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15,277 results for “GENETICS”
Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph
Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large naturalized enclosures for the reintroduction and recovery of the endangered distinct population in central Washington, USA. Reproductive output for females and males decreased as population density and individual homozygosity increased. We identified an interaction indicating that male reproductive output decreased as genetic diversity declined at high population densities, but there was no effect at low densities. Males with high amounts (>50%) of Washington ancestry had higher reproductive output than the other ancestry groups, while reproductive output was decreased for males with high northern Utah/Wyoming ancestry and females with high Oregon/Nevada ancestry. Females and males bred with an average of 3.8 and 3.6 mates per year, respectively, and we found no evidence of positive or negative assortative mating with regards to ancestry. Multiple paternity was confirmed in 81% of litters, and we report the first documented cases of juvenile breeding by pygmy rabbits. This study demonstrates how variation in population density, genetic diversity, and ancestry impact fitness for an endangered species being bred for conservation. Our results advance understanding of basic life history characteristics for a cryptic species that is difficult to study in the wild, and provide lessons for managing populations of vulnerable species in captive and free-ranging populations.
Data from: A genetic assessment of the human-facilitated colonization history of black swans in Australia and New Zealand
Movement of species beyond their indigenous distribution can fundamentally alter the conservation status of the populations involved. If introductions are human-facilitated, introduced species could be considered pests. Characterizing the colonization history of introduced species can, therefore, be critical to formulating the objectives and nature of wildlife management strategies. The black swan (Cygnus atratus) is native to Australia but is considered a reintroduced species in New Zealand, where the endemic population was reported extinct during the 19th century. After the re-introduction of a small number of individuals from Australia, the New Zealand population expanded unexpectedly rapidly, which was attributed to simultaneous waves of migration from Australia. An alternative, but hitherto unformalized, hypothesis is that local extant populations remained and admixed with introduced individuals. To contribute to our understanding of the reintroduction history of the species, we investigated dispersal patterns and demographic histories of seven populations from Australia and New Zealand, using population genetic inferences from a microsatellite dataset. Our results on genetic structure, dispersal rates, and demographic histories provide mixed evidence on the origin of New Zealand black swans. The hypothesis that reintroduced individuals mixed with remaining local individuals and that the subsequent dramatic population expansion may have been due to genetic rescue of the inbred indigenous population cannot be discarded and needs further investigation.
Data from: Demographic, environmental and genetic determinants of mating success in captive koalas (Phascolarctos cinereus)
Many factors have been shown to affect mating behavior. For instance, genes of the major histocompatibility complex (MHC) are known to influence mate choice in a wide variety of vertebrate species. The genetic management of captive populations can be confounded if intrinsic mate choice reduces or eliminates reproductive success between carefully chosen breeding pairs. For example, the San Diego Zoo koala colony only has a 45% copulation rate for matched individuals. Herein, we investigated determinants of koala mating success using breeding records (1984-2010) and genotypes for 52 individuals at four MHC markers. We quantified MHC diversity according to functional amino acids, heterozygosity, and the probability of producing a heterozygous offspring. We then used categorical analysis and logistic regression to investigate both copulation and parturition success. In addition, we also examined age, day length, and average pairwise kinship. Our post-hoc power analysis indicates that at a power level of 1 – β = 0.8, we should have been able to detect strong MHC preferences. However, we did not find a significant MHC effect on either copulation or parturition success with one exception: pairs with lower or no production of a joey had significantly lower MHC functional amino acid diversity in the categorical analysis. In contrast, day length and dam age (or age difference of the pair) consistently had an effect on mating success. These findings may be leveraged to improve the success of attempted pairs, conserve resources, and facilitate genetic management.
Data from: Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve
The giant panda is an example of a species that has faced extensive historical habitat fragmentation and anthropogenic disturbance, and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Non-spatial and spatial capture-recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153-175 and 115-163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with 4 giant panda road-crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution poses a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta-population in both Wolong and throughout their current range.
Data from: Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites
Understanding the genetic architecture of host resistance is key for understanding the evolution of host–parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host–parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host–parasite systems. Only the Pasteuria–Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium–Daphnia system remains unclear.
Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
Data from: Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.
Data from: Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean
Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the center of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef-building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation-by-distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which helped explain an additional 15-21% of genetic variation compared to between-island geographic distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping-stones connecting the central Pacific with the species rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the sub-equatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast-spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale.
FIGURE 3 in Morphological and genetic evidence of the full species status of Iberolacerta cyreni martinezricai (Arribas, 1996)
FIGURE 3.— Canonical Variate Analysis (CVA). Bidimensional representation of the first two canonical axes. OTUs (same abb. as in text) are represented by the centroid and a 95% confidence area. The Minimumlength Spanning Tree (MST) is superimposed. A) Male analysis (75.9% of all variability explained). B) Female analysis (67.3% of all variability explained).
FIGURE 2 in Morphological and genetic evidence of the full species status of Iberolacerta cyreni martinezricai (Arribas, 1996)
FIGURE 2.— ML trees of Iberolacerta. A) ML (GTR+I+G) tree (log likelihood = 2570.17092) using two mitochondrial (cytb and 12S rRNA) and one nuclear gene (cmos). Values above branches are bootstrap supports and, from left to right, they refer to the results using the following methods and models: ML (GTR+I+G) / MP (Ts=Tv) / MP (Ts=1, Tv=4). The black dot indicates the inferred age of the split between I. martinezricai and I. monticola. B) ML (K80) tree (log likelihood = 541.28927) using the cmos nuclear gene only. Values above branches are bootstrap supports and, from left to right, they refer to the results using the following methods and models: ML (K80) / MP (Ts=Tv) / MP (Ts=1, Tv=4).
FIGURE 1 in Morphological and genetic evidence of the full species status of Iberolacerta cyreni martinezricai (Arribas, 1996)
FIGURE 1.— Map of the Iberian Peninsula showing localities of Iberolacerta included in the DNA study. See Table 1 and Fig. 2 for further details.
FIGURE 4 in Morphological and genetic evidence of the full species status of Iberolacerta cyreni martinezricai (Arribas, 1996)
FIGURE 4. UPGMA trees derived from distances among OTUs centroids. Abbreviations as in Fig. 3. MALES. Dendrogram showing three different clusters, one with I. cyreni (GUA and GRE), another with the different I. monticola OTUs clustered progressively and, basal to this, I. martinezricai. This tree reflects very well the original distance matrix (r=0.95). FEMALES. I. cyreni (GRE, GUA) cluster together in a different group to all the rest of I. monticola + I. martinezricai samples analysed. I. monticola from EST appears basal to the other two clusters recovered in the analysis ((FRA + (PIC, CCA, GAL and WCA)). This second tree has a poor fit to the original distance matrix (r=0.73).
Data from: Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (Acer saccharum Marshall)
Due to climate change, the ranges of many North-American tree species are expected to shift northward. Sugar maple (Acer saccharum Marshall) reaches its northern continuous distributional limit in north-eastern North America at the transition between boreal mixed-wood and temperate deciduous forests. We hypothesized that marginal fragmented northern populations from the boreal mixed-wood would have a distinct pattern of genetic structure and diversity. We analyzed 18 microsatellite loci variation in 23 populations distributed along three latitudinal transects (west, central and east) that encompass the continuous-discontinuous species range. Each transect was divided into two zones, continuous (temperate deciduous) and discontinuous (boreal mixed-wood), based on sugar maple stand abundance. Respective positive and negative relationships were found between the distance of each population to the northern limit (D north), and allelic richness (AR) and population differentiation (FST). These relations were tested for each transect separately; the pattern (discontinuous/continuous) remained significant only for the western transect. structure analysis revealed the presence of four clusters. The most northern populations of each transect were assigned to a distinct group. Asymmetrical gene flow occurred from the southern into the four northernmost populations. Southern populations in Québec may have originated from two different postglacial migration routes. No evidence was found to validate the hypothesis that northern populations were remnants of a larger population that had migrated further north of the species range after the retreat of the ice sheet. The northernmost sugar maple populations possibly originated from long distance dispersal.
Data from: Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies
There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.
Data from: Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress resistance-related enzyme activities during early life stages in Atlantic salmon
Oxidative stress (OS) may pose important physiological constraints on individuals, affecting trade-offs between growth and reproduction or ageing and survival. Despite such evolutionary and ecological importance, the results from studies on the magnitude of individual variation in OS resistance and the underlying causes of this variation such as genetic, environmental, and maternal origins, remain inconclusive. Using a high throughput methodology, we investigated the activity levels in three OS resistance-related enzymes (superoxide dismutase, SOD; glutathione reductase, GR; glutathione S-transferase, GST) during the early life stages of 1000 individuals from 50 paternal half-sib families in two populations of Atlantic salmon. Using animal mixed models, we detected the presence of narrow-sense heritability for SOD and GST; that for GST differed between populations due to differences in environmental variance. We found support for the presence of common environmental variation, including maternal effects, for only GR. Using a bivariate animal model, we detected a positive environmental correlation between activity levels of SOD and GST but were unable to detect an additive genetic correlation. Our results complement previous heritability findings for levels of reactive oxygen species or OS resistance by demonstrating the presence of heritability for OS-related enzyme activities. Our findings provide a foundation for future work, such as investigations on the evolutionary importance of variation in enzyme activities. In addition, our findings emphasise the importance of accounting for developmental stage, environmental variance, and kin relationships when investigating the OS-response at the enzyme activity level.
Data from: Environmental factors influence both abundance and genetic diversity in a widespread bird species
Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.
Data from: The evolutionary stability of cross-sex, cross-trait genetic covariances
Although knowledge of the selective agents behind the evolution of sexual dimorphism has advanced considerably in recent years, we still lack a clear understanding of the evolutionary durability of cross-sex genetic covariances that often constrain its evolution. We tested the relative stability of cross-sex genetic covariances for a suite of homologous contact pheromones of the fruit fly Drosophila serrata, along a latitudinal gradient that these traits have diverged in mean. Using a Bayesian framework, which allowed us to account for uncertainty in all parameter estimates, we compared divergence in the total amounts and orientations of genetic variance across populations, finding divergence in orientation but not total variance. We then statistically compared orientation divergence of within-sex (G) to cross-sex (B) covariance matrices. In line with a previous theoretical prediction, we find that the cross-sex covariance matrix, B, is more variable than either male or female within-sex covariance matrix. Decomposition of B matrices into their symmetrical and non-symmetrical components revealed that instability is linked to the degree of asymmetry. We also find that the degree of asymmetry correlates with latitude suggesting a role for spatially varying natural selection in shaping genetic constraints on the evolution of sexual dimorphism.
Data from: Detection of airborne genetically modified maize pollen by real-time PCR
The cultivation of genetically modified (GM) crops has raised in the European Union and other parts of the world numerous concerns about their environmental and economic impact. Especially outcrossing of genetically modified organisms (GMO) was from the beginning a critical issue as airborne pollen has been considered an important way of GMO dispersal. Here, we investigate the use of airborne pollen sampling combined with microscopic analysis and molecular PCR analysis as an approach to monitor GM maize cultivations in a specific area. Field trial experiments in the European Union and South America demonstrated the applicability of the approach under different climate conditions, in rural and semi-urban environment, even at very low levels of airborne pollen. The study documents in detail the sampling of GM pollen, sample DNA extraction and real-time PCR analysis. Our results suggest that this ''GM pollen monitoring by bioaerosol sampling and PCR screening" approach might represent an aid in managing the co-cultivation of GM and non-GM crops, especially in the surveillance of GM-free areas, centres of origin, and natural reserves.
Data from: Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism
Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.
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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)
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DANDI Archive for NWB datasets
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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.