Homoplastic microinversions and the avian tree of life

BMC Evolutionary Biology

Jordan V Smith¹  Jena L Chojnowski²  Michael J Braun³  Edward L Braun⁴  Rebecca T Kimball⁵  Amber J Bonilla⁶  Rauri CK Bowie⁷  Naomi R Iuhasz-Velez⁸  Kin-Lan Han⁹ 

[1] 4869 Pepperwood Way, San Jose, USA;Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, USA;Department of Biological Sciences, Wayne State University, Detroit, USA;Department of Biology, University of Florida, Gainesville, USA;Department of Mathematics, University of Florida, Gainesville, USA;Department of Vertebrate Zoology, Smithsonian Institution, Suitland, USA;Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, USA;Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, USA;Zoology Department, Field Museum of Natural History, Chicago, USA

关键词: Terminal Branch;    Inversion Event;    Avian Genome;    Clathrin Heavy Chain;    Perfect Character;   

DOI  :  10.1186/1471-2148-11-141

学科分类：生物科学（综合）

来源: BioMed Central

【 摘 要 】

Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.

【 授权许可】

CC BY