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247 results for “genetic integration”
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data
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Data from: Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population
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Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone
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Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation
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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
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Literature compilation for: The rise of animal biotelemetry and genetics research data integration
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Data from: Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range
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A machine learning approach to integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning
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Genetic barcoding of museum eggshell improves data integrity of avian biological collections
<p>Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird's egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen's appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species' accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.</p>
Data from: Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data
Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.
Data from: Polyandry and polygyny in a social rodent: an integrative perspective based on social organization, copulations, and genetics
Animal mating systems have fascinated biologists for thousands of years. Ways to describe amating systeminclude determining social organization, observing copulations, or using genetics to assign parentage. Social organization can be difficult to quantify, however, documentation of copulations is often challenging, many copulations do not produce offspring, and genetic variation is sometimes minimal. Here we use data from a 7-year study of wild white-tailed prairie dogs (WTPDs, Cynomys leucurus) living in Colorado USA to estimate the frequencies of polyandry (i.e., copulation with ≥2 males) and polygyny (i.e., copulation with ≥2 females) from three independent approaches: (1) determination of the number of males and females living in the same territory (social organization); (2) observations of copulations; and (3) genetic assignments of paternity from seven polymorphic microsatellites. We predicted that our three approaches would yield similar estimates of polyandry and polygyny. Because a WTPD female's period of sexual receptivity each spring is limited to several hours on a single day, we also predicted that frequencies of polyandry and polygyny would be lower for WTPDs than for animals with longer periods of receptivity. Our results did not support these predictions. For polyandry, observations of copulations and genetics indicated similar overall percentages (27%), but social organization indicated a much lower percentage (2%). For polygyny, observations of copulations indicated the highest overall percentage (84%), then social organization (59%), then genetics (46%). All three approaches showed striking annual variation in the frequencies of WTPD polyandry and polygyny. Long-term studies that integrate behavioral and genetic insights can provide a detailed view of a mating system, but feasibility will depend on ease of capture, visibility of copulations, length of mating season, research objectives, and genetic variation.
Data from: Integrating genetic analysis of mixed populations with a spatially-explicit population dynamics model
Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement in an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses. Incorporation of prior information about stock abundance and movement resulted in more precise and plausible estimates of mixture compositions in time and space. Inclusion of a population dynamics model also allowed robust interpolation of expected catch composition at areas and times with no genetic observations. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.
Maintaining genetic integrity with high promiscuity: Frequent hybridization with low introgression in multiple hybrid zones of Melocactus(Cactaceae)
<p>Hybridization and introgression between species in contact/hybrid zones provide important insight into the genetic and ecological mechanisms of speciation. Cactaceae represents the most important radiation of true succulent angiosperms in the New World. This diversification continues to date, with species experiencing few intrinsic barriers to gene flow and the frequent occurrence of natural hybridization. Here, we used RAD-Seq single-nucleotide polymorphism (SNP) data to investigate the genetic architecture of hybridization in four hybrid zones hosting Melocactus concinnus and four congeneric species (M. ernestii, M. glaucescens, M. paucispinus, and M. zehntneri). Our results revealed that M. concinnusis highly promiscuous in sympatric areas and hybridizes with various species distributed in Morro do Chapéu (Diamantina Plateau, Bahia), eastern Brazil. However, the contemporary genomic introgression among the investigated species is very low (c. 2–5%), confirming that even in the face of hybridization, Melocactus species maintain their genetic integrity. The genomic cline approach showed a large fraction of loci deviating from a model of neutral introgression, where most of the loci are consistent with selection favoring parental genotypes. Our results suggest the occurrence of weak premating but strong <br> postmating reproductive isolation in the analyzed cactus species. Furthermore, as most of the Melocactus species are restricted in distribution, hybridization might negatively affect their integrity if hybrids replace the parental species.</p>
Data from: Approaches to integrating genetic data into ecological networks
As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rican dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci e.g. from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally for mixed templates such as faecal contents of insectivorous bats we use DNA metabarcoding targeting two sequence lengths (157bp, 407bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse and we discuss the implications of this type of resolution on network analysis. Using these data we construct the first molecular-based network of networks containing 3304 interactions between 762 nodes of 8 trophic functions and involving parasitic, mutualistic, and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture
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SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
<p><i>Malus sylvestris</i> (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry and urbanization increasingly endanger <i>Malus sylvestris </i>natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple <i>Malus ×domestica</i> (Borkh.), threatens the genetic integrity of <i>M. sylvestris</i>.</p> <p>The present study investigated the number of hybrids, genetic diversity and genetic structure of 292 putative <i>M. sylvestris</i> that originate from five different natural <i>M. sylvestris</i> populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony.</p> <p>Eighty-seven percent of the wild apple accessions were identified as pure <i>M. sylvestris</i>. The cpDNA analysis showed six private haplotypes for <i>M. sylvestris,</i> whereas three haplotypes were present in <i>M. sylvestris </i>and<i> M. ×domestica.</i> The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure <i>M. sylvestris</i> and <i>M. ×domestica </i>individuals indicating a low gene flow between both species. The genetic diversity within the pure <i>M. sylvestris</i> populations was high with a weak genetic structure between the <i>M. sylvestris</i> populations indicating an unrestricted genetic exchange between these <i>M. sylvestris</i> populations.</p> <p>The clear distinguishing of <i>M. sylvestris</i> and <i>M. ×domestica</i> confirms our expectation of the existence of pure <i>M. sylvestris </i>accessions<i> </i>in this area and supports the argument for the implementation of preservation measures to protect the <i>M. sylvestris </i>populations in<i> </i>Saxony. </p>
FIGURE 9 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 9. Dextral lateral views of specimens of T. catalanensis (A, SMF 100093) indicating inguinal (left arrow) and axillary (right arrow) folds, compared with T. etheridgei (B, SMF 87389), which lacks these folds.
FIGURE 8 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 8. Differences in the mucronation of dorsal scales of Tropidurus catalanensis (above, SMF 100091) and T. torquatus (below, SMF 100097).
FIGURE 5 in Diversity of Tropidurus (Squamata: Tropiduridae) in Paraguay-an integrative taxonomic approach based on morphological and molecular genetic evidence
FIGURE 5. Maximum Likelihood (left) and Bayesian (right) trees inferred using concatenated mitochondrial (16S and COI) and nuclear (PRLR) DNA genes for samples of Tropidurus from Paraguay. Support values on nodes represent SH-aLRT/ UFBoot (in percentages) for ML (only values above 65 are shown), and posterior probability for BI (only values above 70 are shown). See Appendix 3 and Figure 1 for geographic location of samples. Reference bar represents substitutions per site.
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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.