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2,445 results for “Genetics: population”
Data from: Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe
Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech-Slovak border. Even though the population size has been relatively stable over the period studied (2010-2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.
Population fragmentation drives up genetic diversity in signals of individual identity
<p>Many species advertise their unique identity to conspecifics using dedicated individuality signals: one familiar example is human faces. But how unique in the global population do these signals need to be? While human faces are highly variable, each person interacts with many fewer individuals than are found in the total population. This raises the question of how evolutionary mechanisms drive up population-wide diversity when selection occurs at such a local level. We use an individual-based model in which individuals broadcast their identity and quality in separate, genetically-coded signals. Mimicking, for example, scent marking mammal species, females in the model assess males using the quality signal, then attempt to relocate the highest quality male using his identity signal. We ask how population fragmentation affects genetic diversity in the individual identity-signalling region under sexual selection, predicting one of two opposing outcomes: (1) divided populations evolve fewer signal variants globally, since repetition of signals is not costly when individuals interact only with local conspecifics, or (2) stochasticity in mutation and selection cause divergence among subpopulations, increasing the global number of signal variants. We show that local selection drives up global genetic diversity substantially in fragmented populations, even with extremely low rates of dispersal. Because new signal variants arise by mutation and then sweep through their subpopulation, a fragmented population has more global signal variation. This result furthers our understanding of how high levels of diversity in individuality signals are maintained.</p>
Data from: Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus
Body condition is an important determinant of fitness in many natural populations. However, as for many fitness traits, the underlying genes that regulate body condition remain elusive. The dopamine receptor D4 gene (DRD4) is a promising candidate as dopamine is known to play an important role in the regulation of food intake and the metabolism of both glucose and lipids in vertebrates. In this study we take advantage of a large dataset of greater flamingos, Phoenicopterus roseus, to test whether DRD4 polymorphism predicts early body condition (EBC) while controlling for whole genome effects of inbreeding and outbreeding using microsatellite multi-locus heterozygosity (MLH). We typed 670 of these individuals for exon 3 of the homologue of the human DRD4 gene and 10 microsatellite markers. When controlling for effects of yearly environmental variations and differences between sexes, we found strong evidence of an association between exon 3 DRD4 polymorphisms and EBC, with 2.2-2.3% of the variation being explained by DRD4 polymorphism, whereas there was only weak evidence that MLH predicts EBC. Because EBC is most likely a polygenic trait, this is a considerable amount of variation explained by a single gene. This is to our knowledge the first study to show an association between exon 3 DRD4 polymorphism and body condition in nonhuman animals. We anticipate that the DRD4 gene as well as other genes coding for neurotransmitters and their receptors may play an important role in explaining variation in traits that affect fitness.
Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.
Data from: Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing
Though genetic diversity is necessary for population persistence in rapidly changing environments, little is known about how climate-warming influences patterns of intra-population genetic variation. For a pink salmon population experiencing increasing temperatures, we used temporal genetic data (microsatellite = 1993, 2001, 2009; allozyme = 1979, 1981, 1983) to quantify the genetic effective population size (Ne) and genetic divergence due to differences in migration timing and to estimate whether these quantities have changed over time. We predicted that temporal trends toward earlier migration timing and a corresponding loss of phenotypic variation would decrease genetic divergence based on migration timing and Ne. We observed significant genetic divergence based on migration timing and genetic heterogeneity between early- and late-migrating fish. There was also some evidence for divergent selection between early- and late-migrating fish at circadian rhythm genes, but results varied over time. Estimates of Ne from multiple methods were large (>1200) and Ne/Nc generally exceeded 0.2. Despite shifts in migration timing and loss of phenotypic variation, there was no evidence for changes in within-population genetic divergence or Ne over the course of this study. These results suggest that in instances of population stability, genetic diversity may be resistant to climate-induced changes in migration timing.
Data from: Genetic composition of the Warm Springs River Chinook Salmon population maintained following eight generations of hatchery production
Balancing the disparate objectives of fishery augmentation and conservation of an endemic population presents a substantial challenge. In the case of Warm Springs National Fish Hatchery (Warm Springs Hatchery), strategies for achieving both objectives included incorporation of natural fish into the hatchery broodstock and restricting proportions of hatchery fish on the spawning grounds. The hatchery has been more successful in implementing the latter, however, than the former. We analyzed seventy-six SNP markers in Spring Chinook Salmon O. tshawytscha collected from the Warm Springs River in 1976 – 1977 (prior to hatchery produciton) and 2001-2011 (post-hatchery) to examine whether the genetic characteristics of the endemic population had changed during that time. Pre- and post- hatchery collections clustered together when compared to Round Butte Hatchery (a nearby segregated program) and other Columbia River populations. The difference between pre- and post- hatchery collections was non-significant (AMOVA), but post hatchery samples exhibited significantly lower He. We observed some evidence of reduced effective size (Ne) and increased genetic drift in fish produced at Warm Springs Hatchery (relative to natural-origin fish), and even stronger evidence in fish produced at Round Butte Hatchery. We conclude that natural-origin fish returning to the Warm Springs River form a distinct group within the Interior Columbia Basin Spring-run lineage and have changed very little over the past eight generations. We further speculate that differences between hatchery- and natural- origin fish at Warm Springs Hatchery are expected to increase if hatchery operations remain static (little integration of natural-origin fish and incorporation of Round Butte Hatchery fish in broodstock).
Data from: The interplay between local ecology, divergent selection and genetic drift in population divergence of a sexually antagonistic female trait
Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic mating trait in an insect group; the dorsal structures (either rough or smooth) of female diving beetles. Our recent work suggests that the rough structures have a sexually antagonistic function in reducing male mating attempts. For two species (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic drift as an explanation for population divergence in morph frequencies, while for the third (Hygrotus impressopunctatus) we found that divergent selection pulls morph frequencies apart across populations. Furthermore, population morph frequencies in H. impressopunctatus were significantly related to local bioclimatic factors, providing an additional line of evidence for local adaptation in this species. These data therefore suggest that local ecological factors and sexual conflict interact over larger spatial scales to shape population divergence in the polymorphism.
Data from: Spatial population genetic structure of a bacterial parasite in close coevolution with its host
Knowledge of a species' population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a.k.a. 'Red Queen' dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and Western Asia. Using 12 polymorphic VNTR loci, we identified substantial genetic diversity both within and among localities that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, though this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host-specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation-by-distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.
Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)
The central-marginal hypothesis (CMH) predicts that population size, genetic diversity, and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size, and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean center on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core to edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.
Data from: EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly
Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns reflected island-specific selection and that there was little migration between islands. However, genetic studies to test the underlying assumption of restricted migration are lacking and it is also unknown whether the originally described wing-spot patterns have persisted over time. We therefore collected female butterflies from five of Ford's original study locations, including three large islands (St Mary's, St Martin's and Tresco) and two small islands (Tean and St Helen's). Wing-spot patterns had not changed appreciably over time on three of the islands (two large and one small), but were significantly different on the other two. Furthermore, analysis of 176 amplified fragment length polymorphisms revealed significant genome-wide differentiation among the five islands. Our findings are consistent with Ford's conclusions that despite the close proximity of these islands, there is restricted gene flow among them.
Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.
Data from: New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies.
The mutualistic symbioses between reef-building corals and micro-algae form the basis of coral reef ecosystems, yet recent environmental changes threaten their survival. Diversity in host-symbiont pairings on the sub-species level could be an unrecognized source of functional variation in response to stress. The Caribbean elkhorn coral, Acropora palmata, associates predominantly with one symbiont species (Symbiodinium 'fitti'), facilitating investigations of individual-level (genotype) interactions. Individual genotypes of both host and symbiont were resolved across the entire range of the species. Most colonies of a particular animal genotype were dominated by one symbiont genotype (or strain) that may persist in the host for decades or more. While Symbiodinium are primarily clonal, the occurrence of recombinant genotypes indicates sexual recombination is the source of this genetic variation, and some evidence suggests this happens within the host. When these data are examined at spatial scales spanning the entire distribution of A. palmata, gene flow among animal populations was an order of magnitude greater than among populations of the symbiont. This suggests that independent micro-evolutionary processes created dissimilar population genetic structures between host and symbiont. The lower effective dispersal exhibited by the dinoflagellate raises questions regarding the extent to which populations of host and symbiont can co-evolve during times of rapid and substantial climate change. However, these findings also support a growing body of evidence suggesting that genotype by genotype interactions may provide significant physiological variation; influencing the adaptive potential of symbiotic reef corals to severe selection.
Data from: Genetic evidence for high propagule pressure and long-distance dispersal in monk parakeet (Myiopsitta monachus) invasive populations
The monk parakeet (Myiopsitta monachus) is a successful invasive species that does not exhibit life history traits typically associated with colonizing species (e.g., high reproductive rate or long-distance dispersal capacity). To investigate this apparent paradox, we examined individual and population genetic patterns of microsatellite loci at one native and two invasive sites. More specifically, we aimed to evaluate the role of propagule pressure, sexual monogamy, and long-distance dispersal in monk parakeet invasion success. Our results indicate little loss of genetic variation at invasive sites relative to the native site. We also found strong evidence for sexual monogamy from patterns of relatedness within sites, and no definite cases of extra-pair paternity in either the native site sample or the examined invasive site. Taken together, these patterns directly and indirectly suggest that high propagule pressure has contributed to monk parakeet invasion success. In addition, we found evidence for frequent long-distance dispersal at an invasive site (~100km) that sharply contrasted with previous estimates of smaller dispersal distance made in the native range (~2km), suggesting long-range dispersal also contributes to the species' spread within the United States. Overall, these results add to a growing body of literature pointing to the important role of propagule pressure in determining, and thus predicting, invasion success, especially for species whose life history traits are not typically associated with invasiveness.
Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys. The two types of estimate were highly correlated. Overall we found genetic diversity to be only slightly lower in Britain than across a comparable area in Scandinavia where populations are large and continuous. Whilst the ensemble of British fragments maintain diversity levels close to Scandinavian populations, individually they have drifted apart and lost diversity; particularly the smaller populations. An ABC analysis, based on coalescent models, favours demographic scenarios in which Britain maintained high levels of genetic diversity through post-glacial recolonisation. This diversity has subsequently been partitioned into population fragments that have recently lost diversity at a rate corresponding to the current population-size estimates. We conclude that the British population fragments retain sufficient genetic resources to be the basis of conservation and re-planting programmes. Use of markers with different mutation rates gives us greater confidence and insight than one marker set could have alone, and we suggest that RAD-SSRs are particularly useful as high mutation rate marker set with a well-specified ascertainment bias, which are widely available yet often neglected in existing RAD datasets.
Data from: A population genetic signature of human releases in an invasive ladybeetle
Biological invasions have been accelerated by a variety of human activities. Propagule pressure, the number of introduced individuals and independent introductions, is likely to be influenced by these human activities and may be an important factor for successful range expansion in new environments. We tested whether the current distribution of the predatory ladybeetle Coccinella septempunctata in the introduced range (USA) is the result of multiple historical human introductions or natural range expansion from the first established populations in the USA. To test this hypothesis, we compared historical records of propagule size, propagule number, specific introduction locations, and the date of each introduction, with estimates of genetic variation in mitochondrial DNA (COI). Our results indicated that genetic diversity in the introduced range was positively correlated with historical records of propagule size and number, and negatively correlated with distance to nearest introduction point, suggesting that multiple human releases were successful. Higher genetic diversity in populations found near introduction points suggest that initial founder effects were limited, but lower genetic diversity found farther from introduction points is likely the result of serial founder effects during secondary range expansion. These results suggest that the current distribution of C. septempunctata in the introduced range is the result of a combination of human releases and short-range expansion from multiple established populations in introduced range.
Data from: Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins
The Aiptasia-Symbiodinium symbiosis is a promising model for experimental studies of cnidarian-dinoflagellate associations, yet relatively little is known regarding the genetic diversity of either symbiotic partner. To address this we collected Aiptasia from 17 localities throughout the world and examined the genetic diversity of both anemones and their endosymbionts. Based on newly-developed SCAR markers, Aiptasia consisted of two genetically-distinct populations, one Aiptasia lineage from Florida and a second network of Aiptasia genotypes found at other localities. These populations did not conform to the distributions of described Aiptasia species, suggesting that taxonomic re-evaluation is needed in light of molecular genetics. Associations with Symbiodinium further demonstrated the distinctions among Aiptasia populations. According to 18S-RFLP, ITS2-DGGE, and microsatellite flanker region sequencing, Florida anemones engaged in diverse symbioses predominantly with members of Symbiodinium Clades A and B, but also C, whereas anemones from elsewhere harboured only S. minutum within Clade B. Symbiodinium minutum apparently does not form a stable symbiosis with other hosts, which implies a highly-specific symbiosis. Fine-scale differences among S. minutum populations were quantified using six microsatellite loci. Populations of S. minutum had low genotypic diversity and high clonality (R=0.14). Furthermore, minimal population structure was observed among regions and ocean basins, due to allele and genotype sharing. The lack of genetic structure and low genotypic diversity suggest recent vectoring of Aiptasia and S. minutum across localities. This first ever molecular-genetic study of a globally-distributed cnidarian and its Symbiodinium assemblages reveals host-symbiont specificity and widely-distributed populations in an important model system.
Data from: Heterogeneity of genetic architecture of body size traits in a free-living population
Knowledge of the underlying genetic architecture of quantitative traits could aid in understanding how they evolve. In wild populations, it is still largely unknown whether complex traits are polygenic or influenced by few loci with major effect, due to often small sample sizes and low resolution of marker panels. Here, we examine the genetic architecture of five adult body size traits in a free-living population of Soay sheep on St Kilda using 37 037 polymorphic SNPs. Two traits (jaw and weight) show classical signs of a polygenic trait: the proportion of variance explained by a chromosome was proportional to its length, multiple chromosomes and genomic regions explained significant amounts of phenotypic variance, but no SNPs were associated with trait variance when using GWAS. In comparison, genetic variance for leg length traits (foreleg, hindleg and metacarpal) was disproportionately explained by two SNPs on chromosomes 16 (s23172.1) and 19 (s74894.1), which each explained >10% of the additive genetic variance. After controlling for environmental differences, females heterozygous for s74894.1 produced more lambs and recruits during their lifetime than females homozygous for the common allele conferring long legs. We also demonstrate that alleles conferring shorter legs have likely entered the population through a historic admixture event with the Dunface sheep. In summary, we show that different proxies for body size can have very different genetic architecture and that dense SNP helps in understanding both the mode of selection and the evolutionary history at loci underlying quantitative traits in natural populations.
Data from: Does population distribution matter? Influence of a patchy versus continuous distribution on genetic patterns in a wind-pollinated shrub
Aim: Uniform spatial population distributions are predicted to result in lower among-population genetic differentiation and higher within-population genetic diversity than naturally patchy distributions, but there have been surprisingly few attempts to isolate this effect from confounding factors. We studied the widespread wind-pollinated shrub Allocasuarina humilis that is common in a geologically-stable landscape characterised by long-term population persistence to test the influence of semi-continuous versus patchy population distributions on genetic patterns. We also investigated whether A. humilis shows the high population connectedness and genetic diversity typically associated with wind pollination, a relatively uncommon and little-studied syndrome in this landscape. Location: Heath-shrublands ('heath') and forests of south-western Australia. Methods: Populations were sampled from heath and forest regions, which respectively exhibited semi-continuous and patchy population distributions. Genetic structure and diversity were assessed for 27 populations using eight nuclear microsatellite markers and three chloroplast regions. Phylogeographic history was examined using Bayesian phylogeny reconstruction, parsimony analysis and tests of expansion. Results: High haplotype diversity is consistent with long-term population persistence across most of the species' range. Nuclear markers showed low overall population differentiation and no geographical structure over ~900 km, reflecting extensive pollen dispersal. For both marker types, patchily-distributed forest populations were substantially more differentiated with significantly lower within-population diversity than semi-continuous heath populations. Phylogeographic analysis revealed evidence for earlier colonization of heath than forest and recent expansion into wetter forests, consistent with progressive long-term climatic drying. Main conclusions: High population connectedness and genetic diversity probably resulted from wind pollination in combination with dioecy and long life span. Patchy population distributions appear to have influenced genetic structure and diversity through lower pollen and seed dispersal, lower effective population sizes and greater genetic drift. Our approach illustrates the value of minimising confounding variables by testing the effect of a variable ecological trait within a single species.
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population
Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance.
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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.