Hybrid songbirds employ intermediate routes in a migratory divide

Revisiting Perdeck's massive avian migration experiments debunks alternative social interpretations

Whether avian migrants can adapt to their changing world depends on the relative importance of genetic and environmental variation for the timing and direction of migration. In the classic series of field experiments on avian migration, A. C. Perdeck discovered that translocated juveniles failed to reach goal areas, whereas translocated adults performed 'true-goal navigation'. His translocations of > 14 000 common starlings (Sturnus vulgaris) suggested that genetic mechanisms guide juveniles into a population-specific direction, i.e. 'vector navigation'. However, alternative explanations involving social learning after release in juveniles could not be excluded. By adding historical data from translocation sites, data that was unavailable in Perdeck's days, and by integrated analyses including the original data, we could not explain juvenile migrations from possible social information upon release. Despite their highly social behaviour, our findings are consistent with the idea that juvenile starlings follow inherited information and independently reach their winter quarters. Similar to more solitarily migrating songbirds, starlings would require genetic change to adjust the migration route in response to global change.

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.

Reduced hybrid survival in a migratory divide between songbirds

Migratory divides, hybrid zones between populations that use different seasonal migration routes, are hypothesised to contribute to speciation. Specifically, relative to parental species, hybrids at divides are predicted to exhibit (1) intermediate migratory behaviour and (2) reduced fitness as a result. We provide the first direct test of the second prediction here with one of the largest existing avian tracking datasets, leveraging a divide between Swainson's thrushes where the first prediction is supported. Using detection rates as a proxy for survival, our results supported the migratory divide hypothesis with lower survival rates for hybrids than parental forms. This finding was juvenile-specific (vs. adults), suggesting selection against hybrids is stronger earlier in life. Reduced hybrid survival was not explained by selection against intermediate phenotypes or negative interactions among phenotypes. Additional work connecting specific features of migration is needed, but these patterns provide strong support for migration as an ecological driver of speciation.

Night-time neuronal activation of Cluster N in a North American songbird

Night-migrating songbirds utilize the Earth's magnetic field to help navigate to and from their breeding sites each year. A region of the avian forebrain called Cluster N has been shown to be activated during night migratory behavior and it has been implicated in processing geomagnetic information. Previous studies with night-migratory European songbirds have shown that neuronal activity at Cluster N is higher at night than during the day. Comparable work in North American migrants has only been performed in one species of swallows, so extension of examination for Cluster N in other migratory birds is needed. In addition, it is unclear if Cluster N activation is lateralized and the full extent of its boundaries in the forebrain have yet to be described. We used sensory-driven gene expression based on ZENK and the Swainson's thrush, a night-migratory North American songbird, to fill these knowledge gaps. We found elevated levels of gene expression in night- vs. day-active thrushes and no evidence for lateralization in this region. We further examined the anatomical extent of neural activation in the forebrain using 3D reconstruction topology. Our findings demonstrate that Swainson's thrushes possess an extensive bilateral night-activated Cluster N region in the forebrain similar to other European avian species, suggesting that Cluster N is highly conserved in nocturnal migrants.

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.

Migration genetics take flight: genetic and genomic insights into monarch butterfly migration

Monarch butterflies have emerged as a model system in migration genetics. Despite inherent challenges associated with studying the integrative phenotypes that characterize migration, recent research has highlighted genes and transcriptional networks underlying aspects of the monarch's migratory syndrome. Circadian clock genes and the vitamin A synthesis pathway regulate reproductive diapause initiation, while diapause termination appears to involve calcium and insulin signaling. Comparative approaches have highlighted genes that distinguish migratory and nonmigratory monarch populations, as well as genes associated with natural variation in propensity to initiate diapause. Population genetic techniques demonstrate that seasonal migration can collapse patterns of spatial structure at continental scales, whereas loss of migration can drive differentiation between even nearby populations. Finally, population genetics can be applied to reconstruct the monarch's evolutionary history and search for contemporary demographic changes, which can provide relevant context for understanding recently observed declines in overwintering North American monarch numbers.

Diurnal migration patterns in willow warblers differ between the western and eastern flyways

It is a long-standing view that the main mechanism maintaining narrow migratory divides in passerines is the selection against intermediate and suboptimal migratory direction, but empirical proof of this is still lacking. We present novel results from a willow warbler migratory divide in central Sweden from where birds take the typical SW and SE as well as intermediate routes to winter quarters in Africa. We hypothesized that individuals that take the intermediate route are forced to migrate in daytime more often when crossing wide ecological barriers than birds that follow the typical western or eastern flyways. Analyses of geolocator tracks of willow warblers breeding across the entire Sweden, including the migratory divide, provided no support for our hypothesis. Instead, birds that migrated along the western flyway were the most likely to undertake full day flights. The probability of migrating for a full day when crossing major barriers declined linearly from west to east. We speculate that this difference is possibly caused by more challenging conditions in the western part of the Sahara Desert, such as the lack of suitable day-time roost sites. However, it may equally likely be that willow warblers benefit from migrating in daytime if favorable tailwinds offer assistance.

Molecular and acoustic evidence support the species status of Anthus rubescens rubescens and Anthus [rubescens] japonicus (Passeriformes: Motacillidae)

The Buff-bellied Pipit Anthus rubescens comprises two allopatric subspecies groups: A. r. rubescens and A. r. alticola in North America and A. [r.] japonicus in north-east Asia. Despite their great morphological resemblance in breeding plumage, most individuals can be assigned to one or the other subspecies group in non-breeding plumage. Allopatric distributions, morphological differentiation and previously reported molecular divergence suggested the need for additional taxonomic study to assess the rank of these two populations. To resolve the taxonomy of the Buff-bellied Pipit species complex we analysed i) two mitochondrial DNA (mtDNA) loci and ii) nine bioacoustic parameters across 69 sound recordings (338 flight calls) recovered from public databases using principal component analysis and Euclidean distance measures. By comparing our mtDNA and call divergence measures with similar values measured between long-recognised species pairs of the genus, we show that the level of mitochondrial and acoustic divergence between the two Buff-bellied Pipit subspecies groups is typical of species-level divergence in the genus Anthus. Therefore, we recommend splitting the Buff-bellied Pipit species complex into two species: Anthus rubescens (American Pipit) and Anthus japonicus (Siberian Pipit). Our results also suggest that the Water Pipit A. spinoletta deserves taxonomic reassessment as its lineages are highly divergent in acoustics and mtDNA, while mtDNA relationships suggest paraphyly relative to the Rock Pipit A. petrosus. Our work highlights the crucial importance of integrative approaches in taxonomy and the usefulness of bioacoustics in studying cryptic diversity.

Lower survival of hybrid grosbeaks, but not towhees, suggests a molt divide disfavors hybrids

Although avian hybrid zones in the Great Plains have been studied for almost 70 years, we know surprisingly little about the fitness costs to hybrids that keep these zones narrow. We compare age ratios in grosbeaks (Pheucticus ludovicianus and P. melanocephalus) and towhees (Pipilo erythropthalums and P. maculatus), two species pairs that differ in their life histories and molt schedules, to evaluate survival between hybrids and parentals. We then contrast molt and migratory divides as possible sources of selection against hybrids. Hybrid grosbeaks had 27%-33% lower survival relative to their parentals, whereas hybrid towhees had survival rates similar to parentals. Age ratio data for hybrid grosbeaks suggest high mortality in older birds, as expected if selection operates after the first year of life. This pattern is consistent with parental species of grosbeaks having contrasting molt schedules relative to migration, suggesting high mortality costs to hybrids driven by molt biology, which are expressed later in life. Contrasts in molt schedules are absent in towhees. While migratory divides may exist for towhees and grosbeaks, the low adult survival of hybrid grosbeaks suggest that molt may be an important and underappreciated source of selection maintaining this and other narrow avian hybrid zones.

A gradual migratory divide determines not only the direction of migration but also migration strategy of a social migrant bird

Migratory divides separate populations of migratory animals, facilitating the evolution of intraspecific differences in migration strategies. Migration strategies are expected to be different for birds using different flyways and environments, but the knowledge regarding the impact of the flyway on individual migration strategies is scarce. By using satellite tracking and neckband resightings, we reveal the existence and structure of a gradual migratory divide between two European flyway populations of greylag geese Anser anser. Birds breeding at the far end of the Gulf of Bothnia in the Baltic Sea coast use the Western Flyway, those breeding in the Gulf of Finland the Central Flyway and those breeding between these extremes scatter to the two flyways. By using Gaussian process modelling, we show that migration strategies differed between the flyways. The birds using the Western Flyway migrated earlier in autumn, performed longer annual migration and made a clear stopover during migration, whereas the birds using the Central Flyway flew directly to their wintering sites. The gradual migratory divide that also divides migration strategies provides insights into migratory divides on birds with learned migration. Distinct migration strategies in different flyways provide exciting possibilities to further study the factors driving migration strategies.

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.

Autumn migration tracks of Helopsaltes grasshopper‐warblers from Northeast Asia support recent taxonomic assignments

Migration strategies are genetically inherited in most songbirds, and closely related species can exhibit markedly contrasting migration programs. Here, we investigate the autumn migration of one Helopsaltes grasshopper‐warbler from a population near Magadan, North East Russia, based on light‐level geolocation. Although often considered to belong to Middendorff's Grasshopper‐warbler H. ochotensis, recent genetic studies suggest that birds from this population are more closely related to Pallas's Grasshopper‐warbler H. certhiola. We compare the migratory behavior of the Magadan bird with two Pallas's Grasshopper‐warblers tracked from populations in the Kolyma River valley and the Amur region, Russia. We found similar migration patterns in all three tracked individuals, with stopover sites in eastern China and wintering sites in mainland Southeast Asia, within the known range for Pallas's Grasshopper‐warbler. Furthermore, based on morphological data compiled during bird ringing, we were able to confirm the presence of potential “Magadan grasshopper‐warblers” during spring and autumn migration in Thailand. Our scant data provide further evidence that Magadan Helopsaltes, notwithstanding their morphological resemblance to Middendorff's Grasshopper‐warbler, constitute a population of Pallas's Grasshopper‐warbler.

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.

Effects of cavity orientation on nesting success inferred from long-term monitoring of the endangered red-cockaded woodpecker

Animals that create structures often display non-random patterns in the direction of their constructions. This tendency of oriented construction is widely presumed to be an adaptive trait of the constructor’s extended phenotype, but there is little empirical support for this hypothesis. Particularly, for cavity nesting-birds there is a lack of studies examining this issue. In this study of a primary cavity excavator, the endangered red-cockaded woodpecker (Dryobates borealis), we show that cavity entrances exhibited a strong westward bias in all 11 of the populations examined throughout the geographic range of the species in the southeastern United States. This species requires cavities in living pine trees for roosting and nesting that often take many years to complete, resulting in many incomplete excavations on the landscape. We used population monitoring data to show that orientation was stronger among completed cavities than incomplete cavities. There was a significant correlation between latitude and average cavity direction among populations, turning northward with increasing latitude, suggesting adaptation to local conditions. Long-term monitoring data showed that cavity orientation and breeding group size are correlated with egg hatching rates, fledging rates, and the total number of fledglings produced per nest. Our results provide empirical evidence from extensive long-term data that directional orientation in animal constructions is an important feature of the extended animal phenotype and have immediate implications for animal ecology and the conservation of endangered species.

Genomic insights into variation in thermotolerance between hybridizing swordtail fishes

Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.

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.

One fish, two fish, red fish, dead fish: Detecting the genomic footprint of ecological incompatibilities

As we uncover the ubiquity of hybridization in nature, determining how natural selection acts on hybrids has newfound importance for speciation. A study in PLOS Biology uses threespine stickleback to detect a genomic signature of ecological incompatibilities.

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.

Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation

Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome‐wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai‐Tibetan plateau between lowland south‐eastern Chinese R. d. fohkienensis and high‐altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well‐known avian migratory divide, where western lineages take a western migration route around the Qinghai‐Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.

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.

The genomic consequences of hybridization

In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.

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

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

Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup

Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminates how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the female hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the female hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.

Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago

Long-distance dispersal (LDD) outside a species' breeding range contributes to genetic divergence. Previous phylogeographic studies of migratory bird species have not discriminated LDD from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). Haplotype networks of both mitochondrial and nuclear genes of its three subspecies were reconstructed to examine whether the Japanese subspecies of the Brown Shrike (Lanius cristatus superciliosus) diverged from an ancestral CRECS population. A species distribution model (SDM) for the Japanese subspecies was constructed using bioclimatic variables under the maximum entropy algorithm. It was projected backwards to the climate of the last glacial maximum (LGM) to infer the candidate source area of colonization. A migratory route of L. c. superciliosus, which possibly reflects a candidate past colonization route, was tracked by light-level geolocators. Molecular phylogenetic networks suggest that the Japanese subspecies diverged from a population in the CRECS and maintained anciently diverged haplotypes. The SDM inferred that the emerged continental shelf of the ECS and the present CRECS were suitable breeding areas for the Japanese subspecies during the LGM. A major migratory route for L. c. superciliosus was inferred between the CRECS and the Japanese archipelago across the ECS. Our integrative approach supported the LDD hypothesis for divergence of the Japanese subspecies of the Brown Shrike. Shrinkage of the ECS may have been responsible for successful population establishment, due to a sufficient number of migrants overshooting to the Japanese archipelago from the CRECS. Our framework provides a new phylogeographic scenario for this region. Discriminating LDD and vicariance models helps improve our understanding of the phylogeographic histories of migratory species.

Comparative studies on speciation: 30 years since Coyne and Orr

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.

Individual variability and versatility in an eco-evolutionary model of avian migration

Seasonal migration is a complex and variable behaviour with the potential to promote reproductive isolation. In Eurasian blackcaps (Sylvia atricapilla), a migratory divide in central Europe separating populations with southwest (SW) and southeast (SE) autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies. Blackcaps to the west and east of the divide used predominantly SW and SE directions, respectively, but close to the contact zone many individuals took intermediate (S) routes. At 14.0° E, we documented a sharp transition from SW to SE migratory directions across only 27 (10-86) km, implying a strong selection gradient across the divide. Blackcaps wintering in Britain took northwesterly migration routes from continental European breeding grounds. They originated from a surprisingly extensive area, spanning 2000 km of the breeding range. British winterers bred in sympatry with SW-bound migrants but arrived 9.8 days earlier on the breeding grounds, suggesting some potential for assortative mating by timing. Overall, our data reveal complex variation in songbird migration and suggest that selection can maintain variation in migration direction across short distances while enabling the spread of a novel strategy across a wide range.

Earlier and slower or later and faster: Spring migration pace linked to departure time in a Neotropical migrant songbird

Migratory birds travel vast distances and the timing of migratory flights can affect survival and the ability to reproduce. For Neotropical migrant songbirds, early spring departure from wintering sites, early arrival to the breeding grounds and higher reproductive success have been related to the use of suitable habitats and environmental conditions during the non-breeding season. However, how migratory strategies are shaped by winter habitat choice is largely unknown due to the general inability to track birds from specific wintering habitats to stopovers or breeding destinations. We assessed how winter habitat (native forest vs. shade-grown coffee plantations) relates to spring departure date and migration pace in Swainson's Thrush Catharus ustulatus. We also determined the effect of departure date and total migration duration on the arrival date of birds detected near or within their breeding range. We used a novel application of Motus radiotelemetry arrays to track individuals from their wintering grounds in the Andes of South America along their migratory journey to North America. We found variation in migratory strategies between habitats, with birds wintering in native forest departing later than birds in coffee. We present isotopic evidence for native forest being of higher quality than shade-coffee for Swainson's Thrush and hypothesize that moister conditions in forest, as shown by stable isotope (δ¹³ C) analysis of thrush whole blood, provides favourable pre-migratory conditions allowing birds to delay departure from wintering grounds. Habitat, between-site and -year variation in departure date, suggests that birds made facultative adjustments to winter habitat quality and environmental conditions. Independent of habitat, birds that departed later migrated faster and this pattern was maintained along the migration route (n = 44). Migrating earlier and slower or later and faster was unlikely to result in significant differences in arrival time to breeding destinations. Our findings reveal underappreciated complexity in migratory decisions by long-distance migrants that contrast with the current paradigm of earlier departures and arrival from optimal habitats. The next step is to understand the relative fitness benefits of early versus late schedules or whether each strategy is an equally good response to experienced conditions.

Maladaptive migration behaviour in hybrids links to predator-mediated ecological selection

Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and species integrity.

Here, we take advantage of a natural cross‐breeding incident to study migratory behaviour in naturally occurring hybrids as well as in their parental species and explore links between migratory traits and predation risk.

To achieve this, we used electronic tags and passive telemetry to record detailed individual migration patterns (timing and number of migratory trips) in two common freshwater fish species, roach Rutilus rutilus, common bream Abramis brama as well as their hybrids. Next, we scanned for tags regurgitated by a key avian predator (great cormorant Phalacrocorax carbo) at nearby roosting sites, allowing us to directly link migratory behaviour to predation risk in the wild.

We found that hybrid individuals showed a higher number of short, multi‐trip movements between lake and stream habitats as compared to both parental species. The mean date of first lake departure differed between bream and roach by more than 10 days, while hybrids departed in two distinct peaks that overlapped with the parental species' averages. Moreover, the probability of cormorant predation increased with multi‐trip movement frequency across species and was higher for hybrids.

Our data provide novel insights into hybrid viability, with links to predator‐mediated ecological selection. Increased exposure to predators via maladaptive migratory behaviour reduces hybrid survival and can thereby reinforce species integrity.

The importance of intrinsic postzygotic barriers throughout the speciation process

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

Autumn migration direction of juvenile willow warblers (Phylloscopus t. trochilus and P. t. acredula) and their hybrids assessed by qPCR SNP genotyping

BACKGROUNDS

Geographic regions, where two closely related taxa with different migration routes come into contact, are known as migratory divides. Hybrids originating from migratory divides are hypothesized to migrate intermediately relative to the parental populations. Few studies have tested this hypothesis in wild birds, and only in hybrids that have completed the migration back to the breeding grounds. Here, we make use of the well-established migration routes of willow warblers (Phylloscopus trochilus), for which the subspecies trochilus and acredula have migration-associated genetic markers on chromosomes 1 and 5. The genetic approach enabled us to analyze the geographic distribution of juveniles during their first autumn migration, predicting that hybrids should be more frequent in the central flyway over Italy than along the typical SW routes of trochilus and SE routes of acredula.

METHODS

Blood and feather samples were collected from wintering birds in Africa (n = 69), and from juveniles during autumn migration in Portugal (n = 33), Italy (n = 38) and Bulgaria (n = 32). Genotyping was carried out by qPCR SNP assays, on one SNP each on chromosome 1 (SNP 65) and chromosome 5 (SNP 285). Both these SNPs have alternative alleles that are highly fixed (> 97%) in each of the subspecies.

RESULTS

The observed combined genotypes of the two SNPs were associated with the known migration routes and wintering distributions of trochilus and acredula, respectively. We found hybrids (HH) among the juveniles in Italy (5/38) and in Portugal (2/33). The proportion of hybrids in Italy was significantly higher than expected from a background rate of hybrid genotypes (1.5%) in allopatric populations of the subspecies.

CONCLUSIONS

Our genetic approach to assign individuals to subspecies and hybrids allowed us to investigate migration direction in juvenile birds on their first migration, which should better reflect the innate migratory direction than studies restricted to successful migrants. The excess of hybrids in Italy, suggests that they employ an intermediate route relative to the parental populations. Our qPCR SNP genotyping method is efficient for processing large sample sizes, and will therefore be useful in migration research of species with known population genetic structure.

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.

Migration tracking reveals geographic variation in the vulnerability of a Nearctic-Neotropical migrant bird

We compared the vulnerability of a Nearctic-Neotropical migrant (Swainson’s Thrush, Catharus ustulatus) for three geographically-defined breeding populations in California by linking breeding and wintering regions, estimating migration distances, and quantifying relative forest loss. Using data from light-level geolocator and GPS tags, we found that breeding birds from the relatively robust coastal population in the San Francisco Bay area wintered predominantly in western Mexico (n = 18), whereas the far rarer breeding birds from two inland populations that occur near one another in the Sierra Nevada and southern Cascades mountain ranges migrated to farther wintering destinations, with birds from the Lassen region (n = 5) predominantly going to Central America and birds from the Tahoe region (n = 7) predominantly to South America. Landscape-level relative forest loss was greater in the breeding and wintering regions of the two Cascade-Sierra populations than those of coastal birds. Longer migration distances and greater exposure to recent forest loss suggest greater current vulnerability of Cascade-Sierra birds. Our results demonstrate that for some species, quantifying migration distances and destinations across relatively small distances among breeding populations (in this case, 140–250 km apart) can identify dramatically different vulnerabilities that need to be considered in conservation planning.

Evidence of linked selection on the Z chromosome of hybridizing hummingbirds

Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation ( F s t ) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.

Patterns of at-sea behaviour at a hybrid zone between two threatened seabirds

Patterns of behavioural variation and migratory connectivity are important characteristics of populations, particularly at the edges of species distributions, where processes involved in influencing evolutionary trajectories, such as divergence, mutual persistence, and natural hybridization, can occur. Here, we focused on two closely related seabird species that breed in the Mediterranean: Balearic shearwaters (Puffinus mauretanicus) and Yelkouan shearwaters (Puffinus yelkouan). Genetic and phenotypic evidence of hybridization between the two species on Menorca (the eastern and westernmost island in the breeding ranges of the two shearwaters, respectively) has provided important insights into relationships between these recently diverged species. Nevertheless, levels of behavioural and ecological differentiation amongst these populations remain largely unknown. Using geolocation and stable isotopes, we compared the at-sea movement behaviour of birds from the Menorcan ‘hybrid’ population with the nearest neighbouring populations of Balearic and Yelkouan shearwaters. The Menorcan population displayed a suite of behavioural features intermediate to those seen in the two species (including migration strategies, breeding season movements and limited data on phenology). Our findings provide new evidence to support suggestions that the Menorcan population is admixed, and indicate a role of non-breeding behaviours in the evolutionary trajectories of Puffinus shearwaters in the Mediterranean.

The genetics and epigenetics of animal migration and orientation: birds, butterflies and beyond

Migration is a complex behavioural adaptation for survival that has evolved across the animal kingdom from invertebrates to mammals. In some taxa, closely related migratory species, or even populations of the same species, exhibit different migratory phenotypes, including timing and orientation of migration. In these species, a significant proportion of the phenotypic variance in migratory traits is genetic. In others, the migratory phenotype and direction is triggered by seasonal changes in the environment, suggesting an epigenetic control of their migration. The genes and epigenetic changes underpinning migratory behaviour remain largely unknown. The revolution in (epi)genomics and functional genomic tools holds great promise to rapidly move the field of migration genetics forward. Here, we review our current understanding of the genetic and epigenetic architecture of migratory traits, focusing on two emerging models: the European blackcap and the North American monarch butterfly. We also outline a vision of how technical advances and integrative approaches could be employed to identify and functionally validate candidate genes and cis-regulatory elements on these and other migratory species across both small and broad phylogenetic scales to significantly advance the field of genetics of animal migration.

The start of migration correlates with arrival timing, and the total speed of migration increases with migration distance in migratory songbirds: a cross-continental analysis

BACKGROUND

Anthropogenic changes in the climate and environment have globally affected ecological processes such that the spatiotemporal occurrence of the main annual cycle events (i.e., breeding, wintering, moulting, and migration) has shifted in migratory birds. Variation in arrival timing at migratory destinations can be proximately caused by an altered start of migration, total migration distance, and/or total speed of migration. Quantifying the relative contributions of these causes is important because this will indicate the mechanisms whereby birds could potentially adjust their annual cycle in response to global change. However, we have relatively little quantitative information about how each of these factors contributes to variation in arrival timing. My main aims are to estimate how arrival timing is correlated with variation in the start of migration and the total migration distance and how the total speed of migration may change with the total migration distance and body mass in a comprehensive analysis including multiple species.

METHODS

For this purpose, I considered individual tracks covering complete migrations from multiple species and distinguished between within- and between-species effects.

RESULTS

Assuming that the within- and between-species effects quantified under this approach agree with the effects acting at the individual level, starting migration one day later or increasing the total migration distance by 1000 km would result in later arrival timing by 0.4-0.8 days or 2-5 days, respectively. The generality with which the start of migration is correlated with arrival timing within species suggests that this is the general biological mechanism regulating arrival timing, rather than the total migration distance. The total speed of migration was positively correlated with the total migration distance but not with the bird's body mass.

CONCLUSIONS

As the start of migration is endogenously controlled and/or affected by hatching date, directional selection can probably act on existing within-species/within-population variation to alter arrival timing. This factor and the importance of variation in the start of migration for arrival timing suggest that migratory species/populations in which there is sufficient variation in the start of migration and transgenerational processes affect the corresponding timing may present an advantage over others in coping with anthropogenic-induced global changes.

Behavioral Isolation and Incipient Speciation in Birds

Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, in particular, are known for their great diversity in these behaviors, and so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence to evaluate the importance of behavioral isolation in the early stages of avian speciation. Experimentally measured mating preferences indicate that changes in mating behavior can result in premating barriers, with their strength depending on the extent of divergence in mating signals. Differences in migratory and foraging behavior also can play important roles in generating reproductive barriers in the early stages of speciation. However, because premating behavioral isolation is imperfect, extrinsic postzygotic barriers, in the form of selection against hybrids having intermediate phenotypes, also play an important role in avian diversification, especially in completing the speciation process.

A Maladaptive Combination of Traits Contributes to the Maintenance of a Drosophila Hybrid Zone

Drosophila teissieri and D. yakuba diverged approximately 3 mya and are thought to share a large, ancestral, African range [1-3]. These species now co-occur in parts of continental Africa and in west Africa on the island of Bioko [1, 4]. While D. yakuba is a human commensal, D. teissieri seems to be associated with Parinari fruits, restricting its range to forests [4-6]. Genome data indicate introgression, despite no evidence of contemporary hybridization. Here we report the discovery of D. yakuba-D. teissieri hybrids at the interface of secondary forests and disturbed, open habitats on Bioko. We demonstrate that hybrids are the F₁ progeny of D. yakuba females and D. teissieri males. At high temperatures like those found on Bioko, D. teissieri females are generally less receptive to mating, and in combination with temperature effects on egg lay and egg-to-adult viability, this decreases the potential for gene flow between female D. teissieri and male D. yakuba relative to the reciprocal cross. Field and laboratory experiments demonstrate that F₁ hybrids have a maladaptive combination of D. yakuba behavior and D. teissieri physiology, generating additional barriers to gene flow. Nevertheless, analysis of introgressed and non-introgressed regions of the genome indicate that, while rare, gene flow is relatively recent. Our observations identify precise intrinsic and extrinsic factors that, along with hybrid male sterility, limit gene flow and maintain these species. These data contribute to a growing body of literature that suggests the Gulf of Guinea may be a hotspot for hybridization.

Genetic determination of migration strategies in large soaring birds: evidence from hybrid eagles

The relative contributions of genetic and social factors in shaping the living world are a crucial question in ecology. The annual migration of birds to their wintering grounds and back provides significant knowledge in this field of research. Migratory movements are predominantly genetically determined in passerine birds, while in large soaring birds, it is presumed that social (cultural) factors play the largest role. In this study, we show that genetic factors in soaring birds are more important than previously assumed. We used global positioning system (GPS)-telemetry to compare the autumn journeys and wintering ranges of two closely related large raptorial bird species, the greater spotted eagle Clanga clanga and the lesser spotted eagle Clanga pomarina, and hybrids between them. The timing of migration in hybrids was similar to that of one parental species, but the wintering distributions and home range sizes were similar to those of the other. Tracking data were supported by habitat suitability modelling, based on GPS fixes and ring recoveries. These results suggest a strong genetic influence on migration strategy via a trait-dependent dominance effect, although we cannot rule out the contribution of social interactions.