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15,277 results for “GENETICS”
Data from: Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales
The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89–1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.
Data from: Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population
Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (FST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.
Data from: A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity
Twenty-years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-Nucleotide Polymorphisms (SNPs) obtained from ddRAD-sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized trans-oceanic secondary introduction from NE Pacific to Europe. However, the SNPs panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).
Data from: Genetic diversity, population structure and sex-biased dispersal in three co-evolving species
Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analyzed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost's DEST), we detected strong population structuring in all species and less male-biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post-glacial colonization routes - northern populations are as variable as more southern populations. We conclude that conditions for Thompson's geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.
Data from: Stoichiometric traits of stickleback: effects of genetic background, rearing environment, and ontogeny
Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem-effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwa- ter fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichio- metric composition of bodies and excretion) of threespine stickleback. We use two populations from distinct freshwater lineages with contrasting lateral plating pheno- types (full vs. low plating) and their hybrids, which are mostly fully plated. We found that ontogeny, rearing environment, and body condition were the most important pre- dictors of organismal stoichiometry. Although elemental composition was similar be- tween both populations and their hybrids, we found significant divergence in phosphorus allocation among body parts and in phosphorus excretion rates. Overall, body armor differences did not explain variation in whole body phosphorus, phospho- rus allocation, or phosphorus excretion. Evolutionary divergence between these line- ages in both allocation and excretion is likely to have important direct consequences for ecosystems, but may be mediated by evolution of multiple morphological or physi- ological traits beyond plating phenotype.
Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?
Obligate mutualistic nursery pollination systems between insects and plants have led to substantial co-diversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases host plants sharing pollinators are allopatric. However in the case of the species group of Ficus auriculata, forms may co-occur over large parts of their range. We show here that the species group of F. auriculata is constituted by four well-defined genetic entities that share pollinators. We detected hybrids in nature mainly when both parental forms were growing nearby. Controlled crosses showed that F1 offspring could be successfully backcrossed. Hence, despite sharing pollinators and despite hybrid viability, the different forms have preserved their genetic and morphological identity. We propose that ecological differentiation among forms, coupled with limited overlap of reproductive season has facilitated the maintenance of these inter-fertile forms. As such, establishment of pollinator host specificity may not be a prerequisite for sympatric diversification in Ficus.
Data from: Clonality, genetic diversity, and support for the diversifying selection hypothesis, in natural populations of a flower-living yeast
Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights on the ecological and genetic correlates of clonality, and on the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using AFLP markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by AMOVA (Φst = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparths to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality.
Data from: Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star
Poecilogony, or multiple developmental modes in a single species, is exceedingly rare. Several species described as poecilogenous were later demonstrated to be multiple (cryptic) species with a single developmental mode. The Southern Ocean is known to harbor a high proportion of brooders (Thorson's Rule) but with an increasing number of counter examples over recent years. Here we evaluated poecilogony versus crypticism in the brittle star Astrotoma agassizii across the Southern Ocean. This species was initially described from South America as a brooder before some pelagic stages were identified in Antarctica. Reproductive and mitochondrial data were combined to unravel geographic and genetic variation of developmental modes. Our results indicate that A. agassizii is composed of seven well supported and deeply divergent clades (I: Antarctica and South Georgia; II: South Georgia and Subantarctic locations including Kerguelen, Patagonian shelf, and New Zealand; III-VI-VII: Patagonian shelf, IV-V: South Georgia). Two of these clades demonstrated strong size dimorphism when in sympatry and can be linked to differing developmental modes (Clade V: dwarf brooder versus Clade I: giant broadcaster). Based on their restricted geographic distributions and on previous studies, it is likely that Clades III-VI-VII are brooders. Clade II is composed of different morphological species, A. agassizii and A. drachi, the latter originally used as the outgroup. By integrating morphology, reproductive and molecular data we conclude that the variation identified in A. agassizii is best described as crypticism rather than poecilogony.
Data from: The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines
Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks.
Data from: Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes
Background: The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. Methodology/Principal Findings: We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. Conclusions/Significance: All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.
Data from: Genetic differentiation within multiple common grassland plants supports seed transfer zones for ecological restoration
Ecological restoration of grasslands is increasingly based on regional seeds derived from predefined seed transfer zones. However, the degree and spatial pattern of genetic differentiation among provenances of different seed transfer zones is largely unknown. We assessed the genetic differentiation among eight out of 22 German seed transfer zones for seven common grassland species (Arrhenatherum elatius, Centaurea jacea, Daucus carota, Galium album, Hypochaeris radicata, Knautia arvensis and Lychnis flos-cuculi) using AFLP markers. We analysed genetic population structure with AMOVA and Bayesian cluster analysis and tested for isolation by distance and isolation by environment. In all of the investigated species, almost all pairs of provenances were genetically differentiated. Bayesian cluster analysis revealed species-specific numbers and spatial patterns of gene pools, with between two (Arrhenatherum) and eight clusters (Lychnis). Most investigated seed transfer zones represented a unique gene pool in the majority of the species. We found isolation by distance in four species, isolation by environment, driven by climatic seasonality, in three species, and a lack of both in three species. Thus, the observed genetic differentiation appears to be caused by both neutral and adaptive processes. Synthesis and applications. Our study shows that grassland plants are indeed strongly genetically differentiated across Germany supporting the strategy of seed transfer zones for ecological restoration. Although the predefined seed transfer zones are unlikely to match the exact genetic structure of many species, they serve their purpose by capturing a substantial amount of intraspecific genetic variation across species.
Data from: Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations
Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (Fst = 0.32) was more than twice as high as that of the young trees naturally established around native adults (Fst = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity.
Data from: An ecological history of the relict genetic lineage of Arabidopsis thaliana
The combination of extensive population sampling with whole-genome sequencing in the annual plant Arabidopsis thaliana has recently allowed the identification of a genetically differentiated relict lineage. The most important nuclei of relict A. thaliana is found in the Iberian Peninsula and North Africa, although relict accessions have also been found scattered across Atlantic oceanic islands, eastern Mediterranean Basin, South and East Africa and China. We hypothesised that relict A. thaliana long survived and adapted to a wide array of environments in the Iberian Peninsula and North Africa due to the fact that the region repeatedly acted as glacial refugia. Given the lack of evidence to support this hypothesis, we addressed this issue by studying the ecological history of Iberian and North African relict A. thaliana. To this end, we analysed the relationship between the current habitat suitability of relict A. thaliana, estimated with species distribution models, and the vegetation dynamics in the region over the last millennia using pollen fossil data from sediment cores and reconstructions of past distribution ranges of the most important tree species occurring in the region. Overall, our results indicated that a higher current habitat suitability of relict A. thaliana was correlated with more stable vegetation dynamics since the Last Glacial Maximum and during the Holocene. Given that relict A. thaliana is known to harbour genetic variation specific to its relict nature, we also evaluated the differentiation between relict and non-relict A. thaliana accessions at the functional genetic level for the known flowering genes, CRY2 and TSF. Genomic surveys detected the existence of haplogroups of these genes occurring at very high frequency only among relict accessions. Overall, our study reinforced the relict character of this lineage thought to be at the base of the species' early history. We stress the need to sample in depth other geographic areas harbouring relict A. thaliana and conduct further functional genetic analyses between relict and non-relict accessions to keep disentangling the evolutionary trajectory of this annual plant.
Data from: Understanding age-specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis
Many marine species have vastly different capacities for dispersal during larval, juvenile and adult life stages, and this has the potential to complicate the identification of population boundaries and the implementation of effective management strategies such as marine protected areas. Genetic studies of population structure and dispersal rarely disentangle these differences and usually provide only lifetime-averaged information that can be considered by managers. We address this limitation by combining age-specific autocorrelation analysis of microsatellite genotypes, hydrodynamic modelling and genetic simulations to reveal changes in the extent of dispersal during the lifetime of a marine fish. We focus on an exploited coral reef species, Lethrinus nebulosus, which has a circum-tropical distribution and is a key component of a multispecies fishery in northwestern Australia. Conventional population genetic analyses revealed extensive gene flow in this species over vast distances (up to 1500 km). Yet, when realistic adult dispersal behaviours were modelled, they could not account for these observations, implying adult dispersal does not dominate gene flow. Instead, hydrodynamic modelling showed that larval L. nebulosus are likely to be transported hundreds of kilometres, easily accounting for the observed gene flow. Despite the vast scale of larval transport, juvenile L. nebulosus exhibited fine-scale genetic autocorrelation, which declined with age. This implies both larval cohesion and extremely limited juvenile dispersal prior to maturity. The multidisciplinary approach adopted in this study provides a uniquely comprehensive insight into spatial processes in this marine fish.
Data from: Genetic diversity, population structure and phylogeography of Myanmar goats
The diversity of goats in Myanmar is represented by three indigenous breeds, Jade Ni, Nyaung Oo and Waithar Li. This study aimed at characterizing the genetic diversity and relationship of Myanmar goat breeds using microsatellite and mitochondrial DNA variations. A total of 147 goats from all three indigenous breeds were genotyped at 27 microsatellite loci. Genetic diversity in terms of allelic polymorphisms, observed and expected heterozygosities were moderately high. The mean observed heterozygosity within breeds varied between 0.566 ± 0.183 (Nyaung Oo) and 0.595 ± 0.182 (Waithar Li) while the expected heterozygosity varied from 0.605 ± 0.181 (Jade Ni) to 0.647 ± 0.176 (Waithar Li). Considerable heterozygosity deficit ranging from 5.5% to 8.2% was observed in Myanmar goat breeds. Wright's F statistics revealed most of the variations within breeds and only 1.9% of the total observed variation was explained by between breed differences. Principal components and Bayesian clustering analyses showed complete admixture of Nyaung Oo and Waithar Li goats indicating high rate of gene flow among these populations. Population stratification was observed in Jade Ni with a subset of individuals clustering distinctly. Variations in mitochondrial DNA control region revealed 22 distinct haplotypes belonging to two major haplogroups A and B. Haplogroup A was found to predominate Myanmar goats similar to other goat populations in Asia. Comparative analysis of mtDNA variations indicated possible Chinese origin of the maternal haplotypic lineages of Myanmar goats.
Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are susceptible to RNAi-mediated gene knock-down, we developed a simple method for delivery of gene-specific double-stranded RNA that results in significant suppression of target gene transcription levels. The protocol was examined on five genes of interest, and for each, at least 50% knock-down in expression was achieved. While knock-down levels did not reach 100% in any trial, a well-controlled experiment with one heat-shock gene showed unambiguously that such partial gene suppression may cause dramatic changes in phenotype. Copepods with suppressed expression of heat-shock protein beta 1 (hspb1) exhibited dramatically decreased tolerance to high temperatures, validating the importance of this gene during thermal stress, as proposed by a previous study. The application of this RNAi protocol in T. californicus will be invaluable for examining the role of genes putatively involved in reproductive isolation, mitochondrial function and local adaptation.
Data from: Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicates potential for spread of herbicide resistance via gene flow
Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggests the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.
Data from: Contrasting patterns of clonality and fine-scale genetic structure in two rare sedges with differing geographic distributions
For plants with mixed reproductive capabilities, asexual reproduction is more frequent in rare species and is considered a strategy for persistence when sexual recruitment is limited. We investigate whether asexual reproduction contributes to the persistence of two co-occurring, rare sedges that both experience irregular seed set and if their differing geographic distributions have a role in the relative contribution of clonality. Genotypic richness was high (R=0.889±0.02) across the clustered populations of Lepidosperma sp. Mt Caudan and, where detected, clonal patches were small, both in ramet numbers (less than or equal to3 ramets/genet) and physical size (1.3±0.1 m). In contrast, genotypic richness was lower in the isolated L. sp. Parker Range populations, albeit more variable (R=0.437±0.13), with genets as large as 17 ramets and up to 5.8 m in size. Aggregated clonal growth generated significant fine-scale genetic structure in both species but to a greater spatial extent and with additional genet-level structure in L. sp. Parker Range that is likely due to restricted seed dispersal. Despite both species being rare, asexual reproduction clearly has a more important role in the persistence of L. sp. Parker Range than L. sp. Mt Caudan. This is consistent with our prediction that limitations to sexual reproduction, via geographic isolation to effective gene exchange, can lead to greater contributions of asexual reproduction. These results demonstrate the role of population isolation in affecting the balance of alternate reproductive modes and the contextual nature of asexual reproduction in rare species.
Data from: Genetic evidence of female kin clusters in a continuous population of a solitary carnivore, the Eurasian lynx
Large terrestrial carnivores can sometimes display strong family bonds affecting the spatial distribution of related individuals. We studied the spatial genetic relatedness and family structure of female Eurasian lynx, continuously distributed in southern Finland. We hypothesized that closely related females form matrilineal assemblages, clustering together with relatives living in the neighboring areas. We evaluated this hypothesis using tissue samples of 133 legally harvested female lynx (from year 2007 to 2015), genotyped with 23 microsatellite markers, and tested for possible spatial genetic family structure using a combination of Bayesian clustering, spatial autocorrelation, and forensic genetic parentage analysis. The study population had three potential family genetic clusters, with a high degree of admixture and geographic overlap, and showed a weak but significant negative relationship between pairwise genetic and geographic distance. Moreover, parentage analysis indicated that 64% of the females had one or more close relatives (sister, mother, or daughter) within the study population. Individuals identified as close kin consistently assigned to the same putative family genetic cluster. They also were sampled closer geographically than females on average, although variation was large. Our results support the possibility that Eurasian lynx forms matrilineal assemblages, and comparisons with males are now required to further assess this hypothesis.
Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.
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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.