Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

Gamboa, Maribet; Watanabe, Kozo

doi:10.1186/s12864-019-5453-3

Cited by 19 publications

(16 citation statements)

References 68 publications

(84 reference statements)

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“…In this species, southern populations may employ heat-genes in anticipation to heat stress, an adaptation based on the evolutionary history of frequent heat exposure (Gleason & Burton, 2014). Stoneflies are generally weak fliers, with a limited airborne dispersal range within stream corridors, a long water stage during its immature stages (Stewart & Stark, 2008), and an evolutionary history linked with local environmental conditions (Gamboa et al, 2018;Gamboa & Watanabe, 2019). Thus, both local environmental conditions and evolutionary history could influence the stonefly gene expression differences we observed.…”

Section: Discussionmentioning

confidence: 89%

“…Stoneflies are distributed worldwide, with higher species diversity at higher latitudes, and the species has a high diversity and ecological relevance in freshwater ecosystems around the world (DeWalt & Ower, 2019). The seven species selected (Perlodini incertae, Haploperla japonica, Nemoura ovocercia, Taenionema japonicum, Stavsolus japonicus, Amphinemura longispina, and Eocapnia nivalis) have been studied previously for their responses to a latitudinal gradient in Japan using genomic and proteomics approaches, which showed genome-wide signatures of adaptive divergence among populations along the latitude gradient (Gamboa & Watanabe, 2019) using double-digest restriction site-associated DNA sequencing, and a high oxygen-protein expression at higher latitudes using quantitative proteomics and protein differential expression analysis (Gamboa et al, 2017), but, specific gene functions and relative gene expression levels related to the gradient remain to be determined.…”

Section: Introductionmentioning

confidence: 99%

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Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Gamboa

Gotoh

Doloiras-Laraño

et al. 2020

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Latitudinal variation has been known to create strong selection pressure for genomic variation that enables the adaptation and survival of organisms. By altering gene expression patterns, organisms can modify their adaptive potential to heterogeneous environmental conditions along a latitudinal gradient; however, there is a gap in our understanding of how physiological consequences in wild species are affected and how changing environmental conditions act on multiple species. Here, we investigated how seven stream stonefly species sampled from four geographical regions in Japan differ in their responses to latitudinal variations by measuring gene expression (RNA-sequencing) differences within species and gene co-expression among species. We found that a large number of genes (622) were differentially expressed along the latitudinal gradient. The high species-specific gene expression diversity found at higher latitude regions was probably associated with low temperatures and high water discharge, which suggests the adaptive potential of stonefly specie. In contrast, similar gene expression patterns among species was observed at lower latitudes, which suggests that strong environmental stress occurs in warmer regions. Weighted gene co-expression network analysis (WGCNA) identified 22 genes with similar expression patterns among species along the latitudinal gradient. Among the four geographical regions, high differential expression patterns in the co-expressed genes from two regions were found, suggesting that the local environment strongly affects gene expression patterns among species in these regions. Respiration, metabolism, and developmental co-expressed genes exhibited a latitudinal cline, showing clear evidence of divergent adaptive responses to latitude. Our findings demonstrate that stonefly species are differentially adapted to local environmental conditions, and imply that adaptation in gene expression could be shared by multiple species under environmental stress conditions. This study highlights the importance of considering multiple species when evaluating the consequences of environmental changes on aquatic insect communities, and possible mechanisms to cope with environmental changes.

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Section: Discussionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Gamboa

Gotoh

Doloiras-Laraño

et al. 2020

Preprint

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“…Yet the results here provide exciting opportunities to investigate the relationships between ecological or behavioural traits and environmental drivers of selection across species, which can be further assessed with common garden or physiological experiments. This is one of the rst comparative seascape genomic studies to date, and it is imperative that future seascape genomic studies aim to understand how climatic change will impact not just individual species, but communities [72]. Multispecies GEAA studies remain a challenge due to costs associated with highthroughput sequencing and the lack of annotated genomes in non-model species, particularly marine invertebrates [73,74].…”

Section: Discussionmentioning

confidence: 99%

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

Nielsen

Henriques

Beger

et al. 2020

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Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

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“…It is important to combine genetic, ecological components and phenotypes in interpreting adaptation and phylogeographical patterns we observed from empirical studies (Gamboa & Watanabe 2019). Under the rapid genetic technological development, taking advantage of molecular genetic approaches to access genetic diversity can enhance understanding of the process of underlying speciation in heterogeneous freshwater systems (Nosil et al 2017).…”

Section: Introductionmentioning

confidence: 99%

ddRAD-seq Reveals Cryptic Phylogeographic Structure and Adaptive Population Differentiation of Hyporhamphus Intermedius in Heterogeneous Environments from China Mainland

Wang¹,

Lai²,

Bi³

et al. 2020

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BackgroundSpecies differentiation and local adaptation in heterogeneous environments have been getting a large focus but poor knowledge of the mechanism. With widespread in coastal areas and the hyperdiverse freshwater systems in China, Hyporhamphus intermedius is an excellent material for phylogeography and local adaptation research. Here, 156 individuals were sampled in 8 sites from heterogeneous aquatic habitats to comprehend environmental and genetic contributions to phenotypic divergence. Results32,744 SNPs among populations and obvious population differentiation was found by ddRAD-seq among groups from the different watersheds. Population genetic structure was partly geographic, successfully classifying all individuals into three genetic subgroups corresponding to the North, the South and the Plateau Lakes with more migrations within region. Due to the transplant event, the strikingly increasing divergence in a short time indicated the tendency of local differentiation for introduced populations in the Plateau Lakes. Dorsal and anal traits varied widely between the Southern and others, which highlighted previously unrecognized lineages. Furthermore, we inferred the whole population is in response to balancing selection from neutrality test with positive value (Tajima's D=2.773), and demographic history underlay two main split events from the northern ancestral population. Subgroup ranges appear to counterparts to geographic regions with heterogeneous hydrological factors, indicating these features are likely important drivers of diversification.ConclusionsAccordingly, our results revealed that genetic polymorphism and divergence of Hyporhamphus intermedius in heterogeneous environments might be ascribed to a consequence of balancing selection, gene flow at microscales, and the impact of abiotic factors, verifying potentially that genetic differences among populations are the result of both genetic canalization and plastic responses to environmental heterogeneity.

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Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

Cited by 19 publications

References 68 publications

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

ddRAD-seq Reveals Cryptic Phylogeographic Structure and Adaptive Population Differentiation of Hyporhamphus Intermedius in Heterogeneous Environments from China Mainland

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Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

Cited by 19 publications

References 68 publications

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

ddRAD-seq Reveals Cryptic Phylogeographic Structure and Adaptive Population Differentiation of&nbsp;Hyporhamphus Intermedius&nbsp;in&nbsp;Heterogeneous&nbsp;Environments from China Mainland

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ddRAD-seq Reveals Cryptic Phylogeographic Structure and Adaptive Population Differentiation of Hyporhamphus Intermedius in Heterogeneous Environments from China Mainland