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479 results for “genomic evolution”
Hard edges, soft edges, and species range evolution: A genomic analysis of the Cumberland Plateau salamander
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Insights from the timber rattlesnake (<em>Crotalus horridus</em>) genome for MHC gene architecture and evolution in threatened rattlesnakes
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Data for: Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae
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Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
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Data from: Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies
<p>Sex chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inferences. Rapidly evolving complex sex chromosome systems represent a rare opportunity to study the mechanisms of sex chromosome evolution at unprecedented resolution. Three cryptic species of wood white butterflies – <i><span>Leptidea juvernica</span></i>, <i><span>L. sinapis</span></i>, and <i><span>L. reali</span></i> – have each a unique set of multiple sex chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridization (array-CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in <i><span>L. juvernica</span></i>, we identified Z-linked <i><span>Leptidea</span></i> orthologs of <i><span>Bombyx mori</span></i> genes and mapped them by fluorescence <i><span>in situ</span></i> hybridization (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex chromosomes. In addition, we identified W-homologs of Z-linked orthologs and characterized their molecular differentiation. Our results suggest that the multiple sex chromosome system evolved in a common ancestor of these three <i><span>Leptidea</span></i> species as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations and fissions. Thus, the sex chromosome turnover could not play a role in reproductive isolation between the <i><span>Leptidea </span></i>species studied. However, we suggest that subsequent species-specific rearrangements of multiple sex chromosomes, along with different rates of neo-W chromosome degeneration and significantly increased number of Z-linked genes could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.</p>
Data from: Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs
<p>The blue king crab, <i>Paralithodes platypus</i>, which belongs to the Lithodidae family, is a commercially and ecologically important species. However, a high-quality reference genome for the king crab has not yet been reported. Here, we assembled the first chromosome-level blue king crab genome, which contains 104 chromosomes and an N50 length of 51.15 Mb. Furthermore, we determined that the large genome size can be attributed to the insertion of long interspersed nuclear elements and long tandem repeats. Genome assembly assessment showed that 96.54% of the assembled transcripts could be aligned to the assembled genome. Phylogenetic analysis showed the blue king crab to have a close relationship with the Eubrachyura crabs, from which it diverged 272.5 million years ago. Population history analyses indicated that the effective population of the blue king crab declined sharply and then gradually increased from the Cretaceous and Neogene periods, respectively. Furthermore, gene families related to developmental pathways, steroid and thyroid hormone synthesis, and inflammatory regulation, were expanded in the genome, suggesting that these genes contributed substantially to the environmental adaptation and unique body plan evolution of the blue king crab. The high-quality reference genome reported here provides a solid molecular basis for further study of the blue king crab's development and environmental adaptation.</p>
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution
<p>The reissner lamprey<i> Lethenteron reissneri</i> belonging to Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the most direct ancestor of vertebrates. However, the genetic mechanisms underlying the adaptive evolution of lampreys remain unclear. Here, we supplied the genome data and annotation data of <em>Lethenteron reissneri</em>. Total 5 files were uploaded, including the assembled genome of <i>Lethenteron reissneri</i>, the gene annotation file in gff format, the gene function annotation file, the LIP gene sequences of 50 species used in the article, and the readme file. This study not only provides the first chromosome-level reference genome in Cyclostomata, but also indicates the unique biology and adaptive evolution of lampreys.</p>
The tepary bean genome provides insight into evolution and domestication under heat stress
<p>Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Analysis of the tepary genome revealed mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid, hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.</p>
Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure
<p>Physiological states can determine the ability of organisms to handle stress. Does this mean that the same selection pressure will lead to different evolutionary outcomes, depending on the organisms' physiological state? If yes, what will be the genomic signatures of such adaptation(s)? We used experimental evolution in <i>Escherichia coli</i> followed by whole-genome whole-population sequencing to investigate these questions. The sensitivity of <i>Escherichia coli</i> to ultraviolet (UV) radiation depends on the growth phase during which it experiences the radiation. We evolved replicate <i>E. coli</i> populations under two different conditions of UV exposures, namely exposure during the lag and the exponential growth phases. Initially, the UV sensitivity of the ancestor was greater during the exponential phase than the lag phase. However, at the end of 100 cycles of exposure, UV resistance evolved to similar extents in both treatments. Genome analysis showed that mutations in genes involved in DNA repair, cell membrane structure and RNA polymerase were common in both treatments. However, different functional groups were found mutated in populations experiencing lag and exponential UV treatment. In the former, genes involved in transcriptional and translational regulations and cellular transport were mutated, whereas the latter treatment showed mutations in genes involved in signal transduction and cell adhesion. Interestingly, the treatments showed no phenotypic differences in a number of novel environments. Taken together, these results suggest that selection pressures at different physiological stages can lead to differences in the genomic signatures of adaptation, which need not necessarily translate into observable phenotypic differences.</p>
Data from: Evolution of sociality in spiders leads to depleted genomic diversity at both population and species level
Across several animal taxa, the evolution of sociality involves a suite of characteristics, a 'social syndrome', that includes cooperative breeding, reproductive skew, primary female biased sex-ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genome-wide diversity in spider species that differ in level of sociality, reproductive skew, and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within population diversity were 6-10 fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genome-wide diversity, likely to limit their evolutionary potential.
Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)
Premise of Study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated ten transcriptomes and incorporated existing RNA-seq data to infer a multi-locus nuclear phylogeny of the Cypripedioideae and to determine if a whole genome duplication event (WGD) correlated to the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. Methods: Transcriptome data was used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. Key results: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. Conclusions: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.
Data from: Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous non-biological models in parallel at reasonable cost, particularly with shotgun sequencing. Here we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies - swallowtails of the family Papilionidae - that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6,621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced dataset (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 million years ago (Ma) (95% credibility interval: 68.6-142.7 Ma) and Papilionidae around 71.4 Ma (49.8-103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
Data from: Molecular cytogenetic and genomic insights to chromosomal evolution
This review summarizes aspects of the extensive literature on the patterns and processes underpinning chromosomal evolution in vertebrates and especially placental mammals. It highlights the growing synergy between molecular cytogenetics and comparative genomics, particularly with respect to fully or partially sequenced genomes, and provides novel insights into changes in chromosome number and structure across deep division of the vertebrate tree of life. The examination of basal numbers in the deeper branches of the vertebrate tree suggest a haploid (n) chromosome number of 10–13 in an ancestral vertebrate, with modest increases in tetrapods and amniotes most probably by chromosomal fissioning. Information drawn largely from cross-species chromosome painting in the data-dense Placentalia permits the confident reconstruction of an ancestral karyotype comprising n=23 chromosomes that is similarly retained in Boreoeutheria. Using in silico genome-wide scans that include the newly released frog genome we show that of the nine ancient syntenies detected in conserved karyotypes of extant placentals (thought likely to reflect the structure of ancestral chromosomes), the human syntenic segmental associations 3p/21, 4pq/8p, 7a/16p, 14/15, 12qt/22q and 12pq/22qt predate the divergence of tetrapods. These findings underscore the enhanced quality of ancestral reconstructions based on the integrative molecular cytogenetic and comparative genomic approaches that collectively highlight a pattern of conserved syntenic associations that extends back ~360 million years ago.
Data from: Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)
Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and FST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.
Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation". Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated chromosome rearrangements. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, chromosome rearrangements impact multiple cellular processes and these effects need to be considered together, along with those of genic divergence. Understanding the effects of chromosome rearrangements together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
Data from: Evolution of floral diversity: genomics, genes and gamma
A salient feature of flowering plant diversification is the emergence of a novel suite of floral features coinciding with the origin of the most species-rich lineage, Pentapetalae. Advances in phylogenetics, developmental genetics and genomics, including new analyses presented here, are helping to reconstruct the specific evolutionary steps involved in the evolution of this clade. The enormous floral diversity among Pentapetalae appears to be built on a highly conserved ground plan of five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast, lability in the number and arrangement of component parts of the flower characterize the early-diverging eudicot lineages subtending Pentapetalae. The diversification of Pentapetalae also coincides closely with ancient hexaploidy, referred to as the gamma whole-genome triplication, for which the phylogenetic timing, mechanistic details and molecular evolutionary consequences are as yet not fully resolved. Transcription factors regulating floral development often persist in duplicate or triplicate in gamma-derived genomes, and both individual genes and whole transcriptional programmes exhibit a shift from broadly overlapping to tightly defined expression domains in Pentapetalae flowers. Investigations of these changes associated with the origin of Pentapetalae can lead to a more comprehensive understanding of what is arguably one of the most important evolutionary diversification events within terrestrial plants.
Data from: Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers
Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates.
Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.
Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus. We found that a genomic region consistently governs variation in several of the traits that distinguish these contrasting forms. Additionally, some of the taxon specific traits controlled by this QTL cluster have evolved repeatedly during the adaptation to the same habitats, suggesting that it could mediate divergence between locally adapted forms. This cluster contains footprints of divergent natural selection across the range of S. lautus, which suggests that it could have been instrumental for the rapid diversification of this species.
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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.