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15,277 results for “GENETICS”
Data from: Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia
Invasive populations are often associated with low levels of genetic diversity due to population bottlenecks at the initial stages of invasion. Despite this, the ability of invasive species to adapt rapidly in response to novel environments is well documented. Epigenetic mechanisms have recently been proposed to facilitate the success of invasive species by compensating for reduced levels of genetic variation. Here, we use MS-AFLP and microsatellite analyses to compare levels of epigenetic and genetic diversity and differentiation across 15 sites in the introduced Australian house sparrow population. We find patterns of epigenetic and genetic differentiation that are consistent with historical descriptions of three distinct, introductions events. However unlike genetic differentiation, epigenetic differentiation was higher among sample sites than among invasion clusters, suggesting that patterns of epigenetic variation are more strongly influenced by local environmental stimuli or sequential founder events than the initial diversity in the introduction population. Interestingly, we fail to detect correlations between pairwise site comparisons of epigenetic and genetic differentiation, suggesting that some of the observed epigenetic variation has arisen independently of genetic variation. We also fail to detect the potentially compensatory relationship between epigenetic and genetic diversity that has been detected in a more recent house sparrow invasion in Africa. We discuss the potential for this relationship to be obscured by recovered genetic diversity in more established populations, and highlight the importance of incorporating introduction history into population-wide epigenetic analyses.
Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations
Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using the STRUCTURE software gave very similar results, with three main clusters, each containing two sub-clusters, while Bayesian cluster analysis in the Geneland software, exploiting the spatial coordinates of the provenances, resulted in five clusters in accordance with the former results. The implications of the findings for conservation and use of genetic resources of the species are discussed.
Data from: Shaping species with ephemeral boundaries: the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert region
Aim: We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location: Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods: We examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai. Results: Gopherus morafkai was found to comprise genetically and geographically distinct 'Sonoran' and 'Sinaloan' lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection. Main conclusions: The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.
Data from: Diet- and genetically-induced obesity differentially affect the fecal microbiome and metabolome in Apc1638N mice
Obesity is a risk factor for colorectal cancer (CRC), and alterations in the colonic microbiome and metabolome may be mechanistically involved in this relationship. The relative contribution of diet and obesity per se are unclear. We compared the effect of diet- and genetically-induced obesity on the intestinal microbiome and metabolome in a mouse model of CRC. Apc1638N mice were made obese by either high fat (HF) feeding or the presence of the Leprdb/db (DbDb) mutation. Intestinal tumors were quantified and stool microbiome and metabolome were profiled. Genetic obesity, and to a lesser extent HF feeding, promoted intestinal tumorigenesis. Each induced distinct microbial patterns: taxa enriched in HF were mostly Firmicutes (6 of 8) while those enriched in DbDb were split between Firmicutes (7 of 12) and Proteobacteria (5 of 12). Parabecteroides distasonis was lower in tumor-bearing mice and its abundance was inversely associated with colonic Il1b production (p<0.05). HF and genetic obesity altered the abundance of 49 and 40 fecal metabolites respectively, with 5 in common. Of these 5, adenosine was also lower in obese and in tumor-bearing mice (p<0.05) and its concentration was inversely associated with colonic Il1b and Tnf production (p<0.05). HF and genetic obesity differentially alter the intestinal microbiome and metabolome. A depletion of adenosine and P.distasonis in tumor-bearing mice could play a mechanistic role in tumor formation. Adenosine and P. distasonis have previously been shown to be anti-inflammatory in the colon and we postulate their reduction could promote tumorigenesis by de-repressing inflammation.
Data from: Geography best explains global patterns of genetic diversity and post-glacial co-expansion in marine turtles
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to post-glacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial dataset encompassing 23 previously identified lineages from all 7 marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian Model Averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.
Data from: Geographical isolation and environmental heterogeneity contribute to the spatial genetic patterns of Quercus kerrii (Fagaceae)
Southwest China is one of the major global biodiversity hotspots. The Tanaka line, extending within southwestern China from its northwest to its southeast, is an important biogeographical boundary between the Sino-Japanese and Sino-Himalayan floristic regions. Understanding the evolutionary history of the regional keystone species would assist with both reconstructing historical vegetation dynamics and ongoing biodiversity management. In this research, we combined phylogeographic methodologies and species distribution models (SDMs) to investigate the spatial genetic patterns and distribution dynamics of Quercus kerrii, a dominant evergreen oak inhabiting southwest China lowland evergreen broadleaved forests (EBLFs). A total of 403 individuals were sampled from 44 populations throughout southwest China. SDMs and mismatch distribution analysis indicated that Q. kerrii has undergone northward expansion since the Last Glacial Maximum (LGM). Quantitative analysis revealed that the range expansion of Q. kerrii since the LGM exceeded that of the sympatric mid-elevation species Quercus schottkyana, likely owing to their contrasting distribution elevations and habitat availabilities. The historical climate change since the LGM and the latitude gradient of the region played an important role in shaping the genetic diversity of Q. kerrii. The genetic differentiation index and genetic distance surface of Q. kerrii populations east of the Tanaka line exceeded those to its west. The long-term geographic isolation and environmental heterogeneity between the two sides of the Tanaka line might increase species divergence patterns and local adaptation. This study provides new insights into the historical dynamics of subtropical EBLFs and the changing biota of southwest China.
Data from: Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation
The ways that plant-feeding insects have diversified is central to our understanding of terrestrial ecosystems. Obligate nursery pollination mutualisms provide highly relevant model systems of how plants and their insect associates have diversified and the over 800 species of fig trees (Ficus) allow comparative studies. Fig trees can have one or more pollinating fig wasp species (Agaonidae) that breed within their figs, but factors influencing their number remain to be established. In some widely distributed fig trees, the plants form populations isolated by large swathes of sea, and the different populations are pollinated by different wasp species. Other Ficus species with continuous distributions may present genetic signatures of isolation by distance, suggesting more limited pollinator dispersal, which may also facilitate pollinator speciation. We tested the hypothesis that Ficus hirta, a species for which preliminary data showed genetic isolation by distance, would support numerous pollinator species across its range. Our results show that across its range Ficus hirta displays clinal genetic variation and is pollinated by nine parapatric species of Valisia. This is the highest number of pollinators reported to date for any Ficus species and it is the first demonstration of the occurrence of parapatric pollinator species on a fig host displaying continuous genetic structure. Future comparative studies across Ficus species should be able to establish the plant traits that have driven the evolution of pollinator dispersal behaviour, pollinator speciation and host plant spatial genetic structure.
Data from: Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature-associated plastic recombination
Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. The frequency of recombination in the model system Drosophila melanogaster has long been known to exhibit phenotypic plasticity in response to temperature. Here were use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate in response to temperature. In contrast to expectation, we find no evidence for enhanced plasticity in recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct.
Data from: Landscape genetics highlights the role of bank vole metapopulation dynamics in the epidemiology of Puumala hantavirus
Rodent host dynamics and dispersal are thought to be critical for hantavirus epidemiology as they determine pathogen persistence and transmission within and between host populations. We used landscape genetics to investigate how the population dynamics of the bank vole Myodes glareolus, the host of Puumala hantavirus (PUUV), vary with forest fragmentation and influence PUUV epidemiology. We sampled vole populations within the Ardennes, a French PUUV endemic area. We inferred demographic features such as population size, isolation and migration with regard to landscape configuration. We next analysed the influence of M. glareolus population dynamics on PUUV spatial distribution. Our results revealed that the global metapopulation dynamics of bank voles were strongly shaped by landscape features, including suitable patch size and connectivity. Large effective size in forest might therefore contribute to the higher observed levels of PUUV prevalence. By contrast, populations from hedge networks highly suffered from genetic drift and appeared strongly isolated from all other populations. This might result in high probabilities of local extinction for both M. glareolus and PUUV. Besides we detected signatures of asymmetric bank vole migration from forests to hedges. These movements were likely to sustain PUUV in fragmented landscapes. In conclusion, our study provided arguments in favour of source-sink dynamics shaping PUUV persistence and spread in heterogeneous, western European temperate landscapes. It illustrated the potential contribution of landscape genetics to the understanding of the epidemiological processes occurring at this local scale.
Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene-flow. We assess patterns of genetic structure and demographic history in twenty seven populations of nine species of flightless endemic Galápagos weevils from nine of the islands and one winged introduced close relative. Analysis of mitochondrial DNA reveals significant population structure and moderately variable, though demographically stable, populations for lowland endemics (Fst= 0.094 to 0.541; π: 0.014 to 0.042; Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203), in contrast to signals of past contractions and expansions in highland specialists on two islands (Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203). We interpret this series of variable and highly structured population groups as a system of long-established independently founded island units, where structuring could be a signal of micro-allopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations and the potentially threatened state of single-island endemics.
Data from: Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects
Species occupying the same geographic range can exhibit remarkably different population structures across the landscape, ranging from highly diversified to panmictic. Given limitations on collecting population-level data for large numbers of species, ecologists seek to identify proximate organismal traits—such as dispersal ability, habitat preference and life history—that are strong predictors of realized population structure. We examined how dispersal ability and habitat structure affect the regional balance of gene flow and genetic drift within three aquatic insects that represent the range of dispersal abilities and habitat requirements observed in desert stream insect communities. For each species, we tested for linear relationships between genetic distances and geographic distances using Euclidean and landscape-based metrics of resistance. We found that the moderate-disperser Mesocapnia arizonensis (Plecoptera: Capniidae) has a strong isolation-by-distance pattern, suggesting migration–drift equilibrium. By contrast, population structure in the flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by genetic drift, while gene flow is the dominant force in the strong-flying Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best-fitting landscape model for M. arizonensis was based on Euclidean distance. Analyses also identified a strong spatial scale-dependence, where landscape genetic methods only performed well for species that were intermediate in dispersal ability. Our results highlight the fact that when either gene flow or genetic drift dominates in shaping population structure, no detectable relationship between genetic and geographic distances is expected at certain spatial scales. This study provides insight into how gene flow and drift interact at the regional scale for these insects as well as the organisms that share similar habitats and dispersal abilities.
Data from: Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray–Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity—a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
Data from: Modelling the dispersal of the two main hosts of the raccoon rabies variant in heterogeneous environments with landscape genetics
Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km2 in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.
Data from: Genetic diversity, population structure and migration scenarios of the marsupial "Monito del Monte" in south-central Chile.
In this study, we quantified the three pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte", in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least two consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the two genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred a) from the Southern cluster to the Northern cluster and b) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.
Data from: Genetic variation in invasive species response to direct and indirect species interactions
Biotic resistance to invasion arises from strong species interactions that decrease the fitness and population growth rates of potential invaders. Strong, direct interactions such as predation and competition are typically thought to drive biotic resistance, but in diverse communities, indirect interactions among species may also affect biotic resistance. Further, genetic variation in traits of the invading species that affect species interactions may allow some genotypes to overcome biotic resistance. We investigated the direct and indirect effects of a native legume (Acmispon wrangelianus) and insect herbivores on the fitness of different genotypes of an invasive legume (Medicago polymorpha) in a California grassland. Insect herbivores decreased Medicago fitness, but only in the presence of Acmispon, suggesting that indirect interactions mediated through insects and Acmispon are important for deterring Medicago invasion. Some Medicago genotypes were less affected by interactions with other species, however. This genetic variance suggests that while biotic resistance reduced the reproductive success of most genotypes, a few genotypes were able to overcome these complex interactions. However, Medicago invasion was unsuccessful in all treatments at several of our sites, suggesting that factors beyond those manipulated here also play a key role at many sites. At sites where biotic resistance is important, spatial and temporal variation in community composition and the genetic composition of the invasion pool may explain the invasion success of Medicago into this community.
Data from: Genetic inference of epiphytic orchid colonization; it may only take one
Colonization of vacant habitat is a fundamental ecological process that affects the ability of species to persist and undergo range modifications in continually shifting landscapes. Thus, understanding factors that affect and limit colonization has important ecological and conservation implications. Epiphytic orchids are increasingly threatened by various factors, including anthropogenic habitat disturbance. As cleared areas (e.g. pastures) are recolonized by suitable host trees, the establishment and genetic composition of epiphytic orchid populations are likely a function of their colonization patterns. We used genetic analyses to infer the prevailing colonization pattern of the epiphytic orchid, Brassavola nodosa. Samples from three populations (i.e. individuals within a tree) from each of five pastures in the dry forest of Costa Rica were genotyped with neutral nuclear and chloroplast markers. Spatial autocorrelation and hierarchical genetic structure analyses were used to assess the relatedness of individuals within populations, among populations within pastures and among populations in different pastures. The results showed significant relatedness within populations (mean r = 0.166) and significant but lower relatedness among populations within a pasture (mean r = 0.058). Our data suggest that colonization of available habitats is by few individuals with subsequent population expansion resulting from in situ reproduction, and that individuals within a tree are not a random sample of the regional seed pool. Furthermore, populations within a pasture were likely colonized by seeds produced by founders of a neighbouring population within that pasture. These results have important ramifications for understanding conservation measures needed for this species and other epiphytic orchids.
Data from: Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents
This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups; (1) samples from the Zanzibar channel, (2) Mozambique, (3) Madagascar, and (4) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (DEST), but the three predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e. East African Coastal Current, North East Madagascar Current and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale – across national boarders.
Data from: Complex genetic effects on early vegetative development shape resource allocation differences between Arabidopsis lyrata populations
Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (USA) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs.
Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the Major Histocompatibility Complex (MHC), are increasingly being incorporated into genetic studies. In this study we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (Ne < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structure of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations we found that the spatial and temporal structure of microsatellite and MHC diversity were correlated, and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.
Data from: Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae).
Few studies have described the genetic diversity within and between populations of polyploid plant species despite the general acceptance of the importance of polyploidy in plant diversification and speciation. The genus Atriplex has a complex evolutionary history in Australia that has included polyploidy and hybridization among perennial forms. The octoploid, dioecious species Atriplex nummularia is proposed to have evolved from an octoploid ancestor in the coastal semi-arid fringe of south-western Australia, and to have spread east and diversified into taxa which occupy edaphically different habitats. Despite interest in the diversification of the genus, and the ecological and economic importance of A. nummularia, there are no descriptions of the genetic structure of the species. Nuclear microsatellite markers and principal coordinate analysis, analysis of molecular variance, Bayesian and phenetic analyses were used to investigate the diversity and taxonomic relationships of two common subspecies of A. nummularia. Genetic diversity was high overall (A = 509, A′ = 42.4, Ho = 0.824, H′ = 2.8), but values were significantly lower in the western subspecies, A. nummularia ssp. spathulata. As in other outbreeding, perennial species, most of the genetic diversity was within populations (FST = 0.125). Clear divergence of subspecies was evident in principal coordinate analysis, neighbor-joining and Bayesian clustering analyses and the differentiation of populations was very low within subspecies (FSC = 0.048). These findings support the taxonomic separation of the two subspecies. Clustering patterns based on Bayesian analyses suggested that the polyploid subspecies of A. nummularia have multiple origins.
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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.