Conservation Genetics Resources最新文献

Metabarcoding is emerging as an alternative to morphological methods in noninvasive carnivore diet analysis based on scats. A number of metabarcoding markers have been developed but their comparative performance to recover DNA from scats remains mostly untested. We tested three markers covering a wide taxonomic range of prey items and compared them with the results of a morphological analysis. Morphological and genetic methods performed comparably regarding the identity of detected prey species, but the number of identified species varied strongly between markers. Only one, 12S-V5, amplified successfully in all samples and proved to be robust and reliable when working with the highly degraded DNA obtained from scats.

The sea urchin Tripneustes gratilla holds substantial ecological and economic importance in tropical marine ecosystems. To better understand the population structure and genetic diversity of T. gratilla, here we developed a suite of 29 polymorphic microsatellite makers based on high-throughput sequencing. The range of alleles characterized by these primers varied from 6 to 19, with an average number of 12.31. The observed and expected heterozygosities ranged from 0.250 to 1.000 and from 0.808 to 0.955, respectively. All the polymorphism information content values of the 29 loci were above 0.5, suggestive of highly informative. Demonstrating adherence to Hardy–Weinberg equilibrium, these 29 primer pairs present robust candidates for conducting population genetics and phylogeographic analyses in T. gratilla, which may provide valuable information for sustainable management and conservation efforts of this urchin.

Acquiring DNA from wild bats (Mammalia: Chiroptera) is typically undertaken utilizing highly invasive (but non-lethal) sampling techniques comprising wing biopsies and occasional blood samples. While non-invasive sampling is possible through the extraction of DNA from faecal samples, it is not always possible to acquire samples from individual bats whilst conducting fieldwork, and as such, this method is primarily applicable to roost occupancy identification. Similarly, wing swabbing is liable to cross-contamination from roost mates. Here we present the first use of oral (buccal) swabbing for successful, species-resolution DNA sequencing of Vespertilionidae and Rhinolophidae in 10 bat species (nine Vespertilionidae and one Rhinolophidae) from the UK.

Thirty polymorphic microsatellites were developed and characterised for the aquaculture important species, Green chromide, Etroplus suratensis through Illumina Sequencing with a mean read quality (Phred score) of 35.8 and the microsatellite primers were designed from the sequenced information, considering various attributes such as the number of repeats, Tm, GC content, Product size, etc. using the software PRIMER 3.0 web tool. The allele numbers ranged from 6 to 18. The mean observed heterozygosity was 0.745 and the mean expected heterozygosity was 0.762. The average PIC value for 30 microsatellite primers was 0.80 and all the loci had PIC values > 0.75. The identified polymorphic loci would help in revealing the genetic stock identification among the Pearlspot population.

Leiobagrus kingi is a species endemic to southwest China, it is listed as an endangered species. Due to habitat destruction, over-fishing and water pollution, the wild population of L. kingi has decreased dramatically in recent years. Insufficient molecular markers have limited the effective conservation of this species. In the present study, 35 novel single-nucleotide polymorphism (SNP) markers in L. kingi were isolated and characterized based on restriction site-associated DNA sequencing (RAD-seq). The minor allele frequency ranged from 0.043 to 0.481, and the observed and expected heterozygosities ranged from 0.077 to 0.678 and 0.105 to 0.505, respectively. Polymorphic information content ranged from 0.072 to 0.411. Among these SNPs, five loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.01). The novel polymorphic SNPs will be useful for future investigation of population structure and conservation genetics for this species.

A set of single nucleotide polymorphisms (SNP) was developed from the transcriptome of 10 individuals of the sea rose Pentapora fascialis (Cheilostomata) collected in Banyuls-sur-Mer Bay (NW Mediterranean sea). 53,042 putative SNPs were identified and mapped on a de novo assembled transcriptome. A selected set of 320 SNPs with highest coverage and uniquely mapped in the assembled transcriptome was tested using a MassARRAY System on 95 individuals sampled in natural rocks and artificial reefs distributed over a hundred kilometers in the NW Mediterranean (outisde Banyuls-sur-Mer Bay). A total of 177 SNPs were successfully genotyped and found to be polymorphic. Among these, 154 SNPs were in Hardy-Weinberg equilibrium over all samples, with significant linkage disequilibrium in only 21 pairs of SNPs. The newly developed loci will be a valuable tool for population genetics studies of this calcifying bryozoan species whose erect structure makes it an engineering species and a target for conservation plans.

Burbot populations in the Upper Kootenay watershed, transecting the US-Canada border, are subject to intense monitoring and management after severe declines beginning in the 1970s. Genetic monitoring is a high-priority goal for the East Kootenay Burbot Scientific Working Group, but managers do not currently have a genetic marker panel with enough resolution to understand genetic population structure and family structure in the Upper Kootenay burbot populations. Here, we detail the process of developing and optimizing a cost-effective GTseq panel to aid in the conservation of Upper Kootenay burbot. The final GTseq panel contains 331 markers with sufficient variation to accurately infer population structure and reconstruct pedigrees.

The giant panda (Ailuropoda melanoleuca), as an endemic species of China, is also a flagship species of wildlife Conservation. However, the accuracy of individual identification of giant pandas is typically problematic due to the high error rate of microsatellite typing methods. In this study, a panel of 61 SNP makers was developed for individual identification. Of these, 55 polymorphic SNP markers were successfully genotyped. The observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) ranged from 0.056 to 0.611 (mean 0.352), 0.131–0.509 (mean 0.389) and 0.099–0.389(mean 0.305), respectively. No SNPs significantly deviated from Hardy–Weinberg equilibrium (P < 0.05). Our study provides a framework for improving the accuracy of individual identification of giant pandas, especially for poor quality samples collected from the wild.

Feces of animals that forage on nectar and fruit, including many species of bats, often contain DNA that is low in quality and quantity. We developed an approach based on DNA from feces gathered passively to generate microsatellite data for individual lesser long-nosed bats (Leptonycteris yerbabuenae), which are important pollinators for columnar cacti and agave across much of Mexico and in the southwestern U.S. We collected feces from roosts near the U.S-Mexico border and developed a two-step amplification approach to characterize five highly polymorphic microsatellite loci from fecal DNA. Addition of a multiplex PCR step improved amplification success and conserved DNA extracts with a minimal increase in cost. In our initial screening of 433 samples, five focal loci distinguished individuals reliably, with a probability of identity (i.e., the probability of two unrelated individuals having the same microsatellite profile by chance) of 7.5E-09. Repeated analyses revealed a genotyping error rate < 2%. We explore the benefits and limits of our approach for population studies of lesser long-nosed bats and other nectivorous and frugivorous species that provide key ecosystem services and are often of conservation concern.

Globally, many pond turtles (Family Emydidae) are of conservation concern due to contracting ranges, increasingly fragmented habitats, and declining populations. One of these turtles, the diamondback terrapin (Malaclemys terrapin), is of concern within the United States, but surveying potential estuarine habitat for the presence of the species requires high levels of time and effort. Here a species-specific, probe-based qPCR assay for identifying terrapin DNA from environmental DNA (eDNA) is described. To expand the utility of this tool, the assay was designed to allow for potential detection of at least 19 other pond turtles taxa and the utility was tested by designing a second species-specific probe for red-eared slider (Trachemys scripta elegans) with a different fluorophore, which can be used simultaneously with the terrapin probe to detect either species. Probes were found to be species-specific and effective at detecting low levels of DNA for the target species, the diamondback terrapin (10 fg/µL) and the red-eared slider (100 fg/µL) in laboratory conditions. The assay also showed species-specific detection in environmental samples taken from field locations where one species or the other were known to reside. Through citizen science approaches, this assay could be used for discovering novel terrapin habitats, monitoring invasive red-eared slider populations or surveying other emydids, with species-specific probes, at a fraction of the cost of traditional surveys.