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

Abstract

We propose a simple statistical approach for using Dispersal-Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P(r Y ) = n t=1 F(r Y ) t Pt where Y is a node, and F(r Y ) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y , t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage "x", where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp * F(r Y ) on the Bayesian consensus tree when both variables are <100%, where pp is the posterior probability and F(r Y ) is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and of Aesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation of pp * F(r y ) at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil's distribution area. The P was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution (extinction and dispersal events) along the stems of A. californica and sect. Parryana. Key words Aesculus, biogeography, DIVA, fossil wildcards, MrBayes, phylogenetic uncertainty.Studies in historical biogeography based on phylogeny have accumulated rapidly due to the recent increase in availability of molecular phy...

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

“…Results obtained from S-DIVA were identical to those reported from manual calculations by Harris and Xiang (2009). The ''Tree View'' screen of RASP.…”

“…The application of DEC across a distribution of phylogenetic trees has been tentatively termed ''BayesLagrange'', and may be considered a non-parametric Bayesian method (similar to Bayes-DIVA in Harris and Xiang, 2009;Johns, 1957).…”

Multiple windows of colonization to Macaronesia by the dispersal-unspecialized Scrophularia since the Late Miocene

“…This method circumvents the problems about uncertainty in phylogeny and ancestral area optimization attached to the initial DIVA method (Ronquist, 1997), as previously proposed by Harris and Xiang (2009) Nylander et al (2008) in their Bayes-DIVA method. All (pruned) trees from the Bayesian distribution obtained from BEAST were analyzed to account for phylogenetic uncertainty, and results were summarized on the MCC tree.…”

“…All (pruned) trees from the Bayesian distribution obtained from BEAST were analyzed to account for phylogenetic uncertainty, and results were summarized on the MCC tree. Four analyses were conducted with RASP to calculate the probabilities of ancestral ranges at nodes following Fernández-Mazuecos and Vargas (2011), with the "allow reconstruction" option in effect (Harris and Xiang, 2009) and without that option (Nylander et al, 2008), and, for both alternatives, setting the maximum number of areas in ancestral ranges to two or four.…”

Phylogenetics and Biogeography of Apios (Fabaceae) Inferred from Sequences of Nuclear and Plastid Genes

“…We used S-DIVA (statistical dispersal-vicariance analysis; Yu et al 2010; available at http://mnh.scu.edu.cn/soft/blog/RASP) and the reconstructed species trees from BEST to infer the ancestral area of Apios and of the EAS-ENA disjunction because S-DIVA analyses take into consideration the uncertainty of phylogenetic reconstructions (Harris and Xiang 2009). Two areas of endemism were used on the basis of the distribution of the extant species: EAS and ENA.…”