IHB OpenIR  > 鱼类生物学及渔业生物技术研究中心  > 期刊论文
Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda
Zhang, Dong1,2,3; Zou, Hong1,2; Hua, Cong-Jie1,2; Li, Wen-Xiang1,2; Mahboob, Shahid4,5; Al-Ghanim, Khalid Abdullah4; Al-Misned, Fahad4; Jakovlic, Ivan6; Wang, Gui-Tang1,2
2019-07-01
Source PublicationGENOME BIOLOGY AND EVOLUTION
ISSN1759-6653
Volume11Issue:7Pages:1797-1812
Abstract

The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

Keywordbase composition skew GC skew mitochondrial phylogenomics Cymothoida replication origin inversion compositional heterogeneity
DOI10.1093/gbe/evz121
Funding OrganizationDeanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China
Indexed BySCI
Language英语
Funding ProjectDeanship of Scientific Research at King Saud University[RGP 1435-012] ; Earmarked Fund for China Agriculture Research System[CARS-45-15] ; National Natural Science Foundation of China[31872604] ; National Natural Science Foundation of China[31572658]
WOS Research AreaEvolutionary Biology ; Genetics & Heredity
WOS SubjectEvolutionary Biology ; Genetics & Heredity
WOS IDWOS:000484039500008
WOS KeywordTRANSFER-RNA GENES ; DEEP-SEA ; COMPOSITIONAL HETEROGENEITY ; MOLECULAR EVOLUTION ; MULTIPLE REVERSALS ; CYMOTHOID ISOPODS ; CRUSTACEA ; GENOME ; DNA ; TREE
PublisherOXFORD UNIV PRESS
Funding OrganizationDeanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Deanship of Scientific Research at King Saud University ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; Earmarked Fund for China Agriculture Research System ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/33353
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorJakovlic, Ivan; Wang, Gui-Tang
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Minist Agr, Key Lab Aquaculture Dis Control, Wuhan, Hubei, Peoples R China
2.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Hubei, Peoples R China
3.Univ Chinese Acad Sci, Beijing, Peoples R China
4.King Saud Univ, Dept Zool, Coll Sci, Riyadh, Saudi Arabia
5.GC Univ, Dept Zool, Faisalabad, Pakistan
6.Biotransduct Lab, Wuhan, Hubei, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Dong,Zou, Hong,Hua, Cong-Jie,et al. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda[J]. GENOME BIOLOGY AND EVOLUTION,2019,11(7):1797-1812.
APA Zhang, Dong.,Zou, Hong.,Hua, Cong-Jie.,Li, Wen-Xiang.,Mahboob, Shahid.,...&Wang, Gui-Tang.(2019).Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda.GENOME BIOLOGY AND EVOLUTION,11(7),1797-1812.
MLA Zhang, Dong,et al."Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda".GENOME BIOLOGY AND EVOLUTION 11.7(2019):1797-1812.
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