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183 results for “Genome conservation”
Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation
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Dataset for: Conservation genomics of federally endangered Texella harvester species (Arachnida, Opiliones, Phalangodidae) from cave and karst habitats of central Texas
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Data from: From promise to practice: pairing non-invasive sampling with genomics in conservation
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Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation
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Data from: Conservation of the genome-wide recombination rate in white-footed mice
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Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
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Data from: Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers
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Data from: Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations
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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
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Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation
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Data from: Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north-western Pacific Acropora digitifera
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Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
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Data From: Characterizing patterns of genomic variation in the threatened Utah prairie dog: implications for conservation and management
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Conservation genomic analysis of the Croatian indigenous Black Slavonian and Turopolje pig breeds
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Hibiscus nextRAD-seq conservation genomics
<p>The Neches River Rose Mallow (<i>Hibiscus dasycalyx</i>) is a rare wildflower endemic to Texas that is federally protected in the US. While previous work suggests that <i>H. dasycalyx</i> may be hybridizing with its widespread congeners, the Halberd-leaved Rose Mallow (<i>H. laevis</i>) and the Wolly Rose Mallow (<i>H. moscheutos</i>), this has not been studied in detail. We evaluated the relative threats to <i>H. dasycalyx</i> posed by hybridization with <i>H. laevis</i> and <i>H. moscheutos</i> by 1) examining their relatedness to one another via modern phylogenomic methods, 2) examining the species' ecological (dis)similarities to one another using ecological niche modeling, and 3) looking for genomic evidence of hybridization among the three species. Our results suggest that <i>H. dasycalyx</i> is very closely related and ecologically similar to <i>H. laevis</i>, and suggest that <i>H. laevis</i> is interbreeding with <i>H. dasycalyx</i> in the wild. Conversely, <i>H. moscheutos</i> appears to be more distantly related to <i>H. dasycalyx</i> and more ecologically dissimilar, and the two are most likely not hybridizing. For these reasons, we believe that <i>H. laevis</i> poses a greater threat to <i>H. dasycalyx</i> than <i>H. moscheutos</i>. We offer some hypotheses as to why <i>H. dasycalyx</i> and <i>H. laevis</i> are coming into secondary contact where hybridization can occur.</p>
Data from: Using genomic tools to maintain diversity and fitness in conservation programmes
Conservation programmes aim at maximising the survival probability of populations, by minimising the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimising the contributions of the parents, to minimise global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers is available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.
Data from: Whole-genome sequencing approaches for conservation biology: advantages, limitations, and practical recommendations
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq), and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in non-model species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons, and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g. structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently though, no single WGR approach fulfills all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many non-model species and fields including conservation biology.
Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes under Selection in Chinese Indigenous Pigs in the Taihu Lake Region
<p>Chinese indigenous pig breeds in the Taihu Lake region (TH) of Eastern China are well-recognized for their exceptional prolificacy. These breeds including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI) and Hongdenglong (HDL). At present, these breeds are facing a great threaten of population decline, lineage admixture and inbreeding depression since Western commercial pigs have dominated Chinese pig industry. To provide better conservation schemes and identify candidate genes under selection for these breeds, we explored genome-wide SNP markers to unravel genetic variability and relatedness, population structure, historical admixture and genomic signatures of selection of 440 pigs representing the most comprehensive lineages of these breeds in TH in a context of 1228 pig from 45 Eurasian breeds.<b> </b>We showed that these breeds were more closely related among each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two regional subgroups, one including JXB and FJ pigs, and the other comprising EHL, MI, HDL, MS and SWT pigs. In additional, HDL pigs were highly inbred, whereas EHL and MS pigs had more abundant genetic diversity. This is attributable to multiple conservation populations of the two breeds. Moreover, we identified a list of candidate genes for body size and prolificacy at the loci putatively under selection. our results would benefit the sustainable conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.</p>
Data from: Inbreeding and selection shape genomic diversity in captive populations: implications for the conservation of endangered species
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.