Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias).
Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.
Department of Zoology, Denver Museum of Nature & Science, Denver, CO.|Department of Biological Sciences, University of Idaho, Moscow, ID.|Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
Brice A J
BA
Sarver
Department of Zoology, Denver Museum of Nature & Science, Denver, CO.
John R
JR
Demboski
Division of Biological Sciences, University of Montana, Missoula, MT.
Jeffrey M
JM
Good
Department of Biological Sciences, University of Idaho, Moscow, ID.
Nicholas
N
Forshee
Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
Samuel S
SS
Hunter
Department of Biological Sciences, University of Idaho, Moscow, ID.|Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.
Jack
J
Sullivan
D000818:Animals; D004272:DNA, Mitochondrial; D051456:Gene Flow; D054629:Genome, Mitochondrial; D006824:Hybridization, Genetic; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D012589:Sciuridae / Q000145:classification* / Q000235:genetics*; D012641:Selection, Genetic; D014481:United States
D004272:DNA, Mitochondrial