Recent speciation and elevated Z‐chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals

Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z‐chromosome (females are heterogametic, ZW). We tested for elevated Z‐differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal Anas gracilis and the dichromatic chestnut teal A. castanea. Despite prominent morphological differences, these two species are genetically indistinguishable at both mitochondrial DNA (mean Φ_ST < 0.0001) and 17 autosomal loci (mean Φ_ST = 0.0056). However, we detected elevated Z‐differentiation (mean Φ_ST = 0.281) and tentative evidence of an island of differentiation on the Z‐chromosome. This elevated differentiation was explained by a high frequency of derived alleles in chestnut teal that were absent in grey teal, which parallels independent evidence for a gain in dichromatism from a monochromatic ancestor. Coalescent estimates of demographic history and simulations indicated that the elevated Z‐differentiation was unlikely to be explained by neutral processes, but instead supported a role of divergent selection. We discuss evidence for models of speciation with gene flow versus adaptive divergence in the absence of gene flow and find that both hypotheses are plausible explanations of the data. Overall, these teal have the weakest background differentiation documented to date for a species showing a large Z‐effect, and they are an excellent model species for studying speciation genomics and the evolution of sexual dichromatism.     

CORRELATED EVOLUTION OF MIGRATION AND SEXUAL DICHROMATISM IN THE NEW WORLD ORIOLES (ICTERUS)

The evolution of sexual dimorphism has long been attributed to sexual selection, specifically as it would drive repeated gains of elaborate male traits. In contrast to this pattern, New World oriole species all exhibit elaborate male plumage, and the repeated gains of sexual dichromatism observed in the genus are due to losses of female elaboration. Interestingly, most sexually dichromatic orioles belong to migratory or temperate‐breeding clades. Using character scoring and ancestral state reconstructions from two recent studies in Icterus, we tested a hypothesis of correlated evolution between migration and sexual dichromatism. We employed two discrete phylogenetic comparative approaches: the concentrated changes test and Pagel's discrete likelihood test. Our results show that the evolution of these traits is significantly correlated (CCT: uncorrected P < 0.05; ML: LRT = 12.470, P < 0.005). Indeed, our best model of character evolution suggests that gains of sexual dichromatism are 23 times more likely to occur in migratory taxa. This study demonstrates that a life‐history trait with no direct relationship with sexual selection has a strong influence on the evolution of sexual dichromatism. We recommend that researchers further investigate the role of selection on elaborate female traits in the evolution of sexual dimorphism.     

Evolution of sexual dichromatism in relation to nesting habits in European passerines: a test of Wallace's hypothesis

Wallace proposed in 1868 that natural rather than sexual selection could explain the striking differences in avian plumage dichromatism. Thus, he predicted that nesting habits, through their association with nest predation, could drive changes in sexual dichromatism by enabling females in cavity nesters to become as conspicuous as males, whereas Darwin (1871, The Descent of Man and Selection in Relation to Sex, John Murray, London) argued that sexual selection was the sole explanation for dichromatism. Sexual dichromatism is currently used as indicating the strength of sexual selection, and therefore testing Wallace's claim with modern phylogentically controlled methodologies is of prime interest for comparing the roles of natural and sexual selection in affecting the evolution of avian coloration. Here, we have related information on nest attendance, sexual dichromatism and nesting habits (open and cavity nesting) to male and female plumage conspicuousness in European passerines. Nest incubation attendance does not explain male or female plumage conspicuousness but nest type does. Moreover, although females of monochromatic and cavity nesting species are more conspicuous than females of other species, males of monochromatic and open nesting species are those with more cryptic plumage. Finally, analyses of character evolution suggest that changes in nesting habits influence the probability of changes in both dichromatism and plumage conspicuousness of males but do not significantly affect those in females. These results strongly suggest a role of nesting habits in the evolution of plumage conspicuousness of males, and a role for sexual selection also in females, both factors affecting the evolution of sexual dichromatism. We discuss our findings in relation to the debate that Darwin and Wallace maintained more than one century ago on the importance of natural and sexual selection in driving the evolution of plumage conspicuousness and sexual dichromatism in birds, and conclude that our results partly support the evolutionary scenarios envisaged by both extraordinary scientists.     

Flight initiation distances in relation to sexual dichromatism and body size in birds from three continents

Predators exert strong selection pressures on their prey. Prey would therefore benefit by adjusting their behaviour to the risk of predation, while predators conversely would benefit from adjusting their behaviour to that of their prey. Extravagant ornamentation has evolved to attract mates and/or successfully compete with conspecifics of the same sex to secure high mating success, even if that occurs at a cost of increased risk of predation. Thus, sexually dichromatic species may be more susceptible to predation than sexually monochromatic species, and the presence of compensation is indicative of such species being more vulnerable. If extravagant ornamentation is costly in terms of predation risk, then we should expect sexually dichromatic species to have longer flight initiation distances (FID) than sexually monochromatic species. If ornamentation is acquired as a handicap with only individuals in prime condition being able to display with the smallest viability cost, we should expect sexually dichromatic individuals to have shorter FID than sexually monochromatic individuals. Such differences among individuals should, on an evolutionary time scale, translate into differences in FID being related to differences in sexual dichromatism among species. We investigated the relationship between FID and sexual dichromatism in phylogenetic analyses, while accounting for effects of continent (Australia, North America, and Europe), body mass, the interaction between sexual dichromatism and body mass and the interaction between sexual dichromatism and continent. In an analysis of 447 species we found shorter FID in sexually dichromatic than in sexually monochromatic species (consistent with the handicap hypothesis because sexually dichromatic species took greater risks), especially so at large body size. FID differed among continents and the relative difference in FID between sexually monochromatic and sexually dichromatic species was larger in Europe than in Australia and North America. These differences among continents may be attributed to latitudinal effects of predation. These findings are important for current ideas about the evolution of secondary sexual characters because they imply covarying continental differences in predation, especially for large bodied sexually dichromatic species.     

Light matters: testing the “Light Environment Hypothesis” under intra‐ and interspecific contexts

The “Light Environment Hypothesis” (LEH) proposes that evolution of interspecific variation in plumage color is driven by variation in light environments across habitats. If ambient light has the potential to drive interspecific variation, a similar influence should be expected for intraspecific recognition, as color signals are an adaptive response to the change in ambient light levels in different habitats. Using spectrometry, avian‐appropriate models of vision, and phylogenetic comparative methods, I quantified dichromatism and tested the LEH in both intra‐ and interspecific contexts in 33 Amazonian species from the infraorder Furnariides living in environments with different light levels. Although these birds are sexually monochromatic to humans, 81.8% of the species had at least one dichromatic patch in their plumage, mostly from dorsal areas, which provides evidence for a role for dichromatism in sex recognition. Furthermore, birds from habitats with high levels of ambient light had higher dichromatism levels, as well as brighter, more saturated, and more diverse plumages, suggesting that visual communication is less constrained in these habitats. Overall, my results provide support for the LEH and suggest that ambient light plays a major role in the evolution of color signals in this group of birds in both intra‐ and interspecific contexts. Additionally, plumage variation across light environments for these drab birds highlights the importance of considering ambient light and avian‐appropriate models of vision when studying the evolution of color signals in birds.     

Sexually selected dichromatism in the hihi Notiomystis cincta: multiple colours for multiple receivers

Why do some bird species show dramatic sexual dichromatism in their plumage? Sexual selection is the most common answer to this question. However, other competing explanations mean it is unwise to assume that all sexual dichromatism has evolved by this mechanism. Even if sexual selection is involved, further work is necessary to determine whether dichromatism results from competition amongst rival males, or by female choice for attractive traits, or both. Here, we test whether sexually dichromatic hihi (Notiomystis cincta) plumage is currently under sexual selection, with detailed behavioural and genetic analyses of a free‐living island population. Bateman gradients measured for males and females reveal the potential for sexual selection, whilst selection gradients, relating reproductive success to specific colourful traits, show that there is stabilizing selection on white ear tuft length in males. By correlating colourful male plumage with different components of reproductive success, we show that properties of yellow plumage are most likely a product of male–male competition, whilst properties of the black and white plumage are an outcome of both male–male competition and female choice. Male plumage therefore potentially signals to multiple receivers (rival males and potential mates), and this may explain the multicoloured appearance of one of the most strikingly dichromatic species in New Zealand.     

Juvenile coloration of Florida Scrub-Jays ( Aphelocoma coerulescens ) is sexually dichromatic and correlated with condition

The Florida Scrub-Jay is a monogamous cooperative breeder in which both males and females display extensive structurally based blue plumage. Juveniles of this species exhibit blue tail and wing feathers that they begin growing as nestlings, and some of these feathers are retained throughout their first year. Although the birds appear to be sexually monochromatic, we assessed whether cryptic dichromatism exists in both the magnitude and pattern of coloration in tail feathers of juvenile Florida Scrub-Jays. We then determined whether variation in plumage coloration is associated with nutritional condition during molt. Tails of juvenile male Florida Scrub-Jays exhibit a greater proportion of UV reflectance than those of females. Mass at age 11 days and ptilochronology of the juvenile tail feathers were used as measures of individual nutritional condition during feather growth, and the latter was found to be positively associated with UV chroma. These data demonstrate that Florida Scrub-Jays are sexually dichromatic and suggest that variation in plumage color may be condition dependent, although we cannot rule out alternative explanations. Juvenile plumage coloration, therefore, has the potential to function as a signal of individual quality in both males and females.     

Melanin‐based sexual dichromatism in the Western Palearctic avifauna implies darker males and lighter females

Melanins are the most common pigments providing coloration in the plumage and bare skin of birds and other vertebrates. Numerous species are dichromatic in the adult or definitive plumage, but the direction of this type of sexual dichromatism (i.e. whether one sex tends to be darker than the other) has not been thoroughly investigated. Using color plates, we analysed the presence of melanin‐based color patches in 666 species belonging to 69 families regularly breeding in the Western Palearctic. Sexual dichromatism based on melanins in at least one integumentary part involved 205 (30.7%) species. The body parts contributing more frequently to dichromatism were the dorsal areas, head and breast, whereas the less dichromatic body parts were the belly and the exposed integumentary parts (i.e. bill and legs). Regarding the phylogenetic spread of dichromatisms, 37 (53.6%) families contained at least one species with melanin‐based sexual dimorphism in the definitive adult plumage. As for the direction of the color difference, males are darker than females in a majority of species, meaning that males tend to produce more eumelanin and females tend to synthesize more pheomelanin. This survey has revealed the high prevalence of melanins in the emergence of sexual dichromatism in birds, at least in the Western Palearctic. Whether the described pattern is due to sexual selection promoting more conspicuous males or to natural selection for more cryptic females remains to be determined. Given that pheomelanin synthesis concurrently consumes the antioxidant glutathione but may also reduces toxic cysteine, sex‐biased physiological factors should also be given consideration in the evolution of bird plumages.     

Factors influencing the evolution of moult in the non‐breeding season: insights from the family Motacillidae

The number of moults per annual cycle and their final spatial pattern (i.e. topography) show high interspecific variation in the order Passeriformes. Factors behind this variability remain obscure, especially for variability in spatial pattern among species. Here, we explored the relative influence of ten ecological, ontogenetic, social and sexual factors on the evolution of autumn moult (feather replacement largely undertaken by migratory species, which is not necessarily an independent episode within their moult cycle) and prealternate moult among Northern Hemisphere species of the family Motacillidae using phylogenetically controlled analyses, ancestral state reconstruction and analyses of correlated evolution. The results strongly support the presence of prealternate moult and absence of autumn moult as ancestral states in this family. A high rate of change between related species indicates phylogenetic independence among prealternate moult patterns and examined factors. Migration distance and gregariousness are the most important factors influencing prealternate moult evolution, and point toward natural selection and sociality as the most important evolutionary drivers of prealternate moult in Motacillidae. Breeding latitude, seasonal plumage change, winter plumage conspicuousness, sexual dichromatism, plumage maturation and extent of preformative moult show a minor influence, and suggest that ontogeny and sexual selection may have played a limited role in shaping prealternate moult in Motacillidae.     

Understanding Phenotypical Character Evolution in Parmelioid Lichenized Fungi (Parmeliaceae,Ascomycota)

Parmelioid lichens form a species-rich group of predominantly foliose and fruticose lichenized fungi encompassing a broad range of morphological and chemical diversity. Using a multilocus approach, we reconstructed a phylogeny including 323 OTUs of parmelioid lichens and employed ancestral character reconstruction methods to understand the phenotypical evolution within this speciose group of lichen-forming fungi. Specifically, we were interested in the evolution of growth form, epicortex structure, and cortical chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, here we employed both maximum-parsimony and maximum-likelihood approaches to reconstruct ancestral character states. We have also implemented binary and multistate coding of characters and performed parallel analyses with both coding types to assess for potential coding-based biases. We reconstructed the ancestral states for nine well-supported major clades in the parmelioid group, two higher-level sister groups and the ancestral character state for all parmelioid lichens. We found that different methods for coding phenotypical characters and different ancestral character state reconstruction methods mostly resulted in identical reconstructions but yield conflicting inferences of ancestral states, in some cases. However, we found support for the ancestor of parmelioid lichens having been a foliose lichen with a non-pored epicortex and pseudocyphellae. Our data suggest that some traits exhibit patterns of evolution consistent with adaptive radiation.     

ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes that may have been involved in the diversification of species in this recent radiation.     

Molecular phylogenetics of the hummingbird genus Coeligena

Advances in the understanding of biological radiations along tropical mountains depend on the knowledge of phylogenetic relationships among species. Here we present a species-level molecular phylogeny based on a multilocus dataset for the Andean hummingbird genus Coeligena. We compare this phylogeny to previous hypotheses of evolutionary relationships and use it as a framework to understand patterns in the evolution of sexual dichromatism and in the biogeography of speciation within the Andes. Previous phylogenetic hypotheses based mostly on similarities in coloration conflicted with our molecular phylogeny, emphasizing the unreliability of color characters for phylogenetic inference. Two major clades, one monochromatic and the other dichromatic, were found in Coeligena. Closely related species were either allopatric or parapatric on opposite mountain slopes. No sister lineages replaced each other along an elevational gradient. Our results indicate the importance of geographic isolation for speciation in this group and the potential interaction between isolation and sexual selection to promote diversification.     

麻雀两性羽色的比较

鸟类对色彩有较强的区分能力。基于鸟类视觉模型的研究发现,在人类看来类似的羽色,在鸟类眼中存在差别。本研究通过量化麻雀（Passer montanus saturatus）羽毛的反射光谱以及身体量度和喉部、耳羽的黑色斑块面积,比较其在雌鸟和雄鸟之间的差异。研究发现,麻雀雌鸟和雄鸟的身体量度、喉部和耳羽的斑块面积在繁殖季和非繁殖季均无显著差异。基于鸟类的视觉模型,麻雀头顶、喉部、耳羽、腰部的羽色,在雌鸟和雄鸟间无明显分化。基于上述结果,我们认为麻雀的雌鸟和雄鸟在外形上没有表现出性二型。     

Blue tits are ultraviolet tits

The blue tit (Parus caeruleus) has been classified as sexually monochromatic. This classification is based on human colour perception yet, unlike humans, most birds have four spectrally distinct classes of cone and are visually sensitive to wavelengths in the near-ultraviolet (300 to 400 nm). Reflectance spectrophotometry reveals that blue tit plumage shows considerable reflection of UV light. For example, the blue crest shows peak reflectance at wavelengths around 352 nm. Furthermore, the blue tit is sexually dichromatic for multiple regions of plumage, including the crest. Choice trials performed in the laboratory indicate that females prefer males with the brightest crests. This study has implications for both intra- and interspecific studies of sexual selection, as well as future classification of dichromatism, which should not ignore the possibility of variation in reflectance in the UV.     

Phylogeny,biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.     

Nest shape explains variation in sexual dichromatism in New World blackbirds

Following Charles Darwin, research on sexual dichromatism has long focused on sexual selection driving ornamentation in males. However, Alfred Russel Wallace proposed another explanation – that dichromatism evolves as a result of selection favoring crypsis in incubating females. Many recent studies suggest that evolutionary changes in sexual dichromatism often result from changes in female, in addition to male, plumage, yet the evolutionary mechanisms driving changes in female plumage remain largely unexplained. To test Wallace's hypothesis, we examined variation in sexual dichromatism and nest shape, a proxy for predation risk, among New World blackbirds (Aves: Icteridae). Phylogenetic models reveal an evolutionary correlation between sexual dichromatism and nest exposure. Specifically, we found that transitions in monochromatic lineages with exposed nests toward either concealed nests or dichromatism were common. Although this evidence supports Wallace's hypothesis that female incubation leads to selection for crypsis or concealment, we also found that transitions to monomorphism were common, even in lineages with exposed nests – a result suggestive of a role for positive selection on female ornamentation. These patterns of plumage evolution support a growing body of work emphasizing the importance of developing and testing hypotheses to explain evolutionary changes in female, as well as male, ornamentation.     

Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum

The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (III) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r > 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satisfactorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal rampant parallel morphological evolution. Most species previously described based on phenetic grounds are thus resolved of polyphyletic origin. Species polyphylly has been increasingly reported among mosses, raising severe reservations regarding current species definition.     

Immune defence,extra-pair paternity,and sexual selection in birds

Secondary sexual characters have been suggested to reliably reflect the ability of individuals to resist debilitating parasites, and females may gain direct or indirect fitness benefits from preferring the most extravagantly ornamented males. Extra-pair paternity provides an estimate of an important component of sexual selection in birds. Species with a high frequency of extra-pair paternity have a variance in realized reproductive success that is greater than the variance in apparent reproductive success, and extra-pair copulations and hence extra-pair paternity by females are often directly associated with the expression of male secondary sexual characters. If sexually dichromatic species have experienced a long period of antagonistic coevolution with their parasites, such species should have evolved larger immune defence organs than sexually monochromatic species. Bird species with sexual dichromatism had larger spleens for their body size than monochromatic species in a comparative analysis. Furthermore, species with a high frequency of extra-pair paternity were sexually dichromatic and had large spleens for their body size. These results are consistent with the hypothesis that females of dichromatic bird species seek extra-pair copulations to obtain indirect fitness benefits in terms of superior resistance of their offspring to virulent parasites.     

More is better: the uses of developmental genetic data to reconstruct perianth evolution

The origin and evolution of the perianth remains enigmatic. While it seems likely that an undifferentiated perianth consisting of tepals arose early in angiosperm evolution, it is unclear when and how differentiated perianths consisting of distinct organs, such as petals and sepals, arose. Phylogenetic reconstructions of ancestral perianth states across angiosperms have traditionally relied on morphological data from extant species, but these analyses often produce equivocal results. Here we describe the use of developmental genetic data as an additional strategy to infer the ancestral perianth character state for different angiosperm clades. By assessing functional data in combination with expression data in a maximum likelihood framework, we provide a novel approach for investigating the evolutionary history of the perianth. Results of this analysis provide new insights into perianth evolution and provide a proof of concept for using this strategy to explore the incorporation of developmental genetic data in character state reconstructions. As the assumptions outlined here are tested and more genetic data are generated, we hope that ancestral state reconstructions based on multiple lines of evidence will converge.     

The contribution of structural-, psittacofulvin- and melanin-based colouration to sexual dichromatism in Australasian parrots

Colour ornamentation in animals is exceptionally diverse, but some colours may provide better signals of individual quality or more efficient visual stimuli and, thus, be more often used as sexual signals. This may depend on physiological costs, which depend on the mechanism of colour production (e.g. exogenously acquired colouration in passerine birds appears to be most sexually dichromatic). We studied sexual dichromatism in a sample of 27 Australasian parrot species with pigment- (melanin and psittacofulvin) and structural-based colouration, to test whether some of these types of colouration are more prominent in sexual ornamentation. Unlike passerines, in which long wavelength colouration (yellow to red) usually involves exogenous and costly carotenoid pigments, yellow to red colouration in parrots is based on endogenously synthesized psittacofulvin pigments. This allows us to assess whether costly exogenous pigments are necessary for these plumage colours to have a prominent role in sexual signalling. Structural blue colouration showed the largest and most consistent sexual dichromatism, both in area and perceptually relevant chromatic differences, indicating that it is often ornamental in parrots. By contrast, we found little evidence for consistent sexual dichromatism in melanin-based colouration. Unlike passerines, yellow to red colouration was not strongly sexually dichromatic: although the area of colouration was generally larger in males, colour differences between the sexes were on average imperceptible to parrots. This is consistent with the idea that the prominent yellow to red sexual dichromatism in passerines is related to the use of carotenoid pigments, rather than resulting from sensory bias for these colours.