Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish

Tong, Chao; Li, Miao

doi:10.1016/j.ijbiomac.2020.01.207

Cited by 13 publications

(11 citation statements)

References 51 publications

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“…For instance, annelids (Horn et al 2019), arthropods (Lee et al 2011), and fish (Velotta et al 2016), including sculpin (Dennenmoser et al 2016) and stickleback (Jones et al 2012b; Kusakabe et al 2016; Hasan et al 2017), have all shown genetic changes in ion channel genes following colonization of freshwater habitats. Our findings are also in line with a recent study (Tong and Li 2020) on adaptation of Gymnocypris przewalskii to a saline-alkaline lake, which showed that rapidly evolving genes, those with an elevated rate of non-synonymous substitutions, are overwhelmingly involved in ion transport. Our findings of gene functions related to transmembrane ion transport could also be in part driven by changes in temperature over the time period sampled (during the summer months).…”

Section: Discussionsupporting

confidence: 92%

“…For example, genes such as Nalcl and Wnk4 show signs of potential selection as shared outliers across multiple estuaries. Nalcn is a salt-sensing gene that was recently found to be rapidly evolving in saline-alkaline lake-dwelling fish (Tong and Li 2020). Similarly, Wnk4 codes for an intracellular chloride sensor (Chen et al 2019) implicated in salinity-tolerance in stickleback (Wang et al 2014).…”

Section: Discussionmentioning

confidence: 99%

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Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

Garcia-Elfring

Paccard

Thurman

et al. 2020

Preprint

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Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection in action under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele frequency changes in these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

Garcia-Elfring

Paccard

Thurman

et al. 2020

Preprint

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show abstract

“…For example, genes such as Nalcl and Wnk4 show signs of potential selection as shared outliers across multiple estuaries. Nalcn is a salt‐sensing gene that was recently found to be rapidly evolving in saline‐alkaline lake‐dwelling fish (Tong & Li, 2020). Similarly, Wnk4 codes for an intracellular chloride sensor (Chen et al, 2019) implicated in salinity‐tolerance in stickleback (Wang, Fan, et al, 2014; Wang, Yang, et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly‐variable estuaries

et al. 2021

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Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time.The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.

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“…Extremely alkaline stress may cause extensive damage to fish, such as inducing cell apoptosis (Monteiro et al 2009; Zhao et al 2016, 2020). However, several fish species can survive in this harsh environment, such as schizothoracine ( Gymnocypris przewalskii ) (Tong, Fei, et al 2017; Tong & Li 2020), Magadi tilapia ( Alcolapia grahami ) (Wilkie & Wood 1996), and Amur ide ( Leuciscus waleckii) (Xu et al 2017). This may also pose a barrier for alkaline tolerant fish as compared with alkaline intolerant fish.…”

Section: Discussionmentioning

confidence: 99%

Genomic signature of shifts in selection and alkaline adaptation in highland fish

Tong

Tang

et al. 2020

Preprint

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Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed mainly related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species and four alkaline intolerant relatives. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of core shared genes associated with ion transport, apoptosis, immune response and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.Significance StatementLittle is known about how wild fish responds to extreme alkaline stress besides hypoxia at high altitude. Comparative genomics has begun to elucidate the genomic basis of alkaline adaptation in lowland fish, such as killifish, but insight from highland fish has lagged behind. The common role of adaptive molecular evolution during alkaline adaptation in highland and lowland fish has rarely been discussed. We address this question by comparing 15 fish omics data. We find numbers of shared orthologs exhibited consistent patterns of molecular evolution in alkaline tolerant species relative to intolerant species. We further identify remarkably consistent signatures of rapidly evolving and positive selection in a substantial shared core of genes in both highland and lowland alkaline tolerant species.

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Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish

Cited by 13 publications

References 51 publications

Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

Using seasonal genomic changes to understand historical adaptation: parallel selection on stickleback in highly-variable estuaries

Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly‐variable estuaries

Genomic signature of shifts in selection and alkaline adaptation in highland fish

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