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Journal ArticleDOI

The delayed rise of present-day mammals

TLDR
The results show that the phylogenetic ‘fuses’ leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today’s mammals.
Abstract
Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.

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Citations
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Genes mirror geography within Europe.

TL;DR: Despite low average levels of genetic differentiation among Europeans, there is a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans.
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An Update of Wallace’s Zoogeographic Regions of the World

TL;DR: A global map of zoogeographic regions is generated by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals, and it is shown that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere.
Journal ArticleDOI

Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees.

TL;DR: A method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance is developed and will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
References
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APE: Analyses of Phylogenetics and Evolution in R language

TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.