Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors.

Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus's arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. Reduced representation bisulfite sequencing was used to assess differences in methylation in Creole and Spanish samples and revealed 334 differentially methylated regions using high stringency parameters (P-value <0.01, ≥4 CpGs within a distance of 200 bp, mean methylation difference >25%) annotated to 263 unique features. Gene ontology analysis revealed candidate genes involved in tropical adaptation processes, including genes differentially hyper- or hypomethylated above 80% in Creole samples displaying biological functions related to immune response (IRF6, PTGDR, FAM19A5, PGLYRP1), nervous system (GBX2, NKX2-8, RPGR), energy management (BTD), heat resistance (CYB561) and skin and coat attributes (LGR6). Our results entail that major environmental changes imposed on Creole cattle have had an impact on their methylomes measurable today, which affects genes implicated in important pathways for adaptation. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models.

Comparing genetic diversity and demographic history in co-distributed wild South American camelids.

Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent-based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1000 individuals. For vicuña, this bottleneck is inferred to have taken place ~3300 years ago, but to have occurred more recently for guanaco at ~2000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.

Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species.

Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.

The genetic legacy of the 19th-century decline of the British polecat: evidence for extensive introgression from feral ferrets.

In the 19th century, the British polecat suffered a demographic contraction, as a consequence of direct persecution, reaching its lowest population in the years that preceded the First World War. The polecat is now recovering and expanding throughout Britain, but introgressive hybridization with feral ferrets has been reported, which could be masking the true range of the polecat and introducing domestic genes into the species. We used a fragment of the mitochondrial DNA control region and 11 microsatellite loci to characterize the frequency and extent of hybridization and introgression between the two species and assess whether the 19th-century decline corresponded to a genetic bottleneck in the polecat. The proportion of admixture detected in the wild was high (31%) and hybrids were more frequently found outside Wales, suggesting that hybridization is more likely to occur along the eastern edge of the polecat's range expansion. The patterns observed in the mitochondrial and nuclear DNA data show that introgression was mediated by crosses between male polecats and female ferrets, whose offspring backcrossed with polecats. No first-generation (F1 ) hybrids were identified, and the broad range of observed admixture proportions agrees with a scenario of past extensive hybridization between the two species. Using several different methods to investigate demographic history, we did not find consistent evidence for a genetic bottleneck in the British polecat, a result that could be interpreted as a consequence of hybridization with ferrets. Our results highlight the importance of the Welsh polecat population for the conservation and restoration of the genetic identity of the British polecat.

Notes on the conservation threats to the western lesser spot-nosed monkey (Cercopithecus petaurista buettikoferi) in the Bijagós Archipelago (Guinea-Bissau, West Africa).

The lesser spot-nosed monkey (Cercopithecus petaurista) is a widely distributed West African guenon, which is generally considered less vulnerable to local extinctions than many sympatric primate species. Guinea-Bissau harbours the westernmost populations of the species, which is thought to be very rare or even extinct on the mainland, but to have putative populations on some islands of the Bijagós Archipelago. However, due to a lack of regional studies, baseline information on these insular populations is missing. We collected baseline data on the anthropogenic activities that possibly threaten the long-term conservation of this primate by using non-systematic ethnographic methodologies. The species was reported to be decreasing in number or rare by locals on two of the islands, and we identified two main conservation threats to it: generalised habitat loss/degradation, and hunting. While subsistence hunting has been recorded before in these areas, we report, to the best of our knowledge for the first time for these islands, the presence of a semi-organised commercial wild meat trade. The carcasses of western lesser spot-nosed monkeys were observed being stored and shipped from seaports to be sold at urban hubs (Bissau and Bubaque Island). The effect of commercial trade on the species could be severe, considering the small, naturally occurring, carrying capacities typical of insular ecosystems. The results of this study highlight the importance of understanding the leading social drivers of wild meat hunting of lesser spot-nosed monkeys on the Bijagós Archipelago, and the need to conduct baseline research on these insular populations, for which qualitative and quantitative methods could be combined.

Missense SNP of the MC1R gene is associated with plumage variation in the Gyrfalcon (Falco rusticolus).

A single nucleotide polymorphism (MC1R: c.376A>G) in the MC1R gene was found to be highly correlated with pigment phenotype in the Gyrfalcon. Homozygous genotypes c.376GG and c.376AA were found to dominate the extreme white and dark plumage types respectively, and heterozygotes occurred mainly in intermediate phenotypes. However, some heterozygotes were associated with extreme phenotypes, indicating that melanism/albinism might also involve other loci.

Molecular tools and analytical approaches for the characterization of farm animal genetic diversity.

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation.

First record of Neoxysomatium brevicaudatum through the non-invasive sampling of Anguis fragilis: complementary morphological and molecular detection.

Relatively few studies have examined the parasite fauna of British reptiles, partly due to the cryptic nature and low population density of these hosts. Here we examined 12 populations of the slow worm Anguis fragilis which, unlike other UK lizards, occurs at locally high population densities. Morphological examination of non-invasively collected faecal samples revealed the presence of Neoxysomatium brevicaudatum and a second unidentified nematode species. Although previously unrecorded from slow worms in the UK, N. brevicaudatum was present in 38% of animals (mean intensity 70.9, range 1-686). Morphological identification was confirmed by sequencing the 18S ribosomal gene. The use of the species-specific, cytochrome oxidase I mitochondrial gene primers proved an efficient alternative to conventional, microscope screening for parasites, although the original identification of N. brevicaudatum was dependent upon morphological characters. Sequencing also identified the second, smaller nematode as belonging to the Rhabdiasidae family: this species was even more common at a prevalence of 83% (mean intensity 102.8, range 1-2000). While increasing our knowledge of the UK macroparasite fauna, this work demonstrates the benefits of a combined morphological-molecular approach.

Turtle groups or turtle soup: dispersal patterns of hawksbill turtles in the Caribbean.

Despite intense interest in conservation of marine turtles, spatial ecology during the oceanic juvenile phase remains relatively unknown. Here, we used mixed stock analysis and examination of oceanic drift to elucidate movements of hawksbill turtles (Eretmochelys imbricata) and address management implications within the Caribbean. Among samples collected from 92 neritic juvenile hawksbills in the Cayman Islands we detected 11 mtDNA control region haplotypes. To estimate contributions to the aggregation, we performed 'many-to-many' mixed stock analysis, incorporating published hawksbill genetic and population data. The Cayman Islands aggregation represents a diverse mixed stock: potentially contributing source rookeries spanned the Caribbean basin, delineating a scale of recruitment of 200-2500 km. As hawksbills undergo an extended phase of oceanic dispersal, ocean currents may drive patterns of genetic diversity observed on foraging aggregations. Therefore, using high-resolution Aviso ocean current data, we modelled movement of particles representing passively drifting oceanic juvenile hawksbills. Putative distribution patterns varied markedly by origin: particles from many rookeries were broadly distributed across the region, while others would appear to become entrained in local gyres. Overall, we detected a significant correlation between genetic profiles of foraging aggregations and patterns of particle distribution produced by a hatchling drift model (Mantel test, r = 0.77, P < 0.001; linear regression, r = 0.83, P < 0.001). Our results indicate that although there is a high degree of mixing across the Caribbean (a 'turtle soup'), current patterns play a substantial role in determining genetic structure of foraging aggregations (forming turtle groups). Thus, for marine turtles and other widely distributed marine species, integration of genetic and oceanographic data may enhance understanding of population connectivity and management requirements.

The population genetic effects of ancestry and admixture in a subdivided cattle breed.

The genetic structure of the Dexter, a minority cattle breed with complex demographic history, was investigated using microsatellite markers and a range of statistical approaches designed to detect both admixture and genetic drift. Modern representatives of two putative ancestral populations, the Devon and Kerry, together with the different populations of the Dexter, which have experienced different demographic histories, were analysed. Breed units showed comparatively high levels of genetic variability (H(E) = 0.63-0.68); however, distinct genetic subgroups were detected within the Dexter, which could be attributed to known demographic events. Much lower diversity was identified in three small, isolated Dexter populations (H(E) = 0.52-0.55) and higher differentiation (F(ST) > 0.13) was found. For one of these populations, where strong selection has taken place, we also found evidence of a demographic bottleneck. Three methods for quantifying breed admixture were applied and substantial method-based variation in estimates for the genetic contribution of the two proposed ancestral populations for each subdivision of the Dexter was found. Results were consistent only in the case of a group consisting of selected Traditional Dexter animals, where the ancestor of the modern Kerry breed was also determined as the greater parental contributor to the Dexter. The inconsistency of estimation of admixture proportions between the methods highlights the potentially confounding role of genetic drift in shaping small population structure, and the consequences of accurately describing population histories from contemporary genetic data.

Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study.

Genetic variability in purebred dogs is known to be highly structured, with differences among breeds accounting for approximately 30% of the genetic variation. However, analysis of the genetic structure in non-cosmopolitan breeds and local populations is still limited. Nine Portuguese native dog breeds, and other peripheral dog populations (five) with regional affinities, were characterized using 16 microsatellites and 225 amplified fragment length polymorphism (AFLP) markers, and the pattern of genetic differentiation was investigated. Although the level of breed differentiation detected is below that of other dog breeds, there is in most cases a correlation between breed affiliation and molecular structure. AFLP markers and Bayesian clustering methods allowed an average of 73.1% of individuals to be correctly assigned to source populations, providing robust genotypic assessment of breed affiliation. A geographical genetic structure was also detected, which suggests a limited influence of African dogs on the Iberian breeds. The sampling effect on the estimation of population structure was evaluated and there was a 2.2% decrease in genetic differentiation among breeds when working animals were included. Genetic diversity of stray dogs was also assessed and there is no evidence that they pose a threat to the preservation of the gene pool of native dog breeds.

Riverine effects on mitochondrial structure of Bornean orangutans (Pongo pygmaeus) at two spatial scales.

We examined mitochondrial DNA control region sequences of 73 Kinabatangan orangutans to test the hypothesis that the phylogeographical structure of the Bornean orangutan is influenced by riverine barriers. The Lower Kinabatangan Wildlife Sanctuary contains one of the most northern populations of orangutans (Pongo pygmaeus) on Borneo and is bisected by the Kinabatangan River, the longest river in Sabah. Orang-utan samples on either side of the river were strongly differentiated with a high Phi(ST) value of 0.404 (P < 0.001). Results also suggest an east-west gradient of genetic diversity and evidence for population expansion along the river, possibly reflecting a postglacial colonization of the Kinabatangan floodplain. We compared our data with previously published sequences of Bornean orangutans in the context of river catchment structure on the island and evaluated the general relevance of rivers as barriers to gene flow in this long-lived, solitary arboreal ape.

Microsatellites and their application to population genetic studies.

Microsatellites may soon become the markers of choice for molecular population genetic studies. However, our knowledge of these simple repetitive sequences and how they evolve in natural populations is far from complete. We highlight some recent results of population studies and advances in our ability to interpret some of the allele frequency distributions that we are beginning to observe.

High performance computation of landscape genomic models including local indicators of spatial association.

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samßada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samßada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samßada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samßada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samßada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.

Dynamics and genetics of a disease-driven species decline to near extinction: lessons for conservation.

Amphibian chytridiomycosis has caused precipitous declines in hundreds of species worldwide. By tracking mountain chicken (Leptodactylus fallax) populations before, during and after the emergence of chytridiomycosis, we quantified the real-time species level impacts of this disease. We report a range-wide species decline amongst the fastest ever recorded, with a loss of over 85% of the population in fewer than 18 months on Dominica and near extinction on Montserrat. Genetic diversity declined in the wild, but emergency measures to establish a captive assurance population captured a representative sample of genetic diversity from Montserrat. If the Convention on Biological Diversity's targets are to be met, it is important to evaluate the reasons why they appear consistently unattainable. The emergence of chytridiomycosis in the mountain chicken was predictable, but the decline could not be prevented. There is an urgent need to build mitigation capacity where amphibians are at risk from chytridiomycosis.

Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo.

When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P1 and P2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size t(i) = T/N(i), where N(i) is the effective population size of population i) and the contribution of one of two parental populations (which we call p1). This method takes into account drift since the admixture event, variation caused by sampling, and uncertainty in the estimation of the ancestral allele frequencies. The method is tested on simulated data sets and then applied to a human data set. We find that (i) for single-locus data, point estimates are poor indicators of the real admixture proportions even when there are many alleles; (ii) biallelic loci provide little information about the admixture proportion and the time since admixture, even for very small amounts of drift, but can be powerful when many loci are used; (iii) the precision of the parameters' estimates increases with sample size n = 50 vs. n = 200 but this effect is larger for the t(i)'s than for p1; and (iv) the increase in precision provided by multiple loci is quite large, even when there is substantial drift (we found, for instance, that it is preferable to use five loci than one locus, even when drift is 100 times larger for the five loci). Our analysis of a previously studied human data set illustrates that the joint estimation of drift and p1 can provide additional insights into the data.

Inbreeding of bottlenecked butterfly populations. Estimation using the likelihood of changes in marker allele frequencies.

Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, sigma2, the variance in the number of descendants left per gene. In all bottlenecked lines, sigma2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in sigma2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability.

Ant workers selfishly bias sex ratios by manipulating female development.

Kin selection theory predicts that social insects should perform selfish manipulations as a function of colony genetic structure. We describe a novel mechanism by which this occurs. First, we use microsatellite analyses to show that, in a population of the ant Leptothorax acervorum, workers' relatedness asymmetry (ratio of relatedness to females and relatedness to males) is significantly higher in monogynous (single-queen) colonies than in polygynous (multiple-queen) colonies. Workers rear mainly queens in monogynous colonies and males in polygynous colonies. Therefore, split sex ratios in this population are correlated with workers' relatedness asymmetry. Together with significant female bias in the population numerical and investment sex ratios, this finding strongly supports kin-selection theory. Second, by determining the primary sex ratio using microsatellite markers to sex eggs, we show that the ratio of male to female eggs is the same in both monogynous and polygynous colonies and equals the overall ratio of haploids (males) to diploids (queens and workers) among adults. In contrast to workers of species with selective destruction of male brood, L. acervorum workers therefore rear eggs randomly with respect to sex and must achieve their favoured sex ratios by selectively biasing the final caste (queen or worker) of developing females.