Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

The Timing and Direction of Introgression Under the Multispecies Network Coalescent

(2019) Mark S. Hibbins et al.   GENETICS

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

(2019) Gustavo A. Bravo et al.   PeerJ

Recombination rate variation shapes barriers to introgression across butterfly genomes

(2019) Simon H. Martin et al.   PLOS BIOLOGY

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

(2019) Ian V. Caldas et al.   Ecology and Evolution

Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating

(2019) Lindell Bromham   TRENDS IN ECOLOGY & EVOLUTION

Rapid morphological evolution in placental mammals post-dates the origin of the crown group

(2019) Thomas J. D. Halliday et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process

(2019) Joëlle Barido-Sottani et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mystacodon selenensis, the earliest known toothed mysticete (Cetacea, Mammalia) from the late Eocene of Peru: anatomy, phylogeny, and feeding adaptations

(2019) Christian de Muizon et al.   GEODIVERSITAS

Recombination-aware phylogenomics reveals the structured genomic landscape of hybridizing cat species

(2019) Gang Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

(2019) Raja Hashim Ali et al.   MOLECULAR BIOLOGY AND EVOLUTION

Congruence, fossils and the evolutionary tree of rodents and lagomorphs

(2019) Robert J. Asher et al.   Royal Society Open Science

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

The soft explosive model of placental mammal evolution

(2018) Matthew J. Phillips et al.   BMC EVOLUTIONARY BIOLOGY

Early African Fossils Elucidate the Origin of Embrithopod Mammals

(2018) Emmanuel Gheerbrant et al.   CURRENT BIOLOGY

Evaluating genomic signatures of “the large X-effect” during complex speciation

(2018) Daven C. Presgraves   MOLECULAR ECOLOGY

A comprehensive genomic history of extinct and living elephants

(2018) Eleftheria Palkopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets

(2018) Mark Springer et al.   Genes

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

(2018) Úlfur Árnason et al.   Science Advances

Partial genomic survival of cave bears in living brown bears

(2018) Axel Barlow et al.   Nature Ecology & Evolution

Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences

(2017) Meng-Yun Chen et al.   Genome Biology and Evolution

Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree

(2017) Mark S Springer et al.   JOURNAL OF HEREDITY

Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage

(2017) M. Feijoo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification

(2017) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

(2017) Thomas W. Davies et al.   PALEOBIOLOGY

Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification

(2017) Liang Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals

(2017) John Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

(2017) Liang Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the importance of homology in the age of phylogenomics

(2017) Mark S. Springer et al.   SYSTEMATICS AND BIODIVERSITY

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica

(2017) Michael Westbury et al.   Nature Communications

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

(2017) Henrique V. Figueiró et al.   Science Advances

Dating placentalia: Morphological clocks fail to close the molecular fossil gap

(2016) Mark N. Puttick et al.   EVOLUTION

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

Advances in Time Estimation Methods for Molecular Data

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

(2016) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New material ofPalaeoamasia kansui(Embrithopoda, Mammalia) from the Eocene of Turkey and a phylogenetic analysis of Embrithopoda at the species level

(2016) Ozan Erdal et al.   PALAEONTOLOGY

The non-uniformity of fossil preservation

(2016) Steven M. Holland   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mammal madness: is the mammal tree of life not yet resolved?

(2016) Nicole M. Foley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

(2016) Thomas John Dixon Halliday et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

(2016) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

(2016) Alexandra Gavryushkina et al.   SYSTEMATIC BIOLOGY

Macroraptorial sperm whales (Cetacea, Odontoceti, Physeteroidea) from the Miocene of Peru

(2016) Olivier Lambert et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

(2016) V. C. Mason et al.   Science Advances

Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon

(2016) Jun J. Sato et al.   Scientific Reports

Resolving the relationships of Paleocene placental mammals

(2015) Thomas J. D. Halliday et al.   BIOLOGICAL REVIEWS

Morphological Phylogenetics in the Genomic Age

(2015) Michael S.Y. Lee et al.   CURRENT BIOLOGY

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

(2015) Konstantinos Angelis et al.   Current Zoology

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

(2015) Gang Li et al.   GENOME RESEARCH

The Time Scale of Recombination Rate Evolution in Great Apes

(2015) Laurie S. Stevison et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

(2015) Dahiana Arcila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

(2015) Frido Welker et al.   NATURE

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Bayesian molecular clock dating of species divergences in the genomics era

(2015) Mario dos Reis et al.   NATURE REVIEWS GENETICS

Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'

(2015) M. Buckley   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution

(2015) Christopher A. Emerling et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Geomolecular Dating and the Origin of Placental Mammals

(2015) Matthew J. Phillips   SYSTEMATIC BIOLOGY

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

(2015) Konstantinos Angelis et al.   Current Zoology

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

(2015) F. G. Marx et al.   Royal Society Open Science

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

(2014) M. dos Reis et al.   Biology Letters

First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism

(2014) David W. Krause et al.   NATURE

Hybrid Speciation in a Marine Mammal: The Clymene Dolphin (Stenella clymene)

(2014) Ana R. Amaral et al.   PLoS One

Anthracobunids from the Middle Eocene of India and Pakistan Are Stem Perissodactyls

(2014) Lisa Noelle Cooper et al.   PLoS One

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life?

(2014) David J. Pattinson et al.   SYSTEMATIC BIOLOGY

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

(2013) James B. Pease et al.   EVOLUTION

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations

(2013) Chang-Fu Zhou et al.   NATURE

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   PLoS One

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

(2013) Vikas Kumar et al.   PLoS One

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

Technical Comment on "The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals"

(2013) M. S. Springer et al.   SCIENCE

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

(2013) Robert S. Sansom et al.   Scientific Reports

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Incorporating phylogenetic uncertainty on phylogeny-based palaeontological dating and the timing of turtle diversification

(2012) Juliana Sterli et al.   CLADISTICS

A phylogenetic blueprint for a modern whale

(2012) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Phylogenetic analysis, taxonomic revision, and dental ontogeny of the Cretaceous Zhelestidae (Mammalia: Eutheria)

(2012) J. DAVID ARCHIBALD et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL

(2011) Nicolas Lartillot et al.   EVOLUTION

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

(2011) A. Hobolth et al.   GENOME RESEARCH

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

(2011) K T J Davies et al.   HEREDITY

Protungulatum, Confirmed Cretaceous Occurrence of an Otherwise Paleocene Eutherian (Placental?) Mammal

(2011) J. David Archibald et al.   JOURNAL OF MAMMALIAN EVOLUTION

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

A Jurassic eutherian mammal and divergence of marsupials and placentals

(2011) Zhe-Xi Luo et al.   NATURE

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The historical biogeography of Mammalia

(2011) M. S. Springer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India

(2011) A. Goswami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Convergent sequence evolution between echolocating bats and dolphins

(2010) Yang Liu et al.   CURRENT BIOLOGY

Natural hybridization generates mammalian lineage with species characteristics

(2010) P. A. Larsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data

(2010) Richard D. Wilkinson et al.   SYSTEMATIC BIOLOGY

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

(2009) Johannes Krause et al.   BMC EVOLUTIONARY BIOLOGY

The Eutherian Mammal Maelestes gobiensis from the Late Cretaceous of Mongolia and the phylogeny of cretaceous eutheria

(2009) John R. Wible et al.   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

(2009) Michael R. McGowen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

(2009) H. Nishihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

A Likelihood Method for Assessing Molecular Divergence Time Estimates and the Placement of Fossil Calibrations

(2009) R. Alexander Pyron   SYSTEMATIC BIOLOGY

The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

(2009) Jun Inoue et al.   SYSTEMATIC BIOLOGY

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

(2009) Mette E. Steeman et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

(2008) Björn M Hallström et al.   BMC EVOLUTIONARY BIOLOGY

Morphology and Placental Mammal Phylogeny

(2008) Mark S. Springer et al.   SYSTEMATIC BIOLOGY