A genomic timescale for placental mammal evolution.
Nicole M FoleyVictor C MasonAndrew J HarrisKevin R BredemeyerJoana DamasHarris A LewinEduardo EizirikJohn GatesyElinor K KarlssonKerstin Lindblad-Tohnull nullMark S SpringerWilliam J MurphyGregory AndrewsJoel C ArmstrongMatteo BianchiBruce W BirrenKevin R BredemeyerAna M BreitMatthew J ChristmasHiram ClawsonJoana DamasFederica Di PalmaMark DiekhansMichael X DongEduardo EizirikKaili FanCornelia FanterNicole M FoleyKarin Forsberg-NilssonCarlos J GarciaJohn GatesySteven GazalDiane P GenereuxLinda GoodmanJenna GrimshawMichaela K HalseyAndrew J HarrisGlenn HickeyMichael HillerAllyson G HindleRobert M HubleyGraham M HughesJeremy JohnsonDavid JuanIrene M KaplowElinor K KarlssonKathleen C KeoughBogdan KirilenkoKlaus-Peter KoepfliJennifer M KorstianAmanda KowalczykSergey V KozyrevAlyssa J LawlerColleen LawlessThomas LehmannDanielle L LevesqueHarris A LewinXue LiAbigail LindKerstin Lindblad-TohAva Mackay-SmithVoichita D MarinescuTomas Marques-BonetVictor C MasonJennifer R S MeadowsWynn K MeyerJill E MooreLucas R MoreiraDiana D Moreno-SantillanKathleen M MorrillGerard MuntanéWilliam J MurphyArcadi NavarroMartin NweeiaSylvia OrtmannAustin OsmanskiBenedict PatenNicole S PaulatAndreas R PfenningBaDoi N PhanKatherine S PollardHenry E PrattDavid A RaySteven K ReillyJeb R RosenIrina RufLouise RyanOliver A RyderPardis C SabetiDaniel E SchäfferAitor SerresBeth ShapiroArian F A SmitMark SpringerChaitanya SrinivasanCynthia SteinerJessica M StorerKevin A M SullivanPatrick F SullivanElisabeth SundströmMegan A SuppleRoss SwoffordJoy-El TalbotEmma TeelingJason Turner-MaierAlejandro ValenzuelaFranziska WagnerOla WallermanChao WangJuehan WangZhiping WengAryn P WilderMorgan E WirthlinJames R XueXiaomeng ZhangPublished in: Science (New York, N.Y.) (2023)
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.