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We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Copper (Cu) appears to be consistently more toxic to anuran species relative to other vertebrate taxa. There are limited Cu toxicity data for salamanders; of the few studies conducted on salamanders, most examined Cu effects on the embryonic, but not the larval, stage. We performed acute toxicity experiments, to quantify LC50s, on Harrison stage 46 larvae (free swimming hatchlings with egg yolk completely absorbed) of three ambystomatid salamander species. Each LC50 experiment used exposure concentrations of 10, 20, 30, 40, 50, and 60 µg/L with 10 replicates per concentration each containing one larva. We found very high toxicity for all species compared to previously published research on the embryo stage. Specifically, the 4-d LC50s for Ambystoma tigrinum and A. opacum were 35.3 and 18.73 µg/L, respectively. The same Cu concentrations caused similar toxicity to A. talpoideum (LC50 = 47.88 µg/L), but exposures required up to 48 d to elicit the same level of mortality. A time-to-event analysis indicated that time to mortality was significantly affected by Cu concentration. Additionally, for A. talpoideum, we observed that elevated levels of Cu decreased growth rate. Comparisons with previously reported Cu toxicity for embryos suggest that, as with fish, Cu may be more toxic to larval salamander stages than for embryos. Further, our data suggest that Cu is an important environmental contaminant that deserves increased scrutiny on the potential for population-level effects where contamination has occurred in wetlands and streams inhabited by salamanders.

Multiple paternity is relatively common across diverse taxa; however, the drivers and implications related to paternal and maternal fitness are not well understood. Several hypotheses have been offered to explain the occurrence and frequency of multiple paternity. One set of hypotheses seeks to explain multiple paternity through direct and indirect benefits including increased genetic diversity or enhanced offspring fitness, whereas another set of hypotheses explains multiple paternity as a by‐product of sexual conflict and population‐specific parameters such as density. Here, we investigate mating system dynamics in a historically studied population of the American alligator (Alligator mississippiensis) in coastal South Carolina. We examine parentage in 151 nests across 6 years and find that 43% of nests were sired by multiple males and that male reproductive success is strongly influenced by male size. Whereas clutch size and hatchling size did not differ between singly sired and multiply sired nests, fertility rates were observed to be lower in multiply sired clutches. Our findings suggest that multiple paternity may exert cost in regard to female fitness, and raise the possibility that sexual conflict might influence the frequency of multiple paternity in wild alligator populations., We examine parentage in 151 nests across 6 years and find that 43% of nests were sired by multiple males and that male reproductive success is strongly influenced by male size. Whereas clutch size and hatchling size did not differ between singly sired and multiple sired nests, fertility rates were observed to be lower in multiply sired clutches.

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 created20 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.

International audience; In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radio- logical fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem at- tributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensi- tive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that ra- diological risk assessments must be designed and informed by rigorous statistical frameworks capable of reveal- ing the causal inference tying radiological exposure to the endpoints selected for measurement.

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. s...

Wild pigs (Sus scrofa) are the most widely distributed invasive wild ungulate in the United States, yet the factors that influence wild pig dispersal and colonization at the regional level are poorly understood. Our objective was to use a population genetic approach to describe patterns of dispersal and colonization among populations to gain a greater understanding of the invasion process contributing to the expansion of this species. We used 52 microsatellite loci to produce individual genotypes for 482 swine sampled at 39 locations between 2014 and 2016. Our data revealed the existence of genetically distinct subpopulations (F ST = 0.1170, p

We developed and characterized 13 polymorphic microsatellite loci in South Texas species of Praticolella von Martens, 1892 (Gastropoda: Polygyridae), some of which have restricted distributions and can be difficult to identify using traditional shell characters. To make this genomic tool more broadly useful in these species, instead of characterizing loci in many individuals of a single species, we tested them across five populations of four different species. Twelve loci amplified in all four species tested, and eleven loci showed deviations from Hardy-Weinberg equilibrium. These loci will be valuable in assessing species identity and population genetic connectivity among South Texas Praticolella.

Mercury (Hg) exposure poses a threat to both fish and human health. Sharks are known to bioaccumulate Hg, however, little is known regarding how Hg is distributed between different tissue groups (e.g. muscle regions, organs). Here we evaluated total mercury (THg) concentrations from eight muscle regions, four fins (first dorsal, left and right pectorals, caudal-from both the inner core and trailing margin of each fin), and five internal organs (liver, kidney, spleen, heart, epigonal organ) from two different shark species, bonnethead (Sphyrna tiburo) and silky shark (Carcharhinus falciformis) to determine the relationships of THg concentrations between and within tissue groups. Total Hg concentrations were highest in the eight muscle regions with no significant differences in THg concentrations between the different muscle regions and muscle types (red and white). Results from tissue collected from any muscle region would be representative of all muscle sample locations. Total Hg concentrations were lowest in samples taken from the fin inner core of the first dorsal, pectoral, and caudal (lower lobe) fins. Mercury concentrations for samples taken from the trailing margin of the dorsal, pectoral, and caudal fins (upper and lower lobe) were also not significantly different from each other for both species. Significant relationships were found between THg concentrations in dorsal axial muscle tissue and the fin inner core, liver, kidney, spleen and heart for both species as well as the THg concentrations between the dorsal fin trailing margin and the heart for the silky shark and all other sampled tissue types for the bonnethead shark. Our results suggest that biopsy sampling of dorsal muscle can provide data that can effectively estimate THg concentrations in specific organs without using more invasive, or lethal methods.

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.

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 from the wild in New Hampshire. 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.

The Neotropical otter, Lontra longicaudis, is an ecologically important species for freshwater ecosystems that is threatened due to habitat destruction and hunting. However, there is limited information regarding the population sizes, genetic diversity, genetic structure and gene flow of the species, which is crucial for the elaboration of conservation plans. The aim of this study was to isolate and characterize microsatellites for L. longicaudis, using Illumina paired-end-sequencing. Initial amplification tests were performed in 48 loci, out of which, 13 yielded high-quality PCR products and thus were further evaluated. Genetic diversity and discrimination power of the 13 microsatellite loci was assessed using 19 non-invasive samples collected in the Jamapa basin in Veracruz, Mexico and blood samples from six captive individuals. All loci were polymorphic, the number of alleles per locus ranged from 4 to 10, the observed heterozygosity from 0.21 to 0.69, and the expected heterozygosity from 0.55 to 0.82. The combined set of 13 microsatellites showed a high power for discriminating among individuals (probability of identity PID = 1.551 × 10−16) and among siblings (probability of identity of siblings PIDSIB = 3.349 × 10−06). A combination of nine loci are sufficient to discriminate among siblings with high confidence (PIDSIB

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.

Many shark populations have experienced severe declines in the past few decades due to increased demand for their products. As fisheries managers, conservation biologists, and other invested groups move to develop new conservation measures to better protect sharks it will be important to understand the potential reactions (behaviors) local fishermen will have to new regulations. To determine the potential behaviors local artisanal fishermen in Costa Rica would have toward new conservation measures for sharks a structured survey (n=72) was distributed to several fishing communities along Costa Rica's Pacific coast. Overall, 89% of fishermen felt that protecting sharks was important with 97% stating a willingness to support shark conservation. However, support dropped to 67% if they would have to change some of their fishing practices. Almost all fishermen surveyed (93%) were in support of the formation of marine protected areas (MPAs). Although, if MPAs restricted their current fishing practices support dropped to between 6% and 65% depending on the restrictiveness of regulations implemented in the MPA. The majority (86%) of the fishermen surveyed also indicated they would be more likely to support new legislative measures to protect sharks if they were included in the decision making process. The results suggest that artisanal fishermen in Costa Rica are willing to protect sharks, but only if their current fishing practices are minimally impacted. It is therefore important that mangers work with these communities to develop management plans that will provide the best protection possible for sharks while also garnering local support to ensure continued compliance.

Chemical contamination is often suggested as an important contributing factor to amphibian population declines, but direct links are rarely reported. Population modeling provides a quantitative method to integrate toxicity data with demographic data to understand the long-term effects of contaminants on population persistence. In this study we use laboratory-derived embryo and larval toxicity data for two anuran species to investigate the potential for toxicity to contribute to population declines. We use the southern toad (Anaxyrus terrestris) and the southern leopard frog (Lithobates sphenocephalus) as model species to investigate copper (Cu) toxicity. We use matrix models to project populations through time and quantify extinction risk (the probability of quasi-extinction in 35 yr). Life-history parameters for toads and frogs were obtained from previously published literature or unpublished data from a long-term (>35 yr) data set. In addition to Cu toxicity, we investigate the role of climate change on amphibian populations by including the probability of early pond drying that results in catastrophic reproductive failure (CRF, i.e., complete mortality of all larval individuals). Our models indicate that CRF is an important parameter for both species as both were unable to persist when CRF probability was >50% for toads or 40% for frogs. Copper toxicity alone did not result in significant effects on extinction risk unless toxicity was very high (>50% reduction in survival parameters). For toads, Cu toxicity and high probability of CRF both resulted in high extinction risk but no synergistic (or greater than additive) effects between the two stressors occurred. For leopard frogs, in the absence of CRF survival was high even under Cu toxicity, but with CRF Cu toxicity increased extinction risk. Our analyses highlight the importance of considering multiple stressors as well as species differences in response to those stressors. Our models were consistently most sensitive to juvenile and adult survival, further suggesting the importance of terrestrial stages to population persistence. Future models will incorporate multiple wetlands with different combinations of stressors to understand if our results for a single wetland result in a population sink within the landscape.

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 .

Although nearly 30 years have passed since the Chernobyl Nuclear Power Plant accident near the town of Pripyat, Ukraine, the status and health of mammal populations within the Chernobyl Exclusion Zone (CEZ) remain largely unknown, and are of substantial scientific and public interest. Information regarding the response of flora and fauna to chronic radiation exposure is important in helping us understand the ecological consequences of past (eg Chernobyl and Fukushima) and potential future nuclear accidents. We present the results of the first remote-camera scent-station survey conducted within the CEZ. We observed individuals of 14 mammalian species in total; for those species with sufficiently robust visitation rates to allow occupancy to be modeled (gray wolf [Canis lupus], raccoon dog [Nyctereutes procyonoides], Eurasian boar [Sus scrofa], and red fox [Vulpes vulpes]), we found no evidence to suggest that their distributions were suppressed in highly contaminated areas within the CEZ. These data support the results of other recent studies, and contrast with research suggesting that wildlife populations are depleted within the CEZ.

The Chernobyl Exclusion Zone (CEZ) is a ~ 4300 km2 area in Belarus and Ukraine that remains heavily contaminated with radiation from the nuclear accident of 1986. Long standing controversy persists on the fate of wildlife within the CEZ following human abandonment of the area. Human residency remains extremely sparse, and the CEZ has become a refuge for some populations of wildlife, including gray wolves (Canis lupus). Using GPS telemetry, we documented the first long-distance movements of a young (1–2 years) male wolf from the CEZ into the surrounding landscape. The wolf traveled 369 km from its home range center over a 21-day period in February 2015. In the 95 days prior to dispersal, the wolf maintained a home range of ~ 28 km2, with daily displacements rarely exceeding 5 km. With the onset of dispersal, daily displacement increased to a mean of 16.8 km. The dispersal of a young wolf is an important observation because it suggests that the CEZ may serve as a source for some wildlife populations outside of the CEZ, and raises questions about the potential spread of radiation-induced genetic mutations to populations in uncontaminated areas.

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.

Quantifying the relationship between demographic patterns and genetic diversity are important in predicting temporal population genetic changes. To make predictions there must be an understanding of the relationship between census size, the effective number of breeders (Nb) and effective population size (Ne). We evaluate the temporal genetic variation between three populations of Ambystoma salamanders, and compare genetic and demographic estimates of Nb and Ne. We sampled two wetlands, RB and GB for A. opacum and sampled A. talpoideum at RB, over a 20-year period. Ambystoma opacum colonized the RB wetland in 1980 and the population has steadily expanded as A. talpoideum has declined towards local extinction; the GB population of A. opacum has remained relatively large and stable over this same time period. Genetic variation at 10 microsatellites remained stable at each population over the sampled time frame, and did not reflect changes in population size. Genetic estimates of Nb also did not reflect demographic trends, and were lower than demographic estimates of Nb. Genetic methods of determining Ne gave similar estimates to demographic methods. Our findings indicate that sample sizes and number of markers typically used in genetic studies do not provide enough precision to monitor population size changes in amphibians, which likely violate many of the assumptions of Nb and Ne estimation models. These findings should be considered when using Ne in conservation and management assessments of amphibian populations.

Ranaviruses are double-stranded DNA viruses that infect amphibians, fish, and rep- tiles, causing global epidemics in some amphibian populations. It is important to identify new spe- cies that may be susceptible to the disease, particularly if they reside in the same habitat as other at-risk species. On the Savannah River Site (SRS) in Aiken, South Carolina, USA, ranaviruses are present in several amphibian populations, but information is lacking on the presence, prevalence, and morbidity of the virus in reptile species. An eastern mud turtle Kinosternon subrubrum captured on the SRS in April 2014 exhibited clinical signs of a ranaviral infection, including oral plaque and conjunctivitis. Quantitative PCR analyses of DNA from liver tissue, ocular, oral, nasal, and cloacal swabs were all positive for ranavirus, and sequencing of the template confirmed in - fection with a FV3-like ranavirus. Histopathologic examination of postmortem tissue samples revealed ulceration of the oral and tracheal mucosa, intracytoplasmic epithelial inclusions in the oral mucosa and tongue sections, individualized and clusters of melanomacrophages in the liver, and bacterial rods located in the liver, kidney, heart, stomach, and small intestine. This is the first report of morbidity and mortality of a mud turtle with a systemic ranaviral infection.

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.

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

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.

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.

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

We isolated and characterized a total of 33 microsatellite loci from the Patagonian sprat Sprattus fuegensis, a recent exploited marine resource with a conservation status unknowing. Loci were screened in 24 individuals from the inshore waters of the Aysen Fjord, Chile. The number of alleles per locus ranged from 7 to 24, observed heterozygosity ranged from 0.217 to 0.875, and the probability of identity values ranged from 0.006 to 0.133. These new loci will provide tools for examining population genetic structure, estimating effective population size and provide information to fisheries management and conservation.

Females sometimes obtain older sires for their offspring through extra-pair interactions, but how female age influences paternity is largely unexplored and interactive effects across the age span of both sexes have not been analyzed. To test whether female choice of sire age varies with female age in the blue-footed booby (Sula nebouxii), we examined associations between ages of both partners and the probability of extra-pair paternity (EPP) in 350 broods of parents up to 22 years old in a single breeding season. Extra-pair paternity enables a female to select an alternative sire for her offspring and could function to avoid or achieve particular combinations of parental ages. A male age × female age interaction revealed that in young females (≤4 years), EPP decreased with increasing age of the social partner, whereas in old females (≥8 years), it increased. Moreover, sires of extra-pair (EP) chicks of young females paired to young males were on average 6.33 years older than the females’ social partners. Since female boobies control copulatory access, this pattern could imply that young females choose old sires for their proven genetic quality and that old females avoid very old males because matings with them may risk infertility or genetic defects in offspring. Taking female age into account and observing across the whole age span may be necessary for understanding female age-based mate choice.

We developed microsatellite loci for the Julimes pupfish, Cyprinodon julimes. Twenty-five loci were screened across 19 individuals from Julimes Spring, Chihuahua, Mexico. The number of alleles per locus ranged from 2 to 14, observed heterozygosity ranged from 0.105 to 0.947, and the probability of identity values ranged from 0.022 to 0.588. We then tested for cross-amplification in the bighead pupfish, C. pachycephalus; twenty-three individuals from San Diego de Alcala, Chihuahua, Mexico, were screened across the 20 loci that amplified cleanly. These new loci will be used for long-term genetic monitoring of these critically endangered species.

Eighteen microsatellite loci were developed for the silky shark Carcharhinus falciformis and screened across a total of 53 individuals from the western Atlantic Ocean, Eastern Tropical Pacific Ocean, and Red Sea. The number of alleles per locus ranged from 3 to 19, observed heterozygosity ranged from 0.158 to 0.917, and the probability of identity values ranged from 0.010 to 0.460. Though believed to be one of the most abundant species of large sharks, C. falciformis were recently listed as “near threatened” globally and “vulnerable” in the Eastern Tropical Pacific by the IUCN, due to reductions in catch rates from both target and non-target fisheries (Dulvy et al. in Aquat Conserv 18:459–482, 2008). Very little information exists about the population structure and genetic diversity of C. falciformis around the world. These new loci will provide effective tools for examining the sustainability of this declining species.

We isolated and characterized a total of 22 microsatellite loci for the leafcutter ant, Acromyrmex lundii. The loci were screened for 24 individuals from southern Brazil and Uruguay. The number of alleles per locus ranged from 5 to 20, the observed heterozygosity ranged from 0.417 to 0.917, and the probability of identity values ranged from 0.011 to 0.38. These genetic markers will be useful for understanding the population and conservation biology of the leafcutter ant A. lundii and closely related species, and will provide novel insights into the evolutionary biology of social parasitism and leafcutter ant mating systems.

Environmental contaminants are implicated in the global decline of amphibian populations. Copper (Cu) is a widespread contaminant that can be toxic at concentrations just above the normal physiological range. In the present study we examined the effects of chronic Cu aqueous exposure on embryos and larvae of southern toads, Anaxyrus (Bufo) terrestris. Measurable levels of Cu were found in larvae, with tissue concentrations up to 27.5 μg Cu/g dry mass. Aqueous concentrations of Cu as low as 10 μg/L significantly reduced survival to the free-swimming stage and no larvae reached metamorphosis at concentrations above 15 μg/L. Clutches from populations with prior Cu exposure had the lowest survivorship. Among several populations there was significant variation in survivorship at different levels of Cu. More data are needed to understand the underlying causes of within- and among-population resilience to anthropogenic stressors.

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

We isolated and characterized a total of 31 microsatellite loci from the mole salamander, Ambystoma talpoideum. Loci were screened in 20 individuals from a single location in Aiken, South Carolina. The number of alleles per locus ranged from 3 to 11, observed heterozygosity ranged from 0.000 to 0.700, and the probability of identity values ranged from 0.031 to 0.400. These new loci will provide tools for examining the genetic diversity, structure, mating system, and adult morph determination of A. talpoideum.

UNLABELLED 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.

Understanding the demography of species over recent history (e.g.