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

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.

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

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

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

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

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

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,

Non-invasive sampling methods are increasingly being used in conservation research as they reduce or eliminate the stress and disturbance resulting from invasive sampling of blood or tissue. Here we present a protocol optimised for obtaining usable genetic material from moulted plumulaceous feather samples. The combination of simple alterations to a ‘user-developed’ method, comprised of increased incubation

The green tide in the Yellow Sea which has been erupting continuously for 13 years, has brought a huge disaster to the ecosystem. There are four Ulva species from the early stage of green tide in the Yellow Sea usually: Ulva prolifera, Ulva compressa, Ulva flexuosa and Ulva linza. With the passage of time, the green tide floating to Qingdao mainly consists of Ulva prolifera. Molecular biological identification

The vulnerable African timber species Nauclea diderrichii is threatened because of its overexploitation and illegal trade. We sampled individuals across Ghana, Nigeria, Cameroon, Congo Brazzaville, Gabon and Democratic Republic of Congo and performed restriction associated DNA sequencing and low coverage MiSeq genome sequencing to discover SNP and INDEL loci. After MassARRAY genotyping of 95 individuals

Assessing population connectivity and identifying conservation units are critical to formulating effective management plans for marine turtles. We combined a multiplexed targeted enrichment capture technique and high-throughput sequencing to discover single nucleotide polymorphisms (SNPs) and to genotype hawksbill turtles (Eretmochelys imbricata) to examine population structure. Our approach discovered

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