期刊
SYSTEMATIC BIOLOGY
卷 61, 期 5, 页码 717-726出版社
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/sys004
关键词
Flanking sequence; genetic markers; phylogenomics; sequence capture; target enrichment; ultraconserved elements
资金
- National Science Foundation [DEB-0614208, DEB-0841729, DEB-0956069]
- Amazon Web Services
- Direct For Biological Sciences
- Division Of Environmental Biology [0841729] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Div Of Biological Infrastructure [0956069] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1136626] Funding Source: National Science Foundation
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据