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101 results for “Microsatellite genotyping”
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"
<p>These data sets were used for analyses in the publication "Bidirectional gene flow between <em>Fagus sylvatica</em> L. and<em> F. orientalis</em> Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a></p> <p>For details about the data, please read the corresponding ReadMe files.</p>
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
<p>Genetic research is a key component to modern wildlife conservation, but it is contingent on the collection of reliable and high-quality genetic samples. Invasive genetic sampling techniques have potential to negatively impact individuals, which may be prohibitive when working with threatened and endangered species. Prior to sample collection, project managers must try to balance the negative impact on individuals included in the study with the demand for DNA and the difficulty of obtaining samples. Although established methods for blood and tissue collection in reptiles meet the need for high-quantity and quality DNA, they inherently require longer handling times and more skill to obtain. Thus, non-invasive DNA collection methods, such as cloacal swabs, may be preferred when animal welfare is a priority. Cloacal swabs are quicker, easier, require less training and reduce handling time. To evaluate cloacal swabbing as an alternative to collecting blood, we obtained both cloacal and blood swabs. We extracted DNA from cloacal and blood cells that were collected from 23 Timber Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280), concentration, and microsatellite genotyping. Our results show high-quality DNA can be obtained from both cloacal swabs and blood samples, but quality and concentration of DNA was significantly lower from cloacal swabs. Further, degradation and contamination affects the performance of cloacal DNA when compared to blood DNA in microsatellite-based genotyping. Although we recommend collecting blood samples whenever possible to obtain the highest-quality DNA, cloacal swabs represent a viable alternative for genetic sampling when using microsatellite loci as genetic markers.</p>
Datasets for microsatellite genotype for natural populations and seedlings from six mother trees, and seedling survival and growth records
Open the record for dataset details and reuse information.
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
Open the record for dataset details and reuse information.
Microsatellite genotypes of bearded vultures (Gypaetus barbatus)
<p>Multilocus microsatellite genotypes of 236 <em>Gypaetus barbatus </em>individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is given as "0".</p>
Microsatellite genotypes
<p>Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits, on evolutionary divergence, and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (<i>Sceloporus arenicolus</i>). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of <i>S. arenicolus</i>. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of <i>S. arenicolus</i>.</p>
Microsatellites genotyping for common and lesser cuckoos
<p>In a parasite species, the dispersal of individuals should be dependent on host species to which they are specialized; thus, any sexual/individual difference in host specificity may influence their dispersal patterns, and hence, population genetic structures. However, such predictions remain poorly verified in generalist avian brood parasites that is composed of multiple lineages of host-specific races. Here, we show the dispersal consequences inferred from spatial genetic structures and their association with host specificity in brood parasitic common cuckoos <i>Cuculus canorus</i> in which female-specific host race formation has been widely accepted. Genetic sampling from adult cuckoos confirmed restricted dispersal in both sexes and resultant genetic structures between populations where different host species breed allopatrically, whereas it was not the case between distant areas inhabited by the same host species. Contrary to the female host race hypothesis, our results demonstrate that male cuckoos may also have host specificity and disperse accordingly, conclusively allowing us to hypothesize the formation of host race including both sexes.</p>
Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata
<p>Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone <i>Diadumene lineata</i> exhibits temperature-dependent fission which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in F<i><sub>is, </sub></i>which makes the meaning of mean multilocus F<i><sub>is</sub></i> unclear.</p>
Metadata: Microsatellite genotypes for Seriatopora hystrix and Acropora millepora in Indonesia
<p>Microsatellite genotypes for <em>Seriatopora hystrix</em> and <em>Acropora millepora</em> in Indonesia as used in the paper "Differences in genetic diversity and divergence between brooding and broadcast spawning corals across two spatial scales in the Coral Triangle region."</p>
Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)
<p>For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant <i>Trachymyrmex septentrionalis</i> using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.</p>
Microsatellite genotypes of A. chlorotica parentage analysis
<p><span>Historical events of population fragmentation, expansion and admixture over geological time may result in complex patterns of reproductive isolation and may explain why, for some taxa, the study of mitochondrial (mt) and nuclear (nu) genetic data results in discordant evolutionary patterns. Complex patterns of taxonomic diversity were recently revealed in earthworms for which distribution is largely the result of paleogeographical events</span><span>. Here, we investigated reproductive isolation patterns in a complex of cryptic species of earthworms in which discordant patterns between mt and nu genetic lineages were previously revealed, the <em>Allolobophora chlorotica</em> aggregate. Using four nu microsatellite markers and a fragment of the <em>cytochrome c oxidase</em> <em>subunit I</em> mt gene we carried out a parentage analysis to investigate </span><span>the mating patterns </span><span>(i) </span><span>between individuals belonging to two divergent mt lineages that cannot be distinguished with nu markers and (ii) between individuals belonging to lineages that are differentiated both at the mt and nu levels. Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mt lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In crosses between lineages that diverged exclusively at the mt level, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest concerning the use of male/female function between mating partners. In crosses between lineages that diverged both at the mt and nu level, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Different degrees of reproductive isolation, from differential sex allocation to post-zygotic isolation, were thus revealed. Lineages appear to be at different stages in the speciation process, which likely explain the observed opposite patterns of mito-nuclear congruence.</span></p>
Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program
<p><span>Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017 – 2020) of the genetically-informed captive breeding program for the Floreana Island Galapagos giant tortoise, </span><em><span>Chelonoidis niger</span></em><span>. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome </span><span>persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, <em>Chelonoidis becki</em>. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. </span><span>We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. </span><span>This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding. </span></p>
Microsatellite genotypes of Cercidiphyllum japonicum seeds and identity numbers of the seed parents
<p>Genotypes at five microsatellite loci of 361 <em>Cercidiphyllum japonicum </em>seeds and identity numbers of their seed-parents in a population distributed over about 80 ha along a stream within Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan. Based on this and another data (<a href="https://doi.org/10.5061/dryad.zcrjdfnb7">https://doi.org/10.5061/dryad.zcrjdfnb7</a>), pattern of gene dispersal via pollen in this population was estimated by neighborhood model approach and Two generation analysis (TwoGener). These data set can be reused for review of the study and would be useful for comparison with other studies on gene dispersal of tree species.</p>
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
Microsatellite genotypes of South African Cape vulture (Gyps coprotheres)
<p>Multilocus microsatellite genotypes of 605 <em>Gyps coprotheres</em> individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is encoded as "0".</p>
Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping non-habituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Roe deer microsatellite genotype data
<p>In the early 1800s, the European roe deer (<em>Capreolus capreolus</em>) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonised Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonisation and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies and explore the opportunity for development of forensic traceability tools. The results concerning the recolonisation origin support natural, multidirectional immigration from neighbouring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad scale geographic origin assignment using nuclear markers to support law enforcement.</p>
Asian elephant microsatellite genotypes: Nakai Plateau and Sepon mines region, Lao PDR
<p class="MsoNormal">Habitat loss and fragmentation are leading contributors to the endangered status of species. In 2006, the Nakai Plateau contained the largest known Asian elephant (<em>Elephas maximus</em>) population in the Lao People's Democratic Republic (Lao PDR), and the population was among those with the highest genetic diversity reported for Asian elephants. In 2008, completion of the Nam Theun 2 hydroelectric dam inundated much of the Plateau, resulting in the loss of 40% of elephant habitat. We<span> studied elephant presence, movements, and the incidence of human–elephant conflict (HEC) on the Nakai Plateau and surrounding areas from 2004-2020, before and for 12 years after dam completion. To examine contemporary population dynamics in the Nakai elephants, we </span>used genetic sampling to compare <span>minimum population numbers, demography, and levels of genetic diversity from the wet and dry seasons in 2018/2019, 10 years after dam completion, </span>with those reported in a pre-dam-completion genetic survey.<span> </span>After dam completion, we found a major increase in HEC locally and the creation of new, serious, and persistent HEC problems as far as 100 km away.<span> </span>While we were unable to compare estimated population sizes before and after dam completion, our data revealed a decrease in genetic diversity, a male-biased sex ratio, and evidence of dispersal from the Plateau by breeding-age females. Our results raise concerns about the long-term viability of this important population as well as that of other species in this region. Given that hydropower projects are of economic importance throughout Laos and elsewhere in southeast Asia, this study has important implications for understanding and mitigating their impact.</p>
Microsatellite genotypes for adult and seedlings of the temperate seagrass (ribbon weed), Posidonia australis, from four meadows at Rottnest Island, Western Australia
<p>Adult shoots and seedings of the ribbon weed (<em>Posidonia australis</em> Hook.f.), a widespread temperate seagrass, were sampled from four meadows around Rottnest Island, Western Australia. The data set contains multilocus genotypes for adult shoots from four meadows and seedlings from three meadows over two consecutive years. The metadata file contains: Pop number (1 – 10), Sample site, Latitude (S), Longitude (E), individual sample code, year of sampling, life stage (adult shoot or seedling), genotypes (2 columns per locus). The seven polymorphic microsatellite loci are: <em>Pa</em>A1, <em>Pa</em>A105, <em>Pa</em>A120, <em>Pa</em>B6, <em>Pa</em>B8, <em>Pa</em>B112, <em>Pa</em>D113. Most genotypes are diploid, however, 3N genotypes are included.</p>
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