Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.
Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.
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劳亚兽哺乳动物系统发育的系统发育解析：探索编码和非编码序列中的系统发育信号
DOI：
10.1093/gbe/evx147
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发表时间：
2017-08-01
影响因子：
3.3
通讯作者：
Zhang P
中科院分区：
文献类型：
--
作者：
Chen MY;Liang D;Zhang P
Laurasiatherian哺乳动物的中间关系是哺乳动物的系统发育学中最有争议的问题之一，主要依赖于编码序列（CDS），很少使用非编码序列，在这里，我们通过数据挖掘公共基因组进行了数据挖掘。 ）和10,259个基因的CD数据集（20,994,285 bp），涵盖了所有主要的Laurasiatheria（Pholidota除外），我们发现内含子数据包含比CDS数据更强大，更一致的系统。进一步的分析表明，从内含子数据对数据进行了高度鲁棒性，但是CDS数据在相同的条件下产生了不稳定的结果，基因树的统计结果表明，CDS和内含子数据最常观察到的基因树拓扑是相同的，这表明CDS数据中的主要系统发育实际上是Insproul in Instrul Inforial Pers。 （Eulipotyphla，（（Chiroptera，Perissodactyla），（Carnivora，cetartiodactyla）），有利于Chiroptera和Perissodactyla之间的密切关系。为了解决整个生命树的快速辐射事件。
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing “hard” polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.
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影响因子：
3.7
作者：
Hallström BM;Schneider A;Zoller S;Janke A
通讯作者：
Janke A
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
64.8
作者：
通讯作者：
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影响因子：
10.7
作者：
Foley NM;Thong VD;Soisook P;Goodman SM;Armstrong KN;Jacobs DS;Puechmaille SJ;Teeling EC
通讯作者：
Teeling EC
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G