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382 results for “Adaptive radiation”
Widespread reticulate evolution in an adaptive radiation
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Data for Predation and resource availability interact to drive life-history evolution in an adaptive radiation of livebearing fish
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Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
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Topographically distinct adaptive landscapes for teeth, skeletons, and size explain the adaptive radiation of Carnivora (Mammalia)
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Tempo and mode of evolution across multiple traits in an adaptive radiation of birds (Vangidae)
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Cranial modularity drives phenotypic diversification and adaptive radiation of Antarctic icefishes
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Testing for adaptive radiation: a new approach applied to Madagascar frogs
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Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation
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Drivers and dynamics of a massive adaptive radiation in cichlid fishes
<p>Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains elusive in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology, and lower pharyngeal jaw shape), scoring of pigmentation patterns, and approximations of the ecology of virtually all ~240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of morphospace expansion. We provide empirical support for two theoretical predictions on how adaptive radiations proceed, the 'early-burst' scenario (for body shape) and the stages model (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per individual heterozygosity, but is not correlated with transposable element content, number of gene duplications, or genome-wide levels of selection in coding sequences.</p>
Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation
Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification and the accumulation of species diversity among clades. However, why the climatic niche evolves more rapidly in some lineages than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a new phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among lineages with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among lineages.
Breaking photoswitch activation depth limit using ionising radiation stimuli adapted to clinical application
<p>This deposit gathers the main raw data and custom codes related to the manuscript "Breaking photoswitch activation depth limit using ionising radiation stimuli adapted to clinical application".</p>
Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika
<p><span>The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in the virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the achromatic environment with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth-related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability, and 11 sites that may be functionally important on the basis of their </span><span>physicochemical properties. Among the strongest candidate sites for deep-water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is th first compralehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.</span></p>
Code and data from: Competition among small individuals hinders adaptive radiation despite ecological opportunity
<p>Ontogenetic diet shifts, where individuals change their resource use during development, are the rule rather than the exception in the animal world. Here, we aim to understand how such changes in diet during development affect the conditions for an adaptive radiation in the presence of ecological opportunity. We use a size-structured consumer–resource model and the adaptive dynamics approach to study the ecological conditions for speciation. We assume that small individuals all feed on a shared resource. Large individuals, on the other hand, have access to multiple food sources on which they can specialize. We find that competition among small individuals can hinder an adaptive radiation to unfold, despite plenty of ecological opportunity for large individuals. When small individuals experience strong competition for food, they grow slowly and only a few individuals are recruited to the larger size classes. Hence, competition for food among large individuals is weak and there is therefore no disruptive selection. In addition, initial conditions determine if an adaptive radiation occurs or not. A consumer population initially dominated by small individuals will not radiate. On the other hand, a population initially dominated by large individuals may undergo adaptive radiation and diversify into multiple species.</p>
Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats
The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale-dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
Data from: Conservation and convergence of genetic architecture in the adaptive radiation of anolis lizards
<p>The G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk-ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.</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: Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones
<p>Genomic data of 9 clownfish (<em>Amphiprion akallopisos, A. bicinctus, A. melanopus, A. nigripes, A. ocellaris, A. preideraion, A. polymnus, A. sebae, Premnas biaculeatus</em>) species and 1 damselfish species (<em>Pomacentrus moluccensis</em>), presented in " Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones".</p> <p>For each species, the following files are available:</p> <p><strong>Species_genome.fasta</strong>: Genome assembly of the species in fasta format. The genome was obtained using Illumina paired-end reads, following a reference-based method. For more information, please refer to the publication</p> <p><strong>Species_genome.Annotation.gff3</strong>: Structural genome annotation of the species, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Fina gene models were obtained with MAKER2. For more information, please refer to the publication</p> <p><strong>Species_genome.proteins.uniprot.fa</strong>: Predicted protein sequences from the genome assembly of the species, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication</p> <p><strong>Species_genome.transcripts.uniprot.fa</strong>: Predicted coding sequences (CDS) from the genome assembly of the species, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication</p> <p>For <em>Amphiprion ocellaris</em> data, additional to the files presented above, we provided as well the secondary results of the genome assembly using a de novo strategy (Aocellaris_GenomeDeNovo.fasta), its structural annotation (Aocellaris_GenomeDeNovo.Annotation.gff3), and its predicted protein (Aocellaris_GenomeDeNovo.proteins.uniprot.fa) and CDS (Aocellaris_GenomeDeNovo.transcripts.uniprot.fa) sequences. For more information, please refer to the publication</p>
Genomics of cold adaptations in the Antarctic notothenioid fish radiation
<p>Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.</p>
Data from: Diversification dynamics in Caribbean rain frogs (Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation
<p><span>Adaptive radiation</span><span> is proposed to play a key role in generating differences in species richness among lineages and geographic regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analyzing <em>i</em>) the temporal patterns of diversification of Caribbean <em>Eleutherodactylus</em> frogs, and <em>ii</em>) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of <em>Eleutherodactylus</em> differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation, which gradually decreases towards the present. <em>Eleutherodactylus</em> diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, <em>Eleutherodactylus</em> shows higher carrying capacity. Our results indicate that ecological opportunity <em>per se</em> is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.</span></p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.