Although genetic techniques are moving toward collecting massive amounts of genome-wide data through genome-scans, microsatellite markers (µsats) still provide a simple and cost-effective method for key applications such as parentage analyses, pedigree tracking, assessing likelihoods of disease conditions and DNA fingerprinting, among others. Newer laboratory protocols using high throughput sequencing

Microsatellites have been a staple of population genetics research for over three decades, and many large datasets have been generated with these markers. Microsatellites have been used, for example, to conduct genetic monitoring and construct large multigeneration pedigrees as well as genotype thousands of individuals from a given species to create high-resolution baselines of spatial genetic structure

The Dugong dugon (dugong) and Chelonia mydas (green sea turtle) are economically and culturally significant marine mega-herbivores whose populations are declining globally. Capture of these animals for study is challenging and stressful for the animals. Ecological questions can be answered using faeces, which can be collected floating on the water’s surface. However, green turtle and dugong faeces

American mink Neovison vison is a semi-aquatic mustelid that has been introduced throughout Europe. Several attempts to eradicate this invasive species have been carried out since its spread. In the Iberian Peninsula, an eradication program has started since 2001, as part of the national action plan for the conservation of European mink Mustela lutreola. Proper detection is crucial for management,

Rhinanthus major and R. minor are two annual plant species that are known to hybridize in nature and in which unilateral introgression is likely to occur. Here we used double-digest restriction site-associated DNA sequencing technology (ddRAD-seq) to detect 16,932 genome-wide SNPs in R. major and R. minor individuals from 9 populations. After screening these SNP markers across both species, we selected

The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed

Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for genetic analyses of pinnipeds. The present study evaluated

Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™

Habitat degradation and land-use change severely threaten the survival of fairy shrimp and the vernal pools in which they live. Limiting effective fairy shrimp conservation management efforts is the ability to readily identify species without the capture and sacrifice of individuals for microscopy. Here we demonstrate that eDNA metabarcoding is an effective non-invasive tool for monitoring fairy shrimp

Microsatellite DNA is among the several molecular tools used for determining genetic variability and inbreeding depression in threatened populations. It has been used extensively for population genetics studies in conservation of crocodilians. Even though single nucleotide polymorphisms have higher precision compared to microsatellite DNA markers, microsatellites offer a cost advantage which is particularly

We present a conservation genetics tool kit, which offers two ready-to-use workflows for the routine application of genetic methods in conservation management. The workflows were optimized for work load and costs and are accompanied by an easy-to-read and richly illustrated manual with guidelines regarding sampling design, sampling of genetic material, necessary permits, laboratory methods, statistical

Analysis of wolves dietary is a currently important theme because of the discussion about wolves preying on livestock as sheep or goats. We developed molecular markers to especially amplify the DNA of the prey out of wolf scat. For this purpose, we used the mitochondrial D-Loop using public available sequences for wolf and seven potential prey species (even-toed ungulates). We developed special primers

After suffering a massive decline (~ 99%) in numbers caused by feeding on livestock carcasses containing the nephrotoxic drug diclofenac, critically endangered Gyps vultures now persist in low numbers in the Indian subcontinent. Most are concentrated near National Parks, likely due to availability of wild carcasses free from toxic veterinary drugs. Quantification of vulture diets is critical to test

The Smallmouth Bass (Micropterus dolomieu; SMB) is a widely distributed black bass species, but the southwestern edge of the species range within the Interior Highlands contains some of the most divergent ecotypes. The Neosho subspecies (M. d. velox) inhabits tributaries of the Arkansas River within the Ozark Mountains and a second lineage is reported from drainages of the Ouachita Mountains. We sought

We describe the development and testing of qPCR assays to detect four species of amphibians and reptiles of conservation concern in the South Central United States through environmental DNA (eDNA) samples. The target species include the Ringed Salamander (Ambystoma annulatum), Three-toed Amphiuma (Amphiuma tridactylum), Crawfish Frog (Rana areolata), and Chicken Turtle (Deirochelys reticularia). A

Although sex assignment is essential to study biology and ecology of an animal, in Xenarthra there is still no standardized assay for genetic sex identification. Here, we evaluate the potential of two nuclear fragments [Zinc finger (~ 400 bp) and Sex-determination region Y (~ 180 bp) genes] for sex identification of seven Xenarthra species. First, we amplified and sequenced both homologous segments

The hybrids of pimelodid catfish provide products of excellent genetic value for aquaculture due to their greater growth in size, resistance to diseases and adaptation to feed concentrate. However, this practice involves risks such as genetic contamination, the commercialization of hybrid products as pure species, the introduction of exotic species and escapes of fish farming products. Thus, the aim

Lined seahorse ( Hippocampus erectus ), an important economic and medicinal fish in China, exists widely in Atlantic Ocean. However, habitat destruction for its spawning and overfishing has led to profound decline the wild populations in recent years. Therefore, to improve the molecular-assisted selection (MAS) and resources conservation of H. erectus , the 100 novel single nucleotide polymorphism

A mini-barcoding system was developed to help identify endangered unionid mussels in the Lake Biwa system in Japan. A single primer set was designed to amplify a ca. 140-bp barcode fragment based on the published mitochondrial 16S rRNA gene sequences (ca. 350 bp) of Japanese unionids. The new primers successfully amplified genomic DNA from the foot tissues of 81 specimens of 12 target taxa from the

We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identified from Pacific walrus DNA. RADSeq was performed on

Rays (Batoidea) are among the most threatened groups of vertebrates. Slow growth and low fecundity make many species vulnerable to overfishing, but increased demand for gill rakers in traditional Chinese medicine and elasmobranch meat means exploitation continues. In response, protection has increased, with manta and devilrays (Mobulidae) and sawfishes (Pristidae) now listed on Convention on International

Green peafowl (Pavo muticus), a representative of the Southeast Asia Phasianidae, is assessed as globally endangered with populations that are declining. It is highly sensitive to human disturbance and habitat change, two threats that are unlikely to be removed soon in present range countries, and that increase the need for long-term continuous effort for in situ conservation. Captive breeding for

Chestnut species have large ecological, cultural and economic importance. Developing genetic markers for these species is of interest for conservation, breeding or evolutionary studies. We designed 192 primer pairs targeting microsatellites detected in the Castanea mollissima reference genome and tested them on C. sativa and C. crenata. We PCR amplified 3 × 50 microsatellites in 106 chestnut trees

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering

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.

We developed single nucleotide polymorphism (SNP) markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) using restriction site-associated DNA sequencing (RAD-seq) genotyping on the Illumina HiSeq4000 platform. In total, we sequenced 44 individuals from seven populations occurring in the Caspian Sea basin. Of the 86 SNP loci, 43 loci were found to be polymorphic and bi-allelic

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

The Chinese longsnout catfish ( Leiocassis longirostris ) is a commercially important aquaculture species in China. The germplasm resources of L. longirostris have been seriously degraded by human activities, therefore, it is very urgent to develop genetic markers of L. longirostris to investigate the natural resources. Here, a total of 55 single nucleotide polymorphism (SNP) loci were identified using

The Chinese perch ( Siniperca chuatsi Basilewsky) is an endemic freshwater fish species in eastern Asian countries. The perch is mainly distributed in the Yangtze River drainage in China. The wild population of S. chuatsi has declined dramatically due to habitat degradation, anthropogenic activities and eutrophication. Unfortunately, researches regarding its genetic markers are scarce. In this study

Guangdong bream (Megalobrama terminalis) is an economically important species. However, wild Guangdong bream resources have declined sharply in recent years as a result of human disturbance and habitat destruction. Thus, it is crucial that the current resources of Guangdong bream are protected. In this study, 30 novel single nucleotide polymorphism (SNP) markers were developed based on restriction

We describe a primer pair that amplifies a 203 base pair fragment containing 4 single nucleotide polymorphisms (SNPs) within the cytochrome b region of the mitochondrial DNA that, when sequenced, conclusively distinguishes Washington state gray wolves from domestic dogs. The method is more efficient and cost-effective than other established methods for genetically distinguishing domestic dogs from

Amorphophallus krausei is a perennial plant which is native to Southeast Asia. Wild populations of A. krausei are declining in China due to anthropogenic threats. Genetic monitoring is an important tool for the conservation of any threatened population, but genetic diversity studies of A. krausei are currently hindered by a lack of molecular markers. To help with conservation genetics studies of this

Yellowtail kingfish, Seriola lalandi, is a globally distributing pelagic marine fish species. In recent years, the wild population has suffered drastic decline due to overfishing and environmental deterioration. Thus, the sustainable utilization and conservation management for this species should be implemented urgently. In the present study, we developed SNP markers using 2b-RAD sequencing method

The bighead carp (Hypophthalmichthys nobilis) is a native freshwater fish species in China. However, the wild fishery resources of H. nobilis have recently suffered a drastic decline. In this study, a total of 106,657 putative SNP loci were identified from the assembled transcripts of H. nobilis. Thirty-seven polymorphic loci were characterized from 60 SNP loci randomly selected for validation by using

Copepods are important ecologically and represent a large amount of aquatic biomass in both freshwater and marine systems. Despite this, the taxonomy of copepods and other meiofauna is not well understood, hampered by tiny sizes, cryptic taxa, intraspecific polymorphisms and total specimen destruction where DNA methods are employed. In this article we highlight these issues and propose a more up-to-date

A recent eDNA-metabarcoding study assessing fish diversity in the Upper Volga catchment did not detect sterlet at any of the sampled stretches, despite recent sightings that suggest its presence. We designed a TaqMan qPCR protocol to test for sterlet in selected eDNA samples from that study. In-silico and in-vitro tests confirm the protocol’s high sensitivity and specificity to sturgeon taxa and potentially

Populations of wild African Grey parrots (Psittacus erithacus) are declining rapidly driven by the removal of individuals for the pet trade and accelerated habitat destruction and fragmentation. African Greys are currently listed as Endangered on the IUCN Red list and are on Appendix I of CITES, which prohibits all trade in wild-caught individuals. The demand for these parrots in the pet trade can

Mauremys reevesii and M. sinensis are economically important freshwater turtle species widely distributed in China. However, due to heavy overexploitation, their wild populations are near extinction and most living resources are no intensively cultured in breeding farms. To set up an effective management and conservation strategy for both species, we carried out extensive restriction site-associated

Spotted steed ( Hemibarbus maculatus ) is a native freshwater fish widely distributed in China, but data regarding its genetic markers are scarce. In this study, we used genotyping by sequencing (GBS) to develop single nucleotide polymorphisms (SNPs) from 56 individuals. We discovered a total of 57,523 genome-wide SNP markers. After applying strict filtering criteria, 166 high-qualified SNPs were obtained

In the original publication of the article, the latitude and longitude values of the eDNA sample site, “Thornton Creek, WA” were published incorrectly in Table 2. The corrected Table 2 is given below.

The red-crowned crane (Grus japonensis) is an endangered wading bird distributed in northeast Asia. The population of G. japonensis is continuing to decline owing to the loss and degradation of habitats. In order to protect G. japonensis, we developed 33 single nucleotide polymorphism (SNP) markers for this species using a genotyping-by-sequencing approach. The minor allele frequency ranged from 0

In this study, 38 single nucleotide polymorphism (SNP) markers were developed and characterized in Patelloida pygmaea. The minor allele frequency raged from 0.0833 to 0.5000. The observed heterozygosity varied from 0.0000 to 1.000, and the expected heterozygosity varied from 0.1197 to 0.5496. Polymorphic information content ranged from 0.1103 to 0.4316. The inbreeding coefficient values varied from − 0

Identifying dead insect larvae by morphology is mostly challenging but often required in ecological studies, which entails a molecular method. In this study, we developed a protocol of Cytochrome Oxidase c Subunit I (COI) DNA barcoding that could quickly identify larval tephritid flies in a Tibetan alpine meadow. The protocol includes two major operations. The first is to build up a comprehensive reference

Armeniaca sibirica L. (Rosaceae) was once an economically important species in China, but the amount of natural germplasm of A. sibirica recently declined dramatically as a consequence of habitat fragmentation and overharvesting; this species has now been listed as endangered in the China Plant Red Data Book. In this study, 72 polymorphic single nucleotide polymorphism (SNP) markers were developed

We developed two quantitative PCR assays for use with environmental DNA (eDNA) to detect numerous species in the genus Cottus that are indigenous to the Pacific coast watersheds of North America. We conducted in vitro assay validations on ten Cottus species and 32 potentially co-occurring non-Cottus species. We demonstrate the efficacy of these assays by field testing eDNA samples collected from streams

Species from the genus Astragalus L. (Fabaceae) are distributed throughout the world, with southwest China being one of the distribution centers of this genus. Many Astragalus species are used by local Chinese people as traditional medicines for enhancing immunity. However, the complexity of morphological characters in many Astragalus species makes it difficult to correctly identify them. DNA barcoding