&lt;em&gt;Sinocyclocheilus sanxiaensis&lt;/em&gt;, a new blind fish from the Three Gorges of Yangtze River provides insights into speciation of Chinese cavefish

Jiang, Weixing; Li, Jie; XiaoZhong, Lei; Wen, Zhenhai; Han, Yuzhang; Yang, Jing; Chang, Junjun

doi:10.24272/j.issn.2095-8137.2019.065

Cited by 20 publications

(31 citation statements)

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“…Due to the lack of a fossil record for the Sinocyclocheilus , we used two alternative approaches to estimate divergence times in Sinocyclocheilus . First, we used a “standard clock” estimate for fish mitochondrial DNA of 2% per million years [ 19 ], as the main approach of this study. We also used two calibration points (C1, C2) based on the approach of Li et al [ 12 ] for exploring potential differences in estimates of divergence times using different approaches.…”

Section: Methodsmentioning

confidence: 99%

“…Sinocyclocheilus species are thought to have shared a common ancestor in the late Miocene, undergoing a spectacular diversification spanning the Pliocene and Pleistocene, across the southwestern parts of China’s 620,000 km 2 of karst habitats [ 18 ], with nearly 75 extant species [ 19 ]. This resulted in an adaptive diversification into subterranean refugia traversing the intersection of the Guizhou, Guangxi and Yunnan provinces around the time of the uplifting of Tibetan/Guizhou plateau [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…Much of the work on Sinocyclocheilus has been taxonomic in nature [ 23 ], and some species are only known from a few specimens or photographs [ 23 – 31 ], and in some cases, only from a single type specimen [ 19 ]. Over the past decade, however, the inventory of Sinocyclocheilus species has steadily increased [ 6 , 19 , 20 , 23 – 25 , 28 – 39 ], indicating that there are more species yet to be discovered. Difficulties in sampling deep caves scattered across the karstic expanse, and the extreme rarity of some species have impeded exploratory and monitoring studies.…”

Section: Introductionmentioning

confidence: 99%

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Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

et al. 2021

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Background Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique opportunities to understand recurrent evolution of stereotypic traits (such as eye loss and sensory expansion) in the context of a deep and diverse phylogenetic group. However, they remain poorly understood in terms of their morphological evolution. Therefore, we explore key patterns of morphological evolution, habitat utilization and geographic distribution in these fishes. Results We constructed phylogenies and categorized 49 species based on eye-related condition (Blind, Micro-eyed, and Normal-eyed), habitat types (Troglobitic—cave-restricted; Troglophilic—cave-associated; Surface—outside caves) and existence of horns. Geometric-morphometric analyses show Normal-eyed morphs with fusiform shapes segregating from Blind/Micro-eyed deeper bodied morphs along the first principal-component axis; second axis accounts for shape complexity related to horns. The body shapes showed a significant association with eye-related condition and horn, but not habitat types. Ancestral reconstructions suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to their ancestral Normal-eyed morphs; Sinocyclocheilus are also pre-adapted for cave dwelling. Our geophylogeny shows an east-to-west diversification spanning Pliocene and Pleistocene, with early-diversifying Troglobitic species dominating subterranean habitats of karstic plains whereas predominantly Surface forms inhabit hills to the west. Evolutionary rates analyses suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 5–20 fold increase in rate of eye regression, possibly explained by limited resource availability. Body size and eye size have undergone reversals, but not horns, a trait entailing considerable time to form. Conclusions Sinocyclocheilus occupied cave habitats in response to drying associated with aridification of China during late Miocene and the Pliocene. The prominent cave-adaptations (eye-regression, horn-evolution) occur in clades associated with the extensive subterranean cave system in Guangxi and Guizhou provinces. Integration of morphology, phylogeny, rate analyses, molecular-dating and distribution show not only several remarkable patterns of evolution, but also interesting exceptions to these patterns signifying the diversification of Sinocyclocheilus as an invaluable model system to explore evolutionary novelty.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

et al. 2021

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“…Guizhou, and Yunnan provinces of China (Jiang et al, 2019;Zhao and Zhang, 2009). The troglomorphic adaptations of Sinocyclocheilus include the development of a specialized sensory system, such as degeneration or complete loss of eyes, degeneration of scales, loss of pigmentation, expansion of pectoral fins, evolution of 'horns' and enhancement of the neuromast system (He et al, 2013;Li et al, 2020;Ma et al, 2020;Meng et al, 2013).…”

mentioning

confidence: 99%

“…The genus is thought to have originated during the Miocene-Pliocene with cave occupation taking place predominantly during the Pliocene-Pleistocene transition in response to an uplift event and aridification of the Qinghai-Tibetan Plateau (Mao et al, 2021). Nearly all of the molecular studies to date on the phylogenetic relationships within Sinocyclocheilus have been based on mtDNA (Chen et al, 2018;Jiang et al, 2019;Liang et al, 2011), limiting some of the diversification-scale analyses as well as insights into the population-level processes that shape this remarkable radiation. This is an important limitation, given that the uniparental nature of mtDNA inheritance might obscure important events of admixture in the history of Sinocyclocheilus while hampering the inference of species limits given that it represents only a single genetic locus.…”

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confidence: 99%

Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Mao

Vasconcellos

Pie

et al. 2022

Molecular Phylogenetics and Evolution

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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 in freshwater fish requires a sound understanding of the evolutionary relationships between surface and troglomorphic 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 troglomorphic 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 646,497Jbp 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 supports the recognition of six major clusters of species congruent with the identified clades based on the spatial arrangement and overlap of the species in the PC 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 10.5 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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Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China

Che,

Zhang,

et al. 2024

Ecology and Evolution

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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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<em>Sinocyclocheilus sanxiaensis</em>, a new blind fish from the Three Gorges of Yangtze River provides insights into speciation of Chinese cavefish

Cited by 20 publications

References 5 publications

Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China

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