Conservation Genetics Resources最新文献

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.

Abstract

Despite the importance of sex-specific information for sturgeon conservation and management, sex identification has been a major challenge outside of mature adults on spawning grounds. Recent work identified a sex-specific locus (AllWSex2) that appears to be broadly conserved across many Acipenserids, but the assay was not validated for all species within the family. We tested the AllWSex2 marker in three sturgeon taxa (shortnose sturgeon Acipenser brevirostrum, Gulf sturgeon A. oxyrhinchus desotoi, and Atlantic sturgeon A. oxyrhinchus oxyrhinchus) from the Atlantic and Gulf of Mexico Coasts of North America to validate its use for sex identification. Our results indicate AllWSex2 is conserved in all three taxa, presenting a new opportunity to derive sex-specific information from tissue samples, which are routinely collected from these taxa. We found high concordance (range: 97–100%) between genotypic and phenotypic/histological methods, suggesting the assay is broadly effective. However, the small amount of discordance between the methods (< 3%) suggests further refinement may be possible.

Sika deer is indigenous to East Asia. Currently the species is extinct or are nearing the verge of extinction, in numerous places. Reduced population size is sensitive to climate change and has poor adaptation as a result of inbreeding. In this study genome-wide Single nucleotide polymorphisms (SNPs) were identified using double-digest restriction site associated digestion (ddRAD) approach and annotated further to identify genes related to fitness. A total 85,001 SNPs were retained following the quality control. Composite Likelihood Ratio (CLR) statistics found 13 stronger selective sweeps, identified sweeps overlapped with genes related to adaptation, reproduction, cellular functions. Average heterozygosity and nucleotide diversity were 0.27 and 0.29 respectively. Admixture analysis furnished a single cluster indicating no further sub-divergence of Sika deer. These findings would help fabricate appropriate genetic improvement programs by inclusion in the SNP chips, in order to get deeper insights into deer genetics, evolution, domestication and conservation.

Graphical Abstract

Bioinformatic analysis for unravelling genomic variants and selective sweep regions in Cervus nippon

In China, the brown trout is a second-level key aquatic wildlife protection animal in the Tibet Autonomous Region. In order to protect the brown trout germplasm resources in the Tibet Autonomous Region, the Institute of Aquatic Sciences of the Academy of Agricultural and Animal Husbandry Sciences of the Tibet Autonomous Region and the Heilongjiang Institute of the Chinese Academy of Aquatic Sciences collaborated on research on the key technologies of brown trout family construction. A fast in silico simulation method was employed in this study to discover numerous polymorphic SSRs. A total of 1,115,563 SSR loci with two to six nucleotide repeat motifs were mined from 40 chromosomes of the brown trout reference genome by GMATA. The whole genome sequences (30×) of 30 brown trout samples were compared to the reference genome’s chromosome sequence. Then, the HipSTR program was employed to carry out in silico genotyping through comparisons and enumerations of repeat count variants on the motifs of the SSR loci among the samples. The loci with monomorphism and high deletion in the SSR genotype data were removed, and the loci with more than one non-reference allele were retained. The final set of polymorphic SSR loci screened was 106,194. Forty-three SSR markers were randomly selected for characteristic analysis. The range of alleles per locus was 3 to 9 (mean = 5). Observed heterozygosity was in the ranged from 0.167 to 1.000. Expected heterozygosity was in the ranged from 0.155 to 0.823. Twenty-three loci significantly deviated from Hardy-Weinberg equilibrium. These SSR markers will provide valuable information for assessing the genetic diversity of constructed brown trout families and for the genetic improvement of brown trout.

Abstract

Triplophysa (Hedinichthys) yarkandensis macroptera is an endemic species in China, that is mainly distributed in Gansu Province. To date, research on this species has been very limited, focusing mainly on its taxonomy, without any available molecular markers. In the present study, we identified 55 SNP markers in T. (Hedinichthys) yarkandensis macroptera. The minor allele frequency ranged from 0.050 to 0.500, and the observed and expected heterozygosity ranged from 0.167 to 1.000 and 0.155 to 0.508, respectively. The polymorphic information content ranged from 0.141 to 0.375. Among these SNP markers, seventeen loci showed significant departures from Hardy-Weinberg equilibrium after Bonferroni correction. These novel SNP markers will be helpful for future studies on genetic management and population conservation in this species.

Three species of catfish, Silurus biwaensis, Silurus lithophilus, and Silurus asotus, are identified in Lake Biwa. Notably, S. biwaensis and S. lithophilus are endemic species in Lake Biwa; however, their detailed distribution and ecology almost remain unknown. In this study, we developed catfish species-specific primer probe sets based on their whole genome. Using these, we analyzed the water samples collected from three tanks where S. biwaensis, S. lithophilus, and S. asotus were experimentally reared, respectively, and established a new detection system after confirming each primer probe set to be effective. Finally, we conducted environmental DNA analysis for catfishes in Lake Biwa using field samples. Overall, our results showed that environmental DNA analysis is a useful monitoring method for confirming the presence of endemic catfishes in Lake Biwa.

The Japanese anchovy, Engraulis japonicus, is an important economic fish that is distributed in the northwest Pacific Ocean. The effective assessment and management of the Engraulis japonicus fishery requires reliable information regarding its population’s genetic structure. The recent development of double digest restriction-site associated DNA sequencing (ddRAD-Seq) methods may contribute to the discovery of SNPs and the assessment of genetic structure. In our study, 98 single nucleotide polymorphism (SNP) markers were developed using ddRAD-Seq. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.8000 and 0.2778 to 0.5000, respectively. The polymorphism information content (PIC) ranged from 0.239198 to 0.375. All loci have been substantiated to follow the Hardy–Weinberg equilibrium. These novel polymorphic SNP markers will play an important role in the genetic research of E.japonicus, which will be beneficial to the development and utilization of E.japonicus resources. This study aims to provide technical support for the research of genetic diversity of E. japonicus populations through the development of SNP markers.

Abstract

Sauger (Sander canadensis) and walleye (Sander vitreus) are closely related North American fish species that are often managed by fishery agencies throughout their ranges. However, genotyping resources for sauger are presently limited to a small set of microsatellite loci. We evaluated whether primers in an existing walleye genotyping-in-thousands panel could amplify single nucleotide polymorphism loci (SNPs) in sauger. We identified 71 primer pairs that amplify 118 SNPs in both species. Allele frequency differences were large enough to confidently distinguish the species and identify hybrids. Additionally, we identified 41 loci with observed heterozygosity > 0.1 in sauger; these markers may be useful for simple population genetic analyses and parentage analysis when few contributors are present and for differentiating highly structured populations.

Abstract

Przewalski’s horse (Equus ferus) is a national protected species in China. It first became extinct in the wild in 1976, and was reintroduced to the Kalamaili National Park (KNP) in Xinjiang, China in 2001. This study aimed to analyze the genetic diversity and structure of the reintroduced population of Przewalski’s horse in KNP. Here, we developed and designed microsatellite molecular markers using 48 feces samples and combined this with published genomic data from the species. A preliminary analysis of genetic diversity within the Przewalski’s horse population in the KNP was conducted using 16 pairs of simple sequence repeat (SSR) markers with high levels of polymorphism and high stability. A total of 199 alleles were amplified using 16 SSR primer pairs, averaging 12.438 at each locus. In the sample of 48 genomes, the average effective number of alleles detected was 2.695, the average expected heterozygosity was 0.577 and the inbreeding coefficient was 0.232. Twelve loci showed significant deviation from Hardy–Weinberg equilibrium following Bonferroni sequential corrections. Our research finds that the genetic diversity of the Przewalski’s horse population in the KNP remains high. This is the first research using newly developed SSR markers to describe the genetic diversity and structure of the reintroduced Przewalski’s horse population in KNP, China. As such, it can inform future reintroductions of the species and conservation measures.

Liobagrus angullicauda is an endemic species to streams along the southeast coast in China. Due to over fishing and habitat destruction, the natural population of L. angullicauda has decreased dramatically in recent years. Insufficient molecular markers have limited the effective conservation and management of this species. In the present study, we reported the isolation and characterization of 33 SNP markers in L. angullicauda. The minor allele frequency ranged from 0.083 to 0.507, and the observed and expected heterozygosities ranged from 0.177 to 0.624 and 0.290 to 0.712, respectively. Polymorphic information content ranged from 0.118 to 0.408. Among these SNPs, only four loci showed significant departures from the Hardy–Weinberg equilibrium (P < 0.05). Cross-amplification was tested in related species Liobagrus nigricauda, Liobagrus marginalus and Liobagrus marginatoides. The novel polymorphic SNPs should be helpful for the future study on genetic management and population conservation for this species.