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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified asExpand
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispeciesExpand
Estimating phylogenetic trees from genome‐scale data
The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods have been proposed toExpand
Coalescent methods for estimating species trees from phylogenomic data
Genome‐scale sequence data have become increasingly available in the phylogenetic studies for understanding the evolutionary histories of species. However, it is challenging to develop probabilisticExpand
A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations
The earliest evolution of mammals and origins of mammalian features can be traced to the mammaliaforms of the Triassic and Jurassic periods that are extinct relatives to living mammals. Here weExpand
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
Significance We produced a genome-scale dataset from representatives of all placental mammal orders to infer diversification timing relative to the Cretaceous–Paleogene (KPg) boundary. OurExpand
Mammalian bipedalism has long been thought to have arisen in response to arid and open environments. Here, we tested whether bipedalism coevolved with environmental changes using molecular andExpand
Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents
The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks and paleontological data. The fossil record tends to support an earlyExpand
Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity
Gatesy and Springer (1) suggest that coalescent methods cannot build a reliable phylogeny from gene trees, particularly from exonic sequences concatenated in silico. However, the authors confuseExpand
Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics
BackgroundBeak morphology exhibits considerable adaptive plasticity in birds, which results in highly varied or specialized forms in response to variations in ecology and life history. As the onlyExpand