Adrienne I. Kovach

Stock Identification of Atlantic Cod in U.S. Waters Using Microsatellite and Single Nucleotide Polymorphism DNA Analyses

Abstract Management of Atlantic cod Gadus morhua in U.S. waters is based on a two-stock model composed of stocks from (1) the Gulf of Maine (GOM) and (2) Georges Bank (GB) and areas south; however, evidence suggests a more fine-scale structuring. We used microsatellite and single nucleotide polymorphism (SNP) analyses to investigate the stock structure of Atlantic cod in U.S. waters. In year 1, we analyzed microsatellite loci in larvae from GB, age-0 juveniles from multiple locations in the GOM, and adults of unknown maturity from GB, Jeffreys Ledge, and the Great South Channel (GSC). In year 2, Atlantic cod collected from spawning aggregations in Ipswich Bay in the spring and at GB, Stellwagen Bank, Chatham, and Ipswich Bay in the winter, along with adults of unknown maturity from Long Island, New York, were surveyed at a modified battery of microsatellites and three SNPs. In year 1, we saw no significant differences in allelic frequencies between our composite sample of adult and juvenile cod from the G...

A Range-Wide Survey to Determine the Current Distribution of New England Cottontails

Abstract The abundance and distribution of New England cottontails (NEC; Sylvilagus transitionalis) have been declining for several decades. Remnant populations in some regions are known to be vulnerable to extirpation but little is known about the status of populations in most areas. We conducted a survey of the historic range (ca. 1960) of NEC to determine the current distribution and relative status of extant populations. Because NEC were sympatric with eastern cottontails (S. floridanus) and snowshoe hares (Lepus americanus) in much of their historic range, identity of resident lagomorphs was based on DNA extracted either from tissue of captured cottontails or from fecal pellets of free-ranging lagomorphs. We searched 2,301 patches of suitable habitat and detected NEC in 162. We identified 5 disjunct populations in approximately 14% of the historic range. Forest maturation and fragmentation are the most plausible explanations for the widespread decline of NEC. Contraction of the historic distribution was toward eastern and southern edges where a variety of anthropogenic disturbances (e.g., brushy edges of highways and railroad corridors and idle portions of agricultural fields) provided habitat. Land-ownership patterns (dominated by small acreages) and land-use activities (expanding development and limited forest management) within the currently occupied range of NEC suggest a continued decline of suitable habitats. As a result, we recommend efforts to enhance remaining populations of NEC that include responses at 2 spatial scales. At the population or landscape scale, current land uses should guide habitat manipulations that expand existing populations. At the regional scale, we recommend consideration should be given to increasing dispersal among remnant populations, possibly by generating “stepping stones” of suitable habitat. In addition to improving long-term viability of NEC, other species of conservation concern that are dependent on early successional habitats will benefit from these efforts.

Fine-Scale Population Structure and Asymmetrical Dispersal in an Obligate Salt-Marsh Passerine, the Saltmarsh Sparrow (Ammodramus caudacutus)

ABSTRACT. Understanding the spatial scale of gene flow can yield valuable insight into the ecology of an organism and guide conservation strategies. Fine-scale genetic structure is uncommon in migratory passerines because of their high vagility and presumed high dispersal abilities. Aspects of the behavior and ecology of some migratory species, however, may promote structure on a finer scale in comparison to their mobility. We investigated population genetic structure in the Saltmarsh Sparrow (Ammodramus caudacutus), a migratory passerine that breeds along the northeastern coast of the United States, where it is restricted exclusively to a narrow strip of patchily distributed tidal marsh habitat. Using genotyping with 10 microsatellite loci, we detected weak but significant population structure among Saltmarsh Sparrows from nine marshes on the breeding grounds between Scarborough, Maine, and Oceanside, New York. Genetic variation among marshes was largely consistent with a pattern of isolation by distance, with some exceptions. One inland marsh was genetically divergent despite its proximity to other sampled marshes, which suggests that mechanisms besides geographic distance influence population genetic structure. Bayesian clustering, multivariate analyses, and assignment tests supported a population structure consisting of five groups. Estimates of migration rates indicated variation in gene flow among marshes, which suggests asymmetrical dispersal and possible source-sink population dynamics. The genetic structure that we found in Saltmarsh Sparrows may result from natal philopatry and breeding-site fidelity, combined with restricted dispersal due to obligate dependence on a patchy habitat. Our findings suggest that fine-scale population structure may be important in some migratory passerines.

Genetic Barcode RFLP Analysis of the Nelson's and Saltmarsh Sparrow Hybrid Zone

Abstract Hybridization between Saltmarsh Sparrow (Ammodramus caudacutus) and Nelsons Sparrow (A. nelsoni) has been documented in areas where the two species occur sympatrically, increasing the difficulty of accurate species identification. We developed a DNA barcoding restriction fragment length polymorphism (RFLP) test to discriminate between Nelsons Sparrows and Saltmarsh Sparrows and applied it to 426 putative Saltmarsh Sparrows sampled from Maine to New York, USA. All individuals were identified in the field as Saltmarsh Sparrows based on morphology, but 34 (8%) had Nelsons specific mitochondrial DNA, indicating they were of hybrid origin. This discrepancy in morphological and genetic data highlights the difficulties associated with accurate field identification and may hinder conservation efforts by confounding attempts to identify and monitor “pure” populations. Mitochondrial DNA of Nelsons Sparrow was prevalent at the most southern point of the previously documented overlap zone and was also found in one individual 150 km south of the overlap zone. Our findings offer new insights into the extent of hybridization between the two species and underscore the need for further investigation into the consequences of hybridization on conservation of Saltmarsh Sparrows.

Genetic Mark-Recapture Population Estimation in Black Bears and Issues of Scale

ABSTRACT Abundance estimates for black bears (Ursus americanus) are important for effective management. Recently, DNA technology has resulted in widespread use of noninvasive, genetic capture—mark—recapture (CMR) approaches to estimate populations. Few studies have compared the genetic CMR methods to other estimation methods. We used genetic CMR to estimate the bear population at 2 study sites in northern New Hampshire (Pittsburg and Milan) in 2 consecutive years. We compared these estimates to those derived from traditional methods used by the New Hampshire Fish and Game Department (NHFG) using hunter harvest and mortality data. Density estimates produced with genetic CMR methods were similar both years and were comparable to those derived from traditional methods. In 2006, the estimated number of bears in Pittsburg was 79 (95% CI = 60–98) corresponding to a density of 15–24 (95% CI) bears/ 100 km2; the 2007 estimate was 83 (95% CI = 67–99; density = 16–24 bears/100 km2). In 2006, the estimated number of bears in Milan was 95 (95% CI = 74–117; density = 16–25 bears/100 km2); the 2007 estimate was 96 (95% CI = 77–114; density = 17–25 bears/100 km2). We found that genetic CMR methods were able to identify demographic variation at a local scale, including a strongly skewed sex ratio (2 M:1 F) in the Milan population. Genetic CMR is a useful tool for wildlife managers to monitor populations of local concern, where abundance or demographic characteristics may deviate from regional estimates. Future monitoring of the Milan population with genetic CMR is recommended to determine if the sex ratio bias continues, possibly warranting a change in local harvest regimes.

Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

BackgroundEvolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits.ResultsGeographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species.ConclusionsOur findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow.

Anthropogenic influences on the spatial genetic structure of black bears

Anthropogenic influences such as hunting pressure and habitat fragmentation can alter the demographic and spatial patterns of wildlife populations. Understanding the consequences of these impacts is a challenge for natural resource managers, which can be overcome by investigations using spatial genetic techniques. We used spatial autocorrelation and landscape genetic analyses to compare the impacts of anthropogenic forces on the spatial genetic structure of two female black bear (Ursus americanus) populations in northern New Hampshire with similar bear densities but varying human densities, hunting pressure and sex ratios. We found evidence of an impact of hunting mortality on the spatial genetic structure of female black bears. The population with greater hunting pressure and a heavily male-biased sex ratio (Milan) exhibited greater spatial genetic structure represented by a pattern of isolation by distance, kin clustering, and reduced dispersal in comparison to the population with a balanced sex ratio (Pittsburg). We did not find a strong effect of fragmenting landscape features on female spatial structure. Major roads were correlated with spatial genetic structure, but only in the population with lower human density and development (Pittsburg). Slope and elevation were also correlated with spatial genetic structure, suggesting terrain plays a role in structuring seasonal female home range boundaries. Our study revealed the utility of using spatial genetic techniques to identify anthropogenic influences on female social organization. These findings highlight the importance of monitoring the impacts of harvest pressure not only on demographics but also the spatial genetic structure of animal populations.

Limited influence of local and landscape factors on finescale gene flow in two pond-breeding amphibians

Dispersal and gene flow within animal populations are influenced by the composition and configuration of the landscape. In this study, we evaluated hypotheses about the impact of natural and anthropogenic factors on genetic differentiation in two amphibian species, the spotted salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus) in a commercial forest in central Maine. We conducted this analysis at two scales: a local level, focused on factors measured at each breeding pond, and a landscape level, focused on factors measured between ponds. We investigated the effects of a number of environmental factors in six categories including Productivity, Physical, Land Composition, Land Configuration, Isolation and Location. Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood frog breeding ponds. We used a hierarchical Bayesian approach in the program GESTE at each breeding pond and a random forest algorithm in conjunction with a network analysis between the ponds. We found overall high genetic connectivity across distances up to 17 km for both species and a limited effect of natural and anthropogenic factors on gene flow. We found the null models best explained patterns of genetic differentiation at a local level and found several factors at the landscape level that weakly influenced gene flow. This research indicates multiscale investigations that incorporate local and landscape factors are valuable for understanding patterns of gene flow. Our findings suggest that dispersal rates in this system are high enough to minimize genetic structuring and that current forestry practices do not significantly impede dispersal.

Genotype‐environment associations support a mosaic hybrid zone between two tidal marsh birds

Abstract Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh‐level characteristics in shaping a hybrid zone between two recently diverged avian taxa – Saltmarsh (Ammodramus caudacutus) and Nelsons (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co‐occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space.

Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone.

Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelsons (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.