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Phylogenomics and the rise of the angiosperms.

Alexandre Rizzo ZuntiniTom CarruthersOlivier MaurinPaul C BaileyKevin LeempoelGrace E BrewerNiroshini EpitawalageElaine FrançosoBerta Gallego-ParamoCatherine McGinnieRaquel NegrãoShyamali R RoyLalita SimpsonEduardo Toledo RomeroVanessa M A BarberLaura R BotiguéJames J ClarksonRobyn S CowanSteven DodsworthMatthew G JohnsonJan T KimLisa PokornyNorman J WickettGuilherme Medeiros AntarLucinda DeBoltKarime GutierrezKasper P HendriksAlina HoewenerAi-Qun HuElizabeth M JoyceIzai A B S KikuchiIsabel LarridonDrew A LarsonElton John de LírioJing-Xia LiuPanagiota MalakasiNatalia A S PrzelomskaToral ShahJuan ViruelTheodore R AllnuttGabriel K AmekaRose L AndrewMarc S AppelhansMontserrat AristaMaría Jesús ArizaJuan ArroyoWatchara ArthanJulien B BachelierC Donovan BaileyHelen F BarnesMatthew D BarrettRussell L BarrettRandall J BayerMichael J BaylyEdward BiffinNicky BiggsJoanne L BirchDiego BogarínRenata BorosovaAlexander M C BowlesPeter C BoyceGemma L C BramleyMarie BriggsLinda M BroadhurstGillian K BrownJeremy J BruhlAnne BruneauSven BuerkiEdie BurnsMargaret ByrneStuart CableAinsley CalladineMartin W CallmanderÁngela CanoDavid J CantrillWarren M Cardinal-McTeagueMónica M CarlsenAbigail J A CarruthersAlejandra de Castro MateoMark W ChaseLars W ChatrouMartin CheekShi-Lin ChenMaarten J M ChristenhuszPascal-Antoine ChristinMark A ClementsSkye C CoffeyJohn G ConranXavier CornejoThomas L P CouvreurIan D CowieLaszlo CsibaIain DarbyshireGerrit DavidseNina M J DaviesAaron P DavisKor-Jent van DijkStephen R DownieMarco F DurettoMelvin R DuvallSara L EdwardsUrs EggliRoy H J ErkensMarcial EscuderoManuel de la EstrellaFederico FabrianiMichael F FayPaola de L FerreiraSarah Z FicinskiRachael M FowlerSue FrisbyLin FuTim FulcherMercè Galbany-CasalsElliot M GardnerDmitry A GermanAugusto GiarettaMarc GibernauLynn J GillespieCynthia C GonzálezDavid J GoyderSean W GrahamAurélie GrallLaura GreenBee F GunnDiego G GutiérrezJan HackelThomas HaevermansAnna L HaighJocelyn C HallTony HallMelissa J HarrisonSebastian A HattOriane HidalgoTrevor Roland HodkinsonGareth D HolmesHelen C F HopkinsChristopher J JacksonShelley A JamesRichard W JobsonGudrun KadereitImalka M KahandawalaKent KainulainenMasahiro KatoElizabeth A KelloggGraham John KingBeata KlejevskajaBente B KlitgaardRonell R KlopperSandra KnappMarcus A KochJames H Leebens-MackFrederic LensChristine J LeonÉtienne Léveillé-BourretGwilym P LewisDe-Zhu LiLan LiSigrid Liede-SchumannTatyana LivshultzDavid LorenceMeng LuPatricia Lu-IrvingJaquelini LuberEve J LucasManuel LujánMabel LumTerry D MacfarlaneCarlos MagdalenaVidal F MansanoLizo E MastersSimon J MayoKristina McCollAngela J McDonnellAndrew E McDougallTodd G B McLayHannah McPhersonRosa Isela MenesesVincent S F T MerckxFabian A MichelangeliJohn D MitchellAlexandre K MonroMichael J MooreTaryn L MuellerKlaus MummenhoffJérôme MunzingerPriscilla MurielDaniel J MurphyKatharina NargarLars NauheimerFrancis J NgeReto NyffelerAndrés OrejuelaEdgardo M OrtizLuis PalazzesiAriane Luna PeixotoSusan K PellJaume PellicerDarin S PenneysOscar A Perez-EscobarClaes PerssonMarc PignalYohan PillonJosé Rubens PiraniGregory M PlunkettRobyn F PowellGhillean T PranceCarmen PuglisiMing QinRichard K RabelerPaul E J ReesMatthew A M RennerEric H RoalsonMichele RoddaZachary S RogersSaba RokniRolf RutishauserMiguel F de SalasHanno SchäferRowan J SchleyAlexander N Schmidt-LebuhnAlison ShapcottIhsan Al-ShehbazKelly A ShepherdMark P SimmonsAndré O SimõesAna Rita G SimõesMichelle SirosEric de Camargo SmidtJames F SmithNeil SnowDouglas Edward SoltisPamela S SoltisRobert John SorengCynthia A SothersJulian R StarrPeter F StevensShannon C K StraubLena StruweJennifer M TaylorIan R H TelfordAndrew H ThornhillIfeanna ToothAnna Trias-BlasiFrank UdovicicTimothy M A UtteridgeJosé Carlos Del ValleG Anthony VerboomHelen P VonowMaria S VorontsovaJurriaan M de VosNoor Al-WattarMichelle WaycottCassiano A D WelkerAdam J WhiteJan J WieringaLuis T WilliamsonTrevor C WilsonSin Yeng WongLisa A WoodsRoseina WoodsStuart WorboysMartin XanthosYa YangYu-Xiao ZhangMeng-Yuan ZhouSue ZmarztyFernando O ZuloagaAlexandre AntonelliSidonie BellotDarren M CraynOlwen M GracePaul Julian KerseyIlia J LeitchHervé SauquetStephen A SmithWolf L EiserhardtFélix ForestWilliam J Baker
Published in: Nature (2024)
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods 1,2 . A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome 3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins 5-7 . However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes 8 . This 15-fold increase in genus-level sampling relative to comparable nuclear studies 9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
Keyphrases
  • genome wide
  • machine learning
  • genome wide identification
  • deep learning
  • copy number
  • dna methylation
  • gene expression
  • case control
  • radiation therapy
  • risk assessment
  • bioinformatics analysis