Screening H3 Histone Acetylation in a Wild Bird, the House Sparrow (Passer Domesticus).

Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen histone acetylation in the house sparrow (Passer domesticus); we studied this species because DNA methylation was important in the spread of this bird globally. This species has one of the broadest geographic distributions in the world, and part of this success is related to the way that it uses methylation to regulate its gene expression. Here, we verify that a commercially available assay that was developed for mammals can be used in house sparrows. We detected high variance in histone acetylation among individuals in both liver and spleen tissue. Further, house sparrows with higher epigenetic potential in the Toll Like Receptor-4 (TLR-4) promoter (i.e., CpG content) had higher histone acetylation in liver. Also, there was a negative correlation between histone acetylation in spleen and TLR-4 expression. In addition to validating a method for measuring histone acetylation in wild songbirds, this study also shows that histone acetylation is related to epigenetic potential and gene expression, adding a new study option for ecological epigenetics.

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

Within-genotype epigenetic variation enables broad niche width in a flower living yeast.

Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species niche as all of the factors that effect the persistence of the species as well as the impact of the species in a given location (Hutchinson 1957; Chase 2011). Many studies have argued that phenotypic plasticity enhances niche width because plastic responses allow organisms to express advantageous phenotypes in a broader range of environments (Bradshaw 1965; Van Valen 1965; Sultan 2001). Further, species that exploit habitats with fine-grained variation, or that form metapopulations, are expected to develop broad niche widths through phenotypic plasticity (Sultan & Spencer 2002; Baythavong 2011). Although a long history of laboratory, greenhouse and reciprocal transplant experiments have provided insight into how plasticity contributes to niche width (Pigliucci 2001), recent advances in molecular approaches allow for a mechanistic understanding of plasticity at the molecular level (Nicotra et al. 2010). In particular, variation in epigenetic effects is a potential source of the within-genotype variation that underlies the phenotypic plasticity associated with broad niche widths. Epigenetic mechanisms can alter gene expression and function without altering DNA sequence (Richards 2006) and may be stably transmitted across generations (Jablonka & Raz 2009; Verhoeven et al. 2010). Also, epigenetic mechanisms may be an important component of an individual's response to the environment (Verhoeven et al. 2010). While these ideas are intriguing, few studies have made a clear connection between genome-wide DNA methylation patterns and phenotypic plasticity (e.g. Bossdorf et al. 2010). In this issue of Molecular Ecology, Herrera et al. (2012) present a study that demonstrates epigenetic changes in genome-wide DNA methylation are causally active in a species' ability to exploit resources from a broad range of environments and are particularly important in harsh environments.

Hybridization between pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon Scaphirhynchus platorynchus.

This study found that introgressive hybridization of the pallid sturgeon Scaphirhynchus albus with the common shovelnose sturgeon Scaphirhynchus platorynchus has probably occurred across the range of S. albus. Bayesian clustering found evidence of hybridization in all management units of S. albus. Some individuals were intermediate at both genetic and morphological characters, and some had discordant results. The results support introgressive hybridization throughout much of the range of S. albus, yet individuals consistent with being pure members of each species were detected in all management units. Simulations demonstrated that it would be very difficult to distinguish introgressed individuals from pure specimens after multiple generations of backcrossing with these microsatellite markers. Using hybrid or backcross fish as broodstock could artificially accelerate the loss of unique genetic variation in S. albus. Additional microsatellite loci or additional genetic markers, along with morphological data may be required to ensure that hybrid or backcross fish are not used. Introgressive hybridization requires at least two generations and generation lengths of S. albus are long, perhaps as long as 30 years. The proportion of individuals consistent with introgressive hybrid origins indicates that hybridization between S. albus and S. platorynchus probably has occurred for several generations and is not a recent phenomenon.

Broad-scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus) populations.

Introduced species offer unique opportunities to study evolution in new environments, and some provide opportunities for understanding the mechanisms underlying macroecological patterns. We sought to determine how introduction history impacted genetic diversity and differentiation of the house sparrow (Passer domesticus), one of the most broadly distributed bird species. We screened eight microsatellite loci in 316 individuals from 16 locations in the native and introduced ranges. Significant population structure occurred between native than introduced house sparrows. Introduced house sparrows were distinguished into one North American group and a highly differentiated Kenyan group. Genetic differentiation estimates identified a high magnitude of differentiation between Kenya and all other populations, but demonstrated that European and North American samples were differentiated too. Our results support previous claims that introduced North American populations likely had few source populations, and indicate house sparrows established populations after introduction. Genetic diversity also differed among native, introduced North American, and Kenyan populations with Kenyan birds being least diverse. In some cases, house sparrow populations appeared to maintain or recover genetic diversity relatively rapidly after range expansion (<50 years; Mexico and Panama), but in others (Kenya) the effect of introduction persisted over the same period. In both native and introduced populations, genetic diversity exhibited large-scale geographic patterns, increasing towards the equator. Such patterns of genetic diversity are concordant with two previously described models of genetic diversity, the latitudinal model and the species diversity model.