2008
DOI: 10.1080/10635150802044003
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Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes (Aves: Turdus)

Abstract: The phylogeny of the thrushes (Aves: Turdus) has been difficult to reconstruct due to short internal branches and lack of node support for certain parts of the tree. Reconstructing the biogeographic history of this group is further complicated by the fact that current implementations of biogeographic methods, such as dispersal-vicariance analysis (DIVA; Ronquist, 1997), require a fully resolved tree. Here, we apply a Bayesian approach to dispersal-vicariance analysis that accounts for phylogenetic uncertainty … Show more

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Cited by 345 publications
(410 citation statements)
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References 60 publications
(105 reference statements)
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“…The final MCC trees were replayed in Figtree (v1.4.3) (http://tree.bio.ed.ac.uk/software/figtree/). BaTS (Bayesian tip‐significance testing) was used to analyze the correlation among the PCV3 sequences and geographical structure 58. The countries of each sequence were used as the taxon labels, such as China, USA, Korea, Italy, and Brazil.…”
Section: Methodsmentioning
confidence: 99%
“…The final MCC trees were replayed in Figtree (v1.4.3) (http://tree.bio.ed.ac.uk/software/figtree/). BaTS (Bayesian tip‐significance testing) was used to analyze the correlation among the PCV3 sequences and geographical structure 58. The countries of each sequence were used as the taxon labels, such as China, USA, Korea, Italy, and Brazil.…”
Section: Methodsmentioning
confidence: 99%
“…S-DIVA is implemented in the software package RASP (Yu et al, 2013). S-DIVA was written to complement the parsimony-based ancestral area reconstruction method DIVA (Ronquist, 1997) but can account for phylogenetic uncertainty using the Bayesian approach developed by Nylander et al (2008). We constrained the maximal number of areas kept in our biogeographical reconstruction to two using the option ''maxareas".…”
Section: Biogeographical Reconstructionsmentioning
confidence: 99%
“…Dispersal-vicariance analysis [DIVA (61,62)] was used to infer ancestral distributions and historical events involved in the biogeographic history of Rubiaceae. To overcome the uncertainty associated with phylogenetic estimation, we use an approach that averages DIVA biogeographic and temporal reconstructions over a Bayesian sample of highly probable trees (in this case n ϭ 1,000), generating credibility support values for alternative phylogenetic relationships (63). Integrating over the posterior distribution of trees often reveals preference for a single or more restricted set of solutions, thus reducing the uncertainty in DIVA optimizations (63).…”
Section: Methodsmentioning
confidence: 99%