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DOI	10.1016/j.ympev.2019.106534
	NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)
	Boutte, Julien 1,4; Fishbein, Mark 2; Liston, Aaron 3; Straub, Shannon C. K.1
通讯作者	Straub, Shannon C. K.
来源期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1055-7903
EISSN	1095-9513
出版年	2019
卷号	139
英文摘要	Targeted genome sequencing approaches allow characterization of evolutionary relationships using a considerable number of nuclear genes and informative characters. However, most phylogenomic analyses only utilize single nucleotide polymorphisms (SNPs). Studies at the species level, especially in groups that have recently radiated, often recover low amounts of phylogenetically informative variation in coding regions, and require non-coding sequences, which are richer in indels, to resolve gene trees. Here, NGS-Indel Coder, a pipeline to detect and omit false positive indels inferred from assemblies of short read sequence data, was developed to resolve the relationships among and within major clades of the American milkweeds (Asclepius), which are the result of a rapid and recent evolutionary radiation, and whose phylogeny has been difficult to resolve. This pipeline was applied to a Hyb-Seq data set of 768 loci including targeted exons and flanking intron regions from 33 milkweed species. Robust species tree inference was improved by excluding small alignment partitions (< 100 bp) that increased gene tree ambiguity and incongruence. To further investigate the robustness of indel coding, data sets that included small and large indels were explored, and species trees derived from concatenated loci versus coalescent methods based on gene trees were compared. The phylogeny of Asclepius obtained using nuclear data was well resolved, and phylogenetic information from indels improved resolution of specific nodes. The Temperate North American, Mexican Highland, and Incarnatae clades were well supported as monophyletic. Asclepius coulteri, which has been considered part of the Sonoran Desert Glade based on plastome analyses, was placed as sister to all the other milkweed species studied here, rather than as a member of that Glade. Two groups within the Temperate North American and Mexican clades were not resolved, and the inferred relationships strongly conflicted when comparing results based on data sets that did or did not include indel characters. This new pipeline represents a step forward in making maximal use of the information content in phylogenomic data sets.
英文关键词	Sub-sampling SNP detection Incomplete lineage sorting Apocynaceae Character coding Gene tree filtering
类型	Article
语种	英语
国家	USA ; France
收录类别	SCI-E
WOS记录号	WOS:000485041900018
WOS关键词	GENE TREES ; ALIGNMENT ; MODEL ; EVOLUTION ; INFERENCE ; GENOMES ; CHLOROPLAST ; PERFORMANCE ; SEQUENCES ; FRAMEWORK
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/217674
作者单位	1.Hobart & William Smith Coll, Dept Biol, 300 Pulteney St, Geneva, NY 14456 USA; 2.Oklahoma State Univ, Dept Plant Biol Ecol & Evolut, Stillwater, OK 74078 USA; 3.Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA; 4.Univ Rennes 1, Agrocampus Ouest, INRA, IGEPP, BP35327, F-35653 Le Rheu, France
推荐引用方式 GB/T 7714	Boutte, Julien,Fishbein, Mark,Liston, Aaron,et al. NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)[J],2019,139.
APA	Boutte, Julien,Fishbein, Mark,Liston, Aaron,&Straub, Shannon C. K..(2019).NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias).MOLECULAR PHYLOGENETICS AND EVOLUTION,139.
MLA	Boutte, Julien,et al."NGS-Indel Coder: A pipeline to code indel characters in phylogenomic data with an example of its application in milkweeds (Asclepias)".MOLECULAR PHYLOGENETICS AND EVOLUTION 139(2019).