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.

Atlantic cod Gadus morhua in US waters are currently managed as 2 stocks: (1) a Gulf of Maine stock and (2) a Georges Bank and south stock. This designation is decades old and warrants re-evaluation in light of concerns that fisheries management units may not reflect biologically meaningful population units. In this study, we used 10 microsatellite loci, the PanI locus, and 5 single nucleotide polymorphism markers to characterize the population genetic structure of cod in US waters. We found significant differentiation among temporally and spatially divergent populations of cod (global F ST = 0.0044), primarily stemming from 2 potentially non-neutral loci, and evidence for a population structure that strongly contradicts the current 2-stock management model. This genetic structure was stable over a 5 yr period. Our results indicate that cod in US waters are broadly structured into 3 groups: (1) a northern spring-spawning coastal complex in the Gulf of Maine (GOM), (2) a southern complex consisting of winter-spawning inshore GOM, offshore GOM and sites south of Cape Cod, Massachusetts, and (3) a Georges Bank population. The strongest differentiation occurs between populations in the northern and southern complex (mean F ST = 0.0085), some of which spawn in the same bays in different seasons. By means of mixture analysis, young-of-the-year fish sampled on juvenile nurseries were assigned to the spawning complex of their origin. Our findings contribute to a growing body of knowledge that Atlantic cod and other marine fish populations are structured on a finer scale than previously thought and that this structure supports biocomplexity and locally adapted populations. As such, it may be warranted to re-evaluate current management units and tailor management plans toward this finer scale.KEY WORDS: Atlantic cod · Microsatellite DNA · Single nucleotide polymorphism · Population genetic structure · Stock identification · Gadus morhua Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 410: [177][178][179][180][181][182][183][184][185][186][187][188][189][190][191][192][193][194][195] 2010 the importance of processes that limit dispersal and promote self-replenishment of local populations, such as sedentary adult life history strategies (Robichaud & Rose 2004, Howell et al. 2008, spawning site fidelity (Taggart 1997), natal homing (Thorrold et al. 2001, Svedäng et al. 2007), egg and larval retention (Jones et al. 1999, 2005, Bradbury et al. 2008) and local adaptation (McIntyre & Hutchings 2003, Conover et al. 2006, Hutchings et al. 2007). The implications of such fine-scale population structure are important for effective management (Palumbi 2003, Bradbury et al. 2008, Reiss et al. 2009).One marine fish species known to exhibit fine-scale population structure in parts of its distribution is Atlantic cod Gadus morhua L. (see reviews in Waldman 2005 andCarvalho 2008). Atlantic cod is one of the most commercially important marine fishes in the world and comprises a p...

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.

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The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species' range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F ST = 0.145; P \ 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.

Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2–36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both barriers and facilitators of dispersal for an early successional habitat specialist in a fragmented landscape.

Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.

The reproductive behaviour of large, solitary mammals is difficult to study. Owing to their secretive nature and wide-ranging habits, aspects of male mating behaviour are poorly documented in solitary than in social species. We used radiotelemetry and microsatellite DNA analysis to investigate the influence of body size on male mating tactics and short-term reproductive success in the black bear, Ursus americanus, a solitary carnivore. We investigated male ranging behaviour and documented male encounters with breeding females to determine whether males employed conditional mating tactics according to their body sizes. We found that male home-range sizes were not positively associated with body size, but encounter rates with breeding females were. Although all males searched widely for females, mating access appeared to be largely determined by fighting ability. Large males encountered more breeding females and had more frequent encounters during the females' estimated receptive periods than did small-and medium-sized males. Paternity was highly skewed toward the three dominant males who fathered 91% of the cubs sampled during the 3-year study. Paternity was correlated with the frequency of male encounters during female receptive periods. Male encounters, however, overestimated the success of medium-sized males and underestimated the overall variance in male reproductive success. Multiple paternity occurred in two of seven litters, indicating that sperm competition is important in black bear mating behaviour. Implications for male lifetime reproductive success are discussed.Résumé : Le comportement reproducteur de grands mammifères solitaires est difficile à étudier. À cause de la nature discrète et des habitudes nomades des mâles des espèces solitaires, plusieurs aspects de leur comportement reproducteur sont beaucoup moins bien connus que chez les espèces sociales. Nous avons utilisé la radiotélémétrie et l'analyse des microsatellites de l'ADN pour étudier l'influence de la taille du corps sur les tactiques d'accouplement du mâle et sur le succès à court terme de la reproduction chez l'ours noir, Ursus americanus, un carnivore solitaire. Nous avons déterminé les comportements de déplacement des mâles et analysé les rencontres des mâles avec des femelles en état de reproduction pour voir si les mâles utilisent des tactiques conditionnelles d'accouplement en fonction de leur taille. Les surfaces des domaines vitaux des mâles ne sont pas en corrélation positive avec leur taille corporelle, mais leurs taux de rencontre de femelles le sont. Bien que tous les mâles fassent des recherches à grande échelle pour trouver des femelles, l'accès aux femelles semble être largement déterminé par leur capacité de lutte. Les grands mâles rencontrent plus de femelles reproductrices et font plus de contacts durant les périodes apparemment réceptives des femelles que ne le font les mâles de petite et moyenne tailles. La paternité est fortement asymétrique et est le fait principalement de trois mâles qui ont engendré 91 % des ourson...