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45 results for “genotypic adaptation”
Fig. 2 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 2. Genotyping of Cryptosporidium spp. in strawcolored fruit bats by small subunit rRNA-based PCRRFLP. Upper panel: SspI RFLP patterns; lower panel: VspI RFLP patterns; M: 100-bp molecular markers; H: C. hominis positive control; P: C. parvum positive control; B1: Cryptosporidium bat genotype XIV; B2: Cryptosporidium bat genotype XV.
Fig. 4 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 4. Phylogeny of Enterocytozoon bieneusi genotypes in bats based on Bayesian inference analysis of sequences of the internal transcribed spacer of the rRNA gene. The posterior probability values are indicated on the branches. Red ones are E. bieneusi genotypes identified in straw-colored fruit bats in the present study. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Skeleton of Struthiomimus altus. Genotype specimen, Amer. Mus. 5339. One-tenth natural size In this panel mount the animal is placed approximately as found. The pollex is too closely appressed to the other digits, see Fig. 3. in Skeletal Adaptations of Ornitholestes, Struthiomimus, Tyrannosaurus
Skeleton of Struthiomimus altus. Genotype specimen, Amer. Mus. 5339. One-tenth natural size In this panel mount the animal is placed approximately as found. The pollex is too closely appressed to the other digits, see Fig. 3.
Multi-location trials and population-based genotyping reveal high diversity and adaptation to breeding environments in a large collection of red clover
<p>This dataset accompanies the article with the same title made available on bioRxiv <a href="https://doi.org/10.1101/2022.12.19.520744">https://doi.org/10.1101/2022.12.19.520744</a> </p>
Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales
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An experimental test of parasite adaptation to common vs. rare host genotypes
<p>A core hypothesis in coevolutionary theory proposes that parasites adapt to specifically infect common host genotypes. Under this hypothesis, parasites function as agents of negative frequency-dependent selection, favoring rare host genotypes. This parasite-mediated advantage of rarity is key to the idea that parasites maintain genetic variation and select for outcrossing in host populations. Here, we report the results of an experimental test of parasite adaptation to common vs. rare host genotypes. We selected the bacterial parasite <i>Serratia marcescens</i> to kill <i>C. elegans</i> hosts in uneven mixtures of host genotypes. To examine the effect of commonness itself, independent of host identity, each of four host genotypes was represented as common or rare in experimental host mixtures. After experimental selection, we evaluated a parasite line's change in virulence, the selected fitness trait, on its rare and common host genotypes. Our results were consistent with a slight advantage for rare host genotypes: on average, parasites lost virulence against rare genotypes but not against common genotypes. The response varied substantially, however, with distinct patterns across host genotype mixtures. These findings support the potential for parasites to impose negative frequency-dependent selection, while emphasizing that the cost of being common may vary with host genotype.</p>
Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.
Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables
<p>Extreme <span>environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, </span><span>m</span><span>odern bony fishes have colonized various aquatic environments, including perpetually dark,</span><span> hypoxic, hypersaline and toxic habitats</span><span>. </span><span>Eurasian perch (</span><em>Perca fluviatilis</em><span>) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.</span></p>
Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
<p>Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (<em>mettl21e</em>) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and<em> de novo</em> variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and <em>de novo</em> mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.</p>
Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
<p>The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, <em>Carex</em> <em>nova</em> and <em>Carex</em> <em>nelsonii</em> (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (<em>C. nelsonii</em>) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (<em>C. nelsonii</em>), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent<em>.</em></p>
Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima
Understanding the effects of the demographic dynamics and environmental heterogeneity on the genomic variation of forest species is important not only for uncovering the evolutionary history of the species but also for predicting their ability to adapt to climate change. In this study, we combined a common garden experiment with range-wide population genomics analyses to infer the demographic history and characterize patterns of local adaptation in a subtropical oak species, Quercus acutissima. We scanned about 8% of the oak genome using a balanced representation of both genic and non-genic regions and identified a total of 55,361 SNPs in 167 trees. Genomic diversity analyses revealed an east-west split in the species distribution range. Coalescent-based model simulations inferred a late Pleistocene divergence in Q. acutissima between the east and west groups as well as subsequent pre-glaciation population expansion events. Consistent with observed genetic differentiation, morphological traits also showed east-west differentiation and the biomass allocation in seedlings was significantly associated with precipitation. Environment was found to have a significant and stronger impact on the non-neutral than the neutral SNPs, and also significantly associated with the phenotypic differentiation, suggesting that apart from the geography, environment had played a role in determining non-neutral and phenotypic variation. Our approach, which combined a common garden experiment with landscape genomics data, validated the hypothesis of local adaptation of this long-lived oak tree of subtropical China. Our study joins the small number of studies that have combined genotypic and phenotypic data to detect patterns of local adaptation.
Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
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Single nucleotide polymorphisms, environmental data and R scripts used in the work: A donor registry: Genomic analyses of Posidonia australis seagrass meadows identifies adaptive genotypes for future-proofing
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Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
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Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables
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Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima
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Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
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An experimental test of parasite adaptation to common vs. rare host genotypes
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Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping
Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine–freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.
Data from: A phenotype-genotype codon model for detecting adaptive evolution
A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here we present a novel approach called the phenotype-genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio ω to a value ω > 1. As it is becoming increasingly clear that ω > 1 can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include (i) a persistent increase/decrease in ω at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and (ii) a transient increase in ω at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site's optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of three real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-means.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.