The Genetics of Seasonal Migration and Plumage Color

Seasonally migratory songbirds have different historic population size characteristics than resident relatives

Modern genomic methods enable estimation of a lineage's long-term effective population sizes back to its origins. This ability allows unprecedented opportunities to determine how the adoption of a major life-history trait affects lineages' populations relative to those without the trait. We used this novel approach to study the population effects of the life-history trait of seasonal migration across evolutionary time. Seasonal migration is a common life-history strategy, but its effects on long-term population sizes relative to lineages that don't migrate are largely unknown. Using whole-genome data, we estimated effective population sizes over millions of years in closely related seasonally migratory and resident lineages in a group of songbirds. Our main predictions were borne out: Seasonal migration is associated with larger effective population sizes (Ne), greater long-term variation in Ne, and a greater degree of initial population growth than among resident lineages. Initial growth periods were remarkably long (0.63-4.29 Myr), paralleling the expansion and adaptation phases of taxon cycles, a framework of lineage expansion and eventual contraction over time encompassing biogeography and evolutionary ecology. Heterogeneity among lineages is noteworthy, despite geographic proximity (including overlap) and close relatedness. Seasonal migration imbues these lineages with fundamentally different population size attributes through evolutionary time compared to closely related resident lineages.

Mechanisms underlying the loss of migratory behaviour in a long-lived bird

Human-induced environmental changes are changing the migration patterns of birds worldwide. Species are adjusting migration timing, shortening and diversifying migratory routes or even transitioning towards residency. While the ultimate causes driving changes in migratory patterns are well established, the underlying mechanisms by which migratory species adapt to environmental change remain unclear. Here, we studied the mechanisms driving the recent and rapid loss of migratory behaviour in Iberian white storks Ciconia ciconia, a long-lived and previously fully migratory species through the African-Eurasian flyway. We combined 25 years of census data, GPS-tracking data from 213 individuals (80 adults and 133 first-year juveniles) tracked up to 7 years and whole-genome sequencing to disentangle whether within- (phenotypic flexibility) or between- (developmental plasticity or microevolution, through selection) individual shifts in migratory behaviour over time explain the observed population-level changes towards residency. Between 1995 and 2020, the proportion of individuals no longer migrating and remaining in Southern Europe year-round increased dramatically, from 18% to 68-83%. We demonstrate that this behavioural shift is likely explained by developmental plasticity. Within first-year birds, 98% crossed the Strait of Gibraltar towards their African wintering grounds, in Morocco or Sub-Saharan Africa. However, the majority shifted towards a non-migratory strategy as they aged-the proportion of migrants decreased to 67% and 33%, in their second and third year of life, respectively. Supporting these findings, only 19% of GPS-tracked adults migrated. We did not find evidence of phenotypic flexibility, as adults were highly consistent in migratory behaviour over multiple years (only 3 individuals changed strategy between years, out of 113 yearly transitions), nor of selection acting on genetic variation, since genomes of adult migrants and residents are essentially undifferentiated and we did not find evidence of selective sweeps in resident birds. Our results suggest that through developmental plasticity, traits that are plastic during specific windows of development become fixed during adulthood. Thus, inter-generational shifts in the frequency of migratory and non-migratory young individuals could drive population changes in migratory behaviour. This can provide a mechanism for long-lived migratory birds to respond to rapid human-driven environmental changes.

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.

Parity-specific differences in spatial genetics and dispersal in the common lizard

Dispersal is a key demographic parameter that plays an important role in determining spatial population dynamics and genetic structure. Linking differences in dispersal patterns to life-history traits is often confounded by inconsistent environmental pressures experienced by different populations. To explore the relationship between dispersal and life history, we focus on a site where oviparous and viviparous lineages of the common lizard (Zootoca vivipara) are found adjacent to each other. We take advantage of this shared environment to investigate parity-specific dispersal patterns using high-resolution, individual-level spatial-genetic autocorrelation and population genomic approaches (11,726 single nucleotide polymorphisms; 293 oviparous and 310 viviparous individuals). We found isolation-by-distance patterns to be present in both the oviparous and viviparous populations. Density was 2.5 times higher in the oviparous population than the viviparous one, though heterozygosity and genetic diversity measures were similar in the two populations. We found marked differences in the extent of genetic neighbourhoods between the lineages, with the viviparous population showing both dispersal (σ) and spatial-genetic autocorrelation (Moran's I) at 2-fold greater geographic distances than the oviparous population. We found clear evidence of male-biased dispersal from genetic estimates in the viviparous population. In the oviparous population, evidence of male-biased dispersal was weak or absent. These differences are likely to be closely linked to specific requirements of the alternative reproductive strategies and may be the demographic consequences of mother-offspring interactions. Fine-scale geographic and individual-level measures are essential to understanding parity mode differences at microevolutionary scales and to better identifying their ecological and evolutionary impacts.

Combining Individual-Based Radio-Tracking With Whole-Genome Sequencing Data Reveals Candidate for Genetic Basis of Partial Migration in a Songbird

Partial migration is a phenomenon where migratory and resident individuals of the same species co-exist within a population, and has been linked to both intrinsic (e.g., genetic) as well as environmental factors. Here we investigated the genomic architecture of partial migration in the common blackbird, a songbird that comprises resident populations in the southern distribution range, partial migratory populations in central Europe, and exclusively migratory populations in northern and eastern Europe. We generated whole-genome sequencing data for 60 individuals, each of which was phenotyped for migratory behavior using radio-telemetry tracking. These individuals were sampled across the species' distribution range, including resident populations (Spain and France), obligate migrants (Russia), and a partial migratory population with equal numbers of migratory and resident individuals in Germany. We estimated genetic differentiation (FST) of single-nucleotide variants (SNVs) in 2.5 kb windows between all possible population and migratory phenotype combinations, and focused our characterization on birds from the partial migratory population in Germany. Despite overall low differentiation within the partial migratory German population, we identified several outlier regions with elevated differentiation on four distinct chromosomes. The region with the highest relative and absolute differentiation was located on chromosome 9, overlapping PER2, which has previously been shown to be involved in the control of the circadian rhythm across vertebrates. While this region showed high levels of differentiation, no fixed variant could be identified, supporting the notion that a complex phenotype such as migratory behavior is likely controlled by a large number of genetic loci.

Mechanisms that Alter Capacity for Adenosine Triphosphate Production and Oxidative Phosphorylation: Insights from Avian Migration

Avian migration is among the most energetically demanding feats observed in animals. Studies evaluating the physiological underpinnings of migration have repeatedly shown that migratory birds display numerous adaptations that ultimately supply the flight muscle mitochondria with abundant fuel and oxygen during long-distance flights. To make use of this high input, the organs and mitochondria of migrants are predicted to display several traits that maximize their capacity to produce adenosine triphosphate (ATP). This review aims to introduce readers to several mechanisms by which organs and mitochondria can alter their capacity for oxidative phosphorylation and ATP production. The role of organ size, mitochondrial volume, substrate, and oxygen delivery to the electron transport system are discussed. A central theme of this review is the role of changes in electron chain complex activity, mitochondrial morphology and dynamics, and supercomplexes in allowing avian migrants and other taxa to alter the performance of the electron transport system with predictable shifts in demand. It is my hope that this review will serve as a springboard for future studies exploring the mechanisms that alter bioenergetic capacity across animal species.

Sexual selection promotes reproductive isolation in barn swallows

Despite the well-known effects of sexual selection on phenotypes, links between this evolutionary process and reproductive isolation, genomic divergence, and speciation have been difficult to establish. We unravel the genetic basis of sexually selected plumage traits to investigate their effects on reproductive isolation in barn swallows. The genetic architecture of sexual traits is characterized by 12 loci on two autosomes and the Z chromosome. Sexual trait loci exhibit signatures of divergent selection in geographic isolation and barriers to gene flow in secondary contact. Linkage disequilibrium between these genes has been maintained by selection in hybrid zones beyond what would be expected under admixture alone. Our findings reveal that selection on coupled sexual trait loci promotes reproductive isolation, providing key empirical evidence for the role of sexual selection in speciation.

Seasonal migration patterns of Siberian Rubythroat (Calliope calliope) facing the Qinghai-Tibet Plateau

BACKGROUND

Small songbirds respond and adapt to various geographical barriers during their annual migration. Global flyways reveal the diverse migration strategies in response to different geographical barriers, among which are high-elevation plateaus. However, few studies have been focused on the largest and highest plateau in the world, the Qinghai-Tibet Plateau (QTP) which poses a significant barrier to migratory passerines. The present study explored the annual migration routes and strategies of a population of Siberian Rubythroats (Calliope calliope) that breed on the north-eastern edge of the QTP.

METHODS

Over the period from 2021 to 2023, we applied light-level geolocators (13 deployed, seven recollected), archival GPS tags (45 deployed, 17 recollected), and CAnMove multi-sensor loggers (with barometer, accelerometer, thermometer, and light sensor, 20 deployed, six recollected) to adult males from the breeding population of Siberian Rubythroat on the QTP. Here we describe the migratory routes and phenology extracted or inferred from the GPS and multi-sensor logger data, and used a combination of accelerometric and barometric data to describe the elevational migration pattern, flight altitude, and flight duration. All light-level geolocators failed to collect suitable data.

RESULTS

Both GPS locations and positions derived from pressure-based inference revealed that during autumn, the migration route detoured from the bee-line between breeding and wintering grounds, leading to a gradual elevational decrease. The spring route was more direct, with more flights over mountainous areas in western China. This different migration route during spring probably reflects a strategy for faster migration, which corresponds with more frequent long nocturnal migration flights and shorter stopovers during spring migration than in autumn. The average flight altitude (1856 ± 781 m above sea level) was correlated with ground elevation but did not differ between the seasons.

CONCLUSIONS

Our finding indicates strong, season-dependent impact of the Qinghai-Tibet Plateau on shaping passerine migration strategies. We hereby call for more attention to the unexplored central-China flyway to extend our knowledge on the environment-migration interaction among small passerines.

Avian migration clocks in a changing world

Avian long-distance migration requires refined programming to orchestrate the birds' movements on annual temporal and continental spatial scales. Programming is particularly important as long-distance movements typically anticipate future environmental conditions. Hence, migration has long been of particular interest in chronobiology. Captivity studies using a proxy, the shift to nocturnality during migration seasons (i.e., migratory restlessness), have revealed circannual and circadian regulation, as well as an innate sense of direction. Thanks to rapid development of tracking technology, detailed information from free-flying birds, including annual-cycle data and actograms, now allows relating this mechanistic background to behaviour in the wild. Likewise, genomic approaches begin to unravel the many physiological pathways that contribute to migration. Despite these advances, it is still unclear how migration programmes are integrated with specific environmental conditions experienced during the journey. Such knowledge is imminently important as temporal environments undergo rapid anthropogenic modification. Migratory birds as a group are not dealing well with the changes, yet some species show remarkable adjustments at behavioural and genetic levels. Integrated research programmes and interdisciplinary collaborations are needed to understand the range of responses of migratory birds to environmental change, and more broadly, the functioning of timing programmes under natural conditions.

Mapping seasonal migration in a songbird hybrid zone -- heritability, genetic correlations, and genomic patterns linked to speciation

Seasonal migration is a widespread behavior relevant for adaptation and speciation, yet knowledge of its genetic basis is limited. We leveraged advances in tracking and sequencing technologies to bridge this gap in a well-characterized hybrid zone between songbirds that differ in migratory behavior. Migration requires the coordinated action of many traits, including orientation, timing, and wing morphology. We used genetic mapping to show these traits are highly heritable and genetically correlated, explaining how migration has evolved so rapidly in the past and suggesting future responses to climate change may be possible. Many of these traits mapped to the same genomic regions and small structural variants indicating the same, or tightly linked, genes underlie them. Analyses integrating transcriptomic data indicate cholinergic receptors could control multiple traits. Furthermore, analyses integrating genomic differentiation further suggested genes underlying migratory traits help maintain reproductive isolation in this hybrid zone.

Genetics and Evolution of Bird Migration

Bird migration has long been a subject of fascination for humankind and is a behavior that is both intricate and multifaceted. In recent years, advances in technology, particularly in the fields of genomics and animal tracking, have enabled significant progress in our understanding of this phenomenon. In this review, we provide an overview of the latest advancements in the genetics of bird migration, with a particular focus on genomics, and examine various factors that contribute to the evolution of this behavior, including climate change. Integration of research from the fields of genomics, ecology, and evolution can enhance our comprehension of the complex mechanisms involved in bird migration and inform conservation efforts in a rapidly changing world.

Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation

Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.

Gene regulation and speciation in a migratory divide between songbirds

Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration - an ecologically important and taxonomically widespread behavior---to gain insight into this topic. We measure gene expression in five brain regions. Differential expression between migratory states was dominated by circadian genes in all brain regions. The remaining patterns were largely brain-region specific. For example, expression differences between the subspecies that interact with migratory state likely help maintain reproductive isolation in this system and were documented in only three brain regions. Contrary to existing work on regulatory mechanisms underlying species-specific traits, two lines of evidence suggest that trans- (vs. cis) regulatory changes underlie these patterns - no evidence for allele-specific expression in hybrids and minimal associations between genomic differentiation and expression differences. Additional work with hybrids shows expression levels were often distinct (transgressive) from parental forms. Behavioral contrasts and functional enrichment analyses allowed us to connect these patterns to mitonuclear incompatibilities and compensatory responses to stress that could exacerbate selection on hybrids and contribute to speciation.

Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics

Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.

Learning and memory in hybrid migratory songbirds: cognition as a reproductive isolating barrier across seasons

Hybrid zones can be used to identify traits that maintain reproductive isolation and contribute to speciation. Cognitive traits may serve as post-mating reproductive isolating barriers, reducing the fitness of hybrids if, for example, misexpression occurs in hybrids and disrupts important neurological mechanisms. We tested this hypothesis in a hybrid zone between two subspecies of Swainson's thrushes (Catharus ustulatus) using two cognitive tests-an associative learning spatial test and neophobia test. We included comparisons across the sexes and seasons (spring migration and winter), testing if hybrid females performed worse than males (as per Haldane's rule) and if birds (regardless of ancestry or sex) performed better during migration, when they are building navigational maps and encountering new environments. We documented reduced cognitive abilities in hybrids, but this result was limited to males and winter. Hybrid females did not perform worse than males in either season. Although season was a significant predictor of performance, contrary to our prediction, all birds learned faster during the winter. The hypothesis that cognitive traits could serve as post-mating isolating barriers is relatively new; this is one of the first tests in a natural hybrid zone and non-food-caching species. We also provide one of the first comparisons of cognitive abilities between seasons. Future neurostructural and neurophysiological work should be used to examine mechanisms underlying our behavioral observations.

Migration direction in a songbird explained by two loci

Migratory routes and remote wintering quarters in birds are often species and even population specific. It has been known for decades that songbirds mainly migrate solitarily, and that the migration direction is genetically controlled. Yet, the underlying genetic mechanisms remain unknown. To investigate the genetic basis of migration direction, we track genotyped willow warblers Phylloscopus trochilus from a migratory divide in Sweden, where South-West migrating, and South-East migrating subspecies form a hybrid swarm. We find evidence that migration direction follows a dominant inheritance pattern with epistatic interaction between two loci explaining 74% of variation. Consequently, most hybrids migrate similarly to one of the parental subspecies, and therefore do not suffer from the cost of following an inferior, intermediate route. This has significant implications for understanding the selection processes that maintain narrow migratory divides.

Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird

The seasonal migration of birds is a fascinating natural wonder. Avian migratory behaviour changes are common and are probably a polygenic process as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotated near-chromosomal level de novo genome assembly, 50 resequenced genomes, hundreds of morphometric data and species distribution information, we investigated population structure and genomic and phenotypic differences associated with differences in migratory behaviour in a songbird species, Yellow-throated Bunting Emberiza elegans (Aves: Emberizidae). Population genomic analyses reveal extensive gene flow between the southern resident and the northern migratory populations of this species. The hand-wing index is significantly lower in the resident populations than in the migratory populations, indicating reduced flight efficiency of the resident populations. Here, we discuss the possibility that nonmigratory populations may have originated from migratory populations though migration loss. We further infer that the alterations of genes related to energy metabolism, nervous system and circadian rhythm may have played major roles in regulating migration change. Our study sheds light on phenotypic and polygenic changes involving migration change.

The Yellow-browed Warbler (Phylloscopus inornatus) as a model to understand vagrancy and its potential for the evolution of new migration routes

Why and how new migration routes emerge remain fundamental questions in ecology, particularly in the context of current global changes. In its early stages, when few individuals are involved, the evolution of new migration routes can be easily confused with vagrancy, i.e. the occurrence of individuals outside their regular breeding, non-breeding or migratory distribution ranges. Yet, vagrancy can in theory generate new migration routes if vagrants survive, return to their breeding grounds and transfer their new migration route to their offspring, thus increasing a new migratory phenotype in the population. Here, we review the conceptual framework and empirical challenges of distinguishing regular migration from vagrancy in small obligate migratory passerines and explain how this can inform our understanding of migration evolution. For this purpose, we use the Yellow-browed Warbler (Phylloscopus inornatus) as a case study. This Siberian species normally winters in southern Asia and its recent increase in occurrence in Western Europe has become a prominent evolutionary puzzle. We first review and discuss available evidence suggesting that the species is still mostly a vagrant in Western Europe but might be establishing a new migration route initiated by vagrants. We then list possible empirical approaches to check if some individuals really undertake regular migratory movements between Western Europe and Siberia, which would make this species an ideal model for studying the links between vagrancy and the emergence of new migratory routes.

Population genomics of an emergent tri-species hybrid zone

Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is, however, evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression probably occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.

Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks

Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

A migratory divide spanning two continents is associated with genomic and ecological divergence

Migratory divides are contact zones between breeding populations with divergent migratory strategies during the nonbreeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide coinciding with genomic differentiation across a hybrid zone between barn swallow (Hirundo rustica) subspecies in China. Individuals west of the hybrid zone, with H. r. rustica ancestry, had comparatively enriched stable-carbon and hydrogen isotope values and overwintered in eastern Africa, whereas birds east of the hybrid zone, with H. r. gutturalis ancestry, had depleted isotope values and migrated to southern India. The two subspecies took divergent migratory routes around the high-altitude Karakoram Range and arrived on the breeding grounds over 3 weeks apart. These results indicate that assortative mating by timing of arrival and/or selection against hybrids with intermediate migratory traits may maintain reproductive isolation between the subspecies, and that inhospitable geographic features may have contributed to the diversification of Asian avifauna by influencing migratory patterns.

Transcriptome signature changes in the liver of a migratory passerine

The liver plays a principal role in avian migration. Here, we characterised the liver transcriptome of a long-distance migrant, the Northern Wheatear (Oenanthe oenanthe), sampled at different migratory stages, looking for molecular processes linked with adaptations to migration. The analysis of the differentially expressed genes suggested changes in the periods of the circadian rhythm, variation in the proportion of cells in G1/S cell-cycle stages and the putative polyploidization of this cell population. This may explain the dramatic increment in the liver's metabolic capacities towards migration. Additionally, genes involved in anti-oxidative stress, detoxification and innate immune responses, lipid metabolism, inflammation and angiogenesis were regulated. Lipophagy and lipid catabolism were active at all migratory stages and increased towards the fattening and fat periods, explaining the relevance of lipolysis in controlling steatosis and maintaining liver health. Our study clears the way for future functional studies regarding long-distance avian migration.

Comparative Genomics and Evolution of Avian Specialized Traits

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.

Transposable elements mark a repeat-rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus)

The genetic basis of bird migration has been the focus of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different migratory routes to wintering grounds in Africa. Their breeding populations overlap in contact areas or "migratory divides" located in central Scandinavia and in eastern Poland. Earlier analyses demonstrated that the genetic differences between these two migratory phenotypes are few and cluster on chromosomes 1 and 5. In addition, an amplified fragment length polymorphism-derived biallelic marker (known as WW2) presents steep clines across both migratory divides but failed to be mapped in the genome. Here, we characterize the WW2 marker and describe its two variants (WW2 ancestral and WW2 derived) as portions of long terminal repeat retrotransposons originating from an ancient infection by an endogenous retrovirus. We used quantitative polymerase chain reaction techniques to quantify copy numbers of the WW2 derived variant in the two subspecies and their hybrids. This, together with genome analyses revealed that WW2 derived variants are much more abundant in P. t. acredula and appear embedded in a large repeat-rich region (>12 Mbp), not associated with the divergent regions of chromosomes 1 or 5. However, it might interact with genetic elements controlling migration direction. Testing this hypothesis further will require knowing the exact location of this region, such as by obtaining more complete genome assemblies preferably in combination with techniques like fluorescence in situ hybridization applied to a willow warbler karyotype, and finally to investigate the copy number of this marker in hybrids with known migratory tracks.

Age-dependent timing and routes demonstrate developmental plasticity in a long-distance migratory bird

Longitudinal tracking studies have revealed consistent differences in the migration patterns of individuals from the same populations. The sources or processes causing this individual variation are largely unresolved. As a result, it is mostly unknown how much, how fast and when animals can adjust their migrations to changing environments.

We studied the ontogeny of migration in a long‐distance migratory shorebird, the black‐tailed godwit Limosa limosa limosa, a species known to exhibit marked individuality in the migratory routines of adults. By observing how and when these individual differences arise, we aimed to elucidate whether individual differences in migratory behaviour are inherited or emerge as a result of developmental plasticity.

We simultaneously tracked juvenile and adult godwits from the same breeding area on their south‐ and northward migrations. To determine how and when individual differences begin to arise, we related juvenile migration routes, timing and mortality rates to hatch date and hatch year. Then, we compared adult and juvenile migration patterns to identify potential age‐dependent differences.

In juveniles, the timing of their first southward departure was related to hatch date. However, their subsequent migration routes, orientation, destination, migratory duration and likelihood of mortality were unrelated to the year or timing of migration, or their sex. Juveniles left the Netherlands after all tracked adults. They then flew non‐stop to West Africa more often and incurred higher mortality rates than adults. Some juveniles also took routes and visited stopover sites far outside the well‐documented adult migratory corridor. Such juveniles, however, were not more likely to die.

We found that juveniles exhibited different migratory patterns than adults, but no evidence that these behaviours are under natural selection. We thus eliminate the possibility that the individual differences observed among adult godwits are present at hatch or during their first migration. This adds to the mounting evidence that animals possess the developmental plasticity to change their migration later in life in response to environmental conditions as those conditions are experienced.

Animal Migration: An Overview of One of Nature's Great Spectacles

The twenty-first century has witnessed an explosion in research on animal migration, in large part due to a technological revolution in tracking and remote-sensing technologies, along with advances in genomics and integrative biology. We now have access to unprecedented amounts of data on when, where, and how animals migrate across various continents and oceans. Among the important advancements, recent studies have uncovered a surprising level of variation in migratory trajectories at the species and population levels with implications for both speciation and the conservation of migratory populations. At the organismal level, studies linking molecular and physiological mechanisms to traits that support migration have revealed a remarkable amount of seasonal flexibility in many migratory animals. Advancements in the theory for why animals migrate have resulted in promising new directions for empirical studies. We provide an overview of the current state of knowledge and promising future avenues of study.

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

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

A new westward migration route in an Asian passerine bird

The evolution of migration routes in birds remains poorly understood as changes in migration strategies are rarely observed on contemporary timescales.^1-3 The Richard's Pipit Anthus richardi, a migratory songbird breeding in Siberian grasslands and wintering in Southeast Asia, has only recently become a regular autumn and winter visitor to western Europe. Here, we examine whether this change in occurrence merely reflects an increase in the number of vagrants, that is, "lost" individuals that likely do not manage to return to their breeding grounds, or represents a new migratory strategy.^4-6 We show that Richard's Pipits in southwestern Europe are true migrants: the same marked individuals return to southern France in subsequent winters and geo-localization tracking revealed that they originate from the western edge of the known breeding range. They make an astonishing 6,000 km journey from Central Asia across Eurasia, a very unusual longitudinal westward route among Siberian migratory birds.^7,8 Climatic niche modeling using citizen-science bird data suggests that the winter niche suitability has increased in southwestern Europe, which may have led to increased winter survival and eventual successful return journey and reproduction of individuals that initially reached Europe as autumn vagrants. This illustrates that vagrancy may have an underestimated role in the emergence of new migratory routes and adaptation to global change in migratory birds.^9,10 Whatever the underlying drivers and mechanisms, it constitutes one of the few documented contemporary changes in migration route, and the first longitudinal shift, in a long-distance migratory bird.

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland

We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.

Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers

Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (F_ST  = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (F_ST  = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high F_ST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.

Fishing for the genetic basis of migratory behavior

For many species, migrating at just the right time is essential for both survival and reproduction. A new study in salmon localizes a small genomic region associated with migration timing, which in turn affects other physiological traits, suggesting that a seemingly complex suite of migration traits is linked by one "simple" phenotype.

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.

Rapid adjustments of migration and life history in hemisphere-switching cliff swallows

Many aspects of bird migration are necessarily innate.¹ However, the extent of deterministic genetic control, environmental influence, and individual decision making in the control of migration remains unclear.^2-8 Globally, few cases of rapid and dramatic life-history changes resulting in novel migration strategies are known. An example is latitudinal trans-hemispheric breeding colonization, whereby a subpopulation suddenly begins breeding on its non-breeding range.^9-13 These life-history reversals demand concomitant changes in the timing of migration, feather molt, and breeding if the population is to remain viable.¹³ Cliff swallows, Petrochelidon pyrrhonota, are long-distance migrants that breed in North America and spend the non-breeding season mostly in South America.¹⁴ However, in 2015, a small population switched hemispheres by breeding successfully in Argentina,⁹ over 8,000 km from the nearest potential source, after presumably failed attempts.^15,16 This provided a unique chance to characterize the early mechanisms of change in migratory behavior and phenology and to assess the possibility of double breeding. We tracked cliff swallows with geolocators following their second and fourth breeding seasons in Argentina, documenting inverted seasonality, three new migratory patterns and non-breeding areas (North America, Mesoamerica, and South America), and a shift of molt phenology by approximately 6 months, all possibly arising within a single generation. These birds did not practice migratory double breeding, although some spent the boreal summer in the traditional breeding range. Our data show that fundamental phenological changes occurred very rapidly during colonization and that phenotypic plasticity can underlie profound changes in the life histories of migratory birds.

Recessive white plumage color mutation of Japanese quail (Coturnix coturnix japonica) revealed morphological variations in the oropharyngeal roof structures, accompanied by behavioral differences

Genetic background of experimental animals contributes mainly to the variations in the experimental outcomes. Therefore, quails of two lines of plumage color (brown and recessive white) were studied to investigate the impact of plumage color mutations on the morphological structures of the oropharyngeal roof and also on the ingestive behavior and quail performance. Feeding intake and feed conversion ratio were higher in the brown quails, associated with nonsignificant increase of the live body weight and body weight gain. In the recessive white quails, ingestive behaviors revealed significant declines. The roof of the oropharynx roof was significantly longer in the recessive white quails; however, the upper beak was significantly longer and narrower in the brown ones. The length of the palate and pharynx showed nonsignificant increase in the recessive white quails. The median palatine ridge was formed of rostral continuous and caudal interrupted parts, and the lengths of these parts were slightly higher in the recessive white quails, meanwhile the lateral palatine ridge length showed a slight increase in the brown birds. Openings of intraepithelial glands were more numerous in the recessive white quails. The brown quails demonstrated more detectable and larger caudally directed conical shaped palatine and pharyngeal papillae, in addition to more considerable palatine salivary glands openings. The infundibular cleft was significantly wider in the recessive white quails, where its edges were characterized by lack of the pharyngeal papillae. The findings of this study will be beneficial for the breeders during selection the suitable quail lines for meat production purposes.

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

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

Monarch Butterfly Migration as an Integrative Model of Complex Trait Evolution

AbstractUnderstanding the genetic architecture of complex trait adaptation in natural populations requires the continued development of tractable models that explicitly confront organismal and environmental complexity. A decade of high-throughput sequencing-based investigations into the genomic basis of migration points to an integrative framework that incorporates quantitative genetics, evolutionary developmental biology, phenotypic plasticity, and epigenetics to explain migration evolution. In this perspective, I argue that the transcontinental migration of the monarch butterfly (Danaus plexippus) can serve as a compelling system to study the mechanism of evolutionary lability of a complex trait. Monarchs show significant phenotypic and genotypic diversity across their global range, with phenotypic switching that allows for explicit study of evolutionary lability. A developmental approach for elucidating how migratory traits are generated and functionally integrated will be important for understanding the evolution of monarch migration traits. I propose a plasticity threshold model to describe migration lability, and I describe novel functional techniques that will help resolve open questions and model assumptions. I conclude by considering the relationships between adaptive genetic architecture, anthropogenic climate change, and conservation management practice and the timeliness of the monarch migration model to illuminate these connections given the rapid decline of the North American migration.

The genetic regulation of avian migration timing: combining candidate genes and quantitative genetic approaches in a long-distance migrant

Plant and animal populations can adapt to prolonged environmental changes if they have sufficient genetic variation in important phenological traits. The genetic regulation of annual cycles can be studied either via candidate genes or through the decomposition of phenotypic variance by quantitative genetics. Here, we combined both approaches to study the timing of migration in a long-distance migrant, the collared flycatcher (Ficedula albicollis). We found that none of the four studied candidate genes (CLOCK, NPAS2, ADCYAP1 and CREB1) had any consistent effect on the timing of six annual cycle stages of geolocator-tracked individuals. This negative result was confirmed by direct observations of males arriving in spring to the breeding site over four consecutive years. Although male spring arrival date was significantly repeatable (R = 0.24 ± 0.08 SE), most was attributable to permanent environmental effects, while the additive genetic variance and heritability were very low (h² = 0.03 ± 0.17 SE). This low value constrains species evolutionary adaptation, and our study adds to warnings that such populations may be threatened, e.g. by ongoing climate change.

Genomic Regions Related to White/Black Tail Feather Color in Dwarf Chickens Identified Using a Genome-Wide Association Study

Although the genetic foundation of chicken body feather color has been extensively explored, that of tail feather color remains poorly understood. In the present study, we used a synthetic chicken dwarf line (DW), derived from hybrids bred between a black tail chicken breed, Rhode Island Red (RIR), and a white tail breed, dwarf layer (DL), to investigate the genetic rules associated white/black tail color. Even though the body feathers are predominantly red, the DW line still comprises individuals with black or white tails after more than 10 generations of self-crossing and selection for the body feather color. We first performed four crosses using the DW chickens, including black-tailed males to females, reciprocal crosses between the black and white, and white males to females to elucidate the inheritance pattern of the white/black tail. We also performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color using black tail chickens from the RIR and DW lines and white individuals from the DW line. In the crossing experiment, we found that (i) the white/black tail feather color is independent of body feather color; (ii) the phenotype is a simple autosomal trait; and (iii) the white is dominant to the black in the DW line. The GWA results showed that seven single-nucleotide polymorphisms (SNPs) on chromosome 24 were significantly correlated with tail feather color. The significant region (3.97-4.26 Mb) comprises nine known genes (NECTIN1, THY1, gga-mir-1466, USP2, C1QTNF5, RNF26, MCAM, CBL, and CCDC153) and five anonymous genes. This study revealed that the white/black tail feather trait is autosome-linked in DW chickens. Fourteen genes were found in the significant ~0.29 Mb genomic region, and some, especially MCAM, are suggested to play critical roles in the determination of white/black tail feather color. Our research is the first study on the genetics underlying tail feather color and could help further the understanding of feather pigmentation in chickens.

Climate-driven flyway changes and memory-based long-distance migration

Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic¹, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.

Hybridization alters growth and migratory life-history expression of native trout

Human-mediated hybridization threatens many native species, but the effects of introgressive hybridization on life-history expression are rarely quantified, especially in vertebrates. We quantified the effects of non-native rainbow trout admixture on important life-history traits including growth and partial migration behavior in three populations of westslope cutthroat trout over five years. Rainbow trout admixture was associated with increased summer growth rates in all populations and decreased spring growth rates in two populations with cooler spring temperatures. These results indicate that non-native admixture may increase growth under warmer conditions, but cutthroat trout have higher growth rates during cooler periods. Non-native admixture consistently increased expression of migratory behavior, suggesting that there is a genomic basis for life-history differences between these species. Our results show that effects of interspecific hybridization on fitness traits can be the product of genotype-by-environment interactions even when there are minor differences in environmental optima between hybridizing species. These results also indicate that while environmentally mediated traits like growth may play a role in population-level consequences of admixture, strong genetic influences on migratory life-history differences between these species likely explains the continued spread of non-native hybridization at the landscape-level, despite selection against hybrids at the population-level.

Avian Population Genomics Taking Off: Latest Findings and Future Prospects

Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the advent of high-throughput sequencing in various taxa. Several features of avian genomes make them particularly amenable for work in this field, including their nucleated red blood cells permitting easy DNA extraction and small, compact genomes. We review the latest findings in the population genomics of birds here, emphasizing questions related to behavior, ecology, evolution, and conservation. Additionally, we include insights in trait mapping and the ability to obtain accurate estimates of important summary statistics for conservation (e.g., genetic diversity and inbreeding). We highlight roadblocks that will need to be overcome in order to advance work on the population genomics of birds and prospects for future work. Roadblocks include the assembly of more contiguous reference genomes using long-reads and optical mapping. Prospects include the integration of population genomics with additional fields (e.g., landscape genetics, phylogeography, and genomic mapping) along with studies beyond genetic variants (e.g., epigenetics).

CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.

Genes and speciation: is it time to abandon the biological species concept?

The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species - are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.

The evolutionary history and genomics of European blackcap migration

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve.

Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage

Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

Transcriptome signatures in the brain of a migratory songbird

Most of the birds's adaptations for migration have a neuroendocrine origin, triggered by changes in photoperiod and the patterns of Earth's magnetic field. Migration phenomenology has been well described in the past decades, yet the genetic structure behind it remains terra incognita. We used RNA-Seq data to investigate which biological functions are linked with the seasonal brain adaptations of a long-distance trans-continental migratory passerine, the Northern Wheatear (Oenanthe oenanthe). We sequenced the wheatear's transcriptomes at three different stages: lean birds, a characteristic phenotype before the onset of migration, during fattening, and at their maximal migratory body mass. We identified a total of 15,357 genes in the brain of wheatears, of which 84 were differentially expressed. These were mostly related to nervous tissue development, angiogenesis, ATP production, innate immune response, and antioxidant protection, as well as GABA and dopamine signalling. The expression pattern of differentially expressed genes is correlated with typical phenotypic changes before migration, such as hyperphagia, migratory restlessness, and a potential increment in the visual and spatial memory capacities. Our work points out, for future studies, biological functions found to be involved in the development of the migratory phenotype -a unique model to study the core of neural, energetic and muscular adaptations for endurance exercise. Comparison of wheatears' transcriptomic data with two other studies with similar goals shows no correlation among the trends in the gene expression. It highlights the complexity and diversity of adaptations for long-distance migration in birds.