The evolution, maintenance and adaptive function of genetic colour polymorphism in birds

Few genetic loci control the green-brown colour polymorphism in the meadow grasshopper Pseudochorthippus parallelus

The green-brown polymorphism in Orthoptera is a prominent example of the coexistence of multiple colour variants, especially since this polymorphism is shared by many species. The processes that maintain phenotypic polymorphisms depend on the underlying genetic and developmental regulation of body colouration, but these are not well understood for Orthoptera. Here we report on the inheritance of the green-brown polymorphism in the meadow grasshopper Pseudochorthippus parallelus, a species with four discrete colour morphs that differ in the distribution of green colouration across the body. We provide the most detailed analysis of the green-brown polymorphism to date using half-sib full-sib breeding and phenotyping of 4,300 offspring. The data strongly support a simple Mendelian control of the presence/absence of green colour in different regions of the body, involving four autosomal loci, two of which are genetically linked. However, estimation of population allele and haplotype frequencies using probabilistic simulations shows weak linkage disequilibrium in the population. The contrast between pedigree and population linkage suggests the presence of long-standing allelic variation and thus corroborates that long-term balancing selection is acting. Our study confirms and extends our understanding of inheritance patterns within the Chorthippus clade, providing unprecedented insights into the number and linkage of loci involved. The results have implications for the maintenance of polymorphisms and suggest that fluctuations in the phenotypic composition of populations can be generated by the segregation of genetic variants even in the absence of fluctuating selection.

The Function of Melanin-Based Colour Polymorphism in Cattle, Sheep and Goats

Natural selection has rarely promoted the evolution of colour polymorphism in wild mammals. However, it is more common in domestic mammals due to artificial selection. For this reason, domestication could provide valuable insights into the mechanisms underlying the evolution of colour diversity. This raises the question of whether the associations between coat colour and other phenotypes in domestic animals are similar to those in free-living animals. Our literature review of cows, goats and sheep suggests that these associations can differ not only between species but also within and between breeds. This pattern holds for all the traits that we considered: morphology, behaviour, physiology, reproduction, milk production and parasitism. The only consistent association we found in the literature was the attraction of flies towards dark-coloured cows. The relationships between same colour morph, cortisol and thermoregulation varied across environments, suggesting a possible condition-dependent expression of multiple traits. We conclude that artificial selection may lead to a different integration of multiple phenotypes compared to animals living in the wild. Therefore, colour variation may not always serve the same functional roles in domestic animals as it does in wild ones.

Lifetime Fitness Variation Across the Geographical Range in a Colour Polymorphic Species

The maintenance of variation (i.e., different phenotypes) for heritable traits that are under selection, despite expectations of selection eroding variation and favouring only the fittest phenotype, represents an evolutionary paradox. Here, we studied variation in life-history traits in five populations of colour polymorphic tawny owls (Strix aluco) across Europe that have been individually studied for 13 years. Tawny owls show heritable plumage colour variation ranging from less pigmented (grey) to more heavily pigmented (brown-red). The breeding life span (BLS), lifetime egg production (LEP), lifetime reproductive success (LRS) and the number of years skipped between breeding attempts (NYS) varied between the study populations, with LEP and LRS varying across colour morphs in a population-specific fashion. Thus, grey tawny owl females have higher lifetime fledgling and egg production than brown-red females in some populations, but vice versa in others. Hence, our findings demonstrate disruptive selection of tawny owl plumage colourations across their European range, which may be one factor maintaining variation in heritable tawny owl colourations.

Repeatable Selection on Large Ancestry Blocks in an Avian Hybrid Zone

Hybrid zones create natural tests of genetic incompatibilities by combining loci from 2 species in the same genetic background in the wild, making them useful for identifying loci involved in both intrinsic and ecological (extrinsic) isolation. Two Swainson's thrush subspecies form a hybrid zone in western North America. These coastal and inland subspecies exhibit dramatic differences in migration routes; their hybrids exhibit poor migratory survival, suggesting that ecological incompatibilities maintain this zone. We used a panel of ancestry informative markers to identify repeated patterns of selection and introgression across 4 hybrid populations that span the entire length of the Swainson's thrush hybrid zone. Two repeatable patterns consistent with selection against incompatibilities-steep genomic clines and few transitions between ancestry states-were found in large genetic blocks on chromosomes 1 and 5. The block on chromosome 1 showed evidence for inland subspecies introgression while the block on chromosome 5 exhibited coastal subspecies introgression. Some regions previously associated with migratory phenotypes, including migratory orientation, or exhibiting misexpression between the subspecies exhibited signatures of selection in the hybrid zone. Both selection and introgression across the genome were shaped by genomic structural features and evolutionary history, with stronger selection and reduced introgression in regions of low recombination, high subspecies differentiation, positive selection within the subspecies, and on macrochromosomes. Cumulatively, these results suggest that linkage among loci interacts with divergent selection and past divergent evolution between species to strengthen barriers to gene flow within hybrid zones.

Environmental and social correlates of the plumage color polymorphism in an urban dweller, feral pigeon (Columba livia f. domestica)

We examined how urban environments affect the abundance, proportion, and diversity of plumage color morphs in feral pigeons. Five major plumage color morphs (black, blue, white, red, and mixed) were counted in sixty 25-ha plots in Poznań City (Poland). Generalized additive models were used to study the correlations among abundance, proportion of morphs, and environmental factors. Anthropogenic food sources were positively correlated with the abundance of black morphs and the proportions of black and red morphs. The blue morph abundance peaked at a moderate percentage of tall building cover, but its proportion decreased. A similar decrease was observed in the mixed plumage morphs. The abundance of blue morphs decreased, whereas the abundance of white morphs and the proportion of red morphs increased as the distance from the city center increased. The plumage color morph diversity (Simpson) index was positively correlated with food sources and hedgerow density but negatively correlated with street density. Color morph diversity in the study area may be sustained by differential responses of morphs to the environmental features of the urban environment. However, the positive correlation between the abundance of morphs indicates social attraction rather than social isolation among plumage color morphs.

A molecular mechanism for bright color variation in parrots

Parrots produce stunning plumage colors through unique pigments called psittacofulvins. However, the mechanism underlying their ability to generate a spectrum of vibrant yellows, reds, and greens remains enigmatic. We uncover a unifying chemical basis for a wide range of parrot plumage colors, which result from the selective deposition of red aldehyde- and yellow carboxyl-containing psittacofulvin molecules in developing feathers. Through genetic mapping, biochemical assays, and single-cell genomics, we identified a critical player in this process, the aldehyde dehydrogenase ALDH3A2, which oxidizes aldehyde psittacofulvins into carboxyl forms in late-differentiating keratinocytes during feather development. The simplicity of the underlying molecular mechanism, in which a single enzyme influences the balance of red and yellow pigments, offers an explanation for the exceptional evolutionary lability of parrot coloration.

Color polymorphic carnivores have faster speciation rates

Variation in coat color is a prominent feature in carnivores, thought to be shaped by environmental factors. As new traits could allow populations to occupy novel niches and habitats, color polymorphism may be maintained by balancing selection. Consequently, color polymorphic species may speciate more rapidly and can give rise to monomorphic daughter species. We thus predicted that, within the Carnivora, (i) speciation rate is higher in polymorphic lineages, (ii) divergence between color polymorphic lineages is more recent, and (iii) within closely related groups, polymorphic lineages are ancestral and monomorphic lineages derived. We also tested whether accelerated speciation rates relate to niche breadth, measured by the number of occupied habitats and range size. We collected data of 48 polymorphic and 192 monomorphic carnivore species, and assessed speciation rates using phylogenetic comparative methods. We found that polymorphic carnivores had higher speciation rates (λ1 = 0.29, SD = 0.13) than monomorphic species (λ0 = 0.053, SD = 0.044). Hidden and quantitative state speciation and extinction models inferred that color polymorphism was the main contributing factor, and that niche breadth was not of influence. Therefore, other selective forces than spatial niche segregation, such as predator-prey coevolution, may contribute to color polymorphism in wild carnivores.

Territorial status is explained by covariation between boldness, exploration, and thermal preference in a colour polymorphic lizard

Colour polymorphic species often exhibit variation in morphology, physiology, and behaviour among morphs. In particular, dominance status may be signalled by the interaction between behaviour and colour morph. Behavioural traits associated with dominance include boldness, exploration, and aggression, which influence access to preferred habitat, territorial defence, and mate acquisition. In ectotherms, the social structure associated with morphs may result in the exploitation of structural niches differing in thermal quality. Hence, social interactions among morphs may generate concordant variation in thermal preference and environmental temperature. However, few studies have assessed thermal preference variation in colour polymorphic species and its covariation with behaviour. Doing so can provide insight into niche specialization and the maintenance of colour polymorphism in populations. Here, we investigated the patterns of covariation in boldness behaviour, exploratory behaviour, and thermal preference in the tree lizard, Urosaurus ornatus. We assessed trait variation between territorial and non-territorial male morphs and between orange and yellow female morphs. Boldness and exploratory behaviour were repeatable in male U. ornatus and bolder individuals were significantly more likely to incur tail loss, a potential consequence of bold behaviour. Territorial male morphs were significantly bolder and more exploratory and preferred higher body temperatures with a narrower T set than non-territorial morphs. Female morphs did not vary in behavioural or thermal traits. This study highlights behavioural mechanisms that underly ecological niche segregation and variable habitat use between morphs in a colour polymorphic species.

Predator perception of aposematic and cryptic color morphs in two Oophaga species

Animals that are toxic often advertise their unprofitability to potential predators through bright aposematic colors while cryptic ones blend in with their natural background to avoid predators. In the poison dart frogs, Oophaga pumilio and O. granulifera, some populations in Costa Rica and Panama display cryptic green and aposematic red color morphs. We herein used reflectance spectra from the dorsum of red and green morphs of these frogs to estimate their perception by the visual systems of three potential predators (birds, lizards, and crabs) against three natural backgrounds (leaves, trunks and leaf litter). Statistical analyses revealed no strong differences in color contrast against backgrounds between the two frog species. However, strong effects of frog morph, predator, background, and their interactions were observed. When viewed against diverse backgrounds, red frogs of both Oophaga species are more color conspicuous to birds and Anoline lizards than to crabs. A strong effect of species was observed on luminance contrast. Concerning the latter, green frogs particularly in O. granulifera appear more conspicuous than red frogs, while birds perceive higher brightness contrasts than lizards or crabs. Our results further support the importance of birds and lizards as Oophaga predators and provide a first quantitative comparison of conspicuousness between these two frog species.

Dark Morph of the Oriental Honey-Buzzard (Pernis ptilorhynchus orientalis) is Attributable to Specific MC1R Haplotypes

A thorough understanding of the development of complex plumages in birds necessitates the acquisition of genetic data pertaining to the mechanism underlying this phenomenon from various avian species. The oriental honey-buzzard (Pernis ptilorhynchus orientalis), a tropical summer migrant to Northeast Asia, including Japan, exemplifies this aspect owing to the diversity of its ventral coloration and intra-feather barring patterns. However, genetic polymorphism responsible for this diversity has not been identified yet. This study aimed to investigate the link between dark-plumed phenotypes of this subspecies and haplotypes of the melanocortin-1-receptor (MC1R) gene. A draft sequence of MC1R was constructed using next generation sequencing and subsequently amplified using designed polymerase chain reaction (PCR) primers. The genome sequences of 32 honey-buzzard individuals were determined using PCR, and 12 MC1R haplotype sequences were obtained. Among these haplotypes, we found that unique haplotypes with nine non-synonymous substitutions and four or five synonymous substitutions in the coding region had a perfect correlation with the dark-plumed phenotype. The lack of correlation between the genotype of ASIP coding region and plumage phenotype reiterated that the dark morph is attributable to specific MC1R haplotypes. The absence of a correlation between genetic polymorphisms of MC1R and the intra-feather barring patterns, as well as the diversity observed within lighter ground color classes (pale and intermediate), implies the involvement of alternative molecular mechanisms in the manifestation of the aforementioned phenotypes.

Sex allocation is color morph-specific and associated with fledging condition in a wild bird

Melanin-based color polymorphism is predicted to evolve and maintain through differential fitness of morphs in different environments, and several empirical studies indicate that life history strategies, physiology, and behavior vary among color morphs. Sex allocation theory predicts that parents should adjust their sex allocation based on differential costs of raising sons and daughters, and therefore, color morphs are expected to modify their brood sex ratio decisions. In color polymorphic tawny owls (Strix aluco), the pheomelanistic brown morph is associated with higher energy requirements, faster growth, and higher parental effort than the gray morph. As hypothesized, we find that brown tawny owl mothers produced more daughters in early broods and more males in late broods, whereas gray mothers did the opposite. At fledging, daughters of early broods and of brown mothers were heavier than those of late broods or gray mothers. Hence, larger and more costly daughters appeared to benefit more than males from being born to brown mothers early in the season. Brown mothers breeding later in the season produced more cheap sons, while gray mothers face fewer challenges under limited resources and favor daughters. These findings suggest that environmental conditions influence brood sex allocation strategies of genetically determined color morphs differently.

The role of historical biogeography in shaping colour morph diversity in the common wall lizard

The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.

Winter-ground microhabitat use by differently coloured phenotypes affects return rate in a long-distance migratory bird

Migratory bird populations are declining globally at alarming rates. Non-breeding site conditions affect breeding populations, but generalising non-breeding habitat conditions over large spatial regions cannot address potential fine-scale differences across landscapes or local populations. Plumage characteristics can mediate the effects of environmental conditions on individual fitness. However, whether different phenotypes use distinctive non-breeding sites, and whether they respond to non-breeding site conditions differently remains largely unknown. Stable isotopes (δ13C, δ15N, δ2H) of inert tissues are useful to infer habitat characteristics and geographic origins where those tissues were grown. We collected winter-grown feathers from pied flycatchers (Ficedula hypoleuca) on their breeding grounds over several years from males whose dorsal plumage colouration ranged continuously from brown to black and assessed their stable isotope values as proxies of local habitat conditions. Based on feather δ2H profiles we found that browner males spent their non-breeding season in drier habitats than black males. Assignment to origin analysis shows potential regional non-breeding ground separation between differently coloured males. High within-individual repeatability of both δ13C and δ15N indicate the pied flycatcher males return yearly to similar areas. Blacker males were more likely to return to the breeding grounds after dry years compared with brown males. The opposite was found in wet years. Our study demonstrates that different phenotypes are exposed to different non-breeding site conditions which can differentially affect individual survivorship. This has important ramifications for population dynamics under predicted climate change scenarios where especially brown phenotype pied flycatcher males may be under a risk of decreasing.

Pleiotropic effects of melanin pigmentation: haemoparasite infection intensity but not telomere length is associated with plumage morph in black sparrowhawks

There is increasing recognition of the potential pleiotropic effects of melanin pigmentation, particularly on immunity, with reports of variation in haemoparasite infection intensity and immune responses between the morphs of colour-polymorphic bird species. In a population of the black sparrowhawk (Accipiter melanoleucus) in western South Africa, light morphs have a higher haemoparasite infection intensity, but no physiological effects of this are apparent. Here, we investigate the possible effects of haemoparasite infection on telomere length in this species and explore whether relative telomere length is associated with either plumage morph or sex. Using quantitative polymerase chain reaction analysis, we confirmed that dark morphs had a lower haemoparasite infection intensity than light morphs. However, we found no differences in telomere length associated with either the haemoparasite infection status or morph in adults, although males have longer telomeres than females. While differences in haemoparasite intensity between morphs are consistent with pleiotropic effects of melanin pigmentation in the black sparrowhawk, we found no evidence that telomere length was associated with haemoparasite infection. Further work is needed to investigate the implications of possible pleiotropic effects of plumage morph and their potential role in the maintenance of colour polymorphism in this species.

Genetic structure, UV-vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies

Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved in the origin and dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, and for investigating whether polymorphisms represent intermediate stages of diversification towards speciation. We investigated phenotypic and genetic differentiation between two colour morphs of the butterfly Fabriciana adippe using a combination of ddRAD-sequencing and comparisons of body size, colour patterns and optical properties of bright wing spots. The silvery-spotted adippe form had larger and darker wings and reflected UV light, while the yellow cleodoxa form displayed more green scales and reflected very little UV, showcasing that they constitute distinct and alternative integrated phenotypes. Genomic analyses revealed genetic structuring according to source population, and to colour morph, suggesting that the phenotypic differentiation reflects evolutionary modifications. We report 17 outlier loci associated with colour morph, including ultraviolet-sensitive visual pigment (UVRh1), which is associated with intraspecific communication and mate choice in butterflies. Together with the demonstration that the wings of the adippe (but essentially not the cleodoxa) morph reflect UV light, that UV reflectance is higher in females than males and that morphs differ in wing size, this suggests that these colour morphs might represent genetically integrated phenotypes, possibly adapted to different microhabitats. We propose that non-random mating might contribute to the differentiation and maintenance of the polymorphism.

A new trophic specialization buffers a top predator against climate-driven resource instability

Intraspecific phenotypic variability is key to respond to environmental changes and anomalies. However, documenting the emergence of behavioral diversification in natural populations has remained elusive due to the difficulty of observing such a phenomenon at the right time and place. Here, we investigated how the emergence of a new trophic strategy in a population subjected to high fluctuations in the availability of its main trophic resource (migrating songbirds) affected the breeding performance, population structure, and population fitness of a specialized color polymorphic predator, the Eleonora's falcon from the Canary Islands. Using long-term data (2007-2022), we found that the exploitation of an alternative prey (a local petrel species) was associated with the growth of a previously residual falcon colony. Pairs in this colony laid earlier and raised more fledglings than in the other established colonies. The specialization on petrels increased over time, independently of annual fluctuations in prey availability. Importantly, however, the positive effect of petrel consumption on productivity was stronger in years with lower food availability. This trophic diversification was further associated with the genetically determined color morph, with dark individuals preying more frequently on petrels than pale ones, which might promote the long-term maintenance of genotypic and phenotypic diversity. We empirically demonstrate how the emergence of an alternative trophic strategy can buffer populations against harsh environmental fluctuations by stabilizing their productivity.

Genetic basis and expression of ventral colour in polymorphic common lizards

Colour is an important visual cue that can correlate with sex, behaviour, life history or ecological strategies, and has evolved divergently and convergently across animal lineages. Its genetic basis in non-model organisms is rarely known, but such information is vital for determining the drivers and mechanisms of colour evolution. Leveraging genetic admixture in a rare contact zone between oviparous and viviparous common lizards (Zootoca vivipara), we show that females (N = 558) of the two otherwise morphologically indistinguishable reproductive modes differ in their ventral colouration (from pale to vibrant yellow) and intensity of melanic patterning. We find no association between female colouration and reproductive investment, and no evidence for selection on colour. Using a combination of genetic mapping and transcriptomic evidence, we identified two candidate genes associated with ventral colour differentiation, DGAT2 and PMEL. These are genes known to be involved in carotenoid metabolism and melanin synthesis respectively. Ventral melanic spots were associated with two genomic regions, including a SNP close to protein tyrosine phosphatase (PTP) genes. Using genome re-sequencing data, our results show that fixed coding mutations in the candidate genes cannot account for differences in colouration. Taken together, our findings show that the evolution of ventral colouration and its associations across common lizard lineages is variable. A potential genetic mechanism explaining the flexibility of ventral colouration may be that colouration in common lizards, but also across squamates, is predominantly driven by regulatory genetic variation.

Heterozygosity is low where rare color variants in wild carnivores prevail

Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.

Multivariate Models of Animal Sex: Breaking Binaries Leads to a Better Understanding of Ecology and Evolution

"Sex" is often used to describe a suite of phenotypic and genotypic traits of an organism related to reproduction. However, these traits-gamete type, chromosomal inheritance, physiology, morphology, behavior, etc.-are not necessarily coupled, and the rhetorical collapse of variation into a single term elides much of the complexity inherent in sexual phenotypes. We argue that consideration of "sex" as a constructed category operating at multiple biological levels opens up new avenues for inquiry in our study of biological variation. We apply this framework to three case studies that illustrate the diversity of sex variation, from decoupling sexual phenotypes to the evolutionary and ecological consequences of intrasexual polymorphisms. We argue that instead of assuming binary sex in these systems, some may be better categorized as multivariate and nonbinary. Finally, we conduct a meta-analysis of terms used to describe diversity in sexual phenotypes in the scientific literature to highlight how a multivariate model of sex can clarify, rather than cloud, studies of sexual diversity within and across species. We argue that such an expanded framework of "sex" better equips us to understand evolutionary processes, and that as biologists, it is incumbent upon us to push back against misunderstandings of the biology of sexual phenotypes that enact harm on marginalized communities.

Colour-specific diet specialization is associated with differences in owlet weight in a polymorphic owl: influence of the trophic quality variation

The niche divergence hypothesis proposes that the evolution and maintenance of colour polymorphism is based on a mechanism of disruptive selection. In a trophic context, the hypothesis predicts that individuals differing in colour vary in their trophic niche, either because they differ in foraging efficiency or feed in different habitats. A major evolutionary conundrum is how these expectations are affected by variation in trophic quality. Using an owl species with colour plumage polymorphism, the Eurasian scops owl Otus scops, we examined diet and habitat segregation during reproduction in relation to plumage colouration and trophic quality. Intensive sampling revealed that trophic quality for scops owls (i.e. abundance of grasshoppers and locusts) varied more among territories than between years, but scops owls did not segregate among territories of different quality by their colouration. However, we found that sex, plumage colouration and territory differences in trophic quality explained differences in the degree of dietary specialization. Brownish males delivered a higher diversity of prey to the nest than greyish ones in high trophic quality territories. We also found that the more diverse the diet provided by males, the heavier the owlets at fledging. Our study provides evidence for a different sensitivity to trophic quality of the colour morphs with potential fitness consequences in scops owls. We highlight the importance of studying the mechanisms leading to the persistence of colour polymorphism in patchy environments, since segregation may pass otherwise unnoticed if only habitats or years with similar conditions are considered.

Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes

Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.

Single-Cell Transcriptome and Pigment Biochemistry Analysis Reveals the Potential for the High Nutritional and Medicinal Value of Purple Sea Cucumbers

The sea cucumber Apostichopus japonicus has important nutritional and medicinal value. Unfortunately, we know little of the source of active chemicals in this animal, but the plentiful pigments of these animals are thought to function in intriguing ways for translation into clinical and food chemistry usage. Here, we found key cell groups with the gene activity predicted for the color morphology of sea cucumber body using single-cell RNA-seq. We refer to these cell populations as melanocytes and quinocytes, which are responsible for the synthesis of melanin and quinone pigments, respectively. We integrated analysis of pigment biochemistry with the transcript profiles to illuminate the molecular mechanisms regulating distinct pigment formation in echinoderms. In concert with the correlated pigment analysis from each color morph, this study expands our understanding of medically important pigment production, as well as the genetic mechanisms for color morphs, and provides deep datasets for exploring advancements in the fields of bioactives and nutraceuticals.

Regional variation in climate change alters the range-wide distribution of colour polymorphism in a wild bird

According to Gloger's rule, animal colouration is expected to be darker in wetter and warmer climates. Such environmental clines are predicted to occur in colour polymorphic species and to be shaped by selection if colour morphs represent adaptations to different environments. We studied if the distribution of the colour polymorphic tawny owl (Strix aluco) morphs (a pheomelanic brown and a pale grey) across Europe follow the predictions of Gloger's rule and if there is a temporal change in the geographical patterns corresponding to regional variations in climate change. We used data on tawny owl museum skin specimen collections. First, we investigated long-term spatiotemporal variation in the probability of observing the colour morphs in different climate zones. Second, we studied if the probability of observing the colour morphs was associated with general climatic conditions. Third, we studied if weather fluctuations prior to the finding year of an owl explain colour morph in each climate zone. The brown tawny owl morph was historically more common than the grey morph in every studied climate zone. Over time, the brown morph has become rarer in the temperate and Mediterranean zone, whereas it has first become rarer but then again more common in the boreal zone. Based on general climatic conditions, winter and summer temperatures were positively and negatively associated with the proportion of brown morph, respectively. Winter precipitation was negatively associated with the proportion of brown morph. The effects of 5-year means of weather on the probability to observe a brown morph differed between climate zones, indicating region-dependent effect of climate change and weather on tawny owl colouration. To conclude, tawny owl colouration does not explicitly follow Gloger's rule, implying a time and space-dependent complex system shaped by many factors. We provide novel insights into how the geographic distribution of pheomelanin-based colour polymorphism is changing.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

LAY SUMMARY

- What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity?- 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity.- Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá.

RESUMEN

Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas.

Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens

Background: Muscle development, egg production, and plumage colors are different between native and broiler chickens. The study was designed to investigate why improved Aseel (PD4) is colorful, stronger, and grew slowly compared with the control broiler (CB).

Methods: A microarray was conducted using the 7th-day embryo (7EB) and 18th-day thigh muscle (18TM) of improved Aseel and broiler, respectively. Also, we have selected 24 Gallus gallus candidate reference genes from NCBI, and total RNA was isolated from the broiler, improved Aseel embryo tissues, and their expression profiles were studied by real-time quantitative PCR (qPCR). Furthermore, microarray data were validated with qPCR using improved Aseel and broiler embryo tissues.

Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥ 1 and false discovery rate (FDR) ≤ 0.05. In total, 8,069 transcripts were differentially expressed between the 7EB and 18TM of PD4 compared to the CB. A further analysis showed that a high number of transcripts are differentially regulated in the 7EB of PD4 (6,896) and fewer transcripts are differentially regulated (1,173) in the 18TM of PD4 compared to the CB. On the 7th^- and 18th-day PD4 embryos, 3,890, 3,006, 745, and 428 transcripts were up- and downregulated, respectively. The commonly up- and downregulated transcripts are 91 and 44 between the 7th- and 18th-day of embryos. In addition, the best housekeeping gene was identified. Furthermore, we validated the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, and fatty acid metabolism genes in PD4 and CB embryo tissues by qPCR, and the results correlated with microarray expression data.

Conclusion: Our study identified DEGs that regulate the myostatin signaling and differentiation pathway; glycolysis and gluconeogenesis; fatty acid metabolism; Jak-STAT, mTOR, and TGF-β signaling pathways; tryptophan metabolism; and PI3K-Akt signaling pathways in PD4. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help improve muscle development, differentiation, egg production, protein synthesis, and plumage formation in PD4 native chickens. Our findings may be used as a model for improving the growth in Aseel as well as optimizing the growth in the broiler.

Genome-Wide Association Study Identifies Candidate Genes for Stripe Pattern Feather Color of Rhode Island Red Chicks

Feather colors of chickens are not only characteristics of breeds but also as phenotypic markers in chicken breeding. Pure-bred Rhode Island Red (RIR) chicks have a stripe pattern and a non-stripe pattern on the back. The stripe pattern of RIR is generally shown as four longitudinal black stripes on the back and is more likely to appear in females. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes controlling the stripe pattern of RIR chicks, and then, based on physical location and biological functions, quantitative RT-PCR analysis was used to validate the differential expression of candidate genes between stripe pattern and non-stripe pattern back skin tissue. The GWAS showed that a major signal contains 768 significant single nucleotide polymorphisms (SNPs) and 87 significant small insertions-deletions (INDELs) spanning 41.78 to 43.05 Mb (~1.27 Mb) on GGA1, corresponding to 16 genes associated with stripe pattern phenotype. Among these 16 genes, KITLG and TMTC3 could be considered candidate genes as they showed different expressions between back skin tissues of stripe pattern and non-stripe pattern chicks in value (p = 0.062) and the significant level (p < 0.05), respectively. This study provided novel insight into the mechanisms underlying feather pigmentation and stripe formation in RIR chicks.

Genetic divergence among threespine stickleback that differ in nuptial coloration

Sexual signals are shaped by their intended and unintended receivers as well as the signalling environment. This interplay between sexual and natural selection can lead to divergence in signals in heterogeneous environments. Yet, the extent to which gene flow is restricted when signalling phenotypes vary across environments and over what spatial scales remains an outstanding question. In this study, we quantify gene flow between two colour morphs, red and black, of freshwater threespine stickleback fish (Gasterosteus aculeatus). We capitalize on the very recent divergence of signalling phenotypes in this system to characterize within-species and among-morph genetic variation and to test for levels of gene flow between colour morphs in Oregon and Washington. Despite limited evidence for assortative mating between allopatric red and black populations, we found that black populations are genetically distinct from nearby red populations and that the black morph appears to have evolved independently at least twice in Oregon and Washington. Surprisingly, we uncovered a group of stickleback in one small coastal stream, Connor Creek, which is genetically and morphologically distinct from the red and black colour morphs and from marine stickleback. Historically, both colour morphs have coexisted in this location and sometimes hybridized, raising new questions about the origins and history of these fish, which were first described as anadromous-black hybrids >50 years ago. Understanding how genetic variation is currently partitioned within and among populations and colour morphs in this system should prompt future studies to assess the relative roles of habitat, ecological and pre- and post-reproductive barriers in the genetic divergence and phenotypic patterns we observe in nature.

Climate mediates color morph turnover in a species exhibiting alternative reproductive strategies

Sexual selection is considered the primary driver of morph turnover in many color polymorphic taxa, yet the potential for other factors (like climate) to contribute to polymorphism maintenance and evolution remains unclear. Appreciation for a role of environmental conditions in the maintenance and evolution of color polymorphisms has grown in recent years, generating evidence suggesting that color morphs linked to sexual selection may also diverge in climate sensitivity. Focusing on the three color components contributing to the male tree lizard (Urosaurus ornatus) color morphs, I reveal a marked concordance between patterns of turnover over space and time, with a general affinity of orange- and yellow-colored males to hotter, more variable conditions, and blue colored males to wetter, cooler conditions. An assessment of long-term turnover in the blue color component in response to recent climate change over the past 60 years reinforces these findings. Overall, behavioral asymmetries attributed to sexual selection likely expose competing morphs to divergent environmental conditions in heterogeneous habitats, creating opportunity for natural selection to shape climate sensitivities that also drive turnover in morph color composition. Ultimately, these processes may favor stark asymmetries in morph persistence over the coming decades.

Intraspecific diversity alters the relationship between climate change and parasitism in a polymorphic ectotherm

Climate-modulated parasitism is driven by a range of factors, yet the spatial and temporal variability of this relationship has received scant attention in wild vertebrate hosts. Moreover, most prior studies overlooked the intraspecific differences across host morphotypes, which impedes a full understanding of the climate-parasitism relationship. In the common lizard (Zootoca vivipara), females exhibit three colour morphs: yellow (Y-females), orange (O-females) and mixed (mixture of yellow and orange, M-females). Zootoca vivipara is also infested with an ectoparasite (Ophionyssus mites). We therefore used this model system to examine the intraspecific response of hosts to parasitism under climate change. We found infestation probability to differ across colour morphs at both spatial (10 sites) and temporal (20 years) scales: M-females had lower parasite infestations than Y- and O-females at lower temperatures, but became more susceptible to parasites as temperature increased. The advantage of M-females at low temperatures was counterbalanced by their higher mortality rates thereafter, which suggests a morph-dependent trade-off between resistance to parasites and host survival. Furthermore, significant interactions between colour morphs and temperature indicate that the relationship between parasite infestations and climate warming was contingent on host morphotypes. Parasite infestations increased with temperature for most morphs, but displayed morph-specific rates. Finally, infested M-females had higher reductions in survival rates than infested Y- or O-females, which implies a potential loss of intraspecific diversity within populations as parasitism and temperatures rise. Overall, we found parasitism increases with warming temperatures, but this relationship is modulated by host morphotypes and an interaction with temperature. We suggest that epidemiological models incorporate intraspecific diversity within species for better understanding the dynamics of wildlife diseases under climate warming.

Viability, behavior, and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs

Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.

Moonlight influence on quality of nestlings of scops owls depends on paternal coloration

Lunar phases might favor the maintenance of color polymorphism via disruptive selection if the different color variants performed differently in terms of prey capture under different moonlight levels. Moonlight, however, may affect prey capture as a side effect of its influence on prey behavior. Here we combine data of parental provisioning and quality of owlets with one ex-situ study of grasshopper activity to test whether Eurasian scops owls (Otus scops) with different plumage color and their prey are differently affected by moonlight. Food provisioning increased from new- to full-moon. However, the effect of moonlight on owlet mass gain and immune response depended on paternal coloration. On the one hand, body mass gain of nestlings of the greyest fathers increased from nights with new- to full-moon, whereas it did not change with moonlight for the brownest fathers. On the other hand, PHA response of nestlings of the brownest fathers increased with high moonlight levels during the first week of life, whereas it did not change with moonlight levels for the greyest fathers. Grasshoppers were more active at new moon than at full or waning moon. Our study provides supporting evidence that moonlight influences the behavior of both scops owls and its prey and suggests that fluctuations in environmental conditions can modulate the advantages of morphs. These results are important because they provide a general insight into a little appreciated mechanism for the maintenance of color polymorphism in natural populations based on the interactive effect of different environmental factors.

Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae

Color polymorphism-two or more heritable color phenotypes maintained within a single breeding population-is an extreme type of intraspecific diversity widespread across the tree of life. Color polymorphism is hypothesized to be an engine for speciation, where morph loss or divergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated diversification rates. Multiple species in the lizard family Lacertidae are color polymorphic, making them an ideal group to investigate the evolutionary history of this trait and its influence on macroevolution. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of diversification. Accounting for phylogenetic uncertainty with multiple phylogenies and simulation studies, we estimate an ancient origin of color polymorphism (111 Ma) within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved few times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net diversification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of diversification.[Color polymorphism; Lacertidae; state-dependent speciation extinction models; trait-dependent diversification.].

A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation

Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,¹ but generally little is known about the factors affecting their maintenance in populations.² We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.³ Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.

High frequency of an otherwise rare phenotype in a small and isolated tiger population

Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.

Variation in Genetic Mechanisms for Plumage Polymorphism in Skuas (Stercorarius)

Coloration is evolutionarily labile and so provides an excellent trait for examining the repeatability of evolution. Here, we investigate the repeatability of the evolution of polymorphic variation in ventral plumage coloration in skuas (Stercorarius: Stercorariidae). In 2 species, arctic (S. parasiticus) and pomarine skuas (S. pomarinus), plumage polymorphism was previously shown to be associated with coding changes at the melanocortin-1 receptor (MC1R) locus. Here, we show that polymorphism in a third species, the south polar skua (S. maccormicki), is not associated with coding variation at MC1R or with variation at a Z-linked second candidate locus, tyrosinase-related protein 1 (TYRP1). Hence, convergent evolution of plumage polymorphisms in skuas is only partly repeatable at the level of the genetic locus involved. Interestingly, the pattern of repeatability in skuas is aligned not with phylogeny but with the nature of the phenotypic variation. In particular, south polar skuas show a strong sex bias to coloration that is absent in the other species, and it may be that this has a unique genetic architecture.

Epistatic interactions between pterin and carotenoid genes modulate intra-morph color variation in a lizard

Color polymorphisms have become a major topic in evolutionary biology and substantial efforts have been devoted to the understanding of the mechanisms responsible for originating such colorful systems. Within-morph continuous variation, on the other hand, has been neglected in most of the studies. Here, we combine spectrophotometric/visual modeling and genetic data to study the mechanisms promoting continuous variation within categorical color morphs of Podarcis muralis. Our results suggest that intra-morph variability in the pterin-based orange morph is greater compared to white and yellow morphs. We also show that continuous variation within the orange morph is partially discriminable by conspecifics. Genotyping results indicate that allelic variants at the BCO2 locus (responsible for deposition of yellow carotenoids) contribute to generate continuous variation in orange individuals. However, other intrinsic and/or extrinsic mechanisms, such as body size, might be involved, opening a new avenue for future research on the drivers of continuous variation within-morphs.

Close encounters of the three morphs: Does color affect aggression in a polymorphic lizard?

Color polymorphism is genetically controlled, and the process generating and maintaining morphs can affect speciation/extinction rates. Color badges are useful signals in intraspecific communication because they convey information about alternative strategies and can potentially decrease unnecessary conflicts among different color morphs. Competition and aggressive interactions among color morphs can contribute to polymorphism maintenance. This could lead to an uneven spatial distribution of morphs in a population because the local frequency of each morph establishes the intensity of the competition and the fitness of each male. We used a polymorphic lizard, Podarcis muralis, to assess if aggression varies among morphs under two contrasting hypotheses: a heteromorphic versus homomorphic aggression. We used laboratory mirror tests after lizard color manipulation, and we verified the consistency of results with an analysis of the spatial distribution of morphs in a wild population. Both the experiments confirmed that aggression is more common during homomorphic than heteromorphic contests. The adoption of alternative behavioral strategies that minimize risks and costs could facilitate the stable coexistence of the phenotypes and reduce competition. A bias in aggression would advantage rarer morph, which would suffer less harassment by common morphs obtaining a fitness advantage. This process would be negatively-frequency-dependent and would stabilize polymorphism, possibly contributing to sympatric speciation.

Birds of different morphs use slightly different strategies to achieve similar reproductive performance following heatwave exposure

Responses to extreme climatic events may differ between individuals of distinct morphs which differ in life-history strategies, resulting in climate change 'winners' and 'losers' within species. We examined the reproductive performance and carry-over effects on offspring of black- and red-headed Gouldian finches Erythrura gouldiae after exposure to simulated heatwaves of moderate or severe intensity. We expected black-headed pairs' reproductive performance to decline after the severe heatwave because only the condition of black-headed females deteriorates during such a heatwave. Supporting the fact that Gouldian finches of different morphs use alternative reproductive strategies, we found that black-headed females initiated egg-laying a month earlier than red-headed females after experiencing a severe heatwave. We also found that this severe heatwave resulted in shorter spermatozoa in males irrespective of their morph. Despite these effects associated with heatwave intensity, the overall reproductive performance of both morphs was not affected by this factor, which was possibly due to an increased nestling provisioning rate by parents after exposure to the severe heatwave. However, offspring still bore the cost of parental exposure to the severe heatwave, as they showed a reduced condition (lower plasma antioxidant capacity and transient lower breathing rate) and higher oxidative damage (at least in fledglings with black-headed parents). These results suggest that inter-morph phenotypic variability in the Gouldian finch does not result in clear differences in reproductive performance following heatwave exposure, despite basal phenotypic differences between morphs. Whether animals using alternative reproductive strategies are, in the end, differently affected by climate changes will likely depend on the capacity of their offspring to recover from altered developmental conditions.

Environmental drivers of sexual dimorphism in a lizard with alternative mating strategies

Understanding the relative importance of sexual and natural selection in shaping morphological traits is a long-standing goal of evolutionary ecology. Male-biased sexual size dimorphism (SSD) is typically associated with male-male competition. Similarly, male polymorphisms are considered a consequence of competitive social interactions. This classic paradigm overlooks the fact that environmental factors mediate social interactions and can lead to ecological adaptations. Common side-blotched lizards, Uta stansburiana, are a model system for this paradigm due to well-known rock-paper-scissors social dynamics between male morphs. SSD in this species has been considered primarily a consequence of social interactions, with male size resulting from the number of morphs in each population and female size being constrained through fecundity benefits. We test if the environment explains intraspecific variation in SSD and number of male morphs in U. stansburiana. By compiling data from 49 populations, we show that environmental variables are stronger predictors of SSD than the number of male morphs. Similarly, we show that the environment mediates SSD and potentially contributes to morph loss in colder environments. We propose that the environment favours smaller males in areas of high seasonality. Our results demonstrate the importance of the environment as a mediator of SSD.

Malar stripe size and prominence in peregrine falcons vary positively with solar radiation: support for the solar glare hypothesis

Many falcons (Falco spp.) exhibit a distinct dark plumage patch below the eye, termed the malar stripe. This stripe is hypothesized to reduce the amount of solar glare reflected into the eyes while foraging, thereby increasing hunting efficiency in bright conditions. Here, we use a novel, global-scale correlative approach to test this 'solar glare hypothesis' in peregrine falcons (Falco peregrinus), the most widespread falcon species, using web-sourced photographs from across the species' global range. We found that the size and prominence of the malar stripe were positively associated with average annual solar radiation, but not with other environmental variables, such as temperature and rainfall. Our results provide the first published evidence for the hypothesis that this plumage feature functions to reduce the amount of solar glare reflected into the falcon's eyes, thereby improving the ability to pinpoint and target agile prey in bright conditions.

Alternative migratory tactics in brown trout (Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes

The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.

Intrapopulation foraging niche variation between phenotypes and genotypes of Spirit bear populations

Foraging niche variation within a species can contribute to the maintenance of phenotypic diversity. The multiniche model posits that phenotypes occupying different niches can contribute to the maintenance of balanced polymorphisms. Using coastal populations of black bears (Ursus americanus kermodei) from British Columbia, Canada, we examined potential foraging niche divergence between phenotypes (black and white "Spirit" coat color) and between genotypes (black-coated homozygote and heterozygous). We applied the Bayesian multivariate models, with biotracers of diet (δ13C and δ15N) together comprising the response variable, to draw inference about foraging niche variation. Variance-covariance matrices from multivariate linear mixed-effect models were visualized as the Bayesian standard ellipses in δ13C and δ15N isotopic space to assess potential seasonal and annual niche variation between phenotypes and genotypes. We did not detect a difference in annual isotopic foraging niche area in comparisons between genotypes or phenotypes. Consistent with previous field experimental and isotopic analyses, however, we found that white phenotype Spirit bears were modestly more enriched in δ15N during the fall foraging season, though with our modest sample sizes these results were not significant. Although also not statistically significant, variation in isotopic niches between genotypes revealed that heterozygotes were moderately more enriched in δ13C along hair segments grown during fall foraging compared with black-coated homozygotes. To the extent to which the pattern of elevated δ15N and δ13C may signal the consumption of salmon (Oncorhynchus spp.), as well as the influence of salmon consumption on reproductive fitness, these results suggest that black-coated heterozygotes could have a minor selective advantage in the fall compared with black-coated homozygotes. More broadly, our multivariate approach, coupled with knowledge of genetic variation underlying a polymorphic trait, provides new insight into the potential role of a multiniche mechanism in maintaining this rare morph of conservation priority in Canada's Great Bear Rainforest and could offer new understanding into polymorphisms in other systems.

Being Dark is Better: A Feral Pigeon Plumage Polymorphism as a Response to Urban Environments in Slovakia

The purpose of this study was to determine the distribution and plumage phenotypes of the feral pigeon, Columba livia forma urbana (Gmelin, 1789), in Slovakia. Censuses carried out in the built-up areas of 16 towns and cities from November to February (2012–2018) counted and evaluated 3,123 individual birds. The most frequent were melanic colored birds (checker, T-pattern and spread phenotypes), which predominated in the population (51.6%, n = 1,613), followed by paler ones (42.1%, n = 1,316) and other types (6.2%, n = 194). A statistically significant difference was confirmed among the melanic and paler plumage phenotypes (χ2 = 81.49, df = 15, p < 0.0001). Correlation confirmed the different importance of city area and human density on the maintenance of dark and/or pale pigeons living in cities.

Relationship between plumage color and eggshell patterns with egg production and egg quality traits of Japanese quails

Aim:

This study was conducted to identify the diversity of feather color and to determine the relationship between plumage color and egg yield as well as eggshell patterns and internal egg quality traits of Japanese quails.

Materials and Methods:

For investigating phenotypic diversity, a total of 600 quails from five breeding farms were evaluated to record head feather, shank, and plumage color. An on-station experiment was also conducted on 360 laying quails to examine the relationship between plumage color and egg production and egg weight during 24 weeks of laying. Eggs collected during this period were also used for identifying eggshell patterns and examining their relationship with internal egg quality characteristics.

Results:

Plumage color was primarily wild-type, with the highest proportion being 56.3% (p<0.001). Brown color was also found at a relatively high proportion in the population (16.7%), followed by black color (11.3%). The egg production and laying rate of quails with wild-type and brown plumage colors also significantly (p=0.001) differed from those of quails with other plumage types. Egg weight was also higher in these quail groups, especially than that of quails with yellow plumage color. Four patterns of eggshell were identified, among which spotted and dark eggshells were predominant (45.2% and 43.1%, respectively); however, patterns did not affect internal egg quality characteristics.

Conclusion:

Plumage color was primarily wild-type in both male and female quails. Egg yield over a 24-week laying period was superior in quails with wild-type and brown plumage colors, whereas a relationship between eggshell patterns and egg quality traits could not be established.