Conservation Genetics Resources最新文献

The Chinese softshell turtle (Pelodiscus sinensis) is a kind of subaquatic reptile with high nutritional value, medicinal value and economic value. However, the number of wild turtles has dropped dramatically due to excessive fishing and habitat destruction. Artificial breeding of the turtle is facing the dilemma of germplasm degradation and lack of seedlings, which seriously hinders the sustainable development of the turtle industry. In the present study, 60 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.0312 to 0.7500 and from 0.0312 to 0.4841, respectively, and the minor allele frequency ranged from 0.3333 to 0.5000. Only four loci showed significant deviation from Hardy–Weinberg equilibrium. The present study will provide a valuable tool for population study and resource conservation.

Environmental DNA (eDNA) surveys have gained popularity as a highly sensitive detection tool that generally outperform traditional detection techniques. eDNA surveys can provide a cost-effective means to identify species’ distributions and recent incursions, informing the control or containment of invasive species. The red-eared slider turtle, Trachemys scripta elegans, is one of the world’s most invasive species and is listed as a priority pest species for management in Australia. In this study, we validate two eDNA assays to detect this invasive turtle in Australia. We demonstrate high sensitivity in a laboratory setting and perfect detection rates in mesocosms for one of these eDNA assays but show that this does not translate to high detection rates in urban waterbodies at sites of known occupancy. In fact, our results suggest eDNA surveys provide sub-optimal performance compared to traditional detection methods for T.s. elegans. We suggest the capacity for eDNA surveys to provide a highly sensitive detection tool must be evaluated in natural environments on a species-by-species basis to understand any limitations and to avoid high error rates from eDNA surveys leading to wasted resources or inappropriate management decisions. For management of T.s. elegans in Australia, clearly defining the utility of certain eDNA based approaches to detect T.s. elegans and their incursions is vital for effective management of this pest species.

The sleepy cod Oxyeleotris lineolata is native to northern Australia. At present, there is little information on the genome information of the sleepy cod. In this study, a total of 48 novel single nucleotide polymorphism (SNP) markers were developed based on whole-genome resequencing. The analysis of the 48 SNP genotypes in 58 fish showed that the observed heterozygosity and expected heterozygosity ranged from 0.3030 to 0.6667 and 0.2133 to 0.8541, respectively. The minor allele frequency ranged from 0.1211 to 0.4899, and the polymorphism information content ranged from 0.1902 to 0.3749. Among these SNPs, seven SNPs were found to deviate from Hardy–Weinberg equilibrium significantly (P < 0.05). These SNP markers could find application in genetic linkage maps and association analysis with growth traits of sleepy cod.

Sampling the DNA of rare animal species should have minimal impacts on individual health. This can be accomplished through non-lethal/non-invasive sampling. Few of these methods have been developed for invertebrates, including the Mollusca, which are in global decline. Tissue clipping the foot is a common non-lethal method for gastropods. However, it causes permanent damage and is inappropriate for smaller snails. This study used Flinders Technology Associates (FTA) cards to sample DNA from snail mucus for species of different sizes and habitat types, and across evolutionarily distant lineages. In a survival assay, the death rate of individuals sampled with FTA cards (12.1%) was greater than in the controls (3.7%), but the difference was not significant. Of 224 individuals representing 27 snail species (17 Hawaiian native, ten non-native) sampled using both FTA cards and tissue clipping, 80.4% of FTA samples and 91.6% of tissue samples amplified for COI, a significant difference. COI sequencing success did not differ significantly between the two methods. For individuals that failed to produce a COI sequence, an attempt was made to sequence 16S. For 16S, amplification and sequencing rates did not differ significantly between FTA and tissue samples. Habitat type and shell size did not affect FTA sampling success. Phylogenetically basal taxa exhibited lower success rates, but this may have been because of difficulty in sampling operculate taxa, and not because of identity. These results indicate that the FTA sampling is a viable non-lethal alternative to tissue clipping and can be used for diverse gastropods.

Koreanohadra koreana (K. koreana) is an endemic species in South Korea that is listed as endangered. While the ecology and phylogenetics of K. koreana have been studied, its morphological similarity to the related species Koreanohadra kurodana (K. kurodana), can make species identification difficult. Furthermore, this has led to confusion when determining essential habitat information for the conservation of K. koreana. To bypass this issue, we have developed a non-invasive species identification method that can genetically differentiate between them. While there are already various non-invasive genomic DNA (gDNA) extraction methods that utilize the mucus from mollusks, they are limited as they require the target species to be physically located. To address this, in this investigation a method of extracting gDNA from the feces of snails was developed. The method utilized a primer set to amplify a cytochrome b fragment from K. koreana but not K. kurodana or other terrestrial snails. The feces of terrestrial snails could thus be used to obtain gDNA to a genetically usable level if collected within 5 days of excretion. This non-invasive species identification method using feces will help to facilitate genetic research without harming the endangered species and if the target species is not physically in the habitat. Moreover, K. koreana and K. kurodana could perhaps be further distinguished, using their habitat information to help facilitate essential conservation measures.

Red sea bream is a commercially valuable fish that is used as ingredients in the food industry. To prevent a decrease in fishing yield, farmed red sea bream is released. However, this may cause a decrease in the genetic diversity of wild populations, so systematic resource management is required. In this study, 68 single nucleotide polymorphism (SNP) markers were developed using a genotyping-by-sequencing (GBS) analysis. The minor allele frequency (MAF) ranged from 0.1802 to 0.5000, the observed heterozygosity (H_o) ranged from 0.0864 to 0.5000, expected heterozygosity (H_e) ranged from 0.2955 to 0.5000, and the polymorphism information content (PIC) ranged from 0.2518 to 0.3750. Of these SNPs, 25 loci significantly deviated from the Hardy–Weinberg equilibrium after a Bonferroni correction (p < 0.00074). These SNP markers will be useful for the further genetic analysis of the red sea bream population.

A non-invasive, fast, and reliable method for sex identification of the giant panda (Ailuropoda melanoleuca) was developed by genotyping five SNPs located at the sex chromosome amelogenin (AMEL) paralogs. The giant panda’s sex can be accurately distinguished by the homozygous or heterozygous SNP genotypes. Mass spectrometry assay and Sanger sequencing both successfully genotyped tissue and fresh fecal samples collected from known-sex giant pandas. Additionally, we simulated the conditions of wild fecal samples, which were naturally degraded for up to two weeks, and successfully genotyped these samples by mass spectrometry assay in parallel. These results suggest that this is a powerful method for sex determination in highly degraded and lower concentrated DNA samples.

The top-mouth culter Erythroculter ilishaeformis is a kind of carnivorous fish that is currently a widely distributed fish in China, which is a commercially important freshwater fish in China. However, only few effective molecular markers on E. ilishaeformis are available. In this study, nine muscles and liver tissues of cDNA libraries of E. ilishaeformis were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 86,574 sequences from 80,945,107 paired-end reads were generated. 55 novel simple sequence repeat (SSR) markers were developed based on high-throughput sequencing. After genetic diversity analysis, observed heterozygosity (Ho) was from 0.1613 to 0.4839. Expected heterozygosity (He) was from 0.1507 to 0.3728. Minor allele frequencies (MAFs) were from 0.3333 to 0.5000, and Hardy-Weinberg values were relatively balanced. These SSR markers developed from transcriptome sequencing will be as a useful tool to exploit populations genetic of E. ilishaeformis.

Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function that can identify sex-linked markers in species with partially non-recombining sex chromosomes. We test the accuracy and speed of our function with an example dataset from a species of conservation concern, the White Shark, Carcharodon carcharias. We further compare our method against other approaches and find that our method detects more sex-linked markers that can be reliably mapped to reference genomes. Overall, we provide a conservation and fisheries-relevant tool that can reliably and efficiently assign sex from genetic data in species with a heterogametic sex and we demonstrate its utility by developing a sex-identification PCR test for White Sharks.