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Che X, Zhang Y, Wu A, Pan X, Wang M, Yang J, Wang X. Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China. Ecol Evol 2024; 14:e10840. [PMID: 38250223 PMCID: PMC10797211 DOI: 10.1002/ece3.10840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus Sinocyclocheilus in the Yunnan-Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, but the samples of different regions of Sinocyclocheilus contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of Sinocyclocheilus. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of Sinocyclocheilus in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus.
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Affiliation(s)
- Xing‐Jin Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuan‐Wei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - An‐Li Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Xiao‐Fu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity ConservationSouthwest Forestry UniversityKunmingChina
| | - Jun‐Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Xiao‐Ai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
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Mao T, Liu Y, Vasconcellos MM, Pie MR, Ellepola G, Fu C, Yang J, Meegaskumbura M. Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity. Mol Phylogenet Evol 2022; 168:107400. [PMID: 35031467 DOI: 10.1016/j.ympev.2022.107400] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 01/19/2023]
Abstract
Troglomorphism-any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs-has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism (stygomorphism) in freshwater fish requires a sound understanding of the evolutionary relationships between surface and stygomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived stygomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (>95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also support the recognition of six major clusters of species congruent with the identified clades in ordination space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.16 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.
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Affiliation(s)
- Tingru Mao
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Yewei Liu
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Mariana M Vasconcellos
- Programa de Pós-Graduação em Ecologia. Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcio R Pie
- Biology Department, Edge Hill University, Ormskirk, Lancashire L39 4QP, United Kingdom
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Chenghai Fu
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China
| | - Jian Yang
- Key Laboratory of Environment Change and Resource Use, Beibu Gulf, Nanning Normal University, Nanning, Guangxi, PR China
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, PR China.
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Qiu Y, Yang J, Jiang W, Chen X, Bian C, Shi Q. A genomic survey on the immune differences among Sinocyclocheilus fishes. Commun Integr Biol 2017; 9:e1255833. [PMID: 28042381 PMCID: PMC5193045 DOI: 10.1080/19420889.2016.1255833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022] Open
Abstract
In our previous work, we reported comparative genomics studies on 3 Sinocyclocheilus fishes, including the surface-dwelling S. graham (Sg), the semi-cave-dewlling S. rhinocerous (Sr) and the cave-restricted S. anshuiensis (Sa). Here, we performed a genomic survey on the immunity differences among the 3 fishes by combination of the genome and transcriptome data. Our results demonstrate that immune-related genetic pathways in Sa and Sr present more similarities than Sg. The innate immune activity in Sa seems to be higher than Sg and Sr, while Sr owns more copy numbers of MHC-related genes (related with the acquired immune system) than Sg and Sa. These differential immune activities in the 3 Sinocyclocheilus species may be due to their differential habitats. Generally speaking, most immunity genes transcribe the lowest levels in Sa when compared with Sg and Sr, which may be associate with a less various microbial environment in the cave-restricted habitat. However, Sr has more members of MHC-related genes than those in Sg and Sa, suggesting a great contribution from the semi-cave-dwelling condition.
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Affiliation(s)
- Ying Qiu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Shenzhen Academy of Marine Sciences, BGI Fisheries, BGI , Shenzhen, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China
| | - Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, China
| | | | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Shenzhen Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China; BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Shenzhen Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China; BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, China; Laboratory of Aquatic Genomics, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Hao Z, Zhang Q, Qu B. Complete mitochondrial genome of a cavefish, Sinocyclocheilus anophthalmus (Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:84-5. [PMID: 24438242 DOI: 10.3109/19401736.2013.873913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this work, we report the complete mitochondrial genome sequence of a cavefish Sinocyclocheilus anophthalmus. The total length of the mitogenome was 16,574 bp and its overall base composition was estimated to be 31.1% for A, 25.5% for T, 26.9% for C and 16.5% for G, indicating an A-T (56.6%)-rich feature in cavefish mitogenome. It contained the typical structure of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The arrangement of these genes was the same as that found in other fishes. All the protein initiation codons were ATG, except for COX1 starting with GTG. The complete mitochondrial genome sequence of the cavefish would provide new insight for cavefish's genetic mechanisms.
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Affiliation(s)
- Zhihui Hao
- a Laboratory of Biological Pharmaceutical , College of Chemical and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao , China
| | - Qidi Zhang
- a Laboratory of Biological Pharmaceutical , College of Chemical and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao , China
| | - Baohan Qu
- a Laboratory of Biological Pharmaceutical , College of Chemical and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao , China
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Meng F, Braasch I, Phillips JB, Lin X, Titus T, Zhang C, Postlethwait JH. Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Mol Biol Evol 2013; 30:1527-43. [PMID: 23612715 PMCID: PMC3684860 DOI: 10.1093/molbev/mst079] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.
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Affiliation(s)
- Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Meng F, Zhao Y, Postlethwait JH, Zhang C. Differentially-expressed opsin genes identified in Sinocyclocheilus cavefish endemic to China. Curr Zool 2013; 59:170-174. [PMID: 24363664 DOI: 10.1093/czoolo/59.2.170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Eye degeneration is a common troglomorphic character of cave-dwelling organisms. Comparing the morphology and molecular biology of cave species and their close surface relatives is a powerful tool for studying regressive eye evolution and other adaptive phenotypes. We compared two co-occurring and closely-related species of the fish genus Sinocyclocheilus, which is endemic to China and includes both surface- and cave-dwelling species. Sinocyclocheilus tileihornes, a cave species, had smaller eyes than Sinocyclocheilus angustiporus, a surface species. Histological and immunohistochemical analyses revealed that the cavefish had shorter cones and more disorderly rods than did the surface-dwelling species. Using quantitative PCR and in situ hybridization, we found that rhodopsin and a long-wavelength sensitive opsin had significantly lower expression levels in the cavefish. Furthermore, one of two short-wavelength-sensitive opsins was expressed at significantly higher levels in the cavefish. Changes in the expression of opsin genes may have played a role in the degeneration of cavefish eyes.
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Affiliation(s)
- Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yahui Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Chunguang Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Lin CJ, Lin HD, Wang JP, Chao SC, Chiang TY. Phylogeography ofHemibarbus labeo(Cyprinidae): secondary contact of ancient lineages of mtDNA. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00407.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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