Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude

Wang, Ying; Shen, Yanjun; Feng, Chenguang; Zhao, Kai; Song, Zhaobin; Zhang, Yanping; Yang, Liandong; He, Shunping

doi:10.1038/srep29690

Cited by 98 publications

(101 citation statements)

References 56 publications

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“…This was consistent with the work of and Li, Yang, Si, Zhang, and Song (2016). The position of C. dabryi indicated that this is a young species (1.37 Ma; not shown in Figure 2) derived from Triplophysa species, and challenged the monophyly of genus/subgenus Triplophysa supported by He, Chen, and Chen (2006) and Wang et al (2016).…”

Section: Three Species Yunnanilus Brevis Nemacheilus Triangularis Andsupporting

confidence: 88%

“…As such, the species may provide clues of earlier geological movements. Wang et al (2016) argued that the Early Miocene uplifts of the Tibetan Plateau led to divergence of the genus Triplophysa. After the collision of the Indian plate with Asian plate in the early Cenozoic, the Tibetan plateau began its uplift (Chung et al, 1998;Ruddiman, 1998;Tapponnier et al, 2001;Yin & Harrison, 2000).…”

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confidence: 99%

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Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Chen

Yang

et al. 2019

Ecology and Evolution

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Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase‐activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.

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Section: Three Species Yunnanilus Brevis Nemacheilus Triangularis Andsupporting

confidence: 88%

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confidence: 99%

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Chen

Yang

et al. 2019

Ecology and Evolution

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“…The 13 PCGs of mitogenome are all key subunits of complexes directly involved in the oxidative phosphorylation (OXPHOS) process, directly providing 95% free energy for cells, which is important for metabolic demands in organisms (Gu et al, ; Wu, Gu, Guo, Huang, & Yang, ). In recent years, the mitogenome has become a powerful system for examining the genetic basis of organismal adaptation to various harsh environments, and signals of positive selection have been detected in mitochondrial genes of various taxa (Korkmaz, Aydemir, Temel, Budak, & Başıbüyük, ; Luo, Yang, & Gao, ; Scott et al, ; Wang et al, ; Yu, Wang, Ting, & Zhang, ; Yuan et al, ; Zhang et al, ; Zhou, Shen, Irwin, Shen, & Zhang, ). Most of these studies focused their attention on vertebrates, whereas few reports examined the adaptive evolution of crustacean mitogenomes to hydrothermal vent environments (Sun, Hui, Wang, & Sha, ; Wang et al, ).…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Sun

Sha

Wang

2019

Ecology and Evolution

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Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication–random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.

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“…Divergence times were crudely estimated by the lognormal relaxed model with rate in 0.01, and the tree prior was set in Yule process for the analysis. Three fossil records were selected as calibration points to estimate divergence time: (i) the oldest catostomid fossil from the early Paleocene (60 million years ago, mya) (Cavender, ); (ii) the oldest known fossil of an extant catostomid genus Ictiobus dating from the middle Miocene about 15 mya (Cavender, ); (iii) the fossil record of the genus Cobitis (13.8–15.9 mya) (Wang et al., ; Zhou, ) (http://www.wahre-staerke.com/). Markov chain analyses were performed by two independent runs of 80,000,000 generations with sampling every 1,000 generations, and posterior probability was estimated by removing 10% of the initial samples as burn‐in.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary relationships of two balitorids (Cypriniformes, Balitoridae) revealed by comparative mitogenomics

et al. 2018

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Balitoridae, a family within the Cypriniformes, inhabit torrential mountain streams in Asia. Although they have long fascinated ichthyologists for their numerous adaptations to this tumultuous environment, the evolutionary history of this group remains poorly understood. In this study, we investigate the evolutionary relationships of the balitorids with particular attention to the phylogenetic placement of two balitorid species, Yaoshania pachychulis and Erromyzon kalotaenia. Both species have extremely limited distributions, they are limited to Mt. Dayaoshan of the Pearl River in China and require dedicated conservation plans. However, little is known about their evolutionary relationships to other balitorids. Here, we examined the evolutionary relationships of Y. pachychulis and E. kalotaenia to each other and other balitorids through sequencing the complete mitochondrial genomes of nine balitorid individuals. For the newly sequenced balitorids, the length of the whole mitogenome, gene arrangement and their base composition are similar to those of other bony fishes. Analyses based on these newly sequenced mitogenomes and an additional 50 previously published mitogenomes show that Y. pachychulis and E. kalotaenia cluster as different clade within the subfamily Gastromyzontinae. The genetic distance between these two species ranges from 0.127 ± 0.003 to 0.132 ± 0.004 which is slightly higher than that between some genera (e.g. the distance between Vanmanenia and Metahomaloptera is 0.127 ± 0.004). Therefore, it is reasonable to assign Y. pachychulis and E. kalotaenia to different genera. Phylogenetic signal assessment suggested that ND1, ND4 and ND5 genes as well as their concatenated subsets perform relatively well in reconstructing the Cobitoidea phylogeny. The divergence time estimation indicated that the balitorids distributed in Mt. Dayaoshan might have originated and evolved following the flattening and uplifting of the Yunnan–Guizhou Plateau during the late Miocene to late Pliocene.

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Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude

Cited by 98 publications

References 56 publications

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Evolutionary relationships of two balitorids (Cypriniformes, Balitoridae) revealed by comparative mitogenomics

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