Conservation Genetics Resources最新文献

Spatial mark-recapture abundance estimates obtained from fecal genotyping are becoming an essential component of conservation of carnivores. The bobcat (Lynx rufus) is a widespread carnivore in California, USA, that until recently lacked robust demographic data. To facilitate a statewide abundance study, we created a single nucleotide polymorphism (SNP) genotyping panel for individual identification. For SNP discovery, we performed restriction site-associated DNA sequencing (RADseq) on 78 samples collected throughout California and subsequently designed a panel of 96 SNPs for sequencing on a microfluidic platform. This panel includes loci to identify sex and differentiate bobcats from other common carnivores. The panel reliably differentiates individuals when using DNA extracted from feces, with 89% of samples amplifying at > 90% of SNPs. Importantly, we found autosomal SNPs were monomorphic in the closely related Canada lynx (L. canadensis) suggesting the panel would still be effective for bobcat study in areas of sympatry. Fecal genotyping provides a cost-effective, noninvasive method for population monitoring and detecting individual movement. Our panel generates standardized genotypes that can be analyzed across laboratories and used for continued bobcat monitoring in California and other western states.

A total of 42 polymorphic simple sequence repeat (SSR) markers were developed and characterized from genome sequences for the “zig-zag eel”, Mastacembelus armatus, to safeguard its natural resources. Polymorphisms of these SSR markers were evaluated in a natural population of 35 individuals. The number of alleles per locus ranged from two to fourteen. The observed heterozygosity and expected heterozygosity varied from 0.031 to 0.813, and from 0.091 to 0.852, respectively. Three SSR loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These loci have been characterized for the first time and will be useful for genetic conservation and marker-assisted breeding of M. armatus.

The application of Genotyping-by-Sequencing (GBS) approaches is often restricted in wildlife monitoring and conservation genetics, as those fields often rely on noninvasively collected samples with low DNA content. Here we selected a subset of informative single-nucleotide polymorphisms (SNPs) from genome-wide data for lineage discrimination of a locally endangered Eurasian rodent, the hazel dormouse (Muscardinus avellanarius), and designed a microfluidic 96 SNP genotyping assay suitable for noninvasively collected samples. Analyses of 43 samples from different European countries confirmed successful discrimination of the Eastern and Western lineage and local substructure within those lineages, proving the suitability of the developed panel for identifying evolutionary significant units and conservation units. Application with 94 hair and scat samples collected in a recent monitoring study on the hazel dormouse in Southern Germany resulted in > 99.5% amplification success showing the applicability of the new tool in genetic wildlife monitoring and conservation studies.

Cuora flavomarginata is an endangered and protected species in China as well as listed as endangered under the criteria of the IUCN. Single nucleotide polymorphisms (SNPs) are an important component of animal genomic diversity, and are invaluable as genetic markers in the fields of evolutionary and conservation genetics. In this study, a total of 40 novel SNP markers were developed based on whole-genome resequencing. The analysis of the 40 SNP genotypes in 56 turtles showed that the observed heterozygosity and expected heterozygosity ranged from 0.1786 to 0.6071 and 0.1641 to 0.5043, respectively. The minor allele frequency ranged from 0.1161 to 0.911, and the polymorphism information content ranged from 0.252 to 0.455. Among these SNPs, only one SNP was found to deviate from Hardy-Weinberg equilibrium significantly after Bonferroni correction (P < 0.01). These SNP markers could be a valuable tool for genetic management and population conservation in this endangered species.

To identify tiger species on the basis of suspected feces or fur samples collected during field surveys, we developed a duplex PCR system that co-amplified two mitochondrial DNA (mtDNA) amplicons to simultaneously generate a mtDNA quality marker (221 bp) from the cytochrome b (MT-CYB) gene and a tiger marker (314 bp) from the NADH dehydrogenase subunit 4 (MT-ND4) gene. Appearance of the former marker indicated sample-derived mtDNA quality, and the tiger marker was present in the tiger samples but absent from non-tiger samples. A blind test of a suspected tiger fecal sample validated reliability of our system, and a parallel experiment using a previously published approach further confirmed the accuracy of our system. This method has significant practical value for the field management and conservation of tigers because it can be used to analyze suspected samples.

Non-invasive genetic sampling can be used in research, monitoring, and conservation of wild animals to, for example, provide insights into diets, identify individuals and estimate population sizes. Non-invasive genetic sampling may be especially useful to monitor elusive species because DNA can be derived from materials such as hairs and faeces without handling individuals. However, the reliability of the results derived from this technique is dependent on the quality of DNA obtained from samples, which can deteriorate from exposure to environmental conditions and sample age. While freshness of the sample is an important factor, the combined effect of different field conditions on the genotyping success is not fully understood. To address this gap, we systematically investigated the effects of sample age and environmental conditions on genotyping success of faeces, in an experimental setting of four treatments that combined rain and temperature conditions typical of central European climates. We compared the performance of a microsatellite marker set and a SNP panel for red fox (Vulpes vulpes), as well as a microsatellite marker set for pine marten (Martes martes) from faeces resampled over 21 days. We found that genotyping success decreased significantly with sample age, however environmental treatments did not impact the success. Furthermore, the SNPs we used amplified more successfully over time than the respective microsatellites. Therefore, the use of SNPs instead of conventional microsatellites, when using faecal samples for analysis relying on correct amplifications, could be advantageous. We recommend to prioritise the collection of fresh faeces regardless of environmental conditions.

Polycystic ovary syndrome (PCOS) and type-2 diabetes mellitus (T2DM) share common genetic features. Transcription factor 7-like-2 (TCF7L2) is consistently studied T2DM susceptibility locus. However, limited studies on TCF7L2 have failed to demonstrate any link with the PCOS risk. Therefore, we investigated the association of TCF7L2 polymorphic variant (rs12255372) with the PCOS risk. We recruited 120 PCOS cases, diagnosed as per Rotterdam 2003 criteria, and an equal number of age-matched controls. Besides a detailed clinical assessment, subjects underwent biochemical and hormonal profiling. Genotyping for rs12255372 was done by PCR-RFLP. Conditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (95%CIs) of genotype-phenotype correlations. The PCOS cases reported fewer menstrual cycles per year and exhibited signs of hyperandrogenism. The heterozygous genotype of rs12255372 was strongly associated with the PCOS risk (OR = 2.00; 95%CI: 1.07-3.76). Unlike controls, only 3 cases harbored TT genotype, and the PCOS risk persisted in the dominant model (GT + TT) as well. Moreover, we found a synergistic effect modification by the variant genotype in the subjects who had family histories of T2DM, hirsutism, or menstrual irregularities. We report a significant association of the TCF7L2 polymorphic variant rs12255372 with the PCOS risk.

The polar bear (Ursus maritimus) is a species particularly vulnerable to the effects of climate change. As the climate warms, polar bears will be forced to move to more suitable habitats which are likely to shrink, adapt to the new conditions, or decline in population size. However, the genomic diversity within and among all 19 subpopulations of polar bears, and therefore their adaptive potential, is currently unknown. In addition, warmer climates are likely to result in more frequent contact between polar bears and grizzly bears (U. arctos), with which they can hybridize. Here we describe the development, quality control, and application of the Ursus maritimus V2 SNP chip. This 8 K SNP chip contains loci explicitly selected to assess both RAD-derived and transcriptome-derived loci, as well as SNPs to detect hybridization between species. A total of 7,239 loci (90.3% of those printed) were successfully genotyped, with over 99% genotype concordance for individuals typed in duplicate on this chip, and between individuals typed here and on the Ursus maritimus V1 SNP chip. Using simulations, we demonstrate that the markers have high accuracy and efficiency to detect hybridization and backcrosses between polar bears and grizzly bears. However, empirical analysis of 371 polar bears, 440 grizzly bears, and 8 known hybrids found no novel instances of recent hybridization. The Ursus maritimus V2 SNP chip provides a powerful tool for monitoring the adaptive potential of this species along with assessing population structure, quantitative genomics, and hybridization in polar bears.

Finless porpoises (Neophocaena asiaeorientalis) currently face population decline caused by significant human activities and are categorized as endangered on the International Union for Conservation of Nature (IUCN) Red List; however, information on their habitats is currently insufficient. Although conducting visual surveys to determine the distribution of cetaceans is common, visual observation of finless porpoises is challenging owing to their specific morphological and ecological characteristics. In this study, we developed an environmental DNA (eDNA) assay for species-specific detection of finless porpoises. To test the utility of the assay, we conducted a visual survey in parallel with an eDNA survey by collecting water samples from 50 sites throughout Osaka Bay. We visually found a finless porpoise at one location and detected eDNA at nine sites, including sites near the visual observation site and those with rare sightings of finless porpoises. Therefore, in this study, we suggest that the use of eDNA analysis for distribution surveys of finless porpoises will enable more efficient surveys. The proposed eDNA technique can not only be applied to the distribution surveys finless porpoises but also to those of other cetacean species.

A total of 20 polymorphic microsatellites were developed and characterized for a potential aquaculture species, Chanos chanos, utilizing the comprehensive whole genome data of C. chanos obtained from the GenBank database (accession number: LR697106). Using the MIcroSAtellite (MISA) tool, potential microsatellite motifs were identified in the assembled contigs and unigenes and with the PRIMER 3 input software (Version 4.1.0), new primers were developed. The number of alleles per locus in C. chanos varied from 9 to 16, with observed heterozygosities ranging from 0.710 to 0.926, while the expected heterozygosities were within the range of 0.720 to 0.902. Among the 20 microsatellite loci, the majority exhibited PIC values > 0.75. Validation of these microsatellite markers proved that these markers can be used as a significant tool for analysing genetic differentiation as well genetic relationships among C. chanos.