Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish.
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ABSTRACT:
SUBMITTER: Tong C
PROVIDER: S-EPMC8126726 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined.Our study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies.Comparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies.
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Project description:Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss) after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively). Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.
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Project description:The majority of empirical population genetic studies have tried to understand the evolutionary processes that have shaped genetic variation in a single sample taken from a present-day population. However, genomic data collected over tens of generations in both natural and laboratory populations are increasingly used to find selected loci underpinning adaptation over these short timescales. Although these studies have been quite successful in detecting selection on large-effect loci, the fitness differences between individuals are often polygenic, such that selection leads to allele frequency changes that are difficult to distinguish from genetic drift. However, one promising signal comes from polygenic selection's effect on neutral sites that become stochastically associated with the genetic backgrounds that lead to fitness differences between individuals. Previous theoretical work has established that the random associations between a neutral allele and heritable fitness backgrounds act to reduce the effective population size experienced by this neutral allele. These associations perturb neutral allele frequency trajectories, creating autocovariance in the allele frequency changes across generations. Here, we show how temporal genomic data allow us to measure the temporal autocovariance in allele frequency changes and characterize the genome-wide impact of polygenic selection. We develop expressions for these temporal autocovariances, showing that their magnitude is determined by the level of additive genetic variation, recombination, and linkage disequilibria in a region. Furthermore, by using analytic expressions for the temporal variances and autocovariances in allele frequency, we demonstrate that one can estimate the additive genetic variation for fitness and the drift-effective population size from temporal genomic data. We also show how the proportion of total variation in allele frequency change due to linked selection can be estimated from temporal data. Overall, we demonstrate that temporal genomic data offer opportunities to identify the role of linked selection on genome-wide diversity over short timescales, and can help bridge population genetic and quantitative genetic studies of adaptation.
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Project description:Local adaptation and adaptive clines are pervasive in natural plant populations, yet the effects of these types of adaptation on genomic diversity are not well understood. With a data set of 202 accessions of Medicago truncatula genotyped at almost 2 million single nucleotide polymorphisms, we used mixed linear models to identify candidate loci responsible for adaptation to three climatic gradients-annual mean temperature (AMT), precipitation in the wettest month (PWM), and isothermality (ITH)-representing the major axes of climate variation across the species' range. Loci with the strongest association to these climate gradients tagged genome regions with high sequence similarity to genes with functional roles in thermal tolerance, drought tolerance, or resistance to herbivores of pathogens. Genotypes at these candidate loci also predicted the performance of an independent sample of plant accessions grown in climate-controlled conditions. Compared to a genome-wide sample of randomly drawn reference SNPs, candidates for two climate gradients, AMT and PWM, were significantly enriched for genic regions, and genome segments flanking genic AMT and PWM candidates harbored less nucleotide diversity, elevated differentiation between haplotypes carrying alternate alleles, and an overrepresentation of the most common haplotypes. These patterns of diversity are consistent with a history of soft selective sweeps acting on loci underlying adaptation to climate, but not with a history of long-term balancing selection.
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Project description:Parallel adaptation is common and may often occur from shared genetic variation, but the genomic consequences of this process remain poorly understood. We first use individual-based simulations to demonstrate that comparisons between populations adapted in parallel to similar environments from shared variation reveal a characteristic genomic signature around a selected locus: a low-divergence valley centred at the locus and flanked by twin peaks of high divergence. This signature is initiated by the hitchhiking of haplotype tracts differing between derived populations in the broader neighbourhood of the selected locus (driving the high-divergence twin peaks) and shared haplotype tracts in the tight neighbourhood of the locus (driving the low-divergence valley). This initial hitchhiking signature is reinforced over time because the selected locus acts as a barrier to gene flow from the source to the derived populations, thus promoting divergence by drift in its close neighbourhood. We next empirically confirm the peak-valley-peak signature by combining targeted and RAD sequence data at three candidate adaptation genes in multiple marine (source) and freshwater (derived) populations of threespine stickleback. Finally, we use a genome-wide screen for the peak-valley-peak signature to discover additional genome regions involved in parallel marine-freshwater divergence. Our findings offer a new explanation for heterogeneous genomic divergence and thus challenge the standard view that peaks in population divergence harbour divergently selected loci and that low-divergence regions result from balancing selection or localized introgression. We anticipate that genome scans for peak-valley-peak divergence signatures will promote the discovery of adaptation genes in other organisms.
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Project description:Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
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