See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/43181884

S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring

biogeographic histories

Article  in  Molecular Phylogenetics and Evolution · August 2010

DOI: 10.1016/j.ympev.2010.04.011 · Source: PubMed

CITATIONS READS

554 2,224

3 authors:

Yan Yu Aj Harris
Sichuan University South China Botanical Garden
82 PUBLICATIONS   1,577 CITATIONS    63 PUBLICATIONS   1,583 CITATIONS   

SEE PROFILE SEE PROFILE

Xing-Jin He
Sichuan University
223 PUBLICATIONS   2,632 CITATIONS   

SEE PROFILE

Some of the authors of this publication are also working on these related projects:

Pan Himalayas View project

Molecular phylogeny; Evolutionary History; Floral Genome Project; Taxionamy View project

All content following this page was uploaded by Xing-Jin He on 12 March 2019.

The user has requested enhancement of the downloaded file.

This article appeared in a journal published by Elsevier. The attached
copy is furnished to the author for internal non-commercial research
and education use, including for instruction at the authors institution
and sharing with colleagues.
Other uses, including reproduction and distribution, or selling or
licensing copies, or posting to personal, institutional or third party
websites are prohibited.
In most cases authors are permitted to post their version of the
article (e.g. in Word or Tex form) to their personal website or
institutional repository. Authors requiring further information
regarding Elsevier’s archiving and manuscript policies are
encouraged to visit:
http://www.elsevier.com/copyright
 Author's personal copy

Molecular Phylogenetics and Evolution 56 (2010) 848–850

Contents lists available at ScienceDirect

Molecular Phylogenetics and Evolution

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

Short Communication

S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring

biogeographic histories
Yan Yu a, A.J. Harris b, Xingjin He a,*
a
College of Life Sciences, Sichuan University, Chengdu 610064, China
b
Curriculum for the Environment and Ecology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

a r t i c l e i n f o a b s t r a c t

Article history: Dispersal-Vicariance Analysis (DIVA) is one of the most widely used methods of inferring biogeographic
Received 4 December 2009 histories. Here we present a simple tool that complements DIVA and uses a Statistical Dispersal-Vicari-
Revised 10 March 2010 ance Analysis (S-DIVA) to statistically evaluate the alternative ancestral ranges at each node in a tree
Accepted 6 April 2010
accounting for phylogenetic uncertainty and uncertainty in DIVA optimization. S-DIVA provides a
Available online 22 April 2010
point-and-click user interface and displays results as, high-resolution, exportable graphics. S-DIVA is
freely available for download for Windows at http://mnh.scu.edu.cn/S-DIVA.
Keywords:
Ó 2010 Elsevier Inc. All rights reserved.
DIVA
Biogeographic
Program
Phylogeny
Statistics

1. Introduction without error (Nylander et al., 2008). A second source of uncertainty

Studies in historical biogeography based on phylogeny have
accumulated rapidly in the literature due to the exponential in-
crease in phylogenetic studies (see Xiang et al., 1998, 2004, 2005,
2006; Wen, 1999; Sanmartín et al., 2001; Donoghue and Smith,
2004; Sanmartín and Ronquist, 2004; Soltis et al., 2006; Harris
et al., 2009; Alexandre et al., 2009). Dispersal-Vicariance Analysis
(DIVA) (Ronquist, 1997, 2001) is one of the most widely used
methods of inferring biogeographic histories. This is evidenced
by an advanced Google scholar search for ‘‘DIVA” and ‘‘biogeogra-
phy” in 2009 returning greater than 50 relevant results. DIVA
reconstructs the ancestral distribution in a phylogeny by optimiz-
ing a three-dimensional cost matrix, in which extinctions and dis-
persals ‘‘cost” more than vicariance (Ronquist, 1997; Lamm and
Redelings, 2009). Although model-based methods for inferring bio-
geography are available (e.g., Ree et al., 2005; Ree and Smith, 2008;
Sanmartín et al., 2008), DIVA remains popular because it provides
rapid results, requires little prior information, and gives results
comparable to the model-based likelihood method Lagrange of
Ree et al. (2005) and Ree and Smith (2008) (e.g., Ree et al., 2005;
Burbrink and Lawson, 2007; Ree and Smith, 2008; Velazco and
Patterson, 2008; Xiang et al., 2008; Xiang et al., 2009).
One problem with the current implementation of DIVA is that it
ignores the uncertainty in phylogenetic inference because ancestral
ranges are reconstructed onto a fixed tree topology assumed to be
in DIVA is that associated with ancestral area optimization; multiple
equally optimal reconstructions often result in multiple ranges sug-
gested at ancestral nodes (Ronquist, 1997; Nylander et al., 2008).
To account for these uncertainties, Nylander et al. (2008) recently
showed the utility of a non-parametric empirical Bayesian approach
to DIVA. Their approach handles phylogenetic uncertainty and
uncertainty in DIVA optimization. Harris and Xiang (2009) proposed
an alternative approach to Bayes-DIVA, which differs in its ability to
handle uncertainty at some nodes.
We have written Statistical Dispersal-Vicariance Analysis (S-
DIVA), a program which complements DIVA, implements the meth-
ods of Nylander et al. (2008) and Harris and Xiang (2009), and deter-
mines statistical support for ancestral range reconstructions using a
novel method, the S-DIVA value. In S-DIVA, the frequencies of an
ancestral range at a node in ancestral reconstructions are averaged
over all trees and each alternative ancestral range at a node is
weighted by the frequency of the node occurring or by some other
measure of support for the node. S-DIVA is easy-to-install, provides
a user-friendly graphical interface, and generates exportable, graph-
ical results (Fig. 1a and b).
2. Description
2.1. Program features

* Corresponding author. Fax: +86 02885415006. The S-DIVA program requires a set of trees from phylogenetic
E-mail address: xjhe@scu.edu.cn (X. He). analysis (a ‘‘trees file”), a final representative tree, and range infor-

1055-7903/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved.
doi:10.1016/j.ympev.2010.04.011
 Author's personal copy

Y. Yu et al. / Molecular Phylogenetics and Evolution 56 (2010) 848–850 849

Fig. 1. Graphical output from S-DIVA. (a) Graphical results of ancestral distributions for simulated phylogeny with 9 species and 3 areas. A, B and C are ranges of terminals. Pie
charts at nodes show probabilities of alternative ancestral ranges; (b) Alternative ancestral ranges of the node of ((4, 9), 2) displayed as a pie chart and bar charts by S-DIVA.
The node of terminals 2, 4 and 9 has two possible ancestral ranges ‘‘AB or BC”, the occurrence of each range is AB: 60%, BC: 40%. Probability of this result may be interpreted as
100% since the frequency of occurrence of the node (pn) is 100%; (c–g) Five optimal reconstructions resulting in probabilities in a and b. Numbered nodes (roman numerals)
correspond to those in Table 1. Note that node numbers are not part of the S-DIVA output.

mation for terminal taxa. Tree file formats generated by the pro-
grams BEAST (Drummond and Rambaut, 2006), PAUP* (Swofford,
2003) and MrBayes (Huelsenbeck and Ronquist, 2003) are currently
supported by S-DIVA. Range information may be loaded as a comma
separated values file or entered directly into S-DIVA through the user
interface. S-DIVA allows users a variety of options, which customize
analyses for individual needs. Dispersal-Vicariance Analyses in
S-DIVA are performed by DIVA 1.2 (Ronquist, 2001).
In an S-DIVA analysis with default settings, ancestral recon-
structions are performed using DIVA 1.2 for all trees in the trees
file. The probability (p) of an ancestral range x at node n on the final
P
tree is calculated as pðxn Þ ¼ m t¼1 Fðxn Þt  pn where t is the selected
tree, m is the total number of sampled trees, F(xn)t is the occurrence
of an ancestral range x at node n for tree t, and pn is the support for
the node. F(xn)t is calculated as the actual frequency of x within the
pool of ancestral range reconstructions (Harris and Xiang, 2009):
Fðxn Þ ¼ i=Dt . The value i is the number of times the range x occurs
in the total number of alternative reconstructions D at node n in
Pm
tree t. S-DIVA output includes t¼1 Fðxn Þ and the frequency of
occurrence of each node of the final tree in the sample of trees.
The latter may be interpreted as pn or an estimate of pn and can
P
thus be multiplied by m t¼1 Fðxn Þ to determine p(xn). Alternatively,
other means, independent of S-DIVA, may be used to determine
pn. Default settings in S-DIVA generally implement the Bayes-DIVA
method described by Nylander et al. (2008) except that i/Dt is used
to calculate F(xn) and trees from sources other than Bayesian anal-
ysis are allowed (e.g., Micó et al., 2009).
The S-DIVA value, SV, of an optimal reconstruction of the final
P
tree, is calculated as SV ¼ c1 n¼1 Pðxn Þ, where c is the total number
of terminal taxa and c  1 is the total number of nodes. The higher
the S-DIVA value the greater the probability of a reconstruction
(Fig. 1a–g, Table 1).
The graphical output of S-DIVA (Fig. 1a and b) is designed for easy
visualization and navigation of results with displays for the final tree,
each node, and each optimal reconstruction. Graphics are high resolu-
tion and may be browsed on-screen or exported as .jpg or .png files.
Other options in S-DIVA include:
1. Perform biogeographic analysis for a user-specified lineage with
an undefined sister group as in the method of Harris and Xiang
(2009) and as an alternative to the Nylander et al. (2008)
method.
2. Estimate the probability of optimal ancestral ranges at a single,
user-specified node.
3. Add distribution information for an omitted taxon at a user-
specified node.
4. Limit analysis to a random sample of trees from the trees file.
5. Exclude the first specified number of trees in the trees file from
analysis by setting a burn-in.
6. Apply DIVA options in S-DIVA through graphical user interface
and command line formats.
S-DIVA has been tested using the simulated dataset of 100 ran-
domly sampled trees from Harris and Xiang (2009). Harris and
Xiang (2009) used these trees to estimate the biogeographic histo-
ries of four lineages using the Bayes-DIVA method of Nylander
et al. (2008) and their own method. Results obtained from S-DIVA
were identical to those reported from manual calculations by Har-
ris and Xiang (2009) except for several slight differences observed
beyond the second significant digit to the right of the decimal.
These differences are probably explained entirely by the greater
precision of S-DIVA calculations compared to the manual method
of Harris and Xiang (2009) using Microsoft Excel.
2.2. Implementation details
The main routine in S-DIVA is written in VB.net and uses the
program DIVA 1.2 for handling DIVA analysis. The S-DIVA web site
 Author's personal copy

850 Y. Yu et al. / Molecular Phylogenetics and Evolution 56 (2010) 848–850

Table 1
Table for optimal reconstructions in Fig. 1c–g.

I II III IV V VI VII VIII SV

1 (Fig. 1c) Range (x) AB AC AB B AB AC A AC –
V(n) 100 100 60 80 80 60 60 60 600
2 (Fig. 1d) Range (x) AB AC AB B AB BC B BC –
V(n) 100 100 60 80 80 40 40 40 540
3 (Fig. 1e) Range (x) AB AC AB AB A AC A AC –
V(n) 100 100 60 20 20 60 60 60 480
4 (Fig. 1f) Range (x) AB AC BC B AB AC A AC –
V(n) 100 100 40 80 80 60 60 60 580
5 (Fig. 1g) Range (x) AB AC BC B AB BC B BC –
V(n) 100 100 40 80 80 40 40 40 520

Calculations of P(xn) assume that pn for all nodes is equal to 1.0.

gives a detailed example illustrating how to use the program.
Example files and a user’s manual are provided with the S-DIVA
download. A web server is available for running S-DIVA analyses
and can be accessed at http://mnh.scu.edu.cn/sdiva_web. The on-
line version of the program offers a full user interface and makes
the software accessible to MAC and Linux users. The S-DIVA web
service is still in beta and we recommend the offline version of
S-DIVA. We are continually working to improve S-DIVA’s function-
ality and usability. Our next objective is for S-DIVA to handle trees
with polytomies.
Acknowledgments
The authors would like to thank Dr. Jenny Xiang (North Carolina
State University) for her helpful comments and Dr. Johan Nylander
(Stockholm University, Sweden), Dr. Xiaoguo Xiang and Dr. Qiang
Zhang (Institute of Botany, Chinese Academy of Sciences, China)
for testing the software.
Funding: This work was supported by grants from the National
Natural Science Foundation of China (Grant No. 30670146), the
National Infrastructure of Natural Resources for Science and
Technology (Grant No. 2005DKA21403), the Research Fund for
the Large-scale Scientific Facilities of the Chinese Academy of Sci-
ences (Grant No. 2009-LSF-GBOWS-01) and Technology Innovation
Team Programs of Inner Mongolia Agricultural University (Grant
No. NDTD201011).
References
Alexandre, A., Johan, A.A.N., Claes, P., Isabel, S., 2009. Tracing the impact of the
Andean uplift on Neotropical plant evolution. Proceedings of the National
Academy of Sciences of the United States of America 106 (24), 9749–9754.
Burbrink, F.T., Lawson, R., 2007. How and when did Old World rat snakes disperse
into the New World. Molecular Phylogenetics and Evolution 43, 173–189.
Donoghue, M.J., Smith, S.A., 2004. Patterns in the assembly of the temperate forest
around the Northern Hemisphere. Philosophical Transactions of the Royal
Society of London: Biology 359, 1633–1644.
Drummond, A.J., Rambaut, A., 2006. BEAST v1.4. http://beast.bio.ed.ac.uk/.
Harris, A.J., Thomas, D.T., Xiang, Q-Y., 2009. Phylogeny, origin, and biogeographic
history of Aesculus L. (Sapindales): an update from combined analysis of DNA
sequences, morphology, and fossils. Taxon 58, 108–126.
Harris, A.J., Xiang, Q-Y., 2009. Estimating ancestral distributions of lineages with
uncertain sister groups: a statistical approach to Dispersal-Vicariance Analysis
and a case using Aesculus L (Sapindaceae) including fossils. Journal of
Systematics and Evolution 47, 349–368.
Huelsenbeck, J.P., Ronquist, F., 2003. MrBayes 3: Bayesian phylogenetic inference
under mixed models. Bioinformatics 19, 1572–1574.
Lamm, K.S., Redelings, B.D., 2009. Reconstructing ancestral ranges in historical
biogeography: properties and prospects. Journal of Systematics and Evolution
47, 369–382.
Micó, E., Sanmartín, I., Galante, E., 2009. Mediterranean diversification of the grass-
feeding Anisopliina beetles (Scarabaeidae, Rutelinae, Anomalini) as inferred by
bootstrap-averaged dispersal-vicariance analysis. Journal of Biogeography 36,
546–560.
Nylander, J.A.A., Olsson, U., Alström, P., Sanmartín, I., 2008. Accounting for
phylogenetic uncertainty in biogeography: a Bayesian approach to Dispersal-
vicariance Analysis of the thrushes (Aves: Turdus). Systematic Biology 57, 257–
268.
Ree, R.H., Smith, S.A., 2008. Maximum likelihood inference of geographic range
evolution by dispersal local extinction and cladogenesis. Systematic Biology 57,
4–14.
Ree, R.H., Moore, B.R., Webb, C.O., Donoghue, M.J., 2005. A likelihood framework for
inferring the evolution of geographic range of phylogenetic trees. Evolution 59,
2299–2311.
Ronquist, F., 1997. Dispersal-vicariance analysis: a new approach to the
quantification of historical biogeography. Systematic Biology 46, 195–203.
Ronquist, F., 2001. DIVA version 1.2. Computer program for MacOS and Win32.
Evolutionary Biology Centre, Uppsala University. Available at http://
www.ebc.uu.se/systzoo/research/diva/diva.html.
Sanmartín, I., Enghoff, H., Ronquist, F., 2001. Patterns of animal dispersal, vicariance
and diversification in the Holarctic. Biological Journal of the Linnean Society 73,
345–390.
Sanmartín, I., Ronquist, F., 2004. Southern Hemisphere biogeography inferred by
event-based models: plant versus animal patterns. Systematic Biology 53, 216–
243.
Sanmartín, I., Van Der Mark, P., Ronquist, F., 2008. Inferring dispersal: a Bayesian
approach to phylogeny-based island biogeography with special reference to the
Canary Islands. Journal of Biogeography 35, 428–449.
Soltis, D.E., Morris, A.B., MacLachlan, J.S., Manos, P.S., Soltis, P.S., 2006. Comparative
phylogeography of unglaciated eastern North America. Molecular Ecology 15,
4261–4293.
Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other
Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts, US.
Velazco, P.M., Patterson, B.D., 2008. Phylogenetics and biogeography of the broad-
nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae). Molecular
Phylogenetics and Evolution 49, 479–489.
Wen, J., 1999. Evolution of the eastern Asian and eastern North American disjunct
distributions in flowering plants. Annual Review of Ecology and Systematics 30,
421–455.
Xiang, Q-Y, Soltis, D.E., Soltis, P.S., 1998. The eastern Asian and eastern and western
North American disjunction: congruent phylogenetic patterns in seven diverse
genera. Molecular Phylogenetics and Evolution 10, 178–190.
Xiang, Q-Y, Zhang, W.H., Ricklefs, R.E., Qian, H., Chen, Z.D., Wen, J., Li, J.H., 2004.
Regional differences in rates of plant speciation and molecular evolution: a
comparison between eastern Asia and eastern North America. Evolution 58,
2175–2184.
Xiang, Q-Y, Manchester, S.R, Thomas, D.T., Zhang, W.H., Fan, C., 2005. Phylogeny,
biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae):
tracking Tertiary plant migration. Evolution 58, 1685–1700.
Xiang, Q-Y, Thomas, D.T., Zhang, W.H., Manchester, S.R., Murrell, Z., 2006. Species
level phylogeny of the genus Cornus (Cornaceae) based on molecular and
morphological evidence – implications for taxonomy and Tertiary
intercontinental migration. Taxon 55, 9–30.
Xiang, Q-Y, Thomas, D.T., 2008. Tracking character evolution and biogeographic
history through time in Cornaceae – does choice of methods matter. Journal of
Systematics and Evolution 46, 349–374.
Xiang, Q-Y, Smith, S.A., Harris, AJ, Feng, C., 2009. Use of fossils in biogeographic
analysis – challenges and possible solutions abstract invited presentation. In:
Fourth International conference of the International Biogeography Society,
Merida, Mexico, 69pp.

View publication stats