BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Bouckaert, Remco R.; Heled, Joseph; Kühnert, Denise; Vaughan, Timothy G.; Wu, Chieh-Hsi; Xie, Donghua; Suchard, Marc A.; Rambaut, Andrew; Drummond, Alexei J.

doi:10.1371/journal.pcbi.1003537

Cited by 5,678 publications

(5,229 citation statements)

References 29 publications

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“…Divergence times were estimated from the Bayesian tree, based on the strict clock model in MrBayes v3.2 (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003), and with the constant population model in BEAST v2.3 (Bouckaert et al., 2014). The MrBayes analysis was run as described above with uniform branch lengths.…”

Section: Methodsmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

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Section: Methodsmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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“…For the spatial expansion analysis, we also estimated the time of expansion (Schenekar & Weiss, 2011). (3) Past changes in effective population size were evaluated using the Extended Bayesian Skyline Plot approach (EBSP) in BEAST 2.4.4 (Bouckaert et al., 2014). For crabs, accurate estimates were not possible, because populations were differentiated and could not be pooled.…”

Section: Methodsmentioning

confidence: 99%

Highly contrasted population genetic structures in a host–parasite pair in the Caribbean Sea

Jossart

Ridder

Lessios

et al. 2017

Ecology and Evolution

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Evolution and population genetic structure of marine species across the Caribbean Sea are shaped by two complex factors: the geological history and the present pattern of marine currents. Characterizing and comparing the genetic structures of codistributed species, such as host–parasite associations, allow discriminating the relative importance of environmental factors and life history traits that influenced gene flow and demographic events. Using microsatellite and Cytochrome Oxidase I markers, we investigated if a host–parasite pair (the heart urchin Meoma ventricosa and its parasitic pea crab Dissodactylus primitivus) exhibits comparable population genetic structures in the Caribbean Sea and how the observed patterns match connectivity regions from predictive models and other taxa. Highly contrasting patterns were found: the host showed genetic homogeneity across the whole studied area, whereas the parasite displayed significant differentiation at regional and local scales. The genetic diversity of the parasitic crabs (both in microsatellites and COI) was distributed in two main groups, Panama–Jamaica–St Croix on the one hand, and the South‐Eastern Caribbean on the other. At a smaller geographical scale, Panamanian and Jamaican parasite populations were genetically more similar, while more genetic differentiation was found within the Lesser Antilles. Both species showed a signature of population expansion during the Quaternary. Some results match predictive models or data from previous studies (e.g., the Western‐Eastern dichotomy in the parasite) while others do not (e.g., genetic differentiation within the Lesser Antilles). The sharp dissimilarity of genetic structure of these codistributed species outlines the importance of population expansion events and/or contrasted patterns of gene flow. This might be linked to differences in several life history traits such as fecundity (higher for the host), swimming capacity of larval stages (higher for the parasite), and habitat availability (higher for the host).

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“…18) to generate and date phylogenetic trees on the basis of Bayesian analysis. Consistent with the phylogenetic ordering of durian, cotton, and cacao first proposed by Alverson et al 19 , our results suggest that cacao first diverged from the shared duriancotton lineage 62-85 million years ago (95% highest posterior density (HPD) interval), followed by the divergence of durian and cotton 60-77 million years ago (Fig.…”

Section: Comparative Phylogenomics Shows Durian Paleopolyploidymentioning

confidence: 99%