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385 results for “Conservation genetics”
Fig. 1. A in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 1. A – map of South Africa; B – map of the river systems in the inlay showing the sampling sites where Spinitectus petterae Boomker, 1993 was collected in Clarias gariepinus (Burchell). Abbreviations: 1 – down-stream of the Vaal River Barrage; 2 – in the Vaal Dam reservoir; 3 – down-stream of the Grootdraai Dam; 4 – Crocodile River.
Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics
<p>Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.</p>
Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: Implications for conservation and management
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Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
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Sexual selection matters in genetic rescue, but productivity benefits fade over time: A multi-generation experiment to inform conservation
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Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics
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Riverscape genetics of non-native Brook Trout to inform native Cutthroat Trout conservation
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Dataset and R code: Genetic diversity of lion populations in Kenya: evaluating past management practices and recommendations for future conservation actions by Chege M et.al
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Data from: Assessment of conservation status of Ferula huber-morathii: Association with population genetic structure and regional climate
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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
<p class="BodyAA">The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.</p>
Data from: Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range
The greater horseshoe bat (<i>Rhinolophus ferrumequinum</i>) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history of <i>R. ferrumequinum</i> colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede <i>R. ferrumequinum</i> gene flow. These results provide important information to improve the delineation of <i>R. ferrumequinum</i> management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.
Data from: Genetic diversity and conservation status of Helianthus verticillatus, an endangered sunflower of the Southern United States
<p>Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in <i>Helianthus verticillatus</i> (whorled sunflower). This endangered, wild relative of the common sunflower, <i>Helianthus annuus</i>, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for <i>H. verticillatus</i>, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of <i>H. verticillatus</i> individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between <i>H. verticillatus</i> collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of <i>H. verticillatus</i> populations in Georgia. Our results can underpin an original recovery plan for <i>H. verticillatus</i> that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.</p>
Mapping the geographic origin of captive and confiscated Hermann's tortoises: a genetic toolkit for conservation and forensic analyses
<p>The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise <em>Testudo hermanni hermanni</em>. Specific allelic ladders were created for each locus and tested on several reference samples. We used the microsatellite panel to (i) increase our understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origins of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show that the microsatellite panel and the reference dataset can play a beneficial role in reintroduction and repatriation projects when confiscated individuals need to be re-assigned to their respective macro-area of origin before release, and can assist future forensic genetic applications in detecting the illegal trade and possession of <em>Testudo hermanni</em> individuals.</p>
Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation
Little is known about the genetic diversity of coho salmon in Alaska, although this area represents half of the species' North American range. In this study, nine microsatellite loci were used to genotype 32 putative coho salmon populations from seven regions of Alaska. The primary objectives were to estimate and evaluate the degree and spatial distribution of neutral genetic diversity within and among populations of Alaskan coho salmon. Genetic analysis yielded four results that provide insight into forces influencing genetic diversity in Alaskan coho salmon and have important conservation implications: 1) significant population differentiation was found within each region; 2) the degree of differentiation (FST = 0.099) among populations was as large or larger than that reported for other Pacific salmon species in Alaska; 3) phenetic clustering of populations showed weak geographic concordance; 4) strong genetic isolation by distance was only apparent at the finest geographic scale (within a drainage). These results suggest that coho salmon populations are small relative to populations of other Pacific salmon, and the genetic diversity within and among coho salmon populations is influenced primarily by genetic drift, and not gene flow. Resource management and conservation actions affecting coho salmon in Alaska must recognize that the populations are generally small, isolated, and probably exhibit local adaptation to different spawning and freshwater rearing habitats. These factors justify managing and conserving Alaskan coho salmon at a fine geographic scale.
Data from: Behavioral syndromes shape evolutionary trajectories via conserved genetic architecture
Behaviors are often correlated within broader syndromes, creating the potential for evolution in one behavior to drive evolutionary changes in other behaviors. Despite demonstrations that behavioral syndromes are common, this potential for evolutionary effects has not been demonstrated. Here we show that populations of field crickets (Gryllus integer) exhibit a genetically conserved behavioral syndrome structure, despite differences in average behaviors. We found that the distribution of genetic variation and genetic covariance among behavioral traits was consistent with genes and cellular mechanisms underpinning behavioral syndromes rather than correlated selection. Moreover, divergence among populations' average behaviors was constrained by the genetically conserved behavioral syndrome. Our results demonstrate that a conserved genetic architecture linking behaviors has shaped the evolutionary trajectories of populations in disparate environments—illustrating an important way for behavioral syndromes to result in shared evolutionary fates.
Data from: Is MHC diversity a better marker for conservation than neutral genetic diversity? a case study of two contrasting dolphin populations
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.
Data from: Genetic structure of the Painted Bunting and its implications for conservation of migratory populations
The Painted Bunting Passerina ciris is a Neotropical songbird which breeds primarily in the United States during the summer and migrates to Mexico, Central America, southern Florida, and the Caribbean over the winter. Male Painted Buntings are brightly coloured, which makes them highly sought after as pets, particularly in Mexico, Central America and Europe. We used short sequence repeats (microsatellite DNA) to investigate the population genetic structure of the Painted Bunting and its implications in conservation management of migratory populations. We found a detectable level of population differentiation as revealed by pairwise FST and RST comparisons and Bayesian clustering analyses, with strong support for differentiation between eastern and western Painted Buntings (e.g. Oklahoma and Georgia FST = 0.1; P = 0.005; RST = 0.18; P = 0.04) in accordance with previous mitochondrial DNA analysis. We recovered additional support for two sub‐groups within the western clade. While linking migrant songbirds captured outside of the United States to their breeding populations remains a challenge, we show that natural levels of population genetic differentiation can be detected via microsatellite DNA markers and exploited in migratory connectivity studies. We also demonstrate the potential utility of our low‐cost markers for population identification of birds recovered from the pet trade by screening a small subset of samples (n = 5) collected as part of wildlife tracking. We discuss the implications of our results for future efforts to understand patterns of population decline in Painted Buntings more generally, as well as how we might expand this methodology to combat illegal pet‐trade activity in this and other songbird species.
Data from: Deciphering genetic mate choice: not so simple in group-housed conservation breeding programs
Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviours. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials, however this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalised linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three non-mutually exclusive mate choice hypotheses: (i) advantage of heterozygous individuals, (ii) advantage of dissimilar mates, and (iii) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that non-genetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
Data from: Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia
<p>Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. <em>Notelaea lloydii</em> is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among the <em>N. lloydii</em> populations. Therefore, we undertook a genome wide Single Nucleotide Polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among <em>N. lloydii</em> populations in south-eastern Queensland (SE-QLD). Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that <em>N. lloydii </em>produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un-bagged flowering and fruiting rates and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of <em>N. lloydii</em> are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.</p>
Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus
<p>The oceanic whitetip shark, <em>Carcharhinus longimanus</em>, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with <em>F</em><sub>ST </sub>but not Φ<sub>ST</sub>) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (Φ<sub>ST</sub> = 0.051; F<sub>ST</sub> = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.</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.