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675 results for “Introgression”
Data from: Translocation precipitates natural hybridisation and pervasive introgression between marine gastropods with divergent developmental modes
<div> <div> <div> <p>Assisted colonisation, the introduction of species beyond their historical range, is increasingly necessary for conserving species. However, empirical evidence of the long-term genetic outcomes of assisted colonisation is grossly lacking. A risk associated with moving species beyond their native range is the possibility of interspecific hybridisation with a closely related species, potentially resulting in outbreeding depression or the genetic swamping of a parental species. Here, we use a combination of genome-wide Single Nucleotide Polymorphism (SNP) markers and mitochondrial DNA sequencing to determine the long-term genetic consequences of introducing the intertidal periwinkle <em>Bembicium vittatum</em> (a direct developer) beyond its native range and into the native range of its congener <em>Bembicium auratum</em> (a species with planktotrophic larval dispersal). We found novel evidence of natural, multigenerational hybridisation between marine invertebrates with different modes of development. Intriguingly, introgression was highly asymmetrical initially, but became more evenly bidirectional as the population became more admixed. There was a significant decline in the frequency of alleles from the introduced <em>B. vittatum</em> over time, providing evidence of genetic swamping. The present study also provides potential evidence of outbreeding depression, in the form of cytonuclear incompatibilities, leading to the observed pattern of asymmetrical introgression. This study reveals the potential for unexpected mixing between species when reproductive barriers are not well understood, resulting in failure of pure <em>B. vittatum</em> to persist at the translocation site, a major concern associated with assisted colonisation. Without long-term genetic monitoring interspecific hybridisation between <em>B. vittatum</em> and <em>B. auratum</em> would have gone undetected, highlighting the importance of long-term monitoring to detect unintentional negative consequences of conservation translocations. Successful assisted colonisation requires an understanding of the potential for interspecific hybridisation between the threatened species and closely related native species, to reduce the risk of adverse outcomes.</p> </div> </div> </div>
Helperfiles for using hmmix for calling archaic introgression into present day humans (both hg19 and hg38)
<p>These files are:</p> <p>1) Strict callability masks from 1000 genomes project in hg19 and hg38 coordinates</p> <p>2) Outgroup files:</p> <p>hg38_Outgroup_1000g_HGDP.txt: Frequencies of derived alleles in 490 present individuals with Sub-Saharan related ancestry: 426 from 1000genomes project and 64 from HGDP (total=490) Only first two columns are used by hmmix. The remaining columns what the reference base (hg38 refgenome), ancestral base, derived bases and the frequency of the derived bases in HGDP and 1000genomes</p> <p>hg19_Outgroup_1000g.txt: Frequencies of derived alleles in 292 present individuals with Sub-Saharan related ancestry from 1000genomes</p> <p>3) The mutation rate files are based on the outgroup files. They report the mutation rate in 1 Mb window scaled by the genomewide mutation rate </p> <p>4) The reference genome for hg19 and hg38</p> <p>5) The ancestral allele calls for hg19 and hg38</p>
Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
<p>Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera <em>Crotalus</em> and <em>Sistrurus</em>), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.</p> <p>La filogenómica nos permite descubrir la señal histórica de los procesos evolutivos a través del tiempo y estimar redes filogenéticas tomando en cuenta estas señales. El conocimiento de datos genómicos incluso permiten distinguir la contribución de la señal filogenética de la hibridación, introgresión, y de polimorfismos ancestrales a lo largo del genoma. En este trabajo nos enfocamos en como estos procesos han contribuido a la discordancia filogenética entre las serpientes de cascabel, un grupo en el que hay numerosos conflictos en las hipótesis filogenéticas obtenidas de un grupo variado de datos moleculares y métodos analíticos. Nosotros abordamos la inestabilidad de la filogenia de las serpientes de cascabel (generos <em>Crotalus</em> y <em>Sistrurus</em>) usando datos genómicos generados de transcriptomas muestreados en la mayoría de las especies conocidas. Estos datos genómicos, analizados con métodos basados en coalescencia y redes filogenéticas, revelaron numerosos casos de especiación rápida donde los arboles de genes individuales conflictúan con el árbol de especies. Además, la historia evolutiva de las serpientes de cascabel esta dominada por una especiación incompleta y una frecuente hibridación, las cuales probablemente han influenciado interpretaciones pasadas de las filogenias. Nosotros presentamos un nuevo marco en el que las relaciones evolutivas de este grupo solo pueden ser entendidas en base a datos de genomicos y métodos analíticos basados en redes filogenéticas. Nuestros datos sugieren que la radiación en redes filogenéticas, como se ha visto dentro de las serpientes de cascabel, solo puede ser entendida en un contexto filogenómico, necesitando aproximaciones similares en nuestro intento de entender la historia evolutiva en otras especies con radiaciones rápidas.</p>
Data for: Whole genome phylogeny of Gallus: Introgression and data-type effects
<p>Multiple sequence alignments and gene trees from the manuscript "Whole genome phylogeny of Gallus: Introgression and data-type effects." The zip file contains a single folder with a README file that provides details the contents and formats of the files that are included.</p>
Figure 1 in Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach
Figure 1. Backcrossing program used in this study to develop improved lines of rice (BC F ).
Data from: Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea)
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggests that strong enough divergent selection can overpower gene flow, leading to islands of divergence. However, there are alternative explanations for these patterns. Independent evidence that islands of divergence are due to divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here we present multiple lines of evidence that islands of divergence in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the outcome of divergent selection in the face of gene flow. We analyzed a SNP dataset across the genome to assess the amount of gene flow, resistance to introgression, and patterns of selection on genes resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with gene flow between the species in sympatry. In addition, highly differentiated SNPs were subject to divergent selection. Finally, despite gene flow in sympatry, SNPs that are highly differentiated in allopatry are resistant to homogenization in sympatry. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
Data from: Genomic architecture and introgression shape a butterfly radiation
We probe the history of rapidly radiating Heliconius butterflies by means of 20 new genome assemblies and employ them to investigate the genomic architecture of gene flow among lineages. By developing a test to distinguish incomplete lineage sorting from introgression, we demonstrate that histories of loci that differ from the species tree arose mostly through introgression. Moreover, these loci are underrepresented in low recombination and gene-rich regions, consistent with the purging of introgressed alleles tightly linked with incompatibility loci. Additionally, our analysis identifies an inversion that captures a color pattern switch locus which was transferred between lineages via introgression and is convergent with a similar rearrangement in another part of the genus. This analysis of multiple de novo genome sequences enables an improved understanding of the importance of introgression and selective processes in adaptive radiation.
Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima
<p>Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion, and influence evolution as selective pressures force adaption. Such disasters occurred on March 11th 2011, in Fukushima, Japan when an earthquake, tsunami, and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Here, we demonstrate, using genetic data, how wild boar (<em>Sus scrofa leucomystax</em>) have persevered against these environmental changes, including an invasion of escaped domestic pigs (<em>Sus scrofa domesticus</em>). Concurrently, we show evidence of successful hybridization between pigs and native wild boar in this area, however in future offspring, the pig legacy has been diluted through time. We speculate that the range expansion dynamics inhibit long-term introgression and introgressed alleles will continue to decrease at each generation while only maternally inherited organelles will persist. Using the gene flow data among wild boar, we assume that offspring from hybrid lineages will continue dispersal north at low frequencies as climates warm. We conclude that future risks for wild boar in this area include intraspecies competition, revitalization of human related disruptions, and disease outbreaks.</p>
Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies
<p>Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the <i>erato</i>-<i>sara</i> clade of <i>Heliconius</i> butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the <i>sara</i> clade and an ancestral population of <i><span>H. telesiphe</span></i>, a likely hybrid speciation origin for <i>H. hecalesia</i>, and gene flow between the sister species <i><span>H. erato</span></i><span> and <i>H. himera</i></span>. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.</p>
Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution
<p>In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism, and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes that interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes, the sex chromosomes) move through time and space.</p>
Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones
<p>The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognised pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or <em>de</em> <em>novo</em> mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six <em>Triturus</em> newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of <em>Triturus</em> species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple <em>Triturus</em> hybrid zones, indicating that MHC introgression between divergent hybridising species may be widespread and adaptive.</p>
Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas
<p>In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (<i>Periparus ater</i>) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western 'spot-winged tit' (<i>P. a. melanolophus</i>) and e<span class="msoDel">E</span>astern Himalayan coal tits (<i>P. a. aemodius</i>) occur across a narrow range of less than 100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern <i>P. a. aemodius</i> into far western populations of phenotypic <i>P. a. melanolophus</i> but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.</p>
Unraveling the myotis norass: Ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
<p>Using sequences from 2615 UCE loci and multiple methodologies we inferred phylogenies for the largest genetic dataset of New World Myotis to date. The resulting phylogenetic trees were populated with short branch lengths and widespread conflict, hallmarks consistent with rapid adaptive radiations. The degree of conflict observed in Myotis has likely contributed to difficulties disentangling deeper evolutionary relationships. Unlike earlier phylogenies based on 1-2 gene sequences, this UCE dataset places M. brandtii outside the New World clades. Introgression testing of a small subset of our samples revealed evidence of historical but not contemporary gene flow, suggesting that hybridization occurs less frequently in the Neotropics than in the Nearctic. We identified several instances of cryptic lineages within described species as well as several instances of potential taxonomic over-splitting. Evidence from Central and South American localities suggests that diversity in those regions is not fully characterized. In light of the accumulated evidence of the evolutionary complexity in Myotis and our survey of the taxonomic implications from our phylogenies it is apparent that the definition of species and regime of species delimitation need to be re-evaluated for Myotis. This will require substantial collaboration and sample sharing between geneticists and taxonomists to build a system that is both robust and applicable in a genus as diverse as Myotis.</p>
Data from: Summary tests of introgression are highly sensitive to rate variation across lineages
<p>The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods is based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the <em>D </em>test (also known as ABBA-BABA test), the <em>D</em><sub>3</sub> test, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and residual variation across gene-tree edges. We do so by simulating gene trees within species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies. For all three methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. The <em>D</em><sub>3</sub> test was the most sensitive, with around 80% type-1 error, such that <em>D</em><sub>3</sub> appears to be more sensitive to a departure from the clock than to the presence of reticulation. For all three tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can obscure one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.</p>
Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome
<p>Abstract</p> <p>A compelling interest in marine biology is to elucidate how species boundaries between sympatric free‐spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single‐nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing. Using 1066 ancestry‐informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual‐level clustering analyses including the principal component analysis, Bayesian model‐based clustering, and triangle plotting based on ancestry–heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast‐spawning molluscs.</p>
Widespread introgression of MHC genes in Iberian Podarcis lizards
<p>Major Histocompatibility Complex (MHC) genes are crucial for the adaptive immune response of jawed vertebrates. Their variation, reaching extreme levels, is driven mainly by an arms race between hosts and pathogens. One hypothesized mechanism contributing to MHC polymorphism is adaptive introgression, the exchange of genetic variants between hybridizing species favoured by selection, yet its effect on MHC variation is poorly understood. Detection of adaptive MHC introgression, though challenging, may be facilitated by the analysis of species complexes forming multiple hybrid zones. Here, we investigated MHC introgression in six hybrid zones formed by seven species of <em>Podarcis</em> lizards inhabiting the Iberian Peninsula. To differentiate adaptive introgression from neutral introgression, we compared the patterns of gene exchange in MHC and genome-wide markers. We found elevated sharing of MHC alleles in the proximity of contact beyond the areas of detectable genome-wide admixture in most hybrid zones and, in half of them, asymmetric MHC exchange. In general, the elevated MHC allele sharing between species pairs with abutting ranges compared to geographically isolated species pairs also supports the prevalence of introgression. Collectively, our results demonstrate widespread MHC introgression in the Iberian <em>Podarcis</em> complex and suggest its adaptiveness. Contrary to previous results from <em>Triturus</em> newts, we did not observe differences in the rate of introgression between MHC classes. Our work adds support to the emerging view of adaptive introgression as a key mechanism shaping MHC diversity. It also raises questions about the effect of elevated MHC variation and factors leading to the asymmetry of adaptive introgression.</p>
Inferring historical introgression with deep learning
<p><span>Resolving the phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample sizes, restricted phylogenetic topologies, or hypothesis testing. To overcome these difficulties, we developed a deep learning-based approach, named ERICA, for inferring genome-wide evolutionary relationships and local introgressed regions from sequence data. ERICA accepts sequence alignments of both population genomic data and multiple genome assemblies, and efficiently identifies discordant genealogy patterns and exchanged regions across genomes when compared with other methods. We further tested ERICA using real population genomic data from Heliconius butterflies that have undergone adaptive radiation and frequent hybridization. Finally, we applied ERICA to characterize hybridization and introgression in wild and cultivated rice, revealing the important role of introgression in rice domestication and adaptation. Taken together, our findings demonstrate that ERICA provides an effective method for teasing apart evolutionary relationships using whole genome data, which can ultimately facilitate evolutionary studies on hybridization and introgression.</span></p>
Data for: Among-species rate variation produces false signals of introgression
<p>The role of interspecific hybridization in the context of diversification dynamics has recently seen increasing attention. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchange of genetic material through hybridization - are far more common than previously thought. Moreover, even highly divergent species were found to hybridize and backcross. These findings raise the question whether commonly used methods for the detection of introgression are applicable to such divergent hybridizing species, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to divergent species, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we were able to show that commonly applied statistical methods, including the D-statistic and tests based on sets of phylogenetic trees, produce false-positive signals of introgression between highly divergent taxa when these have different rates of evolution. These misleading signals are caused by the presence of homoplasies that occur at different rates when rate variation is present. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites and implemented this test in the program Dsuite.</p>
A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle
<p class="MsoNormal"><span>The cattle industry contributes to Uganda's agricultural output. It however faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent developments in genomics and bioinformatics technologies. In the current study, we provided a proof-of-concept conflict resolution method based on the available bovine genomic tools. Briefly, two farmers we refer to as A and B contested for ownership of a group of 9 cattle. To offer objective and data-based guidance to resolving this conflict, we sampled hair samples of the 9 contested cattle as well as 7 and 2 cattle from farmers A and B respectively that were identified by these farmers as the closest relatives of the contested animals. DNA was extracted from each of the collected hair samples and subsequently genotyped on the Illumina BovineSNP50-24 version 3 BeadChip for 53218 DNA Single Nucleotide Polymorphisms (SNP) variants. Upon genotype data cleaning we retained ~30,000 SNPs which were used for different genomic analyses including principal component analysis, identity by state (IBS) analysis, and hierarchical clustering analysis, to establish the genetic relationships within and between the investigated animal groups.</span></p>
ScienceDex guides
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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.