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

Background: Evolutionary 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. Results: Geographic 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. Conclusions: Our 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

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

Background: Evolutionary 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. Results: Geographic 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. Conclusions: Our 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

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

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 Nelson\u27s (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

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

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 Nelson\u27s (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

Relationship of phenotypic variation and genetic admixture in the Saltmarsh–Nelson\u27s sparrow hybrid zone

Hybridization is influential in shaping species\u27 dynamics and has many evolutionary and conservation implications. Identification of hybrid individuals typically relies on morphological data, but the assumption that hybrids express intermediate traits is not always valid, because of complex patterns of introgression and selection. We characterized phenotypic and genotypic variation across a hybrid zone between 2 tidal-marsh birds, the Saltmarsh Sparrow (Ammodramus caudacutus) and Nelson\u27s Sparrow (A. nelsoni) (n = 290), and we sought to identify morphological traits that could be used to classify admixed individuals. Sparrows were sampled from a total of 34 marshes, including 23 sympatric and 11 putatively allopatric marshes. Each individual was scored at 13 plumage traits, and standard morphometric data were collected. We used genotyping analysis at 24 microsatellite loci to categorize individuals into genotypic classes of pure, F1–F2, or backcrossed. Genetic data revealed that 52% of individuals sampled along the geographic transect were of mixed ancestry, and the majority of these were backcrossed. Traits related to the definition of plumage features (streaking, crown, and face) showed less overlap between genotypic classes than traits related to the amount or color of plumage features. Although morphological data performed well in distinguishing between the 2 taxa, pure and backcrossed individuals of each parental type could not be distinguished because of substantial overlap in plumage and morphology. We conclude that the discrimination of pure and hybrid individuals is not possible in the absence of genetic data. Our results have implications for conservation of pure populations, as extensive backcrossing throughout the hybrid zone may present challenges for monitoring pure species identified by morphology alone

Effect of Deer Density on Breeding Birds in Delaware

Previous research has suggested that high deer densities negatively impact bird communities. Most of this research was conducted using a very high deer density compared to no deer. Our research investigated deer impacts across a density gradient to determine an appropriate density for deer management efforts. Using Breeding Bird Survey (BBS) data from 2005- 2006 and Delaware Department of Natural Resources and Environmental Control (DNREC) deer density data for the same time period, we compared avian richness and relative abundance for BBS points to deer density in Delaware. We divided deer densities into 3 categories: low (\u3c12 deer/km2), medium (12-23 deer/km2) and high (\u3e23 deer/km2). We placed birds into the following deer-sensitive guilds: interior obligates, forest ground nesters, shrub nesters, ground gleaners, low canopy foragers, and tropical migrants. The species richness of ground gleaners was higher in high deer densities (F1.36 = 17.05, P = 0.0002). No other guilds\u27 species richness was affected. The relative abundances of ground gleaners (F1.36 = 25.60, P = \u3c0.0001) and tropical migrants (F1.36 = 4.11, P = 0.0501) were lowest in low deer densities. Relative abundance of wood thrush (Hylocichla mustelina) was also lowest in low deer densities (F1.36 = 21.60, P = \u3c0.0001). Richness and abundance of all guilds were positively influenced by the percent forest cover within a 50 m buffer. The effects of deer density on these bird communities were generally opposite of what past literature has suggested. In order to better understand this trend I have also conducted 618 of my own point counts and corresponding vegetation surveys throughout Delaware. This data was collected from May- August 2008 and will be repeated in the summer of 2009

Targeting fatty acid β-oxidation impairs monocyte differentiation and prolongs heart allograft survival

Monocytes play an important role in the regulation of alloimmune responses after heart transplantation (HTx). Recent studies have highlighted the importance of immunometabolism in the differentiation and function of myeloid cells. While the importance of glucose metabolism in monocyte differentiation and function has been reported, a role for fatty acid β-oxidation (FAO) has not been explored. Heterotopic HTx was performed using hearts from BALB/c donor mice implanted into C57BL/6 recipient mice and treated with etomoxir (eto), an irreversible inhibitor of carnitine palmitoyltransferase 1 (Cpt1), a rate-limiting step of FAO, or vehicle control. FAO inhibition prolonged HTx survival, reduced early T cell infiltration/activation, and reduced DC and macrophage infiltration to heart allografts of eto-treated recipients. ELISPOT demonstrated that splenocytes from eto-treated HTx recipients were less reactive to activated donor antigen-presenting cells. FAO inhibition reduced monocyte-to-DC and monocyte-to-macrophage differentiation in vitro and in vivo. FAO inhibition did not alter the survival of heart allografts when transplanted into Ccr2-deficient recipients, suggesting that the effects of FAO inhibition were dependent on monocyte mobilization. Finally, we confirmed the importance of FAO on monocyte differentiation in vivo using conditional deletion of Cpt1a. Our findings demonstrate that targeting FAO attenuates alloimmunity after HTx, in part through impairing monocyte differentiation

Detection of local-scale population declines through optimized tidal marsh bird monitoring design

Evaluating the efficacy of monitoring designs is crucial for the successful monitoring and conservation of populations. For tidal marsh bird species of conservation concern, detecting population declines at local spatial scales within actionable time frames is a top priority. We examined and compared the effectiveness of alternative monitoring strategies for detecting local-scale population declines using count data from 1176 spatially-independent salt marsh sampling points throughout the northeastern United States (Maine to Virginia). We used abundance estimates that accounted for imperfect detection as initial conditions to simulate annual population declines of 5%, 10%, 30%, and 50% over a 5-year sampling period. Under an optimal monitoring design with biennial sampling, we were able to successfully detect annual population declines of ≥30% for each species and for all species combined. However, this required a minimum of 15–20 points per site being sampled. Power to detect declines, although low for detecting smaller annual declines (i.e., \u3c10%), improved substantially when points were visited twice per season, yet a third visit provided a reduced benefit. When testing factors that could potentially influence power to detect declines, we found that the power within sites was positively related to species abundance. Power was similar between biennial sampling (3 of 5 years) and annual sampling (5 of 5 years), suggesting a more cost-effective approach would be to sample every other year. We found that within most sites, detecting annual declines of 10% or less over a relatively short 5-year duration would be difficult. Hence, we recommend that salt marsh bird monitoring programs in the northeastern United States conduct two visits to each site per sampling year, include 15 or more sampling points per site (without confounding spatial independence), and conduct monitoring efforts every other year. This approach will maximize the efficacy of site-level monitoring of tidal marsh birds, which can aid in assessments of coastal wetland conservation and related habitat management efforts

Non-linear regression models for Approximate Bayesian Computation

Approximate Bayesian inference on the basis of summary statistics is well-suited to complex problems for which the likelihood is either mathematically or computationally intractable. However the methods that use rejection suffer from the curse of dimensionality when the number of summary statistics is increased. Here we propose a machine-learning approach to the estimation of the posterior density by introducing two innovations. The new method fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling. The new algorithm is compared to the state-of-the-art approximate Bayesian methods, and achieves considerable reduction of the computational burden in two examples of inference in statistical genetics and in a queueing model.Comment: 4 figures; version 3 minor changes; to appear in Statistics and Computin