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394 results for “Microsatellite data”

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dryad36/100

Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data.

Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.

opencc-zeroOct 2022View details →

dryad36/100

Microsatellite data from Mediterranean mussels (Mytilus galloprovincialis) from the eastern coast of the Adriatic Sea

Microsatellite data from eighteen populations of Mediterranean Mussels from the eastern coast of the Adriatic Sea collected between 9/2015 and 5/2017.

opencc-zeroJan 2023View details →

dryad36/100

Roe deer microsatellite genotype data

In the early 1800s, the European roe deer (Capreolus capreolus) 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.

opencc-zeroFeb 2023View details →

zenodo36/100

Microsatellite data

Scored alleles of 15 microsatellite markers used in a population genetics study of Harmonia axyridis. Includes global samples, but with a strong focus on South Africa.

opencc-by-4.0May 2023View details →

dryad36/100

American Crow SNPs and microsatellite data

Infectious diseases can cause steep declines in wildlife populations, leading to changes in genetic diversity that may affect the susceptibility of individuals to infection and the overall resilience of populations to pathogen outbreaks. Here, we examine evidence for a genetic bottleneck in a population of American crows (Corvus brachyrhynchos) before and after the emergence of West Nile virus (WNV). More than 50% of marked birds in this population were lost over the two-year period of the epizootic, representing a 10-fold increase in adult mortality. Using analyses of SNPs and microsatellite markers, we tested for evidence of a genetic bottleneck and compared levels of inbreeding and immigration in the pre- and post-WNV populations. Counter to expectations, genetic diversity (allelic diversity and the number of new alleles) increased after WNV emergence. This was likely due to increases in immigration, as the estimated membership coefficients were lower in the post-WNV population. Simultaneously, however, the frequency of inbreeding appeared to increase: mean inbreeding coefficients were higher among SNP markers, and heterozygosity-heterozygosity correlations were stronger among microsatellite markers, in the post-WNV population. These results indicate that loss of genetic diversity at the population level is not an inevitable consequence of a population decline, particularly in the presence of gene flow. The changes observed in post-WNV crows could have very different implications for their response to future pathogen risks, potentially making the population as a whole more resilient to a changing pathogen community, while increasing the frequency of inbred individuals with elevated susceptibility to disease.

opencc-zeroMay 2023View details →

dryad36/100

Data from: Novel microsatellite markers for epiphytic bromeliad Tillandsia recurvata L., in an urban landscape in South-eastern Brazil

The authors present seven novel microsatellite markers for Tillandsia recurvata L. The genome assemble sequences of T. recurvata were obtained from NCBI (7.2Gb) (Sayers et al. 2022). The BioProject Accession and accession numbers are PRJNA701548 and SRX10089449, respectively. The microsatellite identification software Krait (0.5.2) (Du et al. 2018) was used to detect suitable microsatellites, both genome-wide and in the noncoding regions of T. recurvata. The single sequence repeats (SSRs) were refined to a minimum number of seven repeats of di-, tri-, or tetra-nucleotide repeat motifs. These sequences were further limited to SSRs of more than 100bp in length and low GC content (<50%). Krait (0.5.2) (Du et al. 2018) was also used to design the primers for the selected SSR sequences, in conjunction with the integrated Primer3 software. The criteria for primer selection included: a primer length of 18-26bp, an optimal melting temperature (Tm) of 54-59°C and GC content of <50%. These designed primers were single-plexed and amplified using the following PCR cycle: initial denaturation (95°C for 3 min), 34 cycles of 95°C for 30s, annealing for 30s (JP01-JP12: 54°C, 4873TD + 35251TD: 56°C, 19286TD: 53°C, 5044TD + 186664TD + 214633TD: 58°C), 72°C for 1 min and a final extension of 72°C for 5 mins. The authors make this information available to other researchers, to continue the investigation of epiphyte genetics.

opencc-zeroJun 2023View details →

zenodo36/100

Raw data containing microsatellite genotypes and otolith microchemistry data for Lutjanus argentiventris individuals from Galapagos (Ecuador) and the Gulf of California (Mexico)

The dataset contains the raw microsatellite genotypes and otolith microchemistry data for yellow snapper (Lutjanus argentiventris) individuals from Galapagos (Ecuador) and the Gulf of California (Mexico), described in the journal publication: Cavole LM, Munguia-Vega A, Miller JA, Salinas-de-Leon P, Marin Jarrin JR, Johnson AF, Laplane ER, Giron-Nava A, Aburto-Oropeza O (2023) Combining otolith chemistry and genetics to infer the population structure of yellow snapper Lutjanus argentiventris. Ecosphere.

opencc-by-4.0Aug 2023View details →

dryad36/100

Macrocystis pyrifera before (2008) and after (2018-19) microsatellite data in Structure format

Given the impacts of climate change and other anthropogenic stressors on marine systems, there is a need to accurately predict how species respond to changing environments and disturbance regimes. The use of genetic tools to monitor temporal trends in populations gives ecologists the ability to estimate changes in genetic diversity and effective population size that may be undetectable by traditional census methods. Although multiple studies have used temporal genetic analysis, they usually involve commercially important species, and rarely sample before and after disturbance. In this study, we run a temporal analysis of giant kelp, Macrocystis pyrifera, genetic diversity over the scope of 10 years (2008-2018) using the same microsatellite marker panel to assess the genetic consequences of disturbance in several populations of giant kelp (Macrocystis pyrifera) in the Southern California Bight. The study is a rare pre- and post-disturbance microsatellite analysis that included declines to giant kelp caused by the 2015/16 El Nino Southern Oscillation event. We used canopy biomass estimated by remote sensing (Landsat) to quantify the extent of disturbance to kelp beds, and sea surface temperature data to understand how kelp was pushed towards its temperature limits during this period. Despite prolonged periods with decreased canopy at several sites, no changes in genetic structure and allelic richness were observed. We argue that giant kelp in the region is best described as a "patchy population" system where true extinctions are rare. We discuss how deep refugia of subsurface sporophytes and cryptic microscopic life stages could have kept genetic diversity through disturbance. Given the increasing effects of climate change and uncertainty in modeling impacts of species with cryptic life history stages, we suggest further investigation to reveal the role such stages play in species resilience. Genetic monitoring studies of sites selected by remote census demographic and climate surveys should be continued in the future given the predicted impacts of climate change.

opencc-zeroAug 2023View details →

dryad36/100

Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms

Red and brown seaweeds are species with high ecological and economic importance. Here we report the feasibility of cost-effective molecular marker development in 6 species from different clades. Microsatellites markers of two brown seaweed species Alaria esculenta, Pylaiella littoralis, and of four red seaweed species Calliblepharis jubata, Gracilaria gracilis, Gracilaria dura and Palmaria palmata were identified and characterized using genomic sequences of Double-Digest Restriction site Associated DNA (ddRAD). A total of 64,623,186 reads were generated from two runs of multiplexed Illumina Miseq sequencing for which 30,636 reads containing microsatellites and 15,443 microsatellite loci with primers pairs were found. Five hundred seventy-six primers pairs were selected for amplification trials and levels of polymorphism. From the 338 that gave a positive amplification, 142 primers pairs were polymorphic. For genetic analyses two or three populations per species from 13 different geographic locations were used. A total of 28 usable polymorphic markers for A. esculenta, 18 for P. littoralis, 11 for C. jubata, 14 for G. gracilis, 21 for G. dura and 13 for P. palmata were developed. The overall number of alleles per locus ranged from 2 to 22. These 105 new microsatellite markers will be useful for further studies of population genetics, breeding programs and conservation genetics of these species. Compared with traditional approaches, our study yielded thousands of microsatellite loci in a short time with affordable costs in six different species. This study based on ddRAD-sequencing for the development of microsatellite markers provides preliminary data using a few individuals from two distinct populations on the genetic structure and reproduction mode of a non-model species as shown with the detection of clonality for the two red algae, C. jubata and G. dura and the detection of highly genetically divergent populations corresponding probably to different cryptic species under the name of P. littoralis.

opencc-zeroSep 2023View details →

dryad36/100

Genotype data of Philippine native pigs, Duroc, Landrace, Large White and Berkshire, using 20 ISAG-FAO recommended microsatellite markers

Microsatellite genotyping is a cost-effective method for the genetic diversity analysis of under-studied populations, such as the Philippine native pigs. We genotyped n = 196 pigs representing 7 Philippine native pig populations (n = 20 to 27 for each population) and 4 commercial transboundary breeds (n = 9 to 11 for each population). Twenty microsatellite markers, recommended by the International Society of Animal Genetics (ISAG)-FAO, were used to generate the dataset for population analysis (S0005, S0155, S0026, S0355, Sw830, Sw2410, Swr1941, Sw632, Sw24, S0228, Sw936, S0097, Sw857, Sw122, Sw2406, IGF1, Sw240, S0090, S0226, Sw72). S0218 was used as a sex marker (data not shown). All loci, except Sw24, did not deviate from Hardy Weinberg equilibrium. Each marker showed an average PIC of 0.779. A total of 260 alleles of length 86 to 272 bp were obtained. Using this dataset, we determined population structure and conservation priorities in the Philippine native pigs. This dataset contains both the raw files (.fsa) and the processed file (.txt). This dataset can be used by colleagues to increase their research coverage and achieve multi-population and multi-country comparisons, especially among Asian indigenous pigs.

opencc-zeroOct 2023View details →

dryad36/100