Genetics and the origin of bird species

Rapid evolution of pre-zygotic reproductive barriers in allopatric populations

IMPORTANCE

A population diversifies into two or more species-such a process is known as speciation. In sexually reproducing microorganisms, which barriers arise first-pre-mating or post-mating? In this work, we quantify the relative strengths of these barriers and demonstrate that pre-mating barriers arise first in allopatrically evolving populations of yeast, Saccharomyces cerevisiae. These defects arise because of the altered kinetics of mating of the participating groups. Thus, our work provides an understanding of how adaptive changes can lead to diversification among microbial populations.

Evolutionary and Ecological Processes Underlying Geographic Variation in Innate Bird Songs

AbstractEcological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.

Hybridization despite elaborate courtship behavior and female choice in Neotropical tree frogs

The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged-breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second-generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification.

Experimental test of selection against hybridization as a driver of avian signal divergence

Signal divergence may be pivotal in the generation and maintenance of new biodiversity by allowing closely related species to avoid some costs of co-occurrence. In birds, closely related, sympatric species are more divergent in their colour patterns than those that live apart, but the selective pressures driving this pattern remain unclear. Traditionally, signal divergence among sympatric species is thought to result from selection against hybridization, but broad evidence is lacking. Here, we conducted field experiments on naïve birds using spectrometer-matched, painted 3D-printed models to test whether selection against hybridization drives colour pattern divergence in the genus Poecile. To address selection for male colour pattern divergence without the influence of learning or the evolution of female discrimination in sympatry, we simulated secondary contact between Poecile species, and conducted mate choice experiments on naïve, allopatric females. We found that female black-capped chickadees (Poecile atricapillus) are equally likely to perform copulation solicitation displays to sympatric and allopatric heterospecific congeners when they are paired with conspecifics, but exhibit a strong preference for less divergent males when presented with paired heterospecific congeners. These results suggest that increased colour pattern divergence among sympatric species can reduce the likelihood of mixed mating in some contexts, and therefore should be favoured by selection against hybridization.

Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

Cryptic species are closely related taxa that are difficult to separate morphologically, but are reproductively isolated. Here we examine the warbling vireo complex (Vireo gilvus), a widespread songbird speculated to be comprised of more than one cryptic species. We included three taxa within the complex: two of the western (Vireo gilvus swainsonii and Vireo gilvus brewsteri) subspecies and the single eastern (Vireo gilvus gilvus) subspecies. We used mtDNA and microsatellite loci to assess the congruence of genetic data to the current subspecies boundaries. We then incorporated bioacoustic, morphometric and ecological niche modelling analyses to further examine differences. We found two genetic groups with mtDNA analysis, splitting eastern and western warbling vireos. Microsatellite analyses revealed four genetic groups: an eastern group, a Black Hills group and two western groups that do not agree with current western subspecies boundaries based on phenotypic data. Our results suggest that eastern and western warbling vireos have been reproductively isolated for a long period of time and therefore may be best treated as separate species. However, more research into areas of contact to examine the presence of hybridization is advised before making a taxonomic revision. Differences between the two western genetic groups appear less clear, requiring additional research.

Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

Contact zones between recently diverged taxa provide opportunities to examine the causes of reproductive isolation and the processes that determine whether two species can coexist over a broad region. The Pacific wren (Troglodytes pacificus) and winter wren (Troglodytes hiemalis) are two morphologically similar songbirds that started diverging about 4 million years ago, older than most sister species pairs of temperate songbirds. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct. To assess evidence for differentiation, hybridization and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genome. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals, two first-generation hybrids (i.e., F₁ 's) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or other evidence of recent breeding success of F₁ 's, indicating very low or zero fitness of F₁  hybrids. Examination of genomic variation shows evidence for only a single backcrossing event many generations ago. The moderate rate of hybridization combined with very low F₁  hybrid fitness is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species.

Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini)

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species Φ_ST > 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species - the Steller's eider (Polysticta stelleri) - via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories.

Disruptions of feather carotenoid pigmentation in a subset of hybrid northern flickers (Colaptes auratus) may be linked to genetic incompatibilities

Hybridization can bring in single individuals alleles that were never designed to work together, which can result in unexpected or transgressive phenotypes. The Yellow-shafted (auratus group) and Red-shafted (cafer group) subspecies groups of the Northern Flicker (Colaptes auratus) differ conspicuously in the coloration of their flight feathers, but hybridize freely where their ranges overlap in western North America. The difference in color is largely the result of the Red-shafted form harboring ketolated products at C4(4') of the carotenoids found in the Yellow-shafted form. Characterizing the carotenoid pigments in a series of birds of intermediate color (presumed hybrids) revealed that most accumulated a product of β-cryptoxanthin with a keto group on its hydroxylated ring (3-hydroxy-echinenone), while a few accumulated the product with a keto group on the unhydroxylated ring (3'-hydroxy-echinenone). Surprisingly, the latter group also had feather barbs that were noticeably yellower than the associated rachis, corresponding to a lower level of ketolation at C4(4'). We assessed possible biochemical explanations for the differences by probing the relative carotenoid concentration data in individuals of varying color. The difference between the hybrids could not be explained by the general level of ketolation of carotenoids or a particular selectivity of the 4-ketolase involved. We present a testable genetic explanation that invokes incompatibilities between divergent alleles of the two parental forms at interacting loci. Because the idiosyncrasies affect oxidation, they may be the product of mitonuclear incompatibilities.

The importance of intrinsic postzygotic barriers throughout the speciation process

Intrinsic postzygotic barriers can play an important and multifaceted role in speciation, but their contribution is often thought to be reserved to the final stages of the speciation process. Here, we review how intrinsic postzygotic barriers can contribute to speciation, and how this role may change through time. We outline three major contributions of intrinsic postzygotic barriers to speciation. (i) reduction of gene flow: intrinsic postzygotic barriers can effectively reduce gene exchange between sympatric species pairs. We discuss the factors that influence how effective incompatibilities are in limiting gene flow. (ii) early onset of species boundaries via rapid evolution: intrinsic postzygotic barriers can evolve between recently diverged populations or incipient species, thereby influencing speciation relatively early in the process. We discuss why the early origination of incompatibilities is expected under some biological models, and detail how other (and often less obvious) incompatibilities may also serve as important barriers early on in speciation. (iii) reinforcement: intrinsic postzygotic barriers can promote the evolution of subsequent reproductive isolation through processes such as reinforcement, even between relatively recently diverged species pairs. We incorporate classic and recent empirical and theoretical work to explore these three facets of intrinsic postzygotic barriers, and provide our thoughts on recent challenges and areas in the field in which progress can be made. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae)

In order to gain insights into the biogeographic processes underlying biotic diversification in the Atlantic Forest (AF), we used a multi-locus approach to examine the evolutionary history of the White-shouldered Fire-eye (Pyriglena leucoptera) and the Fringe-backed Fire-eye (Pyriglena atra), two parapatric sister species endemic to the AF. We sequenced one mitochondrial, three Z chromosome-linked and three anonymous markers of 556 individuals from 66 localities. We recovered four lineages throughout the AF: P. atra and three populations within P. leucoptera. All populations diverged during the late Pleistocene and presented varying levels of admixture. One Z-linked locus showed the highest level of differentiation between the two species. On the other hand, a mitochondrial haplotype was shared extensively between them. Our data supported vicariance driving speciation along with extinction and dispersal as processes underlying intraspecific diversification. Furthermore, signatures of demographic expansion in most populations and areas of genetic admixture were recovered throughout the AF, suggesting that forest fragmentation was also important in differentiation. Genetic admixture areas are located between large rivers suggesting that AF rivers may diminish gene flow. Our results indicated a complex and dynamic biogeographic history of Pyriglena in the AF, with vicariance, extinction, dispersal and secondary contact followed by introgression likely influencing the current patterns of genetic distribution.

The evolution of specialized dentition in the deep-sea lanternfishes (Myctophiformes)

The evolution of heterodonty, the possession of varied tooth morphologies on the jaws of animals, has been relatively unexplored in ray-finned fishes compared to terrestrial vertebrates, and to an even lesser degree in deep-sea fish lineages. Lanternfishes (Myctophiformes) are an abundant and species-rich group endemic to deep-sea pelagic habitats. In this study, we document the presence of heterodonty on the oral jaws of lanternfishes, identifying differing anatomical and positional variations of dentition. We survey the anatomical variation in tooth morphology on the oral jaws of 114 lanternfish species across 37 genera and integrate our findings with a hypothesis of evolutionary relationships of lanternfishes to infer the number of times heterodonty evolved in this lineage. Our results indicate that heterodonty evolved at least six separate times on the oral jaws of lanternfishes, occurring as variable tooth morphologies in combination with villiform teeth. These combinations of tooth types include villiform plus hooked teeth, villiform plus hooked and recurved teeth, villiform plus spade, tricuspid, and hooked teeth, and villiform plus caniniform teeth. The reoccurring evolution of hooked teeth on the premaxilla and dentary in lanternfishes suggests heterodonty may serve an important functional role in their pelagic deep-sea environment. Hooked teeth could aid in securing and retaining prey in the oral cavity and allow for species to specialize on differing food resources, vital attributes for organisms living in open-ocean habitats.

Early life-history features associated with brood parasitism in the cuckoo catfish, Synodontis multipunctatus (Siluriformes: Mochokidae)

The cuckoo catfish, Synodontis multipunctatus, is the only known obligate brood parasite among fishes, exploiting the parental care of mouthbrooding cichlids endemic to Lake Tanganyika. Comparisons of this system to brood parasitism in birds may reveal broader principles that underlie the evolution of this life-history strategy in vertebrates. However, little is known about the features of the cuckoo catfish that enable this species to successfully parasitize cichlids. Here, we examine early ontogeny of the cuckoo catfish and compare it to that of its cichlid hosts as well as a non-parasitic congener. We found that cuckoo catfish embryos develop and hatch in advance of host embryos, and begin feeding on cichlid young just as they start to hatch. Overall timing of ontogeny in the cuckoo catfish was found to be similar to that of the substrate-spawning congener Synodontis lucipinnis, suggesting that more rapid development of the cuckoo catfish relative to cichlids is not a unique adaptation to brood parasitism. However, we found that cuckoo catfish progeny exhibit extensive morphological differences from S. lucipinnis, which may represent adaptations to brood parasitism. These life-history observations reveal both similarities and differences between the cuckoo catfish system and brood parasitism in other lineages. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.

Cryptic ecological and geographic diversification in coral-associated nudibranchs

Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.

Temporally varying disruptive selection in the medium ground finch (Geospiza fortis)

Disruptive natural selection within populations exploiting different resources is considered to be a major driver of adaptive radiation and the production of biodiversity. Fitness functions, which describe the relationships between trait variation and fitness, can help to illuminate how this disruptive selection leads to population differentiation. However, a single fitness function represents only a particular selection regime over a single specified time period (often a single season or a year), and therefore might not capture longer-term dynamics. Here, we build a series of annual fitness functions that quantify the relationships between phenotype and apparent survival. These functions are based on a 9-year mark-recapture dataset of over 600 medium ground finches (Geospiza fortis) within a population bimodal for beak size. We then relate changes in the shape of these functions to climate variables. We find that disruptive selection between small and large beak morphotypes, as reported previously for 2 years, is present throughout the study period, but that the intensity of this selection varies in association with the harshness of environment. In particular, we find that disruptive selection was strongest when precipitation was high during the dry season of the previous year. Our results shed light on climatic factors associated with disruptive selection in Darwin's finches, and highlight the role of temporally varying fitness functions in modulating the extent of population differentiation.

Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

Background

Understanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria.

Results

We set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes.

Conclusion

Overall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1483-3) contains supplementary material, which is available to authorized users.

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.

The effect of isolation, fragmentation, and population bottlenecks on song structure of a Hawaiian honeycreeper

Little is known about how important social behaviors such as song vary within and among populations for any of the endemic Hawaiian honeycreepers. Habitat loss and non-native diseases (e.g., avian malaria) have resulted in isolation and fragmentation of Hawaiian honeycreepers within primarily high elevation forests. In this study, we examined how isolation of Hawai'i 'amakihi (Chlorodrepanis virens) populations within a fragmented landscape influences acoustic variability in song. In the last decade, small, isolated populations of disease tolerant 'amakihi have been found within low elevation forests, allowing us to record 'amakihi songs across a large elevational gradient (10-1800 m) that parallels disease susceptibility on Hawai'i island. To understand underlying differences among populations, we examined the role of geographic distance, elevation, and habitat structure on acoustic characteristics of 'amakihi songs. We found that the acoustic characteristics of 'amakihi songs and song-type repertoires varied most strongly across an elevational gradient. Differences in 'amakihi song types were primarily driven by less complex songs (e.g., fewer frequency changes, shorter songs) of individuals recorded at low elevation sites compared to mid and high elevation populations. The reduced complexity of 'amakihi songs at low elevation sites is most likely shaped by the effects of habitat fragmentation and a disease-driven population bottleneck associated with avian malaria, and maintained through isolation, localized song learning and sharing, and cultural drift. These results highlight how a non-native disease through its influence on population demographics may have also indirectly played a role in shaping the acoustic characteristics of a species.

Interspecific competition, hybridization, and reproductive isolation in secondary contact: missing perspectives on males and females

Research on sexual selection and hybridization has focused on female mate choice and male-male competition. While the evolutionary outcomes of interspecific female preference have been well explored, we are now gaining a better understanding of the processes by which male-male competition between species in secondary contact promotes reproductive isolation versus hybridization. What is relatively unexplored is the interaction between female choice and male competition, as they can oppose one another or align with similar outcomes for reproductive isolation. The role of female-female competition in hybridization is also not well understood, but could operate similarly to male-male competition in polyandrous and other systems where costs to heterospecific mating are low for females. Reproductive competition between either sex of sympatric species can cause the divergence and/or convergence of sexual signals and recognition, which in turn influences the likelihood for interspecific mating. Future work on species interactions in secondary contact should test the relative influences of both mate choice and competition for mates on hybridization outcomes, and should not ignore the possibilities that females can compete over mating resources, and males can exercise mate choice.

Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps

A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S)-5-hydroxy-4-decanolide (RS-HDL). Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL) analysis involving 475 recombinant hybrid males (F₂), 2148 reciprocally backcrossed females (F₃), and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP) markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.

Every inch a finch: a commentary on Grant (1993) 'Hybridization of Darwin's finches on Isla Daphne Major, Galapagos'

One of the most familiar features of the natural world is that most animals and plants fall into distinct categories known as species. The attempt to understand the nature of species and the origin of new species was the enterprise that drove the early development of evolutionary biology and has continued to be a major focus of research. Individuals belonging to the same species usually share a distinctive appearance and way of life, and they can mate together successfully and produce viable offspring. New species may evolve, therefore, either through ecological divergence or through sexual isolation. The balance between these processes will depend on the extent of hybridization, especially in the early stages of divergence. Detecting and measuring hybridization in natural populations, however, requires intensive, long-term field programmes that are seldom undertaken, leaving a gap in our understanding of species formation. The finch community of a small, isolated island in the Galapagos provided an opportunity to discover how frequently hybridization takes place between closely related species in a pristine location, and Peter Grant's paper, published in Philosophical Transactions B in 1993, reports the observations that he and his collaborators made during the first 20 years of what is now one of the classical studies of evolution in action. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Plumage pigment differences underlying the yellow-red differentiation in the Northern Flicker (Colaptes auratus)

Elucidating the processes that create species differences is a central goal of evolutionary biology. The Northern Flicker (Colaptes auratus) exists as two well-differentiated subspecies groups in North America, the Yellow-shafted (auratus group) and Red-shafted Flickers (cafer group), which differ strikingly in the color of the underside and rachises of flight feathers, and of malar and nuchal patches. We investigated the physiological basis of these conspicuous phenotypic differences by identifying and quantifying the pigments involved. The yellow feathers of auratus contained carotenoids commonly found in nature (lutein, β-cryptoxanthin, zeaxanthin and β-carotene). The orange to red shafts/vanes of cafer and hybrids contained these carotenoids as well as mono- and diketo-carotenoids (notably adonirubin, α-doradexanthin, canthaxanthin, astaxanthin), representing oxygenated products at carbon C4(4') of the carotenoids present in auratus. Oxygenation of feather carotenoids at C4(4') correlated closely with shaft/vane redness. Carotenoid hydroxylation at C3(3') and the proportion of carotenoids with ε end-rings also varied with color and belie differences in the activity of several carotenoid-modifying enzymes between the two subspecies groups. Curiously, occasional yellow feathers in red-shafted individuals had the carotenoids of auratus, hence the differences are not constitutive in cafer, underscoring regulatory differences. The red malar stripe of cafer, the black malar stripe and red nuchal patch of auratus all contained similar types and amounts of carotenoids, mostly 3-hydroxy-4-keto-carotenoids. The biochemical differences between two strongly differentiated forms we uncovered shed light on how plumage coloration can change over evolutionary time and point to further avenues of research.

DNA Dispose, but Subjects Decide. Learning and the Extended Synthesis

Adaptation by means of natural selection depends on the ability of populations to maintain variation in heritable traits. According to the Modern Synthesis this variation is sustained by mutations and genetic drift. Epigenetics, evodevo, niche construction and cultural factors have more recently been shown to contribute to heritable variation, however, leading an increasing number of biologists to call for an extended view of speciation and evolution. An additional common feature across the animal kingdom is learning, defined as the ability to change behavior according to novel experiences or skills. Learning constitutes an additional source for phenotypic variation, and change in behavior may induce long lasting shifts in fitness, and hence favor evolutionary novelties. Based on published studies, I demonstrate how learning about food, mate choice and habitats has contributed substantially to speciation in the canonical story of Darwin's finches on the Galapagos Islands. Learning cannot be reduced to genetics, because it demands decisions, which requires a subject. Evolutionary novelties may hence emerge both from shifts in allelic frequencies and from shifts in learned, subject driven behavior. The existence of two principally different sources of variation also prevents the Modern Synthesis from self-referring explanations.

On the Coyne and Orr-igin of species: effects of intrinsic postzygotic isolation, ecological differentiation, x chromosome size, and sympatry on Drosophila speciation

Coyne and Orr found that mating discrimination (premating isolation) evolves much faster between sympatric than allopatric Drosophila species pairs. Their meta-analyses established that this pattern, expected under reinforcement, is common and that Haldane's rule is ubiquitous in Drosophila species divergence. We examine three possible contributors to the reinforcement pattern: intrinsic postzygotic isolation, dichotomized as to whether hybrid males show complete inviability/sterility; host-plant divergence, as a surrogate for extrinsic postzygotic isolation; and X chromosome size, whether roughly 20% or 40% of the genome is X-linked. We focus on "young" species pairs with overlapping ranges, contrasted with allopatric pairs. Using alternative criteria for "sympatry" and tests that compare either level of prezygotic isolation in sympatry or frequency of sympatry, we find no statistically significant effects associated with X chromosome size or our coarse quantifications of intrinsic postzygotic isolation or ecological differentiation. Although sympatric speciation seems very rare in animals, the pervasiveness of the reinforcement pattern and the commonness of range overlap for close relatives indicate that speciation in Drosophila is often not purely allopatric. It remains to determine whether increased premating isolation with sympatry results from secondary contact versus parapatric speciation and what drives this pattern.

Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds

The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation--especially intrinsic, postzygotic isolation--does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed.

The causes and evolutionary consequences of mixed singing in two hybridizing songbird species (Luscinia spp.)

Bird song plays an important role in the establishment and maintenance of prezygotic reproductive barriers. When two closely related species come into secondary contact, song convergence caused by acquisition of heterospecific songs into the birds’ repertoires is often observed. The proximate mechanisms responsible for such mixed singing, and its effect on the speciation process, are poorly understood. We used a combination of genetic and bioacoustic analyses to test whether mixed singing observed in the secondary contact zone of two passerine birds, the Thrush Nightingale (Luscinia luscinia) and the Common Nightingale (L. megarhynchos), is caused by introgressive hybridization. We analysed song recordings of both species from allopatric and sympatric populations together with genotype data from one mitochondrial and seven nuclear loci. Semi-automated comparisons of our recordings with an extensive catalogue of Common Nightingale song types confirmed that most of the analysed sympatric Thrush Nightingale males were ‘mixed singers’ that use heterospecific song types in their repertoires. None of these ‘mixed singers’ possessed any alleles introgressed from the Common Nightingale, suggesting that they were not backcross hybrids. We also analysed songs of five individuals with intermediate phenotype, which were identified as F₁ hybrids between the Thrush Nightingale female and the Common Nightingale male by genetic analysis. Songs of three of these hybrids corresponded to the paternal species (Common Nightingale) but the remaining two sung a mixed song. Our results suggest that although hybridization might increase the tendency for learning songs from both parental species, interspecific cultural transmission is the major proximate mechanism explaining the occurrence of mixed singers among the sympatric Thrush Nightingales. We also provide evidence that mixed singing does not substantially increase the rate of interspecific hybridization and discuss the possible adaptive value of this phenomenon in nightingales.

Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics

We investigate an individual-based model of adaptive radiation based on the biogeographical changes of the Great African Lakes where cichlid fishes radiated. In our model, the landscape consists of a mosaic of three habitat types which may or may not be separated by geographic barriers. We study the effect of the alternation between allopatry and sympatry called landscape dynamics. We show that landscape dynamics can generate a significantly higher diversity than allopatric or sympatric speciation alone. Diversification is mainly due to the joint action of allopatric, ecological divergence, and of disruptive selection increasing assortative mating and allowing for the coexistence in sympatry of species following reinforcement or character displacement. Landscape dynamics possibly increase diversity at each landscape change. The characteristics of the radiation depend on the speed of landscape dynamics and of the number of geographically isolated regions at steady state. Under fast dynamics of a landscape with many fragments, the model predicts a high diversity, possibly subject to the temporary collapse of all species into a hybrid swarm. When fast landscape dynamics induce the recurrent fusion of several sites, diversity is moderate but very stable over time. Under slow landscape dynamics, diversification proceeds similarly, although at a slower pace.

The effects of translocation-induced isolation and fragmentation on the cultural evolution of bird song

Understanding the divergence of behavioural signals in isolated populations is critical to knowing how certain barriers to gene flow can develop. For many bird species, songs are essential for conspecific recognition and mate choice. Measuring the rate of song divergence in natural populations is difficult, but translocations of endangered birds to isolated islands for conservation purposes can yield insights, as the age and source of founder populations are completely known. We found significant and rapid evolution in the structure and diversity of bird song in North Island saddlebacks, Philesturnus rufusater, in New Zealand, with two distinct lineages evolving in < 50 years. The strong environmental filters of serial translocations resulted in cultural bottlenecks that generated drift and reduced song variability within islands. This rapid divergence coupled with loss of song diversity has important implications for the behavioural evolution of this species, demonstrating previously unrecognised biological consequences of conservation management.

Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

BACKGROUND

The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct.

RESULTS

We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years.

CONCLUSIONS

By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.