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2,445 results for “Genetics: population”
Figure 2 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 2. – Landmarks distribution on fish body of Aphanius fasciatus. 1: Eye position, 2: Dorsal opercular limit, 3: Beginning of dorsal fin, 4: End of dorsal fin, 5: Dorsal limit of caudal peduncle, 6: Median limit of caudal peduncle, 7: Ventral limit of caudal peduncle, 8: End of anal fin, 9: Beginning of anal fin, 10: Pelvic fin insertion, 11: Ventral opercula limit, 12: Dorsal limit of pectoral fin, 13: Ventral limit of pectoral fin, 14: Mouth.
Figure 1 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 1. – Map of the west Mediterranean basin with North African sample sites. 1: Mellah lagoon (LM), 2: Mellah marsh (M), 3: Lagoon of Bizerte (BZ), 4: Ayata Lake (LA).
Figure 2 in Extant because important or important because extant? On the scientific importance and conservation of a genetically pure Sicilian population of the threatened Salmo cettii Rafinesque, 1810
Figure 2. – Individual Salmo cettii from Tellesimo Stream (for the morphological and phenotypical characteristics of Sicilian trout see: Duchi, 1988; Fruciano et al., 2014; Duchi, 2018).
Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer
<p>Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N<sub>e</sub>) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N<sub>e</sub> of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N<sub>e</sub>/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased N<sub>e</sub> in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N<sub>e</sub>. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.</p>
Fig. 2. A in Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae) dengue vector from the Brazilian state of Maranhão
Fig. 2. A priori estimate of the probable groups of populations produced by the BAPS (Bayesian Analysis of Population Structure v 6.0) program, indicating a total of two groups.
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1 in Comparative Genetics Of Apodemus Agrarius (Rodentia: Mammalia) From Insular And Continental Eurasian Populations: Cytochrome B Sequence Analyses
Fig. 1. Collectionsitesfor 91 specimensfrom 29 locationsof Apodemusagrarius, usedin thisstudy. ThespecimennumberforeachlocationarelistedinTable 1, andminimum Jukes-Cantordistancesbetween 17 haplotypesfrommainlandKoreaandother 49 haplo- typesfromsevenregions (Taiwan, Jeju, northeasternChina, easternChina, centralChina, Far-easternRussia, andEurope) basedonthecytochrome b completesequencesaregiven
Fig. 1 MapshowingtherangeofthestudypopulationofEasternImperialEaglesinHungaryandthelocationofsampledandnotsampledterritoriesin 2003 in High Turnover Rate Revealed By Non-Invasive Genetic Analyses In An Expanding Eastern Imperial Eagle Population
Fig. 1 MapshowingtherangeofthestudypopulationofEasternImperialEaglesinHungaryandthelocationofsampledandnotsampledterritoriesin 2003 (35 ofthe 61 nesting
Fig. 2 in High Turnover Rate Revealed By Non-Invasive Genetic Analyses In An Expanding Eastern Imperial Eagle Population
Fig. 2. Firstidentification (1999, territorycodeBS-02) andre-identification (2003, BS-03) of afemale. Theterritorieswereapproximately 10 kmawayfromeachotherandtheoriginal BS-02 territorywasvacantin 2001-2002, butitwasoccupiedbyapairwithanewfemale in 2003; differentmarkingsrepresentdifferentgeneticallytaggedfemales, blackmarkings representthenestsfromtheBS-02 territory, greymarkingsrepresentnestsfromtheBS-03 territory; yearsinitalic (nestsmarkedbycircles) representnestingsiteswithoutsamples.
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Data from: Chrysolaena obovata, A SPECIES NATIVE OF BRAZILIAN CERRADO: GENETIC DIVERSITY AND STRUCTURE OF NATURAL POPULATIONS AND POTENTIAL FOR INULIN PRODUCTION
<p><em>Chrysolaena obovata</em> (Less.) M. Dematteis, an herbaceous Asteraceae species widely distributed across different Brazilian Cerrado physiognomies, has underground organs, named rhizophores, that accumulate high concentrations of inulin-type fructans. These carbohydrates are recognized as beneficial soluble fibers for human health and are currently used in the food and pharmaceutical industries. Considering that fructans, in addition to their economic potential, provide plants with greater tolerance to drought, heat and cold, it is important to understand whether their metabolism is conserved in natural populations. In this work, we aimed to investigate if the levels of genetic diversity in the populations studied allow the selection of localities with a high genetic base and higher fructan content for future programs of <em>in</em> <em>situ</em> conservation and genetic improvement for inulin production. Therefore, we characterized the diversity, structure, and gene flow of seven natural populations from Brazilian Cerrado, using nine microsatellite loci (SSR). In addition, we compared whether the fructan composition varied between populations of different Cerrado phytophysiognomies. Overall, we found that <em>C. obovata</em> populations exhibited moderate levels of genetic diversity, low genetic differentiation, and high gene flow. This study identified two populations with less genetic diversity and therefore, greater attention should be given to conservation programs including these populations. Fructan metabolism is conserved in all populations, indicating that <em>C. obovata</em> is an important genetic resource with high potential for inulin production.</p> <p><strong>File descriptions</strong></p> <p>Population_code.txt - Contains a matrix that indicates the population_code, Population_name, Brazilian-state, Phytophysiognomy, Collection coordinates and Altitudes (m).</p> <p>Date_ Diaz et al.xlsx – Contains Genotypes crude of the individuals analyzed. Primer used for nine microsatellite loci (Camacho <em>et al</em> 2017). </p> <p>Carbohydrates_Diaz et al - Contains data for carbohydrates in <em>C. obovata</em> plant rhizophores in each population (BRA, UB, SD, SP).</p> <p><strong>Location: Brazilian Cerrado</strong></p>
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
<p><strong>PREMISE</strong>: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function.</p> <p><strong>METHODS</strong>: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass <em>Leymus chinensis</em>. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.</p> <p><strong>RESULTS</strong>: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.</p> <p><strong>CONCLUSIONS</strong>: We found strong genetic structure among patches of <em>L. chinensis</em>. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.</p>
Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations
<p>The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained. Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both. Color patterns in male bluefin killifish provoke both types of questions. Red and yellow morphs are common in all populations. Blue males are more common in tannin-stained swamps relative to clear springs. Here we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns. We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.</p>
Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles
<p><span>Ocean warming challenges marine organisms' resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures.</span></p> <p><span>Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, <em>Pinctada margaritifera</em>. We benefit from two ecotypes for which local environmental conditions are characterized by either large diurnal variations in the tide-pools (Marquesas archipelago) or lower mean temperature with stable to moderate seasonal variations (Gambier archipelago).</span><br><br><span>We explored the physiological basis of individual responses to elevated temperature<em>, </em>genetic divergence as well as plasticity and acclimation by combining lipidomic and transcriptomic approaches.</span><br><br><span>We show that <em>P. margaritifera</em> has certain capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Genetic variation across populations overlaps with gene expression and involves the mitochondrial respiration machinery, a central physiological process that contributes to species thermal sensitivity and their distribution ranges.</span><br><br><span>Our results present evidence for acclimation potential in <em>P. margaritifera</em> and urge for longer term studies to assess populations resilience in face of climate change.</span></p>
Additional files for manuscript titled 'The double round-robin population unravels the genetic architecture of grain size in barley'
<p>Additional file 1: Parental allele for barley orthologs of genes controlling grain size in rice</p> <p>Additional file 2: Cross-validation of quantitative trait loci (QTLs) detected for grain size characters in rice</p> <p>Additional file 3: Adjusted entry means of recombinant inbred lines of 45 HvDRR sub-populations</p>
Effects of insularity on genetic diversity within and among natural populations
<p>We conducted a review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories. Contradictory to typical expectations, insularity had relatively minor effects on GD within and among population, which points to the more important roles of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen – particularly in systems (i.e. studies) where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same system – suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within - population GD than among - population GD, although a number of biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics highly relevant to current conservation management practices.</p> <p> </p>
Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia
<p><span>Anthropogenic </span>climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in <em>Acropora digitifera</em> across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecasting future genetic offset in random forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming predictions (RCP 2.6), we observed a general pattern of increasing genetic offset with latitude. Under the most extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch in genetic composition, compared to populations in the inshore Kimberley region. The study suggest complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.</p>
Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population
<p>Various aspects of sociality in mammals (e.g., dyadic connectedness) are linked with measures of biological fitness (e.g., longevity). How within- and between-individual variation in relevant social traits arises in uncontrolled wild populations is challenging to determine but is crucial for understanding constraints on the evolution of sociality. We use an advanced statistical method, known as the 'animal model', which incorporates pedigree information, to look at social, genetic, and environmental influences on sociality in a long-lived wild primate. We leverage a longitudinal database spanning 20 years of observation on individually recognized white-faced capuchin monkeys (Cebus capucinus imitator), with a multi-generational pedigree. We analyze two measures of spatial association, using repeat sampling of 376 individuals (mean: 53.5 months per subject, range: 6-185 months per subject). Conditioned on the effects of age, sex, group size, seasonality , and El Niño–Southern Oscillation phases, we show low to moderate long-term repeatability (across years) of the proportion of time spent social (posterior mode [95% Highest Posterior Density interval]: 0.207 [0.169, 0.265]) and of average number of partners (0.144 [0.113, 0.181]) (latent scale). Most of this long-term repeatability could be explained by modest heritability (<em>h<sup>2</sup></em><sub>social</sub>: 0.152 [0.094, 0.207]; <em>h<sup>2</sup></em><sub>partners</sub>: 0.113 [0.076, 0.149]) with small long-term maternal effects (<em>m<sup>2</sup></em><sub>social</sub>: 0.000 [0.000, 0.045]; <em>m<sup>2</sup></em><sub>partners</sub>: 0.000 [0.000, 0.041]). Our models capture the majority of variance in our behavioral traits, with much of the variance explained by temporally changing factors, such as group of residence, highlighting potential limits to the evolvability of our trait due to social and environmental constraints.</p>
On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations
<p>Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In non-redundant systems, exemplified by coevolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.</p>
Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels"
<p>Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels". </p> <p>migrationmatrix14.txt contains the particle tracking matrix, with the total number of particles that migrated from row i to column j (out of a total of 2217864 particles released per population).</p> <p>mussel_microsat_Genepop.txt contains the microsatellite data for each population in Genepop format.</p>
Epidendrum radicans - genetic data of 4 regional populations
<p>Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, <em>Epidendrum radicans</em>, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092 – 0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from <em>in situ</em> reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).</p>
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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.