Borja Mila

• PhD UCLA
• Researcher at Spanish National Research Council

The evolutionary history of insular species is linked to the ecology genetic diversity and structure of the founder population as well as the ancestral population that served as a source. Population genetic studies of insular species have focused on single species and their recent post-colonisation history, ignoring the genetic characteristics of a...

Understanding the factors driving phenotypic and genomic differentiation of insular populations is of major interest to gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study parallel evolution and identify...

Understanding the factors driving phenotypic and genomic differentiation of insular populations is of major interest to gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study parallel evolution and identify...

Oceanic archipelagos are optimal systems for the study of speciation because of their geographic isolation and the diversity of insular habitats. When colonising oceanic archipelagos, island populations diverge from each other by local adaptation mechanisms and by neutral factors such as genetic drift. In this work we aim to understand the role of...

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of...

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and global factors. We argue that volcanic oceanic islands provide useful settings to study the influence of p...

According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands,...

Categorizing individuals into discrete forms in colour polymorphic species can overlook more subtle patterns in coloration that can be of functional significance. Thus, quantifying inter‐individual variation in these species at both within‐ and between‐morph levels is critical to understand the evolution of colour polymorphisms. Here we present ana...

The evolution of host–parasite interactions as host lineages colonize new geographic regions and diversify over evolutionary time is poorly understood. To assess whether haemosporidian parasite diversity has changed during the diversification of an avian host, we surveyed the diversity and prevalence of blood parasite lineages (genera Plasmodium, H...

The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior and evolutionary biology for over a century. It is composed of at least six distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variat...

Colonization of a novel environment by a few individuals can lead to rapid evolutionary change, yet there is scarce evidence of the relative contributions of neutral and selective factors in promoting divergence during the early stages of colonization. We explore the role of neutral and selective forces in the divergence of a unique urban populatio...

Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study,...

Chromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we too...

Colonization of a novel environment by a few 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. We explore the role of neutral and selective forces in the divergence of a unique urban population...

Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fri...

Western New Guinea remains one of the last biologically underexplored regions of the world, and much remains to be learned regarding the diversity and evolutionary history of its fauna and flora. During a recent ornithological expedition to the Kumawa Mountains in West Papua, we encountered an undescribed species of Melanocharis berrypecker (Melano...

The common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing i...

Current bird populations in southern temperate latitudes often represent relicts of glacial refugia from which northern populations expanded as the climate became suitable following the last glacial maximum, 18 000 years before present. Alternatively, these southern populations could be the result of the fragmentation of large distributions and oth...

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.¹,² Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have...

The common chaffinch, Fringilla coelebs, is one of the most common, widespread and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing i...

Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing...

Aim: Oceanic islands have often been colonized by small groups of individuals dispersing from the nearest mainland, giving rise to insular populations characterized by locally adapted phenotypes and low genetic diversity. Alternatively, due to past geo‐climatic changes, the present‐day distribution of the species may not correspond to that found at...

Due to their limited ranges and inherent isolation, island species provide a unique opportunity to study the impact of non-adaptive forces on molecular evolution, especially how effective population size may influence the accumulation of deleterious mutations. By estimating nucleotide diversity at synonymous and non-synonymous sites for a large set...

The presence of congeneric taxa on the same island suggests the possibility of in situ divergence, but can also result from multiple colonizations of previously diverged lineages. Here, using genome-wide data from a large population sample, we test the hypothesis that intra-island divergence explains the occurrence of four geographical forms meetin...

Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome‐wide markers to investigate the diversification of the Reunion grey white eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this speci...

Chromosomal organization is relatively stable among avian species, especially for sex chromosomes. Sylvioidea species, however, harbor a unique pair of neo-sex chromosomes, originating from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. In this study, we took advantage of this unusual event to study...

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...

The relative roles of natural and sexual selection in promoting evolutionary lineage divergence remains controversial and difficult to assess in natural systems. Local adaptation through natural selection is known to play a central role in adaptive radiations, yet secondary sexual traits can vary widely among species in recent radiations, suggestin...

Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., “islands of differentiation” in FST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of g...

Color plays a prominent role in species recognition, therefore understanding the proximate basis of pigmentation can provide insight into reproductive isolation and speciation. Color differences between taxa may be the result of regulatory differences, or be caused by mutations in coding regions of the expressed genes. To investigate these two alte...

Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to test the relative importance of two major evolutionary mechanisms, adaptation to local ecological conditions by natural selection, or mechanisms of reproductive isolation such as assortative mating mediated by sexually selected mating signals or post-zy...

Color plays a prominent role in reproductive isolation, therefore understanding the proximal basis of pigmentation can provide insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) have evolved marked differences in plumage coloration since the Last Glacial Maximum, yet whether color differences are caused by mutations in codi...

Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated...

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...

Patterns of phenotypic and genic frequencies across hybrid zones provide insight into the origin and evolution of reproductive isolation. The Reunion grey white-eye, Zosterops borbonicus, exhibits parapatrically distributed plumage colour forms across the lowlands of the small volcanic island of Reunion (Mascarene archipelago). These forms meet and...

[This corrects the article DOI: 10.1371/journal.pone.0171785.].

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relations...

Accession names of the sound archives used in the bioacoustics analysis. (DOCX)

Adult preserved specimens of Dendropsophus sp. D and E showing variation in dorsal and ventral coloration. (TIF)

Primers used for DNA amplification. (DOCX)

Additional specimens examined. (DOCX)

Genbank accession numbers for DNA sequences used in the phylogenetic analysis. (DOCX)

Supplementary Methods and TablesThis file includes details about methods and parameters used, as well as supplementary results on analyses ofphenotype and whole genome analyses.

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...

Understanding which factors promote disease emergence and transmission remains a major challenge of epidemiology. A problem with research on emerging diseases is that we seldom know to what extent pathogens circulate in natural populations before emergence is already occurring. Moreover, it is critical to determine which pathogen characteristics ar...

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...

Populations that have experienced long periods of geographic isolation will diverge over time. The application of high-throughput sequencing technologies to study the genomes of related taxa now allows us to quantify, at a fine scale, the consequences of this divergence across the genome. Throughout a number of studies, a notable pattern has emerge...

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 differenti...

Following Pleistocene glacial maxima, species that adapted to temperate climates in low-latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during intergl...

The Réunion grey white-eye (Zosterops borbonicus), a small passerine endemic to the island of Réunion (Mascarene archipelago), constitutes an extraordinary case of phenotypic variation within a bird species, with conspicuous plumage colour differentiation at a microgeographical scale. To understand whether natural selection could explain such varia...

Patterns of genetic structure and gene flow among populations help us understand population dynamics and properly manage species of concern. Matrilineal mtDNA sequence data have been instrumental in revealing genetic structure at the intraspecific level, but bi-parentally inherited markers are needed to confirm patterns at the genome level and to a...

Patterns of genetic structure and gene fl ow among populations help us understand population dynamics and properly manage species of concern. Matrilineal mtDNA sequence data have been instrumental in revealing genetic structure at the intraspecifi c level, but bi-parentally inherited markers are needed to confi rm patterns at the genome level and t...

Rock-paper-scissors (RPS) dynamics, which maintain genetic polymorphisms over time through negative frequency-dependent (FD) selection, can evolve in short-lived species with no generational overlap, where they produce rapid morph frequency cycles. However, most species have overlapping generations and thus, rapid RPS dynamics are thought to requir...

Taxonomic classification of birds based exclusively on morphology and plumage traits has often been found to be inconsistent with true evolutionary history when tested with molecular phylogenies based on neutrally-evolving markers. Here we present cytochrome-b gene sequences for the poorly known little brown bustard (Eupodotis humilis) and analyze...

The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km(2)). To understand whether such population differentiati...

Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessar...

Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations and by in situ diversification rate. In this study, we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility o...

Background: The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabr...

Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pool...

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occu...

We used next-generation sequencing (NGS) techniques to develop 14 new microsatellite loci in the great bustard (Otis tarda), an endangered steppe bird. We genotyped 22 individuals of the species in order to quantify levels of polymorphism and found that the number of alleles per locus ranged from 2 to 11 (mean = 4.21), with observed heterozygosity...

Early anthropogenic impacts on the abundance and distribution of wild species are difficult to document, but can help us to understand the causes and relative importance of current declines. Genetic data can be of use in inferring historical demographic events, but the accuracy of these inferences depends on the availability and precision of demogr...

The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of cor...

Recent studies exploring the molecular genetic basis for migratory variation in animals have identified polymorphisms in two genes ( CLOCK and ADCYAP1) that are linked to circadian rhythms and correlate with migratory propensity and phenology among individuals and populations. Results from these initial studies are mixed, however, and additional da...

Aim Niche modelling is increasingly used to predict species' geographical distributions or to infer the evolutionary or ecological processes that constrain them, but relatively few studies have examined the ecological processes governing the distributions of parasites. Among such processes, niche divergence is frequently invoked to explain species...

The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic...

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