Abstract: Rapid and accurate sex-identification of sal- monids has remained an important challenge for aquacul- ture and wild population study and management. A molecular method looking for the presence of the male- specific sdY gene has recently been proposed. However, the size of the amplified fragment (*500pb) and the DNA revealing technique (agarose-gel electrophoresis) preclude its use on partially degraded DNA and in high-throughput population studies running smaller fragments on automated DNA analyzers. Here, we propose an improved molecular method based on the amplification of a shorter section of the sdY gene for sex-determination in Atlantic salmon and brown trout. Designed primers were multiplexed with several microsatellites and provided reliable sexing for 97 % of the individuals tested. We successfully applied this method to both fresh and archived tissues from 16 indi- viduals (9 populations) of brown trout and 19 individuals (14 populations) of Atlantic salmon. This molecular marker also includes important length polymorphism providing useful Y-linked phylogeographic information.

Abstract: The genus Symbiodinium comprises a diverse group of dinoflagellates known for their obligate relationship with reef–building corals. Members of the sub-genus ‘clade C’ are abundant, geographically wide-spread, as well as genetically and ecologically diverse. Coral colonies harboring clade C are often the most exposed to physical stressors. The genotypic diversity, dispersal and genetic connectivity exhibited by these Symbiodinium are the subjects of an increasing number of population genetic studies utilizing microsatellites. Here we describe 18 new microsatellite loci and test their utility across four common clade C types. We obtained multi-locus genotypes with individual level resolution in each of these types. Our results indicate that multi-locus genotypes can be obtained for many members of clade C using a subset of these markers. Data from these markers may assess population dynamics during coral bleaching and recovery as well as resolve boundaries to genetic recombination among these closely related, yet ecologically distinct, lineages.

Abstract: Environmental DNA (eDNA) is increasingly applied as a highly sensitive way to detect aquatic animals non-invasively. However, distinguishing closely related taxa can be particularly challenging. Previous studies of ancient DNA and genetic diet analysis have used blocking primers to enrich target template in the presence of abundant, non-target DNA. Here we apply a blocking primer to increase the specificity of a TaqMan assay for eDNA detection of rare and endangered bull trout (Salvelinus confluentus) in the presence of the closely related (Salvelinus namaycush). We found that addition of a blocking primer substantially increased assay specificity without compromising sensitivity or quantification ability.

Abstract: We describe a set of novel primers for successful amplification of the complete mitochondrial cytochrome b (cyt b) gene of ungulate species. DNA extracted from non-invasively obtained and decomposed samples is found to be degraded and inappropriate for amplification of the complete gene (more than 1 kb) in single PCR amplification. We developed a series of six ungulate-specific conserved primers for the cyt b gene. These primers, in various combinations, amplify 366–1,266 bp fragments. We also used them in multiplex PCR reaction to assess the maximum possible size of the PCR amplification product.

Abstract: Twenty-seven polymorphic trinucleotide microsatellite DNA markers were developed from Saccharina japonica, through paired-end Illumina sequencing data. Sixty-three gametophyte clones of the species, preserved indoor as germplasm resources were genotyped using these markers. The number of alleles ranged from 2 to 7 with an average 4.7 per locus. The gene diversity and expected heterozygosity varied from 0.171 to 0.774 and from 0.174 to 0.793, respectively. Sixteen loci could be successfully amplified in Saccharina longissima with 12 loci being polymorphic. These novel microsatellite DNA markers will be extremely useful in germplasm resource conservation and management of S. japonica and also in its related species S. longissima.

Abstract: 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 microsatellite loci will be useful for genetic studies relevant to the conservation of the koala, a species listed as vulnerable.

Abstract: We describe a simple, cost-effective procedure for the in-house production of a 725 bp size standard that is suitable for use on automatic DNA analyzers. Using an orange fluorescent dye to label fragments of known sizes on the pUC-19 plasmid, our size standard enables the use of all four fluorescent dyes, and thus maximizes throughput on five dye set platforms. Our data suggest this size standard yields qualitatively identical results as those from commercially available size standards at a fraction of the cost.

Abstract: Yellow-horn (Xanthoceras sorbifolium Bunge) is an endangered tree in northern China that has been devastated by humans during the past several decades. We have developed 84 microsatellite markers and tested them in eight trees sampled from four provinces. 38 loci were found to be polymorphic. The number of alleles per locus ranged from 2 to 8, and expected heterozygosity ranged from 0.117 to 0.855. 11 of 38 primers randomly selected also successfully amplified DNA from two population. These markers are essential for assessing the gene flow and mating system of Yellow-horn for conservation of this endangered species.

Abstract: The natural populations of silver carp (Hypophthalmichthys molitrix) have been declining due to habitat fragmentation, over-fishing and water pollution in China. In this study, 159 transcript-associated microsatellites were developed for silver carp by mining transcriptome sequences, and polymorphism of 27 randomly selected loci were further characterized in a wild population. The number of alleles per locus ranged from 4 to 9, the observed and expected heterozygosity ranged from 0.067 to 0.933 and 0.326 to 0.864, respectively. These novel microsatellite markers will be powerful tools to assess the population structure and genetic diversity in silver carp.

Abstract: Ecosystem diversity, species richness and genetic diversity are the three major facets of biodiversity which deserve equal attention for conservation. However, genetic diversity is significant in identification of unique populations for conservation purpose. Aspects of DNA barcoding, loss of genetic diversity in cryptic species and examples of molecular phylogenetic and molecular phylogeographic studies on aquatic insects of headwaters from major biogeographic realms are briefly reviewed in the light of prioritization of taxa and habitats for conservation. Special emphasis is laid on identification of evolutionary significant units for effective conservation in the context of global climate change. Current methodologies for identifying potential loss of intraspecific genetic diversity are also highlighted with suggestions on future research priorities.

Abstract: Genetic diversity and population genetic structure are key components of seagrass resilience and contribute to an understanding of its conservation and management. We isolated 29 polymorphic microsatellite (SSR) markers from a widely distributed pioneer seagrass, Cymodocea rotundata, by two methods; next generation sequencing and compound SSR marker isolation. Twenty-nine markers had 2–14 alleles per locus, and the observed and expected heterozygosity ranged from 0 to 0.688, and 0.113 to 0.770, respectively. These loci will facilitate investigation of the genetic diversity and population genetic connectivity and structure of C. rotundata.

Abstract: We developed 17 variable microsatellite markers for the threatened Saiga antelope. Using one Illumina Miseq lane resulted in 105,948 unique fragments containing a microsatellite motif. Eighty-one ordered primer pairs resulted in 26 analyzable fragments, of which 17 markers showed variability in at least one population from Kazakhstan. Number of alleles ranged from 2 to 11 and values of heterozygosity varied from 0.08 to 0.91 (HO) and 0.08 to 0.88 (HE). The markers are currently used to delineate conservation units and to help understanding annual migration dynamics in this species.

Abstract: The brown algal genus Laminaria (Phaeophyceae, Laminariales) is ecologically and economically important. Laminaria ochroleuca is the genus member with the southernmost distribution in the Northern hemisphere, from Southern Great Britain to Morocco. Here we describe the characterization of 15 microsatellite loci that can be used to study genetic diversity at different spatial scales and its dynamics in declining southern populations. These loci identified a number of alleles ranging from 3 to 26 (mean = 9). Expected heterozygosities range from 0.0824 to 0.9401. We also tested cross-amplification of these microsatellite markers in two other species within the genus, L. hyperborea and L. digitata. A total of eight and ten alleles cross-amplified in L. hyperborea and L. digitata, respectively. These 15 variable microsatellite loci are an important molecular tool to conduct population genetics studies in L. ochroleuca and other species within the genus.

Abstract: Predation by invasive salmonids threatens the conservation of the endangered Australian freshwater fish Macquarie perch (Macquaria australasica). Predation is difficult to detect visually because larval fish are rapidly digested. Here, we present PCR primers that will enable the detection of M. australasica from trace samples, removing the need to detect undigested larval fish to confirm predation. We tested these primers on DNA from all fish species present in an upstream section of the Cotter River, a key locality for the species. We demonstrate the primers to be species-specific, amplifying DNA from M. australasica only.

Abstract: The genomic content of the non-model plant Frangula alnus remains largely unexplored. However, because of its occurrence over a wide latitudinal range and its invasive nature in the US and Canada, F. alnus may serve as an excellent study species in tree conservation genomic research. We used pooled paired-end sequencing of Restriction-site Associated DNA to discover SNPs in the insect pollinated shrub F. alnus. We identified 7,383 SNPs from which the corresponding contig sequences were annotated to the available plant genomes. An enrichment analysis showed an excess of putatively adaptive and plastic gene ontology terms.

Abstract: Sixteen polymorphic microsatellite primers were developed for Pseudoplatystoma reticulatum and provided an efficient multiplex protocol to amplify these loci in four multiplex PCRs. Most microsatellites here obtained showed moderate to high polymorphism levels in P. reticulatum and P. corruscans, as well as interspecific allelic differences, and represents useful genetic markers for population studies in these fishes.

Abstract: Ash (Fraxinus, Oleaceae) species occur on most continents, within a wide range of forest tree communities. Emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), introduced into the U.S. from Asia in the late twentieth century, has caused widespread mortality, primarily in green ash, Fraxinus pennsylvanica Marsh. (Section: Melioides) and now impacts other North American ash species. The development and successful reintroduction of resistant trees requires genetic tools to evaluate population dynamics and aid in species identification. Here, we report 15 novel EST-SSR markers developed in green ash, most of which amplify and are polymorphic across 18 species of Fraxinus, including six species native to North America. The high average polymorphism information content (0.741) and allelic richness (15.3) revealed in six disparate populations of green ash indicate that these markers also have utility for investigating population dynamics in this species.

Abstract: The large scale loach (Paramisgurnus dabryanus) is endemic to China and is one of the most abundant edible fish in East Asia. The species is invasive in Japan, competing and hybridizing with the native Misgurnus anguillicaudatus. In this study, microsatellites were developed for the first time in this species using biotinylated probes for hybridization and library screening. Twelve polymorphic microsatellite loci were isolated and characterized in farmed fish. The number of alleles varied between two and five, and the observed and expected heterozygosity ranged from 0.32 to 1.00 and 0.51 to 0.75, respectively. Three loci (Pda14-102, Pda15-139, Pda18-104) deviated significantly from Hardy–Weinberg equilibrium values (P < 0.01). These microsatellite markers could prove useful for genetic identification and population management of P. dabryanus in the future.

Abstract: Seventeen polymorphic microsatellite markers were developed for Eurasian perch, using double-restriction-site-associated DNA approach combined with Ion Torrent PGM™ sequencing. In test panel of 48 individuals from two populations, the average number of alleles per locus was 10.2, ranging from 2 to 24. These variable microsatellites will be invaluable resource for population genetic studies in perch.

Abstract: Thirteen polymorphic microsatellite loci have been isolated and characterized from Cynoglossus semilaevis for the purpose of protecting its wild resources. They had between three and nine alleles. Observed and expected heterozygosities varied from 0.57 to 0.93, and from 0.56 to 0.82, respectively. All the loci conformed to Hardy–Weinberg equilibrium after Bonferroni correction. No significant linkage disequilibrium was detected among the loci (P > 0.004). They have provided sufficient level of genetic diversity to investigate the fine-scale population structure and species conservation and management in the C. semilaevis.

Abstract: Lady’s slipper orchid (Cypripedium calceolus) serves as a flagship species for plant conservation in many European countries. Its populations are threatened by over-collecting and loss of suitable habitat. Information on local and regional genetic structure can help to develop appropriate conservation strategies. A total of fifteen novel microsatellite markers were developed using MiSeq sequencing. All loci found to be polymorphic, with the number of alleles per locus ranging from 2 to 8. Observed heterozygosity ranged from 0.19 to 0.89. The developed microsatellite markers will be useful to analyze genetic diversity and genetic structure of C. calceolus populations.

Abstract: Twelve novel microsatellite markers were developed for the naked mole-rat, Heterocephalus glaber, a species characterized by a social structure analogous to that seen in eusocial insects. All but one locus (Hglab01) were found to be polymorphic across the 33 samples screened, with the number of alleles ranging from one to seven (average 3.58). Average observed and expected estimates of heterozygosity were 0.328 and 0.533, respectively. These are the first microsatellites developed for H. glaber and provide a useful tool for further population and mating system studies.

Abstract: Next generation sequencing was used to develop 15 new polymorphic microsatellite markers for the commercially and recreationally important fish mulloway (Argyrosomus japonicus). Improved knowledge of the genetic structure of the species is necessary for fisheries and environmental management. In a population of mulloway, we found that genetic variation and heterozygosity were high in most of our loci (mean number of alleles per locus = 9.46; mean heterozygosity = 0.660). To test the usefulness of our new markers for genetic research on other sciaenids, we cross amplified samples from eight other related sciaenid species, including three that form important fisheries and others that have significant conservation issues. We found that most of our new primers pairs produced scorable profiles in each of the other important sciaenids.

Abstract: Sixteen polymorphic, dinucleotide microsatel- lite loci were developed for Rhoadsia altipinna, a small characid fish from impacted rivers in south western Ecua- dor. None of the loci were in linkage disequilibrium or deviated significantly from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Variability was relatively high with allelic richness ranging between 2 and 22 alleles per locus (average = 9.125), observed hetero- zygosity ranging between 0.125 and 0.958 (aver- age = 0.695), and expected heterozygosity ranging between 0.120 and 0.952 (average = 0.736).

Abstract: The mitochondrial genome of the Australia eastern long-necked turtle Chelodina longicollis is 16,437 bp, containing 37 genes, with overall gene organisation and nucleotide composition typical of mitogenomes of other vertebrates. We identified a presumptive light strand replication initiation site (OL) in the WANCY region, a feature thought to be absent from the side-necked turtles (Pleurodira). The tRNAser2 of C. longicollis lacks a D-arm. This is the fifth mitogenome published for the Pleurodira, the third for the Chelidae and the first turtle mitogenome generated using next-generation sequencing. It will assist the development of primers and strategies for examining mitochondrial variation across the side-necked turtles.

Abstract: Seventeen polymorphic microsatellite loci were isolated and characterized from an important marine fish Larimichthys polyactis. The number of alleles per locus ranged from 4 to 21. The observed and expected heterozygosity ranged from 0.4583 to 0.9167 and from 0.7154 to 0.9566, respectively. These microsatellite loci could be useful for analyses of genetic diversity, population genetic structure, and management of L. polyactis.

Abstract: The marbled rockfish, Sebastiscus marmoratus, is an important commercially near-shore fish inhabiting littoral rocky bottoms from Japan to the East China Sea. Eleven polymorphic microsatellite loci were isolated from S. marmoratus and the polymorphism of these loci was observed in 32 samples from one wild population. The number of alleles ranged from 2 to 8. The polymorphism information content ranged from 0.155 to 0.752. The levels of the observed and expected heterozygosity were 0.186–0.969 and 0.170–0.782, respectively. Only one locus (Sm3-63) deviated from Hardy–Weinberg equilibrium. These microsatellite markers can provide a useful tool for further study on genetic diversity and conservation of S. marmoratus.

Abstract: Cinnamomum kanehirae, an endemic species in Taiwan, has become rare and endangered because of intensive logging and illegal felling performed to obtain medicinal fungus. To facilitate C. kanehirae conservation, 15 novel microsatellites were developed using a magnetic bead enrichment method. Most of these markers were obtained using cross-species amplification. The number of alleles and observed and expected heterozygosities across loci ranged from 2 to 13, 0.000 to 1.000, and 0.152 to 0.897. These novel markers are useful for population and conservation genetic studies on C. kanehirae and for developing appropriate conservation strategies.

Abstract: Dacrydium pectinatum de Laub. (Podocarpaceae) is the sole species of Dacrydium in China. Excessive logging for more than 30 years has resulted in its vulnerable status in China. Fifteen microsatellites were developed for D. pectinatum, 12 of which displayed polymorphisms. The number of alleles ranged from one to seven, the expected and observed heterozygosities varied from 0.000 to 0.819 and from 0.000 to 1.000, respectively. Significant linkage disequilibrium and deviations from the Hardy–Weinberg equilibrium were found. These microsatellite markers give a comprehensive understanding of the forces driving population evolution and local adaptation of D. pectinatum, which may also contribute to its management and conservation.