[dinosaur] Inferring the mammal tree: Species-level sets of phylogenies

Ben Creisler
[email protected]

A new paper that may be of interest:

Free pdf:


Nathan S. Upham, Jacob A. Esselstyn & Walter Jetz (2019)
Inferring the mammal tree: Species-level sets of phylogenies for questions
in ecology, evolution, and conservation.
PLoS Biology 17(12): e3000494.
doi: https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1371_journal.pbio.3000494&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=fSkxWyY9dLFwkVksiNbkDFNctBBCpXW9dcE6YjNXVW4&s=pPBLnAKWbYvTuh_4MA7uXONmELXCfgi6ATIkBW3QIbk&e= 
https://urldefense.proofpoint.com/v2/url?u=https-3A__journals.plos.org_plosbiology_article-3Fid-3D10.1371_journal.pbio.3000494&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=fSkxWyY9dLFwkVksiNbkDFNctBBCpXW9dcE6YjNXVW4&s=D5QVMnh7dX4gxZkw_a3PkhVKuU8gRuSBiYJta6Kt3QE&e= 

Free pdf:
https://urldefense.proofpoint.com/v2/url?u=https-3A__journals.plos.org_plosbiology_article_file-3Fid-3D10.1371_journal.pbio.3000494-26type-3Dprintable&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=fSkxWyY9dLFwkVksiNbkDFNctBBCpXW9dcE6YjNXVW4&s=VwD1Uxz5ePC1aCy_GPjORi4Mbnlq7FC0VPMo9iDSwho&e= 


Big, time-scaled phylogenies are fundamental to connecting evolutionary
processes to modern biodiversity patterns. Yet inferring reliable
phylogenetic trees for thousands of species involves numerous trade-offs
that have limited their utility to comparative biologists. To establish a
robust evolutionary timescale for all approximately 6,000 living species of
mammals, we developed credible sets of trees that capture root-to-tip
uncertainty in topology and divergence times. Our "backbone-and-patch"
approach to tree building applies a newly assembled 31-gene supermatrix to
two levels of Bayesian inference: (1) backbone relationships and ages among
major lineages, using fossil node or tip dating, and (2) species-level
"patch" phylogenies with nonoverlapping in-groups that each correspond to
one representative lineage in the backbone. Species unsampled for DNA are
either excluded ("DNA-only" trees) or imputed within taxonomic constraints
using branch lengths drawn from local birth–death models ("completed"
trees). Joining time-scaled patches to backbones results in species-level
trees of extant Mammalia with all branches estimated under the same
modeling framework, thereby facilitating rate comparisons among lineages as
disparate as marsupials and placentals. We compare our phylogenetic trees
to previous estimates of mammal-wide phylogeny and divergence times,
finding that (1) node ages are broadly concordant among studies, and (2)
recent (tip-level) rates of speciation are estimated more accurately in our
study than in previous "supertree" approaches, in which unresolved nodes
led to branch-length artifacts. Credible sets of mammalian phylogenetic
history are now available for download at https://urldefense.proofpoint.com/v2/url?u=http-3A__vertlife.org_phylosubsets&d=DwIFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=fSkxWyY9dLFwkVksiNbkDFNctBBCpXW9dcE6YjNXVW4&s=flrKmIwwt0IxilRKsRiji4Q3J_yLepYfbTSFokuQhA8&e= ,
enabling investigations of long-standing questions in comparative biology.