NIGPAS OpenIR
Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates
Noah, Katherine E.1; Hao, Jiasheng2; Li, Luyan3; Sun, Xiaoyan (孙晓燕)3; Foley, Brian4; Yang, Qun (杨群)3; Xia, Xuhua1,5
2020-02-01
发表期刊EVOLUTIONARY BIOINFORMATICS
ISSN1176-9343
卷号16页码:12
摘要

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such "big data" sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new "principled" codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

关键词Deep phylogeny alignment method codon degeneration method arthropods land colonization
DOI10.1177/1176934320903735
收录类别SCI
语种英语
关键词[WOS]MULTIPLE SEQUENCE ALIGNMENT ; RIBOSOMAL-RNA ; MODEL CHOICE ; GENES ; INFERENCE ; ARACHNIDA ; TREE ; UNCERTAINTY ; ALGORITHM ; EVOLUTION
资助项目Natural Science and Engineering Research Council (NSERC) of Canada[RGPIN/2018-03878] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDB26000000] ; Chinese Academy of Sciences[KZCX2-YWJC104]
WOS研究方向Evolutionary Biology ; Mathematical & Computational Biology
WOS类目Evolutionary Biology ; Mathematical & Computational Biology
WOS记录号WOS:000511999000001
项目资助者Natural Science and Engineering Research Council (NSERC) of Canada ; Strategic Priority Research Program of Chinese Academy of Sciences ; Chinese Academy of Sciences
出版者SAGE PUBLICATIONS LTD
文献类型期刊论文
条目标识符http://ir.nigpas.ac.cn/handle/332004/31419
专题中国科学院南京地质古生物研究所
通讯作者Yang, Qun (杨群); Xia, Xuhua
作者单位1.Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
2.Anhui Normal Univ, Coll Life Sci, Wuhu, Peoples R China
3.Chinese Acad Sci, Nanjing Inst Geol & Paleontol, Nanjing, Peoples R China
4.Los Alamos Natl Lab, Theoret Biol & Biophys Grp, Los Alamos, NM USA
5.Univ Ottawa, Ottawa Inst Syst Biol, Ottawa, ON, Canada
推荐引用方式
GB/T 7714
Noah, Katherine E.,Hao, Jiasheng,Li, Luyan,et al. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates[J]. EVOLUTIONARY BIOINFORMATICS,2020,16:12.
APA Noah, Katherine E..,Hao, Jiasheng.,Li, Luyan.,Sun, Xiaoyan .,Foley, Brian.,...&Xia, Xuhua.(2020).Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates.EVOLUTIONARY BIOINFORMATICS,16,12.
MLA Noah, Katherine E.,et al."Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates".EVOLUTIONARY BIOINFORMATICS 16(2020):12.
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