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315 results for “gene diversity”
VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes
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Habitats and environmental variables investigated in a diversity survey on Polynucleobacter bacteria revealed by amplicon sequencing of priB genes
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Sequential introgression of a carotenoid processing gene underlies sexual ornament diversity in a genus of manakins
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Data for: Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma
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Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
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FIGURE 1 in Uncovering a hidden diversity: a new species of freshwater shrimp Macrobrachium (Decapoda: Caridea: Palaemonidae) from Neotropical region (Brazil) revealed by morphological review and mitochondrial genes analyses
FIGURE 1. Characterization and location of the São Francisco river basin in Brazil. The red border indicates the location of Grande Sertão Veredas National Park and the distribution range of Macrobrachium veredensis sp. nov. Modified from MMA 2006 and ANA 2016.
Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype
<p><span><span>Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident </span><span><span>European </span></span><span>brook lamprey (</span><i><span><span>Lampetra planeri</span></span></i><span>) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) a </span><span><span>positive effect of</span></span><span> admixture with the closely related anadromous</span><span><span> river lamprey</span></span><span> (</span><i><span><span>L. fluviatilis</span></span></i><i><span><span>)</span></span></i><span> ecotype on </span><i><span><span>L. planeri</span></span></i><span> genetic diversity. We genotyped 2472 individuals, including 225 </span><i><span><span>L. fluviatilis</span></span></i><span>, sampled </span><span><span>from</span></span><span> 81 sites upstream and downstream barriers to migration, in 29 </span><span><span>western </span></span><span>European rivers. Linear modelling revealed a strong positive relationship between </span><span><span>genetic diversity and</span></span><span> the distance </span><span><span>from </span></span><span><span>the</span></span><span><span> river</span></span><span> source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal </span><span><span>mediated by</span></span><span> water flow. Downstream </span><i><span><span>L. planeri </span></span></i><span>populations in sympatry with </span><i><span><span>L. fluviatilis </span></span></i><span>displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic </span><span><span>make-</span></span><span>up of upstream </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>whereas admixture between ecotypes maintains higher levels of genetic diversity in </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>sympatric</span><i><span> </span></i><span>with </span><i><span><span>L. fluviatilis</span></span></i><span>. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks. </span></span></p>
The evolution of hemocyanin genes in Tectipleura - a multitude of conserved introns in highly diverse gastropods
<p><strong>Background</strong>: Hemocyanin is the oxygen transporter of most molluscs. Thus, it is an essential protein of these animals which needs to be adapted perfectly to their environments. In Tectipleura, which is a very large and diverse gastropod group with >27,000 species living in all kinds of habitats, several hemocyanin genes have already been identified. They evolved independently from each other within different lineages due to multiple gene duplications and represent potential adaptations to different environments or lifestyles. The aim of this study is to explore the evolution of these genes by analyzing their exon-intron architectures for characteristic features indicating adaptations.</p> <p><strong>Results</strong>: We reconstructed gene architectures of ten hemocyanin genes of four species of Tectipleura: (i) Aplysia californica (ii) Lymnaea stagnalis (iii) Cornu aspersum and (iv) Helix pomatia . Their hemocyanin genes comprise 53 introns each, which is conspicuously more than in known hemocyanin genes of Cephalopoda (9-11), Vetigastropoda (15) and Caenogastropoda (28-33). The gene structures of Tectipleura hemocyanins are identical in terms of number and locations of the introns with exception of only one hemocyanin of Lymnaea stagnalis that comprises one additional intron. Deeper analyses reveal that introns which vary between gene structures of different molluscan lineages most probably evolved more recently through independent intron gains.</p> <p><strong>Conclusions</strong>: The strong conservation of the large number of introns in hemocyanin genes in Tectipleura for over 200 million years suggests a selective pressure on the gene structure. While we have not found characteristic positions or sequence motifs of introns that are conserved, it may be simply the great number of introns that offers increased possibilities of gene regulation and thus may facilitate habitat shifts, adaptive radiation and speciation. This hypothesis is supported by the increased number of introns within hemocyanin genes of Pomacea canaliculata which evolved independently from those of Tectipleura. This species belongs to Caenogastropoda, the sister group of Heterobranchia (where Tectipleura belong to) which is also very diverse and comprises species living in different habitats. Thus, our study provides first evidence that a multitude of introns may contribute to adaptive gene diversity of animals.</p>
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Data from: Mining for NRPS and PKS genes revealed a high diversity in the Sphagnum bog metagenome
Sphagnum bog ecosystems are among the oldest vegetation forms harboring a specific microbial community and are known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome shows a rich secondary metabolism, the genes have not yet been explored. To analyze nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), the diversity of NRPS and PKS genes in Sphagnum-associated metagenomes was investigated by in silico data mining and sequence-based screening (PCR amplification of 9,500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid gene sequences. The occurrence of NRPS sequences was strongly dominated by the members of the Protebacteria phylum, especially by species of the Burkholderia genus, while PKS sequences were mainly affiliated with Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR amplification screening, displaying amino acid identities of 48% to 91% to annotated sequences of members of the phyla Proteobacteria, Actinobacteria, and Cyanobacteria. Some of the identified metagenomic clones showed the closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of as-yet-undescribed bioactive metabolites. This report highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications.
Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.
Data from: Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species
Heteroecious holocyclic aphids exhibit both sexual and asexual reproduction and alternate among primary and secondary hosts. Most of these aphids can feed on several related hosts, and invasions to new habitats may limit the number of suitable hosts. For example, the aphid specialist Aphis glycines survives only on the primary host buckthorn (Rhamnus spp.) and the secondary host soybean (Glycine max) in North America where it is invasive. Owing to this specialization and sparse primary host distribution, host colonization events could be localized and involve founder effects, impacting genetic diversity, population structure and adaptation. We characterized changes in the genetic diversity and structure across time among A. glycines populations. Populations were sampled from secondary hosts twice in the same geographical location: once after secondary colonization (early season), and again immediately before primary host colonization (late season). We tested for evidence of founder effects and genetic isolation in early season populations, and whether or not late-season dispersal restored genetic diversity and reduced fragmentation. A total of 24 single-nucleotide polymorphisms and 6 microsatellites were used for population genetic statistics. We found significantly lower levels of genotypic diversity and more genetic isolation among early season collections, indicating secondary host colonization occurred locally and involved founder effects. Pairwise FST decreased from 0.046 to 0.017 in early and late collections, respectively, and while genetic relatedness significantly decreased with geographical distance in early season collections, no spatial structure was observed in late-season collections. Thus, late-season dispersal counteracts the secondary host colonization through homogenization and increases genetic diversity before primary host colonization.
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: Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on males and females. If such conflict is pervasive, it could potentially lead to genomic heterogeneity in levels of genetic diversity an idea that so far has not been empirically tested on a genome-wide scale. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sexual conflict, for which we use sex-biased gene expression as a proxy, relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to diversity levels also in intergenic DNA and introns. We find signatures of balancing selection in sex-biased genes but also note that relaxed purifying selection could potentially explain part of the observed patterns. The finding of significant genetic differentiation between males and females for male-biased (and gonad-specific) genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus indicate that sexual antagonism could potentially be considered as one viable explanation to the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.
Data from: Contracting patterns of diversity and population differentiation at the innate immunity gene Toll-like receptor 2 (TLR2) in two sympatric rodent species
Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defence may be evolutionarily more dynamic than has previously been appreciated.
Data from: Recent population decline and selection shape diversity of taxol-related genes
Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane related genes are unknown. We examined variation at five main taxol-related genes of T. baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site-frequency spectrum and Zeng's compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT, and balancing selection for DBAT. In addition, neutrality tests based on site-frequency spectrum found that while a recent reduction in population size may explain most of statistics' values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defense-related genes. Such natural selection processes may have produced taxane variants still undiscovered.
Data from: Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicates potential for spread of herbicide resistance via gene flow
Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggests the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.
Lower St. Lawrence Estuary bacterial 16S rRNA gene diversity
<p>The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is among the largest and most productive coastal ecosystems in the world.<b> </b>Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modeling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free-living or particle-associated). Assemblages from the upper waters represent sets of co-occurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters., and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically-active bacterial community that is compositionally distinct compared to surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine Myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.</p>
Data from: Patterns of diversity and spatial variability of β-defensin innate immune genes in a declining wild population of tree swallows
Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.
Data from: High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations
Range expansion is a widespread biological process, with well described theoretical expectations for the genomic outcomes accompanying the colonization of novel ranges. However, comparatively few empirical studies address the genome-wide consequences associated with the range expansion process, particularly in recent or on-going expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction enzyme assisted sequencing approach (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well-publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts.
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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.
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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.
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