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NGS-μsat : bioinformatics framework supporting high throughput microsatellite genotyping from next generation sequencing platforms Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-11 Denis Roy, Sarah J. Lehnert, Clare J. Venney, Ryan Walter, Daniel. D. Heath
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
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Efficient genotyping with backwards compatibility: converting a legacy microsatellite panel for muskellunge ( Esox masquinongy ) to genotyping-by-sequencing chemistry Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-06 Kristen M. Gruenthal, Wesley A. Larson
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
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Using DNA to distinguish between faeces of Dugong dugon and Chelonia mydas : non-invasive sampling for IUCN-listed marine megafauna Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-05 S. J. Tol, M. Harrison, R. Groom, J. Gilbert, D. Blair, R. Coles, B. C. Congdon
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
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A cost-effective PCR–RFLP method for monitoring invasive American mink: preliminary field test in control areas of Spain Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-04 Ettore Emanuele Dettori, Alessandro Balestrieri, Loreto García Román, Victor Manuel Zapata-Perez, Angelo Ruiu, Laura Carcangiu, Francisco Robledano-Aymerich
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,
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Development of a large set of diagnostic SNP markers using ddRAD-seq to study hybridization in Rhinanthus major and R. minor (Orobanchaceae) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-03 Khaled Mirzaei, Renate A. Wesselingh
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
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A panel of 96 SNPs to identify individuals and differentiate subspecies of elk ( Cervus canadensis ) for microfluidic and other genotyping platforms Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-03 Benjamin N. Sacks, Gunmeet K. Bali, Zachary T. Lounsberry, Stevi L. Vanderzwan
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
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Enabling pinniped conservation by means of non-invasive genetic population analysis Conserv. Genet. Resour. (IF 1.107) Pub Date : 2021-01-03 Kristina Steinmetz, Sinéad Murphy, Oliver Ó Cadhla, James Barnett, Luca Mirimin
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
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Development of nuclear SNP markers for Mahogany ( Swietenia spp.) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-08-12 Birte Pakull, Lasse Schindler, Malte Mader, Birgit Kersten, Celine Blanc-Jolivet, Maike Paulini, Maristerra R. Lemes, Sheila E. Ward, Carlos M. Navarro, Stephen Cavers, Alexandre M. Sebbenn, Omar di Dio, Erwan Guichoux, Bernd Degen
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™
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eDNA metabarcoding bioassessment of endangered fairy shrimp ( Branchinecta spp.) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-07-31 Zachary Gold, Adam R. Wall, Emily E. Curd, Ryan P. Kelly, N. Dean Pentcheff, Lee Ripma, Paul H. Barber, Regina Wetzer
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
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The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-08-09 Gaurav Vashistha, Sharma Deepika, Parag Madhukar Dhakate, Faiyaz A. Khudsar, David Kothamasi
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
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Ready-to-use workflows for the implementation of genetic tools in conservation management Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-08-16 Rolf Holderegger, Benedikt R. Schmidt, Christoph Grünig, Robert Meier, Daniela Csencsics, Martin Gassner, Christian Rellstab, André Stapfer
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
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Development of D-Loop mitochondrial markers for amplification of prey DNA from wolf scat Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-09-23 Hilke Schroeder, Stefanie Palczewski, Bernd Degen
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
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Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-09-23 Mousumi Ghosh-Harihar, Nehal Gurung, Harsh Shukla, Ishani Sinha, Awadhesh Pandit, Vibhu Prakash, Rhys E. Green, Uma Ramakrishnan
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
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A conservation-oriented SNP panel for Smallmouth Bass ( Micropterus dolomieu ), with emphasis on Interior Highlands lineages Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-09-21 James M. Long, Andrew T. Taylor, Vince Buonaccorsi
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
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Development and validation of four environmental DNA assays for species of conservation concern in the South-Central United States Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-09-15 Cameron D. Siler, Elyse S. Freitas, Tamaki Yuri, Lara Souza, Jessa L. Watters
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
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Molecular sexing of Xenarthra: a tool for genetic and ecological studies Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-09-04 Carmen Elena Barragán-Ruiz, Eliana Paviotti-Fischer, Karen Giselle Rodríguez-Castro, Arnaud L. J. Desbiez, Pedro Manoel Galetti Jr.
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
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An economic method for the identification of catfish hybrids using microsatellites: a case study of Pseudoplatystoma metaense × Leiarius marmoratus hybrids Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-08-24 Laura Vanessa Solarte-Murillo,Iván David Sandoval-Herrera,Jaime Alberto Marín-Colorado,José Ariel Rodríguez-Pulido
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
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Isolation and characterization of 100 SNP markers in lined seahorse ( Hippocampus erectus ) using RAD sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-08-02 Ke-Cheng Zhu,Qiwei Ma,Dian-Chang Zhang
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
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A DNA mini-barcoding system for endangered unionid mussels in the Lake Biwa system in Japan Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-07-11 Kohji Mabuchi, Kazuya Nishida
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
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A little SNP of this, a little SNP of that: The discovery of 116 single nucleotide polymorphism markers to enable the rapid identification of individual Pacific walrus ( Odobenus rosmarus divergens ) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-19 Geoffrey M. Cook, Daniel J. Prince, Sean M. O’Rourke, Timothy L. King, Michael R. Miller, Cara J. Lewis, Michael S. Eackles, Patrick R. Lemons, Suresh A. Sethi, Jeffrey B. Olsen, John K. Wenburg
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
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A new minibarcode assay to gacilitate species identification from processed, degraded or historic ray (batoidea) samples Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-18 Gregory J. Wannell, Andrew M. Griffiths, Anastasia Spinou, Romina Batista, Marina Barreira Mendonça, Wolmar Benjamin Wosiacki, Bonnie Fraser, Sabine Wintner, Athanasios I. Papadopoulos, Grigorios Krey, Chrysoula Gubili
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
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Identification of hybrid green peafowl using mitochondrial and nuclear markers Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-15 Han Yu Du, Xin Yuan Zhang, Thi Dao Dinh, Yue Ma, Cheng Zong, Guang Long Li, Thomas D. Dahmer, Yan Chun Xu
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
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Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-09 Benoit Laurent, Clément Larue, Emilie Chancerel, Erwan Guichoux, Rémy J. Petit, Teresa Barreneche, Cécile Robin, Olivier Lepais
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
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DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-05 George N. Ude, David O. Igwe, Chrysten Brown, Myron Jackson, Alusine Bangura, Onyinye Ozokonkwo-Alor, Onyinye C. Ihearahu, Obih Chosen, Michael Okoro, Christabel Ene, Venatus Chieze, Mariam Unachukwu, Christie Onyia, George Acquaah, James Ogbonna, Aditi Das
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
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Development of a quantitative PCR assay for detecting Egeria densa in environmental DNA samples Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-06-02 Dorothy M. Chase, Lauren M. Kuehne, Julian D. Olden, Carl O. Ostberg
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.
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Characterization of single nucleotide polymorphism markers for the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) based on RAD sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-05-25 Majidreza Khoshkholgh,Sajad Nazari
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
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Who is who? High Resolution Melting analysis to discern between hare species using non-invasive sampling Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-05-18 Maria Buglione, Simona Petrelli, Tommaso Notomista, Gabriele de Filippo, Romano Gregorio, Domenico Fulgione
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
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De novo discovery of SNPs for genotyping endangered sun parakeets ( Aratinga solstitialis ) in Guyana Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-05-14 Robert Spitzer, Anita J. Norman, Helena Königsson, Bastian Schiffthaler, Göran Spong
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)
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An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata , in the western Atlantic Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-05-02 Ryan N. Lehman, Gregg R. Poulakis, Rachel M. Scharer, Katherine E. Schweiss, Jill M. Hendon, Nicole M. Phillips
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
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Sex identification PCR–RFLP assay tested in eight species of Sebastes rockfish Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-04-29 Felix Vaux, Hannah M. Aycock, Sandra Bohn, Leif K. Rasmuson, Kathleen G. O’Malley
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
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Development of a massively parallel, genotyping-by-sequencing assay in American badger ( Taxidea taxus ) highlights the need for careful validation when working with low template DNA Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-04-04 Michael E. Donaldson, Katelyn Jackson, Yessica Rico, Josh B. Sayers, Danielle M. Ethier, Christopher J. Kyle
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
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Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey ( Rhinopithecus roxellana ) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-04-03 Chen Ling, Wu Lixia, Hou Rong, Shen Fujun, Zhang Wenping, Tang Yao, Yuan Yaohua, Zhao Bo, Zhang Liang
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
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A novel environmental DNA detection approach for the wading birds Platalea leucorodia , Recurvirostra avosetta and Tringa totanus Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-04-02 Robin Schütz, Ralph Tollrian, Maximilian Schweinsberg
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.
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An efficient molecular sexing of the globally vulnerable Saunders’s Gull ( Saundersilarus saundersi ) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-30 Wei Lei, Chang’an Liu, Kuixing Shangguan, Shengling Zhou, Guoxiang Liao, Dongxu Gao
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
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Molecular sexing is a viable alternative to probing for determining sex in the imperiled Louisiana Pine Snake ( Pituophis ruthveni ) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-29 Aron D. Katz, Sarah Pearce, Christopher Melder, Jinelle H. Sperry, Mark A. Davis
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
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Biobanking in amphibian and reptilian conservation and management: opportunities and challenges Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-10 Julie Strand, Helena Thomsen, Julie B. Jensen, Cecilie Marcussen, Trine B. Nicolajsen, Mathias B. Skriver, Isabella M. Søgaard, Tariq Ezaz, Stig Purup, Henrik Callesen, Cino Pertoldi
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
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Multiplex microsatellite PCR panels for the neotropical red mangrove, Rhizophora mangle : combining efforts towards a cost-effective and modifiable tool to better inform conservation and management Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-06 John Paul Kennedy, Hayley Craig, Antonella Jara-Cavieres, Agnessa Lundy, Richard F. Preziosi, Jennifer K. Rowntree
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
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Development of 85 SNP markers for the endangered plant species Prunus mira (Rosaceae) based on restriction site-associated DNA sequencing (RAD-seq) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-05 Wenquan Bao, Dun Ao, Tana Wuyun, Lin Wang, Yu-e Bai
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
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Development of a set of SNP markers for population genetics of the red gorgonian ( Paramuricea clavata ), an emblematic species of the Mediterranean coralligenous Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-04 M. Padrón, M. Milhes, M. Massot, E. Guichoux
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
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Development of new SNPs loci on Quercus robur and Quercus petraea for genetic studies covering the whole species’ distribution range Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-04 Celine Blanc-Jolivet, Svetlana Bakhtina, Ruslan Yanbaev, Yulai Yanbaev, Malte Mader, Erwan Guichoux, Bernd Degen
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
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Development of SNP markers and validation 24 SNPs in darkbarbel catfish ( Pelteobagrus vachelli ) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-03-02 Chengtao Guo, Yuhong Wang, Weihua Hu, Jie Mei, Wenjie Guo
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
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Characterization of 55 SNP markers in Chinese longsnout catfish Leriocassis Longirostris Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-26 Wei Zhao,Jian Zhou,Zhe Li,Tingsen Jing,Li Zhao,Hua Ye
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
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Development of SNPs in Siniperca chuatsi Basilewsky using high-throughput sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-24 Mingsong Xiao,Kelin Qian,Fangyin Bao
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
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Isolation and characterization of 30 SNP markers in Guangdong bream ( Megalobrama terminalis ) by next-generation sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-24 Jiping Yang, Xinhui Li, Yuefei Li, Shuli Zhu, Weitao Chen, Jie Li
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
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Development of a mitochondrial DNA marker that distinguishes domestic dogs from Washington state gray wolves Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-20 Ellen M. Reese,Misa Winters,Rebecca K. Booth,Samuel K. Wasser
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
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Development of SNP markers for conservation genetic monitoring of Amorphophallus krausei based on RAD sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-19 Si Yin, Xuemei Ding, Yuehui Yan, Lizhou Tang, Haibo Wang, Chao Liu, Yong Gao
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
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Development of SNP markers for yellowtail kingfish ( Seriola lalandi ) by 2b-RAD simplified genome sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-19 Aijun Cui, Bin Wang, Yan Jiang, Xuezhou Liu, Yongjiang Xu
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
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Development of SNP markers for the bighead carp ( Hypophthalmichthys nobilis ) by using transcriptomic sequences Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-02-18 Rui An, Jianjun Fu, Bingjie Jiang, Wenbin Zhu, Lanmei Wang, Mingkun Luo, Zaijie Dong
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
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Non-destructive genome skimming for aquatic copepods Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-01-21 Vinod Vakati, Steven Dodsworth
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
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Development of a TaqMan qPCR protocol for detecting Acipenser ruthenus in the Volga headwaters from eDNA samples Conserv. Genet. Resour. (IF 1.107) Pub Date : 2020-01-09 Tamara Schenekar, Martin Schletterer, Steven J. Weiss
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
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Testing microsatellite loci for individual identification of captive African grey parrots ( Psittacus erithacus ): a molecular tool for parentage analysis that will aid in monitoring legal trade Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-12-06 Sandi Willows-Munro, Courtneë Kleinhans
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
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SNP discovery in Mauremys reevesii and M. sinensis using restriction site-associated DNA sequence (RAD-seq) Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-29 Qiming Xie, Chaozhen Rong, Xilei Li, Nianyue Lai, Tiantian Chen, Qingqing Li, Shiping Su
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
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Development of SNP in spotted steed ( Hemibarbus maculatus Bleeker) using GBS sequencing Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-22 Liu Huifen,Wang Jing,Zhang Limin,Fang Fugui,Zhang Meng,Ma Xiao,Tian Xue,Li Xuejun,Nie Guoxing
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
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Correction to: Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacifc coast watersheds of North America Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-21 Marshal S. Hoy, Carl O. Ostberg
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.
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Development and characterization of 33 SNP markers for the red-crowned crane ( Grus japonensis ) using a genotyping-by-sequencing approach Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-16 Nan Xu, Yining Chen, Jiaming Zhang, Qingzheng Zhang, Jing Yang, Jingjing Li, Hongyi Liu
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
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Development and characterization of 38 SNP markers in the true limpet Patelloida pygmaea Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-16 Ruoran Li, Yunhui Wang, Xiaoyue Sun, Yanran Xu, Jiangyong Qu, Xumin Wang
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
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A protocol for fast identification of larval tephritid flies with a community-wide COI reference bank Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-15 Yuran Dong,Tan Li,Xinqiang Xi,Shucun Sun
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
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Development and characterization of 72 SNP markers in Armeniaca sibirica based on transcriptomics Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-14 Wenquan Bao, Dun Ao, Tana Wuyun, Lin Wang, Shulan Bai, Yu-e Bai
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
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Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacific coast watersheds of North America Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-13 Marshal S. Hoy, Carl O. Ostberg
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
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Species identification in complex groups of medicinal plants based on DNA barcoding: a case study on Astragalus spp. ( Fabaceae ) from southwest China Conserv. Genet. Resour. (IF 1.107) Pub Date : 2019-11-13 Dequan Zhang, Bei Jiang
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
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