Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias

doi:10.1093/sysbio/syu049

	Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias
	Liu, Yang ; Cox, Cymon J.; Wang, Wei 2; Goffinet, Bernard
	2014
发表期刊	SYSTEMATIC BIOLOGY
ISSN	1063-5157
卷号	63 期号:6 页码:862-878
摘要	Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.
关键词	Compositional heterogeneity early land plants evolutionary saturation mitochondrial genome phylogenomics synonymous codon-usage bias
学科领域	Evolutionary Biology
DOI	10.1093/sysbio/syu049
收录类别	SCI
语种	英语
WOS关键词	PHYLOGENETIC-RELATIONSHIPS ; HORIZONTAL TRANSFER ; ANGIOSPERM PHYLOGENY ; NUCLEOTIDE-SEQUENCES ; MULTIGENE PHYLOGENY ; STREPTOPHYTE ALGAE ; CHLOROPLAST GENOME ; MULTIPLE ALIGNMENT ; ORGANELLAR GENOME ; BAYES FACTORS
WOS研究方向	Evolutionary Biology
WOS记录号	WOS:000344695900002
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
EISSN	1076-836X
资助机构	National Science Foundation [EF 0531557, DEB 0919284, DEB-1146295] ; Division Of Environmental Biology [1146295] Funding Source: National Science Foundation
作者邮箱	bernard.goffinet@uconn.edu
作品OA属性	Green Submitted, hybrid
引用统计	被引频次：92[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27294
专题	系统与进化植物学国家重点实验室
作者单位	1.Univ Connecticut, Dept Ecol & Evolutionary Biol, Storrs, CT 06269 USA 2.Cox, Cymon J.] Univ Algarve, Ctr Ciencias Mar, P-8005319 Faro, Portugal 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Liu, Yang,Cox, Cymon J.,Wang, Wei,et al. Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias[J]. SYSTEMATIC BIOLOGY,2014,63(6):862-878.
APA	Liu, Yang,Cox, Cymon J.,Wang, Wei,&Goffinet, Bernard.(2014).Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias.SYSTEMATIC BIOLOGY,63(6),862-878.
MLA	Liu, Yang,et al."Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias".SYSTEMATIC BIOLOGY 63.6(2014):862-878.

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