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Coyotes (Canis latrans) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (Lynx rufus) and gray foxes (Urocyon cinereoargenteus) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (Odocoileus virginianus) and wild turkeys (Meleagris gallopavo). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020–2021. We collected 180 scat samples along 295.9 kilometers (71.1–122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcoding and species-specific mtDNA fragment analysis (153 were coyote, 20 bobcat, and seven gray fox). Overall, we found evidence that two species, coyote and bobcat, consumed deer while all three consumed turkeys. Frequency of deer in the diet varied across sites for coyotes from 62–86% and wild turkey was present with a frequency of occurrence of 9% for coyotes, 5% for bobcats, and 14% for gray fox. Vertebrate diet specialization was evident across predator species with high frequency of deer in coyote diets, rabbits and small mammals in bobcat diets, and herpetofauna in gray fox diets. During deer fawning and wild turkey nesting and brood rearing, dietary overlap appears to be mediated by disparate selection of prey items, which reduced competition among coyotes, bobcats, and gray foxes. Use of DNA metabarcoding may augment our understanding of dietary preferences within this predator guild by providing increased resolution of diet composition among important game species. [ABSTRACT FROM AUTHOR]

Understanding the demography of species over recent history (e.g. <100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods, it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically based demographic inference on salamander species with documented population declines ( Ambystoma talpoideum) and expansions ( A. opacum), patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated dd RAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning. [ABSTRACT FROM AUTHOR]

The creation of wetlands, such as urban and industrial ponds, has increased in recent decades, and these wetlands often become enriched in pollutants over time. One metal contaminant trapped in created wetlands is copper (Cu2+). Copper concentrations in sediments and overlying water may affect amphibian species that breed in created wetlands. The authors analyzed the Cu concentration in dried sediments from a contaminated wetland and the levels of aqueous Cu released after flooding the sediments with different volumes of water, mimicking low, medium, and high pond-filling events. Eggs and larvae of Ambystoma opacum Gravenhorst, a salamander that lays eggs on the sediments in dry pond beds that hatch on pond-filling, were exposed to a range of Cu concentrations that bracketed potential aqueous Cu levels in created wetlands. Embryo survival varied among clutches, but increased Cu levels did not affect embryo survival. At Cu concentrations of 500 µg/L or greater, however, embryos hatched earlier, and the aquatic larvae died shortly after hatching. Because Cu concentrations in sediments increase over time in created wetlands, even relatively tolerant species such as A. opacum may be affected by Cu levels in the posthatching environment. Environ Toxicol Chem 2014;33:1631-1637. © 2014 SETAC [ABSTRACT FROM AUTHOR]

Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance. [ABSTRACT FROM AUTHOR]

Exposure to environmental contaminants contributes to the global decline of amphibian populations. The impacts of organic contaminants on amphibians are well documented. However, substantially less is known concerning the potential effects of metals on amphibian populations. Copper (Cu) is an essential element, but it can be toxic at concentrations only slightly higher than the normal physiological range. The present study examines the effects of chronic Cu exposure on embryos and larvae of southern leopard frogs, Lithobates (Rana) sphenocephalus. Groups of eggs from multiple clutches were collected from two wetlands and exposed to a range of Cu concentrations (0-150 µg/L) until they reached the free-swimming stage, and then individual larvae were reared to metamorphosis. Higher Cu concentrations significantly reduced embryo survival to the free-swimming stage but did not further reduce survival to metamorphosis. Larval period was affected by Cu treatment, but the clutch from which larvae originated (i.e., parentage) explained a higher proportion of the variation. Embryo survival to hatching varied significantly among clutches, ranging from 42.9 to 79.2%. Measurable levels of Cu were found in larvae with body burdens up to 595 µg Cu/g dry mass in the 100 µg/L treatment, and larval Cu body burdens were higher than in metamorphs. The present study also demonstrated that higher initial egg density ameliorated embryo mortality at higher Cu levels and should be accounted for in future studies. Environ. Toxicol. Chem. 2012; 31: 1587-1594. © 2012 SETAC [ABSTRACT FROM AUTHOR]

Molecular data have been used to show northward post-Pleistocene range expansions from a refugium in the southeastern United States for several mammal species. Fossil and historical records indicate that gray foxes (Urocyon cinereoargenteus) were not present in the northeastern United States until well after the Pleistocene (ca. 900). To test the hypothesis that gray foxes experienced a post-Pleistocene range expansion we conducted a phylogeographic analysis of gray foxes from across the eastern United States. We sequenced a variable portion of the mitochondrial control region (411 base pairs) from 229 gray fox tissue samples from 15 states, representing the range of all 3 East Coast subspecies. Phylogeographic analyses indicated no clear pattern of genetic structuring of gray fox haplotypes across most of the eastern United States. However, when haplotype frequencies were subdivided into a northeastern and a southern region, we detected a strong signal of differentiation between the Northeast and the rest of the eastern United States. Indicators of molecular diversity and tests for demographic expansion confirmed this division and suggested a very recent expansion of gray foxes into the northeastern states. Our results support the hypothesis that gray foxes 1st colonized the Northeast during a historical period of hemisphere-wide warming, which coincided with the range expansion of deciduous forest. We present the 1st study that analyzes the phylogeographic patterns of the gray fox in the eastern United States. [ABSTRACT FROM AUTHOR]

We developed a model to examine the amount of sperm that males should transfer to females under different conditions of sperm precedence. Following a previous model (Parker's), we assume the existence of nonrandom mating roles in which there are males that always mate first and others that always mate second. However, we alter Parker's model by introducing the possibility that males are non-optimal in their sperm allocation (because males make mistakes or are interrupted, or because of phenotypic variation among males). We predicted that when males behave optimally, their sperm expenditures will be equal for most levels of sperm precedence, regardless of whether they mate first or second. However, when the possibility that males behave non-optimally is included, we predicted (i) a positive correlation between the allocations of first and second males when there is second-male precedence, (ii) a negative correlation when there is first-male precedence, and (iii) no correlation when there is no precedence. We discuss these and other predictions and provide supporting evidence from the literature.Nous avons conçu un modèle pour déterminer la quantité de sperme que les mâles doivent transférer aux femelles dans différentes conditions de préséance de sperme. D'après un modèle antérieur (Parker), nous supposons des rôles sexuels non aléatoires, système dans lequel certains mâles sont toujours les premiers à s'accoupler, et d'autres, s'accouplent toujours en second. Cependant, nous modifions le modèle de Parker pour tenir compte de la possibilité que les mâles n'optimisent pas l'allocation de leur sperme (à cause d'erreurs ou d'interruptions ou alors à cause de leur variation phénotypique). Lorsqu'ils optimisent leur comportement, les mâles devraient tous avoir les mêmes dépenses de sperme pour la plupart des conditions de préséance de sperme, indépendamment de l'ordre qu'ils suivent pour s'accoupler. Cependant, en tenant compte de la possibilité que les mâles n'aient pas nécessairement un comportement optimal, nous prédisons (i) une corrélation positive entre les allocations des premiers et des seconds partenaires mâles lorsqu'il y préséance de sperme chez les mâles qui s'accouplent en second, (ii) une corrélation négative quand la préséance va aux mâles qui s'accouplent en premier et (iii) l'absence de corrélation quand il n'y a pas de préséance. Nous examinons ces hypothèses et d'autres et nous appuyons nos prédictions par des données tirées de la littérature.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite markers were developed and characterized to evaluate genetic diversity and population structure in Lilaeopsis schaffneriana subsp. recurva, an endangered species endemic to wetlands dispersed throughout southeastern Arizona, USA, and northern Sonora, Mexico. • Methods and Results: Eight loci (one of which was monomorphic) were developed and characterized in 48 individuals from two populations. The total number of alleles was 35, ranging from one to 10 per locus. Many of the primers amplified in L. carolinensis, L. chinensis, L. masonii, L. occidentalis, L. schaffneriana subsp. schaffneriana, Oxypolis fendleri, and Eryngium lemmonii. • Conclusions: Development of these novel microsatellite loci will facilitate a deeper understanding of genetic diversity, mode of reproduction, and population structure not only in L. schaffneriana subsp. recurva, but also in apiaceous relatives. [ABSTRACT FROM AUTHOR]

Globally, human activities have resulted in rapid environmental changes that present unique challenges for wildlife. However, investigations of local adaptation in response to simultaneous exposure to multiple anthropogenic selection pressures are rare and often generate conflicting results. We used an in situ reciprocal transplant design within a quantitative genetic framework to examine how adaptive evolution and phenotypic plasticity contribute to the persistence of an amphibian population inhabiting an environment characterized by high levels of multiple toxic trace elements. We found evidence of phenotypic divergence that is largely consistent with local adaptation to an environment contaminated with multiple chemical stressors, tied to potential trade‐offs in the absence of contaminants. Specifically, the population derived from the contaminated environment had a reduced risk of mortality and greater larval growth and in the contaminated environment, relative to offspring from the naïve population. Further, while survival in the uncontaminated environment was not compromised in offspring from the contaminant‐exposed population, they did show delayed development and reduced growth rates over larval development, relative to the naïve population. We found no evidence of reduced additive genetic variation in the contaminant‐exposed population, suggesting long‐term selection in a novel environment has not reduced the evolutionary potential of that population. We also saw little evidence that past selection in the ASH environment had reduced trait plasticity in the resident population. Maternal effects were prominent in early development, but we did not detect any trends suggesting these effects were associated with the maternal transfer of toxic trace elements. Our results demonstrate the potential for adaptation to multiple contaminants in a wild amphibian population, which may have facilitated long‐term persistence in a heavily impacted environment. [ABSTRACT FROM AUTHOR]

A correction to the article "Microsatellite development for an endangered riparian inhabitant, Lilaeopsis schaffneriana subsp. recurva (Apiaceae)" that was published in the April, 2012 issue is presented.

Ecological stoichiometry uses information on a few key biological elements (C, N and P) to explain complex ecological patterns. Although factors driving variation in these elements are well established, expanding stoichiometric principles to explore dynamics of the many other essential elements comprising biological tissues (i.e. the ionome) is needed to determine their metabolic relationships and better understand biological control of elemental flows through ecosystems.In this paper, we report observations of ionomic variation in two species of salamander (Ambystoma opacum and A. talpoideum) across ontogenic stages using specimens from biological collections of two wetlands sampled over a 30‐year period. This unique data set allowed us to explore the extent of ionomic variation between species, among ontogenic stages, between sites and through time.We found species‐ and, to a lesser extent, site‐specific differences in C, N and P along with 13 other elements forming salamander ionomes but saw no evidence of temporal changes. Salamander ionomic composition was most strongly related to ontogeny with relatively higher concentrations of many elements in adult males (i.e. Ca, P, S, Mg, Zn and Cu) compared to metamorphic juveniles, which had greater amounts of C, Fe and Mn.In addition to patterns of individual elements, covariance among elements was used to construct multi‐elemental nutrient balances, which revealed differences in salamander elemental composition between species and sites and changes in elemental proportions across ontogenic development. These multi‐elemental balances distinguished among species‐site‐ontogenic stage groups better than using only C, N and P.Overall, this study highlights the responsiveness of consumer ionomes to life‐history and environmental variation while reflecting underlying relationships among elements tied to biological function. As such, ionomic studies can provide important insights into factors shaping consumer elemental composition and for predicting how these changes might affect higher‐order ecological processes. [ABSTRACT FROM AUTHOR]

Abstract: Species with complex life cycles are susceptible to environmental stressors across life stages, but the carryover and latent effects between stages remain understudied. For species with biphasic life histories, such as pond‐breeding amphibians, delayed effects of aquatic conditions can influence terrestrial juveniles and adults directly or indirectly, usually mediated through fitness correlates such as body size. We collected adult southern toads (Anaxyrus terrestris) from 2 source populations—a natural reference wetland and a metal‐contaminated industrial wetland—and exposed their offspring to 2 aquatic stressors (a metal contaminant, copper [Cu], and a dragonfly predator cue) in outdoor mesocosms (n = 24). We then reared metamorphs in terraria for 5 mo to examine delayed effects of early life stage environmental conditions on juvenile performance, growth, and survival. Larval exposure to Cu, as well as having parents from a contaminated wetland, resulted in smaller size at metamorphosis—a response later negated by compensatory growth. Although Cu exposure and parental source did not affect larval survival, we observed latent effects of these stressors on juvenile survival, with elevated Cu conditions and metal‐contaminated parents reducing postmetamorphic survival. Parental source and larval Cu exposure affected performance at metamorphosis through carryover effects on body size but, 1 mo later, latent effects of parental source and larval predator exposure directly (i.e., not via body size) influenced performance. The carryover and latent effects of parental source population and aquatic Cu level on postmetamorphic survival and juvenile performance highlight the importance of conducting studies across life stages and generations. Environ Toxicol Chem 2018;37:2660–2669. © 2018 SETAC [ABSTRACT FROM AUTHOR]

Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs) remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485), with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus. [ABSTRACT FROM AUTHOR]

Exposure to agrochemicals can have lethal and sublethal effects on amphibians. Most toxicology studies only examine exposure during the aquatic larval stage. Survival of the juvenile stage is the most important for population persistence and it is critical to understand the potential impacts of exposure during this life stage. We investigated how short-term exposure to triclopyr, an herbicide commonly used in forestry management, might impact several juvenile traits. To determine if juveniles perceived exposure as an environmental stressor, we measured their release of corticosterone. We also examined dispersal traits by measuring foraging and hopping behavior. We found no evidence that exposure negatively impacted these traits or was a stressor. Our results provide a preliminary assessment of the potential impact of triclopyr on juvenile amphibians, but we recommend additional research on the effects of agrochemicals on juvenile amphibians. [ABSTRACT FROM AUTHOR]

One barrier to establishing catch limits to help protect shark populations is a lack of accurate species-specific extraction rates. This is due to many species looking similar, distinguishing characteristics (fins and head) of sharks commonly being removed, or sharks being grouped together in fisheries data. For this study, we collected elasmobranch (shark and ray) tissue samples from the central markets in San Jose (10 fish vendors or pescadarias) and Heredia (5 pescadarias) from June 2013 to September 2014. We used DNA barcoding techniques to amplify approximately 1050 bp of the NADH dehydrogenase subunit 2 (NADH2) gene (n = 833). We found that at least nine species of shark ( Alopias pelagicus , Carcharhinus falciformis , C. limbatus , C. obscurus , Mustelus lunulatus , Nasolamia velox , Rhizoprionodon longurio , Sphyrna lewini , S. zygaena ) and one ray ( Dasyatis longa ) are being sold in local markets, with C. falciformis representing 87.3% of shark samples tested (n = 637) and D. longa representing 100% of ray samples tested (n = 85). Our results suggest that C. falciformis continues to be under intense fishing pressure in the waters around Costa Rica despite recent concern over continued population declines. Although the number of Endangered S. lewini (4%) being sold in the markets is much less than for C. falciformis (87.3%), the numbers are still concerning given their current conservation status. [ABSTRACT FROM AUTHOR]

Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes. [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite loci were developed for the epiphytic pencil orchid Dendrobium calamiforme for population genetic and phylogeographic investigation of this Australian taxon. • Methods and Results: Nineteen microsatellite loci were identified from an Illumina paired-end shotgun library of D. calamiforme. Polymorphism and genetic diversity were assessed in 24 individuals from five populations separated by a maximum distance of ∼80 km. All loci were polymorphic with two to 14 alleles per locus, expected heterozygosity ranging from 0.486 to 0.902, and probability of identity values ranging from 0.018 to 0.380. • Conclusions: These novel markers will serve as valuable tools for investigation of levels of genetic diversity as well as patterns of gene flow, genetic structure, and phylogeographic history. [ABSTRACT FROM AUTHOR]

Individual variation in sexual fidelity and extrapair paternity (EPP) is widely attributed to environmental heterogeneity, but the only variables known to be influential are food abundance and density of conspecific breeders (potential extrapair partners). Habitat structure is thought to impact EPP but is rarely measured and, when considered, is usually confounded with food abundance and predation pressure. To sidestep these confounds, we tested whether EPP is associated with habitat structure variables and with local conspecific density in a species whose nesting habitat is not used for feeding and lacks predators. In a blue-footed booby, Sula nebouxii , colony, the probability of EPP in a female's nest was highest in parts of the study plot where there were few obstacles to locomotion, and was quadratically related to local density of sexually active males, even though local males did not sire the EP chicks. The probability of a male breeder siring EP (extrapair) chicks elsewhere was quadratically related to local density of sexually active males around his nest. From these patterns we infer that both sexes may foray for EP interactions, that males and females nesting at intermediate density are most likely to be accessed by forayers, and that obstacles in the vicinity of a female's nest constrain access of foraying males. To our knowledge, this is the first demonstration that individual variation in EPP is associated with habitat structure in the absence of confounding variation in food availability, predation pressure or breeder quality, and the first evidence that EPP opportunities of female and male breeders are reduced by high density of conspecific breeders above a particular threshold. [ABSTRACT FROM AUTHOR]

Abstract: Despite mounting evidence that extra-pair copulations (EPCs) are common in the Canidae, no studies have examined the most basal member of this family, the gray fox (Urocyon cinereoargenteus). In this study we explored the possibility that gray foxes may be socially, but not genetically, monogamous. Multiple paternity was confirmed in one litter and suspected in three others (n=7), thus 14.3–57.1% of all litters had more than one father. In this high-density population, multiple paternity may be one strategy to reduce inbreeding, although only one pair was significantly related to each other (r=0.36). Mother–daughter pairs were more common than father–son pairs. These results coupled with a previous study showing a female-biased sex ratio suggest male-biased dispersal and the potential for helper females. [Copyright &y& Elsevier]

Background: Boiga irregularis is a widespread invasive species on Guam and has led to extirpation of most of the island's native avifauna. There are presently no microsatellite markers for this invasive species, hence we developed highly polymorphic microsatellite markers to allow for robust population genetic studies on Guam. Findings: We isolated and characterized 33 microsatellite loci for the brown tree snake, B. irregularis. The loci were screened across 32 individuals from Guam. The number of alleles per locus ranged from three to ten, with an average of 4.62. The expected (He) and observed heterozygosity (Ho) ranged from 0.294 to 0.856 and from 0.031 to 0.813, with an average of 0.648 and 0.524, respectively. Significant deviations from Hardy-Weinberg equilibrium were detected at seven loci after Bonferoni correction. Probability of identity values ranged from 0.043 to 0.539. Conclusions: These genetic markers are useful for understanding a suite of post-invasion population genetic parameters, sources of invasions, and effectiveness of management strategies for this invasive species. [ABSTRACT FROM AUTHOR]

Elasmobranchs represent one of the most imperiled taxa, yet few nations have developed catch limits and no international or bilateral catch limits exist. One barrier to establishing catch limits is a lack of accurate species-specific extraction rates due to many species looking similar, distinguishing characteristics (fins and head) being removed, or grouping of all elasmobranchs together in fisheries data. To better understand the species-specific impacts fisheries are having on elasmobranchs we used forensic genetic techniques to identify the types and quantities of shark species landed in Costa Rican artisanal small-scale and mid-scale fisheries. We collected elasmobranch tissue samples from fishermen in three locations along Costa Rica's Pacific Coast: Coyote, Bejuco, and Ojochal, from April 2013 to September 2014. We used DNA barcoding techniques, utilizing a 1044 base pair region of the NADH dehydrogenase subunit 2 gene, to identify to species 275 of the 416 samples collected. Within these fisheries, seven species of shark and one ray were identified, with the scalloped hammerhead shark (Sphyrna lewini) accounting for ∼75−80% of all sharks landed. Observed total lengths (TL) for the scalloped hammerhead shark (10.9–99 cm) in these fisheries suggests the sharks sampled were all either juveniles or neonates. Based on these data it is likely that the areas from which these samples were collected represent nursery grounds for the scalloped hammerhead shark. The quantity of young scalloped hammerhead sharks removed from these areas, and ones similar to them, by these artisanal fisheries could be of great importance when determining future conservation measures for this species. Our findings also indicate that sharks caught in these artisanal fisheries do not appear to represent those sold in markets around San Jose. [ABSTRACT FROM AUTHOR]

Highlights • Offspring of parents from a copper (Cu) contaminated site were more tolerant Cu than those from reference sites. • Population exposure history to other metal contaminants was not associated with Cu tolerance. • Cu tolerance not associated with maternal factors, including transfer of metals to eggs or egg size. • Patterns of tolerance suggestive of adaptation, rather than acclimatization, to a common environmental contaminant. Abstract Human activities have radically shaped the global landscape, affecting the structure and function of ecosystems. Habitat loss is one of the most visible changes to the landscape and a primary driver of species declines; however, anthropogenic environmental contamination also threatens population persistence, but is not as readily observed. Aquatic organisms are especially susceptible to chemical perturbations, which can negatively impact survival and fitness related traits. Some populations have evolved tolerance to chemical stressors, which could mitigate the consequences associated with contamination. Amphibians are experiencing global declines due to multiple stressors and are particularly at risk to aquatic chemical stressors due to their permeable skin and reliance on wetlands for reproduction and larval development. However, amphibians also have substantial plasticity in response to environmental variation. We designed our study to examine whether tolerance to heavy metals is greater in Southern toad (Anaxyrus terrestris) larvae from wetlands with a history of contamination. Considering many of the most common trace elements elicit acute toxicity by disrupting osmotic- and ionic-regulation, we hypothesized that alterations to these aspects of physiology resulting from multigenerational exposure to trace element mixtures would be the most likely routes by which tolerance would evolve. We used copper (Cu) as a proxy for heavy metal exposure because it is a widely distributed aquatic stressor known to cause osmotic stress that can also cause mortality at levels commonly encountered in the environment. We found considerable within and among population variation in Cu tolerance, as measured by time to death. Larvae from populations living in sites contaminated with mixtures of heavy metals associated with coal fly ash were no more tolerant to Cu than those from reference sites. However, larvae from a population inhabiting a constructed wetland complex with high Cu levels were significantly more tolerant; having half the risk of mortality as reference animals. This wetland complex was created < 20 years ago, thus if elevated Cu tolerance in this population is due to selection in the aquatic habitat, such adaptation may occur rapidly (i.e. ∼10 generation). Our results provide evidence that amphibians may be able to evolve tolerance in response to trace element contamination, though such tolerance may be specific to the combination of contaminants present. [ABSTRACT FROM AUTHOR]

We isolated and characterized a total of 13 microsatellite loci from Cordulegaster sarracenia (Odonata: Cordulegastridae). Loci were screened in 24 individuals from Louisiana and Texas. Within C. sarracenia, the number of alleles per locus ranged from 0 to 5, and observed and expected heterozygosities ranged from 0.000 to 0.556 and 0.000 to 0.613, respectively. Overall differentiation among study populations was very high (FST = 0.423), suggesting significant geographic population structure with low diversity within populations. Twelve of the 13 primers amplified in C. sayi, C. diastatops, C. maculata, and C. obliqua and polymorphism levels are reported. These new genetic markers will provide tools for addressing a number of population genetic and demographic questions relating to conservation of this rare dragonfly species. [ABSTRACT FROM AUTHOR]

Round whitefish ( Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning. [ABSTRACT FROM AUTHOR]

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045–0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies. [ABSTRACT FROM AUTHOR]

This study reports the development, characterization, and cross-species transferability of 20 genomic microsatellite markers for Aronia melanocarpa, an important nutraceutical fruit crop. The markers were developed with Illumina paired-end genomic sequencing technology using DNA from Professor Ed cultivar that was originally collected fromthe wild in NewHampshire. The markers were highly polymorphic and transferable to Aronia arbutifolia and Aronia prunifolia genomes. The average number of alleles per locus was 9.1, 4.5, and 5.6 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. The polymorphism information content (PIC) of loci ranged from 0.38 to 0.95 for all taxa, with an average of 0.80, 0.68, and 0.87 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. This is the first study to develop microsatellite markers in the Aronia genus. These markers will be very useful in studying the genetic diversity and population structure of wild Aronia and expediting the breeding efforts of this emerging fruit crop through marker-assisted selection. [ABSTRACT FROM AUTHOR]

Ligumia nasuta (Say, 1817; Eastern Pondmussel) is an imperiled freshwater mussel (Unionidae) in eastern North America. Population declines in the Laurentian Great Lakes resulting from the introduction of dreissenid mussels and habitat destruction in the 20th Century have greatly reduced and limited its distribution. To properly inform restoration and management efforts for L. nasuta , fine-scale genetic analyses must be performed on the remnant populations. This study used Illumina paired-end shotgun sequencing to identify potential microsatellite loci for L. nasuta , utilizing two samples to develop the Illumina paired-end shotgun library. Forty-eight primer pairs were tested on the remaining 24 samples. Twenty-nine of the 48 microsatellite primer sets screened were successfully amplified using 24 L. nasuta samples collected from the Great Lakes watershed. The estimated fragment size ranged from 167 to 445 base-pairs (bp) and the number of alleles per locus varied between 5 and 16 (mean = 9.7). Only five of the loci deviated significantly from Hardy–Weinberg expectations after Bonferroni corrections. The development of these new microsatellite loci will greatly facilitate future genetic studies on L. nasuta . [ABSTRACT FROM AUTHOR]

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment. [ABSTRACT FROM AUTHOR]

Background: A priority for conservation is the identification of endemic populations. We developed microsatellite markers for common raven (Corvus corax), a bird species with a Holarctic distribution, to identify and assess endemic populations in Alaska. Results: From a total of 50 microsatellite loci, we isolated and characterized 15 loci. Eight of these loci were polymorphic and readily scoreable. Eighteen to 20 common ravens from Fairbanks, Alaska were genotyped showing the following variability: 3-8 alleles per locus, 0.25-0.80 observed heterozygosity (Ho), and 0.30-0.80 expected heterozygosity (He). All loci were in Hardy-Weinberg equilibrium and linkage equilibrium and many loci amplified and were polymorphic in related taxa. Conclusions: These loci will be used to identify endemic populations of common raven and assess their genetic diversity and connectivity. [ABSTRACT FROM AUTHOR]

Many metals are acutely toxic to aquatic organisms at high concentrations and for some metals, such as copper (Cu), even low-level chronic contamination may be cause for conservation concern. Amphibian susceptibility to Cu has been examined in only a few species, and susceptibility is highly variable. The lethal and sublethal effects were examined of chronic aqueous Cu exposure on embryonic and larval eastern narrowmouth toads, Gastrophryne carolinensis. Copper levels as low as 10 μg Cu/L reduced embryonic and larval survival. Embryonic survivorship varied within- and between-source populations, with embryos derived from uncontaminated-wetland parents having greater survival at lower Cu levels than embryos from parents from a metal-contaminated constructed wetland. At 30 μg/L, embryos from the contaminated site had greater survival. Overall survival from oviposition to metamorphosis was 68.9% at 0 μg/L and 5.4% at 10 μg/L. Similarly, embryos exposed to ≥50 μg/L demonstrated developmental delays in transition from embryo to free-swimming larva. These results demonstrate a negative population-specific response to environmentally relevant levels of Cu. Environ Toxicol Chem 2015;34:575-582. © 2014 SETAC [ABSTRACT FROM AUTHOR]

Major Histocompatibility Complex (MHC) variability plays a key role in pathogen resistance, but its relative importance compared to environmental and demographic factors that also influence resistance is unknown. We analyzed the MHC II DRB exon 2 for 165 raccoons ( Procyon lotor ) in Missouri (USA). For each animal we also determined the presence of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to two highly virulent pathogens, canine distemper virus (CDV) and parvovirus. We investigated the role of MHC polymorphism and other demographic and environmental factors previously associated with predicting seroconversion. In addition, using an experimental approach, we studied the relative importance of resource availability and contact rates. We found important associations between IgG antibody presence and several MHC alleles and supertypes but not between IgM antibody presence and MHC. No effect of individual MHC diversity was found. For CDV, supertype S8, one allele within S8 (Prlo-DRB ∗ 222), and a second allele (Prlo-DRB ∗ 204) were positively associated with being IgG+, while supertype S4 and one allele within the supertype (Prlo-DRB ∗ 210) were negatively associated with being IgG+. Age, year, and increased food availability were also positively associated with being IgG+, but allele Prlo-DRB ∗ 222 was a stronger predictor. For parvovirus, only one MHC allele was negatively associated with being IgG+ and age and site were stronger predictors of seroconversion. Our results show that negative-frequency dependent selection is likely acting on the raccoon MHC and that while the role of MHC in relation to other factors depends on the pathogen of interest, it may be one of the most important factors predicting successful immune response. [ABSTRACT FROM AUTHOR]

Crawfish Frogs (Lithobates areolatus) are a North American ranid, considered near threatened globally with populations in decline throughout their range. We studied populations of Crawfish Frogs on local and regional scales at their northeastern range limit to (1) assess the level of genetic diversity within populations, (2) estimate fine-scale genetic structure, and (3) estimate genetic differentiation between populations at the regional level. We used 10 microsatellite loci to genotype frogs collected from three regional sites in Indiana separated by 50- 172 km and at one of these sites within a network of three breeding ponds <1 km apart. Heterozygosity estimates revealed high levels of diversity within these populations (mean Ho: 0.54-0.67 per site), which is encouraging for future management. The degree of population subdivision was low at the regional level (FST = 0.071 for sites within 172 km). Genetic differentiation was related to geographic distance between sampling sites, as predicted by an isolation-by-distance model. We observed no genetic differentiation between individuals sampled from ponds approximately 250 m apart and slight divergence of individuals from a pond approximately 750 m away. This suggests ponds within 1 km form a genetically distinct single breeding unit composed of multiple subpopulations. Finally, we observed high genetic differentiation between southwest and southeast Indiana sites indicating historical (rather than recent) isolation of these sites. These data will be applied to a regional management plan in an attempt to recover Crawfish Frogs along the northeastern extreme of their range. [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. • Methods and Results: A total of 42 polymorphic loci were identified from a sample of 24 individuals from a single population in Ohio, USA. The number of alleles per locus ranged from two to nine, and median observed heterozygosity was 0.435. • Conclusions: This large number of polymorphic loci will enable researchers to quantify male fitness, patterns of multiple paternity, selfing, and biparental inbreeding in large natural populations of this species. These markers will also permit detailed study of fine-scale patterns of genetic structure. [ABSTRACT FROM AUTHOR]

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample - a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. [ABSTRACT FROM AUTHOR]

Abstract: Earthworms are important components of soil ecosystems worldwide, and have been used extensively as indicator species in ecotoxicology studies. Our understanding of mating systems, population structure, and genetic diversity in earthworms is limited by the current lack of available genetic tools. To address this gap, we developed 16 novel microsatellite markers for the compost earthworm Eisenia fetida, one of the most widely studied earthworm species. We tested the new markers in 3 putative populations of worms from commercial vermiculture operations in Canada and the U.S.A. All 16 loci were variable in at least one population, with the number of alleles per locus ranging from 3 to 10, observed heterozygosity from 0.000 to 0.783, and polymorphic information content from 0.032 to 0.587. One group had significantly reduced heterozygosity compared to the other 2, but overall there were only minor genetic differences among the tested suppliers, suggesting a possible bottleneck for this species in North America. The microsatellite loci we describe here will be extremely useful tools for future field and laboratory studies of E. fetida. Body size and condition in adult worms varied significantly by supplier, and breeding success and cocoon production were significantly higher in breeding pairs from one supplier compared to the other two. In the absence of evidence for genetic divergence among populations, our results suggest that the early rearing environment may be an important factor affecting adult breeding performance. We caution that the source of worms may affect the outcome of laboratory experiments involving growth and reproduction. [Copyright &y& Elsevier]

Background: Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results: A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1). Conclusion: We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly. [ABSTRACT FROM AUTHOR]

Premise of the study: Microsatellite markers were developed in Actaea racemosa to analyze population genetic structure, compare genetic diversity across the species' range, and provide a genetic context for studies of phytochemical variation. Methods and Results: A total of seven polymorphic loci were screened in 60 individuals from 12 localities. The number of alleles per locus ranged from three to six, and observed heterozygosity ranged from 0.133 to 0.900. Most of the loci tested cross-amplified in A. pachypoda, A. podocarpa, and A. rubra, indicating the utility of these markers for the genus. Conclusions: These new loci will provide tools for population genetics studies, including the characterization of genetic variation in A. racemosa and other eastern North American species of Actaea. [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite markers were isolated and characterized in Berberis thunbergii , an invasive and ornamental shrub in the eastern United States, to assess genetic diversity among populations and potentially identify horticultural cultivars. • Methods and Results: A total of 12 loci were identifi ed for the species. Eight of the loci were polymorphic and were screened in 24 individuals from two native (Tochigi and Ibaraki prefectures, Japan) and one invasive (Connecticut, USA) population and 21 horticultural cultivars. The number of alleles per locus ranged from three to seven, and observed heterozygosity ranged from 0.048 to 0.636. • Conclusions: These new markers will provide tools for examining genetic relatedness of B. thunbergii plants in the native and invasive range, including phylogeographic studies and assessment of rapid evolution in the invasive range. These markers may also provide tools for examining hybridization with other related species in the invasive range. [ABSTRACT FROM AUTHOR]

* Premise of the study: We isolated and characterized microsatellite markers in Polygonum cespitosum Blume, an herbaceous annual plant species introduced into North America from Asia that has recently become invasive. * Methods and Results: A total of 12 polymorphic and 3 monomorphic loci were screened in 1-2 individuals from each of 20 populations from the introduced and native range, for a total of 24 samples. The number of alleles per locus in the polymorphic loci ranged from 3 to 9, and expected heterozygosity ranged from 0.156 to 0.838. * Conclusions: These new loci will provide tools for examining genetic relatedness among introduced and native populations of this and other related species. [ABSTRACT FROM AUTHOR]

We developed and optimized 15 polymorphic microsatellite loci in the jungle perch, Kuhlia rupestris. Loci were screened in a single population ( n = 24) from Fraser Island, Queensland, Australia. Number of alleles per locus ranged from 3 to 19 and observed heterozygosity from 0.25 to 1. No significant linkage disequilibrium was detected between any pair of loci. Genotype proportions for these loci in the population sampled were in Hardy–Weinberg equilibrium. [ABSTRACT FROM AUTHOR]

Measurements of external contaminant exposures on individual wildlife are rare because of difficulties in using contaminant monitors on free-ranging animals. Most wildlife contaminant exposure data are therefore simulated with computer models. Rarely are empirical exposure data available to verify model simulations, or to test fundamental assumptions inherent in exposure assessments. We used GPS-coupled contaminant monitors to quantify external exposures to individual wolves (Canis lupus) living within the Belarus portion of Chernobyl's 30-km exclusion zone. The study provided data on animal location and contaminant exposure every 35 min for 6 months, resulting in ~6600 individual locations and 137Cs external exposure readings per wolf, representing the most robust external exposure data published to date on free ranging animals. The data provided information on variation in external exposure for each animal over time, as well as variation in external exposure among the eight wolves across the landscape of Chernobyl. The exposure data were then used to test a fundamental assumption in screening-level risk assessments, espoused in guidance documents of the U.S. Environmental Protection Agency and U.S. Department of Energy, — Mean contaminant concentrations conservatively estimate individual external exposures. We tested this assumption by comparing our empirical data to a series of simulations using the ERICA modeling tool. We found that modeled simulations of mean external exposure (10.5 mGy y−1), based on various measures of central tendency, under-predicted mean exposures measured on five of the eight wolves wearing GPS-contaminant monitors (i.e., 12.3, 26.3, 28.0, 28.8 and 35.7 mGy y−1). If under-prediction of exposure occurs for some animals, then arguably the use of averaged contaminant concentrations to predict external exposure is not as conservative as proposed by current risk assessment guidance. Thus, a risk assessor's interpretation of simulated exposures in a screening-level risk analysis might be misguided if contaminant concentrations are based on measures of central tendency. We offer three suggestions for risk assessors to consider in order to reduce the probability of underestimating exposure in a screening-level risk assessment. Unlabelled Image • GPS-coupled contaminant monitors worn by wolves within Chernobyl's exclusion zone. • Measured external exposure at 35-min intervals on 8 wolves for 6 months • Empirical data compared to model simulations of external exposure • Simulations using mean contaminant levels under-predicted exposure on 5 of 8 wolves. • Findings question current exposure assessment guidance of USEPA and USDOE. [ABSTRACT FROM AUTHOR]