Molecular Phylogenetics and Evolution 118 (2018) 286–305

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Molecular Phylogenetics and Evolution

journal homepage: www.elsevier.com/locate/ympev

Rampant polyphyly in the Arracacia clade (Apiaceae) and an assessment of MARK

the phylogenetic utility of 20 noncoding plastid loci
⁎
Clark A. Dandersona, , Stephen R. Downiea, Michael Hermannb
a
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
b
Crops for the Future, Serdang, Selangor, Malaysia

A R T I C L E I N F O A B S T R A C T

Keywords: The Arracacia clade (Apiaceae, Apioideae) is a heterogeneous assemblage of 12 genera, comprising 111 known
Arracacha species distributed in high montane temperate and sub-alpine habitats of meso- and South America. Previous
Intergenic spacer studies have indicated that the genera Arracacia, Coulterophytum, and Prionosciadium are polyphyletic, but for the
Intron most part relationships among the members of the clade are largely unknown. Initially, cladistic analyses of
Noncoding cpDNA
nrDNA ITS sequences were carried out on 212 accessions (122 taxa), representing 92 species of the Arracacia
Páramo
clade and outgroups from the closely-related páramo genera Cotopaxia, Niphogeton, and Perissocoeleum and
Rapid species radiation
members of the Perennial Endemic North American clade and its allies. Using the ITS results to inform sampling
of a small subset of taxa, a pilot study examining the phylogenetic utility of 20 noncoding chloroplast loci was
subsequently performed to identify those regions most useful at resolving relationships. A cost-benefit analysis
determined that five loci (trnQ–5′rps16, trnD–trnT, rpl32–trnL, psbD–trnT, ndhA intron) would maximize re-
solution and branch support in the clade. Cladistic analyses of four of these loci (trnQ–5′rps16, trnD–trnT,
rpl32–trnL, ndhA intron) and the ITS region, separately and combined, revealed that Arracacia, Coaxana,
Coulterophytum, Prionosciadium, and Rhodosciadium are each polyphyletic and that Donnellsmithia and
Myrrhidendron are each monophyletic. Although most relationships in the Arracacia clade and among the closely-
related genera Cotopaxia, Niphogeton, and Perissocoeleum are poorly resolved and supported, ten groups are
recognized for future revisionary studies. Polyploidy and rapid species radiation have likely confounded generic
circumscriptions and interpretation of relationships.

1. Introduction extremely limited sampling, recognized the group as monophyletic-

The Arracacia clade of Apiaceae subfamily Apioideae tribe Selineae
represents a morphologically heterogeneous assemblage of 12 genera
and 111 known species distributed in high montane temperate and sub-
alpine (páramos) habitats of meso- and South America (Downie et al.,
2010; Mathias, 1965). These species are also variable in their life his-
tory, with species ranging from herbaceous annuals, biennials, or per-
ennials to woody perennials. In the genus Arracacia, the entire range of
life histories are observed (Constance, 1949; Hermann, 1997; Mathias
and Constance, 1944–1945). The largest genera of the clade are Arra-
cacia (41 spp.), Donnellsmithia (19 spp.), Prionosciadium (20 spp.), and
Rhodosciadium (15 spp.). The remaining genera are either monotypic
(Dahliaphyllum, Enantiophylla, Mathiasella, and Ottoa) or consist of two
to four species each (Coaxana, Coulterophytum, Myrrhidendron, and
Neonelsonia). Based in part on Drude’s (1897–1898) treatment of
Apiaceae, Pimenov and Leonov (1993) placed these genera in four
tribes. Previous molecular phylogenetic studies, while based on an
hence, the name Arracacia clade (Downie et al., 2000b, 2001, 2002).
These same studies also revealed that the genera Arracacia, Coulter-
ophytum, and Prionosciadium are each not monophyletic.
The largest genus Arracacia is distributed throughout Mexico,
Central America, and South America (Constance, 1949; Mathias and
Constance, 1944–1945) and contains the only native umbellifer do-
mesticated in South America, arracacha (A. xanthorrhiza). Arracacha is
cultivated for its tuberous storage roots, which are prepared in a way
similar to potatoes, and is a major food staple for approximately
80–100 million people (Hermann, 1997). Attempts to delimit Arracacia
from other members of the Arracacia clade have wrought frustration to
taxonomists for over a century (Constance, 1949; Constance and
Affolter, 1995; Coulter and Rose, 1895a, 1900; Hemsley, 1880; Watson,
1886). Arracacia is morphologically diverse, with characters pertaining
to the stylopodium, leaf complexity, carpophore type, and fruit shape,
ribs, and vittae showing considerable variation (Mathias and
Constance, 1944–1945). Coaxana, Coulterophytum, Donnellsmithia,

⁎
Corresponding author at: Department of Biology, Auburn University at Montgomery, P.O. Box 244023, Montgomery, AL 36124, USA.
E-mail address: cdanders@aum.edu (C.A. Danderson).

http://dx.doi.org/10.1016/j.ympev.2017.10.006
Received 10 March 2017; Received in revised form 4 October 2017; Accepted 6 October 2017
Available online 07 October 2017
1055-7903/ © 2017 Elsevier Inc. All rights reserved.
C.A. Danderson et al.
Neonelsonia, and Ottoa are similar to Arracacia in their laterally flat-
tened fruits, while in all other genera of the Arracacia clade the fruits
are dorsally compressed, and often strongly so. Arracacia is also vari-
able in its involucre appearance, and the variation seen in this character
across its species encompasses the same range of variation encountered
among all other genera. Investigations of the relationships among se-
lected South American Arracacia species have been conducted using
AFLPs, microsatellites, and principal component and canonical dis-
criminant analyses of morphological characters (Blas, 2005; Blas et al.,
2008a,b; Hermann, 1997; Knudsen, 2003; Morillo et al., 2004). These
studies focused specifically on determining the origin and genetic di-
versity of the South American species of Arracacia most-closely related
to, and often confused with, A. xanthorrhiza. Relationships among the
wild polycarpic (perennial), monocarpic (annual), and cultivated
(polycarpic) forms of A. xanthorrhiza were highlighted. These studies
did not include representatives of all the South American Arracacia
species, nor did they sample adequately Mexican and Central American
Arracacia species and other genera of the Arracacia clade.
The relationship between Coulterophytum and Enantiophylla, as well
as the relationship of these two taxa to other members of the Arracacia
clade, has yet to be investigated. When Coulterophytum was first de-
scribed (Robinson, 1892), it was noted that its overall habit and in-
florescence appearance was reminiscent of Arracacia; however, it dif-
fered from Arracacia primarily by having slightly compressed mericarps
with contracted stipe-like bases. Soon after, Coulter and Rose (1893)
erected the monotypic genus Enantiophylla. They reported that this
genus was similar to Coulterophytum in many ways, including its fruit
being contracted into a stipe-like base. They observed that Enantiophylla
differed from Coulterophytum in its opposite leaf arrangement, more
compressed fruit, and its prominent dorsal and intermediate ribs and
winged lateral ribs. Additional species have since been described for
Coulterophytum (Coulter and Rose, 1900; Rose, 1905), one of which, C.
brevipes, was subsequently transferred to Arracacia because its fruit
lacked a stipe-like base (Constance and Affolter, 1995). Prionosciadium
and Rhodosciadium are easily distinguished from Arracacia by their
strongly dorsally compressed fruits (Mathias and Constance,
1944–1945), but they too are difficult to differentiate from each other.
Considering the problems with morphology in delimiting genera
within the Arracacia clade, an assessment of their evolutionary re-
lationships using molecular data is warranted, as molecular markers
have been useful in resolving relationships in other problematic clades
of Apiaceae. To date, the nuclear ribosomal DNA (nrDNA) internal
transcribed spacer (ITS) region comprises the most comprehensive da-
tabase for Apiaceae phylogenetic study (Downie et al., 2001, 2010).
These sequences are readily obtainable, even from old herbarium spe-
cimens, and the phylogenies at low taxonomic levels are generally
congruent with those inferred using chloroplast markers (Downie et al.,
2010). Several chloroplast DNA (cpDNA) noncoding regions (e.g.,
rpoC1 and rps16 introns, and the trnT–trnL–trnF, trnQ–rps16–5′trnK, and
rpl32–trnL intergenic spacers) have also been favored (Bone et al., 2011;
Calviño et al., 2006, 2010; Carlson et al., 2011; Downie et al., 2000b;
Feist et al., 2012; George et al., 2014; Liao et al., 2013; Sun and
Downie, 2010). Some difficulties encountered in successfully resolving
low-level relationships using cpDNA data are determining which loci to
examine and how many of them to use. Shaw et al. (2005, 2007, 2014)
examined the potential utility of noncoding cpDNA regions at eluci-
dating lower-level relationships in angiosperms, Downie and Jansen
(2015) investigated the variability of 74 noncoding loci from five
plastid genomes in Apiaceae, and Spooner et al. (2017) explored the
phylogenetic utility of the entire plastid genome at resolving relation-
ships within Daucus (Apiaceae). While these studies provided great
insights into what regions are likely to provide the most informative
characters, it was noted that the efficacy of these loci at resolving inter-
and intrageneric relationships varied among lineages (Downie and
Jansen, 2015; Mort et al., 2007; Shaw et al., 2007, 2014; Spooner et al.,
2017). There is a cost-benefit aspect in carrying out a molecular
287
Molecular Phylogenetics and Evolution 118 (2018) 286–305
systematic study, in which the cost of adding more loci outweighs the
benefit of gained phylogenetic resolution and branch support. By
screening many loci over a small subset of well-chosen taxa, the
minimal number of loci necessary to maximize resolution and support
in a larger sampling of taxa may be achieved. Shaw et al. (2014) noted
that of the 178 papers they reviewed, only 28 reported doing such a
screening. The number of regions screened varied from four to 15 and
rarely was information provided on those loci excluded from further
analysis. The number of noncoding cpDNA loci ultimately used varied
from one to six, with most studies using only two or three. This suggests
that some studies may not be using enough loci to obtain optimal re-
solution or support. Following these observations, Shaw et al. (2014)
suggested the need for screening of multiple noncoding cpDNA prior to
carrying out a lower-level phylogenetic study and requested that in-
formation on both the regions screened and those omitted from further
analysis be provided so as to further understanding of the phylogenetic
utility and performance of these regions across different lineages.
In this paper, we use results of an ITS phylogeny of the Arracacia
clade to inform selection of taxa for inclusion in a pilot study examining
the utility of 20 plastid noncoding loci for resolving relationships. We
ascertain the minimum number of plastid loci necessary to maximize
phylogenetic resolution and branch support in this subset of taxa and
then use these regions in conjunction with ITS sequences to infer re-
lationships within the large, widespread, and economically important
Arracacia clade. Specifically, our goals at the outset of this study were
to elucidate intergeneric and interspecific relationships within the
Arracacia clade; ascertain the degree of polyphyly of the large, complex
genera Arracacia, Donnellsmithia, Prionosciadium, and Rhodosciadium;
report on the phylogenetic placements of the four monotypic genera;
and identify major clades for subsequent systematic and evolutionary
studies. Concomitantly, we provide insight on the efficacy of 20 plastid
loci in resolving phylogenetic relationships within a major clade of
Apiaceae and present details on how these loci perform in this lineage
regardless of their ability to resolve relationships. The results of this
investigation will provide the foundation for a much-needed revision of
the genera comprising the Arracacia clade and suggest plastid loci that
should be considered in other studies of Apiaceae phylogeny.
2. Materials and methods
2.1. Accessions examined
The 212 accessions of Apiaceae (representing 122 taxa) considered
in our molecular studies, including taxonomic authorities, voucher or
source information, and GenBank reference numbers are provided in
Appendix A. These accessions represent 92 of the 111 known species of
the Arracacia clade, plus the undescribed species Coulterophytum ja-
liscanum ined., C. reflexipes ined., and Prionosciadium gomez-pompai
ined. based on annotated specimens. Details of sampling are as follows:
Arracacia (30 of its 41 species were sampled), Coaxana (2 of 2 spp.),
Coulterophytum (2 of 4 spp.), Dahliaphyllum (1 of 1 sp.), Donnellsmithia
(13 of 19 spp.), Enantiophylla (1 of 1 sp.), Mathiasella (1 of 1 sp.),
Myrrhidendron (4 of 4 spp.), Neonelsonia (1 of 2 spp.), Ottoa (1 of 1 sp.),
Prionosciadium (20 of 20 spp.), and Rhodosciadium (13 of 15 spp.). All
material used for molecular analysis, with the exception of leaf frag-
ments for 25 accessions of Arracacia andina, A. elata, A. equatorialis, A.
moschata, A. xanthorrhiza, and Neonelsonia acuminata that were pro-
vided to us directly by Bioversity International, Cali, Colombia, were
obtained from herbarium specimens. Many of these herbarium speci-
mens were annotated previously to species by the late Lincoln Con-
stance and/or Mildred Mathias, foremost authorities on these plants.
As outgroups for the ITS study, representatives of the circumboreal
genus Angelica (A. ampla, A. archangelica, and A. arguta) and the
Perennial Endemic North American clade (Cymopterus globosus,
Musineon divaricatum, Neoparrya lithophila, Oreoxis humilis, Polytaenia
texana, Shoshonea pulvinata, Taenidia integerrima, Tauschia kelloggii, and
C.A. Danderson et al.
Zizia aurea) were included (Sun et al., 2004; Downie et al., 2010).
Previous and ongoing molecular systematic studies have demonstrated
a close relationship among these taxa and those of the Arracacia clade
(Downie et al., 2002; Plunkett and Downie, 1999; Sun et al., 2004;
James F. Smith et al., Boise State University, unpubl. data). Ad-
ditionally, 10 species (11 accessions) of the genera Cotopaxia, Nipho-
geton, and Perissocoeleum were included because their close relation-
ships to Arracacia, Prionosciadium, and Rhodosciadium have been
suggested in past treatments based on fruit, bract, and pollen characters
(Mathias and Constance, 1952, 1967). Aethusa cynapium was used to
root the trees as higher-level studies have consistently placed it as a
sister taxon to a clade comprising many of the aforementioned taxa
(Downie et al., 2000c, 2002). For the combined cpDNA and ITS study,
the trees were rooted with Aethusa cynapium and seven species of Ni-
phogeton and Cotopaxia because of the inability to recover cpDNA se-
quences from the degraded DNA extractions of the other outgroup taxa.
2.2. DNA extraction, purification, and sequencing
Protocols for DNA extraction, PCR amplification, purification, and
sequencing of previously published ITS sequences are provided else-
where (Downie and Katz-Downie, 1996; Downie et al., 1998, 2000a;
Katz-Downie et al., 1999; Sun et al., 2004). For all newly procured data,
20 mg of leaf material was used. DNA was isolated using either a
DNeasy Plant Mini kit (Qiagen Inc., Valencia, CA) or a PureLinkTM
Genomic Plant DNA Purification kit (Invitrogen Corporation, Carlsbad,
CA).
All ITS and cpDNA loci examined herein used a similar protocol to
generate sequences. Each 25-µL PCR reaction consisted of 10.5 µL of
sterile water (11.0 µL in the cpDNA reactions), 5.0 µL of 5X green or
colorless GoTaq Flexi Polymerase buffer (Promega Corp., Madison, WI),
4 µL of 1.25 µM dNTPs (Invitrogen Corp.), 2 µL of 25 µM MgCl2 buffer
(2.75 µL in the cpDNA reactions), 0.5 µL of 20 µM concentrations of
both the forward and reverse primers, 0.25 µL (1.25 units) of GoTaq
Flexi DNA polymerase (Promega Corp.), and 1.0 µL of unquantified
template DNA. ITS PCR reactions also contained 1.25 µL of DMSO to
relax secondary structure. In the case that a particular accession was
hard to amplify, a 1:10 or 1:100 dilution of the DNA was used and/or
the amount of DNA polymerase was adjusted to 0.5 µL (2.5 units), 1 µL
(5 units), or 1.5 µL (7.5 units). The thermocycler programs used for
nrDNA and cpDNA amplifications have been presented previously
(Downie and Katz-Downie, 1996; Shaw et al., 2007).
The resultant PCR products were purified using either QIAquick
PCR Purification or Gel Extraction kits (Qiagen Inc.) or the modified
ExoSAP method of Werle et al. (1994). In the ExoSAP method, 2.25 µL
of sterile water, 0.25 µL (5 units) of Exonuclease I (New England Bio-
labs, Ipswich, MA), and 0.5 µL (0.5 units) of Shrimp Alkaline Phos-
phatase (Promega Corp.) were added directly to the PCR template
tubes, and the tubes were placed in a PCR thermocycler for incubation
(37 °C for 30 min) and heat inactivation (80 °C for 15 min). Sequence
reactions of the purified PCR products were carried out using an ABI
Prism Big Dye Terminator vers. 3.1 Ready Reaction Cycle Sequencing
kit (Applied Biosystems, Foster City, CA). All primers used for ampli-
fication were also used for sequencing. The sequencing reaction pro-
tocol has been described in detail elsewhere (Calviño et al., 2006). Both
DNA strands were sequenced in their entirety using an ABI 3730XL
high-throughput DNA capillary sequencer.
2.3. Sequence alignment and phylogenetic analyses
Sequences were aligned manually using Mesquite vers. 3.10
(Maddison and Maddison, 2016). Gaps were scored as binary characters
using the simple indel coding method outlined in Simmons and
Ochoterena (2000). The data sets were examined with and without gaps
included. Sequence characteristics were obtained for all regions, as well
as for the various combinations analyzed. Uncorrected pairwise
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
nucleotide distances were obtained using the pairwise distances option
in PAUP∗ vers. 4.0a151 (Swofford, 2002). Only positions of un-
ambiguous alignment were included in the analyses.
2.3.1. ITS
In the ITS study, all 212 accessions of Apiaceae were included.
Identical sequences of different accessions of the same taxon were each
represented by single terminals in the phylogenetic analyses
(Supplementary Table 1); as a result, 170 terminals were identified.
Sequence data for 31 of these accessions were obtained from previous
studies (Downie and Katz-Downie, 1996; Downie et al., 1998, 2002;
Katz-Downie et al., 1999; Sun et al., 2004).
Maximum parsimony (MP) analyses of ITS data sets with and
without gaps scored as additional characters were carried out using the
parsimony ratchet approach of Nixon (1999) implemented using
PAUPRat (Sikes and Lewis, 2001) and PAUP∗ via the CIPRES Science
Gateway (Miller et al., 2010). In these analyses, characters were treated
as unordered, transformations were weighted equally, and gaps were
treated as missing data. For a starting tree, a single search using random
stepwise addition of taxa, TBR branch swapping, MULTREES, and
saving no more than one shortest tree was implemented. The ratchet
parameters selected were 200 replicates with 20% of the characters
being perturbed based on a random number seed. The best tree for each
iteration was saved and used to start the next search. To ensure that the
shortest tree was recovered, 10 ratchet runs were conducted and the
tree lengths compared. The best trees saved in memory were then used
to construct the strict consensus (SC) tree. Clade support was assessed
by utilizing 1000 bootstrap (BS) support replicates and 100 random
addition sequence replicates with the heuristic search option
(Felsenstein, 1985).
Bayesian analysis was carried out on both ITS data sets using
MrBayes vers. 3.2.6 (Ronquist et al., 2012). As there was no appreciable
difference in resolution between data sets, results of only the “sequence
with gaps excluded” data set are presented. The best evolutionary
model of nucleotide substitution for the entire ITS region was selected
using the Akaike information criterion (AIC; Akaike, 1974) estimator in
jModelTest vers. 2.1.7 (Darriba et al., 2012). Two independent runs,
with four chains each, of 5,000,000 generations were run simulta-
neously using the default, uniform priors. The model parameters were
sampled at a frequency of 100 generations. The starting trees were
chosen at random and all parameters were unlinked. Stationarity was
determined by graphing the likelihood scores in Microsoft Excel and
utilizing the Compare analysis in AWTY (Wilgenbusch et al., 2004).
Stationarity was reached at 500,000 generations and the first 5000 trees
were discarded as burn-in. A Bayesian majority-rule (MR) consensus
tree was calculated from the remaining 45,000 trees and posterior
probabilities (PP) were estimated. Maximum likelihood (ML) analysis
was also performed using RAxML-HPC2 on XSEDE (Stamatakis, 2014)
via the CIPRES Science Gateway. To obtain the best tree, 1000 ML
searches were run using the model selected by jModelTest. One thou-
sand BS searches were executed using the rapid bootstrapping option.
To assess whether topological differences among the MP, ML, and
Bayesian trees were significant, Shimodaira-Hasegawa (parametric;
Shimodaira and Hasegawa, 1999) and Templeton (non-parametric;
Templeton, 1983) tests were implemented in PAUP∗. For the Shimo-
daira-Hasegawa (SH) test, the RELL resampling method with 1000 re-
plicates was used.
2.3.2. Pilot cpDNA
The 20 noncoding chloroplast loci examined and the primer se-
quences used for PCR amplification and DNA sequencing are presented
in Table 1. In a pilot study to assess the efficacy of these regions at
resolving relationships, these 20 loci were sequenced in nine species
(Aethusa cynapium, Arracacia ebracteata, A. xanthorrhiza, Coaxana pur-
purea, Enantiophylla heydeana, Mathiasella bupleuroides, Myrrhidendron
donnell-smithii, Ottoa oenanthoides, and Rhodosciadium argutum) that
C.A. Danderson et al. Molecular Phylogenetics and Evolution 118 (2018) 286–305

Table 1
The 20 cpDNA regions examined and the primer sequences used for PCR amplification and sequencing.

Region Primer Sequence (5′–3′) Reference

3′rps16–5′trnK rps16-2: TTT CTC GAG CCG TAC GAG GAG Lee and Downie (2006)
trnK: TAC TCT ACC GTT GAG TTA GC
rps16 intron 5′ exon (rps16): TTT AAA ACG ATG TGG TAG AAA GCA Lee and Downie (2006)
3′ exon (rps16): TCG GGA TCG AAC ATC AAT TGC AAC
trnQ–5′rps16 trnQ: CCC GCT ATT CGG AGG TTC GA Lee and Downie (2006)
rps16-1R: ATC GTG TCC TTC AAG TCG CA
trnS–5′trnG trnSGCU: AGA TAG GGA TTC GAA CCC TCG Shaw et al. (2005)
5′ trnG2S: TTT TAC CAC TAA ACT ATA CCC GC
trnG intron 5′ trnG2G: GCG GGT ATA GTT TAG TGG TAA AA Shaw et al. (2005)
3′ trnGUUC: GTA GCG GGA ATC GAA CCC GCA TC
atpI–atpH atpI: TAT TTA CAA GYG GTA TTC AAG CT Shaw et al. (2007)
atpH: CCA AYC CAG CAG CAA TAA C
rpoB–trnC rpoB: CKA CAA AAY CCY TCR AAT TG Shaw et al. (2005)
trnCGCAR: CAC CCR GAT TYG AAC TGG GG
petN–psbM ycf6F: ATG GAT ATA GTA AGT CTY GCT TGG GC Shaw et al. (2005)
psbMR: ATG GAA GTA AAT ATT CTY GCA TTT ATT GCT
trnD–trnT trnDGUC: ACC AAT TGA ACT ACA ATC CC Demesure et al. (1995)
trnTGGU: CTA CCA CTG AGT TAA AAG GG
psbD–trnT psbD: CTC CGT ARC CAG TCA TCC ATA Shaw et al. (2007)
trnT(GGU)-R: CCC TTT TAA CTC AGT GGT
trnS–trnfM trnSUGA: GAG AGA GAG GGA TTC GAA CC Demesure et al. (1995)
trnfMCAU: CAT AAC CTT GAG GTC ACG GG
trnT–5′trnL TabA: CAT TAC AAA TGC GAT GCT CT Taberlet et al. (1991)
TabB: TCT ACC GAT TTC GCC ATA TC
trnL intron TabC: CGA AAT CGG TAG ACG CTA CG Taberlet et al. (1991)
TabD: GGG GAT AGA GGG ACT TGA AC
ndhJ–3′trnL ndhJ: ATG CCY GAA AGT TGG ATA GG Shaw et al. (2007)
TabE: GGT TCA AGT CCC TCT ATC CC Taberlet et al. (1991)
3′trnV–ndhC trnV(CAC)x2: GTC TAC GGT TCG ART CCG TA Shaw et al. (2007)
ndhC: TAT TAT TAG AAA TGY CCA RAA AAT ATC ATA TTC
psbJ–petA psbJ: ATA GGT ACT GTA RCY GGT ATT Shaw et al. (2007)
petA: AAC ART TYG ARA AGG TTC AAT T
petL–psbE petL: AGT AGA AAA CCG AAA TAA CTA GTT A Shaw et al. (2007)
psbE: TAT CGA ATA CTG GTA ATA ATA TCA GC
ndhF–rpl32 ndhF: GAA AGG TAT KAT CCA YGM ATA TT Shaw et al. (2007)
rpl32-R: CCA ATA TCC CTT YYT TTT CCA A
rpl32–trnL rpl32-F: CAG TTC CAA AAA AAC GTA CTT C Shaw et al. (2007)
trnL(UAG): CTG CTT CCT AAG AGC AGC GT
ndhA intron ndhAx1: GCY CAA TCW ATT AGT TAT GAA ATA CC Shaw et al. (2007)
ndhAx2: GGT TGA CGC CAM ARA TTC CA

represent both disparate lineages and closely related taxa based on
results of the ITS analyses. These regions were chosen because their
utility at resolving lower taxonomic level relationships had been sug-
gested in other studies, both in Apiaceae and other angiosperms
(Calviño et al., 2010; Miller et al., 2009; Shaw et al., 2005, 2007).
MP analyses using PAUP∗ were run on data partitions constructed
from all 20 cpDNA loci, ITS only (excluding 5.8S), and combined
cpDNA and ITS data sets, as well as on data sets constructed to include
the incremental addition of cpDNA loci to determine how much re-
solution and branch support could be gained for these nine species. The
combination of cpDNA loci considered in each of these analyses was
chosen on the basis of their overall sequence variability, number of
parsimony informative (PI) characters, sequence divergence within the
ingroup, and the ease of obtaining these sequences. For each data set,
heuristic searches were performed for 100,000 replicates using random
addition of taxa, TBR branch swapping, gaps treated as missing data,
and the MULTREES option. BS values were estimated as described
previously.
Regression analyses, performed in Microsoft Excel, were used to
determine whether the total number of variables sites, or potentially
informative characters (PICs), is a good indicator of the amount of PI
characters a region contains (Shaw et al., 2005; Mort et al., 2007). The
effect of aligned sequence length on the phylogenetic utility of the re-
gion, in terms of both the total number of variable characters and the
number of PI characters, was also investigated (Miller et al., 2009; Mort
et al., 2007; Shaw et al., 2005). Regression analyses were implemented
including and excluding the ITS region.
2.3.3. Combined cpDNA and ITS
On the basis of results of the pilot cpDNA study, four highly variable
cpDNA regions were identified (trnQ–5′rps16, trnD–trnT, rpl32–trnL,
ndhA intron) and subjected to further study. While psbD–trnT was dis-
covered to be among the most variable regions, it was excluded from
consideration as it was difficult to recover complete sequences for many
taxa. The ndhA intron was utilized due to its high level of variability
and ease of PCR amplification. Sequence data for these four regions
were obtained for 88 accessions of the Arracacia clade. We included
Niphogeton (6 species), Cotopaxia asplundii, and Aethusa cynapium as
outgroups, with A. cynapium used to root the trees. In total, 96 term-
inals were considered. ITS sequences for 12 of these accessions were
obtained previously (Downie et al., 1998, 2002).
MP analyses of partitioned and combined data sets (including
scored gaps) were carried out using an approach identical to the ITS
study. Prior to combining ITS and cpDNA data, their congruence was
determined by visual inspection of the topologies and supporting BS
values resulting from the partitioned analyses (see Supplementary
Figs. 1 and 2, respectively). Trees were considered incongruent if they
showed “hard” incongruence-that is, different topologies with high BS
values-rather than “soft” incongruence-different topologies with low BS
values (Magee et al., 2009; Seelanan et al., 1997; Wiens, 1998). In
addition, congruence was tested using the incongruence length differ-
ence (ILD) test conducted using the partition homogeneity test in
PAUP∗ (Farris et al., 1995). For the ILD test, 100 replicates were con-
sidered implementing simple stepwise addition of taxa, MULTREES,
and TBR branch-swapping. Following the MP analyses, the model of

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evolution was estimated for the combined data and Bayesian analysis
was performed following a similar approach as implemented pre-
viously, except that two independent runs, with four chains each, of
7,000,000 generations were run simultaneously using the default,
uniform priors. Stationarity was reached at 200,000 generations, and
the first 2000 trees were discarded as burn-in. A Bayesian MR consensus
tree was calculated from the remaining 68,000 trees and PP were es-
timated. Significance of topological differences among the trees were
examined using the SH (with RELL resampling and 1000 replicates) and
Templeton tests. ML analysis of the combined data set was executed
using the same approach as the ITS study.
3. Results
3.1. ITS
Alignment of ITS sequences for 170 terminals required the in-
troduction of 45 indels, each ranging from one to 18 bp in size, and
resulted in an aligned length of 635 bp. Six positions were ambiguous
and excluded from subsequent analysis. Of the remaining positions, 263
were PI and 119 were autapomorphic. Six indels were PI. The max-
imum pairwise sequence divergence for the entire ITS region across all
terminals was 13.4% (between Donnellsmithia ovata and Arracacia va-
ginata). The maximum sequence divergences for the four largest genera
of the Arracacia clade were as follows: Arracacia-11.1% (between A.
edulis and A. schneideri); Donnellsmithia-12.1% (between D. mexicana
and D. ovata); Prionosciadium-11.1% (between P. diversifolium and P.
humile); and Rhodosciadium-8.9% (between R. nelsonii and R. pringlei).
Sequence heterogeneity was detected in Arracacia fruticosa 3835,
Rhodosciadium dissectum 3820, and R. purpureum 3887. In A. fruticosa, a
C–T polymorphism was located at position 211 in ITS-1, R. dissectum
had an A–G polymorphism at position 58 in ITS-1 and a C–G poly-
morphism at position 464 in ITS-2, and R. purpureum had a C–T poly-
morphism at position 38 and two A–T polymorphisms at positions 167
and 174 in ITS-1.
MP analysis of these ITS sequence data with six gaps included as
additional informative characters resulted in 1316 saved trees, each of
1326 steps (consistency index [CI] = 0.387-this and all following CI
values are without uninformative characters; retention index
[RI] = 0.678). Three of the six PI gaps were homoplastic. The sequence
only data set resulted in 1059 saved trees, each of 1315 steps
(CI = 0.385; RI = 0.677). The topologies of the SC trees for both data
sets were wholly congruent, as were the BS values for many nodes. As
such, results of the “sequence with gaps” data set were not considered
further.
jModelTest selected the GTR + G model of nucleotide substitution
for the Bayesian analysis. Results of the SH tests indicated significant
differences between the topologies of the MP and ML trees and between
the MP and Bayesian trees (P = .001 and P = .049, respectively), but
did not indicate significant differences between the ML and Bayesian
trees (P = .059). The Templeton tests indicated significant differences
between all three tree topologies (MP and ML: P < 0.0001; MP and
Bayesian: P = .0236; ML and Bayesian: P = .0001). Visual inspection of
these trees revealed that these differences are attributable to poorly
supported lineages. Examination of a single MP tree showed the pre-
sence of long terminal branches and short internal branches, indicating
the presence of numerous autapomorphies. The presence of these long
branches may result in long-branch attraction in the MP tree
(Felsenstein, 2003), providing an explanation for the differing topolo-
gies. Therefore, in light of these observations, only the Bayesian MR
consensus tree is presented (Fig. 1), with posterior probabilities and BS
values from the MP and ML analyses included above the congruent
nodes (PP/MP/ML).
All analyses of ITS data reveal that the relationships among the taxa
comprising the Arracacia clade are largely unresolved and poorly sup-
ported. The genera Arracacia, Coaxana, Coulterophytum, Prionosciadium,
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
and Rhodosciadium are each highly polyphyletic. The majority of spe-
cies of Prionosciadium (12 spp.) and Rhodosciadium (11 spp.) formed a
weakly supported clade with four species of Arracacia (PP = 0.98, MP
BS < 50%, ML BS = 64%). Coulterophytum (4 spp.) and Enantiophylla
heydeana formed a clade with two species of Arracacia (PP = 0.99, MP
BS = 64%, ML BS = 82%). Coaxana purpurea allies with Arracacia eb-
racteata (PP = 0.99, MP BS = 61%, ML BS = 73%). The genus
Donnellsmithia (13 spp.) is monophyletic (PP = 1.0, MP BS < 50%, ML
BS = 76%). The genus Myrrhidendron formed a monophyletic group
(PP = 1.0, MP BS = 91%, ML BS = 95%); however, in the Bayesian MR
and ML trees, this genus formed a clade with eight species of Arracacia
(PP = 0.99, ML BS = 51%). The monotypic genus Mathiasella formed a
highly supported clade with Prionosciadium humile and P. simplex
(PP = 1.0, MP BS = 100%, ML BS = 100%). The monotypic genus
Dahliaphyllum formed a clade with Arracacia filipes (PP = 0.81, MP
BS < 50%, ML BS < 50%). The remaining two genera, Neonelsonia
and Ottoa, were placed within the Arracacia clade; yet, their relation-
ships to the other genera remained unresolved. The genera Cotopaxia,
Niphogeton, and Perissocoeleum formed a grade at the base of the
Arracacia clade.
3.2. Pilot cpDNA
Sequence characteristics of 20 noncoding cpDNA loci and the ITS
region (excluding 5.8S) for nine species, separate and combined, are
presented in Table 2. A 31-bp inversion was present within the
psbJ–petA region in A. cynapium. The top four cpDNA loci exhibiting the
greatest number of variable characters were rpl32–trnL, ndhF–rpl32,
trnQ–5′rps16, and trnD–trnT (Fig. 2) and the top four cpDNA loci having
the greatest number of PI characters were rpl32–trnL, trnQ–5′rps16,
trnD–trnT, and psbD–trnT (Fig. 3). When considering that some regions,
such as trnT–5′trnL and trnL intron and trnS–5′trnG and trnG intron, are
often co-amplified and sequenced, the trnS–trnG–trnG region becomes
the fifth best in providing variable and PI characters. Of the four introns
included, the ndhA intron demonstrated the greatest number of variable
and PI characters (43 and 6, respectively), making it one of the most
variable loci. The ITS region outperformed all cpDNA loci in both
numbers of variable and PI characters (117 and 23, respectively).
When considering only the cpDNA loci, there was a significant re-
lationship between the number of variable characters and aligned
length (F1,18 = 11.5, P = .003); consideration of the ITS region ren-
dered this relationship insignificant (F1,19 = 0.006, P = .94). There was
no significant relationship between the number of PI characters and
aligned length, excluding and including ITS (F1,18 = 3.73, P = .07 and
F1,19 = 0.29, P = .6, respectively). There was a significant relationship
between the number PI characters and the number of variable char-
acters, excluding and including ITS (F1,18 = 14.44, P = .001 and
F1,19 = 58.29, P = 3.33E−07, respectively). Ten of the 21 inferred
cpDNA PI gaps were homoplastic, and there was no significant re-
lationship between the length of PI gaps and their degree of homoplasy
(F1,19 = 0.717, P = .408). When comparing the variability of the 16
cpDNA intergenic spacer regions to that of the four introns, the inter-
genic spacers had a mean percent variability of 4.08% (SD = 1.17) and
the introns had a mean percent variability of 3.4% (SD = 0.96).
Results of MP analysis revealed that the cpDNA only data set had
the greatest resolution of relationships (Fig. 4). As such, the cpDNA only
tree was used as the hypothetical relationship tree for all the other data
sets to be evaluated against. A comparison of the recovered nodes and
associated BS values resulting from nine MP analyses of ITS only,
cpDNA only, gaps only, and the incremental addition of five cpDNA
noncoding regions with ITS on this hypothetical relationship tree are
presented in Table 3.
3.3. CpDNA and ITS
Sequence characteristics of the cpDNA trnQ–5′rps16, trnD–trnT,
C.A. Danderson et al. Molecular Phylogenetics and Evolution 118 (2018) 286–305

Fig. 1. Majority-rule consensus tree of 45,000 trees derived from Bayesian analysis of 212 nrDNA ITS sequences represented by 170 terminals. The number in parentheses following a
terminal corresponds with the number of identical accessions represented by that terminal (Supplementary Table 1). Numbers on the branches represent posterior probability values and
maximum parsimony and maximum likelihood bootstrap support (PP/MP/ML; only those greater than 0.5% and 50% are shown). Branch lengths are proportional to the number of the
expected nucleotide substitutions (scale bar corresponds to 1 substitution per 10 sites). Taxa in italicized bold were used in the cpDNA pilot study. Cult = cultivated; mono = monocarpic;
poly = polycarpic.

rpl32–trnL, and ndhA intron regions and ITS, separately and combined,
for 96 accessions, are presented in Table 4. MP analysis of the cpDNA
only matrix (trnQ–5′rps16, trnD–trnT, rpl32–trnL, ndhA intron plus PI
indels) resulted in 1796 saved 974-step trees (CI = 0.514; RI = 0.805).
MP analysis of the ITS only (plus PI indels) matrix resulted in 1837
saved trees, each of 1011 steps (CI = 0.409; RI = 0.578). The ILD test
showed that there was significant incongruence between the cpDNA
and ITS data sets (P = .01). Visual examination of the SC trees (see
Supplementary Figs. 1 and 2) revealed that most differences were due
to “soft” incongruence, with one possible instance of “hard” incon-
gruence. This “hard” incongruence was between the relationship of
Mathiasella to Prionosciadium humile and P. simplex. In the cpDNA tree,
Mathiasella was sister taxon to P. simplex (BS = 100%), and in the ITS
SC tree it was sister taxon to P. humile (BS = 91%). In both trees, all
three of these taxa formed a clade (BS = 100%). As Mathiasella and P.
simplex are missing large portions of the 5.8S gene, it was suspected that
these missing data might have had an effect on the recovered re-
lationships. To test this, another MP analysis using the same para-
meters, but with the 5.8S region excluded, was run. The resulting SC
tree (not shown) had the same topology, yet the BS value for the re-
lationship between Mathiasella and P. simplex reduced from 91% to
73%, making the incongruence “soft”. With this caveat in mind, the two
data sets were combined for simultaneous analysis. MP analysis of the
combined data set resulted in 1945 saved 2075-step trees (CI = 0.421;
RI = 0.660).
jModelTest selected the GTR + I + G model of nucleotide sub-
stitution for the Bayesian analysis. SH tests indicated significant dif-
ferences between the topologies of the MP and ML trees and between

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Fig. 1. (continued)
the MP and Bayesian trees (P = .002 and P = .001, respectively), but
did not indicate significant differences between the ML and Bayesian
trees (P = .279). Templeton tests indicated significant differences be-
tween the MP and ML topologies and between the ML and Bayesian
topologies (P = .0004 and P = .0039, respectively); however, the
topologies of the MP and Bayesian were not significantly different
(P = .0251). Once more, visual inspection of these trees showed dif-
ferences attributable to poorly supported lineages. The Bayesian MR
consensus tree (Fig. 5) is presented with PP and BS values from the MP
and ML analyses included above the congruent nodes (PP/MP/ML). The
analyses of the combined cpDNA and ITS data resulted in greater re-
solution of the recovered clades than either data set alone.
Based on results of combined cpDNA and ITS data, eight major
clades are informally recognized in the Arracacia clade, and two are
recognized among the taxa of Niphogeton and Cotopaxia (Fig.5). Al-
though many of these clades have low support values, they were either
consistently recovered in the MP, ML, and Bayesian analyses or were
not in conflict. Still, the relationships among these newly recognized
clades remain largely unresolved. All analyses support the prior
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
observations that the genera Arracacia, Coulterophytum, and Prio-
nosciadium are polyphyletic. To these we add Coaxana and Rhodoscia-
dium, and also Niphogeton from the outgroup representatives. Excluded
from these 10 major clades because of dubious phylogenetic placements
are Dahliaphyllum almedae, Neonelsonia acuminata, and Ottoa oe-
nanthoides, plus five species of Arracacia (A. filipes, A. compacta, A.
fruticosa, A. anomala, and A. elata).
Rhodosciadium Group (Clade 1) – This clade (PP = 0.58, MP
BS < 50%, ML BS < 50%) contains 26 species (29 terminals) of
Arracacia, Prionosciadium, and Rhodosciadium, including the type of
Rhodosciadium, R. pringlei. Four species of Arracacia (A. quadrifida, A.
tolucensis, A. longipedunculata, and A. hemsleyana) are dispersed
throughout this clade. Based on the ITS phylogeny (Fig. 1), Prio-
nosciadium lilacinum, P. megacarpum, P. saraviki, and P. townsendii
should be included in this group, as well.
Arracacia xanthorrhiza Group (Clade 2) – This clade (PP = 0.75,
MP BS < 50%, ML BS < 50%) contains five species (7 terminals) of
Arracacia and Prionosciadium. The domesticated species and type of the
genus Arracacia, A. xanthorrhiza, the recently discovered wild
C.A. Danderson et al.
Fig. 1. (continued)
polycarpic and monocarpic Andean populations of A. xanthorrhiza, and
the South American species A. andina and A equatorialis form a well-
supported clade (PP = 1.0, MP BS = 96%, ML BS = 100%).
Additionally, Prionosciadium madrense, the type of Prionosciadium,
should be included in this group (Fig. 1).
Coulterophytum Group (Clade 3) – This clade (PP = 0.98, MP
BS < 50%, ML BS = 52%) contains four species of Coulterophytum and
Enantiophylla including their types (C. laxum and E. heydeana), as well
as two species of Arracacia (A. brandegei and A. ternata). Enantiophylla
arises from within a paraphyletic Coulterophytum and is sister taxon to
C. pubescens (PP = 1.0, MP BS = 97%, ML BS = 99%). The unpublished
species of Coulterophytum, C. reflexipes ined., should also be included in
this group (Fig. 1). The two undescribed species of Coulterophytum, C.
jaliscanum ined. and C. reflexipes ined., have a relatively low ITS se-
quence divergence between them (0.6%), but a 2.9 and 3.5% sequence
divergence between them and the two other species of Coulterophytum.
Donnellsmithia Group (Clade 4) – Donnellsmithia is a strongly
supported monophyletic group in all analyses (PP = 1.0, MP BS = 99%,
ML BS = 100%).
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
Myrrhidendron Group (Clade 5) – The Myrrhidendron group
(PP = 0.99, MP BS < 50%, ML BS = 55%) consists of four species
comprising the woody genus Myrrhidendron (including its type, M.
donnell-smithii) and six species of Arracacia (A. bracteata, A. donnell-
smithii, A. molseedii, A. pringlei, A. ravenii, and A. rigida). The genus
Myrrhidendron is strongly supported as monophyletic (PP = 1.0, MP
BS = 98%, ML BS = 100%).
Coaxana Group (Clade 6) – This group (PP = 1.0, MP BS = 93%,
ML BS = 98%) contains six species of Arracacia (A. aegopodioides, A.
atropurpurea, A. ebracteata, A. macvaughii, A. moschata, and A. nelsonii)
and two species of Coaxana (including its type, C. purpurea). Coaxana
forms a clade (PP = 0.96, MP BS = 84%, ML BS = 77%) with A. eb-
racteata, with the latter being sister taxon to C. purpurea (PP = 1.0, MP
BS = 81%, ML BS = 89%).
Mathiasella Group (Clade 7) – The Mathiasella group (PP = 1.0,
MP BS = 100%, ML BS = 100%) contains the monotypic genus
Mathiasella and two morphologically anomalous species of
Prionosciadium, P. humile and P. simplex. Arracacia anomala allies with
this clade in the MP SC tree (not shown), but with a BS value of <
C.A. Danderson et al. Molecular Phylogenetics and Evolution 118 (2018) 286–305

Table 2
Sequence characteristics of the 20 cpDNA loci investigated, as well as nrDNA ITS (excluding the 5.8S region), for the nine taxa included in the pilot cpDNA study.

Metrics 3′rps16–5′trnK rps16 Intron trnQ–5′rps16 trnS–5′trnG trnG Intron atpI–atpH

# of Taxa 9 9 9 9 9 9
Aligned Length (bp) 762 862 1384 573 741 1143
Length Variation 696–732 857–862 1185–1299 525–563 705–729 749–1136
# Indels (Size in bp) 12 (1–27) 4 (1–4) 16 (1–172) 6 (1–36) 7 (1–16) 5 (1–388)
# Inversions 0 0 0 0 0 0
# Variable Characters 38 32 61 23 30 25
% Variablilty 5.14 3.76 4.44 4.34 4.10 2.21
# Excluded Positions 23 12 10 43 10 14
# Constant Positions 713 822 1329 513 708 1109
# Autapomorphies 21 25 39 12 22 16
# Parsimony Informative Sites 5 3 6 5 1 4
# Parsimony Informative Gaps 1 0 3 0 2 0
Sequence Divergence (%)
Including Outgroup 0–2.79 0.12–2.37 0.08–2.32 0.19–1.85 0–1.85 0.14–1.75
Including Ingroup 0–1.33 0.12–0.83 0.08–0.90 0.19–1.63 0–1.15 0.14–0.95

Metrics rpoB–trnC petN–psbM trnD–trnT psbD–trnT trnS–trnfM trnT–5′trnL

# of Taxa 9 9 9 9 7 9
Aligned Length (bp) 1354 1155 1197 1505 1104 798
Length Variation 1211–1317 1124–1139 814–1160 1421–1456 1078–1094 605–793
# Indels (Size in bp) 10 (1–98) 10 (1–15) 14 (1–312) 10 (1–24) 6 (1–9) 5 (1–193)
# Inversions 0 0 0 0 0 0
# Variable Characters 45 37 56 47 33 30
% Variablilty 3.32 3.23 4.74 3.20 3.05 3.76
# Excluded Positions 0 12 16 36 22 0
# Constant Positions 1319 1116 1139 1432 1055 773
# Autapomorphies 33 24 35 29 25 23
# Parsimony Informative Sites 2 3 7 8 2 2
# Parsimony Informative Gaps 1 1 2 1 0 0
Sequence Divergence (%)
Including Outgroup 0.08–1.91 0.18–1.35 0.25–2.29 0.07–1.36 0.38–1.60 0.13–2.69
Including Ingroup 0.08–0.58 0.18–0.98 0.25–1.29 0.07–0.93 0.38–0.85 0.13–0.76

Metrics trnL Intron ndhJ–3′trnL 3′trnV–ndhC psbJ–petA petL–psbE ndhF–rpl32

# of Taxa 9 9 9 9 9 8
Aligned Length (bp) 518 872 1091 1012 1009 1057
Length Variation 494–516 820–849 1062–1077 553–971 576–1009 978–1021
# Indels (Size in bp) 4 (1–16) 11 (1–18) 8 (1–9) 15 (1–375) 4 (2–432) 15 (1–36)
# Inversions 0 0 0 1 0 0
# Variable Characters 9 37 35 43 31 63
% Variablilty 1.74 4.24 3.21 4.31 3.10 6.20
# Excluded Positions 0 0 0 14 10 41
# Constant Positions 513 846 1064 971 972 968
# Autapomorphies 3 25 23 22 22 45
# Parsimony Informative Sites 2 1 4 5 5 3
# Parsimony Informative Gaps 0 2 2 1 1 0
Sequence Divergence (%)
Including Outgroup 0–0.60 0.12–1.71 0.19–1.61 0–1.69 0–1.83 0.31–3.14
Including Ingroup 0–0.60 0.12–1.08 0.19–0.75 0–1.09 0–1.01 0.31–1.43

Metrics rpl32–trnL ndhA Intron CpDNA Only ITS Only Combined CpDNA & ITS

# of Taxa 9 9 9 9 9
Aligned Length (bp) 1038 1087 20262 445 20707
Length Variation 933–978 1063–1078 18277–19437 424–440 187801–19876
# Indels (Size in bp) 22 (1–31) 10 (1–13) 194 (1–432) 8 (1–14) 202 (1–432)
# Inversions 0 0 1 0 1
# Variable Characters 68 43 786 117 902
% Variablilty 6.77 3.98 3.94 26.29 4.42
# Excluded Positions 33 6 302 0 302
# Constant Positions 959 1048 19369 336 19705
# Autapomorphies 35 28 507 86 593
# Parsimony Informative Sites 11 5 84 23 107
# Parsimony Informative Gaps 3 1 21 0 21
Sequence Divergence (%)
Including Outgroup 0.22–3.30 0.09–2.10 0.22–1.79 3.89–11.90 0.34–2.03
Including Ingroup 0.22–1.83 0.09–0.95 0.22–0.73 3.89–11.66 0.34–0.99

50%. As this relationship has little support, A. anomala is not con- A. hintonii, and A. schneideri).
sidered within the Mathiasella group. Niphogeton Group (Clade 9) – This group (PP = 1.0, MP
Arracacia edulis Group (Clade 8) – This group (PP = 1.0, MP BS = 88%, ML BS = 86%) contains five of six species of Niphogeton,
BS = 75%, ML BS = 88%) contains three species of Arracacia (A. edulis, including its type N. ternata. Niphogeton josei should also be included in

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120

100

80
Variable Characters

60

40

20

0
rpl32-trnL
ndhF-rpl32

ndhA intron

trnG intron
trnT-5'trnL
atpI-atpH
trnS-5'trnG
trnL intron
ITS
trnQ-5'rps16
trnD-trnT
psbD-trnT
rpoB-trnC
psbJ-petA

3'rps16-5'trnK
petN-psbM
ndhJ-3'trnL
3'trnV-ndhC
trnS-trnfM
rps16 intron
petL-psbE
Fig. 4. Single minimal length 670-step (hypothetical relationship) tree based on 20 non-
coding cpDNA loci from equally weighted maximum parsimony analyses of eight taxa
representing different clades and levels of relationship in the Arracacia clade and the
outgroup Aethusa cynapium. The nodes of the tree are numbered above the branches and
numbers below the branches represent bootstrap support estimates (only those greater
Fig. 2. The total number of variable characters (autapomorphies + PI than 50% are shown).
sites + gaps + inversions) for each of the 20 non-coding cpDNA loci and the nrDNA ITS
region (excluding 5.8S). The white bars stacked on the black bars indicate the total
number of variable characters for those regions that are often combined (i.e., not being monophyletic (Downie et al., 2000b, 2002). In contrast,
trnT–trnL–trnL and trnS–trnG–trnG). Donnellsmithia and Myrrhidendron are each monophyletic. Donnells-
mithia shares several features with Arracacia, such as leaf morphology,
25 lateral compression of fruit, short styles, and a stylopodium that is
usually lacking or depressed; it differs from Arracacia in that its in-
volucre and involucel are usually wanting, it usually has oval to ellip-
20 soid or obcordate fruit without a tapering of the apex, it is not woody in
habit, and its seed is not sulcate in cross-section under the vittae. As
such, its monophyly stands in stark contrast to those highly poly-
PI Characters

15 phyletic genera that also share features with Arracacia. Myrrhidendron is

morphologically unique and easy to distinguish from other members of
the clade by the presence of very large linear or oblong, dorsally
10 compressed fruits and cleft to toothed bracts and bracteoles.
In Apiaceae subfamily Apioideae, the recognition of tribes, sub-
tribes, and genera has traditionally been based largely on fruit mor-
5 phology and anatomy, particularly such features as fruit compression,
the presence/absence of lateral and/or dorsal wings, ribs and vittae,
fruit shape, and the shape of the seed in cross-section (Downie and Katz-
0 Downie, 1996). These features have been demonstrated to be unreliable
rpl32-trnL

psbJ-petA
ndhA intron
trnQ-5'rps16
trnD-trnT
psbD-trnT

3'rps16-5'trnK
3'trnV-ndhC
petL-psbE
trnS-5'trnG
petN-psbM
atpI-atpH
ndhF-rpl32
rpoB-trnC
ndhJ-3'trnL
rps16 intron
trnG intron
trnS-trnfM
trnT-5'trnL
trnL intron
ITS

in the delimitation of other large apioid genera, such as Cymopterus,

Fig. 3. The total number of PI characters (PI sites + gaps) for each of the 20 non-coding
cpDNA loci and the nrDNA ITS region (excluding 5.8S). The white bars stacked on the
black bars indicate the total number of PI characters for those regions that are often
combined (i.e., trnT–trnL–trnL and trnS–trnG–trnG).
this group (Fig. 1).
Cotopaxia Group (Clade 10) – The genus Cotopaxia (represented
by its type, C. asplundii) forms a clade with Niphogeton stricta (PP = 0.9,
MP BS = 63%, ML BS = 59%). Niphogeton scabra should also be in-
cluded in this group (Fig. 1).
4. Discussion
4.1. Polyphyly and rapid species radiation
One of the most salient features of the Arracacia clade is the high
degree of polyphyly of its genera, most notably Arracacia, Coaxana,
Coulterophytum, Prionosciadium, and Rhodosciadium. This is in agree-
ment with previous studies, albeit based on limited sampling, where
Arracacia, Coulterophytum, and Prionosciadium were revealed as each
Lomatium, and Peucedanum (Downie et al., 2002; Spalik et al., 2004;
Sun et al., 2004). The problem with using fruit compression, fruit shape,
and the presence/absence of wings is that they are adaptations for
dispersal and, therefore, prone to convergence, with different patterns
of development resulting in morphological similarities (Downie et al.,
2002; Heywood, 1986; Theobald, 1971). Vittae and the presence of
ribbed fruit may also be prone to convergence as they are adaptations to
protect the developing seed from herbivory (Downie et al., 2002; Spalik
et al., 2001). In the Arracacia clade, the variability of fruit shapes ex-
hibited is impressive, with fruit being ovoid, ellipsoid, lanceolate,
obovoid, clavate, oblong, and orbicular. Equally variable is rib shape
and number, the number of vittae, and the appearance of the seed in
cross-section, especially in Arracacia, Prionosciadium, and Rhodoscia-
dium (Constance, 1949; Constance and Affolter, 1995; Constance and
Breedlove, 1994; Constance and Hitchcock, 1954; Coulter and Rose,
1895a,b, 1900, 1927; Mathias and Constance, 1944–1945, 1973). The
convergence of these characters and their widespread use in delimiting
genera within the Arracacia clade has no doubt confounded the tax-
onomy of the group, resulting in its high degree of polyphyly.
Another salient feature of the Arracacia clade is the considerable
lack of resolution apparent among the basal nodes of all phylogenies
estimated herein. Large polytomies abound, and all trees show a pattern
of short, basal branches and longer terminal ones characteristic of rapid

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C.A. Danderson et al. Molecular Phylogenetics and Evolution 118 (2018) 286–305

Table 3
Comparison of the recovered nodes and associated bootstrap values of the hypothetical tree (Fig. 4). (1) = ITS only; (2) = cpDNA only; (3) = gaps only; (4) = ITS + rpl32–trnL;
(5) = ITS + rpl32–trnL + trnD–trnT; (6) = ITS + rpl32–trnL + trnD–trnT + trnQ–5′rps16; (7) = ITS + rpl32–trnL + trnD–trnT + trnQ–5′rps16 + psbD–trnT; (8) = ITS + rpl32–trnL + trnD–trnT
+ trnQ–5′rps16 + psbD–trnT + ndhA intron; (9) = combined cpDNA and ITS. – = Node absent in SC tree. + = Node present in SC tree, but not in BS 50% majority-rule tree. CI values are
without uninformative characters included.

Node (1) (2) (3) (4) (5) (6) (7) (8) (9)

Node 1 77 100 92 100 100 100 100 100 100

Node 2 – + – – – – – – –
Node 3 – 91 – – + + + 60 86
Node 4 54 91 – – 97 95 99 99 93
Node 5 69 100 84 94 97 99 100 100 100
Node 6 – + – – – – – – –
# Trees 3 1 40 10 1 2 2 2 3
Tree Length 137 670 34 188 237 290 333 369 810
CI 0.628 0.695 0.618 0.695 0.694 0.686 0.687 0.705 0.670

Table 4
Sequence characteristics of the four loci of cpDNA (trnQ–5′rps16, trnD–trnT, rpl32–trnL, and ndhA intron) and nrDNA ITS region, separately and combined, for 96 accessions of the
Arracacia clade and outgroups.

Locus

Metrics trnQ–5′rps16 trnD–trnT rpl32–trnL ndhA Intron

Aligned Length (bp) 1506 1374 1181 1139

Length Variation (bp) 684–1299 809–1160 780–978 1030–1093
# Indels (Size in bp) 53 (1–599) 57 (1–342) 85 (1–212) 31 (1–44)
# Excluded Positions 0 54 82 1
# Constant Positions 1313 1190 920 1001
# Autapomorphies 142 83 118 92
# Parsimony Informative Sites (%) 51 (3.4) 47 (3.6) 61 (5.6) 45 (4.0)
# Parsimony Informative Gaps (Size in bp) 8 (6–172) 12 (6–342) 8 (2–17) 3 (8–13)
# Inversions (Size in bp) 1 (100) 0 0 1 (33)
Sequence Divergence (%) 0–1.9 0–2.2 0–3.2 0–1.5

Metrics CpDNA Only ITS Only Combined CpDNA & ITS

Aligned Length (bp) 5200 634 5834

Length Variation (bp) 3808–4480 586–602 4407–5010
# Indels (Size in bp) 226 (1–599) 46 (1–18) 272 (1–599)
# Excluded Positions 137 3 140
# Constant Positions 4424 284 4708
# Autapomorphies 435 150 585
# Parsimony Informative Sites (%) 204 (4.0) 197 (31.2) 401 (7.0)
# Parsimony Informative Gaps (Size in bp) 31 (2–342) 3 (3–14) 34 (2–342)
# Inversions (Size in bp) 2 (33–100) 0 2 (33–100)
Sequence Divergence (%) 0–1.5 0–13.2 0.1–2.7

radiations. Such a branching pattern has previously been demonstrated
in other genera of Apiaceae exhibiting rapid species radiations, such as
Cymopterus, Eryngium, Lomatium, and Osmorhiza (Calviño et al., 2008;
Downie et al., 2002; Hardig and Soltis, 1999; Soltis et al., 1995; Sun
et al., 2004; Wen et al., 2002; Yoo et al., 2002). Pairwise sequence
divergences between taxa in the Arracacia clade were generally low,
with the maximum value for ITS being 13.4%, a value comparable to
that seen in Cymopterus and other members of the Perennial Endemic
North American clade of umbellifers (Downie et al., 2002). As the loci
utilized herein are known to be fast-evolving (Calviño et al., 2010;
Downie and Jansen, 2015; Miller et al., 2009; Shaw et al., 2005, 2007,
2014) and some close-related relationships are resolved throughout the
trees (e.g., Arracacia xanthorrhiza, A. equatorialis, and A. andina), there
is little reason to doubt the appropriateness of these loci for inferring
inter- and infrageneric relationships. We have also shown that the ad-
dition of more regions does not result in greater resolution, as implied
by the pilot cpDNA study. Considering that the lack of phylogenetic
signal is not due to the use of inappropriate markers, an alternative
explanation is one of rapid species radiation. Such a phenomenon ap-
pears to be a common evolutionary process for many other taxa en-
demic to continental, or western, North America (Herschkovitz and
Zimmer, 2000; Rieseberg et al., 1991; Schwarzbach and Kadereit, 1995;
Wojciechowski et al., 1999).
The base chromosome number of the Arracacia clade, as it is in
other members of Apiaceae subfamily Apioideae, is x = 11; however,
numerous instances of polyploidy and aneuploidy have been reported
in the group, which may be indicative of past hybridization events
confounding generic circumscriptions and interpretation of relation-
ships. Additional evidence for hybridization within the Arracacia clade
may be the ITS sequence heterogeneity exhibited by some taxa, al-
though hybridization has yet to be confirmed. In Arracacia,
Donnellsmithia, and Rhodosciadium, as examples, there are recorded
instances of triploidy and even tetraploidy (Constance et al., 1976a,b;
Moore, 1971). Aneuploidy has been shown to occur in Arracacia,
Donnellsmithia, Ottoa, Prionosciadium, and Rhodosciadium (Bell and
Constance, 1966; Constance et al., 1976a,b; Moore, 1971). This pattern
of polyploidy has been noted in other taxonomically complex Mexican
and Central American Apiaceae genera, such as Eryngium, and it has
been suggested that this high degree of polyploidy may primarily be a
result of local ecological gradients that are associated with isolation,
speciation, endemism, and hybridization. Many of these polyploid taxa
demonstrate relatively high incidence of survival in their geographic

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C.A. Danderson et al.
origins and in less optimal environments to which they have migrated
(Bell, 1964). This widespread presence of polyploidy throughout the
Arracacia clade may also be an indicator of rapid species radiation. As a
result of rapid radiations, intrinsic prezygotic and postzygotic isolation
mechanisms may not have had enough time to evolve, allowing for
introgressive hybridization (Wiens et al., 2006). It is also possible that
the rapid species radiation is a result of hybridization (Seehausen,
2004), as polyploidy can be promoted by introgressive hybridization
(Tate et al., 2005). Other South American páramo genera (Gentianella
and Halenia in Gentianaceae and Valeriana in Valerianaceae) have de-
monstrated rapid species radiation, and it appears that this might be a
common feature of the recently formed páramo ecosystem. Coloniza-
tion of the rising Andes and the páramo has often been compared to the
colonization of recently formed islands in that colonizing species have
many unoccupied niches that they can rapidly take advantage of due to
the lack of a native flora (Bell and Donoghue, 2005; von Hagen and
Kadereit, 2001; Kadereit and von Hagen, 2003). While hydridization
has yet to be confirmed in the Arracacia clade, the results of this study
and others suggest that further investigations on this topic for the group
are warranted.
4.2. Phylogenetic utility of ITS and cpDNA markers
ITS sequences are the most prevalent type of molecular data used in
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
Fig. 5. Majority-rule consensus tree of 68,000
trees derived from Bayesian analysis of combined
cpDNA (trnQ–5'rps16, trnD–trnT, rpl32–trnL,
ndhA intron) and nrDNA ITS sequences from 96
taxa. Numbers on the branches represent pos-
terior probability values and maximum parsi-
mony and maximum likelihood bootstrap support
(PP/MP/ML; only those greater than 0.5% and
50% are shown). Branch lengths are proportional
to the number of the expected nucleotide sub-
stitutions (scale bar corresponds to 1 substitution
per 100 sites). Ten major clades are identified.
Cult = cultivated; mono = monocarpic; poly
= polycarpic.
phylogenetic studies of Apiaceae to date (Downie et al., 2001, 2010)
and have previously proved useful in resolving infrageneric relation-
ships in subfamily Apioideae (Downie et al., 2004; Feist and Downie,
2008; Neves and Watson, 2004). Within the Arracacia clade, ITS se-
quences failed to resolve deep-level relationships and many branches
were poorly supported (Fig.1), despite its large number of PI sites. This
overall lack of resolution is likely due to a combination of high levels of
homoplasy of these data and, as discussed previously, rapid species
radiation.
Until recently, most studies utilizing cpDNA in Apiaceae systematic
studies considered only a handful of regions, most notably matK
(Plunkett and Downie, 1999; Plunkett et al., 1996), rpoC1 intron (Downie
et al., 1998, 2000b; Plunkett and Downie, 1999), rpl16 intron (Downie
et al., 2000b), rps16 intron (Calviño et al., 2006; Downie et al., 2002; Lee
and Downie, 2000; Sun and Downie, 2004), and portions or all of
trnT–trnL–trnF (Downie et al., 2002; Sun and Downie, 2010). These loci
were often used in conjunction with ITS and were utilized at taxonomic
levels from family down to infrageneric, with variable success. At lower
taxonomic levels, usage of rps16 intron and trnT–trnL–trnF resulted in
largely unresolved trees and poorly supported relationships (Downie
et al., 2002; Sun and Downie, 2004; Yoo et al., 2002). Only recently have
more variable regions, such as psbI–psbK–trnQ–rps16–5′trnK (primarily
the region trnQ–5′trnK), trnD–trnT, and rpl32–trnL, been employed (Bai
et al., 2015; Bone et al., 2011; Calviño and Downie, 2007; Calviño et al.,
C.A. Danderson et al.
2008; Carlson et al., 2011; Feist et al., 2012; George et al., 2014; Lee and
Downie, 2006; Liao et al., 2013; Magee et al., 2010; Nicolas and Plunkett,
2009, 2012).
To examine how many regions are necessary to maximize resolution
and branch support in a phylogeny while simultaneously reducing the
amount of time and cost involved with increased sequencing, we per-
formed a cost-benefit analysis. From this analysis, the tree derived from
the cpDNA only data set (representing all 20 loci) was the most-re-
solved, with all nodes recovered (Fig. 4). The addition of the five best
regions (trnQ–5′rps16, trnD–trnT, psbD–trnT, rpl32–trnL, ndhA intron) to
ITS were enough to recover most of the nodes of this most-resolved,
hypothetical relationship tree. This result is similar to Calviño et al.
(2010) in which six cpDNA regions obtained the same set of major
clades as did 11 cpDNA regions combined. However, the current study
differed in what plastid regions were used. Calviño et al. (2010) ex-
amined the utility of only 11 loci and based their choices on the number
of PI characters rather than the number of variable characters. They did
not sample psbD–trnT, atpI–atpH, and petL–psbE which ranked highly in
Shaw et al. (2007) and had more variable characters than trnD–trnT,
trnS–trnfM, and rpoB–trnC.
Of the five cpDNA regions used to reveal the most-resolved, hy-
pothetical relationship tree, the one most widely used in recent mole-
cular systematic investigations is rpl32–trnL. Miller et al. (2009) noted
that rpl32–trnL was one of the more promising regions for infrageneric
studies and, as a result, the region has since been used extensively (e.g.,
Calviño et al., 2010; Carlson et al., 2011; Carter et al., 2014; Chen et al.,
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
Fig. 5. (continued)
2010; George et al., 2014; Herden et al., 2016; Liao et al., 2013; Lu and
Morden, 2014; Magee et al., 2015; Nazaire and Hufford, 2014; Peterson
et al., 2010, 2015; Schulte et al., 2014; Sinitsyna et al., 2016; Stern and
Bohs, 2016). TrnD–trnT may be the next most commonly implemented
region (e.g., Calviño et al., 2010; Fisher et al., 2014; Gagnon et al.,
2015; Gostel et al., 2016; Halpin and Fishbein, 2013; Liede-Schumann
et al., 2014; Miller et al. 2009; Nicolas and Plunkett, 2009; Simon et al.,
2016). TrnQ–5′rps16 has also experienced wide usage and is most often
used in conjunction with rps16 intron and 3′rps16–5′trnK (e.g., Lu and
Morden, 2014; Nazaire and Hufford, 2014; Santos et al., 2016; Schulte
et al., 2014; Silveira and Simpson, 2013; Sinitsyna et al., 2016). This
region, with the included rps16 intron, has been used frequently in
Apiaceae studies (Bai et al., 2015; Calviño and Downie, 2007; Calviño
et al., 2008, 2010; Feist et al. 2012; Lee and Downie, 2006; Magee et al.,
2010). In contrast, the ndhA intron has been utilized very little (e.g.,
Carter et al., 2014; Fisher et al., 2014; Ocampo et al., 2013; Peterson
et al., 2010, 2014, 2015; Skema, 2014; Small et al., 1998). Due to
functional and structural constraints required of group II plastid in-
trons, it is more conserved than intergenic spacers (Kelchner, 2002). In
Shaw et al. (2007) and Downie and Jansen (2015), this intron ranked
12 th out of 34 and 15 th out of 74 cpDNA loci, respectively. In both
studies it is the most variable of all plastid introns. Similarly, psbD–trnT
is rarely used (e.g., Kempton, 2012; Nazaire and Hufford, 2014;
Ocampo et al., 2013). Prior to Shaw et al. (2007) and Downie and
Jansen (2015), this region was noted by Daniell et al. (2006) as being
highly variable, and our study agrees with this assessment. Due to its
C.A. Danderson et al.
variability and number of PI characters, further consideration of
psbD–trnT should be given when attempting to elucidate lower-level
relationships.
CpDNA loci are indeed variable in their phylogenetic utility and
what may be a useful marker in one lineage may not be appropriate in
another. As such, the necessity of performing pilot studies by examining
multiple regions cannot be overstated. Consideration should also be
extended to regions demonstrating low levels of variability in other
groups, as with the case of the ndhA intron. It appears unlikely that
there is a common region that can elucidate lower-level relationships
across all angiosperm lineages.
4.3. Characterization of major clades
Rhodosciadium Group (Clade 1) – The species of Prionosciadium
and Rhodosciadium comprising this clade are similar to each other in
that they all have strongly dorsally compressed fruits. However,
members of Prionosciadium lack a stylopodium, have a tendency to be
taller, have less compound leaves, and do not die back to the ground
every year (Constance and Breedlove, 1994; Mathias and Constance,
1944–1945). Species of Prionosciadium and Rhodosciadium are easily
distinguished from those of Arracacia in that the latter have laterally
compressed fruits (Mathias and Constance, 1944–1945). We are not yet
aware of any shared morphological feature that can be used to support
the union of the species comprising this clade.
Arracacia xanthorrhiza Group (Clade 2) – As circumscribed, this
group contains three species of Arracacia distributed in South America
and three species of Prionosciadium distributed in Mexico. In his revi-
sion of South American Arracacia, Constance (1949) noted that A. an-
dina, A. equatorialis, and A. xanthorrhiza are probably closely related, a
hypothesis supported by our study. Hermann (1997) discovered wild
populations of A. xanthorrhiza in Peru and Ecuador, and hypothesized
that Ecuador may be the likely ancestral origin of the cultivated arra-
cacha based on features of overall morphological similarity, perennial
life cycle, and altitudinal distribution. He also confirmed the morpho-
logical similarities among A. andina, A. equatorialis, and A. xanthorrhiza.
The members of Prionosciadium in this group differ from the species of
Arracacia primarily in their strongly dorsally flattened fruits and their
different geographic distribution.
The cultivated form of A. xanthorrhiza formed a highly supported
clade with the wild polycarpic forms of A. xanthorrhiza, suggesting that
the ancestor of cultivated arracacha may be polycarpic, as indicated
previously by Hermann (1997). The wild monocarpic A. xanthorrhiza
forms a weakly supported sister group to a clade containing all acces-
sions of the polycarpic A. equatorialis and the cultivated and wild
polycarpic forms of A. xanthorrhiza. The accessions of A. andina form a
sister lineage to all other Arracacia in this group. All previous studies
including A. andina have regarded it as the closest relative to A. xan-
thorrhiza due to its similar morphology and life cycle; these studies have
also suggested that it should be subsumed into A. xanthorrhiza (Blas,
2005; Blas et al., 2008a; Constance, 1949; Hermann, 1997; Knudsen,
2003). We agree with this suggestion and propose that A. equatorialis
also be subsumed within A. xanthorrhiza.
Coulterophytum Group (Clade 3) – In all trees, the monotypic
Enantiophylla arises out of a clade containing Coulterophytum laxum and
C. pubescens. This relationship comes as no surprise, as both
Coulterophytum and Enantiophylla share a similar stipe-like contraction
of the base of the mericarps that is found nowhere else in the Arracacia
clade (Constance and Affolter, 1995; Coulter and Rose, 1893). As such,
we recommend that E. heydeana be transferred into Coulterophytum. The
low sequence divergence values between C. jaliscanum ined. and C.
reflexipes ined. suggest that if these taxa were to be described as new
species, only a single species may be warranted.
Donnellsmithia Group (Clade 4) – Members of the monophyletic
genus Donnellsmithia are similar morphologically to those of Arracacia
in their variable leaf complexity, laterally flattened fruit, and number of
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
fruit vittae. These genera differ in that Donnellsmithia is never woody,
the fruit is oval to ellipsoid or obcordate with narrow or filiform ribs,
the involucre and involucel are usually wanting, and the seed is not
sulcate in cross-section under the vittae.
Myrrhidendron Group (Clade 5) – The monophyletic genus
Myrrhidendron is readily distinguished from the species of Arracacia in
this clade on the basis of its fruit which are dorsally flattened, linear to
oblong in shape, and very large (8–20 mm long) and its cleft to toothed
bracts and bracteoles (Constance, 1949; Coulter and Rose, 1927;
Mathias and Constance, 1944–1945). No obvious morphological or
anatomical features support the relationship of these Arracacia species
to Myrrhidendron.
Coaxana Group (Clade 6) – Arracacia ebracteata clearly arises from
within the genus Coaxana. Arracacia ebracteata was originally described
as a species of Coaxana (Rose, 1905), but was later transferred to Ar-
racacia by Mathias and Constance (1973) on the basis that its mericarp
rib morphology was subequal and unwinged, whereas the ribs of C.
bambusioides and C. purpurea were heteromorphic and conspicuously
thin-winged. Notwithstanding carpology, they noted that A. ebracteata
was very similar to Coaxana in their sharing of conspicuously flaring
purplish leaf sheaths and purplish flowers. We recommend that A. eb-
racteata be transferred back to Coaxana and that the description of
Coaxana be emended to include this variation in fruit carpology.
Mathiasella Group (Clade 7) – Mathias and Constance (1941),
when describing Prionosciadium simplex, commented that it was closely
related to P. humile and that these two species were anomalous as they
have a small slender stature and simple inflorescence compared to the
tall, stout plants with complex, branching inflorescences that typify all
other species of Prionosciadium. Mathiasella is easily separated from
these two species by its involucre and involucel morphology (Constance
and Hitchcock, 1954). Closer examination of specimens will be needed
to determine if any morphological or anatomical features are shared by
the three species comprising this clade.
Arracacia edulis Group (Clade 8) – The three species (A. edulis, A.
hintonii, and A. schneideri) that make up this clade are anomalous in the
genus Arracacia in that they have a depressed and inconspicuous sty-
lopodium (Constance and Affolter, 1995; Mathias and Constance,
1944–1945). Although three other species of Arracacia (A. anomala, A.
compacta, and A. filipes) also have depressed stylopodia, they are readily
separated from this group on the basis of other morphological char-
acters. Due to the group’s anomalous nature, it is very probable that
they will be treated as a genus other than Arracacia in future revi-
sionary study.
Niphogeton and Cotopaxia Groups (Clades 9 and 10) – Among
outgroups considered, we included the genera Cotopaxia, Niphogeton, and
Perissocoeleum. With the addition of Austropeucedanum, the group has been
considered closely related to Arracacia, Prionosciadium, and Rhodosciadium
(Mathias and Constance, 1952, 1967). Austropeucedanum, Cotopaxia, Ni-
phogeton, and Perissocoeleum are largely restricted to páramo habitats of
South America. Results of the phylogenetic analyses affirm the close re-
lationships of Cotopaxia, Niphogeton, and Perissocoeleum to each other and
with the Arracacia clade. These genera differ from members of the Arra-
cacia clade primarily by the absence of inflexed petal tips (Mathias and
Constance, 1951, 1967). Based on the absence of this feature and results of
the phylogenetic analyses, we maintain these genera outside of the Arra-
cacia clade. Members of Niphogeton occur in two distinct clades and, thus,
the genus is not monophyletic. Niphogeton stricta (and N. scabra in the ITS
trees) allies with Cotopaxia asplundii. Mathias and Constance (1952) noted
that C. asplundii was similar in appearance to N. scabra and N. stricta.
Further sampling of Niphogeton, Perissocoeleum, and Cotopaxia from across
their range is required.
Eight taxa, including the monotypic genera Dahliaphyllum and
Ottoa, could not be placed unambiguously into one of the eight major
groups comprising the Arracacia clade. Whether additional sequence
data are better able to place these taxa into one of these eight major
clades or new major clades must be recognized remain to be seen.
C.A. Danderson et al.
5. Conclusions
The phylogenetic relationships of the complex assemblage of genera
belonging to the Arracacia clade remain largely unresolved, although
we have made some progress in delimiting major clades. Extensive
polyphyly of genera suggests drastic changes to the prevailing tax-
onomy are required, and rapid species radiations suggest that this will
be no small task. Resolution of relationships will also be confounded
because of the extensive polyploidy of the group, possibly due to hy-
bridization. We recognize eight major clades within the Arracacia clade
and two among its closest allies, with these ten clades providing the
necessary foundation for future revisionary studies of the group.
Morphological and fruit anatomical studies will be required to identify
non-DNA synapomorphies supporting each of these major clades.
An examination of 20 noncoding cpDNA loci in eight species of the
Arracacia clade and the outgroup Aethusa indicated that the trnQ–5′rps16,
trnD–trnT, psbD–trnT, and rpl32–trnL intergenic spacer regions and the
ndhA intron were the fastest evolving, as assessed by the greatest number
of variable and PI characters. A subsequent cost-benefit analysis, set up to
determine how many of these 20 regions would be necessary to maximize
resolution and branch support, revealed that five highly variable loci plus
the ITS region resulted in a similar amount of resolution as using all 20
noncoding cpDNA loci and ITS. Future molecular systematic studies of
the Arracacia clade, or any other major clade within the Apiaceae, would
benefit by the inclusion of these markers.
Acknowledgements
The authors thank the curators of herbaria CAS, F, GH, ILL, ILLS, ISU,
MICH, MO, NY, TEX, LL, UC, and US for access to specimens. We also thank
D. S. Katz-Downie, C. I. Calviño, and J. Stratton for assistance in the la-
boratory, and two anonymous reviewers for comments on a previous ver-
sion of the manuscript. Funding for this project was supported by NSF grant
DEB 0089452 to S.R. Downie, a Herbert H. Ross Memorial Fund award
(Illinois Natural History Survey), a Francis M. and Harlie M. Clark research
support grant, and a Harold C. and Sonja L. Labinsky award. This paper
represents a portion of a Ph.D. dissertation submitted by C.A. Danderson to
the Graduate College of the University of Illinois at Urbana-Champaign.
Appendix A
Accessions of Apiaceae from which the sequences for the nrDNA ITS
and cpDNA studies were obtained, with corresponding DNA accession
number, voucher information, taxonomic authorities, and GenBank
reference numbers.
A.1. Outgroup taxa
Aethusa cynapium L., DNA #127, Downie 127 (ILL), ITS-
GQ862376, 3′rps16-5′trnK-JQ304814, rps16 intron-JQ304823, trnQ-
5′rps16-JQ304832, trnS-5′trnG-JQ304841, trnG intron-JQ304850, atpI-
atpH-JQ304859, rpoB-trnC-JQ304868, petN-psbM-JQ304877, trnD-trnT-
JQ304886, psbD-trnT-JQ304895, trnS-trnfM-JQ304904, trnT-5′trnL-
JQ304911, trnL intron-JQ304920, ndhJ-3′trnL-JQ304929, 3′trnV-ndhC-
JQ304938, psbJ-petA-JQ304947, petL-psbE-JQ304956, ndhF-rpl32-
JQ304965, rpl32-trnL-JQ304973, ndhA intron-JQ304982. Angelica
ampla A. Nelson, DNA #1108, Hartman 25821 (RM), ITS-U79597,
U79598B. Angelica archangelica L., DNA #79, Downie 79 (ILL), ITS-
AH003539A. Angelica arguta Nutt. ex Torr. & A. Gray, DNA #773,
Raiche 364.90 (UC), ITS-U79599, U79600B. Cotopaxia asplundii
Math. & Const., DNA #3372, Baslev 2189 (MO), ITS-JQ304991, trnQ-
5′rps16-JX141821, rpl32-trnL-JX141984, ndhA intron-JX142071.
Cymopterus globosus (S. Wats.) S. Wats., DNA #819, Lyons-Weiler s.n.,
ITS-U78398, U78458B. Musineon divaricatum (Pursh) Nutt. ex
Torr. & A. Gray, DNA #1097, Nelson 30905 (RM), ITS-AF358506,
AF358573D. Neoparrya lithophila Math., DNA #944, Hartman 17360
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Molecular Phylogenetics and Evolution 118 (2018) 286–305
(RM), ITS-AF358509, AF358576D. Niphogeton azorelloides
Math. & Const., DNA #3701, Holm-Nielsen 16373 (F), ITS-GQ862482,
trnQ-5′rps16-JX141844, trnD-trnT-JX141921, rpl32-trnL-JX142007,
ndhA intron-JX142094. Niphogeton chirripoi (Suesseng.)
Math. & Const., DNA #3612, Weston 6058 (ISU), ITS-GQ862483, trnQ-
5′rps16-JX141845, trnD-trnT-JX141922, rpl32-trnL-JX142008, ndhA in-
tron-JX142095. Niphogeton dissecta (Benth.) Macbr., DNA #3371,
Grifo & Solomon 1013 (MO), ITS-JQ304992, trnQ-5′rps16-JX141846,
trnD-trnT-JX141923, rpl32-trnL-JX142009, ndhA intron-JX142096.
Niphogeton glaucescens (H. B. K.) Macbr., DNA #3706, Cuatrescasas
5535 (F), ITS-GQ862484; DNA #3707, Asplund 16822 (F), ITS-
GQ862485, trnQ-5′rps16-JX141847, trnD-trnT-JX141924, rpl32-trnL-
JX142010, ndhA intron-JX142097. Niphogeton josei Math. & Const.,
DNA #3700, Cuatrecasas 9427 (F), ITS-GQ862486. Niphogeton scabra
(Wolff) Macbr., DNA #3703, Hutchinson & Tovar 4267 (F), ITS-
GQ862487. Niphogeton stricta (Wolff) Math. & Const., DNA #3704,
Davis, Franquemont, King, & Sperling 1557 (F), ITS-GQ862488, trnQ-
5′rps16-JX141848, trnD-trnT-JX141925, rpl32-trnL-JX142011, ndhA in-
tron-JX142098. Niphogeton ternata (Willd. ex Schult.)
Math. & Const., DNA #3705, Skenar 8108 (F), ITS-GQ862489, trnQ-
5′rps16-JX141849, trnD-trnT-JX141926, rpl32-trnL-JX142012, ndhA in-
tron-JX142099. Oreoxis humilis Raf., DNA #1100, Hartman 11718
(RM), ITS-AF358512, AF358579D. Perissocoeleum barclagiae
Math. & Const., DNA #3373, Castañeda 4531 (MO), ITS-JQ304993.
Polytaenia texana (J. M. Coult. & Rose) Math. & Const., DNA #1508,
Barrie 1403 (RM), ITS-AY146867, AY146933E. Shoshonea pulvinata
Evert & Const., DNA #1105, Evert 10623 (RM), ITS-U78400, U78460B.
Taenidia integerrima (L.) Drude, DNA #763, Downie 763 (ILL), ITS-
U78399, U78459B. Tauschia kelloggii (A. Gray) Macbr., DNA #2220,
Ahart 6972 (UC), ITS-AY146883, AY146949E. Zizia aurea (L.) W. D.
Koch, DNA #8, Downie 8 (ILL), AH003554C.
A.2. Ingroup taxa
Arracacia aegopodioides J. M. Coult. & Rose, DNA #567,
Breedlove 72231 (CAS), ITS-AF358467, AF358534D, trnQ-5′rps16-
JX141790, trnD-trnT-JX141876, rpl32-trnL-JX141953, ndhA intron-
JX142040; DNA #3298, Anderson 13082 (UC), ITS-GQ862378; DNA
#3427, Vaughan, Dwyer, Spellman, & Wunderlin 1065 (MO), ITS-
GQ862377. Arracacia andina Britton, DNA #3251, Vásconez & Velasco
5 (COL), ITS-GQ862379; DNA #3252, Hermann & Montalvo 1586 plant
10 (COL), ITS-GQ862380, trnQ-5′rps16-JX141791, trnD-trnT-JX141877,
rpl32-trnL-JX141954, ndhA intron-JX142041; DNA #3253,
Hermann & Montalvo 1586 plant 11 (COL), ITS-GQ862381. Arracacia
anomala Math. & Const., DNA #3674, White 3495 (MICH), ITS-
GQ862382, trnQ-5′rps16-JX141792, trnD-trnT-JX141878, rpl32-trnL-
JX141955, ndhA intron-JX142042. Arracacia atropurpurea
Benth. & Hook. f. ex Hemsl., DNA #3426, Garcia & Pérez 3726 (MO),
ITS-GQ862383, trnQ-5′rps16-JX141793, trnD-trnT-JX141879, rpl32-
trnL-JX141956, ndhA intron-JX142043; DNA #3475, Zamudio & Díaz
4467 (MO), ITS-GQ862384. Arracacia bracteata J. M. Coult. & Rose,
DNA #573, Breedlove 72536 (CAS), ITS-AF358468, AF358535D, trnQ-
5′rps16-JX141794, trnD-trnT-JX141880, rpl32-trnL-JX141957, ndhA in-
tron-JX142044; DNA #3303, Cruden 1212 (UC), ITS-GQ862385.
Arracacia brandegei J. M. Coult. & Rose, DNA #504, Breedlove 43405
(UC), ITS-U30570, U30571B; DNA #3425, Moran 18886 (MO), ITS-
GQ862386, trnQ-5′rps16-JX141795, trnD-trnT-JX141881, rpl32-trnL-
JX141958, ndhA intron-JX142045. Arracacia compacta Rose, DNA
#3616, Cruden 1092 (ISU), ITS-GQ862387, trnQ-5′rps16-JX141796,
trnD-trnT-JX141882, rpl32-trnL-JX141959, ndhA intron-JX142046.
Arracacia donnell-smithii J. M. Coult. & Rose, DNA #3423, Breedlove
22815 & Smith (MO), ITS-GQ86238, trnQ-5′rps16- JX141797, trnD-trnT-
JX141883, rpl32-trnL-JX141960, ndhA intron-JX142047. Arracacia
ebracteata (Rose) Math. & Const., DNA #3421, Breedlove 39913 (MO),
ITS-GQ862389, 3′rps16-5′trnK-JQ304815, rps16 intron-JQ304824,
trnQ-5′rps16-JQ304833, trnS-5′trnG-JQ304842, trnG intron-JQ304851,
C.A. Danderson et al.
atpI-atpH-JQ304860, rpoB-trnC-JQ304869, petN-psbM-JQ304878, trnD-
trnT-JQ304887, psbD-trnT-JQ304896, trnS-trnfM-JQ304905, trnT-
5′trnL-JQ304912, trnL intron-JQ304921, ndhJ-3′trnL-JQ304930, 3′trnV-
ndhC-JQ304939, psbJ-petA-JQ304948, petL-psbE-JQ304957, ndhF-
rpl32-JQ304966, rpl32-trnL-JQ304974, ndhA intron-JQ304983; DNA
#3468, Breedlove 37333 (MO), ITS-GQ862390. Arracacia edulis S.
Wats., DNA #3682, Straw & Forman 1995 (MICH), ITS-GQ862391,
trnQ-5′rps16-JX141798, trnD-trnT-JX141884, rpl32-trnL-JX141961,
ndhA intron-JX142048. Arracacia elata Wolff, DNA #3236, Hermann
1451 plant 2 & Montalvo (COL), ITS-GQ862393, trnQ-5′rps16-JX141799,
rpl32-trnL-JX141962, ndhA intron-JX142049; DNA #3257, Vásconez 8
(COL), ITS-GQ862395; DNA #3285, Hermann & Montalvo 1585 (COL),
ITS-GQ862392; DNA #3286, Hermann 1451 plant 1 & Montalvo (COL),
ITS-GQ862394. Arracacia equatorialis Const., DNA #3243,
Hermann & Montalvo 1605 plant 3 (COL), ITS-GQ862396, trnQ-5′rps16-
JX141800, trnD-trnT-JX141885, rpl32-trnL-JX141963, ndhA intron-
JX142050; DNA #3246, Hermann & Montalvo 1614 (COL), ITS-
GQ862397; DNA #3247, Hermann & Montalvo 1605 plant 4 (COL), ITS-
GQ862398. Arracacia filipes Math. & Const., DNA #3683, Breedlove
18922 (MICH), ITS-GQ862399, trnQ-5′rps16-JX141801, trnD-trnT-
JX141886, rpl32-trnL-JX141964, ndhA intron-JX142051. Arracacia
fruticosa Rose, DNA #3835, Breedlove 72204 & Mahoney (CAS), ITS-
GQ862400, trnQ-5′rps16-JX141802, trnD-trnT-JX141887, rpl32-trnL-
JX141965, ndhA intron-JX142052. Arracacia hemsleyana J. M.
Coult. & Rose, DNA #3836, Breedlove 63612 & Anderson (CAS), ITS-
GQ862401, trnQ-5′rps16-JX141803, rpl32-trnL-JX141966, ndhA intron-
JX142053; DNA #3868, Johnston s.n. (TEX), ITS-JQ304994. Arracacia
hintonii Const. & Affolter, DNA #3785, Hinton et al. 22472 (TEX), ITS-
GQ862403, trnQ-5′rps16-JX141804, trnD-trnT-JX141888, rpl32-trnL-
JX141967, ndhA intron-JX142054; DNA #3786, Hinton et al. 19159
(TEX), ITS-GQ862404; DNA #3787, Hinton et al. 18410 (TEX), ITS-
GQ862405. Arracacia longipedunculata J. M. Coult. & Rose, DNA
#3685, Roe & Rose 1850 (MICH), ITS-GQ862406, trnQ-5′rps16-
JX141805, trnD-trnT-JX141889, rpl32-trnL-JX141968, ndhA intron-
JX142055; DNA #3867, Hinton 1142 (F), ITS-JQ304995. Arracacia
macvaughii Math. & Const., DNA #3686, Denton 1969 (MICH), ITS-
GQ862407, trnQ-5′rps16-JX141806, trnD-trnT-JX141890, rpl32-trnL-
JX141969, ndhA intron-JX142056; DNA #3687, Barriga & Cols. 6906
(MICH), ITS-GQ862408. Arracacia molseedii Math. & Const., DNA
#3429, Cedillo 609 & Lorence (MO), ITS-GQ862409, trnQ-5′rps16-
JX141807, trnD-trnT-JX141891, rpl32-trnL-JX141970, ndhA intron-
JX142057. Arracacia moschata DC., DNA #3234, Vásconez & Vacas 11
(COL), ITS-GQ862414; DNA #3235, Hermann 1471 plant 2 & Vásconez
(COL), ITS-GQ862415; DNA #3237, C. P. 33, ITS-GQ862410, trnQ-
5′rps16-JX141808, trnD-trnT-JX141892, rpl32-trnL-JX141971, ndhA in-
tron-JX142058; DNA #3238, Hermann 1427 (COL), ITS-GQ862411;
DNA #3239, Hermann 1541 & Korntheuer (COL), ITS-GQ862412; DNA
#3256, Vásconez & Vacas 14 (COL), ITS-GQ862416; DNA #3287,
Hermann 1471 plant 1 & Vásconez (COL), ITS-GQ862417; DNA #3289,
Hermann 1623 & Korntheuer (COL), ITS-GQ862413. Arracacia nelsonii
J. M. Coult. & Rose, DNA #560, Breedlove 72434 (UC), ITS-U30556,
U30557B, trnQ-5′rps16-JX141809, trnD-trnT-JX141893, rpl32-trnL-
JX141972, ndhA intron-JX142059; DNA #3300, Steyermark 48965
(UC), ITS-GQ862418; DNA #3424, Breedlove 41107 (MO), ITS-
GQ862419. Arracacia pringlei J. M. Coult. ex Rose, DNA #3678,
Breedlove 8105 & Raven (MICH), ITS-GQ862420, trnQ-5′rps16-
JX141810, trnD-trnT-JX141894, rpl32-trnL-JX141973, ndhA intron-
JX142060. Arracacia quadrifida Const. & Affolter, DNA #3614,
Degener & Degener 26275 (ISU), ITS-GQ862421, trnQ-5′rps16-JX141811,
trnD-trnT-JX141895, rpl32-trnL-JX141974, ndhA intron-JX142061;
DNA #3866, Molseed 384 (ISU), ITS-JQ304996. Arracacia ravenii
Const. & Affolter, DNA #3428, Snow 212 with Whittemore (MO), ITS-
GQ862422; DNA #3470, Ton 9529 & Mtz. de Lopez (MO), ITS-
GQ862423, trnQ-5′rps16-JX141812, trnD-trnT-JX141896, rpl32-trnL-
JX141975, ndhA intron-JX142062. Arracacia rigida J. M.
Coult. & Rose, DNA #3422, Ventura 1183 (MO), ITS-GQ862424; DNA
301
Molecular Phylogenetics and Evolution 118 (2018) 286–305
#3677, Ventura 3057 (MICH), ITS-GQ862425, trnQ-5′rps16-JX141813,
trnD-trnT-JX141897, rpl32-trnL-JX141976, ndhA intron-JX142063.
Arracacia schneideri Math. & Const., DNA #3432, Chittenden 106 with
Atkins (MO), ITS-GQ862426, trnQ-5′rps16-JX141814, trnD-trnT-
JX141898, rpl32-trnL-JX141977, ndhA intron-JX142064. Arracacia
ternata Math. & Const., DNA #3675, Bartlett 10379 (MICH), ITS-
GQ862427, trnQ-5′rps16-JX141815, trnD-trnT-JX141899, rpl32-trnL-
JX141978, ndhA intron-JX142065; DNA #3676, Bartlett 10153 (MICH),
ITS-GQ862428. Arracacia tolucensis var. tolucensis (H. B. K.) Hemsl.,
DNA #569, Ornduff 8560 (UC), ITS-AF358469, AF358536D, trnQ-
5′rps16-JX141817, trnD-trnT-JX141901, rpl32-trnL-JX141980, ndhA in-
tron-JX142067; DNA #3302, McVaugh 12277 (UC), ITS-GQ862429.
Arracacia tolucensis (H. B. K.) Hemsl. var. multifida (S. Wats.)
Math. & Const., DNA #556, cult. UC Berkeley, L. Constance pers. coll.
C-2355, ITS-AF358470, AF358537D, trnQ-5′rps16-JX141816, trnD-trnT-
JX141900, rpl32-trnL-JX141979, ndhA intron-JX142066; DNA #3301,
Bell 16761 & Duke (UC), ITS-GQ862430. Arracacia vaginata J. M.
Coult. & Rose, DNA #3672, Ton 970 (MICH), ITS-GQ862431; DNA
#3673, Breedlove 6859 (MICH), ITS-GQ862432. Arracacia xanthor-
rhiza Bancr. cultivated, DNA #3240, Hermann 1559 (COL), ITS-
GQ862433; DNA #3241, Hermann 1560 (COL), ITS-GQ862434; DNA
#3242, Hermann 836 (COL), ITS-GQ862435; DNA #3244, Hermann
1516 (COL), ITS-GQ862436, 3′rps16-5′trnK-JQ304816, rps16 intron-
JQ304825, trnQ-5′rps16-JQ304834, trnS-5′trnG-JQ304843, trnG intron-
JQ304852, atpI-atpH-JQ304861, rpoB-trnC-JQ304870, petN-psbM-
JQ304879, trnD-trnT-JQ304888, psbD-trnT-JQ304897, trnS-trnfM-
JQ304906, trnT-5′trnL-JQ304913, trnL intron-JQ304922, ndhJ-3′trnL-
JQ304931, 3′trnV-ndhC-JQ304940, psbJ-petA-JQ304949, petL-psbE-
JQ304958, ndhF-rpl32-JQ304967, rpl32-trnL-JQ304975, ndhA intron-
JQ304984; DNA #3245, Hermann 1554 (COL), ITS-GQ862437.
Arracacia xanthorrhiza Bancr. monocarpic, DNA #3249, Hermann
764 (COL), ITS-GQ862441; DNA #3260, Hermann 1003 (COL), ITS-
GQ862442; DNA #3261, Cruz 108 (COL), ITS-GQ862443, trnQ-5′rps16-
JX141819, trnD-trnT-JX141903, rpl32-trnL-JX141982, ndhA intron-
JX142069; DNA #3262, Hermann 1627 & Cruz (COL), ITS-GQ862444;
DNA #3290, Blas 1 (COL), ITS-GQ862445. Arracacia xanthorrhiza
Bancr. polycarpic, DNA #3248, Hermann & Montalvo 1612 plant 3
(COL), ITS-GQ862438, trnQ-5′rps16-JX141818, trnD-trnT-JX141902,
rpl32-trnL-JX141981, ndhA intron-JX142068; DNA #3250,
Hermann & Montalvo 1612 plant 5 (COL), ITS-GQ862439; DNA #3259,
Hermann & Montalvo 1612 (COL), ITS-GQ862440. Coaxana bambu-
sioides Math. & Const., DNA #3515, Reveal, Peterson, Harley, & Broome
4297 (MO), ITS-GQ862446; DNA #3518, Breedlove 36014 (MO), ITS-
GQ862447, trnQ-5′rps16-JX141820, trnD-trnT-JX141904, rpl32-trnL-
JX141983, ndhA intron-JX142070; DNA #3821, Breedlove 61980
(CAS), ITS-GQ862448. Coaxana purpurea J. M. Coult. & Rose, DNA
#515, Breedlove 72745 (UC), ITS-U30572, U30573B; DNA #3297,
Breedlove 12248 (UC), ITS-GQ862449, 3′rps16-5′trnK-JQ304817, rps16
intron-JQ304826, trnQ-5′rps16-JQ304835, trnS-5′trnG-JQ304844, trnG
intron-JQ304853, atpI-atpH-JQ304862, rpoB-trnC-JQ304871, petN-
psbM-JQ304880, trnD-trnT-JQ304889, psbD-trnT-JQ304898, trnT-
5′trnL-JQ304914, trnL intron-JQ304923, ndhJ-3′trnL-JQ304932, 3′trnV-
ndhC-JQ304941, psbJ-petA-JQ304950, petL-psbE-JQ304959, rpl32-trnL-
JQ304976, ndhA intron-JQ304985. Coulterophytum jaliscanum
McVaugh ined., DNA #840, Iltis et al. 1299 (UC), ITS-AF358473,
AF358540D, trnQ-5′rps16-JX141822, trnD-trnT-JX141905, rpl32-trnL-
JX141985, ndhA intron-JX142072. Coulterophytum laxum B. L. Rob.,
DNA #565, Iltis 298 & Cochrane (UC), ITS-U30560, U30561B, trnQ-
5′rps16-JX141823, trnD-trnT-JX141906, rpl32-trnL-JX141986, ndhA in-
tron-JX142073. Coulterophytum pubescens J. M. Coult. & Rose, DNA
#3619, Rzedowski 26206 (MICH), ITS-GQ862450, trnQ-5′rps16-
JX141824, rpl32-trnL-JX141987, ndhA intron-JX142074.
Coulterophytum reflexipes Const. & Affolter ined., DNA #3822,
Breedlove 64455 & Anderson (CAS), ITS-GQ862451. Dahliaphyllum al-
medae Const. & Breedlove, DNA # 796, Breedlove 61970 (UC), ITS-
U78395, U78455B, trnQ-5′rps16-JX141825, trnD-trnT-JX141907, rpl32-
C.A. Danderson et al.
trnL-JX141988, ndhA intron-JX142075. Donnellsmithia ampulliformis
Math. & Const., DNA #3697, Koch, Fryxell, & Altman 87154 (F), ITS-
GQ862452, trnQ-5′rps16-JX141826, rpl32-trnL-JX141989, ndhA intron-
JX142076. Donnellsmithia biennis (J. M. Coult. & Rose)
Math. & Const., DNA #3783, Barrie 1517 with Luckow (TEX), ITS-
GQ862453, trnQ-5′rps16-JX141827, trnD-trnT-JX141908, rpl32-trnL-
JX141990, ndhA intron-JX142077. Donnellsmithia breedlovei
Math. & Const., DNA #3613, Breedlove 12374 (ISU), ITS-GQ862454,
trnQ-5′rps16-JX141828, trnD-trnT-JX141909, rpl32-trnL-JX141991,
ndhA intron-JX142078. Donnellsmithia cordata (J. M. Coult. & Rose)
Math. & Const., DNA #3833, Breedlove 61872 (CAS), ITS-GQ862455,
trnQ-5′rps16-JX141829, rpl32-trnL-JX141992, ndhA intron-JX142079.
Donnellsmithia dissecta (J. M. Coult. & Rose) Math. & Const., DNA
#3293, Juárez 1657 (UC), ITS-GQ862456, trnQ-5′rps16-JX141830,
trnD-trnT-JX141910, rpl32-trnL-JX141993, ndhA intron-JX142080.
Donnellsmithia guatemalensis J. M. Coult. & Rose, DNA #3517,
Tenorio 14847, Martínez, Droege, & Díaz (MO), ITS-GQ862457, trnQ-
5′rps16-JX141831, trnD-trnT-JX141911, rpl32-trnL-JX141994, ndhA in-
tron-JX142081. Donnellsmithia juncea var. juncea (Humb. & Bonpl.
ex Spreng.) Math. & Const., DNA #3511, Paredes 10 (MO), ITS-
GQ862458; DNA #3512, Saynes 717 (MO), ITS-GQ862459, trnQ-
5′rps16-JX141832, trnD-trnT-JX141912, rpl32-trnL-JX141995, ndhA in-
tron-JX142082. Donnellsmithia juncea (Humb. & Bonpl. ex Spreng.)
Math. & Const. var. purpurea (J. M. Coult. & Rose) Math. & Const.,
DNA #3824, Breedlove 63923 & Anderson (CAS), ITS-GQ862460, trnQ-
5′rps16-JX141833, trnD-trnT-JX141913, rpl32-trnL-JX141996, ndhA in-
tron-JX142083. Donnellsmithia mexicana (B. L. Rob.)
Math. & Const., DNA #3827, Breedlove 36156 (CAS), ITS-GQ862461,
trnQ-5′rps16-JX141834, trnD-trnT-JX141914, rpl32-trnL-JX141997,
ndhA intron-JX142084. Donnellsmithia ovata (J. M. Coult. & Rose)
Math. & Const., DNA #3829, Breedlove 59147 & Almeda (CAS), ITS-
GQ862462, trnQ-5′rps16-JX141835, rpl32-trnL-JX141998, ndhA intron-
JX142085. Donnellsmithia pinnatisecta (Riley) Math. & Const., DNA
#3513, Téllez 11023 (MO), ITS-GQ862463, trnQ-5′rps16-JX141836,
trnD-trnT-JX141915, rpl32-trnL-JX141999, ndhA intron-JX142086.
Donnellsmithia reticulata (J. M. Coult. & Rose) Math. & Const., DNA
#3832, Breedlove 61546 (CAS), ITS-GQ862464, trnQ-5′rps16-
JX141837, rpl32-trnL-JX142000, ndhA intron-JX142087.
Donnellsmithia serrata (J. M. Coult. & Rose) Math. & Const., DNA
#3521, Tenorio 20420 with Alvarado & Martínez (MO), ITS-GQ862465,
trnQ-5′rps16-JX141838, trnD-trnT-JX141916, rpl32-trnL-JX142001,
ndhA intron-JX142088; DNA #3828, Breedlove 26735 (CAS), ITS-
GQ86246. Donnellsmithia ternata (S. Wats.) Math. & Const., DNA
#3671, Hinton et al. 23305 (MICH), ITS-GQ862467, trnQ-5′rps16-
JX141839, trnD-trnT-JX141917, rpl32-trnL-JX142002, ndhA intron-
JX142089. Enantiophylla heydeana J. M. Coult. & Rose, DNA #572,
Iltis et al. 3187 (UC), ITS-U30558, U30559B, 3′rps16-5′trnK-JQ304818,
rps16 intron-JQ304827, trnQ-5′rps16-JQ304836, trnS-5′trnG-JQ304845,
trnG intron-JQ304854, atpI-atpH-JQ304863, rpoB-trnC-JQ304872,
petN-psbM-JQ304881, trnD-trnT-JQ304890, psbD-trnT-JQ304899, trnS-
trnfM-JQ304907, trnT-5′trnL-JQ304915, trnL intron-JQ304924, ndhJ-
3′trnL-JQ304933, 3′trnV-ndhC-JQ304942, psbJ-petA-JQ304951, petL-
psbE-JQ304960, ndhF-rpl32-JQ304968, rpl32-trnL-JQ304977, ndhA in-
tron-JQ304986; DNA #3433, Flores-Franco, Calzada, & Solís 2840 (MO),
ITS-GQ862468. Mathiasella bupleuroides Const. & C. L. Hitchc., DNA
#802, Hinton et al. 22234 (UC), ITS-U78394, U78454B, 3′rps16-5′trnK-
JQ304819, rps16 intron-JQ304828, trnQ-5′rps16-JQ304837, trnS-
5′trnG-JQ304846, trnG intron-JQ304855, atpI-atpH-JQ304864, rpoB-
trnC-JQ304873, petN-psbM-JQ304882, trnD-trnT-JQ304891, psbD-trnT-
JQ304900, trnS-trnfM-JQ304908, trnT-5′trnL-JQ304916, trnL intron-
JQ304925, ndhJ-3′trnL-JQ304934, 3′trnV-ndhC-JQ304943, psbJ-petA-
JQ304952, petL-psbE-JQ304961, ndhF-rpl32-JQ304969, rpl32-trnL-
JQ304978, ndhA intron-JQ304987. Myrrhidendron donnell-smithii J.
M. Coult. & Rose, DNA #561, Grantham & Parsons 0433–90 (UC), ITS-
U30554, U30555B; DNA #563, Grantham & Parsons 0198–90 (UC), ITS-
U30554, U30555B; DNA #3484, Alfaro 1727 (MO), ITS-GQ862471;
302
Molecular Phylogenetics and Evolution 118 (2018) 286–305
DNA #3495, Almeda 2208, Flowers, & Wyatt (MO), ITS-GQ862470,
3′rps16-5′trnK-JQ304820, rps16 intron-JQ304829, trnQ-5′rps16-
JQ304838, trnS-5′trnG-JQ304847, trnG intron-JQ304856, atpI-atpH-
JQ304865, rpoB-trnC-JQ304874, petN-psbM-JQ304883, trnD-trnT-
JQ304892, psbD-trnT-JQ304901, trnT-5′trnL-JQ304917, trnL intron-
JQ304926, ndhJ-3′trnL-JQ304935, 3′trnV-ndhC-JQ304944, psbJ-petA-
JQ304953, petL-psbE-JQ304962, ndhF-rpl32-JQ304970, rpl32-trnL-
JQ304979, ndhA intron-JQ304988; DNA #3496, Morales 1151, Poveda,
Jímenez, & Lépiz (MO), ITS-GQ862469. Myrrhidendron glaucescens J.
M. Coult. & Rose, DNA #3489, Ølgaard, Brandbyge, Roth, & Sperling
34452 (MO), ITS-GQ862472, trnQ-5′rps16-JX141840, rpl32-trnL-
JX142003, ndhA intron-JX142090. Myrrhidendron maxonii J. M.
Coult. & Rose, DNA #3492, Hammel 2811 (MO), ITS-GQ862473; DNA
#3516, D’Arcy, Hammel, Hill, Schwartz, & Wolcott 12898 (MO), ITS-
GQ862474; DNA #3519, McPherson 9491 (MO), ITS-GQ862475, trnQ-
5′rps16-JX141841, trnD-trnT-JX141918, rpl32-trnL-JX142004, ndhA in-
tron-JX142091. Myrrhidendron pennellii J. M. Coult. & Rose, DNA
#3491, Arbelaez, Vélez, Carvajal, & Uribe 630 (MO), ITS-GQ862476,
trnQ-5′rps16-JX141842, trnD-trnT-JX141919, rpl32-trnL-JX142005,
ndhA intron-JX142092. Neonelsonia acuminata (Benth.) J. M.
Coult. & Rose, DNA #3231, Hermann 1512 (CUVC), ITS-GQ862477,
trnQ-5′rps16-JX141843, trnD-trnT-JX141920, rpl32-trnL-JX142006,
ndhA intron-JX142093; DNA #3232, Vásconez & Montalvo 18 (COL),
ITS-GQ862478; DNA #3233, Vásconez & Velasco 3 (COL), ITS-
GQ862479; DNA #3295, Panero 3483 with Dávila & Calzada (UC), ITS-
GQ862481; DNA #3430, Roldán, Mosquera, Niño, Correa, & Giraldo
3194 (MO), ITS-GQ862480. Ottoa oenanthoides var. oenanthoides H.
B. K., DNA #3254, Moran 7744 & Feist (ILLS), ITS-GQ862490, 3′rps16-
5′trnK-JQ304821, rps16 intron-JQ304830, trnQ-5′rps16-JQ304839,
trnS-5′trnG-JQ304848, trnG intron-JQ304857, atpI-atpH-JQ304866,
rpoB-trnC-JQ304875, petN-psbM-JQ304884, trnD-trnT-JQ304893, psbD-
trnT-JQ304902, trnS-trnfM-JQ304909, trnT-5′trnL-JQ304918, trnL in-
tron-JQ304927, ndhJ-3′trnL-JQ304936, 3′trnV-ndhC-JQ304945, psbJ-
petA-JQ304954, petL-psbE-JQ304963, ndhF-rpl32-JQ304971, rpl32-trnL-
JQ304980, ndhA intron-JQ304989. Ottoa oenanthoides H. B. K. var.
major (Wedd.) Math. & Const. in Lasser, DNA #3708,
Charpin & Jacquemoud 13650 (F), ITS-GQ862491. Prionosciadium
acuminatum B. L. Rob. ex J. M. Coult. & Rose, DNA #770, Breedlove
36448 (CAS), ITS-AF358517, AF358584D, trnQ-5′rps16-JX141850,
trnD-trnT-JX141927, rpl32-trnL-JX142013, ndhA intron-JX142100;
DNA #3486, Anderson 12577 (MO), ITS-GQ862492; DNA #3661,
Roberts & Keil 10230 (MICH), ITS-GQ862514. Prionosciadium bellii
Math. & Const., DNA #3476, Soto Núñez, Román de Soto & Soto 6486
(MO), ITS-GQ862509; DNA #3659, Anderson & Anderson 5000 (MICH),
ITS-GQ862493, trnQ-5′rps16-JX141851, trnD-trnT-JX141928, rpl32-
trnL-JX142014, ndhA intron-JX142101. Prionosciadium cuneatum J.
M. Coult. & Rose, DNA #3870, Feddema 723 (MICH), ITS-JQ304997.
Prionosciadium dissectum J. M. Coult. & Rose, DNA #3480,
Miller & Téllez 3213 (MO), ITS-GQ862495; DNA #3481, Bell
16657 & Duke (MO), ITS-GQ862496, trnQ-5′rps16-JX141852, trnD-trnT-
JX141929, rpl32-trnL-JX142015, ndhA intron-JX142102.
Prionosciadium diversifolium Rose, DNA #3467, Breedlove 25999
(MO), ITS-GQ862497, trnQ-5′rps16-JX141853, trnD-trnT-JX141930,
rpl32-trnL-JX142016, ndhA intron-JX142103; DNA #3609,
Degener & Degener 26230 (ISU), ITS-GQ862498. Prionosciadium filifo-
lium J. M. Coult. & Rose, DNA # 3660, McVaugh 17648 (MICH), ITS-
GQ862499, trnQ-5′rps16-JX141854, trnD-trnT-JX141931, rpl32-trnL-
JX142017, ndhA intron-JX142104. Prionosciadium gomez-pompai
Const. & Affolter ined., DNA #3696, Baéz & Paredes 30 (F), ITS-
GQ862500; DNA #3888, Avendano 00028 (F), ITS-JQ304998.
Prionosciadium humile Rose, DNA #3610, Beetle 14980 (ISU), ITS-
GQ862501, trnQ-5′rps16-JX141855, trnD-trnT-JX141932, rpl32-trnL-
JX142018, ndhA intron-JX142105. Prionosciadium lilacinum
Math. & Const., DNA #3479, Andreason, Oliver, & Verhoek-Williams 644
(MO), ITS-GQ862502. Prionosciadium linearifolium J. M.
Coult. & Rose, DNA #3658, McVaugh 18660 (MICH), ITS-GQ862503,
C.A. Danderson et al.
trnQ-5′rps16-JX141856, trnD-trnT-JX141933, rpl32-trnL-JX142019,
ndhA intron-JX142106. Prionosciadium macrophyllum J. M.
Coult. & Rose, DNA #3782, McVaugh 24699 (MICH), ITS-GQ862504,
trnD-trnT-JX141934, rpl32-trnL-JX142020. Prionosciadium madrense
S. Wats., DNA #3477, Torres 3724 & Tenorio (MO), ITS-GQ862505;
DNA #3478, Bell 16602 & Duke (MO), ITS-GQ862506; DNA #3667,
Maysilles 8184 (MICH), ITS-GQ862507; DNA #3781, Maysilles 7810
(MICH), ITS-GQ862508; DNA #3872, Pennington 229 (TEX), ITS-
JQ304999. Prionosciadium megacarpum J. M. Coult. & Rose, DNA
#3873, Molseed & Rice 230 (ISU), ITS-JQ305000; DNA #3874, Soto
Núñez 5292 (NY), ITS-JQ305001. Prionosciadium nelsonii J. M.
Coult. & Rose, DNA #3473, Breedlove 39629 (MO), ITS-GQ862510,
trnQ-5′rps16-JX141857, trnD-trnT-JX141935, rpl32-trnL-JX142021,
ndhA intron-JX142107; DNA #3474, Breedlove 26373 (MO), ITS-
GQ862511. Prionosciadium saraviki Laferr., DNA #3879, Van
Devender 97–885, Reina, Larson, Merlin, & Martinez (CAS), ITS-
JQ305002; DNA #3880, Pennington 174 (TEX), ITS-JQ305003.
Prionosciadium serratum J. M. Coult. & Rose, DNA #3876, Flores
1639, with Tellez, Tenorio, & Cadena (MICH), ITS-JQ305004.
Prionosciadium simplex Math. & Const., DNA #497, Breedlove 63487
(CAS), ITS-AF358518, AF358585D, trnQ-5′rps16-JX141858, trnD-trnT-
JX141936, rpl32-trnL-JX142022, ndhA intron-JX142108.
Prionosciadium thapsoides var. thapsoides (DC.) Math. & Const.,
DNA #3611, Molseed 355 (ISU), ITS-GQ862512, trnQ-5′rps16-
JX141859, trnD-trnT-JX141937, rpl32-trnL-JX142023, ndhA intron-
JX142109; DNA #3662, McVaugh 18355 (MICH), ITS-GQ862494; DNA
#3878, Nevling & Gomez-Pompa 2153 (F), ITS-JQ305005.
Prionosciadium thapsoides (DC.) Math. & Const. var. pringlei (S.
Wats.) Math. & Const., DNA #3788, Correll & Gentry 22826 (LL), ITS-
GQ862513, trnQ-5′rps16-JX141860, trnD-trnT-JX141938, rpl32-trnL-
JX142024, ndhA intron-JX142110; DNA #3877, Bye, Jr. 6693 (GH),
ITS-JQ305006. Prionosciadium townsendii Rose, DNA #3882, Fryxell
3801 (MICH), ITS-JQ305007. Prionosciadium turneri
Const. & Affolter, DNA # 568, Turner s.n. (UC), ITS-U30568, U30569B,
trnQ-5′rps16-JX141861, trnD-trnT-JX141939, rpl32-trnL-JX142025,
ndhA intron-JX142111; DNA #3294, McVaugh 15566 (UC), ITS-
GQ862515. Prionosciadium watsonii J. M. Coult. & Rose ex S. Wats.,
DNA #496, Breedlove 61338 (CAS), ITS-AF358519, AF358586D, trnQ-
5′rps16-JX141862, trnD-trnT-JX141940, rpl32-trnL-JX142026, ndhA in-
tron-JX142112. Rhodosciadium argutum (Rose) Math. & Const., DNA
#551, Rzedowski 41342 (UC), ITS-U30566, U30567B, 3′rps16-5′trnK-
JQ304822, rps16 intron-JQ304831, trnQ-5′rps16-JQ304840, trnS-
5′trnG-JQ304849, trnG intron-JQ304858, atpI-atpH-JQ304867, rpoB-
trnC-JQ304876, petN-psbM-JQ304885, trnD-trnT-JQ304894, psbD-trnT-
JQ304903, trnS-trnfM-JQ304910, trnT-5′trnL-JQ304919, trnL intron-
JQ304928, ndhJ-3′trnL-JQ304937, 3′trnV-ndhC-JQ304946, psbJ-petA-
JQ304955, petL-psbE-JQ304964, ndhF-rpl32-JQ304972, rpl32-trnL-
JQ304981, ndhA intron-JQ304990. Rhodosciadium diffusum (J. M.
Coult. & Rose) Math. & Const., DNA #3520, Meléndez JMM306 (MO),
ITS-GQ862516; DNA #3522, Breedlove 52134 (MO), ITS-GQ862517,
trnQ-5′rps16-JX141863, rpl32-trnL-JX142027, ndhA intron-JX142113;
DNA #3665, Bell 16654 & Duke (MICH), ITS-GQ862519; DNA #3669,
Rzedowski 44348 (MICH), ITS-GQ862518. Rhodosciadium dissectum J.
M. Coult. & Rose, DNA #3820, Breedlove 69538 (CAS), ITS-GQ862520,
trnQ-5′rps16-JX141864, trnD-trnT-JX141941, rpl32-trnL-JX142028,
ndhA intron-JX142114. Rhodosciadium glaucum var. glaucum J. M.
Coult. & Rose, DNA #3487, Tenorio 20373 (MO), ITS-GQ862521, trnQ-
5′rps16-JX141865, trnD-trnT-JX141942, rpl32-trnL-JX142029, ndhA in-
tron-JX142115; DNA #3883, Turner 15190 (TEX), ITS-JQ305008.
Rhodosciadium glaucum var. lineare J. M. Coult. & Rose, DNA
#3666, Anderson & Anderson 4754 (MICH), ITS-GQ862522, trnQ-
5′rps16-JX141866, trnD-trnT-JX141943, rpl32-trnL-JX142030, ndhA in-
tron-JX142116. Rhodosciadium longipes (Rose) Math. & Const., DNA
#3699, Pringle 10297 (F), ITS-GQ862523, trnQ-5′rps16-JX141867, trnD-
trnT-JX141944, rpl32-trnL-JX142031, ndhA intron-JX142117; DNA
#3884, Breedlove 59537 & Almeda (NY), ITS-JQ305009.
303
Molecular Phylogenetics and Evolution 118 (2018) 286–305
Rhodosciadium macvaughiae Math. & Const., DNA #3668, González
437 (MICH), ITS-GQ862524, trnQ-5′rps16-JX141868, trnD-trnT-
JX141945, rpl32-trnL-JX142032, ndhA intron-JX142118; DNA #3826,
Breedlove 64190 & Anderson (CAS), ITS-GQ862525. Rhodosciadium
montanum (J. M. Coult. & Rose) Math. & Const., DNA #3494,
Rzedowski 44731 (MO), ITS-GQ862526, trnQ-5′rps16-JX141869, trnD-
trnT-JX141946, rpl32-trnL-JX142033, ndhA intron-JX142119; DNA
#3885, McVaugh 18357 (MICH), ITS-JQ305010; DNA #3886, Denton
1951 (MICH), ITS-JQ305011. Rhodosciadium nelsonii (J. M.
Coult. & Rose) Math. & Const., DNA #3488, Breedlove 37546 (MO),
ITS-GQ862527, trnQ-5′rps16-JX141870, trnD-trnT-JX141947, rpl32-
trnL-JX142034, ndhA intron-JX142120. Rhodosciadium nudicaule (J.
M. Coult. & Rose) Drude, DNA #3523, Martin 555 (MO), ITS-
GQ862528, trnQ-5′rps16-JX141871, trnD-trnT-JX141948, rpl32-trnL-
JX142035, ndhA intron-JX142121. Rhodosciadium pringlei S. Wats.,
DNA #3664, Flores 4046 (MICH), ITS-GQ862529; DNA #3670,
McVaugh 19800 (MICH), ITS-GQ862530, trnQ-5′rps16-JX141872, trnD-
trnT-JX141949, rpl32-trnL-JX142036, ndhA intron-JX142122.
Rhodosciadium purpureum (Rose) Math. & Const., DNA #3493, Koch
77130 (MO), ITS-GQ862531, trnQ-5′rps16-JX141873, trnD-trnT-
JX141950, rpl32-trnL-JX142037, ndhA intron-JX142123; DNA #3887,
Pringle s.n. (LL), ITS-JQ305012. Rhodosciadium tolucense (H. B. K.)
Math., DNA #3482, Escobedo 1586 (MO), ITS-GQ862533, trnQ-5′rps16-
JX141874, trnD-trnT-JX141951, rpl32-trnL-JX142038, ndhA intron-
JX142124; DNA #3483, Fuentes 637 (MO), ITS-GQ862532; DNA
#3684, Zamudio 3910 (MICH), ITS-GQ862534. Rhodosciadium tuber-
osum J. M. Coult. & Rose, DNA #3663, Rzedowski 16789 (MICH), ITS-
GQ862535, trnQ-5′rps16-JX141875, trnD-trnT-JX141952, rpl32-trnL-
JX142039, ndhA intron-JX142125.
Notes: ADownie and Katz-Downie (1996); BDownie et al. (1998);
C
Katz-Downie et al. (1999); DDownie et al. (2002); ESun et al. (2004).
Appendix B. Supplementary material
Supplementary data associated with this article can be found, in the
online version, at http://dx.doi.org/10.1016/j.ympev.2017.10.006.
References
Akaike, H., 1974. A new look at the statistical model identification. IEEE Trans. Autom.
Control 19, 716–723.
Bai, X., Ma, X.-G., Gao, Y.-D., Zhao, C., He, X.-J., 2015. Intraspecific differentiation of
Pleurospermum hookeri (Apiaceae), and its interspecific relationships with two close
relatives in the genus Pleurospermum. J. Syst. Evol. 53, 308–320.
Bell, C.D., Donoghue, M.J., 2005. Phylogeny and biogeography of Valerianaceae
(Dipsacales) with special reference to the South American valerians. Org. Divers.
Evol. 5, 147–159.
Bell, C.R., 1964. Incidence of polyploidy correlated with ecological gradients. Evolution
18, 510–511.
Bell, C.R., Constance, L., 1966. Chromosome numbers in Umbelliferae. III. Am. J. Bot. 53,
512–520.
Blas, R., 2005. Diversity of Arracacia species in Peru. Ph.D. thesis. Gembloux, Belgium:
Gembloux Agricultural University. 154p.
Blas, R., Ghislain, M., del Rosario Herrera, M., Baudoin, J.-P., 2008a. Genetic diversity
analysis of wild Arracacia species according to morphological and molecular markers.
Genet. Resour. Crop Evol. 55, 625–642.
Blas, R., Hermann, M., Baudoin, J.-P., 2008b. Analysis of the geographic distribution and
relationships among the Peruvian wild species of Arracacia. Genet. Resour. Crop Evol.
55, 643–655.
Bone, T.S., Downie, S.R., Affolter, J.M., Spalik, K., 2011. A phylogenetic and biogeo-
graphic study of the genus Lilaeopsis (Apiaceae tribe Oenantheae). Syst. Bot. 36,
789–805.
Calviño, C.I., Downie, S.R., 2007. Circumscription and phylogeny of Apiaceae subfamily
Saniculoideae based on chloroplast DNA sequences. Mol. Phylogenet. Evol. 44,
175–191.
Calviño, C.I., Martínez, S.G., Downie, S.R., 2008. The evolutionary history of Eryngium
(Apiaceae, Saniculoideae): rapid radiations, long distance dispersals, and hybridiza-
tions. Mol. Phylogenet. Evol. 46, 1129–1150.
Calviño, C.I., Martínez, S.G., Downie, S.R., 2010. Unraveling the taxonomic complexity of
Eryngium L. (Apiaceae, Saniculoideae): phylogenetic analysis of 11 non-coding
cpDNA loci corroborates rapid radiations. Plant Divers. Evol. 128, 137–149.
Calviño, C.I., Tilney, P.M., van Wyk, B.-E., Downie, S.R., 2006. A molecular phylogenetic
study of southern African Apiaceae. Am. J. Bot. 93, 1828–1847.
Carlson, K.I., Mansfield, D.H., Smith, J.F., 2011. A new species in the Lomatium
C.A. Danderson et al.
foeniculaceum (Apiaceae) clade revealed through combined morphometric and phy-
logenetic analyses. Syst. Bot. 36, 495–507.
Carter, B.E., Nostratinia, S., Shevock, J.R., 2014. A revisitation of species circumscriptions
and evolutionary relationships in Scouleria (Scouleriaceae). Syst. Bot. 39, 4–9.
Chen, C.L., Liao, F.S., Cheng, S.H., 2010. Phylogenetic analysis in the genera Phaius and
Cephalantheropsis using rpl32–trnL marker. Acta Hort. 878, 107–113.
Constance, L., 1949. The South American species of Arracacia (Umbelliferae) and some
related genera. Bull. Torrey Bot. Club 76, 39–52.
Constance, L., Affolter, J.M., 1995. Three new species and a new combination in Arracacia
Bancroft (Umbelliferae/Apiaceae). Brittonia 47, 320–327.
Constance, L., Breedlove, D.E., 1994. Dahliaphyllum, a new arborescent umbellifer from
Guerrero. Acta Botánica Mexicana 26, 83–87.
Constance, L., Hitchcock, C.L., 1954. Mathiasella, a new genus of North American
Umbelliferae. Am. J. Bot. 41, 56–58.
Constance, L., Chuang, T.-I., Bell, C.R., 1976a. Chromosome numbers in Umbelliferae. V.
Am. J. Bot. 63, 608–625.
Constance, L., Chuang, T.-I., Bye, R.A., 1976b. Chromosome numbers in Chihuahuan
Umbelliferae. Bot. Mus. Leaflets (Harvard Univ.) 24, 241–247.
Coulter, J.M., Rose, J.N., 1893. Notes on North American Umbelliferae. III. Bot. Gaz. 18,
54–56.
Coulter, J.M., Rose, J.N., 1895a. Report on Mexican Umbelliferae, mostly from the state
of Oaxaca, recently collected by C.G. Pringle and E.W. Nelson. Contributions from the
U.S. Natl. Herbarium 3, 289–309.
Coulter, J.M., Rose, J.N., 1895b. Deanea, a new genus of Umbelliferae-with plate XXVII.
Bot. Gaz. 20, 372–373.
Coulter, J.M., Rose, J.N., 1900. A synopsis of Mexican and Central American
Umbelliferae. Proc. Washington Academy Sci. 1, 111–159.
Coulter, J.M., Rose, J.N., 1927. Revision of the genus Myrrhidendron. J. Wash. Acad. Sci.
17, 213–215.
Daniell, H., Lee, S.-B., Grevich, J., Saski, C., Quesada-Vargas, T., Guda, C., Tomkins, J.,
Jansen, R.K., 2006. Complete chloroplast genome sequences of Solanum bulbocas-
tanum, Solanum lycopersicum and comparative analyses with other Solanaceae gen-
omes. Theor. Appl. Genet. 112, 1503–1518.
Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. JModelTest 2: more models, new
heuristics and parallel computing. Nat. Methods 9, 772.
Demesure, B., Sodzi, N., Petit, R.J., 1995. A set of universal primers for amplification of
polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants.
Mol. Ecol. 4, 129–131.
Downie, S.R., Jansen, R.K., 2015. A comparative analysis of whole plastid genomes from
the Apiales: expansion and contraction of the inverted repeat, mitochondrial to
plastid transfer of DNA, and identification of highly divergent noncoding regions.
Syst. Bot. 40, 336–351.
Downie, S.R., Katz-Downie, D.S., 1996. A molecular phylogeny of Apiaceae subfamily
Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer se-
quences. Am. J. Bot. 83, 234–251.
Downie, S.R., Hartman, R.L., Sun, F.-J., Katz-Downie, D.S., 2002. Polyphyly of the spring-
parsleys (Cymopterus): molecular and morphological evidence suggests complex re-
lationships among the perennial endemic genera of western North American
Apiaceae. Can. J. Bot. 80, 1295–1324.
Downie, S.R., Katz-Downie, D.S., Spalik, K., 2000a. A phylogeny of Apiaceae tribe
Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer se-
quences. Am. J. Bot. 87, 76–95.
Downie, S.R., Katz-Downie, D.S., Watson, M.F., 2000b. A phylogeny of the flowering
plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences:
towards a suprageneric classification of subfamily Apioideae. Am. J. Bot. 87,
273–292.
Downie, S.R., Plunkett, G.M., Watson, M.F., Spalik, K., Katz-Downie, D.S., Valiejo-Roman,
C.M., Terentieva, E.I., Troitsky, A.V., Lee, B.-Y., Lahham, J., El-Oqlah, A., 2001.
Tribes and clades within Apiaceae subfamily Apioideae: the contribution of mole-
cular data. Edin. J. Bot. 58, 301–330.
Downie, S.R., Ramanath, S., Katz-Downie, D.S., Llanas, E., 1998. Molecular systematics of
Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA in-
ternal transcribed spacer and plastid rpoC1 intron sequences. Am. J. Bot. 85,
563–591.
Downie, S.R., Spalik, K., Katz-Downie, D.S., Reduron, J.-P., 2010. Major clades within
Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS
sequences. Plant Divers. Evol. 128, 111–136.
Downie, S.R., Sun, F.-J., Katz-Downie, D.S., Colletti, G.J., 2004. A phylogenetic study of
Perideridia (Apiaceae) based on nuclear ribosomal DNA ITS sequences. Syst. Bot. 29,
737–751.
Downie, S.R., Watson, M.F., Spalik, K., Katz-Downie, D.S., 2000c. Molecular systematics
of Old World Apioideae (Apiaceae): relationships among some members of tribe
Peucedaneae sensu lato, the placement of several island-endemic species, and re-
solution within the apioid superclade. Can. J. Bot. 78, 506–528.
Drude, C.G.O., 1897–1898. Umbelliferae. In: Engler, A., Prantl, K. (Eds.), Die natürlichen
Pflanzenfamilien, vol.3, no. 8. Wilhelm Engelmann, Leipzig, Germany, pp. 63–250.
Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C., 1995. Testing the significance of incon-
gruence. Cladistics 10, 315–319.
Feist, M.A., Downie, S.R., 2008. A phylogenetic study of Oxypolis and Ptilimnium
(Apiaceae) based on nuclear rDNA ITS sequences. Syst. Bot. 33, 447–458.
Feist, M.A.E., Downie, S.R., Magee, A.R., Liu, M., 2012. Revised generic delimitations for
Oxypolis and Ptilimnium (Apiaceae) based on leaf morphology, comparative fruit
anatomy, and phylogenetic analysis of nuclear rDNA ITS and cpDNA trnQ–trnK in-
tergenic spacer sequence data. Taxon 61, 402–418.
Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap.
Evolution 39, 783–791.
304
Molecular Phylogenetics and Evolution 118 (2018) 286–305
Felsenstein, J., 2003. Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
Fisher, A.E., Clark, L.G., Kelchner, S.A., 2014. Molecular phylogeny estimation of the
bamboo genus Chusquea (Poaceae: Bambusoideae: Bambuseae) and description of
two new subgenera. Syst. Bot. 39, 829–844.
Gagnon, E., Hughes, C.E., Lewis, G.P., Bruneau, A., 2015. A new cryptic species in a new
cryptic genus in the Caesalpinia group (Leguminosae) from the seasonally dry inter-
Andean valleys of South America. Taxon 64, 468–490.
George, E.E., Mansfield, D.H., Smith, J.F., Hartman, R.L., Downie, S.R., Hinchliff, C.E.,
2014. Phylogenetic analysis reveals multiple cases of morphological parallelism and
taxonomic polyphyly in Lomatium (Apiaceae). Syst. Bot. 39, 662–675.
Gostel, M.R., Phillipson, P.B., Weeks, A., 2016. Phylogenetic reconstruction of the myrrh
genus, Commiphora (Burseraceae), reveals multiple radiations in Madagascar and
clarifies infrageneric relationships. Syst. Bot. 41, 67–81.
von Hagen, K.B., Kadereit, J.W., 2001. The phylogeny of Gentianella (Gentianaceae) and
its colonization of the southern hemisphere as revealed by nuclear and chloroplast
DNA sequence variation. Org. Divers. Evol. 1, 69–79.
Halpin, K.M., Fishbein, M., 2013. A chloroplast phylogeny of Agavaceae subfamily
Chlorogaloideae: implications for the tempo of evolution on serpentine soils. Syst.
Bot. 38, 996–1011.
Hardig, T.M., Soltis, P.S., 1999. An ITS-based phylogenetic analysis of the Euryptera
species group in Lomatium (Apiaceae). Plant Syst. Evol. 219, 65–78.
Hemsley, W.B., 1880. Umbelliferae. In: Godman, F.D., Salvert, O. (Eds.), Biologia centrali-
americana; or, contributions to the knowledge of the flora and fauna of Mexico and
Central America. Botany, vol. 1. R.H. Porter and Dulau and Co., London, United
Kingdom. pp. 563–565.
Herden, T., Hanelt, P., Friesen, N., 2016. Phylogeny of Allium L. subgenus Anguinum (G.
Don. ex WDJ Koch) N. Friesen (Amaryllidaceae). Mol. Phylogenet. Evol. 95, 79–93.
Hermann, M., 1997. Arracacha. Arracacia xanthorrhiza Bancroft. In: Hermann, M., Heller,
J. (Eds.), Andean Roots and Tubers: Ahipa, Arracacha, Maca and Yacon. IPGRI,
Rome, Italy, pp. 75–172.
Herschkovitz, M.A., Zimmer, E.A., 2000. Ribosomal DNA evidence and disjunctions of
western American Portulacaceae. Mol. Phylogenet. Evol. 15, 419–439.
Heywood, V.H., 1986. The Umbelliferae: an impossible family? Acta Universitatis
Upsaliensis. Symb. Bot. Upsal. 26, 173–180.
Kadereit, J.W., von Hagen, K.B., 2003. The evolution of flower morphology in
Gentianaceae-Swertiinae and the role of key innovations and niche width for the
diversification of Gentianella and Halenia in South America. Int. J. Plant Sci. 164,
S441–S452.
Katz-Downie, D.S., Valiejo-Roman, C.M., Terentieva, E.I., Troitsky, A.V., Pimenov, M.G.,
Lee, B.-Y., Downie, S.R., 1999. Towards a molecular phylogeny of Apiaceae subfamily
Apioideae: additional information from nuclear ribosomal DNA ITS sequences. Plant
Syst. Evol. 216, 167–195.
Kelchner, S.A., 2002. Group II introns as phylogenetic tools: structure, function, and
evolutionary constraints. Am. J. Bot. 89, 1651–1669.
Kempton, E.A., 2012. Systematics of Eriogonoideae s. s. (Polygonaceae). Syst. Bot. 37,
723–737.
Knudsen, S.R., 2003. Reproduction biology of the Andean root crop arracacha (Arracacia
xanthorrhiza Bancroft var. xanthorrhiza) and the taxonomic status of the South
American Arracacia Bancroft species with special emphasis on the position of culti-
vated arracacha and related wild species. Ph.D. thesis. Copenhagen, Denmark:
Botanical Section, Department of Ecology, The Royal Veterinary and Agricultural
University, 150p.
Lee, B.-Y., Downie, S.R., 2000. Phylogenetic analysis of cpDNA restriction sites and rps16
intron sequences reveal relationships among Apiaceae tribes Caucalideae, Scandiceae
and related taxa. Plant Syst. Evol. 221, 35–60.
Lee, C.S., Downie, S.R., 2006. Phylogenetic relationships within Cicuta (Apiaceae tribe
Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data. Can. J. Bot.
83, 453–468.
Liao, C., Downie, S.R., Li, Q., Yu, Y., He, X., Zhou, B., 2013. New insights into the phy-
logeny of Angelica and its allies (Apiaceae) with emphasis on East Asian species, in-
ferred from nrDNA, cpDNA, and morphological evidence. Syst. Bot. 38, 266–281.
Liede-Schumann, S., Nikolaus, M., Silva, U.C.S., Rapini, A., Mangelsdorff, R.D., Meve, U.,
2014. Phylogenetics and biogeography of the genus Metastelma (Apocynaceae-
Asclepiadoideae-Asclepiadeae: Metastelmatinae). Syst. Bot. 39, 594–612.
Lu, P.-L., Morden, C.W., 2014. Phylogenetic relationships among the dracaenoid genera
(Asparagaceae: Nolinoideae) inferred from chloroplast DNA loci. Syst. Bot. 39,
90–104.
Maddison, W.P., Maddison, D.R., 2016. Mesquite: a modular system for evolutionary
analysis. Version 3, 10. http://mesquiteproject.org.
Magee, A.R., Calviño, C.I., Liu, M.R., Downie, S.R., Tilney, P.M., van Wyk, B.-E., 2010.
New tribal delimitations for the early diverging lineages of Apiaceae. Taxon 59,
567–580.
Magee, A.R., Nicolas, A.N., Tilney, P.M., Plunkett, G.M., 2015. Phylogenetic relationships
and generic realignments in the early diverging subtribe Pentziinae (Asteraceae,
Anthemidae). Bot. J. Linn. Soc. 178, 633–647.
Magee, A.R., van Wyk, B.-E., Tilney, P.M., Downie, S.R., 2009. Generic delimitations and
relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina, the
North African genera Krubera and Stoibrax, and a new monotypic genus of the sub-
family Apioideae (Apiaceae). Syst. Bot. 34, 580–594.
Mathias, M.E., 1965. Distribution patterns of certain Umbelliferae. Ann. Mo. Bot. Gard.
52, 387–398.
Mathias, M.E., Constance, L., 1941. Three new species of Mexican Umbelliferae. Bull.
Torrey Bot. Club 68, 254–256.
Mathias, M.E., Constance, L., 1944–1945. Umbelliferae. In: North American flora, vol.
28B. The New York Botanical Garden, New York, pp. 43–265.
Mathias, M.E., Constance, L., 1951. A revision of the Andean genus Niphogeton
C.A. Danderson et al.
(Umbelliferae). Univ. Calif. Publ. Bot. 23, 405–426.
Mathias, M.E., Constance, L., 1952. New South American Umbelliferae. Bull. Torrey Bot.
Club 79, 359–370.
Mathias, M.E., Constance, L., 1967. Some Umbelliferae of the Andean paramos of South
America. Brittonia 19, 212–226.
Mathias, M.E., Constance, L., 1973. New and reconsidered Mexican Umbelliferae.
Contrib. Univ. Mich. Herbarium 11, 1–24.
Miller, J.S., Kamath, A., Levin, R.A., 2009. Do multiple tortoises equal a hare? The utility
of nine noncoding plastid regions for species-level phylogenies in tribe Lycieae
(Solanaceae). Syst. Bot. 34, 796–804.
Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES science gateway for
inference of large phylogenetic trees, in: Proceedings of the Gateway Computing
Environments Workshop (GCE), 14 Nov. 2010, New Orleans, Louisiana, U.S.A.,
pp. 1–8.
Moore, D.M., 1971. Chromosome studies in the Umbelliferae. In: Heywood, V.H. (Ed.),
The Biology and Chemistry of the Umbelliferae. Academic Press, London, U.K., pp.
233–255.
Morillo, E., Second, G., Pham, J.L., Risterucci, A.M., 2004. Development of DNA micro-
satellite markers in the Andean root crop arracacha: Arracacia xanthorrhiza Banc.
(Apiaceae). Mol. Ecol. Notes 4, 680–682.
Mort, M.E., Archibald, J.K., Randle, C.P., Levsen, N.D., O’Leary, T.R., Topalov, K.,
Wiegand, C.M., Crawford, D.J., 2007. Inferring phylogeny at low taxonomic levels:
utility of rapidly evolving cpDNA and nuclear ITS loci. Am. J. Bot. 94, 173–183.
Nazaire, M., Hufford, L., 2014. Phylogenetic systematics of the genus Mertensia
(Boraginaceae). Syst. Bot. 39, 268–303.
Neves, S.S., Watson, M.F., 2004. Phylogenetic relationships within Bupleurum (Apiaceae)
based on nuclear ribosomal DNA ITS sequence data. Ann. Bot. 93, 379–398.
Nicolas, A.N., Plunkett, G.M., 2009. The demise of subfamily Hydrocotyloideae
(Apiaceae) and the re-alignment of its genera across the entire order Apiales. Mol.
Phylogenet. Evol. 53, 134–151.
Nicolas, A.N., Plunkett, G.M., 2012. Untangling generic limits in Azorella, Laretia, and
Mulinum (Apiaceae: Azorelloideae): insights from phylogenetics and biogeography.
Taxon 61, 826–840.
Nixon, K.C., 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis.
Cladistics 15, 407–414.
Ocampo, G., Koteyeva, N.K., Voznesenskaya, E.V., Edwards, G.E., Sage, T.L., Sage, R.F.,
Columbus, J.T., 2013. Evolution of leaf anatomy and photosynthetic pathways in
Portulacaceae. Am. J. Bot. 100, 2388–2402.
Peterson, P.M., Romaschenko, K., Arrieta, Y.H., 2014. A molecular phylogeny and new
subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae). Taxon
63, 1212–1243.
Peterson, P.M., Romaschenko, K., Arrieta, Y.H., 2015. A molecular phylogeny and clas-
sification of the Eleusininae with a new genus, Mirachne (Poaceae: Chloridoideae:
Cynodonteae). Taxon 64, 445–467.
Peterson, P.M., Romaschenko, K., Johnson, G., 2010. A classification of the Chloridoideae
(Poaceae) based on multi-gene phylogenetic trees. Mol. Phylogenet. Evol. 55,
580–598.
Pimenov, M.G., Leonov, M.V., 1993. The Genera of the Umbelliferae: A Nomenclator.
Royal Botanic Gardens, Kew, U.K.
Plunkett, G.M., Downie, S.R., 1999. Major lineages within Apiaceae subfamily Apioideae:
a comparison of chloroplast restriction site and DNA sequence data. Am. J. Bot. 86,
1014–1026.
Plunkett, G.M., Soltis, D.E., Soltis, P.S., 1996. Evolutionary patterns in Apiaceae: in-
ferences based on matK sequence data. Syst. Bot. 21, 477–495.
Rieseberg, L.H., Beckstrom-Sternberg, S.M., Liston, A., Arias, D.M., 1991. Phylogenetic
and systematic inferences from chloroplast DNA and isozymes variation in Helianthus
sect. Helianthus (Asteraceae). Syst. Bot. 16, 50–76.
Robinson, B.L., 1892. XII. Contribution from the Gray Herbarium of Harvard University.
Descriptions of new plants collected in Mexico by C. G. Pringle in 1890 and 1891,
with notes upon a few other species. Proc. Am. Acad. Arts Sci. 27, 165–185.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B.,
Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient Bayesian
phylogenetic inference and model choice across a large model space. Syst. Biol. 61,
539–542.
Rose, J.N., 1905. Studies of Mexican and Central American plants-No. 4. Contributions
from the U.S. Natl. Herbarium 8, 281–339.
Santos, M.F., Sano, P.T., Forest, F., Lucas, E., 2016. Phylogeny, morphology and cir-
cumscription of Myrcia sect. Sympodiomyrcia (Myrcia s.l., Myrtaceae). Taxon 65,
759–774.
Schulte, L.J., Clark, J.L., Novak, S.J., Ooi, M.T.-Y., Smith, J.F., 2014. Paraphyly of section
Stygnanthe (Columnea, Gesneriaceae) and a revision of the species of section
Angustiflorae, a new section inferred from ITS and chloroplast DNA data. Syst. Bot. 39,
613–636.
Schwarzbach, A.E., Kadereit, J.W., 1995. Rapid radiation of North American desert
genera of the Papaveraceae: evidence from restriction site mapping and PCR-ampli-
fied chloroplast DNA fragments. Plant Syst. Evol. 9, 159–170.
Seehausen, O., 2004. Hybridization and adaptive radiation. Trends Ecol. Evol. 19,
198–207.
Seelanan, T., Schnabel, A., Wendel, J.F., 1997. Congruence and consensus in the cotton
tribe (Malvaceae). Syst. Bot. 22, 259–290.
Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Winder,
C.T., Schilling, E.E., Small, R.L., 2005. The tortoise and the hare II: relative utility of
21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 92,
142–166.
Shaw, J., Lickey, E.B., Schilling, E.E., Small, R.L., 2007. Comparison of whole chloroplast
genome sequences to choose noncoding regions for phylogenetic studies in
305
Molecular Phylogenetics and Evolution 118 (2018) 286–305
angiosperms: the tortoise and the hare III. Am. J. Bot. 94, 275–288.
Shaw, J., Shafer, H.L., Leonard, O.R., Kovach, M.J., Schorr, M., Morris, A.B., 2014.
Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic
inferences in angiosperms: the tortoise and the hare IV. Am. J. Bot. 101, 1987–2004.
Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with ap-
plications to phylogenetic inference. Mol. Biol. Evol. 16, 1114–1116.
Sikes, D.S., Lewis, P.O., 2001. Beta software, version 1. PAUPRat: PAUP∗ implementation
of the parsimony ratchet. Distributed by the authors. Department of Ecology and
Evolutionary Biology, University of Connecticut, Storrs, U.S.A.
Silveira, M.A., Simpson, M.G., 2013. Phylogenetic systematics of the mesa mints:
Pogogyne (Lamiaceae). Syst. Bot. 38, 782–794.
Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic
analyses. Syst. Bot. 49, 369–381.
Simon, M.F., Pastore, J.F.B., Souza, A.F., Borges, L.M., Scalon, V.R., Ribeiro, P.G., Santo-
Silva, J., Souza, V.C., Queiroz, L.P., 2016. Molecular phylogeny of Stryphnodendron
(Mimosoideae, Leguminosae) and generic delimitations in the Piptadenia group. Int.
J. Plant Sci. 177, 44–59.
Sinitsyna, T.A., Herden, T., Friesen, N., 2016. Dated phylogeny and biogeography of the
Eurasian Allium section Rhizirideum (Amaryllidaceae). Plant Syst. Evol. 302,
1311–1328.
Skema, C., 2014. Reevalauation of species delimitations in Dombeya section Hilsenbergia
(Dombeyaceae). Syst. Bot. 39, 541–562.
Small, R.L., Ryburn, J.A., Cronn, R.C., Seelanan, T., Wendel, J.F., 1998. The tortoise and
the hare: choosing between noncoding plastome and nuclear Adh sequences for
phylogeny reconstruction in a recently diverged plant group. Am. J. Bot. 85,
1301–1315.
Soltis, P.S., Novak, S.J., Hardig, T.M., Soltis, D.E., 1995. Phylogenetic relationships and
rapid radiation in Lomatium (Apiaceae). Am. J. Bot. 82, 163 (Abstract).
Spalik, K., Reduron, J.-P., Downie, S.R., 2004. The phylogenetic position of Peucedanum
sensu lato and allied genera and their placement in tribe Selineae (Apiaceae, sub-
family Apioideae). Plant Syst. Evol. 243, 189–210.
Spalik, K., Wojewódzka, A., Downie, S.R., 2001. The evolution of fruit in Scandiceae
subtribe Scandicinae (Apiaceae). Can. J. Bot. 79, 1358–1374.
Spooner, D.M., Ruess, H., Iorizzo, M., Senalik, D., Simon, P., 2017. Entire plastid phy-
logeny of the carrot genus (Daucus, Apiaceae): concordance with nuclear data and
mitochondrial and nuclear DNA insertions to the plastid. Am. J. Bot. 104, 296–312.
Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis
of large phylogenies. Bioinformatics 2014. http://dx.doi.org/10.1093/
bioinformatics/btu033.
Stern, S., Bohs, L., 2016. An eight marker phylogeny of Solanum sect. Micracantha
(Solanaceae). Syst. Bot. 41, 120–127.
Sun, F.-J., Downie, S.R., 2004. A molecular systematic investigation of Cymopterus and its
allies (Apiaceae) based on phylogenetic analyses of nuclear (ITS) and plastid (rps16
intron) DNA sequences. South African J. Bot. 70, 407–416.
Sun, F.-J., Downie, S.R., 2010. Phylogenetic relationships among the perennial, endemic
Apiaceae subfamily Apioideae of western North America: additional data from the
cpDNA trnF–trnL–trnT region continue to support a highly polyphyletic Cymopterus.
Plant Divers. Evol. 128, 151–172.
Sun, F.-J., Downie, S.R., Hartman, R.L., 2004. An ITS-based phylogenetic analysis of the
perennial, endemic Apiaceae subfamily Apioideae of western North America. Syst.
Bot. 29, 419–431.
Swofford, D.L., 2002. PAUP∗: phylogenetic analysis using parsimony (∗and other
methods), version 4. Sinauer Associates, Sunderland, Massachusetts, U.S.A.
Taberlet, P., Gielly, L., Pautou, G., Bouvet, J., 1991. Universal primers for amplification of
three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17, 1105–1109.
Tate, J.A., Soltis, D.E., Soltis, P.E., 2005. Polyploidy in plants. In: Gregory, T.R. (Ed.), The
Evolution of the Genome. Elsevier Academic Press, Amsterdam, Netherlands, pp.
372–426.
Templeton, A.R., 1983. Phylogenetic inference from restriction endonuclease cleavage
site maps with particular reference to the evolution of humans and the apes.
Evolution 37, 221–244.
Theobald, W.L., 1971. Comparative anatomical and developmental studies in the
Umbelliferae. In: Heywood, V.H. (Ed.), The Biology and Chemistry of the
Umbelliferae. Academic Press, London, U.K., pp. 177–197.
Watson, S., 1886. XXI. Contributions to American botany. 1. Lists of plants collected by
Dr. Edward Palmer in the state of Jalisco, Mexico, in 1886. Proc Am. Acad. Arts Sci.
22, 396–465.
Wen, J., Lowry II, P.P., Walck, J.L., Yoo, K.-O., 2002. Phylogenetic and biogeographic
diversification in Osmorhiza (Apiaceae). Ann. Mo. Bot. Gard. 89, 414–428.
Werle, E., Schneider, C., Renner, M., Völker, M., Fiehn, W., 1994. Convenient single-step,
one tube purification of PCR products for direct sequencing. Nucleic Acids Res. 22,
4354–4355.
Wiens, J.J., 1998. Combining data sets with different phylogenetic histories. Syst. Biol.
47, 568–581.
Wiens, J.J., Engstrom, T.N., Chippindale, P.T., 2006. Rapid diversification, incomplete
isolation, and the “speciation clock” in North American salamanders (genus
Plethodon): testing the hybrid swarm hypothesis or rapid radiation. Evolution 60,
2585–2603.
Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A System for Graphical
Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. < http://ceb.
csit.fsu.edu/awty > .
Wojciechowski, M.F., Sanderson, M.J., Hu, J.-M., 1999. Evidence of the monophyly of
Astragalus (Fabaceae) and its major subgroups based on nuclear ribosomal DNA ITS
and chloroplast DNA trnL intron data. Syst. Bot. 24, 409–437.
Yoo, K.-O., Lowry II, P.P., Wen, J., 2002. Discordance of chloroplast and nuclear ribo-
somal DNA data in Osmorhiza (Apiaceae). Am. J. Bot. 89, 966–971.