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1,598 results for “genetic diversity”
Data from: When can refuges mediate the genetic effects of fire regimes? A simulation study of the effects of topography and weather on neutral and adaptive genetic diversity in fire-prone landscapes
Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection-driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which microrefuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically complex landscapes, with fire refuges and fire-prone "hotspots" apparent. Interannual weather variability reduced the effect of topography on fire patterns, with refuges less apparent under high weather variability. Neutral genetic diversity was correlated with long-term fire frequency under spatially heterogeneous fire regimes, being higher in fire refuges than fire-prone areas, except under high dispersal or low fire severity (low mortality). This generated different spatial genetic structures in fire-prone and fire-refuge components of the landscape, despite similar dispersal. In contrast, genetic diversity was only associated with time since the most recent fire in flat landscapes without predictable refuges and hotspots. Genetic effects of selection driven by fire-related conditions depended on selection pressure, migration distance and spatial heterogeneity in fire regimes. Allele frequencies at a locus conferring higher fitness under successional environmental conditions followed a pattern of "temporal adaptation" to contemporary conditions under strong selection pressure and high migration. However, selected allele frequencies were correlated with spatial variation in long-term mean fire frequency (relating to environmental predictability) under weak dispersal, low selection pressure and strong spatial heterogeneity in fire regimes.
Data from: Effect of habitat fragmentation on the genetic diversity of peripheral populations of beech in Central Italy
Fragmentation can affect the demographic and genetic structure of populations near the boundary of their bio-geographic range. Higher genetic differentiation among populations coupled with lower level of within population variability is expected as a consequence of reduced population size and isolation. The effects of these two factors have been rarely disentangled. Given their high gene flow, anemophilous forest trees should be more affected, in terms of loss of genetic diversity, by small population size rather than geographic isolation alone. We studied the impact of distance from the main range (a measure of isolation) and reduced population size on the within and among population components of genetic variability. We assayed 11 isozyme loci in 27 marginal populations of European beech (Fagus sylvatica L.) in Central Italy. Populations were divided in three groups with an increasing level of fragmentation. In the most fragmented group the within population genetic variability was slightly smaller and the among population differentiation significantly larger than in the other two groups. These results support the role of random genetic drift having a larger impact on the most fragmented group, while gene flow seems to balance genetic drift in the two less fragmented ones. Given that average distance from the main range is not different between the intermediate and the most fragmented group, but average population size is smaller, we can conclude that gene flow is effective, even at relatively long distances, in balancing the effect of fragmentation if population size is not too small.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account
The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.
Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and feral populations over 4 years in an agricultural landscape of 41 km2. We used exact compatibility and maximum likelihood assignment methods to assign these plants to cultivars. Even pure lines and hybrid cultivar seed lots contained several genotypes. The cultivar diversity in fields reflected the conventional view of agroecosystems quite well: that is, there was a succession of cultivars, some grown for longer than others because of their good performance, some used for one year and then abandoned, and others gradually adopted. Three types of field emerged: fields sown with a single cultivar, fields sown with two cultivars, and unassigned fields (too many cultivars or unassigned plants to reliably assign the field). Field plant diversity was higher than expected, indicating the persistence of cultivars that were grown for only one year. The cultivar composition of feral populations was similar to that of field plants, with an increasing number of cultivars each year. By using genetic tools, we found a link between the cultivars of field plants in a particular year and the cultivars of feral population plants in the following year. Feral populations on road verges were more diverse than those on path verges. All of these findings are discussed in terms of their consequences in the context of coexistence with genetically modified crops.
Data from: Genetic diversity of the imperiled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation
The Mediterranean bath sponge Spongia officinalis is an iconic species with high socio-economic value and imperiled present and future status due to unregulated harvesting, mortality incidents and lack of established knowledge regarding its ecology. This study aims to assess genetic diversity and population structure of the species at different geographic sectors and levels of geographic distance along its distribution. For this purpose, 11 locations in the eastern Mediterranean (Aegean Sea), western Mediterranean (Provence coast), and the Strait of Gibraltar were sampled; specimens were analysed using partial mitochondrial cytochrome oxidase subunit I (COI) sequences, along with a set of 8 microsatellite loci. According to our results (i) no genetic differentiation exists among the acknowledged Mediterranean morphotypes and presumably S. officinalis can be viewed as a single, morphologically variable species; (ii) a notable divergence was recorded in the Gibraltar region, indicating the possible existence of a cryptic species; (iii) restriction to gene flow was evidenced between the Aegean Sea and Provence giving two well-defined regional clusters, thus suggesting the existence of a phylogeographic break between the two systems; (iv) low levels of genetic structure, not correlated to geographic distance, were observed inside geographic sectors, implying mechanisms (natural or anthropogenic) that enhance dispersal and gene flow, promoting population connectivity; (v) the genetic diversity of S. officinalis is maintained high in most studied locations despite pressure from harvesting and the influence of devastating epidemics. These findings provide a basis towards the effective conservation and management of the species.
Data from: Genetic signatures of ecological diversity along an urbanization gradient
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
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: Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic Forest
Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.
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: 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: On the origin of sweet potato (Ipomoea batatas (L.) Lam) genetic diversity in New Guinea, a secondary centre of diversity
New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.
Data from: A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii
Seagrass cover has declined in many areas of the world in a trend that has accelerated over the past several decades. This raises concern for both the impact the decline in cover has on coastal ecosystems and the effect it may have on seagrass evolutionary potential, as genotypic and genomic variation is lost. We used 8 microsatellite loci to investigate genetic diversity, structure, and connectivity in the seagrass Halodule wrightii from the Gulf of Mexico (Texas, USA) and western Atlantic (Bermuda). We examined how estimates correlated with changes in H. wrightii abundance and distribution on the Texas Gulf coast over the past 50 yr. Results show that, compared to other species, H. wrightii from this region exhibits variable clonal diversity (R = 0.02-0.81), moderate allelic diversity (mean AR = 4.09), and relatively high heterozygosity (mean He = 0.56). The patterns of genetic diversity and structure, however, do not entirely coincide with either geography or recent historical trends in seagrass distribution in this region. Results from a basin in which seagrasses have recently been expanding were consistent with expectations, as they were for an isolated site near the limit of H. wrightii's range. Results from basins in which seagrasses have been experiencing decline and/or fragmentation, however, were mixed. Genetic structure on the Texas coast was relatively weak and coincided more strongly with tidal range than with geographic barriers or distance. Rapid expansion and the discovery of identical multi-locus genotypes at several sites raises the possibility of migration via drifting vegetative fragments, as the geographic distance among certain multi-locus genotypes cannot be explained by rhizome growth models.
Data from: Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae)
Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63 % of seeds are sired by male trees located within 30 m of the mother. On average, 27 % of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had gre ater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.
Data from: Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated to environmental factors.
Data from: Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex
Background: Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller's Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the Meselson effect and Muller's Ratchet. Dugesiidae planarians show outstanding regeneration capabilities, allowing them to naturally reproduce by fission, either strictly or combined with sex (facultative). Therefore, they are an ideal model to analyze the genetic footprint of fissiparous reproduction, both when it is alternated with sex and when it is the only mode of reproduction. Results: In the present study, we generate and analyze intraindividual cloned data of a nuclear and a mitochondrial gene of sexual, fissiparous and facultative wild populations of the species Dugesia subtentaculata. We find that most individuals, independently of their reproductive strategy, are mosaics. However, the intraindividual haplotype and nucleotide diversity of fissiparous and facultative individuals is significantly higher than in sexual individuals, with no signs of Muller's Ratchet. Finally, we also find that this high intraindividual genetic diversity of fissiparous and facultative individuals is composed by different combinations of ancestral and derived haplotypes of the species. Conclusions: The intraindividual analyses of genetic diversity point out that fissiparous reproduction leaves a very special genetic footprint in individuals, characterized by mosaicism combined with the Meselson effect (named in the present study as the mosaic Meselson effect). Interestingly, the different intraindividual combinations of ancestral and derivate genetic diversity indicate that haplotypes generated during periods of fissiparous reproduction can be also transmitted to the progeny through sexual events, resulting in offspring showing a wide range of genetic diversity and putatively allowing purifying selection to act at both intraindividual and individual level. Further investigations, using Dugesia planarians as model organisms, would be of great value to delve into this new model of genetic evolution by the combination of fission and sex.
Population structure and genetic diversity of sheep breeds in the Kyrgyzstan
<p><span>Sheep are a main livestock </span><span>species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. </span>The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of <span>large-scale livestock improvements</span>, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n=31), Gissar (n=30), Kyrgyz coarse wool (n=13), Aykol (n=31), and Tien-Shan (n=24) breeds were genotyped with the OvineSNP50 BeadChip or the <span>Ovine Infinium HD BeadChip </span>(Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (F<sub>ROH</sub> = 0.034), while the maximum was found in the Alai breed (F<sub>ROH</sub> = 0.071). Short ROH segments (ROH≤4Mb) were predominant in all breeds. Long ROH segments (ROH>16Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (<i>Ne<sub>5</sub>=</i>660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (<i>Ne<sub>5</sub> </i>=176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.</p>
A comparison of neutral genetic differentiation and genetic diversity among migratory and resident populations of Golden-crowned-Kinglets (Regulus satrapa)
<p>Many animals migrate seasonally between breeding and non-breeding territories and these annual movements can have a profound effect on population genetic structure. We genotyped 283 individuals from 11 populations at seven variable microsatellite loci and compared patterns of neutral genetic differentiation and neutral genetic diversity among migratory and resident breeding populations of the Golden-crowned Kinglet (Regulus satrapa), a widespread North American songbird. We predicted that resident populations would exhibit greater genetic differentiation and lower genetic diversity than migratory populations because migratory behaviour is thought to enhance gene flow. The magnitude of genetic differentiation and genetic diversity among migratory and resident populations was comparable, and the greatest levels of differentiation were observed for pairwise comparisons between Ontario and all western populations. Distance-based redundancy models and redundancy models revealed that patterns of neutral genetic differentiation and neutral genetic diversity follow an isolation-by-distance model and are not correlated with migratory behaviour. Overall it appears that genetic patterns are more closely associated with Pleistocene glacial history as proposed in a previous study.</p>
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Data from: Partial support for the central–marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird
Large-scale population comparisons have contributed to our understanding of the evolution of geographic range limits and species boundaries, as well as the conservation value of populations at range margins. The central–marginal hypothesis (CMH) predicts a decline in genetic diversity and an increase in genetic differentiation toward the periphery of species' ranges due to spatial variation in genetic drift and gene flow. Empirical studies on a diverse array of taxa have demonstrated support for the CMH. However, nearly all such studies come from widely distributed species, and have not considered if the same processes can be scaled down to single populations. Here, we test the CMH on a species composed of a single population: the Island Scrub-Jay (Aphelocoma insularis), endemic to a 250 km2 island. We examined microsatellite data from a quarter of the total population and found that homozygosity increased toward the island's periphery. However, peripheral portions of the island did not exhibit higher genetic differentiation. Simulations revealed that highly localized dispersal and small total population size, but not spatial variation in population density, were critical for generating fine-scale variation in homozygosity. Collectively, these results demonstrate that microevolutionary processes driving spatial variation in genetic diversity among populations can also be important for generating spatial variation in genetic diversity within populations.
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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.