Introgressive hybridization and natural selection in Darwin's finches

Fluctuating selection in a Monkeyflower hybrid zone

While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus, we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus-like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus, specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species.

Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression

Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.

Metazoa-level USCOs as markers in species delimitation and classification

Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.

Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats

Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.

Avian introgression patterns are consistent with Haldane's Rule

According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.

Sexually dichromatic hybrids between two monochromatic duck species, the Chiloé wigeon and the Philippine duck

Captive bird hybrids can provide important data on certain traits, such as hybrid viability and fertility. In this paper, we describe four hybrids between the Chiloé wigeon (Anas sibilatrix) and the Philippine duck (Anas luzonica). These two species diverged about 13 million years ago and are found on different continents, making the occurrence of wild hybrids extremely unlikely. Hence, these captive hybrids provide a unique opportunity to learn more about the outcome of hybridization between these highly divergent species. One pair of hybrids mated and produced six unfertilized eggs, suggesting that hybrids between these species are infertile. Morphologically, the hybrids were slightly larger than the parental species, but had intermediate bill lengths. With regard to plumage patterns, the hybrids displayed characteristics of both parental species: Males developed the iridescent green head pattern of the Chiloé wigeon, whereas the females showed the dark crown and eye stripe of the Philippine duck. Interestingly, Chiloé wigeon and Philippine duck are both sexually monochromatic whereas the hybrids showed clear sexual dimorphism. These hybrids can thus lead to novel insights into the genetic and developmental basis of sexual mono- and dichromatism in ducks.

Adaptive introgression of the beta-globin cluster in two Andean waterfowl

Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.

Behavioural response to songs between genetically diverged allopatric populations of Darwin's small tree finch in the Galápagos

Empirical data that identify contemporary mechanisms of divergence shed light on how species could multiply. In this study, we measured population genetic structure, song syllable diversity and response to simulated intruder song in Darwin's small tree finch (Camarhynchus parvulus) on Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to test whether the magnitude of contemporary behavioural response in resident birds was consistent with patterns of genetic or cultural differences between populations. We analysed genetic structure and the occurrence of song syllable types, and experimentally measured the response of resident birds to intruder bird song from different geographical origin (i.e., island) or syllable type. We discovered a weak signal of population genetic structure between Santa Cruz and Floreana Islands. Although some song syllables occurred on both islands, others were unique to each island; Santa Cruz Island males used more unique syllables than Floreana Island males. Both Santa Cruz and Floreana resident males discriminated their response towards a simulated intruder song based on the geographical origin of the intruder song, but not on the syllable type sung by the intruder. We conclude that the populations are diverging in genetic and cultural traits and identified a signal of contemporary behavioural response that could maintain divergence upon secondary contact.

Hybridization and cryptic speciation in the Iberian endemic plant genus Phalacrocarpum (Asteraceae-Anthemideae)

Understanding the role and impact of reticulation in phylogenetic inquiry has improved with extended use of high throughput sequencing data. Yet, due to the dynamism of genomes over evolutionary time, disentangling old hybridization events remains a serious challenge. Phalacrocarpum (DC.) Willk. is one of the 27 Iberian endemic plant genera, currently considered monotypic but including three subspecies. Its uncertain phylogenetic relationships within tribe Anthemideae (Asteraceae) point to an Early Miocene divergence from its sister group, and its persistent taxonomic instability has been proposed to be due to hybridization. We aim at understanding the evolutionary history of this genus using SNPs called from a genotyping-by-sequencing (GBS) analysis, Sanger sequences-from three plastid DNA regions (psbJ-petA, petB-petD, trnH-psbA) and the nuclear ribosomal ITS regions (cloned)-as well as leaf morphometric multivariate analysis. SNP data and Sanger sequences strongly support the unforeseen existence of a cryptic species in the eastern populations of P. oppositifolium subsp. anomalum. Broad molecular and morphometric patterns of variation found in conflictive populations from the Sanabria Valley region convincingly identify a recent previously undocumented hybrid zone. By contrast, evidence is less conclusive on relationships between subspecies hoffmannseggii, oppositifolium and a second conflictive group distributed along the Galician-Portuguese border (Orense massifs). Although genetic clustering analysis of SNP data suggests that the former subspecies was the maternal progenitor in hybridization events that gave rise to the other two groups, we found considerable uniqueness of ITS ribotypes and plastid haplotypes in them. This result, in the context of Pleistocene climatically-driven range shifts in NW Iberian Peninsula, can be due to periods of isolation, genetic bottlenecks and drift superimposed on old hybridization events. Our study confirms the idea that unravelling old hybridization events may be compromised by the suite of evolutionary processes accumulated subsequently, particularly in areas with a history of climatic instability.

Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes

Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.

Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective

The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.

Hybridization fluctuates with rainfall in Darwin’s tree finches

Hybridization in natural populations may be an adaptive response to shifting climatic regimes, but understanding this can be limited by the timing of sampling effort and confident identification of hybrids. On the Galapagos Islands, Darwin’s finches regularly hybridize; the islands also show extreme annual variation in rainfall, but the effect of annual rainfall on the frequency of finch hybridization is little known. Across a 20-year period on Floreana Island, we compare patterns of hybridization in sympatric Darwin’s tree finches (N = 425; Camaryhnchus spp.) and test for an effect of annual rainfall on (1) the frequency of hybrids (C. pauper × C. parvulus) and (2) the percentage of male hybrid birds produced per year (hybrid recruitment). Annual rainfall correlated with recruitment positively for hybrids, negatively for C. parvulus and not at all for C. pauper. Furthermore, the percentage of hybrids (range: 12–56%) and C. parvulus did not change with sampling year, but the critically endangered C. pauper declined. Our findings indicate that hybrid recruitment is recurring and variable according to annual rainfall in Camarhynchus Darwin’s finches.

Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives

Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.

OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression

Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain "overlay" of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.

Urbanization erodes niche segregation in Darwin's finches

Urbanization is influencing patterns of biological evolution in ways that are only beginning to be explored. One potential effect of urbanization is in modifying ecological resource distributions that underlie niche differences and that thus promote and maintain species diversification. Few studies have assessed such modifications, or their potential evolutionary consequences, in the context of ongoing adaptive radiation. We study this effect in Darwin's finches on the Galápagos Islands, by quantifying feeding preferences and diet niche partitioning across sites with different degrees of urbanization. We found higher finch density in urban sites and that feeding preferences and diets at urban sites skew heavily toward human food items. Furthermore, we show that finches at urban sites appear to be accustomed to the presence of people, compared with birds at sites with few people. In addition, we found that human behavior via the tendency to feed birds at non-urban but tourist sites is likely an important driver of finch preferences for human foods. Site differences in diet and feeding behavior have resulted in larger niche breadth within finch species and wider niche overlap between species at the urban sites. Both factors effectively minimize niche differences that would otherwise facilitate interspecies coexistence. These findings suggest that both human behavior and ongoing urbanization in Galápagos are starting to erode ecological differences that promote and maintain adaptive radiation in Darwin's finches. Smoothing of adaptive landscapes underlying diversification represents a potentially important yet underappreciated consequence of urbanization. Overall, our findings accentuate the fragility of the initial stages of adaptive radiation in Darwin's finches and raise concerns about the fate of the Galápagos ecosystems in the face of increasing urbanization.

How to Make a Weed: The Saga of the Slender False Brome Invasion in the North American West and Lessons for the Future

Historical herbarium collections and genetic analyses indicate that slender false brome (Brachypodium sylvaticum) was first introduced in test gardens in Oregon in the early 1900 s as part of the USDA’s plant introduction program. A small number of naturalized populations were established, but it was not until several decades later that this alien species became an aggressive invader. The Oregon invasive strains of false brome were generated as a consequence of mating among genetically divergent lineages. The resulting hybrid populations contained high levels of genetic variation that fueled the evolution of specific adaptations to the Pacific Northwest climate and ultimately generated genetically superior lineages. Although the false brome invasion has caused significant ecological and economic harm and is expected to continue spreading across western North America, understanding the circumstances that have promoted its success may provide valuable lessons for the management of native plants under pressure from global climate change.

Parallel introgression and selection on introduced alleles in a native species

As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.

The sarolga: conservation implications of genetic and visual evidence for hybridization between the brolga Antigone rubicunda and the Australian sarus crane Antigone antigone gillae

To investigate the extent of suspected hybridization between the brolga Antigone rubicunda and the Australian sarus crane Antigone antigone gillae, first noted in the 1970s, we analysed the genetic diversity of 389 feathers collected from breeding and flocking areas in north Queensland, Australia. We compared these with 15 samples from birds of known identity, or that were phenotypically typical. Bayesian clustering based on 10 microsatellite loci identified nine admixed birds, confirming that Australian cranes hybridize in the wild. Four of these were backcrosses, also confirming that wild Australian crane hybrids are fertile. Genetic analyses identified 10 times more hybrids than our accompanying visual field observations. Our analyses also provide the first definitive evidence that both brolgas and sarus cranes migrate between the Gulf Plains, the principal breeding area for sarus cranes, and major non-breeding locations on the Atherton Tablelands. We suggest that genetic analysis of shed feathers could potentially offer a cost-effective means to provide ongoing monitoring of this migration. The first observations of hybrids coincided with significantly increased opportunities for interaction between the two species when foraging on agricultural crops, which have developed significantly in the Atherton Tablelands flocking area since the 1960s. As the sarus crane is declining in much of its Asian range, challenges to the genetic integrity of the Australian sarus crane populations have international conservation significance.

Genomic insights into the vulnerability of sympatric whitefish species flocks

The erosion of habitat heterogeneity can reduce species diversity directly but can also lead to the loss of distinctiveness of sympatric species through speciation reversal. We know little about changes in genomic differentiation during the early stages of these processes, which can be mediated by anthropogenic perturbation. Here, we analyse three sympatric whitefish species (Coregonus spp) sampled across two neighbouring and connected Swiss pre-alpine lakes, which have been differentially affected by anthropogenic eutrophication. Our data set comprises 16,173 loci genotyped across 138 whitefish using restriction-site associated DNA sequencing (RADseq). Our analysis suggests that in each of the two lakes, the population of a different, but ecologically similar, whitefish species declined following a recent period of eutrophication. Genomic signatures consistent with hybridization are more pronounced in the more severely impacted lake. Comparisons between sympatric pairs of whitefish species with contrasting ecology, where one is shallow benthic and the other one more profundal pelagic, reveal genomic differentiation that is largely correlated along the genome, while differentiation is uncorrelated between pairs of allopatric provenance with similar ecology. We identify four genomic loci that provide evidence of parallel divergent adaptation between the shallow benthic species and the two different more profundal species. Functional annotations available for two of those loci are consistent with divergent ecological adaptation. Our genomic analysis indicates the action of divergent natural selection between sympatric whitefish species in pre-alpine lakes and reveals the vulnerability of these species to anthropogenic alterations of the environment and associated adaptive landscape.

Role of sexual imprinting in assortative mating and premating isolation in Darwin's finches

Global biodiversity is being degraded at an unprecedented rate, so it is important to preserve the potential for future speciation. Providing for the future requires understanding speciation as a contemporary ecological process. Phylogenetically young adaptive radiations are a good choice for detailed study because diversification is ongoing. A key question is how incipient species become reproductively isolated from each other. Barriers to gene exchange have been investigated experimentally in the laboratory and in the field, but little information exists from the quantitative study of mating patterns in nature. Although the degree to which genetic variation underlying mate-preference learning is unknown, we provide evidence that two species of Darwin's finches imprint on morphological cues of their parents and mate assortatively. Statistical evidence of presumed imprinting is stronger for sons than for daughters and is stronger for imprinting on fathers than on mothers. In combination, morphology and species-specific song learned from the father constitute a barrier to interbreeding. The barrier becomes stronger the more the species diverge morphologically and ecologically. It occasionally breaks down, and the species hybridize. Hybridization is most likely to happen when species are similar to each other in adaptive morphological traits, e.g., body size and beak size and shape. Hybridization can lead to the formation of a new species reproductively isolated from the parental species as a result of sexual imprinting. Conservation of sufficiently diverse natural habitat is needed to sustain a large sample of extant biota and preserve the potential for future speciation.

Unpacking the species conundrum: philosophy, practice and a way forward

The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as 'individuals' while the criteria for categorization treats them as 'classes'. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an 'inclusive' probabilistic approach for understanding and delimiting species. Finally, we provide aWallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and 'inclusive' probabilistic approaches may work best for delimitation.

Genomic islands of divergence or opportunities for introgression?

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci ('genomic islands of divergence') that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush (Catharus ustulatus), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

Admixture mapping identifies introgressed genomic regions in North American canids

Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.

A beak size locus in Darwin's finches facilitated character displacement during a drought

Ecological character displacement is a process of morphological divergence that reduces competition for limited resources. We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin's finches on Daphne Major in the Galápagos Islands: The medium ground finch diverged from its competitor, the large ground finch, during a severe drought. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin's finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event: Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59). Thus, a major locus has apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin's finches.