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Determining the amount and distribution of genetic variation represents a fundamental step for the inference of evolutionary processes acting on populations of endangered species. For these species, adaptive evolutionary potential is highly reduced by the loss of genetic variation due to drift. Here, we examined genetic diversity at the mitochondrial control region (CR), 17 microsatellites, and six Toll-like receptor (TLR) genes, known to play a key role on the innate immune response of vertebrates in the Antioquia wren (AW) Thryophilus sernai, an endangered passerine bird inhabiting the remnant fragments of tropical dry forest in the northernmost part of the Cauca river canyon, Colombia. We found very low variation for the three types of markers. The CR showed scarce variability, while only six of the 17 microsatellites analyzed and two of the six TLRs sequenced were polymorphic. Population structure analyses suggest the occurrence of one single population in the area. Selection tests could not detect signatures of positive selection for the variable sites in the species, and assessment of amino acid changes found within the lineage do not suggest any functional effects that could be associated to selection in either polymorphic TLR loci. Comparisons with species showing widespread and restricted distribution supports a low TLR variability typical of small populations. These results suggest current low evolutionary potential for the species, as its reduced genetic diversity is expected to increase extinction risk by limiting the ability to cope with environmental changes. Our study supports current evidence suggesting drift as the main driver shaping TLR variation.

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here, we describe patterns of geographic differentiation of 2 disjunct populations of Diglossa brunneiventris separated by ∼1,000 km along the Andes. Diglossa brunneiventris vuilleumieriis isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the 2 D. brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other 3 species within the carbonaria complex (D. gloriosa, D. humeralis, and D. carbonaria). We also constructed ecological niche models for each D. brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the 2 D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.LAY SUMMARYDiglossa brunneiventris has two disjunct populations separated by more than 1,000 km along the Andes (longer than the span of Ecuador).Although similar in coloration, the two populations exhibit differences in body size and wing length.Whether these two populations belong to the same species and how recently they were separated are still open questions.We provide molecular and climatic evidence that suggests the two populations are not sister taxa.Genetic evidence suggests the northern population is related to populations of Diglossa humeralis from the Eastern Andes in Colombia, while the southern population is more related to populations of D. humeralis from Ecuador and southern Colombia.The northern population has a restricted and fragmented range and its conservation status depends on evidence for its recognition as an independent lineage.

Understanding the spatial scale at which selection acts upon adaptive genetic variation in natural populations is fundamental to our understanding of evolutionary ecology, and has important ramifications for conservation. The environmental factors to which individuals of a population are exposed can vary at fine spatial scales, potentially generating localized patterns of adaptation. Here, we compared patterns of neutral and major histocompatibility complex (MHC) variation within an island population of Berthelot's pipit (Anthus berthelotii) to assess whether landscape-level differences in pathogen-mediated selection generate fine-scale spatial structuring in these immune genes. Specifically, we tested for spatial associations between the distribution of avian malaria, and the factors previously shown to influence that distribution, and MHC variation within resident individuals. Although we found no overall genetic structure across the population for either neutral or MHC loci, we did find localized associations between environmental factors and MHC variation. One MHC class I allele (ANBE48) was directly associated with malaria infection risk, while the presence of the ANBE48 and ANBE38 alleles within individuals correlated (positively and negatively, respectively) with distance to the nearest poultry farm, an anthropogenic factor previously shown to be an important determinant of disease distribution in the study population. Our findings highlight the importance of considering small spatial scales when studying the patterns and processes involved in evolution at adaptive loci.

How the environment influences the transmission and prevalence of disease in a population of hosts is a key aspect of disease ecology. The role that environmental factors play in host-pathogen systems has been well studied at large scales, that is, differences in pathogen pressures among separate populations of hosts or across land masses. However, despite considerable understanding of how environmental conditions vary at fine spatial scales, the effect of these parameters on host-pathogen dynamics at such scales has been largely overlooked. Here, we used a combination of molecular screening and GIS-based analysis to investigate how environmental factors determine the distribution of malaria across the landscape in a population of Berthelot's pipit (Anthus berthelotii, Bolle 1862) on the island of Tenerife (Canary Islands, Spain) using spatially explicit models that account for spatial autocorrelation. Minimum temperature of the coldest month was found to be the most important predictor of malaria infection at the landscape scale across this population. Additionally, anthropogenic factors such as distance to artificial water reservoirs and distance to poultry farms were important predictors of malaria. A model including these factors, and the interaction between distance to artificial water reservoirs and minimum temperature, best explained the distribution of malaria infection in this system. These results suggest that levels of malaria infection in this endemic species may be artificially elevated by the impact of humans. Studies such as the one described here improve our understanding of how environmental factors, and their heterogeneity, affect the distribution of pathogens within wild populations. The results demonstrate the importance of measuring fine-scale variation - and not just regional effects - to understand how environmental variation can influence wildlife diseases. Such understanding is important for predicting the future spread and impact of disease and may help inform disease management programmes as well as the conservation of specific host species.

Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analyzed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here we focused on diversity at toll-like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen-mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation, and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales. This article is protected by copyright. All rights reserved.

Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population., Synopsis Genomic studies of human genetic variation are useful for investigating human evolutionary history, as well as for designing strategies for identifying disease-related genes. Despite its large population and its increasing complex genetic disease burden as a result of modernization, India has been excluded from most of the largest genomic surveys. The authors performed an extensive investigation of Indian genetic diversity and population relationships, sampling 15 groups of India-born immigrants to the United States and genotyping each individual at 1,200 genetic markers genome-wide. Populations from India, and groups from South Asia more generally, form a genetic cluster, so that individuals placed within this cluster are more genetically similar to each other than to individuals outside the cluster. However, the amount of genetic differentiation among Indian populations is relatively small. The authors conclude that genetic variation in India is distinctive with respect to the rest of the world, but that the level of genetic divergence is smaller in Indians than might be expected for such a geographically and linguistically diverse group.