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

Song and genetic divergence within a subspecies of white-crowned sparrow (Zonotrichia leucophrys nuttalli)

Animal culture evolves alongside genomes, and the two modes of inheritance-culture and genes-interact in myriad ways. For example, stable geographic variation in culture can act as a reproductive barrier, thereby facilitating genetic divergence between "cultural populations." White-crowned sparrows (Zonotrichia leucophrys) are a well-established model species for bird song learning and cultural evolution, as they have distinct, geographically discrete, and culturally transmitted song types (i.e., song dialects). In this study, we tested the hypothesis that divergence between culturally transmitted songs drives genetic divergence within Nuttall's white-crowned sparrows (Z. l. nuttalli). In accordance with sexual selection theory, we hypothesized that cultural divergence between mating signals both preceded and generated genetic divergence. We characterized the population structure and song variation in the subspecies and found two genetically differentiated populations whose boundary coincides with a major song boundary at Monterey Bay, California. We then conducted a song playback experiment that demonstrated males discriminate between songs based on their degree of divergence from their local dialect. These results support the idea that discrimination against non-local songs is driving genetic divergence between the northern and southern populations. Altogether, this study provides evidence that culturally transmitted bird songs can act as the foundation for speciation by sexual selection.

A genomic basis of vocal rhythm in birds

Vocal rhythm plays a fundamental role in sexual selection and species recognition in birds, but little is known of its genetic basis due to the confounding effect of vocal learning in model systems. Uncovering its genetic basis could facilitate identifying genes potentially important in speciation. Here we investigate the genomic underpinnings of rhythm in vocal non-learning Pogoniulus tinkerbirds using 135 individual whole genomes distributed across a southern African hybrid zone. We find rhythm speed is associated with two genes that are also known to affect human speech, Neurexin-1 and Coenzyme Q8A. Models leveraging ancestry reveal these candidate loci also impact rhythmic stability, a trait linked with motor performance which is an indicator of quality. Character displacement in rhythmic stability suggests possible reinforcement against hybridization, supported by evidence of asymmetric assortative mating in the species producing faster, more stable rhythms. Because rhythm is omnipresent in animal communication, candidate genes identified here may shape vocal rhythm across birds and other vertebrates.

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

Maintenance of local adaptation despite gene flow in a coastal songbird

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.

Assortative mating for between-patch dispersal status in a wild bird population: Exploring the role of direct and indirect underlying mechanisms

Previous studies have reported functional integration between dispersal and other phenotypic traits allowing individuals to alleviate dispersal costs, and such associations can affect dispersal evolution in return. In sexually reproducing species, assortative mating according to dispersal can shape the maintenance of such trait associations. Despite the potentially crucial consequences of dispersal in natural populations, assortative mating for dispersal and its underlying mechanisms remain largely unexplored. Here, we assessed assortative mating for between-patch dispersal status in a fragmented population of a small passerine bird, the collared flycatcher, and explored whether such assortative mating could result from (i) direct mate choice based on dispersal-related behavioural (aggressiveness and boldness) and morphological traits (tarsus and wing length), (ii) biased mating due to spatio-temporal heterogeneity in the distribution of dispersal phenotypes and/or (iii) post-mating adjustment of dispersal phenotype or dispersal-related traits. We found intrinsic assortative mating (i.e. positive among-pair correlation) for current dispersal status (in the year of mating) but not for natal dispersal status, even though we could not exclude it due to limited power. We also found assortative mating for boldness and age category (yearlings vs. older adults), and the probability for pair members to be assorted for current dispersal status was higher when both pair members were of similar boldness score and of the same age compared with mixed-age pairs. Mate choice based on boldness and age thus appears as a possible mechanism underlying assortative mating for dispersal status. Our analyses however remained correlative, and only an experimental manipulation of these traits could allow inferring causal links. Non-random mating for dispersal-related traits may affect the evolution of dispersal syndromes in this population. More work is nevertheless needed to fully assess the evolutionary implications of age- and behaviour-based assortative mating for dispersal.

Larval environmental conditions influence plasticity in resource use by adults in the burying beetle, Nicrophorus vespilloides

Recent studies have shown that intraspecific patterns of phenotypic plasticity can mirror patterns of evolutionary diversification among species. This appears to be the case in Nicrophorus beetles. Within species, body size is positively correlated with the size of carrion used to provision larvae and parental performance. Likewise, among species, variation in body size influences whether species exploit smaller or larger carrion and the extent to which larvae depend on parental care. However, it is unclear whether developmental plasticity in response to carcass size, parental care, or both underlie transitions to new carcass niches. We examined this by testing whether variation in the conditions experienced by Nicrophorus vespilloides larvae influenced their ability to breed efficiently upon differently sized carcasses as adults. We found that the conditions experienced by larvae during development played a critical role in determining their ability to use large carcasses effectively as adults. Specifically, individuals that developed with parental care and on large carcasses were best able to convert the resources on a large carcass into offspring when breeding themselves. Our results suggest that parentally induced plasticity can be important in the initial stages of niche expansion.

Morphological ghosts of introgression in Darwin's finch populations

Many species of plants, animals, and microorganisms exchange genes well after the point of evolutionary divergence at which taxonomists recognize them as species. Genomes contain signatures of past gene exchange and, in some cases, they reveal a legacy of lineages that no longer exist. But genomic data are not available for many organisms, and particularly problematic for reconstructing and interpreting evolutionary history are communities that have been depleted by extinctions. For these, morphology may substitute for genes, as exemplified by the history of Darwin's finches on the Galápagos islands of Floreana and San Cristóbal. Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris in 1835. The populations became extinct in the next few decades, partly due to destruction of Opuntia cactus by introduced goats, whereas Geospiza fortis has persisted to the present. We used measurements of large samples of G. fortis collected for museums in the period 1891 to 1906 to test for unusually large variances and skewed distributions of beak and body size resulting from introgression. We found strong evidence of hybridization on Floreana but not on San Cristóbal. The skew is in the direction of the absent G. magnirostris We estimate introgression influenced 6% of the frequency distribution that was eroded by selection after G. magnirostris became extinct on these islands. The genetic residuum of an extinct species in an extant one has implications for its future evolution, as well as for a conservation program of reintroductions in extinction-depleted communities.

Estimating hybridization rates in the wild: Easier said than done?

Hybridization has important effects on the evolutionary trajectories of natural populations but estimates of this process in the wild and at the individual-level are lacking. Justyn et al. attempted to fill this gap using the citizen science database eBird but there are limitations to this approach. Here, we outline and directly test these limitations using literature searches, case studies, and a comparison between eBird and Birds of North America (BNA), a database that documents hybridization using the scientific literature. We use a hybrid zone between Lazuli and Indigo buntings to highlight the importance of considering geographic range when estimating rates of hybridization and two literature searches to show the importance of considering cryptic hybrids (those that cannot be identified using phenotypic traits) when quantifying these rates. We also use BNA and a case study of hybrid White-faced and Glossy Ibises to show that citizen scientists are underreporting hybrids compared with experts. Justyn et al. highlighted an important gap in the literature, but their results likely represent the lower limit of hybridization between birds and a more nuanced interpretation of their results (e.g., considering extrinsic postzygotic selection) is needed.

Character displacement drives trait divergence in a continental fauna

Coexisting (sympatric) pairs of closely related species are often characterized by exaggerated trait differences. This widespread pattern is consistent with adaptation for reduced similarity due to costly interactions (i.e., "character displacement")-a classic hypothesis in evolutionary theory. But it is equally consistent with a community assembly bias in which lineages with greater trait differences are more likely to establish overlapping ranges in the first place (i.e., "species sorting"), as well as with null expectations of trait divergence through time. Few comparative analyses have explicitly modeled these alternatives, and it remains unclear whether trait divergence is a general prerequisite for sympatry or a consequence of interactions between sympatric species. Here, we develop statistical models that allow us to distinguish the signature of these processes based on patterns of trait divergence in closely related lineage pairs. We compare support for each model using a dataset of bill shape differences in 207 pairs of New World terrestrial birds representing 30 avian families. We find that character displacement models are overwhelmingly supported over species sorting and null expectations, indicating that exaggerated bill shape differences in sympatric pairs result from enhanced divergent selection in sympatry. We additionally detect a latitudinal gradient in character displacement, which appears strongest in the tropics. Our analysis implicates costly species interactions as powerful drivers of trait divergence in a major vertebrate fauna. These results help substantiate a long-standing but equivocally supported linchpin of evolutionary theory.

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.

Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

Pattern blending enriches the diversity of animal colorations

Animals exhibit a fascinating variety of skin patterns, but mechanisms underlying this diversity remain largely unknown, particularly for complex and camouflaged colorations. A mathematical model predicts that intricate color patterns can be formed by "pattern blending" between simple motifs via hybridization. Here, I analyzed the skin patterns of 18,114 fish species and found strong mechanistic associations between camouflaged labyrinthine patterns and simple spot motifs, showing remarkable consistency with the pattern blending hypothesis. Genomic analyses confirmed that the coloring on multiple labyrinthine fish species has originated from pattern blending by hybridization, and phylogenetic comparative analyses have further substantiated the pattern blending hypothesis in multiple major fish lineages. These findings provide a plausible mechanistic explanation for the characteristic diversity of animal markings and suggest a novel evolutionary process of complex and camouflaged colorations by means of pattern blending.

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.

Triad hybridization via a conduit species

Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.

Designing mate choice experiments

The important role that mate choice plays in the lives of animals is matched by the large and active research field dedicated to studying it. Researchers work on a wide range of species and behaviours, and so the experimental approaches used to measure animal mate choice are highly variable. Importantly, these differences are often not purely cosmetic; they can strongly influence the measurement of choice, for example by varying the behaviour of animals during tests, the aspects of choice actually measured, and statistical power. Consideration of these effects are important when comparing results among studies using different types of test, or when using laboratory results to predict animal behaviour in  natural populations. However, these effects have been underappreciated by the mate choice literature to date. I focus on five key experimental considerations that may influence choice: (i) should mating be allowed to occur, or should a proxy behavioural measure of preference be used instead? (ii) Should subjects be given a choice of options? (iii) Should each subject be tested more than once, either with the same or different stimuli? (iv) When given a choice, how many options should the subject choose between? (v) What form should the experimental stimuli take? I discuss the practical advantages and disadvantages of common experimental approaches, and how they may influence the measurement of mate choice in systematic ways. Different approaches often influence the ability of animals to perceive and compare stimuli presented during tests, or the perceived costs and benefits of being choosy. Given that variation in the design of mate choice experiments is likely unavoidable, I emphasise that there is no single 'correct' approach to measuring choice across species, although ecological relevance is crucial if the aim is to understand how choice acts in natural populations. I also highlight the need for quantitative estimates of the sizes of potentially important effects, without which we cannot make informed design decisions.

How phenotypic matching based on neutral mating cues enables speciation in locally adapted populations

Maynard Smith's (American Naturalist, 1966, 100, 637) suggestion that in some cases a prerequisite for speciation is the existence of local ecological adaptations has not received much attention to date. Here, we test the hypothesis using a model like that of Maynard Smith but differing in the way animals disperse between niches. In previous studies, males disperse randomly between niches but females stay put in their natal niche. As a first step toward generalizing the model, we here analyze the case that equal proportions of the two sexes disperse between niches before breeding. Supporting Maynard Smith's (1966) hypothesis, we find that once local adaptations are established, a neutral mating cue at an independent locus can rapidly enable speciation in populations with a suitable mechanism for phenotype matching. We find that stable ecological polymorphisms are relatively insensitive to the strength of selection, but depend crucially on the extent of dispersal between niches, with a threshold of ~5% if population sizes in two niches are equal. At higher levels of dispersal, ecological differentiation is lost. These results contrast with those of earlier studies and shed light on why parapatric speciation is limited by the extent of gene flow. Our testable model provides a candidate explanation for the rapid speciation rates, diversity of appearance and occurrence of "species flocks" observed among some African cichlids and neotropical birds and may also have implications for the occurrence of punctuational change on phylogenies.

Hybridization increases population variation during adaptive radiation

Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.

The reach of gene-culture coevolution in animals

Culture (behaviour based on socially transmitted information) is present in diverse animal species, yet how it interacts with genetic evolution remains largely unexplored. Here, we review the evidence for gene-culture coevolution in animals, especially birds, cetaceans and primates. We describe how culture can relax or intensify selection under different circumstances, create new selection pressures by changing ecology or behaviour, and favour adaptations, including in other species. Finally, we illustrate how, through culturally mediated migration and assortative mating, culture can shape population genetic structure and diversity. This evidence suggests strongly that animal culture plays an important evolutionary role, and we encourage explicit analyses of gene-culture coevolution in nature.

Adult sex ratio influences mate choice in Darwin's finches

The adult sex ratio (ASR) is an important property of populations. Comparative phylogenetic analyses have shown that unequal sex ratios are associated with the frequency of changing mates, extrapair mating (EPM), mating system and parental care, sex-specific survival, and population dynamics. Comparative demographic analyses are needed to validate the inferences, and to identify the causes and consequences of sex ratio inequalities in changing environments. We tested expected consequences of biased sex ratios in two species of Darwin's finches in the Galápagos, where annual variation in rainfall, food supply, and survival is pronounced. Environmental perturbations cause sex ratios to become strongly male-biased, and when this happens, females have increased opportunities to choose high-quality males. The choice of a mate is influenced by early experience of parental morphology (sexual imprinting), and since morphological traits are highly heritable, mate choice is expressed as a positive correlation between mates. The expected assortative mating was demonstrated when the Geospiza scandens population was strongly male-biased, and not present in the contemporary Geospiza fortis population with an equal sex ratio. Initial effects of parental imprinting were subsequently overridden by other factors when females changed mates, some repeatedly. Females of both species were more frequently polyandrous in male-biased populations, and fledged more offspring by changing mates. The ASR ratio indirectly affected the frequency of EPM (and hybridization), but this did not lead to social mate choice. The study provides a strong demonstration of how mating patterns change when environmental fluctuations lead to altered sex ratios through differential mortality.