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genolike_map20_q20_snp16_maf002_ind32_430K.beagle Input file of genotype likelihoods in Beagle format (.beagle.gz) for PCANGSD analysis. ORJUSTRUx8_biall_dp450_q40_perpopmiss075_hwe00001_maf002_LD02_neutral01 Dataset of 16,858 independent neutral SNPs from 64 samples in vcf format for STRUCTURE analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ_neutral01 Dataset of 15,209 neutral SNPs used in the PCA intended for population structure correction in the redundancy analysis (RDA). ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_noZ Dataset of 15,252 SNPs used in the redundancy analysis. ORJU06x12_biall_dp450_q40_maf002_nomissing_hwe00001_sel01_BAYESCENV Subset of 49 SNP outliers identified with BayScEnv for the second redundancy analysis in the manuscript. ORJUGEO_coords_ALLSAMPLES Table of sample location and geographic coordinates for all sequenced samples of the study. ORJUGEO_coords_ClimVariables Sample data and WorldClim environmental data (Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology.) for each one of the samples included in the genotype-environment association analyses., The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (i) drift in geographic isolation, (ii) differentiation along continuous selective gradients, and (iii) isolation by adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci., Peer reviewed

Data for microsatellites, spectrophotometry and melanins dosage This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds included in the pedigree analysis, 3) Spectrophotometry measurements and 4) Results from the dosage of melanins for 12 individuals. Localities coordinates are also provided. All_data_microsats_spectro_melanindosage.xlsx Unfiltered VCF file for 42 individuals SNPs calls for individual GBS data from the same three localities as in Pooled RAD-seq. Colors and localities for each individuals are provided in a separate excel file. Highlands_dataset.recode.vcf Information about individuals included in the GBS VCF file Morph and localities for each individual included in the GBS study. Localities_Morphs_individuals_VCF.xlsx, Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection., Peer reviewed

Microsatellite allele dataset Microsatellite genotypes of all individuals (n=590) separeted by locality (n=25). Genepop format was selected to create the dataset. chough_microsatellite_genotypes-GENEPOP.txt Field monitoring data The dataset includes the population of ringing, province of recapture/resighting and individual identity of the records for which the distance of movements was calculated (n = 9862). Field_monitoring_data.xls, Social barriers have been shown to reduce gene flow and contribute to genetic structure among populations in species with high cognitive capacity and complex societies, such as cetaceans, apes and humans. In birds, high dispersal capacity is thought to prevent population divergence unless major geographic or habitat barriers induce isolation patterns by dispersal, colonization or adaptation limitation. We report that Iberian populations of the red-billed chough, a social, gregarious corvid with high dispersal capacity, show a striking degree of genetic structure composed of at least 15 distinct genetic units. Monitoring of marked individuals over 30 years revealed that long-distance movements over hundreds of kilometres are common, yet recruitment into breeding populations is infrequent and highly philopatric. Genetic differentiation is weakly related to geographic distance and habitat types used are overall qualitatively similar among regions and regularly shared by individuals of different populations, so that genetic structure is unlikely to be due solely to isolation by distance or isolation by adaptation. Moreover, most population nuclei showed relatively high levels of genetic diversity, suggesting a limited role for genetic drift in significantly differentiating populations. We propose that social mechanisms may underlie this unprecedented level of genetic structure in birds through a pattern of isolation by social barriers not yet described, which may have driven this remarkable population divergence in the absence of geographic and environmental barriers., Peer reviewed

ZoboGrad-GENEPOP Individual genotypes of the 401 individuals at 12 microsatellite loci. This file is provided in the universal GENEPOP format. The first section corresponds to a list of the name of the loci. Then, each row represent a single individual: first column is the individual identifier and the following columns correspond to the length (concatenation of 2 x 3 digits) of the different alleles at the 12 loci (one column each). Sampling localities are separated by a empty lines. ZoboGrad-Morpho File summarizing the morphological data for each individual. Each line corresponds to a single individual with informations about sampling localities, ringer and all the morphological variables measured: weight (g), wing length (mm), tail length (mm), tarsus length (mm), bill length (mm), bill depth (mm) and bill width (mm)., Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variation among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using eleven microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact mid-way up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients., Peer reviewed

Phased DNA sequences and aminoacids This file contains all the phased sequences used in the study, with heterozygous gaps resolved. Fasta containing aminoacids translations are also provided for markers used in MK tests. Phased_DNA_sequences_and_amino_acids.zip Informations about individuals This file contains for each individual included in the study its identifier, its color form/morph, the locality where it was sampled and its sex. Individual_information.xlsx, Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits five plumage color variants that can be grouped into three color forms which occupy discrete geographic regions in the lowlands of Réunion and a fourth form which comprises two color morphs (grey and brown), occurs at high elevation, and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of seven candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied may beare involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other non-model species., Peer reviewed

2016_06_27 MalesSpecMorph_museum Colorimetric Spectra and Morphological variable measures per museum skin, males. SNP calls output from the GBS Bioinformatics pipeline SNP calls in HapMap format with basic filtering on missingness and allele frequency for 95 Junco samples, generated by the Cornell University’s Institute for Genomic Diversity (IGD). c1.snpmerged.filtered.hmp, Natural systems composed of closely-related taxa that vary in the degree of phenotypic divergence and geographic isolation, provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and color, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage color, and use mitochondrial DNA genes, a nuclear intron, and genome-wide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation-in-action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates., Peer reviewed

[Methods] All methods and protocols are described in detail in the article. [Usage Notes] All methods and protocols are described in detail in the article., Colonization of a novel environment by a small group of individuals can lead to rapid evolutionary change, yet evidence of the relative contributions of neutral and selective factors in promoting divergence during the early stages of colonization remain scarce. Here, we use genome-wide SNP data to test the role of neutral and selective forces in driving the divergence of a unique urban population of the Oregon junco (Junco hyemalis oreganus), which became established on the campus of the University of California at San Diego (UCSD) in the early 1980s. Previous studies based on microsatellite loci documented significant genetic differentiation of the urban population as well as divergence in sexual signaling and life-history traits relative to nearby montane populations. However, the geographic origin of the colonization and the factors involved in the onset of the differentiation process remained uncertain. Our genome-wide SNP dataset confirmed the marked genetic differentiation of the UCSD population, and phylogenomic analysis identified the coastal subspecies pinosus from central California as its sister group instead of the neighboring mountain population. Demographic inference based on site frequency spectra recovered a time of separation from pinosus as recent as 20 to 32 generations, and a strong bottleneck at the time of colonization, suggesting a relevant role of founder effects and drift in the genetic differentiation of the UCSD population. However, we also found significant associations between environmental parameters characterizing the urban habitat of UCSD and genome-wide variants linked to functional genes. Some of the identified gene functions, like heavy metal detoxification and high-pitched hearing, have been reported as potentially adaptive in birds inhabiting urban environments. These results suggest that the interplay between founder events and directional selection may result in rapid shifts in both neutral and adaptive loci across the genome, and reveal the UCSD population of juncos as an ongoing case of divergence following the colonization of an anthropic environment., Ministerio de Ciencia e Innovación, Award: CGL-2011-25866. Ministerio de Ciencia e Innovación, Award: CGL-2015-66381. National Science Foundation, Award: IOS-1257527., Peer reviewed