Brazilian elodea (Egeria densa) is an invasive freshwater plant that demonstrates widespread ecological impacts in freshwater ecosystems and causes substantial economic damage. Here, we developed an environmental DNA assay for detection of E. densa to provide resource managers with a tool for early detection, identification, and monitoring of invasive populations.

Identification of the species is a crucial step in many ecological studies. Sometimes, this could become a challenge, because of animal elusive behavior, low density population or for sympatric species leaving similar signs that are impossible to discriminate based only on their morphology. Here, we set up non-invasive molecular method to discern between the Italian hare (Lepus corsicanus) and the

Parrots (Psittaciformes) are among the most endangered groups of birds today and remain threatened by habitat loss and exploitation for the live bird trade. Under such conditions, reliable and non-invasive monitoring techniques are crucial for successful conservation measures. In this study, we developed a panel of 86 high quality SNPs for genotyping endangered sun parakeets (Aratinga solstitialis)

The Critically Endangered Smalltooth Sawfish, Pristis pectinata, was once widespread in the tropical and subtropical waters of the Atlantic Ocean, but following substantial declines over the past century, the remaining population(s) are currently confined to Florida in the U.S., and the Bahamas. Recent research and verified public encounter reports suggest that the core population in south and southwest

The phenotypic identification of sex in Sebastes rockfish is difficult and often impractical from a management perspective, and the genetic basis of sex determination in the genus is currently uncertain. We tested a previously developed sex identification polymerase chain reaction restriction fragment length polymorphism (PCR–RFLP) assay in eight species of Sebastes rockfish. Results indicated that

Non-invasive DNA sampling to identify and enumerate species is critical to population monitoring and for developing effective management strategies. However, individual DNA identification is often limited by degraded and low template DNA (LT-DNA) that routinely yields partial profiles prone to technical artifacts, thus limiting their utility/reliability. Massively parallel, genotyping-by-sequencing

Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite

Wading birds play an important role in coastal and wetland ecosystems. As a result of anthropogenic disturbances, numbers of wading birds have declined over the past years, and therefore, the monitoring of bird species is crucial to preserve their habitats and counteract this. Due to known limitations of conventional monitoring, molecular approaches are increasingly becoming complementary methods.

Efficient sexing of the globally vulnerable Saunders’s Gull (Saundersilarus saundersi) is urgently needed in the conservation research and practical management. The universal P2/P8 molecular sexing method has been proved to be invalid for this gull. Here, the improved molecular sexing procedure of Saunders’s Gull is described. The gene sequences of chromo-helicase-DNA binding protein (CHD)-Z and CHD-W

Determining sex is critical for demographic monitoring of endangered species, but this task can be particularly challenging in reptiles that are sexually monomorphic. Conventional sexing methods are invasive, often inaccurate, can cause injury, and, for sexually immature individuals, equivocal. Molecular approaches have been established as viable alternatives but have not been compared with conventional

Numerous species from the classes Amphibia and Reptilia are facing extinction as a result of habitat loss and increasing anthropogenic impact on the environment; to be more specific, 32% amphibian and 20% reptilian species are either threatened or endangered. The aim of this review is to highlight the status of biobanking as one of the many tools within conservation of amphibians and reptilians. Moreover

Better-informed mangrove conservation and management practices are needed as the ecosystem services provided by these intertidal forests continue to be threatened by increasing anthropogenic pressures and climate change. Multiple layers of knowledge are required to achieve this goal, including insights into population genetics of mangrove species. Understanding the importance of population-genetic

Prunus mira, an important economic fruit crop and ancestral peach species, is widely distributed along the Yarlung Zangbo Grand Canyon and tributary basins in the Tibetan plateau. Due to infrastructure construction and deforestation, natural habitat of P. mira has been severely damaged, leading to reduction in its distribution range and population size and it is listed as a critically endangered species

Transcriptome sequencing was used for the development of single nucleotide polymorphisms (SNP) for the red gorgonian (Paramuricea clavata). A total of 20,736 SNPs were identified, and 1718 had a coverage of over 100 reads. Of the 480 SNPs tested, 347 SNPs were successfully genotyped at 95 samples from the NW Mediterranean using a MassARRAY System. This set of markers will be of great value for population

We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci in Quercus robur and Quercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within Russia and Germany. We successfully screened a selected

Darkbarbel catfish (Pelteobagrus vachelli) is an important commercial fish species in China. However, its wild populations have undergone a dramatic decline in recent years because of overfishing and habitat destruction for its spawning. Therefore, it is extremely urgent to develop sufficient molecular markers for the effective conservation and molecular-aided selection of this species. In the present

Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign

During the 1950s and 1970s the osprey (Pandion haliaetus) experienced a dramatic population crash and remains of conservation concern in several parts of the world. We isolated 37 microsatellite loci and assessed these in ospreys sampled in the UK and Norway (using mouth swabs/feathers). From 26 loci variable in four ospreys, we selected 13, combined these into two multiplex-PCR sets and included a

The technique to produce hybrid Tulu or Nar camels from crosses between dromedary and Bactrian camels is common throughout Middle Eastern and Central Asian countries. Formerly, these hybrids were highly valued as strong and persistent pack animals but today are bred to improve milk or wool quality in the respective species and for camel wrestling. We developed a diagnostic single nucleotide polymorphism

We report the development of 14 new microsatellite markers in the Queensland koala (Phascolarctos cinereus adustus). Ten unrelated Queensland koala individuals from the San Diego Zoo, USA, were genotyped. The number of alleles per locus ranged from 2 to 7, with an average of 5.14 alleles per locus. Across all loci, the average observed and expected heterozygosity values were both 0.69. These polymorphic

The giant water bug (Abedus herberti) is a large flightless insect that is a keystone predator in aridland aquatic habitats. Extended droughts, possibly due to climate change and groundwater pumping, are causing once-perennial aquatic habitats to dry, resulting in serious conservation concern for some populations. A. herberti also exhibits exclusive male parental care, which has made it a model organism

Ten microsatellite markers were developed for Robinsonia (Asteraceae), a genus endemic to the Juan Fernández Archipelago, Chile. Polymorphisms of these markers were tested using one population each of R. evenia, R. gayana, and R. gracilis. The number of alleles for these markers ranged from 2 to 17 per locus, and expected heterozygosity ranged from 0 to 0.847 by population. A significant deviation

PolyAna (available at http://www.biol.sc.edu/~austin/) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous.

Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. Sarracenia species naturally hybridize with each other, and hybrid swarms have been identified. A number of the taxa within the genus are considered endangered. In order to facilitate evolutionary, ecological and conservation genetic analyses within the genus,

Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica,

Genome size—the total haploid content of nuclear DNA— is constant in all cells in individuals within a species, but differs among species. Consequently, the genome size is a quantifiable genetic signature that not only characterizes a species, but it can reflect chromatin modifications, which play fundamental roles in most biological processes that are involved in the manipulation and expression of

An efficient protocol for the isolation of high-quality DNA from tissues is essential to many aspects of molecular biology. Shed skin is often overlook as a source for high-quality DNA in molecular studies involving frog. In this study, DNA from shed skin of frog was extracted using phenol–chloroform, the DNeasy extraction kit (Qiagen) and an improved salting-out protocol, in comparison with those

Environmental DNA (eDNA) techniques show promise in facilitating the study and conservation of threatened species. The advantages of high sensitivity and high efficiency have been demonstrated by studies across various taxa. Asian turtles, one of the most threatened vertebrate groups, are facing extinction due to overexploitation for use as traditional Chinese medicine, food, and pets. Most species

We clarify the contribution of gene introgression in the recovery of the sable Martes zibellina, which has undergone significant population declines by the end of the nineteenth century. To verify the contribution of interspecific gene introgression, variation among the sable and the pine marten Martes martes was investigated utilizing restriction fragment analysis of the mitochondrial cytochrome b

Erythrophleum fordii is an economically important evergreen species. Due to its multipurpose values, it is currently heavily exploited and endangered. To better understand the evolutionary adaptations of E. fordii for germplasm resource protection, ninety polymorphic functional single nucleotide polymorphism (SNP) loci were characterized. The observed and expected heterozygosities ranged from 0.129

Novel single nucleotide polymorphism loci were identified for teak (Tectona grandis Linn. f.) using a combined Next Generation Sequencing approach on the Illumina MiSeq system with genotyping on the Agena MassARRAY iPLEX™ platform. Three hundred and forty four putative loci were identified through sequencing of DNA fragments following a modified double digest Restriction Associated DNA Sequencing method

In this study, 26 single nucleotide polymorphism (SNP) markers were developed and characterized in Nipponacmea schrenckii. The minor allele frequency raged from 0.0238 to 0.3571. The observed heterozygosity and expected heterozygosity ranged from 0.0000 to 0.2381 and from 0.0929 to 0.4866, respectively. Polymorphic information content ranged from 0.0866 to 0.3538. The inbreeding coefficient values

Accurate determination of sex ratios is an important metric for the conservation and management of wild Atlantic salmon populations. Previously published primers for a male-specific gene were shown to be unreliable at determining sex due to the presence of deletions in the forward primer-binding site. A new forward primer, used in conjunction with the existing reverse primer, greatly improved reliability

As a vulnerable species in the Red List of China’s Vertebrates, Schizothorax waltoni (S. waltoni) is mainly distributed in the middle reaches of Yarlung Tsangpo River in Tibet. Due to its delicate meat and delicious taste, S. waltoni is the main economic fish in the producing area. But recently, it has undergone a drastic population decline due to the overfishing of fishery resources, the invasion

As part of the species recovery plan for the critically endangered pygmy hog (Porcula salvania), a conservation-breeding program was initiated, to bolster its wild population. For successful conservation-breeding, it is essential to maintain 90% of the founder genetic diversity over time. Therefore, in the present study, we assessed the genetic diversity of a captive population of pygmy hog across

We describe novel hybrid primers for the successful amplification and sequencing of the mitochondrial cytochrome b (cytb) gene in the family Siganidae. We aligned 403 cytb sequences from 29 species and found multiple potential conserved hybrid primers (< twofold degeneracy). The best set was selected, and successfully amplified and sequenced ~ 1100 bp of cytb in the Siganidae.

Recent field survey in Ranipur Wildlife Sanctuary (RWS), Chitrakoot, Uttar Pradesh, India amazed us to locate several bird carcasses on the railway track and prompted to identify the species and possible reasons of mortality from the deteriorated body remains. Surprisingly, DNA analysis with conserved mitochondrial genes i.e. Cytochrome b (Cyt b) and 16S rRNA, identified carcass originated from a Critically

Snow leopards (Panthera uncia) are an enigmatic, high-altitude species whose challenging habitat, low population densities and patchy distribution have presented challenges for scientists studying its biology, population structure, and genetics. Molecular scatology brings a new hope for conservation efforts by providing valuable insights about snow leopards, including their distribution, population

Computation of Patterson’s D-statistic and its five-taxon derivatives are important phylogenetic methods for the quantification of reticulated evolution, yet are limited in application by the lack of a single, comprehensive program to efficiently perform all necessary calculations from common phylogenetic and population genetic program file formats. To increase accessibility for a broad range of researchers

Coilia ectenes, also called Coilia nasus, is an ecologically important species endemic to China. Due to habitat fragmentation, over-harvesting and water pollution, the natural germplasm of C. ectenes has declined dramatically in the recent decades. Thus, developing sufficient molecular markers for the conservation and molecular-aided selection of this species is urgent. In this study, 50 polymorphic

The Chinese longsnout catfish (Leiocassis longirostris Günther) is a semi-migratory freshwater species. Leiocassis longirostris is mainly inhabiting the main stream of the Yangtze River and rarely found in lakes due to over fishing, environmental pollution and other human disturbances. Novel single nucleotide polymorphisms (SNPs) were screened based on high-throughput sequencing in Leiocassis longirostris

Grass carp is one of the most important freshwater aquaculture fish in China. Though a few molecular markers had been reported, it was not enough for grass carp germplasm improvement and protection. In order to verify the effectiveness and practicability of insert/deletion mutations reported in grass carp genome, 85 insert/deletion mutations were randomly selected and analyzed. After simple sequence

Hucho bleekeri, also called Sichuan taimen, is a species endemic to Yangtze River drainage in China. Due to habitat destruction, heavy fishing and pollution, the wild population of H. bleekeri has declined rapidly in recent years. Insufficient molecular markers have limited the effective conservation of this species. In the present study, 34 novel single nucleotide polymorphism (SNP) markers were developed

The largemouth bass Micropterus salmoides was introduced into Guandong province of China in 1983, and is now one of the China’s primary cultured fish species. After a long period of farming, the populations are facing the stringent challenges of germplasm resources degraded, and genetic improvement is urgently needed. Thus, developing sufficient molecular markers for the conservation and molecular-aided

Analysis of environmental DNA (eDNA) through non-invasive sampling continues to gain popularity in the surveillance of organisms. Methodological improvement to ensure maximum DNA recovery from the samples would benefit future studies. We investigated the effects of DNA extraction methods and filter preservation methods on eDNA yield by analyzing field-collected water samples for eDNA of the Eastern

In this study we tested a newly-developed instrument (an automatized DNA extractor MAxWell16-Promega), in order to test if DNA isolation can be performed more efficiently on feacal samples collected from three different species: bears, wolfs and capercaillies. We also evaluate a simple method for samples preservation in the field, which include the preservation of faeces in vials filled with ethanol

A rapid allelic discrimination real-time polymerase chain reaction (qPCR) assay has been developed for the confirmation of lion (Panthera leo) or tiger (P. tigris) DNA. The method includes a low cost allele specific PCR assay designed for each SNP variant where the genotype is determined by incorporation and subsequent fluorescence of FAM or HEX following PCR. The described method was able to accurately

Triplophysa siluroides is an endemic species to the upper reaches of the Yellow River. Due to over fishing and habitat destruction, the natural population of T. siluroides 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 50 SNP markers

To assist in efforts to monitor the distribution and abundance of lake sturgeon Acipenser fulvescens, a species of conservation concern in Canada and the United States, we developed two quantitative PCR (qPCR) environmental DNA assays targeting the cytochrome c oxidase 1 (COI) and cytochrome b (cyt b) genes. Neither assay amplified DNA from the closely-related shortnose sturgeon Acipenser brevirostrum

Stacksbinder (available at https://ps.agr.ryukoku.ac.jp/stacksbinder/) is a web-based tool for summarizing the output of software Stacks, which is widely used to analyze restriction site-associated DNA sequencing (RAD-Seq) data. Although summarization is an essential step in RAD-Seq analysis, no specific tools exist for summarizing and visualizing these data. Stacksbinder generates a summary report

We described here the successful identification of three economic aquaculture mussel species in China and their hybrids by high resolution melting curve analysis (HRM) of single nucleotide polymorphisms (SNPs). The nuclear 18S ribosomal RNA gene sequences from Mytilus edulis, Mytilus coruscus, and Perna viridis were aligned and amplified. In total, 8 SNP sites were detected from the 79-bp amplicon

Unfortunately, in the original publication of the article, the voucher number in the second paragraph was published erroneously as “YNUSM20160817008”. The corrected voucher number should read as “YNUST201406180002”.