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1. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

Author

Lifu Qian, Hui Wang, Jie Yan, Tao Pan, Shanqun Jiang, Dingqi Rao, and Baowei Zhang

Subjects
Mitochondrial genome, Gene rearrangement, Hotspots, Duplicate control regions, Snakes, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. Results In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. Conclusions The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.

Published
2018
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2. Long-term sky islands generate highly divergent lineages of a narrowly distributed stream salamander (Pachyhynobius shangchengensis) in mid-latitude mountains of East Asia

Author

Wenbo Shi, Hui Wang, Pablo Orozco-terWengel, Peng Yan, Baowei Zhang, Lifu Qian, Tao Pan, Zhonglou Sun, Chao-Chao Hu, Guiyou Wu, and Xiao-Bing Wu

Subjects
0106 biological sciences, 0301 basic medicine, China, Genotype, Evolution, Population, Population demography, Urodela, Niche conservatism, Biology, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, Genetic diversity, Gene flow, 03 medical and health sciences, Sky island, Rivers, QH359-425, Animals, Cluster Analysis, education, Ecology, Evolution, Behavior and Systematics, Ecosystem, Phylogeny, Demography, Ecological niche, Islands, education.field_of_study, Pachyhynobius, Ecology, Asia, Eastern, Pachyhynobius shangchengensis, Genetic Variation, biology.organism_classification, Genetic divergence, Phylogeography, 030104 developmental biology, Taxon, Microsatellite Repeats, Research Article
Abstract

Background Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands. Results The Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon’s distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions. Conclusions Our results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence. Electronic supplementary material The online version of this article (10.1186/s12862-018-1333-8) contains supplementary material, which is available to authorized users.

Published
2019

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