Coalescent-based species tree estimation with

Transcription

Coalescent-based species tree estimation with
many hundreds of taxa and thousands of genes
Siavash Mirarab
University of Texas at Austin
BXBF;Core Eudicots/Rosids;Draba sachalinensis
UVQL;Core Eudicots/Rosids;Draba magellanica
LAPO;Core Eudicots/Rosids;Draba oligosperma
LJQF;Core Eudicots/Rosids;Draba ossetica
HABV;Core Eudicots/Rosids;Draba aizoides
GTSV;Core Eudicots/Rosids;Draba hispida
TZWR;Core Eudicots/Rosids;Arabis alpina
VMNH;Core Eudicots/Rosids;Sinapis alba
IPWB;Core Eudicots/Rosids;Brassica nigra
CSUV;Core Eudicots/Rosids;Cochlearia officinalis
Arath_TAIR10;Genome;Arabidopsis_thaliana
LVUS;Core Eudicots/Rosids;Cleome violacea
QSKP;Core Eudicots/Rosids;Polanisia trachysperma
VDKG;Core Eudicots/Rosids;Cleome gynandra
UPZX;Core Eudicots/Rosids;Cleome viscosa
RTTY;Core Eudicots/Rosids;Salvadora sp.
SWPE;Core Eudicots/Rosids;Reseda odorata
UAXP;Core Eudicots/Rosids;Gyrostemon ramulosus
JOIS;Core Eudicots/Rosids;Koeberlinia spinosa
DZTK;Core Eudicots/Rosids;Batis maritima
CRNC;Core Eudicots/Rosids;Limnanthes douglasii
MYZV;Core Eudicots/Rosids;Tropaeolum peregrinum
HYZL;Core Eudicots/Rosids;Akania lucens
Carpa_ASGPBv0.4;Genome;Carica_papaya
CZPV;Core Eudicots/Rosids;Moringa oleifera
OLXF;Core Eudicots/Rosids;Hibiscus cannabinus
ZSAB;Core Eudicots/Rosids;Hoheria angustifolia
WYIG;Core Eudicots/Rosids;Dombeya burgessiae
Theca_v1.1;Genome;Theobroma cacao
ATFX;Core Eudicots/Rosids;Muntingia calabura
PKMO;Core Eudicots/Rosids;Cistus inflatus
WMUK;Core Eudicots/Rosids;Schizolaena sp.
KPTE;Core Eudicots/Rosids;Bixa orellana
PUDI;Core Eudicots/Rosids;Daphne giraldii
AWJM;Core Eudicots/Rosids;Edgeworthia papyrifera
RJIM;Core Eudicots/Rosids;Melia azedarach
UVDC;Core Eudicots/Rosids;Azadirachta indica
UHJR;Core Eudicots/Rosids;Citrus x paradisi
QICX;Core Eudicots/Rosids;Ailanthus altissima
IKFD;Core Eudicots/Rosids;Quassia amara
FCCA;Core Eudicots/Rosids;Boswellia sacra
JSZD;Core Eudicots/Rosids;Bursera simaruba
YUOM;Core Eudicots/Rosids;Rhus radicans
BCAA;Core Eudicots/Rosids;Kirkia wilmsii
VFFP;Core Eudicots/Rosids;Acer negundo
HBHB;Core Eudicots/Rosids;Aesculus pavia
WAXR;Core Eudicots/Rosids;Litchi chinensis
OBTI;Core Eudicots/Rosids;Peganum harmala
YZVJ;Core Eudicots/Rosids;Cephalotus follicularis
THHD;Core Eudicots/Rosids;Elaeocarpus sylvestris
TIUZ;Core Eudicots/Rosids;Cunonia capensis
JHCN;Core Eudicots/Rosids;Oxalis sp.
KKDQ;Core Eudicots/Rosids;Salix viminalis
IEPQ;Core Eudicots/Rosids;Salix dasyclados
GLVK;Core Eudicots/Rosids;Salix eriocephala
RZTJ;Core Eudicots/Rosids;Salix fargesii
TDTF;Core Eudicots/Rosids;Salix sachalinensis
LFOG;Core Eudicots/Rosids;Salix purpurea
INQX;Core Eudicots/Rosids;Salix acutifolia
Poptr_v3.0;Genome;Populus trichocarpa
SIZE;Core Eudicots/Rosids;Passiflora caerulea
ZIWB;Core Eudicots/Rosids;Passiflora_sp
EZZT;Core Eudicots/Rosids;Passiflora edulis
COAQ;Core Eudicots/Rosids;Malesherbia fasciculata
LPGY;Core Eudicots/Rosids;Viola tricolor
NJLF;Core Eudicots/Rosids;Viola canadensis
XNLP;Core Eudicots/Rosids;Manihot grahamii
Manes_v4.1;Genome;Manihot esculenta
VVPY;Core Eudicots/Rosids;Croton tiglium
PAZJ;Core Eudicots/Rosids;Ricinus communis
RHAU;Core Eudicots/Rosids;Euphorbia mesembryanthemifolia
PXYR;Core Eudicots/Rosids;Euphorbia pekinensis
RVGH;Core Eudicots/Rosids;Drypetes deplanchei
ZTLR;Core Eudicots/Rosids;Rhizophora mangle
RPPC;Core Eudicots/Rosids;Erythroxylum coca
VNMY;Core Eudicots/Rosids;Bischofia javanica
YGAT;Core Eudicots/Rosids;Phyllanthus sp.
FWCQ;Core Eudicots/Rosids;Garcinia oblongifolia
OSIP;Core Eudicots/Rosids;Garcinia livingstonei
BNDE;Core Eudicots/Rosids;Hypericum perforatum
NFXV;Core Eudicots/Rosids;Mammea americana
ZBVT;Core Eudicots/Rosids;Chrysobalanus icaco
HBUQ;Core Eudicots/Rosids;Licania michauxii
CKDK;Core Eudicots/Rosids;Ochna serrulata
TVCU;Core Eudicots/Rosids;Ochna mossambicensis
XPBC;Core Eudicots/Rosids;Galphimia gracilis
OODC;Core Eudicots/Rosids;Linum bienne
POZS;Core Eudicots/Rosids;Linum usitatissimum
MYVH;Core Eudicots/Rosids;Linum grandiflorum
BHYC;Core Eudicots/Rosids;Linum lewisii
AEPI;Core Eudicots/Rosids;Linum leonii
BVOF;Core Eudicots/Rosids;Linum perenne
HNCF;Core Eudicots/Rosids;Linum hirsutum
TXMP;Core Eudicots/Rosids;Linum strictum
VXOD;Core Eudicots/Rosids;Linum tenuifolium
KCPT;Core Eudicots/Rosids;Linum macraei
AXPJ;Core Eudicots/Rosids;Linum flavum
IHCQ;Core Eudicots/Rosids;Crossopetalum rhacoma
MFEA;Core Eudicots/Rosids;Stackhousia spathulata
WWKL;Core Eudicots/Rosids;Tapiscia sinensis
UDUT;Core Eudicots/Rosids;Larrea tridentata
KVAY;Core Eudicots/Rosids;Tribulus eichlerianus
ZHMB;Core Eudicots/Rosids;Krameria lanceolata
IMZV;Core Eudicots/Rosids;Oenothera grandis
ARYD;Core Eudicots/Rosids;Oenothera laciniata
YHLF;Core Eudicots/Rosids;Oenothera rhombipetala
KBRW;Core Eudicots/Rosids;Oenothera clelandii
ROLB;Core Eudicots/Rosids;Oenothera elata
IDAU;Core Eudicots/Rosids;Oenothera elata
BZDF;Core Eudicots/Rosids;Oenothera biennis
ZINQ;Core Eudicots/Rosids;Oenothera grandiflora
DZLN;Core Eudicots/Rosids;Oenothera picensis
GVCB;Core Eudicots/Rosids;Oenothera affinis
HKMQ;Core Eudicots/Rosids;Oenothera villaricae
CJGZ;Core Eudicots/Rosids;Oenothera nana
EQYT;Core Eudicots/Rosids;Oenothera berlandieri
SJAN;Core Eudicots/Rosids;Oenothera serrulata
AXNH;Core Eudicots/Rosids;Oenothera filiformis
PMTB;Core Eudicots/Rosids;Oenothera gaura
JKNQ;Core Eudicots/Rosids;Oenothera suffulta suffulta
UJGI;Core Eudicots/Rosids;Oenothera rosea
TLCA;Core Eudicots/Rosids;Oenothera speciosa
FEDW;Core Eudicots/Rosids;Epilobium sp.
YNUE;Core Eudicots/Rosids;Punica granatum
RJNQ;Core Eudicots/Rosids;Lagerstroemia indica
AJJE;Core Eudicots/Rosids;Terminalia neotaliala
Eucgr_v1.1;Genome;Eucalyptus grandis
AYMT;Core Eudicots/Rosids;Eucalyptus leucoxylon
NEBM;Core Eudicots/Rosids;Syzygium micranthum
FGDU;Core Eudicots/Rosids;Syzygium paniculatum
SWGX;Core Eudicots/Rosids;Tetrazygia bicolor
WWQZ;Core Eudicots/Rosids;Medinilla magnifica
YGCX;Core Eudicots/Rosids;Geranium maculatum
HJMP;Core Eudicots/Rosids;Astragalus membranaceus
MYMP;Core Eudicots/Rosids;Astragalus propinquus
KNMB;Core Eudicots/Rosids;Lathyrus sativus
JTQQ;Core Eudicots/Rosids;Glycyrrhiza lepidota
PEZP;Core Eudicots/Rosids;Glycyrrhiza glabra
RMWJ;Core Eudicots/Rosids;Wisteria floribunda
KEGA;Core Eudicots/Rosids;Glycine soja
TVSH;Core Eudicots/Rosids;Bituminaria bituminosa
Phavu_v1.0;Genome;Phaseolus vulgaris
SUAK;Core Eudicots/Rosids;Codariocalyx motorius
NXOH;Core Eudicots/Rosids;Apios americana
VLNB;Core Eudicots/Rosids;Gompholobium polymorphum
CMFF;Core Eudicots/Rosids;Lupinus polyphyllus
TTRG;Core Eudicots/Rosids;Lupinus angustifolius
SLYR;Core Eudicots/Rosids;Cladrastis lutea
ZSSR;Core Eudicots/Rosids;Xanthocercis zambesiaca
ZCDJ;Core Eudicots/Rosids;Acacia argyrophylla
PJSX;Core Eudicots/Rosids;Acacia pycnantha
XOOE;Core Eudicots/Rosids;Desmanthus illinoensis
KZED;Core Eudicots/Rosids;Senna hebecarpa
GEHT;Core Eudicots/Rosids;Gleditsia triacanthos
VHZV;Core Eudicots/Rosids;Gleditsia sinensis
QZXQ;Core Eudicots/Rosids;Gymnocladus dioicus
JETM;Core Eudicots/Rosids;Bauhinia tomentosa
RKFX;Core Eudicots/Rosids;Cercis canadensis
RKLL;Core Eudicots/Rosids;Copaifera officinalis
OQHZ;Core Eudicots/Rosids;Quillaja saponaria
OHAE;Core Eudicots/Rosids;Polygala lutea
PGKL;Core Eudicots/Rosids;Phellodendron amurense
DXQW;Core Eudicots/Rosids;Juglans nigra
INSP;Core Eudicots/Rosids;Myrica cerifera
LWDA;Core Eudicots/Rosids;Alnus serrulata
CWZU;Core Eudicots/Rosids;Betula pendula
LNER;Core Eudicots/Rosids;Casuarina equisetifolia
NHUA;Core Eudicots/Rosids;Castanea crenata
UZWG;Core Eudicots/Rosids;Castanea pumila
HENI;Core Eudicots/Rosids;Quercus shumardii
SVVG;Core Eudicots/Rosids;Fagus sylvatica
TJLC;Core Eudicots/Rosids;Nothofagus obliqua
QIEH;Core Eudicots/Rosids;Cotoneaster transcaucasicus
BLVL;Core Eudicots/Rosids;Sorbus koehneana
VCIN;Core Eudicots/Rosids;Malus baccata
EAVM;Core Eudicots/Rosids;Amelanchier canadensis
TJQY;Core Eudicots/Rosids;Kerria japonica
ZPKK;Core Eudicots/Rosids;Aruncus dioicus
Prupe_v1.0;Genome;Prunus persica
NCVK;Core Eudicots/Rosids;Prunus prostrata
SXCE;Core Eudicots/Rosids;Physocarpus opulifolius
SQCF;Core Eudicots/Rosids;Dryas octopetala
XFFT;Core Eudicots/Rosids;Cercocarpus ledifolius
IANR;Core Eudicots/Rosids;Rosa palustris
QNOC;Core Eudicots/Rosids;Sanguisorba minor
DHAW;Core Eudicots/Rosids;Geum quellyon
EDHN;Core Eudicots/Rosids;Ficus religiosa
XVJB;Core Eudicots/Rosids;Morus nigra
WKCY;Core Eudicots/Rosids;Urtica dioica
ACFP;Core Eudicots/Rosids;Boehmeria nivea
AQGE;Core Eudicots/Rosids;Humulus lupulus
BJSW;Core Eudicots/Rosids;Cannabis sativa
KYAD;Core Eudicots/Rosids;Celtis occidentalis
CQMG;Core Eudicots/Rosids;Ulmus alata
WVEF;Core Eudicots/Rosids;Rhamnus caroliniana
EILE;Core Eudicots/Rosids;Rhamnus japonica
ZHEE;Core Eudicots/Rosids;Ziziphus jujuba
RBYC;Core Eudicots/Rosids;Elaeagnus pungens
OCTM;Core Eudicots/Rosids;Begonia sp.
NNGU;Core Eudicots/Rosids;Coriaria nepalensis
AXAF;Core Eudicots/Rosids;Thladiantha villosula
HDWF;Core Eudicots/Rosids;Francoa appendiculata
VYGG;Core Eudicots/Rosids;Stachyurus praecox
PTLU;Core Eudicots/Rosids;Staphylea trifolia
DRIL;Core Eudicots;Kalanchoe crenato-diagremontiana
ZJUL;Core Eudicots;Rhodiola rosea
KWGC;Core Eudicots;Crassula perforata
VJPU;Core Eudicots;Boerhavia dominii
ZBTA;Core Eudicots;Boerhavia coccinea
EGOS;Core Eudicots;Allionia incarnata
DVXD;Core Eudicots;Allionia incarnata
JGAB;Core Eudicots;Mirabilis jalapa
JAFJ;Core Eudicots;Bougainvillea spectabilis
SFKQ;Core Eudicots;Hilleria latifolia
AZBL;Core Eudicots;Petiveria alliacea
MRKX;Core Eudicots;Phytolacca bogotensis
BKQU;Core Eudicots;Phytolacca americana
GIWN;Core Eudicots;Sarcobatus vermiculatus
HZTS;Core Eudicots;Sesuvium portulacastrum
EDIT;Core Eudicots;Sesuvium verrucosum
GJNX;Core Eudicots;Cypselea humifusa
BERS;Core Eudicots;Zaleya pentandra
OMYK;Core Eudicots;Trianthema portulacastrum
BJKT;Core Eudicots;Delosperma echinatum
IWIS;Core Eudicots;Portulaca pilosa
GCYL;Core Eudicots;Portulaca suffruticosa
LDEL;Core Eudicots;Portulaca amilis
CPLT;Core Eudicots;Portulaca grandiflora
KDCH;Core Eudicots;Portulaca umbraticola
BYNZ;Core Eudicots;Portulaca umbraticola
LLQV;Core Eudicots;Portulaca cryptopetala
EZGR;Core Eudicots;Portulaca oleracea
UQCB;Core Eudicots;Portulaca molokiniensis
CPKP;Core Eudicots;Lophophora williamsii
JLOV;Core Eudicots;Pereskia aculeata
LKKX;Core Eudicots;Talinum sp.
CTYH;Core Eudicots;Basella alba
RNBN;Core Eudicots;Mollugo cerviana
SCAO;Core Eudicots;Mollugo nudicaulis
NXTS;Core Eudicots;Mollugo verticillata
KJAA;Core Eudicots;Mollugo pentaphylla
BWRK;Core Eudicots;Alternanthera sessilis
ZBPY;Core Eudicots;Alternanthera brasiliana
OHKC;Core Eudicots;Alternanthera caracasana
EYRD;Core Eudicots;Alternanthera tenella
CUTE;Core Eudicots;Blutaparon vermiculare
HDSY;Core Eudicots;Aerva persica
PDQH;Core Eudicots;Aerva lanata
XSSD;Core Eudicots;Amaranthus cruentus
WMLW;Core Eudicots;Amaranthus retroflexus
AAXJ;Core Eudicots;Atriplex prostrata
ONLQ;Core Eudicots;Atriplex hortensis
CBJR;Core Eudicots;Atriplex rosea
SMMC;Core Eudicots;Chenopodium quinoa
FVXD;Core Eudicots;Beta maritima
Betvu_v1.1;Genome;Beta_vulgaris
WGET;Core Eudicots;Kochia scoparia
SKNL;Core Eudicots;Saponaria officinalis
SHEZ;Core Eudicots;Dianthus caryophyllus
OLES;Core Eudicots;Schiedea membranacea
FZQN;Core Eudicots;Silene latifolia
TJES;Core Eudicots;Spergularia media
RXEN;Core Eudicots;Polycarpaea repens
YNFJ;Core Eudicots;Microtea debilis
RUUB;Core Eudicots;Physena madagascariensis
CVDF;Core Eudicots;Simmondsia chinensis
WOBD;Core Eudicots;Limonium spectabile
CGGO;Core Eudicots;Plumbago auriculata
FYSJ;Core Eudicots;Polygonum convolvulus
WQUF;Core Eudicots;Nepenthes alata
EHNF;Basal Eudicots;Dillenia indica
DAYQ;Core Eudicots;Mitella pentandra
CTSS;Core Eudicots;Tellima breviflora
SLOI;Core Eudicots;Tiarella polyphylla
ERIA;Core Eudicots;Heuchera sanguinea
OOVX;Core Eudicots;Boykinia jamesii
CKKR;Core Eudicots;Astilbe chinensis
UHBY;Core Eudicots;Oresitrophe rupifraga
CIAC;Core Eudicots;Bergenia sp.
YKFU;Core Eudicots;Peltoboykinia watanabei
FCBJ;Core Eudicots;Saxifraga stolonifera
SYHW;Core Eudicots;Ribes aff. giraldii
UWFU;Core Eudicots;Itea virginica
LMVB;Core Eudicots;Liquidambar styraciflua
IUSR;Core Eudicots;Myriophyllum aquaticum
TOKV;Core Eudicots;Aphanopetalum resinosum
HQRJ;Core Eudicots;Loropetalum chinense
OMDH;Core Eudicots;Loropetalum chinense
YKQR;Core Eudicots;Hamamelis virginiana
NUZN;Core Eudicots;Cercidiphyllum japonicum
FYTP;Core Eudicots;Daphniphyllum macropodum
HTDC;Core Eudicots;Tamarix chinensis
HTIP;Core Eudicots;Paeonia lactiflora
BSEY;Core Eudicots;Daenikera sp.
QKMG;Core Eudicots;Phoradendron serotinum
XGFU;Core Eudicots;Exocarpos cupressiformis
RSPO;Core Eudicots;Santalum acuminatum
VGVI;Core Eudicots;Dendropemon caribaeus
XKPS;Core Eudicots;Ximenia americana
STKY;Core Eudicots;Balanophora fungosa
XMBA;Core Eudicots/Asterids;Poliomintha bustamanta
WHNV;Core Eudicots/Asterids;Micromeria fruticosa
IYDF;Core Eudicots/Asterids;Thymus vulgaris
PHCE;Core Eudicots/Asterids;Prunella vulgaris
FUMQ;Core Eudicots/Asterids;Nepeta cataria
PUCW;Core Eudicots/Asterids;Agastache rugosa
FDMM;Core Eudicots/Asterids;Rosmarinus officinalis
EQDA;Core Eudicots/Asterids;Salvia spp.
TAGM;Core Eudicots/Asterids;Melissa officinalis
BAHE;Core Eudicots/Asterids;Solenostemon scutellarioides
FYUH;Core Eudicots/Asterids;Lavandula angustifolia
SNNC;Core Eudicots/Asterids;Leonurus japonicus
EAAA;Core Eudicots/Asterids;Marrubium vulgare
GETL;Core Eudicots/Asterids;Pogostemon sp.
ATYL;Core Eudicots/Asterids;Scutellaria montana
UCNM;Core Eudicots/Asterids;Ajuga reptans
LRRR;Core Eudicots/Asterids;Teucrium chamaedrys
GNPX;Core Eudicots/Asterids;Oxera neriifolia
RTNA;Core Eudicots/Asterids;Oxera pulchella
DMLT;Core Eudicots/Asterids;Vitex agnus-castus
Mimgu_v2.0;Genome;Mimulus guttatus
FAMO;Core Eudicots/Asterids;Conopholis americana
FROP;Core Eudicots/Asterids;Epifagus virginiana
VYDM;Core Eudicots/Asterids;Orobanche fasciculata
EJCM;Core Eudicots/Asterids;Lindenbergia philippensis
OWAS;Core Eudicots/Asterids;Rehmannia glutinosa
UMUL;Core Eudicots/Asterids;Paulownia fargesii
MQIV;Core Eudicots/Asterids;Phyla dulcis
PSHB;Core Eudicots/Asterids;Lantana camara
GCFE;Core Eudicots/Asterids;Verbena hastata
UTQR;Core Eudicots/Asterids;Tabebuia umbellata
XAYK;Core Eudicots/Asterids;Kigelia africana
TKEK;Core Eudicots/Asterids;Mansoa alliacea
WOHL;Core Eudicots/Asterids;Schlegelia parasitica
EDXZ;Core Eudicots/Asterids;Schlegelia violacea
ZRIN;Core Eudicots/Asterids;Uncarina grandidieri
NBMW;Core Eudicots/Asterids;Sanchezia sp.
WEAC;Core Eudicots/Asterids;Strobilanthes dyeriana
AYIY;Core Eudicots/Asterids;Ruellia brittoniana
PCGJ;Core Eudicots/Asterids;Anisacanthus quadrifidus
MXFG;Core Eudicots/Asterids;Pinguicula agnata
JCMU;Core Eudicots/Asterids;Pinguicula caudata
HRUR;Core Eudicots/Asterids;Utricularia sp.
GRFT;Core Eudicots/Asterids;Buddleja sp.
XRLM;Core Eudicots/Asterids;Buddleja lindleyana
SIBR;Core Eudicots/Asterids;Celsia arcturus
XXYA;Core Eudicots/Asterids;Verbascum sp.
EJBY;Core Eudicots/Asterids;Anticharis glandulosa
GDZS;Core Eudicots/Asterids;Byblis gigantea
YKZB;Core Eudicots/Asterids;Plantago maritima
PTBJ;Core Eudicots/Asterids;Plantago virginica
GNRI;Core Eudicots/Asterids;Digitalis purpurea
YRHD;Core Eudicots/Asterids;Antirrhinum braun-blanquetii
XISJ;Core Eudicots/Asterids;Antirrhinum majus
CLRW;Core Eudicots/Asterids;Bacopa caroliniana
DTNC;Core Eudicots/Asterids;Sinningia tuberosa
RWKR;Core Eudicots/Asterids;Saintpaulia ionantha
DCCI;Core Eudicots/Asterids;Calceolaria pinifolia
COBX;Core Eudicots/Asterids;Polypremum procumbens
KTAR;Core Eudicots/Asterids;Chionanthus retusus
YZGX;Core Eudicots/Asterids;Cyrilla racemiflora
TORX;Core Eudicots/Asterids;Olea europaea
MZLD;Core Eudicots/Asterids;Ligustrum sinense
YADI;Core Eudicots/Asterids;Asclepias syriaca
DSUV;Core Eudicots/Asterids;Asclepias curassavica
JCLQ;Core Eudicots/Asterids;Apocynum androsaemifolium
YFQX;Core Eudicots/Asterids;Apocynum androsaemifolium
JGYZ;Core Eudicots/Asterids;Holarrhena pubescens
EDEQ;Core Eudicots/Asterids;Wrightia natalensis
MGVU;Core Eudicots/Asterids;Allamanda cathartica
QEHE;Core Eudicots/Asterids;Rauvolfia tetraphylla
UOYN;Core Eudicots/Asterids;Catharanthus roseus
GGJD;Core Eudicots/Asterids;Strychnos spinosa
KPUM;Core Eudicots/Asterids;Exacum affine
ECTD;Core Eudicots/Asterids;Gentiana acaulis
HGSM;Core Eudicots/Asterids;Gelsemium sempervirens
KTWL;Core Eudicots/Asterids;Kaliphora madagascariensis
PCNH;Core Eudicots/Asterids;Psychotria marginata
DNQA;Core Eudicots/Asterids;Psychotria douarrei
ZSGF;Core Eudicots/Asterids;Psychotria ipecacuanha
WQRD;Core Eudicots/Asterids;Galium boreale
JWEY;Core Eudicots/Asterids;Heliotropium tenuifolium
ABEH;Core Eudicots/Asterids;Heliotropium greggii
MZOB;Core Eudicots/Asterids;Heliotropium mendocinum
MDJK;Core Eudicots/Asterids;Heliotropium texanum
OUER;Core Eudicots/Asterids;Heliotropium convolvulaceum
IDGE;Core Eudicots/Asterids;Heliotropium racemosum
OEKO;Core Eudicots/Asterids;Heliotropium filiforme
NIGS;Core Eudicots/Asterids;Heliotropium karwinskyi
DIHD;Core Eudicots/Asterids;Heliotropium tenellum
XVRU;Core Eudicots/Asterids;Heliotropium calcicola
SMUR;Core Eudicots/Asterids;Lennoa madreporoides
HANM;Core Eudicots/Asterids;Pholisma arenarium
EMAL;Core Eudicots/Asterids;Ehretia acuminata
YQIJ;Core Eudicots/Asterids;Phacelia campanularia
DKFZ;Core Eudicots/Asterids;Mertensia paniculata
Solly_iTAGv2.3;Genome;Solanum lycopersicum
DLAI;Core Eudicots/Asterids;Solanum lasiophyllum
GHLP;Core Eudicots/Asterids;Solanum dulcamara
DLJZ;Core Eudicots/Asterids;Solanum ptychanthum
LQJY;Core Eudicots/Asterids;Solanum xanthocarpum
NMDZ;Core Eudicots/Asterids;Solanum sisymbriifolium
UGJI;Core Eudicots/Asterids;Lycopersicon cheesmanii
AIOU;Core Eudicots/Asterids;Brugmansia sanguinea
JNVS;Core Eudicots/Asterids;Datura metel
LWCK;Core Eudicots/Asterids;Lycium barbarum
OSMU;Core Eudicots/Asterids;Lycium sp.
BOLZ;Core Eudicots/Asterids;Atropa belladonna
MKZR;Core Eudicots/Asterids;Nicotiana sylvestris
NAUM;Core Eudicots/Asterids;Ipomoea lindheimeri
EMBR;Core Eudicots/Asterids;Ipomoea pubescens
VXKB;Core Eudicots/Asterids;Ipomoea purpurea
XQRV;Core Eudicots/Asterids;Ipomoea purpurea
QSLH;Core Eudicots/Asterids;Ipomoea hederacea
NHAG;Core Eudicots/Asterids;Ipomoea nil
OQBM;Core Eudicots/Asterids;Ipomoea indica
IZNU;Core Eudicots/Asterids;Ipomoea lobata
ERWT;Core Eudicots/Asterids;Ipomoea coccinea
ALUC;Core Eudicots/Asterids;Ipomoea quamoclit
CPOC;Core Eudicots/Asterids;Convolvulus arvensis
AHRN;Core Eudicots/Asterids;Cuscuta pentagona
QZZU;Core Eudicots/Asterids;Pyrenacantha malvifolia
ASMV;Core Eudicots/Asterids;Ilex vomitoria
SXML;Core Eudicots/Asterids;Ilex paraguariensis
DFYF;Core Eudicots/Asterids;Ilex sp.
QACK;Core Eudicots/Asterids;Helwingia japonica
GIPR;Core Eudicots/Asterids;Aucuba japonica
SZUO;Core Eudicots/Asterids;Eucommia ulmoides
HXCD;Core Eudicots/Asterids;Flaveria vaginata
QXWF;Core Eudicots/Asterids;Flaveria kochiana
JEPE;Core Eudicots/Asterids;Flaveria bidentis
ZCUA;Core Eudicots/Asterids;Flaveria trinervia
NVSO;Core Eudicots/Asterids;Flaveria palmeri
LYPZ;Core Eudicots/Asterids;Flaveria pubescens
UYED;Core Eudicots/Asterids;Flaveria sonorensis
JYMN;Core Eudicots/Asterids;Flaveria brownii
YRBQ;Core Eudicots/Asterids;Flaveria angustifolia
AQZD;Core Eudicots/Asterids;Flaveria pringlei
BIDT;Core Eudicots/Asterids;Flaveria cronquistii
UBLN;Core Eudicots/Asterids;Xanthium strumarium
DUNJ;Core Eudicots/Asterids;Helenium autumnale
AFQQ;Core Eudicots/Asterids;Inula helenium
MHYG;Core Eudicots/Asterids;Conyza canadensis
DESP;Core Eudicots/Asterids;Erigeron canadensis
TEZA;Core Eudicots/Asterids;Solidago canadensis
XRCX;Core Eudicots/Asterids;Aster tataricus
DOVJ;Core Eudicots/Asterids;Leontopodium alpinum
GUMF;Core Eudicots/Asterids;Anthemis tinctoria
OAGK;Core Eudicots/Asterids;Matricaria matricarioides
DUQG;Core Eudicots/Asterids;Tanacetum parthenium
BMSE;Core Eudicots/Asterids;Senecio rowleyanus
KGJF;Core Eudicots/Asterids;Tragopogon porrifolius
KFZY;Core Eudicots/Asterids;Tragopogon castellanus
FUPX;Core Eudicots/Asterids;Tragopogon pratensis
DDRL;Core Eudicots/Asterids;Tragopogon dubius
JNKW;Core Eudicots/Asterids;Cicerbita plumieri
RFSD;Core Eudicots/Asterids;Lactuca graminifolia
CFRN;Core Eudicots/Asterids;Carthamus lanatus
EYKJ;Core Eudicots/Asterids;Silybum marianum
HUQC;Core Eudicots/Asterids;Scaevola mossambicensis
IXVJ;Core Eudicots/Asterids;Menyanthes trifoliata
TPEM;Core Eudicots/Asterids;Platyspermation crassifolium
GIOY;Core Eudicots/Asterids;Corokia cotoneaster
AUIP;Core Eudicots/Asterids;Phelline lucida
FXGI;Core Eudicots/Asterids;Stylidium adnatum
IZLO;Core Eudicots/Asterids;Lobelia siphilitica
IHPC;Core Eudicots/Asterids;Platycodon grandiflorus
TQKZ;Core Eudicots/Asterids;Angelica archangelica
CWYJ;Core Eudicots/Asterids;Heracleum lanatum
WEQK;Core Eudicots/Asterids;Centella asiatica
AJFN;Core Eudicots/Asterids;Myodocarpus sp.
SUVN;Core Eudicots/Asterids;Hedera helix
EDBB;Core Eudicots/Asterids;Polyscias fruticosa
OINM;Core Eudicots/Asterids;Hydrocotyle umbellata
SALZ;Core Eudicots/Asterids;Pittosporum resiniferum
NTEO;Core Eudicots/Asterids;Pittosporum sahnianum
QIKZ;Core Eudicots/Asterids;Griselinia racemosa
MVSE;Core Eudicots/Asterids;Griselinia littoralis
SBZH;Core Eudicots/Asterids;Pennantia corymbosa
JTRM;Core Eudicots/Asterids;Dipsacus asper
FFFY;Core Eudicots/Asterids;Valeriana officinalis
GSZA;Core Eudicots/Asterids;Lonicera japonica
CAQZ;Core Eudicots/Asterids;Symphoricarpos sp.
HLJG;Core Eudicots/Asterids;Viburnum odoratissimum
ZJRC;Core Eudicots/Asterids;Sambucus canadensis
CLMX;Core Eudicots/Asterids;Escallonia rubra
CLNU;Core Eudicots/Asterids;Escallonia sp. cv. Newport
PPPZ;Core Eudicots/Asterids;Rhododendron scopulorum
WXVX;Core Eudicots/Asterids;Ledum palustre
AVJK;Core Eudicots/Asterids;Cavendishia cuatrecasasii
SERM;Core Eudicots/Asterids;Sarcodes sanguinea
LRTN;Core Eudicots/Asterids;Monotropa uniflora
QAUE;Core Eudicots/Asterids;Actinidia chinensis
HUSX;Core Eudicots/Asterids;Roridula gorgonias
UFHF;Core Eudicots/Asterids;Galax urceolata
ADHK;Core Eudicots/Asterids;Galax urceolata
AXBO;Core Eudicots/Asterids;Sinojackia xylocarpa
JPDJ;Core Eudicots/Asterids;Symplocos tinctoria
NGRR;Core Eudicots/Asterids;Ternstroemia gymnanthera
ODDO;Core Eudicots/Asterids;Ardisia humilis
DAAD;Core Eudicots/Asterids;Ardisia revoluta
PTFA;Core Eudicots/Asterids;Jacquinia sp.
VKJD;Core Eudicots/Asterids;Maesa lanceolata
KVFU;Core Eudicots/Asterids;Diospyros malabarica
WRPP;Core Eudicots/Asterids;Synsepalum dulcificum
OXYP;Core Eudicots/Asterids;Sideroxylon reclinatum
BEFC;Core Eudicots/Asterids;Manilkara zapota
YSRZ;Core Eudicots/Asterids;Fouquieria macdougalii
FNEN;Core Eudicots/Asterids;Phlox sp.
WVMY;Core Eudicots/Asterids;Phlox drummondii
JEXA;Core Eudicots/Asterids;Impatiens balsamifera
BNTL;Core Eudicots/Asterids;Souroubea exauriculata
VUSY;Core Eudicots/Asterids;Nyssa ogeche
XONJ;Core Eudicots/Asterids;Camptotheca acuminata
BFJL;Core Eudicots/Asterids;Cornus florida
FWBF;Core Eudicots/Asterids;Alangium chinense
ZETY;Core Eudicots/Asterids;Hydrangea quercifolia
QURC;Core Eudicots/Asterids;Dichroa febrifuga
VTLJ;Core Eudicots/Asterids;Caiophora chuquitensis
BBBA;Core Eudicots/Rosids;Tetrastigma obtectum
SZPD;Core Eudicots/Rosids;Tetrastigma voinierianum
Vitvi_Genoscope.12X;Genome;Vitis vinifera
BGZG;Core Eudicots/Rosids;Cissus quadrangularis
QUTB;Basal Eudicots;Aextoxicon punctatum
HAEU;Basal Eudicots;Berberidopsis beckleri
XMQO;Basal Eudicots;Gunnera manicata
IWMW;Basal Eudicots;Buxus sempervirens
SWOH;Basal Eudicots;Trochodendron aralioides
SIIK;Basal Eudicots;Hakea drupacea
RQUG;Basal Eudicots;Hakea prostrata
GRRW;Basal Eudicots;Grevillea robusta
VQFW;Basal Eudicots;Platanus occidentalis
FAKD;Basal Eudicots;Nelumbo sp.
Nelnu_v1.0;Genome;Nelumbo nucifera
QCOU;Basal Eudicots;Papaver setigerum
RQNK;Basal Eudicots;Papaver somniferum
BEKN;Basal Eudicots;Papaver rhoeas
SSDU;Basal Eudicots;Papaver bracteatum
IRAF;Basal Eudicots;Argemone mexicana
XHKT;Basal Eudicots;Sanguinaria canadensis
XMVD;Basal Eudicots;Chelidonium majus
EVOD;Basal Eudicots;Eschscholzia californica
UDHA;Basal Eudicots;Ceratocapnos vesicaria
ZGQD;Basal Eudicots;Corydalis linstowiana
AUGV;Basal Eudicots;Capnoides sempervirens
NMGG;Basal Eudicots;Hypecoum procumbens
Aquco_v1.1;Genome;Aquilegia_coerulea
GBVZ;Basal Eudicots;Thalictrum thalictroides
ZUHO;Basal Eudicots;Anemone hupehensis
UPOG;Basal Eudicots;Anemone pulsatilla
VGHH;Basal Eudicots;Hydrastis canadensis
WFBF;Basal Eudicots;Podophyllum peltatum
YHFG;Basal Eudicots;Nandina domestica
CCID;Basal Eudicots;Akebia trifoliata
QTJY;Basal Eudicots;Euptelea pleiosperma
AALA;Basal Eudicots;Meliosma cuneifolia
ABSS;Magnoliids;Sassafras albidum
BCGB;Magnoliids;Cinnamomum camphora
KAYP;Magnoliids;Lindera benzoin
WIGA;Magnoliids;Persea borbonia
VYLQ;Magnoliids;Cassytha filiformis
KRJP;Magnoliids;Peumus boldus
BSVG;Magnoliids;Gyrocarpus americanus
MAQO;Magnoliids;Gomortega keule
WAIL;Magnoliids;Laurelia sempervirens
WPHN;Magnoliids;Idiospermum australiense
FALI;Magnoliids;Calycanthus floridus
PSJT;Magnoliids;Uvaria microcarpa
YZRI;Magnoliids;Annona muricata
DHPO;Magnoliids;Eupomatia bennettii
XQWC;Magnoliids;Michelia maudiae
WBOD;Magnoliids;Magnolia grandiflora
OBPL;Magnoliids;Myristica fragrans
XSZI;Magnoliids;Peperomia fraseri
MUNP;Magnoliids;Piper auritum
CSSK;Magnoliids;Houttuynia cordata
OPDF;Magnoliids;Saururus cernuus
QDVW;Magnoliids;Saruma henryi
PAWA;Magnoliids;Aristolochia elegans
WKSU;Magnoliids;Drimys winteri
SJEV;Magnoliids;Canella winterana
WZFE;Chloranthales;Ascarina rubricaulis
OSHQ;Chloranthales;Sarcandra glabra
NPND;Basalmost angiosperms;Ceratophyllum demersum
XFJG;Monocots;Maianthemum canadense
RCUX;Monocots;Maianthemum sp.
UZXL;Monocots;Disporopsis pernyi
RQZP;Monocots;Nolina bigelovii
HOKG;Monocots;Nolina atopocarpa
TCYS;Monocots;Peliosanthes minor
LSJW;Monocots;Ruscus sp.
MVRF;Monocots;Sansevieria trifasciata
ONBE;Monocots;Eriospermum lancifolia
FGRF;Monocots;Asparagus densiflorus
MUMD;Monocots;Lomandra longifolia
CMCY;Monocots;Hesperaloe parviflora
PLBZ;Monocots;Chlorogalum pomeridianum
ICNN;Monocots;Yucca filamentosa
YBML;Monocots;Yucca brevifolia
KXSK;Monocots;Agave tequilana
SVTS;Monocots;Drimia altissima
KOFB;Monocots;Urginea maritima
IXEM;Monocots;Brodiaea sierrae
DPFW;Monocots;Zephyranthes treatiae
JDTY;Monocots;Rhodophiala pratensis
LDME;Monocots;Amaryllis belladonna
DMIN;Monocots;Phycella aff. cyrtanthoides
ZKPF;Monocots;Traubia modesta
TRRQ;Monocots;Narcissus viridiflorus
GJPF;Monocots;Allium sativum
KBXS;Monocots;Allium commutatum
PRFO;Monocots;Agapanthus africanus
BLAJ;Monocots;Hemerocallis spp.
JHUL;Monocots;Hemerocallis sp.
WTDE;Monocots;Johnsonia pubescens
FCEL;Monocots;Phormium tenax
JVBR;Monocots;Aloe vera
SART;Monocots;Xeronema callistemon
LTZF;Monocots;Sisyrinchium angustifolium
RDYY;Monocots;Cyanastrum cordifolium
KYNE;Monocots;Cyanella orchidiformis
YJUG;Monocots;Curculigo sp.
EMJJ;Monocots;Borya sphaerocephala
VTUS;Monocots;Goodyera pubescens
LELS;Monocots;Haemaria discolor
XZME;Monocots;Drakaea elastica
MTHW;Monocots;Platanthera clavellata
JSAG;Monocots;Masdevallia yuangensis
CNTZ;Monocots;Oncidium sphacelatum
THDM;Monocots;Vanilla planifolia
AFLV;Monocots;Xerophyllum asphodeloides
OOSO;Monocots;Helonias bullata
MWYQ;Monocots;Smilax bona-nox
THEW;Monocots;Lilium sargentiae
QNPH;Monocots;Colchicum autumnale
NHIX;Monocots;Colchicum autumnale
GDKK;Monocots;Gloriosa superba
VQYB;Monocots/Commelinids;Neurachne lanigera
ZENX;Monocots/Commelinids;Neurachne alopecuroidea
XUAB;Monocots/Commelinids;Paraneurachne muelleri
BXAY;Monocots/Commelinids;Neurachne minor
NNOK;Monocots/Commelinids;Neurachne tenuifolia
ZMGN;Monocots/Commelinids;Neurachne munroi
BPKH;Monocots/Commelinids;Neurachne annularis
XBKS;Monocots/Commelinids;Thyridolepis mitchelliana
WCOR;Monocots/Commelinids;Thyridolepis multiculmis
SOHV;Monocots/Commelinids;Panicum miliaceum
ROEI;Monocots/Commelinids;Cymbopogon nardus
Sorbi_v2.1;Genome;Sorghum bicolor
YPIC;Monocots/Commelinids;Microstegium vimineum
YXNR;Monocots/Commelinids;Triodia aff. bynoei
EFCZ;Monocots/Commelinids;Eleusine coracana
RCAH;Monocots/Commelinids;Uniola paniculata
YLWW;Monocots/Commelinids;Uniola paniculata
HATH;Monocots/Commelinids;Aristida stricta
IADP;Monocots/Commelinids;Deschampsia cespitosa
RMVB;Monocots/Commelinids;Avena fatua
Orysa_v7.0;Genome;Oryza sativa
WXNT;Monocots/Commelinids;Joinvillea ascendens
BSTR;Monocots/Commelinids;Chondropetalum tectorum
PWSG;Monocots/Commelinids;Cyperus papyrus
WBIB;Monocots/Commelinids;Lepidosperma gibsonii
XPAF;Monocots/Commelinids;Mapania palustris
CIEA;Monocots/Commelinids;Juncus inflexus
BYPY;Monocots/Commelinids;Brocchinia reducta
PPQR;Monocots/Commelinids;Typha angustifolia
BRUD;Monocots/Commelinids;Typha latifolia
LSKK;Monocots/Commelinids;Orchidantha maxillarioides
UOEL;Monocots/Commelinids;Strelitzia reginae
XHHU;Monocots/Commelinids;Heliconia sp.
Musac_v1.0;Genome;Musa acuminata
LEMW;Monocots/Commelinids;Curcuma longa
BDJQ;Monocots/Commelinids;Zingiber officinale
JNUB;Monocots/Commelinids;Maranta leuconeura
TZNS;Monocots/Commelinids;Canna sp.
HXJE;Monocots/Commelinids;Serenoa repens
HWUP;Monocots/Commelinids;Sabal bermudana
Elagu_v2.0;Genome;Elaeis guineensis
NSPR;Monocots/Commelinids;Nypa fruticans
VVVV;Monocots;Ludovia sp.
DGXS;Monocots;Freycinetia multiflora
VBHQ;Monocots;Stemona tuberosa
SILJ;Monocots;Talbotia elegans
QOXT;Monocots;Xerophyta villosa
OCWZ;Monocots;Dioscorea villosa
COCP;Monocots;Triglochin maritima
BYQM;Monocots;Posidonia australis
DWZT;Monocots;Sagittaria latifolia
MFIN;Monocots;Pistia stratiotes
YMES;Monocots;Typhonium blumei
Spipo_v2;Genome;Spirodella polyrhiza
MTII;Monocots;Acorus americanus
VZCI;Basalmost angiosperms;Illicium floridanum
NWMY;Basalmost angiosperms;Kadsura heteroclita
FZJL;Basalmost angiosperms;Austrobaileya scandens
PZRT;Basalmost angiosperms;Nymphaea sp.
WTKZ;Basalmost angiosperms;Nuphar advena
Ambtr_v1.0.27;Genome;Amborella_trichopoda
URDJ;Basalmost angiosperms;Amborella trichopoda
XQSG;Conifers;Microbiota decussata
BUWV;Conifers;Platycladus orientalis
CGDN;Conifers;Tetraclinis sp.
FRPM;Conifers;Calocedrus decurrens
XMGP;Conifers;Juniperus scopulorum
QNGJ;Conifers;Cupressus dupreziana
UEVI;Conifers;Fokienia hodginsii
AIGO;Conifers;Chamaecyparis lawsoniana
NKIN;Conifers;Thujopsis dolabrata
VFYZ;Conifers;Thuja plicata
RMMV;Conifers;Callitris macleayana
JDQB;Conifers;Neocallitropsis pancheri
IFLI;Conifers;Callitris gracilis
AUDE;Conifers;Widdringtonia cedarbergensis
GKCZ;Conifers;Diselma archeri
YYPE;Conifers;Austrocedrus chilensis
OVIJ;Conifers;Papuacedrus papuana
ETCJ;Conifers;Pilgerodendron uviferum
FHST;Conifers;Taxodium distichum
OXGJ;Conifers;Glyptostrobus pensilis
GMHZ;Conifers;Cryptomeria japonica
QFAE;Conifers;Sequoiadendron giganteum
HBGV;Conifers;Sequoia sempervirens
NRXL;Conifers;Metasequoia glyptostroboides
XIRK;Conifers;Athrotaxis cupressoides
QSNJ;Conifers;Taiwania cryptomerioides
ZQVF;Conifers;Cunninghamia lanceolata
ZYAX;Conifers;Taxus cuspidata
WWSS;Conifers;Taxus baccata
YLPM;Conifers;Pseudotaxus chienii
BTTS;Conifers;Austrotaxus spicata
NVGZ;Conifers;Cephalotaxus harringtonia
HQOM;Conifers;Torreya nucifera
EFMS;Conifers;Torreya taxifolia
IAJW;Conifers;Amentotaxus argotaenia
YFZK;Conifers;Sciadopitys verticillata
SCEB;Conifers;Podocarpus coriaceus
XLGK;Conifers;Podocarpus rubens
UUJS;Conifers;Nageia nagi
VGSX;Conifers;Retrophyllum minus
ROWR;Conifers;Falcatifolium taxoides
QHBI;Conifers;Falcatifolium taxoides
IZGN;Conifers;Dacrydium balansae
FMWZ;Conifers;Dacrycarpus compactus
HILW;Conifers;Acmopyle pancheri
MHGD;Conifers;Microcachrys tetragona
QCGM;Conifers;Saxegothaea conspicua
ZQWM;Conifers;Lagarostrobos franklinii
CDFR;Conifers;Manoao colensoi
JZVE;Conifers;Parasitaxus usta
JRNA;Conifers;Phyllocladus hypophyllus
BBDD;Conifers;Microstrobos fitzgeraldii
OWFC;Conifers;Halocarpus bidwillii
KLGF;Conifers;Sundacarpus amarus
EGLZ;Conifers;Prumnopitys andina
MIXZ;Conifers;Agathis robusta
ACWS;Conifers;Araucaria sp.
RSCE;Conifers;Wollemia nobilis
XTZO;Conifers;Araucaria rulei
DZQM;Conifers;Pinus radiata
Pinta_v2.0;Genome;Pinus taeda
MFTM;Conifers;Pinus jeffreyi
JBND;Conifers;Pinus ponderosa
IIOL;Conifers;Pinus parviflora
AWQB;Conifers;Picea engelmannii
NPRL;Conifers;Cathaya argyrophylla
WVWN;Conifers;Larix speciosa
IOVS;Conifers;Pseudotsuga wilsoniana
GAMH;Conifers;Tsuga heterophylla
AREG;Conifers;Nothotsuga longibracteata
AQFM;Conifers;Pseudolarix amabilis
VSRH;Conifers;Abies lasiocarpa
JUWL;Conifers;Keteleeria evelyniana
GGEA;Conifers;Cedrus libani
TOXE;Gnetales;Welwitschia mirabilis
GTHK;Gnetales;Gnetum montanum
VDAO;Gnetales;Ephedra sinica
KAWQ;Cycadales;Stangeria eriopus
GNQG;Cycadales;Encephalartos barteri
WLIC;Cycadales;Dioon edule
XZUY;Cycadales;Cycas micholitzii
SGTW;Ginkgoales;Ginkgo biloba
URCP;Leptosporangiate Monilophytes;Athyrium filix-femina
AFPO;Leptosporangiate Monilophytes;Athyrium sp.
UFJN;Leptosporangiate Monilophytes;Diplazium wichurae
FCHS;Leptosporangiate Monilophytes;Deparia lobato-crenata
HTFH;Leptosporangiate Monilophytes;Onoclea sensibilis
VITX;Leptosporangiate Monilophytes;Blechnum spicant
YJJY;Leptosporangiate Monilophytes;Woodsia scopulina
YQEC;Leptosporangiate Monilophytes;Woodsia ilvensis
MROH;Leptosporangiate Monilophytes;Thelypteris acuminata
OCZL;Leptosporangiate Monilophytes;Homalosorus pycnocarpos
LHLE;Leptosporangiate Monilophytes;Cystopteris fragilis
RICC;Leptosporangiate Monilophytes;Cystopteris reevesiana
XXHP;Leptosporangiate Monilophytes;Cystopteris fragilis
YOWV;Leptosporangiate Monilophytes;Cystopteris protrusa
HNDZ;Leptosporangiate Monilophytes;Cystopteris utahensis
HEGQ;Leptosporangiate Monilophytes;Gymnocarpium dryopteris
BMIF;Leptosporangiate Monilophytes;Odontosororia sp.
PSKY;Leptosporangiate Monilophytes;Asplenium nidus
KJZG;Leptosporangiate Monilophytes;Asplenium platyneuron
CJNT;Leptosporangiate Monilophytes;Polypodium glycyrrhiza
ZRAV;Leptosporangiate Monilophytes;Polypodium hesperium
YLJA;Leptosporangiate Monilophytes;Polypodium amorphum
ZQYU;Leptosporangiate Monilophytes;Phlebodium pseudoaureum
UJWU;Leptosporangiate Monilophytes;Pleopeltis polypodioides
ORJE;Leptosporangiate Monilophytes;Phymatosorus grossus
OQWW;Leptosporangiate Monilophytes;Davallia fejeensis
NWWI;Leptosporangiate Monilophytes;Nephrolepis exaltata
FQGQ;Leptosporangiate Monilophytes;Polystichum acrostichoides
JBLI;Leptosporangiate Monilophytes;Bolbitis repanda
WGTU;Leptosporangiate Monilophytes;Leucostegia immersa
RFRB;Leptosporangiate Monilophytes;Didymochlaena truncatula
MTGC;Leptosporangiate Monilophytes;Dennstaedtia davallioides
ZXJO;Leptosporangiate Monilophytes;Parahemionitis cordata
DCDT;Leptosporangiate Monilophytes;Gaga arizonica
YCKE;Leptosporangiate Monilophytes;Notholaena montieliae
XDDT;Leptosporangiate Monilophytes;Argyrochosma nivea
GSXD;Leptosporangiate Monilophytes;Myriopteris rufa
BMJR;Leptosporangiate Monilophytes;Adiantum raddianum
WCLG;Leptosporangiate Monilophytes;Adiantum aleuticum
SKYV;Leptosporangiate Monilophytes;Vittaria lineata
WQML;Leptosporangiate Monilophytes;Cryptogramma acrostichoides
POPJ;Leptosporangiate Monilophytes;Pteris vittata
FLTD;Leptosporangiate Monilophytes;Pteris ensiformis
UJTT;Leptosporangiate Monilophytes;Pityrogramma trifoliata
PIVW;Leptosporangiate Monilophytes;Ceratopteris thalictroides
YIXP;Leptosporangiate Monilophytes;Lindsaea microphylla
NOKI;Leptosporangiate Monilophytes;Lindsaea linearis
VVRN;Leptosporangiate Monilophytes;Lonchitis hirsuta
UWOD;Leptosporangiate Monilophytes;Plagiogyria japonica
PNZO;Leptosporangiate Monilophytes;Culcita macrocarpa
EWXK;Leptosporangiate Monilophytes;Thyrsopteris elegans
GANB;Leptosporangiate Monilophytes;Cyathea (Alsophila) spinulosa
CVEG;Leptosporangiate Monilophytes;Azolla cf. caroliniana
KIIX;Leptosporangiate Monilophytes;Pilularia globulifera
PBUU;Leptosporangiate Monilophytes;Lygodium japonicum
CQPW;Leptosporangiate Monilophytes;Anemia tomentosa
QIAD;Leptosporangiate Monilophytes;Hymenophyllum bivalve
TRPJ;Leptosporangiate Monilophytes;Hymenophyllum cupressiforme
TWFZ;Leptosporangiate Monilophytes;Crepidomanes venosum
MEKP;Leptosporangiate Monilophytes;Dipteris conjugata
XDVM;Leptosporangiate Monilophytes;Sticherus lobatus
VIBO;Leptosporangiate Monilophytes;Osmunda javanica
UOMY;Leptosporangiate Monilophytes;Osmunda sp.
RFMZ;Leptosporangiate Monilophytes;Osmundastrum cinnamomeum
EEAQ;Eusporangiate Monilophytes;Sceptridium dissectum
BEGM;Eusporangiate Monilophytes;Botrypus virginianus
DJSE;Eusporangiate Monilophytes;Ophioglossum vulgatum
QVMR;Eusporangiate Monilophytes;Psilotum nudum
ALVQ;Eusporangiate Monilophytes;Tmesipteris parva
UGNK;Eusporangiate Monilophytes;Marattia attenuata
DFHO;Eusporangiate Monilophytes;Danaea nodosa
JVSZ;Eusporangiate Monilophytes;Equisetum hyemale
CAPN;Eusporangiate Monilophytes;Equisetum diffusum
WAFT;Lycophytes;Diphasiastrum digitatum
ENQF;Lycophytes;Lycopodium annotinum
PQTO;Lycophytes;Lycopodium deuterodensum
XNXF;Lycophytes;Dendrolycopodium obscurum
UPMJ;Lycophytes;Pseudolycopodiella caroliniana
ULKT;Lycophytes;Lycopodiella appressa
CBAE;Lycophytes;Huperzia myrsinites
GAON;Lycophytes;Huperzia squarrosa
GKAG;Lycophytes;Huperzia lucidula
YHZW;Lycophytes;Huperzia selago
ZZEI;Lycophytes;Phylloglossum drummondii
ZZOL;Lycophytes;Selaginella stauntoniana
Selmo_v1.0;Genome;Selaginella moellendorffii
LGDQ;Lycophytes;Selaginella apoda
ABIJ;Lycophytes;Selaginella lepidophylla
KJYC;Lycophytes;Selaginella willdenowii
JKAA;Lycophytes;Selaginella wallacei
ZYCD;Lycophytes;Selaginella acanthonota
ZFGK;Lycophytes;Selaginella kraussiana
KUXM;Lycophytes;Selaginella selaginoides
PKOX;Lycophytes;Isoetes tegetiformans
PYHZ;Lycophytes;Isoetes sp.
TMAJ;Mosses;Neckera douglasii
QMWB;Mosses;Anomodon attenuatus
JADL;Mosses;Rhynchostegium serrulatum
VBMM;Mosses;Claopodium rostratum
WSPM;Mosses;Loeskeobryum brevirostre
MIRS;Mosses;Climacium dendroides
LNSF;Mosses;Stereodon subimponens
EEMJ;Mosses;Thuidium delicatulum
TAVP;Mosses;Calliergon cordifolium
IGUH;Mosses;Leucodon julaceus
ZACW;Mosses;Leucodon brachypus
QKQO;Mosses;Pseudotaxiphyllum elegans
DHWX;Mosses;Fontinalis antipyretica
WNGH;Mosses;Aulacomnium heterostichum
CMEQ;Mosses;Orthotrichum lyellii
JMXW;Mosses;Bryum argenteum
XWHK;Mosses;Rosulabryum cf. capillare
BGXB;Mosses;Plagiomnium insigne
ORKS;Mosses;Philonotis fontana
YWNF;Mosses;Hedwigia ciliata
GRKU;Mosses;Syntrichia princeps
FFPD;Mosses;Ceratodon purpureus
NGTD;Mosses;Dicranum scoparium
VMXJ;Mosses;Leucobryum albidum
RGKI;Mosses;Leucobryum glaucum
RDOO;Mosses;Racomitrium varium
ABCD;Mosses;Racomitrium elongatum
BPSG;Mosses;Scouleria aquatica
ZQRI;Mosses;Timmia austriaca
YEPO;Mosses;Physcomitrium sp.
Phypa_v3.0;Genome;Physcomitrella patens
KEFD;Mosses;Encalypta streptocarpa
AWOI;Mosses;Diphyscium foliosum
HRWG;Mosses;Buxbaumia aphylla
SZYG;Mosses;Polytrichum commune
ZTHV;Mosses;Atrichum angustatum
HVBQ;Mosses;Tetraphis pellucida
WOGB;Mosses;Andreaea rupestris
UHLI;Mosses;Sphagnum recurvum
GOWD;Mosses;Sphagnum lescurii
RCBT;Mosses;Sphagnum palustre
SKQD;Mosses;Takakia lepidozioides
IRBN;Liverworts;Scapania nemorosa
OFTV;Liverworts;Barbilophozia barbata
YBQN;Liverworts;Odontoschisma prostratum
WZYK;Liverworts;Bazzania trilobata
RTMU;Liverworts;Calypogeia fissa
LGOW;Liverworts;Schistochila sp.
KRUQ;Liverworts;Porella navicularis
UUHD;Liverworts;Porella pinnata
BNCU;Liverworts;Radula lindenbergiana
TGKW;Liverworts;Frullania sp.
HPXA;Liverworts;Ptilidium pulcherrimum
NRWZ;Liverworts;Metzgeria crassipilis
YFGP;Liverworts;Pallavicinia lyellii
PIUF;Liverworts;Pellia cf. epiphylla
JHFI;Liverworts;Pellia neesiana
JPYU;Liverworts;Marchantia polymorpha
HMHL;Liverworts;Marchantia paleacea
TFYI;Liverworts;Marchantia emarginata
ILBQ;Liverworts;Conocephalum conicum
WJLO;Liverworts;Ricciocarpos natans
TXVB;Liverworts;Lunularia cruciata
HERT;Liverworts;Sphaerocarpos texanus
TCBC;Hornworts;Nothoceros vincentianus
DXOU;Hornworts;Nothoceros aenigmaticus
AKXB;Hornworts;Phaeomegaceros coriaceus
WEEQ;Hornworts;Phaeoceros carolinianus
FAJB;Hornworts;Paraphymatoceros hallii
BSNI;Hornworts;Anthoceros agrestis
TWUW;Hornworts;Anthoceros agrestis
ANON;Hornworts;Leiosporoceros dussii
HJVM;Green Algae;Cosmarium ochthodes
STKJ;Green Algae;Cosmarium ochthodes
WDGV;Green Algae;Cosmarium subtumidum
GBGT;Green Algae;Xanthidium antilopaeum
MOYY;Green Algae;Pleurotaenium trabecula
MCHJ;Green Algae;Micrasterias fimbriata
WCQU;Green Algae;Staurodesmus convergens
BHBK;Green Algae;Cosmarium tinctum
RPRU;Green Algae;Staurodesmus omearii
QWFV;Green Algae;Bambusina borreri
GGWH;Green Algae;Onychonema laeve
DFDS;Green Algae;Desmidium aptogonum
MNNM;Green Algae;Cosmarium granatum
ISHC;Green Algae;Staurastrum sebaldi
GYRP;Green Algae;Euastrum affine
RQFE;Green Algae;Cosmocladium cf. constrictum
HIDG;Green Algae;Cosmarium broomei
RPQV;Green Algae;Phymatodocis nordstedtiana
YSQT;Green Algae;Penium exiguum
AEKF;Green Algae;Penium margaritaceum
DRFX;Green Algae;Closterium lunula
KEYW;Green Algae;Gonatozygon kinahanii
XRTZ;Green Algae;Roya obtusa
SNOX;Green Algae;Planotaenium ohtanii
FFGR;Green Algae;Netrium digitus
KMNX;Green Algae;Nucleotaenium eifelense
NBYP;Green Algae;Mesotaenium kramstae
MFZO;Green Algae;Zygnemopsis sp.
JOJQ;Green Algae;Cylindrocystis cushleckae
HKZW;Green Algae;Mesotaenium caldariorum
ZRMT;Green Algae;Mougeotia sp.
RPGL;Green Algae;Cylindrocystis brebissonii
VAZE;Green Algae;Cylindrocystis sp.
YOXI;Green Algae;Cylindrocystis brebissonii
WSJO;Green Algae;Mesotaenium braunii
WDCW;Green Algae;Mesotaenium endlicherianum
HAOX;Green Algae;Spirogyra sp.
TPHT;Green Algae;Spirotaenia sp.
QPDY;Green Algae;Coleochaete irregularis
VQBJ;Green Algae;Coleochaete scutata
DRGY;Green Algae;Chaetosphaeridium globosum
Chabr_v0.1;Genome;Chara braunii
MWXT;Green Algae;Chara vulgaris
FQLP;Green Algae;Klebsormidium subtile
Klefl_v1.0;Genome;Klebsormidium flaccidum
FPCO;Green Algae;Interfilum paradoxum
BFIK;Green Algae;Entransia fimbriata
AZZW;Green Algae;Chlorokybus atmophyticus
NNHQ;Green Algae;Spirotaenia minuta
KYIO;Green Algae;Mesostigma viride
XMCL;prasinophytes/Prasinococcales;Prasinococcus capsulatus
WDWX;Green Algae;Dunaliella primolecta
ZDIZ;Green Algae;Dunaliella tertiolecta
RHVC;Green Algae;Dunaliella salina
UKUC;Green Algae;Dunaliella salina
SYJM;Green Algae;Dunaliella salina
ZFXU;Green Algae;Asteromonas gracilis
QRTH;Green Algae;Chloromonas perforata
PRIQ;Green Algae;Pleurastrum insigne
ZLQE;Green Algae;Stephanosphaera pluvialis
KFEB;Green Algae;Haematococcus pluvialis
GUBD;Green Algae;Brachiomonas submarina
MULF;Green Algae;Chlamydomonas bilatus
VALZ;Green Algae;Chlamydomonas noctigama
JRGZ;Green Algae;Chlamydomonas moewusii
TSBQ;Green Algae;Chlamydomonas sp.
GFUR;Green Algae;Chloromonas subdivisa
LNIL;Green Algae;Pteromonas angulosa
ACRY;Green Algae;Pteromonas sp.
ZIVZ;Green Algae;Phacotus lenticularis
JWGT;Green Algae;Volvox aureus
WRSL;Green Algae;Volvox aureus
Volca_v2.0;Green Algae;Volvox aureus
RNAT;Green Algae;Eudorina elegans
RYJX;Green Algae;Pandorina morum
ISPU;Green Algae;Volvox globator
KUJU;Green Algae;Gonium pectorale
Chlre_v5.5;Genome;Chlamydomonas reinhardii
IHOI;Green Algae;Chloromonas oogama
BCYF;Green Algae;Chlamydomonas cribrum
JKKI;Green Algae;Lobomonas rostrata
QWRA;Green Algae;Vitreochlamys sp.
USIX;Green Algae;Neochlorosarcina sp.
IRYH;Green Algae;Heterochlamydomonas inaequalis
XDLL;Green Algae;Oogamochlamys gigantea
OFUE;Green Algae;Lobochlamys segnis
LBRP;Green Algae;Chloromonas reticulata
AJUW;Green Algae;Chloromonas rosae
AOUJ;Green Algae;Chlamydomonas sp.
UTRE;Green Algae;Chloromonas tughillensis
RUIF;Green Algae;Carteria obtusa
VIAU;Green Algae;Carteria crucifera
FXHG;Green Algae;Hafniomonas reticulata
XKWQ;Green Algae;Pediastrum duplex
XTON;Green Algae;Pediastrum duplex
VJDZ;Green Algae;Botryosphaerella sudetica
PZIF;Green Algae;Scenedesmus dimorphus
MWAN;Green Algae;Neodesmus pupukensis
OTQG;Green Algae;Ankistrodesmus sp.
FOYQ;Green Algae;Microspora cf. tumidula
BZSH;Green Algae;Golenkinia longispicula
ENAU;Green Algae;Spermatozopsis similis
MXDS;Green Algae;Spermatozopsis exsultans
DZPJ;Green Algae;Cylindrocapsa geminella
VFIV;Green Algae;Fritschiella tuberosa
JMUI;Green Algae;Stigeoclonium helveticum
RAWF;Green Algae;Uronema belkae
ISGT;Green Algae;Uronema sp.
IJMT;Green Algae;Aphanochaete repens
BAZF;Green Algae;Chaetopeltis orbicularis
DVYE;Green Algae;Oedogonium cardiacum
SDPC;Green Algae;Oedogonium foveolatum
CQQP;Green Algae;Ochlochaete sp.
OAEZ;Green Algae;Percursaria percursa
OQON;Green Algae;Entocladia endozoica
LSHT;Green Algae;Bolbocoleon piliferum
NQYP;Green Algae;Pirula salina
KSFK;Green Algae;Desmochloris halophila
GJIY;Green Algae;Pseudoneochloris marina
LETF;Green Algae;Planophila sp
CBNG;Green Algae;Planophila laetevirens
AJAU;Green Algae;Helicodictyon planctonicum
JIWJ;Green Algae;Acrosiphonia sp.
KADG;Green Algae;Ignatius tetrasporus
ALZF;Green Algae;Halochlorococcum marinum
NSTT;Green Algae;Oltmannsiellopsis viridis
GYBH;Green Algae;Codium fragile
JTIG;Green Algae;Bryopsis plumosa
VHIJ;Green Algae;Blastophysa cf. rhizopus
VBLH;Green Algae;Cladophora glomerata
NATT;Green Algae;Trentepohlia annulata
YDCQ;Green Algae;Cephaleuros virescens
Chlva_v1.0;Genome;Chlorella variabilis
EEJO;Green Algae;Ettlia oleoabundans
AKCR;Green Algae;Parachlorella kessleri
BILC;Green Algae;Prototheca wickerhamii
JQFK;Green Algae;Picochlorum atomus
MNCB;Green Algae;Eremosphaera viridis
MFYC;Green Algae;Nannochloris atomus
PFUD;Green Algae;Geminella sp.
QYXY;Green Algae;Botryococcus terribilis
ETGN;Green Algae;Botryococcus braunii
GXBM;Green Algae;Coccomyxa pringsheimii
NKXU;Green Algae;Trebouxia arboricola
ZNUM;Green Algae;Leptosira obovata
EATP;Green Algae;Microthamnion kuetzingianum
WCLV;Green Algae;Prasiola crispa
WXRI;Green Algae;Stichococcus bacillaris
HVNO;prasinophytes;Tetraselmis chui
HHXJ;prasinophytes;Tetraselmis striata
DUMA;prasinophytes;Tetraselmis cordiformis
FMVB;prasinophytes;Scherffelia dubia
PUAN;Green Algae;Pedinomonas tuberculata
RRSV;Green Algae;Pedinomonas minor
AYPS;Green Algae;unidentified species
TGNL;Green Algae;Picocystis salinarum
ISIM;prasinophytes;Nephroselmis pyriformis
MMKU;prasinophytes;Nephroselmis olivacea
Ostlu_v2.0;Genome;Ostreococcus lucimarinus
MCPK;prasinophytes;Bathycoccus prasinos
Micpu_v3.0;Genome;Micromonas pusilla
QXSZ;prasinophytes;Mantoniella squamata
XOAL;prasinophytes;Dolichomastix tenuilepis
BTFM;prasinophytes;Monomastix opisthostigma
TNAW;prasinophytes;Pyramimonas parkeae
XIVI;prasinophytes;Cymbomonas sp.
JMTE;prasinophytes;Pseudoscourfieldia marina
MXEZ;prasinophytes;Pycnococcus provasolii
EGNB;Green Algae;Scourfieldia sp.
XJGM;prasinophytes/Prasinococcales;coccoid-prasinophyte
HYHN;prasinophytes/Prasinococcales;Prasinoderma coloniale
PQED;Glaucophyta (Algae);Gloeochaete wittrockiana
POOW;Glaucophyta (Algae);Glaucocystis cf. nostochinearum
JKHA;Glaucophyta (Algae);Cyanoptyche gloeocystis
YTYU;Glaucophyta (Algae);Cyanophora paradoxa
QFND;Glaucophyta (Algae);Cyanophora paradoxa
ULXR;Chromista (Algae);Scytosiphon dotyi
VRGZ;Chromista (Algae);Petalonia fascia
JCXF;Chromista (Algae);Scytosiphon lomentaria
QLMZ;Chromista (Algae);Colpomenia sinuosa
ASZK;Chromista (Algae);Punctaria latifolia
RAPY;Chromista (Algae);Saccharina sculpera
SRSQ;Chromista (Algae);Saccharina japonica
FIDQ;Chromista (Algae);Undaria pinnatifida
FSQE;Chromista (Algae);Desmarestia viridis
JGGD;Chromista (Algae);Sargassum muticum
VYER;Chromista (Algae);Sargassum hemiphyllum
YRMA;Chromista (Algae);Sargassum thunbergii
LDRY;Chromista (Algae);Sargassum fusiforme
RWXW;Chromista (Algae);Sargassum horneri
HFIK;Chromista (Algae);Sargassum vachellianum
FIKG;Chromista (Algae);Sargassum henslowianum
FOMH;Chromista (Algae);Sargassum integerrimum
LIRF;Chromista (Algae);Dictyopteris undulata
APTP;Chromista (Algae);Ishige okamurae
VKVG;Chromista (Algae);Synura sp.
DBYD;Chromista (Algae);Synura petersenii
BOGT;Chromista (Algae);Mallomonas sp.
MJMQ;Chromista (Algae);Hemiselmis virescens
ROZZ;Chromista (Algae);Chroomonas sp.
BAKF;Chromista (Algae);Cryptomonas curvata
IRZA;Chromista (Algae);Proteomonas sulcata
IAYV;Chromista (Algae);Rhodomonas sp.
NMAK;Chromista (Algae);Pavlova lutheri
VJED;Chromista (Algae);Pavlova lutheri
LLEN;Chromista (Algae);Pavlova lutheri
RFAD;Chromista (Algae);Pavlova lutheri
EBWI;Chromista (Algae);Ochromonas sp.
BAJW;Chromista (Algae);Isochrysis sp.
LXRN;Chromista (Algae);Prymnesium parvum
LJPN;Red Algae;Gracilaria blodgettii
VNAL;Red Algae;Gracilaria vermiculophylla
FTRP;Red Algae;Gracilaria chouae
PWKQ;Red Algae;Gracilaria sp.
IKWM;Red Algae;Gracilaria lemaneiformis
ZJOJ;Red Algae;Grateloupia filicina
IKIZ;Red Algae;Grateloupia livida
URSB;Red Algae;Grateloupia turuturu
PYDB;Red Algae;Grateloupia catenata
UGPM;Red Algae;Chondrus crispus
WEJN;Red Algae;Mazzaella japonica
SBLT;Red Algae;Gloiopeltis furcata
CKXF;Red Algae;Ahnfeltiopsis flabelliformis
IEHF;Red Algae;Dumontia simplex
IHJY;Red Algae;Kappaphycus alvarezii
BWVJ;Red Algae;Betaphycus philippinensis
JEBK;Red Algae;Eucheuma denticulatum
UYFR;Red Algae;Symphyocladia latiuscula
XAXW;Red Algae;Neosiphonia japonica
YSBD;Red Algae;Heterosiphonia pulchra
VZWX;Red Algae;Ceramium kondoi
PVGP;Red Algae;Porphyridium purpureum
OBUY;Red Algae;Porphyridium cruentum
ZULJ;Red Algae;Pyropia yezoensis
JJZR;Red Algae;Rhodochaete parvula
LLXJ;Red Algae;Chroodactylon ornatum
RSOF;Red Algae;Glaucosphaera vacuolata
RTLC;Red Algae;Rhodella violacea
Cyame_v1.0;Red Algae;
phylogenomics
gene 1
gene 2
gene 999
gene 1000
ACTGCACACCG ACTGC-CCCCG AATGC-CCCCG -CTGCACACGG
CTGAGCATCG CTGAGC-TCG ATGAGC-TC- CTGA-CAC-G
AGCAGCATCGTG AGCAGC-TCGTG AGCAGC-TC-TG C-TA-CACGGTG
CAGGCACGCACGAA AGC-CACGC-CATA ATGGCACGC-C-TA AGCTAC-CACGGAT
Orangutan
Chimpanzee
Gorilla
Human
“gene” here refers to a portion of
refer
“c-genes”:
theto
genome
(not a functional gene)
I’ll use the term “gene” to
recombination-free orthologous stretches of the genome
2
Gene tree discordance
gene 1
Gorilla Human Chimp Orang.
gene1000
Gorilla Chimp Human Orang.
3
The species tree
Gorilla Human Chimp Orangutan
gene 1
gene1000
3
A gene tree
The species tree
Gorilla Human Chimp Orangutan
gene 1
gene1000
Causes of gene tree discordance include:
•
Incomplete Lineage Sorting (ILS)
•
Duplication and loss
•
Horizontal Gene Transfer (HGT)
3
A gene tree
•
A random process related to having multiple
versions of each gene in a population
Tracing alleles
through generations
4
•
•
Omnipresent; most likely for short times
between speciation events and/or large
population size
4
Tracing alleles
through generations
•
•
Omnipresent; most likely for short times
between speciation events and/or large
population size
•
We have statistical models of ILS (multi-species coalescent)
•
Tracing alleles
through generations
The species tree defines the probability
distribution on gene trees, and is
identifiable from the distribution on gene
trees [Degnan and Salter, Int. J. Org. Evolution, 2005]
4
Impact of genome-scale data on error?
Error
?
gene 1
gene 2
gene 999
gene 1000
Data
A. Theoretical statistical guarantees: assuming data are generated under
the multi-species coalescent model, we aspire to statistical consistency
B. Simulation studies, generating synthetic data according to the multispecies coalescent model and models of sequence evolution
5
Simulation studies
True(model)speciestree
Truegenetrees
Sequencedata
Finch Falcon Owl Eagle Pigeon
Finch Owl Falcon Eagle Pigeon
Es�matedspeciestree
Es�matedgenetrees
Error metric: percentage of branches in true tree that are missing from the estimated tree
6
Species tree estimation from phylogenomic data (Approach 1: concatenation)
gene 1
gene 2
gene 999
gene 1000
7
gene 1
gene 2
gene 999
gene 1000
ACTGCACACCG CTGAGCATCG AGCAGCATGCGATG CAGAGCACGCACGAA ACTGC-CCCCG CTGAGC-TCG AGCAGC-TGCGATG AGCA-CACGC-CATA AATGC-CCCCG ATGAGC-TC- AGCAGC-TGC-ATG ATGAGCACGC-C-TA -CTGCACACGGCTGA-CAC-G C-TA-CAC-GGATGAGC-TAC-CACGGAT
Concatenation
7
gene 1
gene 2
gene 999
gene 1000
Orangutan
Chimpanzee
Gorilla
Human
Concatenation
7
gene 1
gene 2
gene 999
gene 1000
Orangutan
Chimpanzee
Gorilla
Human
Concatenation
Statistically inconsistent & positively misleading
Error
(proof for unpartitioned maximum likelihood)
[Roch and Steel, Theo. Pop. Gen., 2014]
Mixed accuracy in simulations [Kubatko and Degnan, Systematic Biology, 2007] [Mirarab, et al., Systematic Biology, 2014]
7
Data
Species tree estimation from phylogenomic data (Approach 2: summary methods)
gene 1
gene 2
gene 999
gene 1000
8
gene 1
gene 2
gene 999
gene 1000
Chimp
Gorilla Gorilla
Chimp Chimp
Gorilla Orang.
Chimp
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
8
Chimp
gene 1
gene 2
gene 999
gene 1000
Gorilla Gorilla
Chimp Chimp
Gorilla Orang.
Orangutan
Chimpanzee
Gorilla
Human
Chimp
Summary method
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
8
Chimp
gene 1
gene 2
gene 999
gene 1000
Gorilla Gorilla
Chimp Chimp
Gorilla Orang.
Orangutan
Chimpanzee
Gorilla
Human
Chimp
Summary method
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Error
Can be statistically consistent
•
MP-EST (maximum pseudo-likelihood)
[Liu, Yu, Edwards, BMC Evol. Bio., 2010]
•
NJst, STAR, STELLS, … BUCKy-population
8
Data
Chimp
gene 1
gene 2
gene 999
gene 1000
Gorilla Gorilla
Chimp Chimp
Gorilla Orang.
Orangutan
Chimpanzee
Gorilla
Human
Chimp
Summary method
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Error
Can be statistically consistent
•
MP-EST (maximum pseudo-likelihood)
Error-free gene trees
[Liu, Yu, Edwards, BMC Evol. Bio., 2010]
•
NJst, STAR, STELLS, … BUCKy-population
Data
Co-estimation [Heled and Drummond, MBE, 2010]: accurate but not scalable
Site-based (i.e., no gene trees) [Chifman and Kubatko, Bioin., 2014]: newer …
8
A F LOC K OF G EN OM E S
Large-scale phylogenomics
90. J. F. Storz, J. C. Opazo, F. G. Hoffmann, Mol. Phylogenet. Evol.
66, 469–478 (2013).
91. F. G. Hoffmann, J. F. Storz, T. A. Gorr, J. C. Opazo, Mol. Biol.
Evol. 27, 1126–1138 (2010).
ACKN OW LEDG MEN TS
Genome assemblies and annotations of avian genomes in this
study are available on the avian phylogenomics website
(http://phybirds.genomics.org.cn), GigaDB (http://dx.doi.org/
10.5524/101000), National Center for Biotechnology Information
(NCBI), and ENSEMBL (NCBI and Ensembl accession numbers
are provided in table S2). The majority of this study was
supported by an internal funding from BGI. In addition, G.Z. was
supported by a Marie Curie International Incoming Fellowship
grant (300837); M.T.P.G. was supported by a Danish National
Research Foundation grant (DNRF94) and a Lundbeck Foundation
grant (R52-A5062); C.L. and Q.L. were partially supported by a
Danish Council for Independent Research Grant (10-081390);
and E.D.J. was supported by the Howard Hughes Medical Institute
and NIH Directors Pioneer Award DP1OD000448.
RESEARCH ARTICLE
Whole-genome analyses resolve
early branches in the tree of life
of modern birds
Erich D. Jarvis,1*† Siavash Mirarab,2* Andre J. Aberer,3 Bo Li,4,5,6 Peter Houde,7
Cai Li,4,6 Simon Y. W. Ho,8 Brant C. Faircloth,9,10 Benoit Nabholz,11
Jason T. Howard,1 Alexander Suh,12 Claudia C. Weber,12 Rute R. da Fonseca,6
F LOC K OF G EN OM E S
Jianwen Li,4 Fang Zhang,4 Hui Li,4 Long Zhou,4 Nitish Narula,7,13 Liang Liu,14
Ganesh Ganapathy,1 Bastien Boussau,15 Md. Shamsuzzoha Bayzid,2
Volodymyr Zavidovych,1 Sankar Subramanian,16 Toni Gabaldón,17,18,19
Mol. Phylogenet. Evol.
RESEARCH ARTICLE
Salvador Capella-Gutiérrez,17,18 Jaime Huerta-Cepas,17,18 Bhanu Rekepalli,20
The Avian Genome Consortium
1
1
1
2
Kasper Munch,21 Mikkel Schierup,21 Bent Lindow,6 Wesley C. Warren,22
C. Opazo, Mol. Biol.
Chen Ye, Shaoguang Liang, Zengli Yan, M. Lisandra Zepeda,
2
2
David Ray,23,24,25 Richard E. Green,26 Michael W. Bruford,27 Xiangjiang Zhan,27,28
Paula F. Campos, Amhed Missael Vargas Velazquez,
José Alfredo Samaniego,2 María Avila-Arcos,2 Michael D. Martin,2
Andrew Dixon,29 Shengbin Li,30 Ning Li,31 Yinhua Huang,31
Ross Barnett,2 Angela M. Ribeiro,3 Claudio V. Mello,4 Peter V. Lovell,4
Elizabeth P. Derryberry,32,33 Mads Frost Bertelsen,34 Frederick H. Sheldon,33
n genomes in this
Daniela Almeida,3,5 Emanuel Maldonado,3 Joana Pereira,3
35
35
6
Robb T. Brumfield,33 Claudio V. Mello,35,36 Peter V. Lovell,35 Morgan Wirthlin,35
cs website
Kartik Sunagar, , Siby Philip, , Maria Gloria Dominguez-Bello,
http://dx.doi.org/
Michael Bunce,7 David Lambert,8 Robb T. Brumfield,9
Maria Paula Cruz Schneider,36,37 Francisco Prosdocimi,36,38 José Alfredo Samaniego,6
hnology Information
Frederick H. Sheldon,9 Edward C. Holmes,10 Paul P. Gardner,11
Amhed Missael Vargas Velazquez,6 Alonzo Alfaro-Núñez,6 Paula F. Campos,6
ccession numbers
Tammy E. Steeves,11 Peter F. Stadler,12 Sarah W. Burge,13
Bent Petersen,39 Thomas Sicheritz-Ponten,39 An Pas,40 Tom Bailey,41 Paul Scofield,42
s study was
Eric Lyons,14 Jacqueline Smith,15 Fiona McCarthy,16
n addition, G.Z. was
Frederique Pitel,17 Douglas Rhoads,18 David P. Froman19
Michael Bunce,43 David M. Lambert,16 Qi Zhou,44 Polina Perelman,45,46
Erich D. Jarvis,1*† Siavash Mirarab,2* Andre J. Aberer,3 Bo Li,4,5,6 Peter Houde,7
oming Fellowship
Amy C. Driskell,47 Beth Shapiro,26 Zijun Xiong,4 Yongli Zeng,4 Shiping Liu,4
9,10
11
a Danish National
1
Cai Li,4,6 Simon Y. W. Ho,8 Brant C. Faircloth,
Benoit
Nabholz,
China National GeneBank,
BGI-Shenzhen,
Shenzhen 518083,
Zhenyu Li,4 Binghang Liu,4 Kui Wu,4 Jin Xiao,4 Xiong Yinqi,4 Qiuemei Zheng,4
Lundbeck Foundation
1
12
12
6
Jason
T.
Howard,
Alexander
Suh,
Claudia
C.
Weber,
Rute
R.
da
Fonseca,
China. 2Centre
for GeoGenetics,
Natural
History
Museum of
lly supported by a
Yong Zhang,4 Huanming Yang,48 Jian Wang,48 Linnea Smeds,12 Frank E. Rheindt,49
4
7,13
Denmark,
University
of Copenhagen,
Voldgade
1350
Jianwen Li,4 Fang Zhang,4 Hui Li,4 Long
Zhou,
Nitish
Narula,
Liang
1Øster
2 5-7,Liu,
314
k
ant (10-081390);
3
Michael Braun,50 Jon Fjeldsa,51 Ludovic Orlando,6 F. Keith Barker,52
Interdisciplinar de
Copenhagen, Denmark. CIMAR/CIIMAR, Centro
ghes Medical Institute
Ganesh Ganapathy,1 Bastien Boussau,15Investigação
Md. Shamsuzzoha
Bayzid,2
Marinha e Ambiental, Universidade do Porto, Rua
Knud Andreas Jønsson,51,53,54 Warren Johnson,55 Klaus-Peter Koepfli,56
448.
16
17,18,19
Volodymyr Zavidovych,1 Sankar Subramanian,
Gabaldón,
dos Bragas, 177,Toni
4050-123
Porto, Portugal. 4Department of
Stephen O’Brien,57,58 David Haussler,59 Oliver A. Ryder,60 Carsten Rahbek,51,54
17,18
20
Neuroscience
Oregon
Health &
Science University
Salvador Capella-Gutiérrez,17,18 Jaime Behavioral
Huerta-Cepas,
Bhanu
Rekepalli,
5
Eske Willerslev,6 Gary R. Graves,51,61 Travis C. Glenn,62 John McCormack,63
21
21 Portland, OR 97239,6 USA. Departamento de Biologia,
22 Faculdade
2
Kasper
Munch,
Mikkel
Schierup,
Bent
Lindow,
Wesley
C.
Warren,
64
Lisandra Zepeda,
de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169Hans Ellegren,12 Per Alström,65,66 Scott V. Edwards,67
27
27,28 Dave Burt,
6
David Ray,23,24,25 Richard E. Green,26 007
Michael
W. Bruford,
Xiangjiang
azquez,2
Department of Biology,
University ofZhan,
Puerto
Porto, Portugal.
Alexandros Stamatakis,3,68 David P. Mindell,69 Joel Cracraft,70 Edward L. Braun,71
31 Campus, JGD 224, San Juan,
Michael D. Martin,2
Ponce de Leon,
Rio Piedras
Andrew Dixon,29 Shengbin Li,30 Ning Rico,
Li,31Av Yinhua
Huang,
4
4
Gene
sequence
data
Estimated
gene
trees6,43† Guojie Zhang4,77†
7
Tandy Warnow,2,72† Wang
Jun,48,73,74,75,76initial
† M. Thomas
P. Gilbert,
Mello, Peter V. Lovell,
and Environmental DNA laboratory,
PR 009431-3360, USA.
Elizabeth P. Derryberry,32,33 Mads Frost
Bertelsen,34 Trace
Frederick
H. Sheldon,33
a Pereira,3
Department
of
Environment
and
Agriculture,
Curtin
University,
Perth,
35,36
35
35
Robb T. Brumfield,33 Claudio V. Mello,Western
Peter 6102,
V. Lovell,
MorganFutures
Wirthlin,
Dominguez-Bello,6
To better determine the history of modern birds, we performed a genome-scale phylogenetic
Research
Australia
Australia. 8Environmental
36,37
36,38
6
umfield,9
Institute, Prosdocimi,
Griffith University, Nathan, José
Queensland
4121, Australia.
Maria
Paula
Cruz
Schneider,
Francisco
Alfredo
Samaniego,
analysis
of 48 species representing all orders of Neoaves using phylogenomic methods
9
Paul P. Gardner,11
6
6
Museum of Natural Science, Louisiana
State University, Baton6
created
to
handle genome-scale data. We recovered a highly resolved tree that confirms
Amhed
Missael
Vargas
Velazquez,
Alonzo
Alfaro-Núñez,
Paula
F.
Campos,
13
10
W. Burge,
for Infectious
Rouge,39
LA 70803, USA.40Marie Bashir Institute41
Bent Petersen,39 Thomas Sicheritz-Ponten,
An
Pas, Charles
TomPerkins
Bailey,
PaulofScofield,42previously controversial sister or close relationships. We identified the first divergence in
rthy,16
Diseases and
Biosecurity,
Centre, School
44
45,46
. Froman19
Neoaves, two groups we named Passerea and Columbea, representing independent lineages
Sciences and
Sydney Perelman,
Medical School, The University of
Michael Bunce,43 David M. Lambert,16Biological
Qi Zhou,
Polina
11
47
26
4NSW 2006, Australia. 4
School
of
Biological
Sydney,
Sydney
of diverse and convergently evolved land and water bird species. Among Passerea, we infer
Amy C. Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping
Liu,4
Sciences, University
of Canterbury, Christchurch
8140, New Zealand.
4
4
4
enzhen 518083,
the common ancestor of core landbirds to have been an apex predator and confirm independent
12
Zhenyu Li,4 Binghang Liu,4 Kui Wu,4 Jin
Xiao,
Xiong
Yinqi,
Qiuemei
Zheng,
(partitioned)
Bioinformatics Group, Department of Computer Science, and
ory Museum of
4
48
48
12
49gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to
Yong
Zhang,
Huanming
Yang,
Jian
Wang,
Linnea
Smeds,
Frank
E.
Rheindt,
Interdisciplinary
Center
for
Bioinformatics,
University
of
Leipzig,
oldgade 5-7, 1350
sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved
European Molecular
Hr̈telstrasse
16-18,6D-04107
Leipzig,Barker,
Germany. 1352
Michael Braun,50 Jon Fjeldsa,51 Ludovic
Orlando,
F. Keith
tro Interdisciplinar de
Biology
Laboratory,
European
Bioinformatics
Institute,56
Hinxton,
challenging to resolve, which was best explained by massive protein-coding sequence
51,53,54
55
de do Porto, Rua
Knud Andreas Jønsson,
WarrenCambridge
Johnson,
Klaus-Peter
Koepfli,
14
CB10 1SD, UK. School of Plant Sciences, BIO5 Institute,
Department of
convergence and high levels of incomplete lineage sorting that occurred during a rapid
57,58
59
60
51,54
Stephen O’Brien,
David Haussler, University
Oliver
A. Ryder,
Rahbek,
of Arizona,
Tucson, AZ Carsten
85721, USA. 15
Division of Genetics
ence University
radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
6
51,61 and Genomics, The Roslin62
63
Institute
and
Royal
(Dick)
School
of
Eske Willerslev, Gary R. Graves,
Travis C. Glenn, John McCormack,
Biologia, Faculdade
Veterinary
Studies, The Roslin Institute Building,
64
12
65,66
67 University of
ampo Alegre, 4169Dave Burt, Hans Ellegren, Per Alström,
Scott V. Edwards,
he diversification of species is not always
trasting species trees. Resolving such timing and
Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.
niversity of Puerto
69
70
71
16
Alexandros Stamatakis,3,68 David P. Mindell,
Joel
Cracraft,
Edward University
L. Braun,
gradual
but
can
occur
in
rapid
radiations,
phylogenetic relationships is important for comDepartment
of
Veterinary
Science
and
Microbiology,
of
JGD 224, San Juan,
6,43
Arizona,
1117 EThomas
Lowell Street,
Office Box
210090-0090,
parative genomics, which can inform about human
Tandy Warnow,2,72† Wang Jun,48,73,74,75,76
† M.
P.Post
Gilbert,
† GuojieTucson,
Zhang4,77† especially after major environmental changes
tal DNA laboratory,
17
de Génétiquesupergene
Cellulaire, INRA Chemin alignments
AZ 85721, USA. Laboratoire
Incompatibility Graph
Binned
Supergene
trees
(weighted)
Species
urtin University, Perth,
(1, 2). Paleobiological (3–7) and molecular
(8)
traits and
diseases
(22).
de Borde-Rouge,
Auzeville,
BP 52627a, 31326
CASTANET-TOLOSAN
To better determine the history of modern
birds, we
performed
genome-scale
phylogenetic
tal Futures Research
evidence suggests that such “big bang” radiaRecent avian studies based on fragments of 5
CEDEX, France. 18Department of Biological Sciences, Science and
d 4121, Australia.
analysis of 48 species representing all orders
of Neoaves using phylogenomic methods tions occurred for neoavian birds (e.g., songbirds,
[~5000 base pairs (bp) (8)] and 19 [31,000 bp (17)]
Engineering 601, University of Arkansas, Fayetteville, AR 72701, USA.
niversity, Baton
created to handle genome-scale data. We19Department
recovered
a highly
resolved
tree
thatCorvallis,
confirms parrots, pigeons, and others) and placental mamof Animal
Sciences,
Oregon State
University,
genes recovered some relationships inferred from
for Infectious
OR
97331,
USA.
previously
controversial
sister
or
close
relationships.
We
identified
the
first
divergence
in mals, representing 95% of extant avian and mamre, School of
morphological data (15, 23) and DNA-DNA hyNeoaves, two groups we named Passerea and Columbea, representing independent lineages
, The University of
malian species, after the Cretaceous to Paleogene
bridization (24), postulated new relationships,
of Biological
of diverse and convergently evolved landSUPPLEMENTARY
and water birdMATERIALS
species. Among Passerea, we infer
(K-Pg)
mass
extinction
event
about
66
million
years
and contradicted many others. Consistent with
h 8140, New Zealand.
the common ancestor of core landbirds towww.sciencemag.org/content/346/6215/1311/suppl/DC1
have been an apex predator and confirm independent
ago (Ma). However, other nuclear (9–12) and mitomost previous molecular and contemporary morer Science, and
Textpigeons and flamingoes as belonging to
gains of vocal learning. Among Columbea,Supplementary
we identify
ersity of Leipzig,
chondrial (13, 14) DNA studies propose an earlier,
phological studies (15), they divided modern
Downloaded from www.sciencemag.org on December 11, 2014
Avian phylogenomics [Jarvis, Mirarab, et al., Science, 2014]
Whole-genome analyses resolve
early branches in the tree of life
of modern birds
g
g
g
T
Downloaded from www.sciencemag.org on December 11, 2014
g
9
tree
Phylotranscriptomic analysis of the origin and early
diversification of land plants
PNAS PLUS
1KP: Plant whole transcriptomes
Norman J. Wicketta,b,1,2, Siavash Mirarabc,1, Nam Nguyenc, Tandy Warnowc, Eric Carpenterd, Naim Matascie,f,
Saravanaraj Ayyampalayamg, Michael S. Barkerf, J. Gordon Burleighh, Matthew A. Gitzendannerh,i, Brad R. Ruhfelh,j,k,
Eric Wafulal, Joshua P. Derl, Sean W. Grahamm, Sarah Mathewsn, Michael Melkoniano, Douglas E. Soltish,i,k,
Pamela S. Soltish,i,k, Nicholas W. Milesk, Carl J. Rothfelsp,q, Lisa Pokornyp,r, A. Jonathan Shawp, Lisa DeGironimos,
Dennis W. Stevensons, Barbara Sureko, Juan Carlos Villarrealt, Béatrice Roureu, Hervé Philippeu,v, Claude W. dePamphilisl,
Tao Chenw, Michael K. Deyholosd, Regina S. Baucomx, Toni M. Kutchany, Megan M. Augustiny, Jun Wangz, Yong Zhangv,
Zhijian Tianz, Zhixiang Yanz, Xiaolei Wuz, Xiao Sunz, Gane Ka-Shu Wongd,z,aa,2, and James Leebens-Mackg,2
a
Whole transcriptomes for 103 plant species
•
1,200 in the next phase
Edited by Paul O. Lewis, University of Connecticut, Storrs, CT, and accepted by the Editorial Board September 29, 2014 (received for review December 23, 2013)
•
400-800 single copy “genes”
Reconstructing the origin and evolution of land plants and their
algal relatives is a fundamental problem in plant phylogenetics, and
is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite
advances in molecular systematics, some hypotheses of relationships
remain weakly resolved. Inferring deep phylogenies with bouts of
rapid diversification can be problematic; however, genome-scale
data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on
the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely
resulting from the difficulty and cost of data generation. To address
this limitation, transcriptome data for 92 streptophyte taxa were
generated and analyzed along with 11 published plant genome
sequences. Phylogenetic reconstructions were conducted using up
Significance
•
Spans ~1 billion years of evolution
•
Many unanswered questions about plant evolution
Early branching events in the diversification of land plants and
closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate
reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the
embryo, vascular tissue, seeds, and flowers. We investigated
relationships among streptophyte algae and land plants using
the largest set of nuclear genes that has been applied to this
problem to date. Hypothesized relationships were rigorously
tested through a series of analyses to assess systematic errors in
phylogenetic inference caused by sampling artifacts and model
10
EVOLUTION
•
Chicago Botanic Garden, Glencoe, IL 60022; bProgram in Biological Sciences, Northwestern University, Evanston, IL 60208; cDepartment of Computer Science,
University of Texas, Austin, TX 78712; dDepartment of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; eiPlant Collaborative,
Tucson, AZ 85721; fDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; gDepartment of Plant Biology, University of
Georgia, Athens, GA 30602; hDepartment of Biology and iGenetics Institute, University of Florida, Gainesville, FL 32611; jDepartment of Biological Sciences,
Eastern Kentucky University, Richmond, KY 40475; kFlorida Museum of Natural History, Gainesville, FL 32611; lDepartment of Biology, Pennsylvania State
University, University Park, PA 16803; mDepartment of Botany and qDepartment of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
n
Arnold Arboretum of Harvard University, Cambridge, MA 02138; oBotanical Institute, Universität zu Köln, Cologne D-50674, Germany; pDepartment of
Biology, Duke University, Durham, NC 27708; rDepartment of Biodiversity and Conservation, Real Jardín Botá nico-Consejo Superior de Investigaciones
Cientificas, 28014 Madrid, Spain; sNew York Botanical Garden, Bronx, NY 10458; tDepartment fur Biologie, Systematische Botanik und Mykologie,
Ludwig-Maximilians-Universitat, 80638 Munich, Germany; uDépartement de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale
Centre-Ville, Montreal, QC, Canada H3C 3J7; vCNRS, Station d’ Ecologie Expé rimentale du CNRS, Moulis, 09200, France; wShenzhen Fairy Lake Botanical
Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China; xDepartment of Ecology and Evolutionary Biology, University of
Michigan, Ann Arbor, MI 48109; yDonald Danforth Plant Science Center, St. Louis, MO 63132; zBGI-Shenzhen, Bei shan Industrial Zone, Yantian District,
Shenzhen 518083, China; and aaDepartment of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
Number of species impacts
estimation error in the species tree
1000 genes, “medium” levels of ILS, simulated species trees
[Mirarab and Warnow, ISMB, 2015]
11
Designing summary methods:
ideas from the literature
locus 1
locus 2
locus 999
locus 1000
ACTGCACACCG CTGAGCATCG AGCAGCATCGTG CAGGCACGCACGAA Chimp
Gorilla
Gorilla
Chimp
Orang.
Chimp
Gorilla
Chimp
ACTGC-CCCCG CTGAGC-TCG AGCAGC-TCGTG AGC-CACGC-CATA AATGC-CCCCG ATGAGC-TC- AGCAGC-TC-TG ATGGCACGC-C-TA -CTGCACACGG
CTGA-CAC-G
C-TA-CACGGTG AGCTAC-CACGGAT
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Summary method
Orangutan
Chimpanzee
Gorilla
Human
12
locus 1
locus 2
locus 999
p1 = 30% p2 = 30% p3 = 40%
locus 1000
Gorilla
Gorilla
Chimp
Orang.
Chimp
Gorilla
Chimp
CTGA-CAC-G
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Summary method
Orangutan
Chimpanzee
Gorilla
Human
12
Orang.
Chimp
Gorilla
Chimp
Human
Gorilla
Human
Orang. Human
Chimp
Gorilla
Orang.
locus 1
locus 2
locus 999
p1 = 30% p2 = 30% p3 = 40%
locus 1000
Gorilla
Gorilla
Chimp
Orang.
Chimp
Gorilla
Chimp
CTGA-CAC-G
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Summary method
Chimpanzee
Gorilla
Human
Chimp
Gorilla
Chimp
Human
Gorilla
Human
Orang. Human
Chimp
Gorilla
Orang.
Dominant
•
Orangutan
Orang.
For 4 species, the dominant quartet
topology is the species tree [Allman, et al. 2010], [Degnan, 2014]
12
locus 1
locus 2
locus 999
p1 = 30% p2 = 30% p3 = 40%
locus 1000
Gorilla
Gorilla
Chimp
Orang.
Chimp
Gorilla
Chimp
CTGA-CAC-G
Human
Orang. Human
Orang. Human
Orang. Human
Gorilla
Summary method
Chimpanzee
Human
Gorilla
Chimp
Human
Gorilla
Human
Orang. Human
Chimp
Gorilla
Orang.
For 4 species, the dominant quartet
topology is the species tree [Allman, et al. 2010], [Degnan, 2014]
•
Gorilla
Chimp
Dominant
•
Orangutan
Orang.
For >4 species, the dominant topology
may be different from the species tree [Degnan and Rosenberg, 2006, 2009]
12
More than 4 species
(probabilities are made-up just as an example)
Gorilla
Human
Orangutan Chimp
Chimp
Gorilla
Orang.
Chimp
Gorilla
Chimp
Human
Orang.
Human
Gorilla
Human
Orang.
50%
Gorilla Human Chimp Orang. Dog
1. Break gene trees into
quartets of species
✓ ◆
n
4
2. Find the dominant tree
for all quartets of taxa
3. Combine quartet trees Example: BUCKy-pop. [Larget, et al., Bioinformatics,
2010]
Gorilla
Dog
Human
Chimp
25%
Chimp
Gorilla
Human
Dog
Dog
Chimp
Gorilla
Chimp
Human
Gorilla
Human
Dog
55%
Gorilla
Human
Orangutan Dog
dog
Human
21%
Orang.
dog
Gorilla
dog
Orang.
Human
Gorilla
Human
Orang.
87%
Gorilla
Orang.
Chimp
Gorilla
Chimp
Dog
Orang.
Dog
Gorilla
Dog
Orang.
88%
6%
Chimp
Dog
Orang.
Chimp
Dog
Chimp
Human
Orang.
Human
Dog
Human
Orang.
95%
13
6%
Chimp
6%
Dog
Human
Orangutan Chimp
24%
Gorilla
7%
Gorilla
Dog
Orangutan Chimp
25%
2%
3%
ASTRAL: weighting by frequency
(probabilities are made-up just as an example)
Gorilla
Human
Orangutan Chimp
Chimp
Gorilla
Orang.
Chimp
Gorilla
Chimp
Human
Orang.
Human
Gorilla
Human
Orang.
50%
Gorilla Human Chimp Orang. Dog
✓ ◆
n
into 4
1. Break gene trees
quartets of species
2. Find the tree that
“satisfies” the maximum
number of weighted
quartets from gene trees
Gorilla
Dog
Human
Chimp
25%
Chimp
Gorilla
Human
Dog
Dog
Chimp
Gorilla
Chimp
Human
Gorilla
Human
Dog
55%
Gorilla
Human
Orangutan Dog
dog
Human
19%
Orang.
dog
Gorilla
dog
Orang.
Human
Gorilla
Human
Orang.
87%
Gorilla
Orang.
Chimp
Gorilla
Chimp
Dog
Orang.
Dog
Gorilla
Dog
Orang.
88%
6%
Chimp
Dog
Orang.
Chimp
Dog
Chimp
Human
Orang.
Human
Dog
Human
Orang.
95%
14
6%
Chimp
6%
Dog
Human
Orangutan Chimp
26%
Gorilla
7%
Gorilla
Dog
Orangutan Chimp
25%
2%
3%
ASTRAL
[Mirarab, et al., ECCB/Bioinformatics, 2014]
•
Optimization Problem (suspected NP-Hard):
Find the species tree with the maximum number of induced
quartet trees shared with the collection of input gene trees
Score(T ) =
a gene tree
X
t2T
Set of quartet trees
induced by T
(Q(T ) \ Q(t))
15
all input gene trees
ASTRAL
[Mirarab, et al., ECCB/Bioinformatics, 2014]
•
Optimization Problem (suspected NP-Hard):
Find the species tree with the maximum number of induced
quartet trees shared with the collection of input gene trees
Score(T ) =
a gene tree
•
X
t2T
Set of quartet trees
induced by T
(Q(T ) \ Q(t))
all input gene trees
Theorem: Statistically consistent under the multispecies coalescent model when solved exactly
15
Exact solution
•
We developed a dynamic programming algorithm to
solve the problem exactly
•
•
Exponential running time (still feasible for <18 species)
Developed a constrained version of the problem that can
be solved exactly in polynomial time
•
Runs for 1000 species and 1000 genes in about a day
•
Remains statistically consistent
16
Dynamic programming
L
A
L-A
17
Dynamic programming
L
A
A’
•
A-A’
A’
L-A
A-A’
A’
A-A’
Recursively break subsets of
species into smaller subsets
17
Dynamic programming
L
A’
L-A
u
•
A-A’
A’
A-A’
A’
A’
A-
A’
L-A
A
A-A’
•
17
w(u):
Compare u against input
gene trees and compute quartets
from gene trees satisfied by u
Dynamic programming
L
A’
Exponential
L-A
u
•
A-A’
A’
A-A’
A’
A’
A-
A’
L-A
A
A-A’
•
17
w(u):
Compare u against input
gene trees and compute quartets
from gene trees satisfied by u
Constrained version
L
A1
A
L-A
A4
A2
A6
A10
A5
A8
A9
A3
A’
A-A’
A’
A-A’
A’
A7
A-A’
18
Constrained version
L
A1
A
L-A
A4
A2
A6
A10
A5
A8
A9
A3
A’
•
A-A’
A’
A-A’
A’
A7
A-A’
Restrict “branches” in the species tree to a given constraint set X.
18
Asymptotic running time
•
for k genes of n species
19
Asymptotic running time
•
•
for k genes of n species
Surprise: running time is better than ⇥(n4 )
✓ ◆
n
• Don’t we have to at least list all 4 quartets?
✓ ◆
n
• No! we calculate scores without listing 4 quartets
19
Choosing the constraint set X
In ASTRAL-I:
•
X = {all bipartitions in all gene trees}
•
Motivation: given large number of gene trees, each
species tree branch appears in at least one gene tree (used in Phylonet-MDC [Than et al., 2009, Yun, et al., 2011])
•
Theorem: the default constrained version of ASTRAL
is also statistically consistent
20
Choosing the constraint set X
In ASTRAL-I:
•
X = {all bipartitions in all gene trees}
•
•
Motivation: given large number of gene trees, each
species tree branch appears in at least one gene tree (used in Phylonet-MDC [Than et al., 2009, Yun, et al., 2011])
•
Theorem: the default constrained version of ASTRAL
is also statistically consistent
ASTRAL-II [Mirarab and Warnow, ISMB, 2015]: We use heuristic
algorithms to further augment the constraint set X
20
Number of species impacts
estimation error in the species tree
21
Species tree topological error (FN)
ASTRAL: accurate and scalable
16%
ASTRAL−II
MP−EST
12%
8%
4%
10
50
100
200
500
1000
number of species
22
16%
ASTRAL−II
MP−EST
12%
8%
4%
10
50
100
200
500
1000
number of species
22
16%
12%
ASTRAL−II
ASTRAL−II
NJst
MP−EST
MP−EST
8%
4%
10
50
100
200
500
1000
number of species
22
Running time as function of # species
ASTRAL−II
NJst
Running time (hours)
MP−EST
20
10
0
10 50 100
200
500
1000
number of species
23
Varying the level of ILS
1000 genes
30%
200 genes
50 genes
ASTRAL−II
NJst
CA−ML
20%
10%
0%
10M
2M
500K
10M
2M
500K
10M
tree length (controls the amount of ILS)
200 species, simulated species trees
24
2M
500K
Deep ILS
1000 genes
30%
200 genes
50 genes
ASTRAL−II
NJst
CA−ML
20%
10%
10M
2M
500K
10M
2M
500K
10M
2M
tree length (controls the amount of ILS)
200 species, simulated species trees, deep ILS
25
500K
10M
0.4
ASTRAL−II
2M
ASTRAL−II (true gt)
CA−ML
0.3
1e−06
0.2
0.1
0.0
0.4
0.3
1e−07
True gene trees?
0.2
0.1
0.0
50
200
1000
genes
26
50
200
1000
Simulation properties
rate
tree height
1e−06
1e−07
10M
2M
500K
15
10
5
late an UPGMA tree and
euristic adds relatively few
next heuristic, which is our
0
0%
20%
40%
60%
80%
RF distance (true species tree vs true gene trees)
(b) Gene tree estimation error
4
density
nsus of the gene trees at
0, 5/100, 1/10, 1/4, 1/3).
ensus tree, we resolve the
artitions implied by those
the polytomy by applying
matrix, starting from the
e sample one taxon from
use the greedy consensus
mple to find a resolution
any multifunctions in this
We repeat this process at
dy consensus trees include
(a) True gene tree discordance
20
density
om one of the children of
u0
quartet trees that put
2
of leaves outside the node
n each of the input k nodes
re O(n2 k) computations.
maximum number of input
ASTRAL-II
3
2
1
0
0%
25%
50%
75%
100%
RF distance (true vs estimated)
27
Fig. 1. Characteristics of the simulation (a) RF distance between the true
Similar to concatenation with some interesting
differences (e.g., recovered bryophytes)
ASTRAL took only about 10 minutes (serial
Gnepine
Conifers monophyletic
running time) on 103 taxa and 400 genes
Gnetifer
Angiosperms
cots + magnoliids
icots + mag/Chlor
s + Chloranthales
+ Chlor, monocots
nocots + eudicots
604genes.trimExt.unpart
untrim.unpart
604genes.trimExt.gamma.unpart
50genes.unpart
604genes.trimExt.Bayes.CATGTR
untrim.unpart
50genes50sites.unpart
604genes.trimExt.Bayes.CAT
50genes.unpart
50genes50sites.part
50genes50sites.gamma.part
untrim.unpart
50genes50sites.part
50genesChara.unpart
50genes.unpart
50genes50sites.25X.unpart
50genesChara.unpart
50genes33taxa.unpart
50genes50sites.part
50genesChara.unpart
50genes50sites25X.unpart
untrim.unpart
untrim50genes.unpart
untrim.unpart
50genes
50genes.unpart
50genes50sites.part
50genes.25X
untrim.unpart
50genes33taxa
50genes.unpart
50genes50sites.part
50genesChara.unpart
untrim
50genes50sites.part
50genesChara.unpart
untrim.gamma
50genes
50genesChara.unpart
50genes.25X
50genes33taxa
untrim
untrim.gamma untrim.unpart
untrim.unpart
50genes.unpart
50genes
50genes.unpart
50genes.25X
50genes50sites.part
50genes33taxa
50genes50sites.part
untrim
50genesChara.unpart
untrim
50genes
50genesChara.unpart
50genes
50genes.25X
50genes.25X
50genes33taxa
untrim
untrim.gamma
50genes
untrim.unpart
50genes.25X
50genes.unpart
50genes33taxa
untrim
50genes50sites.part
untrim
50genes
untrim.gamma
50genes.25X
50genesChara.unpart
50genes
50genes33taxa
50genes.25X
50genes33taxa
Gymnosperms
Gnepine
Gnetifer
Gnetales-sister
ons
Charales-sister
Coleochaetales-sister
NA
Angiosperms
Eudicots + magnoliids
The ASTRAL tree:
all
ASTRAL on plants dataset
Bryophytes
Mosses + liverworts
Bryophytes monophyletic
Hornworts-sister
Liverworts-basal
Hornworts-basal
NA
Bryophytes
Mosses + liverworts
Hornworts-sister
Liverworts-basal
Hornworts-basal
Gymnosperms
Gnepine
Gnetifer
AA
Gnetales-sister
High support
im.unpart
es.unpart
im.unpart
tes.unpart
es.unpart
sites.part
tes.unpart
mma.part
sites.part
ra.unpart
mma.part
5X.unpart
ra.unpart
xa.unpart
5X.unpart
xt.unpart
xa.unpart
ma.unpart
xt.unpart
ma.unpart
tes.unpart
.CATGTR
5X.unpart
ayes.CAT
untrim
im.unpart
50genes
es.unpart
enes.25X
tes.unpart
es33taxa
sites.part
mma.part
untrim
ra.unpart
m.gamma
5X.unpart
50genes
xa.unpart
im.unpart
enes.25X
xt.unpart
es.unpart
es33taxa
ma.unpart
es.unpart
sites.part
.CATGTR
untrim
mma.part
m.gamma
ra.unpart
im.unpart
50genes
Angiosperms
er to land
plants
Eudicots + mag/Chlor
•
Eudicots
+
magnoliids
atophyceae-sister
Magnoliids + Chloranthales
Mag + Chlor, monocots
Charales-sister
gnoliids + Chloranthales
Monocots + eudicots
eochaetales-sister
Monocots + •
eudicots ANA-grade angiosperms
Bryophytes
Amborella + Nuphar
osses + liverworts
NA-grade
angiosperms
Amborella-sister
ytesAmborella
monophyletic
+•Nuphar
Hornworts-sister
Amborella-sister
Liverworts-basal
Hornworts-basal
untrim.unpart
50genes.unpart
50genes50sites.part
untrim.unpart
50genes.unpart
50genesChara.unpart
50genes50sites.part
50genesChara.unpart
Bryophytes
Mosses + liverworts
Hornworts-sister
Liverworts-basal
Hornworts-basal
1 and 2
im.unpart
es.unpart
tes.unpart
sites.part
mma.part
ra.unpart
5X.unpart
xa.unpart
xt.unpart
ma.unpart
.CATGTR
Gymnosperms
•
Gnepine
fers monophyletic
Gnetifer
Gnetales-sister
im.unpart
es.unpart
tes.unpart
sites.part
mma.part
ra.unpart
5X.unpart
xa.unpart
xt.unpart
ma.unpart
.CATGTR
ayes.CAT
g.
Summary ofStrong
support
land
plant(Weak
relationships
across
52 supermatrix a
Support for hypotheses
Weak
Support of
Compatible
Rejection) ANA-grade
Strong
Rejection
ade 4.
angiosperms
ANA-grade
angiosperms
angiosperms
mborella
+ Nuphar for hypotheses of land plantAmborella
+ Nuphar
Amborella
Nuphar
of
support
relationships
across
supermatrix
coalescent-b
ata
matrix
(Table S2). Occupancy-based
gene
trimming
was52
carried
out
by+and
removing
gene
pport
Compatible (Weak Rejection)
Strong Rejection
Amborella-sister Weak Support
Amborella-sister
Amborella-sister
ehypotheses
S2).
Occupancy-based
gene
trimming
was
carried
out byfor
removing
genes
>50
oftrimming
land et
plant
relationships
across
52
supermatrix
and
coalescent-based
analyses
gnment.
Site
columns
in the
aligmment
which
>50%
offor
thewhich
full
taxon
[Wickett,
Mirarab,
al.,removed
PNAS,
2014]
mming
removed
columns
in
thecarried
aligmment
for
whichwas
>50%
of the
full
taxon
set
were
repre
28removing
as
performed
onacross
gene
trees
when
a terminal
branch
25-times
than
the
median
b
cy-based
gene
trimming
was
outcoalescent-based
by
genes
forlonger
which
>50%
the
full
tax
nt
relationships
52
supermatrix
and
analyses
including
permutations
A
ygnematophyceae-sister
Charales-sister
NA
Codon
positions
1 and 2
to land plants
Mag + Chlor,Sister
monocots
Monocots
+ eudicots
Zygnematophyceae-sister
1 and 2
Gymnosperms
Gnepine
Gnetifer
Gnetales-sister
Matrix type
Supermatrix
Alignment
Angiosperms DNA to AA
all
ANA-grade angiosperms
Amborella + Nuphar
Amborella-sisterBryophytes
Charales-sister
Mosses + liverworts
Hornworts-sister
Liverworts-basal
Hornworts-basal
Gymnosperms
Gnetales-sister
Angiosperms
Strong Support
Strong Support
Weak Support
Monocots + eudicots
all
NA
Matrix type
AA Alignment
DNA
ASTRAL
Supermatrix
NA CodonNA
positionsNA
Concatenation-ML
AA
DNA
DNA
to AA
to AA
AA
1 and
1 and
2 2
ASTRAL
all
NA
Sister to land plants
Zygnematophyceae-sister
Charales-sister
Bryophytes
Mosses + liverworts
Hornworts-sister
Liverworts-basal
Hornworts-basal
Gymnosperms
Gnepine
Gnetifer
Gnetales-sister
Angiosperms
Weak
Support
Compatible (Weak Rejec
CompatibleMonocots
(Weak Rejection)
Strong Rej
+ eudicots
ASTRAL-II on biological datasets
(ongoing collaborations)
•
1200 plants with ~ 400 genes (1KP consortium)
•
250 avian species with 2000 genes (with LSU, UF, and Smithsonian)
•
200 avian species with whole genomes (with Genome 10K, international)
•
250 suboscine species (birds) with ~2000 genes (with LSU and Tulane)
•
140 Insects with 1400 genes (with U. Illinois at Urbana-Champaign)
•
50 Hummingbird species with 2000 genes (with U. Copenhagen and
Smithsonian)
•
40 raptor species (birds) with 10,000 genes (with U. Copenhagen and Berkeley)
•
38 mammalian species with 10,000 genes (with U. of Bristol, Cambridge, and
Nat. Univ. of Ireland)
29
Summary
•
Genome-scale sequence data provides a wealth of information
•
Yet, reconstruction of species phylogenies remains challenging
•
•
Scalability to many species: ASTRAL
•
Limited data per gene: statistical binning
•
Impact of model violations
•
Recombination
•
Missing data
•
Multiple sources of gene tree discordance
Many interesting statistical and computational questions and need
for method development
30
Acknowledgments
…
Tandy Warnow
Keshav Pingali
S.M. Bayzid Nam Nguyen (now at UIUC)
Jim Leebens-‐mack Norman Wickett Gane Wong (UGA)
(U Chicago)
(U of Alberta)
Théo Zimmermann
HMMI international student fellowship Guojie Zhang Tom Gilbert Erich Jarvis Bastien Boussau (BGI, China) (U Copenhagen) (Duke, HMMI) (Université Lyon)
…
Ed Braun (U Florida)

Coalescent-based species tree estimation with

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