Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus: Analysis of variability of the control region (D-loop) of mitochondrial DNA

Maltsev, A. N.; Stakheev, V. V.; Bogdanov, A. S.; Fomina, E.S.; Котенкова, Е. В.

doi:10.1134/s0012496615060058

Cited by 13 publications

(7 citation statements)

References 10 publications

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“…However, even the sufficiently extended Cox1 fragment constituting more than three quarters of the entire gene appeared to be unsuitable for the identification of individuals of the subspecies M. m. musculus, M. m. wagneri, M. m. gansuensis, and M. m. domesticus from Transcaucasia, despite the fact that the animals were "pure" for the nuclear Brca1 gene. Thus, our results of Cox1 gene analysis are consistent with the data of other authors who studied the mitochondrial genes D-loop and Cytb [7,[16][17][18] and can be explained either by the stabilizing selection of mtDNA in house mice of the subspecies M. m. musculus, M. m. wagneri, and M. m. gansuensis or by large-scale introgression from any one subspecies to the gene pool of other subspecies due to hybridization [16]. It should be noted that the presence of foreign mtDNA can be traced in our sample in some individuals with well distinguishable Cox1 gene mitotypes and best explains the differences in the topology of the dendrograms constructed on the basis of the nuclear and mitochondrial genes.…”

Section: Discussionsupporting

confidence: 92%

“…The results of recent studies of mtDNA fragments-the control region (D-loop) and the cytochrome b gene (Cytb)-showed a complete, approximately the same, though noticeably inferior to the allospecies of "wild" mice, genetic differentiation of the subspecies M. m. domesticus, M. m. musculus, M. m. castaneus, M. m. gentilulus, M. m. bactrianus, a new subspecies M. m. isatissus, and an unclassified form from Nepal [7,8,16,17]. However, despite the rather high variability of the mitochondrial genes, the subspecies M. m. musculus, M. m. wagneri, and M. m. gansuensis did not form individual clades on dendrograms [7,[16][17][18]. Distinguishing subclusters, which often included mice originating from very distant regions and belonging to different subspecies, had an apparently random nature.…”

Section: Genomics Transcriptomicsmentioning

confidence: 92%

“…This might be the cause of the insufficiently successful determination of the subspecies affiliation of house mice on the basis of the mitochondrial genes [7,[16][17][18]. To test this hypothesis, we analyzed the variability of the fragment of the mitochondrial gene Cox1 in M. musculus individuals identified as homozygous ("pure") members of groups I-V on the basis of the nuclear gene Brca1 and originating from the regions remote from the hybridization zones.…”

Section: Species Groupmentioning

confidence: 99%

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Variability of Fragments of Nuclear Brca1 Gene, Exon 11, and Mitochondrial Cox1 Gene in House Mice Mus musculus

et al. 2020

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To clarify genetic differences between subspecies of the house mouse Mus musculus, their distribution, and hybridization, we first conducted a comparative analysis of variability of nucleotide sequences of fragments of the nuclear gene Brca1, exon 11 (2331 bp), and mitochondrial gene Cox1 (1260 bp) in 40 house mice from West and East Europe, Transcaucasia, Siberia, and Central and South Asia. Brca1 genotypes were divided into five main groups, which differed in a number of fixed substitutions. Genotypes of each group are characteristic for the certain geographical region and the following subspecies: M. m. musculus, M. m. domesticus, M. m. castaneus, and M. m. wagneri together with M. m. gansuensis; a fifth group corresponds to an unidentified subspecies or a distinct genetic form of M. musculus from India (Sikkim State). Besides the homozygous specimens, we revealed mice, which were heterozygous for all diagnostic loci simultaneously; these specimens were determined as hybrid. Hybrid mice were mainly found in the zones of contact of subspecies, but in some cases, quite far from one of the parent subspecies (possibly, due to transportation). In two hybrid mice (from Bakhtiari Province of Iran and Transbaikalia of Russia), unique Brca1 haplotypes were detected. It cannot be ruled out that, at least partly, they may be characteristic of the M. m. bactrianus and M. m. gansuensis subspecies, respectively. Thus, the results of the study showed that the nuclear Brca1 gene is a promising molecular genetic marker for the analysis of variability, differentiation, and hybridization of house mice as well for subspecific identification of M. musculus specimens. Despite more rapid evolution of the Cox1 gene, it is not well suited for discrimination of M. m. musculus, M. m. wagneri, M. m. gansuensis specimens and Transcaucasian representatives of M. m. domesticus due to introgression and long-term maintenance of foreign mitochondrial DNA in populations. However, Cox1 gene analysis (along with the diagnostics of animals by nuclear DNA) may be useful for estimation of population differences in M. m. castaneus and M. m. domesticus subspecies.

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Section: Discussionsupporting

confidence: 92%

Section: Genomics Transcriptomicsmentioning

confidence: 92%

Section: Species Groupmentioning

confidence: 99%

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Variability of Fragments of Nuclear Brca1 Gene, Exon 11, and Mitochondrial Cox1 Gene in House Mice Mus musculus

et al. 2020

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“…The mitochondrial DNA (mtDNA) D-loop sequence is widely used in population genetic analysis because it does not encode proteins and is not affected by selection (Liao et al, 2016;Maltsev et al, 2015). In the present study, wild M. nipponense populations were sampled from eight different natural water bodies in Yixing city, including reservoirs, brooks, and shallow lakes, and D-loop sequences were employed to examine their genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Xiong

Jiang

Zhang

et al. 2023

Aquat. Living Resour.

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This article presents a study of D-loop sequences to characterize the genetic diversity of wild Macrobrachium nipponense populations in Yixing natural waters including two reservoirs (Hengshan reservoir, HS; Youche reservoir, YC), 3 brooks (Linjin Dang, LJD; Magong Dushan Dang, MDD; Yangshan Dang, YSD) and 3 shallow lakes (Dongjiu lake, DJ; Xijiu lake, XJ; Tuanjiu lake, XJ), and compared the genetic differentiation and population structure with wild populations of Taihu Lake (TH), Yangtze River (YZ), and the main local artificially bred varieties “Taihu No. 2” (TH-2). A 747 bp D-loop sequence fragment was amplified in 321 individuals and the results exhibited a higher content of A+T (80.03%) than C+G (19.97%). A total of 110 haplotypes were identified. The h and π value proved the diversity of these populations was at the same level with high genetic diversity. TH-2 and YZ showed remarkable diversity, and XJ is even better. Fst estimates suggested that YZ and TH-2 were significant differentiation with other Yixing populations (P < 0.05). Three populations from shallow lake (DJ, XJ and TJ) displayed significant differentiated with the left Yixing ones (P < 0.05). The pairwise genetic distance, as well as haplotype network results, also suggested that all these 11 populations did not diverge at the species level (<15%). The P values of Tajima's D and Fu Fs were relatively greater than 0.1 (P > 0.1) and the nucleotide mismatch distribution analysis showed multiple peaks, giving a conclusion that the populations did not exhibited expansion. All these results suggested that TH-2 and YZ have remarkable diversity, and the germplasm resources and genetic diversity of M. nipponense in Yixing are very good and are suitable for original materials of breeding.

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“…It possessed four officially recognized indigenous breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, Yushu) and two improved breeds (Datong and Ashdan). Mitochondrial DNA (mtDNA) owns the characteristics of maternal inheritance and high variation rate, that making it as an important molecular marker to explore the evolution history, origin and genetic diversity of mammals (Bruford et al, 2003;Lunkina et al, 2004;Srivastava et al, 2015;Maltsev et al, 2015). The mammalian cytochrome b gene (Cytb ), located in the functional region of mitogenome, is a mitochondrial oxidative phosphorylation complex protein encoding 379 amino acids (Hatefi, 2018).…”

Section: Introductionmentioning

confidence: 99%

Maternal genetic diversity, differentiation and phylogeny of wild yak and four domestic yak breeds in Qinghai, China inferred from mitochondrial Cytb variations

et al. 2023

Preprint

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Yak (Bos grunniens) is a unique livestock animal originating from the Qinghai-Tibet Plateau in China. In the current study, we investigated the maternal genetic diversity, differentiation and phylogeny of wild yak population and four domestic yak breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, and Yushu) in Qinghai, China by analyzing 166 mitochondrial cytochrome b (Cytb) gene sequence variations. Our results indicated that the haplotype and nucleotide diversities of wild yak were 0.883±0.044 and 0.004±0.002, while the total haplotype and nucleotide diversities of four Qinghai domestic yak breeds were 0.646±0.040 and 0.003±0.001, respectively. Among the four Qinghai domestic yak breeds, the haplotype diversity was found to be highest in Yushu yak breed (Hd = 0.770±0.053), while the lowest was recorded in Huanhu yak breed (Hd = 0.501±0.088). Estimates of FST values showed a moderate genetic differentiation between wild yak and Huanhu yak (FST = 0.058) as well as that between Huanhu yak and Yushu yak breeds (FST = 0.052), but a weak genetic differentiation was observed between the other yak breeds/populations (-0.021＜FST＜0.037). Additionally, the clustering analysis based on RST values showed that Xueduo yak and Huanhu yak were clustered into one group, and each of the other three yak breeds/populations was separated into one group, respectively. Overall, the clustering relationship between wild yak and Yushu yak was closer. Maternal phylogenetic analysis showed that wild yak and four local yak breeds/populations in Qinghai represented in three maternal lineages (Mt-Ⅰ, Mt-Ⅱ, and Mt-Ⅲ), indicating three maternal origins in yak. Our study would provide valuable information for the conservation and utilization of wild yak and Qinghai domestic yak breeds.

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Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus: Analysis of variability of the control region (D-loop) of mitochondrial DNA

Cited by 13 publications

References 10 publications

Variability of Fragments of Nuclear Brca1 Gene, Exon 11, and Mitochondrial Cox1 Gene in House Mice Mus musculus

Variability of Fragments of Nuclear Brca1 Gene, Exon 11, and Mitochondrial Cox1 Gene in House Mice Mus musculus

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Maternal genetic diversity, differentiation and phylogeny of wild yak and four domestic yak breeds in Qinghai, China inferred from mitochondrial Cytb variations

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