Implications of Hybridization, NUMTs, and Overlooked Diversity for DNA Barcoding of Eurasian Ground Squirrels

被引：33

作者：

Ermakov, Oleg A. ^{[1
]}

Simonov, Evgeniy ^{[2
,3
]}

Surin, Vadim L. ^{[4
]}

Titov, Sergey V. ^{[1
]}

Brandler, Oleg V. ^{[5
]}

Ivanova, Natalia V. ^{[6
]}

Borisenko, Alex V. ^{[6
]}

机构：

[1] Penza State Univ, Dept Zool & Ecol, Penza, Russia

[2] Russian Acad Sci, Inst Systemat & Ecol Anim, Siberian Branch, Novosibirsk, Russia

[3] Tomsk State Univ, Tomsk 634050, Russia

[4] Russian Acad Med Sci, Hematol Res Ctr, Moscow, Russia

[5] Russian Acad Sci, NK Koltsov Dev Biol Inst, Moscow, Russia

[6] Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada

来源：

PLOS ONE | 2015年 / 10卷 / 01期

基金：

俄罗斯基础研究基金会;

关键词：

SPECIES IDENTIFICATION; MITOCHONDRIAL PSEUDOGENES; MOLECULAR-IDENTIFICATION; MAXIMUM-LIKELIHOOD; SPERMOPHILUS-MAJOR; RIBOSOMAL-RNA; RODENTIA; PHYLOGENY; EVOLUTION; TAXONOMY;

D O I：

10.1371/journal.pone.0117201

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.

引用

页数：19

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