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dc.contributor.author Chen, Xin
dc.contributor.author Lemmon, Alan R.
dc.contributor.author Lemmon, Emily Moriarty
dc.contributor.author Pyron, R. Alexander
dc.contributor.author Burbrink, Frank T.
dc.date.accessioned 2017-04-17T21:48:51Z
dc.date.available 2017-04-17T21:48:51Z
dc.date.issued 2017-03-24
dc.identifier doi:10.5061/dryad.r43s0
dc.identifier.citation Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT (2017) Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Molecular Phylogenetics and Evolution 111: 206-218.
dc.identifier.issn 1055-7903
dc.identifier.uri http://hdl.handle.net/10255/dryad.142939
dc.description Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents. We estimate species trees inferred from phylogenomic scale data (304 loci) while exploring several strategies that consider topological error from each individual gene tree. With a dated species tree, we examine taxonomy and test previous hypotheses that suggest the ratsnakes originated in the Old World (OW) and dispersed to New World (NW). Furthermore, we determine if dispersal to the NW represented a source of ecological opportunity, which should show elevated rates of species diversification. We show that ratsnakes originated in the OW during the mid-Oligocene and subsequently dispersed to the NW by the mid-Miocene; diversification was also elevated in a subclade of NW taxa. Finally, the optimal biogeographic region-dependent speciation model shows that the uptick in ratsnake diversification was associated with colonization of the NW. We consider several alternative explanations that account for regionally distinct diversification rates.
dc.relation.haspart doi:10.5061/dryad.r43s0/1
dc.relation.haspart doi:10.5061/dryad.r43s0/2
dc.relation.haspart doi:10.5061/dryad.r43s0/3
dc.relation.haspart doi:10.5061/dryad.r43s0/4
dc.relation.haspart doi:10.5061/dryad.r43s0/5
dc.relation.haspart doi:10.5061/dryad.r43s0/6
dc.relation.haspart doi:10.5061/dryad.r43s0/7
dc.relation.haspart doi:10.5061/dryad.r43s0/8
dc.relation.haspart doi:10.5061/dryad.r43s0/9
dc.relation.isreferencedby doi:10.1016/j.ympev.2017.03.017
dc.title Data from: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes
dc.type Article
prism.publicationName Molecular Phylogenetics and Evolution
dryad.citationInProgress false

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Title gene_fasta_87taxa
Downloaded 10 times
Description Genes used to build the phylogeny
Download gene_fasta_87taxa.zip (1.896 Mb)
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Title Species tree from MPEST
Downloaded 7 times
Description Time-calibrated species tree using MPEST for topological inference and MCMCtree for the time
Download tree_oldcal.tre (6.336 Kb)
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Title Species tree inferred using ASTRAL
Downloaded 5 times
Download rat_astral_II.tre (3.761 Kb)
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Title gene trees for each locus
Downloaded 6 times
Description Gene trees were built using Bayesian inference method with 1000 posterior probability trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download rootedtrees-20170409T045003Z-001.zip (371.0 Mb)
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Title bootstrap gene trees for each locus
Downloaded 5 times
Description Gene trees were built using maximum likelihood method with 1000 bootstrap gene trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download bstree_1000-20170409T044850Z-001.zip (426.6 Mb)
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Title maximum likelihood gene tree for each locus
Downloaded 5 times
Description The gene tree for each locus inferred using Maximum likelihood method. These gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download mltrees304.zip (509.4 Kb)
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Title Gene tree for each locus inferred using Bayesian inference method
Downloaded 8 times
Description These gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download ppcontrees.zip (468.8 Kb)
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Title convert full sequence code to full species name
Downloaded 6 times
Description This is a bash script used to convert the tip names on species tree from sequence code to full species names
Download changetreetipnames.sh (5.47 Kb)
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Title convert sequence code to full species name
Downloaded 5 times
Description This is a bash script used to convert the tip names on species tree from full species name to short sequence code.
Download changetreetipnames2.sh (5.47 Kb)
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