MRBAYES: Bayesian inference of phylogenetic trees

Huelsenbeck, John P.; Ronquist, Fredrik

doi:10.1093/bioinformatics/17.8.754

Cited by 20,309 publications

(13,301 citation statements)

References 13 publications

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“…The Bayesian network was assembled in MrBayes v3.2 (Huelsenbeck & Ronquist, 2001) with the generalized time reversible model, a gamma‐distributed rate variation, and allowance for invariable sites (GTR + Γ + I). The analysis was conducted as two simultaneous runs with eight chains for 5,000,000 generations, a 25% burn‐in, final PSRF > 0.999, ESS > 1,000, and standard deviation of split frequencies < 0.01.…”

Section: Methodsmentioning

confidence: 99%

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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%

“…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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“…This concatenated sequence was used as an input for a Bayesian phylogenetic analysis performed using MrBayes v 3.2 (Huelsenbeck and Ronquist 2001). The analysis was carried out partitioning by gene and applying the Jones model to each partition, as it was the one with the highest posterior probability (1.0) with parameters unlinked across partitions.…”

Section: Methodsmentioning

confidence: 99%

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

et al. 2018

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The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2 Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and Core Eukaryotic Genes Mapping Approach (CEGMA) analysis reveals that our assembly captures almost all protein-coding genes. RNA-seq was performed and 93.1% of the reads aligned to the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.

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“…According to the results of the Akaike Information Criterion in MrModeltest v2.3 (Nylander, 2004), the GTR + Γ + I model was selected as the best model of sequence evolution. Based on the selected model, phylogenetic reconstruction was performed with MrBayes v3.1 (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003). The Bayesian analysis consisted of two runs each with four simultaneous Markov chains for 20,000,000 generations.…”

Section: Methodsmentioning

confidence: 99%

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

Greve

Haase

Hutterer

et al. 2017

Ecology and Evolution

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The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio‐ and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP‐ and mtDNA‐tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.

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MRBAYES: Bayesian inference of phylogenetic trees

Abstract: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

Cited by 20,309 publications

References 13 publications

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

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

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

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