Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq

Kang, Jingliang; Ma, Xiuhui; He, Shunping

doi:10.1038/s41598-017-02853-3

Cited by 19 publications

(18 citation statements)

References 89 publications

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“…Indeed, much of our understanding of gene flow and population genetic patterns in fluvial systems comes from studies of fish and aquatic insects (e.g. Faulks, Gilligan, & Beheregaray, ; Finn & Adler, ; Finn, Blouin, & Lytle, ; Fluker, Kuhajda, & Harris, ; Fluker, Kuhajda, Lang, & Harris, ; Kang, Ma, & He, ; Lecaudey, Schliewn, Osinov, Taylor, Bernatchez, Schliewn, & Osinov, ; Robinson, Simmons, Williams, & Moyer, ; Stobie, Oosthuizen, Cunningham, & Bloomer, ). Moreover, hypotheses that predict diversity patterns across riverine landscapes have been mostly developed with data on freshwater insects and fish (reviewed by Davis et al, ; Hughes et al, ).…”

Section: Introductionmentioning

confidence: 99%

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

et al. 2019

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Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD‐seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream‐biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.

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Section: Introductionmentioning

confidence: 99%

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

et al. 2019

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“…RAD sequencing is generally used in marine organisms and plant research, to develop SNP molecular markers, but less applied in insect research. The researchers used this method to analyze the genetic structure and genetic diversity of white perch Morone Americana [15], Nujiang catfish Creteuchiloglanis macropterus [35], American lobster Homarus americanus [36], Sweetpotato Ipomoea batatas [37], and other organisms. All of them obtained good results.…”

Section: Discussionmentioning

confidence: 99%

Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

Chen

Wang

Li³

et al. 2020

Insects

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To determine population genomic structure through high-throughput sequencing techniques has revolutionized research on non-model organisms. The coconut leaf beetle, Brontispa longissima (Gestro), is a widely distributed pest in Southern China. Here, we used restriction site-associated DNA (RAD) genotyping to assess the invasion pathway by detecting and estimating the degree of genetic differentiation among 51 B. longissima accessions collected from Southern China. A total of 10,127 SNPs were obtained, the screened single nucleotide polymorphism (SNP) information was used to construct the phylogenetic tree, FST analysis, principal component analysis, and population structure analysis. Genetic structure analysis was used to infer the population structure; the result showed that all accessions were divided into Hainan population and non-Hainan population. The Hainan population remained stable, only the Sansha population differentiated, and the non-Hainan populations have gradually differentiated into smaller sub-populations. We concluded that there are two sources of invasion of B. longissima into mainland China: Taiwan and Hainan. With the increase of the invasion time, the Hainan population was relatively stable, and the Taiwan population was differentiated into three sub-populations. Based on the unrooted phylogenetic tree, we infer that Taiwan and Hainan are the two invasive base points. The Taiwan population invaded Fujian, Guangdong, and Guangxi, while the Hainan population invaded Yunnan and Sansha. Our results provide strong evidence for the utility of RAD sequencing (RAD-seq) in population genetics studies, and our generated SNP resource could provide a valuable tool for population genomics studies of B. longissima in the future.

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“…For example, some studies have focused on metabolic rate, as reported in highland westslope cutthroat trout (Oncorhynchus clarkii) as compared with introduced lowland rainbow trout (Oncorhynchus mykiss) in the Oldman River basin (Canada): Fish at high altitudes have a lower metabolic rate [3]. Kang and co-workers [4] investigated the genetic mechanism of high-altitude adaptation in Creteuchiloglanis macropterus (Siluriformes) and found that many genes were involved in energy metabolism and hypoxia, which might be an important resource for studying adaptations to a high-altitude environment. Li and co-workers [5] characterized the mitochondrial genomes of two species ("morphologically primitive" clade and "morphologically specialized" clade) of schizothoracine fishes.…”

Section: Introductionmentioning

confidence: 99%

Hepatic Steatosis in a Bullhead (Cottus gobio) Population from a High-Mountain Lake (Carnic Alps): Adaptation to an Extreme Ecosystem?

Pastorino

Prearo

Pizzul

et al. 2019

Water

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The aim of this study was to describe liver alterations observed in a bullhead (Cottus gobio) population from a high-mountain lake (Dimon Lake; 1857 m a.s.l.) located in Carnic Alps (Northeast Italy). Two fish sampling campaigns (summer and autumn) were performed in 2017 to explore the possible causes of this phenomenon. In addition, to investigate the typical liver features of C. gobio, control specimens were captured from Degano Creek in the same seasons. Total length, weight, and liver weight were recorded in fish from both sampling sites. In addition, Fulton’s condition factor (K) and hepatosomatic index (HSI) were calculated. Stomach contents were also analyzed. Liver from each specimen was sampled, and histological examination was carried out. Liver steatosis (L) (nuclear displacement and cytoplasm vacuolization) were histologically evaluated by assigning a semiquantitative severity score. A significant difference in L was found between Dimon Lake and Degano Creek in both summer (Mann–Whitney test; p = 0.0001) and autumn (Mann–Whitney test; p < 0.0001). Regarding HSI, a significant difference was also recorded between Dimon Lake and Degano Creek in summer (Mann–Whitney test; p < 0.0001) and also in autumn (Mann–Whitney test; p < 0.0001), but no seasonal change in K values was recorded between the two sites in both summer (Mann–Whitney test; p = 0.8589) and autumn (Mann–Whitney test; p = 0.6415). A significant positive correlation between HSI and L was found (ρS 0.573). The causes of this abnormality might be related to adaptation by the fish to the high-altitude environment, accumulating lipids in the liver to tackle the adverse season, which lasts for 6 months of the year. Nonetheless, our study does not preclude steatosis induced by a nearly exclusive chironomids diet in bullhead from Dimon Lake.

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Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq

Cited by 19 publications

References 89 publications

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla

Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

Hepatic Steatosis in a Bullhead (Cottus gobio) Population from a High-Mountain Lake (Carnic Alps): Adaptation to an Extreme Ecosystem?

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