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219 results for “fine structure”
Data from: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers
An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.
Data from: Fine scale genetic structure among greater sage-grouse leks in central Nevada
Background: Mating systems that reduce dispersal and lead to non-random mating might increase the potential for genetic structure to arise at fine geographic scales. Greater sage-grouse (Centrocercus urophasianus) have a lek-based mating system and exhibit high site fidelity and skewed mating ratios. We quantified population structure by analyzing variation at 27,866 single-nucleotide polymorphisms in 140 males from ten leks (within five lek complexes) occurring in a small geographic region in central Nevada. Results: Lek complexes, and to a lesser extent individual leks, formed statistically identifiable clusters in ordination analyses, providing evidence for fine-scale geographic genetic differentiation. Lek geography predicted genetic differentiation even at a small geographic scale, which could be sharpened by strong site fidelity. Relatedness was also higher among individuals within lek complexes (and leks), suggesting that reproductive skew, where few males participate in most of the successful matings, could also potentially contribute to genetic differentiation. Models incorporating a habitat resistance surface as a proxy for potentially reduced movement due to landscape features indicated that both geographic distance and habitat suitability (i.e. preferred habitat) predicted genetic structure, with no significant effect of man-made barriers to movement (i.e. power lines and roads). Finally, we illustrate how data sets containing fewer loci (<4000) had less statistical precision and failed to detect the full degree of genetic structure. Conclusion: Our results suggest that habitat features and lek site geography of sage-grouse shape fine scale genetic structure, and highlight how larger data sets can have increased precision and accuracy for quantifying ecologically relevant genetic structure over small geographic scales.
Data from: Deciphering the fine-structure of tribal admixture in the Bedouin population using genomic data
The Bedouin Israeli population is highly inbred and structured with a very high prevalence of recessive diseases. Many studies in the past two decades focused on linkage analysis in large, multiple consanguineous pedigrees of this population. The advent of high-throughput technologies motivated researchers to search for rare variants shared between smaller pedigrees, integrating data from clinically similar yet seemingly non-related sporadic cases. However, such analyses are challenging because, without pedigree data, there is no prior knowledge regarding possible relatedness between the sporadic cases. Here, we describe models and techniques for the study of relationships between pedigrees and use them for the inference of tribal co-ancestry, delineating the complex social interactions between different tribes in the Negev Bedouins of southern Israel. Through our analysis, we differentiate between tribes that share many yet small genomic segments because of co-ancestry versus tribes that share larger segments because of recent admixture. The emergent pattern is well correlated with the prevalence of rare mutations in the different tribes. Tribes that do not intermarry, mostly because of social restrictions, hold private mutations, whereas tribes that do intermarry demonstrate a genetic flow of mutations between them. Thus, social structure within an inbred community can be delineated through genomic data, with implications to genetic counseling and genetic mapping.
Data from: Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India
Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) (1800 km2). Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho =0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060), and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.
Data from: Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation
The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species' biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a highly valued aromatic resin obtained from the bark of the tree. This study assessed the genetic diversity and fine-scale spatial genetic structure (FSGS) of two cohorts (adults and seedlings) from two populations (Guba-Arenja and Kurmuk) in Western Ethiopia and inferred intra-population gene dispersal in the species, using microsatellite markers. The expected heterozygosity (HE) was 0.664–0.724. The spatial analyses based on kinship coefficient (Fij) revealed a significant positive genetic correlation up to a distance of 130 m. Spatial genetic structure was relatively weak (Sp = 0.002–0.014) indicating that gene dispersal is extensive within the populations. Based on the FSGS patterns found, we estimate indirectly gene dispersal distances of 103 and 124 m for the two populations studied. The high heterozygosity, the low fixation index and the low Sp values found in this study are consistent with outcrossing as the (predominant) mating system in B. papyrifera. We suggest that seed collection for ex situ conservation and reforestation programmes of B. papyrifera should use trees separated by distances of at least 100 m but preferably 150 m to limit genetic relatedness among seeds from different trees.
Data from: Genetic rescue by distant trees mitigates qualitative pollen limitation imposed by fine-scale spatial genetic structure
Restricted seed dispersal frequently leads to fine-scale spatial genetic structure (i.e., FSGS) within plant populations. Depending on its spatial extent and the mobility of pollinators, this inflated kinship at the immediate neighbourhood can critically impoverish pollen quality. Despite the common occurrence of positive FSGS within plant populations, our knowledge regarding the role of long-distance pollination preventing reproductive failure is still limited. Using microsatellite markers, we examined the existence of positive FSGS in two low-density populations of the tree Pyrus bourgaeana. We also designed controlled crosses among trees differing in their kinship to investigate the effects of increased local kinship on plant reproduction. We used six pollination treatments and fully monitored fruit production, fruit and seed weight, proportion of mature seeds per fruit, and seed germination. Our results revealed positive FSGS in both study populations and lower fruit initiation in flowers pollinated with pollen from highly-genetically related individuals within the neighbourhood, with this trend intensifying as the fruit development progressed. Besides, open-pollinated flowers exhibited lower performance of compared to those pollinated by distant pollen donors, suggesting intense qualitative pollen limitation in natural populations. We found positive fine-scale spatial genetic structure is translated into impoverished pollen quality from nearby pollen donors which negatively impacts the reproductive success of trees in low-density populations. Under this scenario of intrapopulation genetic rescue by distant pollen donors, the relevance of highly-mobile pollinators for connecting spatially and genetically distant patches of trees may be crucial to safeguarding population recruitment.
Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish
<p>The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such quantifying diversity is central to combatting ongoing wide spread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in northeastern Canada, Arctic charr (<i>Salvelinus alpinus</i>). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic charr in northeastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the SNP panel and with the microsatellite loci (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery, and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.</p>
Data from: Contrasting patterns of clonality and fine-scale genetic structure in two rare sedges with differing geographic distributions
For plants with mixed reproductive capabilities, asexual reproduction is more frequent in rare species and is considered a strategy for persistence when sexual recruitment is limited. We investigate whether asexual reproduction contributes to the persistence of two co-occurring, rare sedges that both experience irregular seed set and if their differing geographic distributions have a role in the relative contribution of clonality. Genotypic richness was high (R=0.889±0.02) across the clustered populations of Lepidosperma sp. Mt Caudan and, where detected, clonal patches were small, both in ramet numbers (less than or equal to3 ramets/genet) and physical size (1.3±0.1 m). In contrast, genotypic richness was lower in the isolated L. sp. Parker Range populations, albeit more variable (R=0.437±0.13), with genets as large as 17 ramets and up to 5.8 m in size. Aggregated clonal growth generated significant fine-scale genetic structure in both species but to a greater spatial extent and with additional genet-level structure in L. sp. Parker Range that is likely due to restricted seed dispersal. Despite both species being rare, asexual reproduction clearly has a more important role in the persistence of L. sp. Parker Range than L. sp. Mt Caudan. This is consistent with our prediction that limitations to sexual reproduction, via geographic isolation to effective gene exchange, can lead to greater contributions of asexual reproduction. These results demonstrate the role of population isolation in affecting the balance of alternate reproductive modes and the contextual nature of asexual reproduction in rare species.
Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada
The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.
Data from: RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
FIGURE 7 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 7. Chauliops conica sp. nov.: (a) pygophore, dorsal view; (b) spermatheca; (c) aedeagus; (d) paramere. Each scale bar equal 0.1 mm.
FIGURE 6 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 6. Chauliops quaternaria sp. nov.: (a) aedeagus; (b) paramere; (c) spermatheca. Each scale bar equal 0.1 mm.
FIGURE 5 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 5. (a) C. zhengi: anterior trichobothrium of sternum VI; (b) C. horizontalis: trichobothrium of sternum III; (c) Malcus auriculatus Štys (Malcinae): trichobothria of sternum VII; (d) Sphragisticus nebulosus (Fallén) (Rhyparochromidae): innermost trichobothrium of sternum IV; (e) Ninus insignis Stål (Ninidae): middle trichobothrium of sternum III; (f) Plinthisus maculatus (Kiritshenko) (Plinthisinae): trichobothrium of sternum III.
FIGURE 2 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 2. (a) C. bisontula: mesotergum and scutellum (ca = "cell" area; p = projection of posterior margin of mesotergum); (b) C. horizontalis: fore wing; (c) C. bisontula: meso- and metapleuron; (d) C. bisontula: scent gland; (e) C. zhengi: thoracic segments, ventral view; (f) C. horizontalis: waxy hairs on mesopleuron, enlarged.
FIGURE 3 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 3. (a) C. horizontalis: foreleg; (b) C. quaternaria sp. nov.: apex of mesotibia; (c) C. horizontalis: tibial comb; (d) C. conica sp. nov.: tibial comb; (e) C. zhengi: pretarsus of midleg; (f) C. quaternaria sp. nov.: pretarsus of hindleg.
FIGURE 8 in Notes on fine structures of Chauliops with descriptions of two new species from China (Insecta: Hemiptera: Heteroptera: Malcidae)
FIGURE 8. (a) Chauliops conica sp. nov., dorsal view; (b) Chauliops conica sp. nov., lateral view; (c) Chauliops quaternaria sp. nov., dorsal view; (d) Chauliops fallax Scott, dorsal view; (e) Chauliops bisontula Banks, dorsal view; (f) Chauliops horizontalis Zheng, dorsal view; (g) Chauliops zhengi Xue et Bu, dorsal view. Scale bar equal 1 mm.
Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.
<p>This database contains the coordinates of individuals of <em>Aechmea mariae-reginae</em> and <em>Werauhia ampla</em> in phorophytic trees and the genotypes for 8 microsatellite loci.</p>
Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia
<p>Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. <i>Eleginops maclovinus</i> is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of <i>E</i>. <i>maclovinus</i>. We use Restriction-site Associated DNA (RAD) sequencing and outlier tests to obtain 11,712 neutral, 338 adaptive loci, and 78 loci associated to environmental variables. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 to 14,454 and were influenced more by locality than salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in <i>E</i>. <i>maclovinus</i> populations. These results suggest a complex interaction between genetic drift, geneflow, and natural selection in this area. Our findings suggest that at least two to three genetic units exist in this area, and the information should be integrated into the management of this species. We discuss the significance of these results for fishery management and suggest future directions to improve our understanding of how <i>E</i>. <i>maclovinus</i> is adapted to the dynamic waters of Northern Patagonia.</p>
Data: Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon
<p>Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.</p>
Few juveniles or males were collected. Only four males from groups 7, 8, 9, and 11, all in clade D, were included in the dataset. The male in Fig. 13E–H conforms to the general morphological description of males in Lobocriconema with an undifferentiated labial region, the absence of a stylet, a degenerate pharyngeal region, a FIGURE 7. SEM images of specimens representing clades D (A–H) and B (I). NID numbers are associated with unique specimens, all are females except image C. A) Lobocriconema sp., face view with conspicuous labial disc surrounded by irregular labial structure, Nine-Mile Prairie, Nebraska, NID 4533. B) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Big Thicket National Preserve, Texas, NID 4560. C) Lobocriconema sp., juvenile, head with visible submedian lobes, body scales with fine terminal projections, Spring Creek Prairie, Nebraska, NID 4514. D) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Nine-Mile Prairie, Nebraska, NID 4527 E) Lobocriconema sp., cephalic profile with protruding stylet, Nine-Mile Prairie, Nebraska, NID 4529. F) Lobocriconema sp., head profile lacking submedian lobes, Tunica Hills, Louisiana, NID 4574. G) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4533. H) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4526. I) Lobocriconema sp., face view lacking submedian lobes, Great Smoky Mountains National Park, Purchase Knob, NID 4570. in Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions
Few juveniles or males were collected. Only four males from groups 7, 8, 9, and 11, all in clade D, were included in the dataset. The male in Fig. 13E–H conforms to the general morphological description of males in Lobocriconema with an undifferentiated labial region, the absence of a stylet, a degenerate pharyngeal region, a FIGURE 7. SEM images of specimens representing clades D (A–H) and B (I). NID numbers are associated with unique specimens, all are females except image C. A) Lobocriconema sp., face view with conspicuous labial disc surrounded by irregular labial structure, Nine-Mile Prairie, Nebraska, NID 4533. B) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Big Thicket National Preserve, Texas, NID 4560. C) Lobocriconema sp., juvenile, head with visible submedian lobes, body scales with fine terminal projections, Spring Creek Prairie, Nebraska, NID 4514. D) Lobocriconema sp., face view lacking submedian lobes and displaying subcuticular labial structure, Nine-Mile Prairie, Nebraska, NID 4527 E) Lobocriconema sp., cephalic profile with protruding stylet, Nine-Mile Prairie, Nebraska, NID 4529. F) Lobocriconema sp., head profile lacking submedian lobes, Tunica Hills, Louisiana, NID 4574. G) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4533. H) Lobocriconema sp., tail with closed vulva, Nine-Mile Prairie, Nebraska, NID 4526. I) Lobocriconema sp., face view lacking submedian lobes, Great Smoky Mountains National Park, Purchase Knob, NID 4570.
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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.