Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383, Wrocław, Poland.
Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245, Białystok, Poland.
Sci Rep. 2022 Sep 30;12(1):16381. doi: 10.1038/s41598-022-20763-x.
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
线粒体 DNA（mtDNA）谱系被认为是种内和种间生物多样性的重要组成部分，可揭示许多分类群的殖民路线和系统地理结构。其中包括广泛分布于全北界的鹿属。我们从 13 个鹿类种中获得了完整的线粒体基因组序列，并将其纳入了 71 个鹿科动物线粒体基因组的全球系统发育分析中。分辨率良好的系统发育树证实鹿属为单系群。基于几个化石校准点的分子年代学研究表明，约 260 万年前，鹿属的两个主要线粒体谱系在中亚地区分离，即西部谱系（包括梅花鹿和马鹿）和东部谱系（包括白唇鹿、加拿大马鹿和日本梅花鹿）。我们还观察到西部谱系的梅花鹿和东部谱系代表中一些线粒体基因组成的趋同变化。日本梅花鹿和梅花鹿的几个亚种在其线粒体蛋白编码基因中积累了大量有害替换，可能是由于种群数量减少导致的漂变。与之前的研究不同，我们发现马鹿的遗迹单倍群 B 与所有其他赤鹿谱系为姐妹群，而中东的单倍群 E 与巴尔干半岛的单倍群 C 具有共同的祖先。与已发表的核基因组树相比，线粒体 DNA 系统发育树可能暗示不同鹿种之间以及南亚鹿、爪哇鹿和黇鹿的共同祖先之间存在古老的 mtDNA 渗入。
