Temperate origins of long-distance seasonal migration in New World songbirds

Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives)

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonisation in bar-tailed godwits

In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non-stop flights of any landbird. Using nextRAD sequencing of 14,318 single-nucleotide polymorphisms and scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in two main lineages at the last glacial maximum, when much of their present-day breeding range persisted in a vast, unglaciated Siberian-Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine-scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non-breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations.

The importance of migratory drop-off for island colonization in birds

Seasonal migration is an underappreciated driver of animal diversification. Changes in migratory behaviour may favour the establishment of sedentary founder populations and promote speciation if there is sufficient reproductive isolation between sedentary and migratory populations. From a systematic literature review, we here quantify the role of migratory drop-off-the loss of migratory behaviour-in promoting speciation in birds on islands. We identify at least 157 independent colonization events likely initiated by migratory species that led to speciation, including 44 cases among recently extinct species. By comparing, for all islands, the proportion of island endemic species that derived from migratory drop-off with the proportion of migratory species among potential colonizers, we showed that seasonal migration has a larger effect on island endemic richness than direct dispersal. We also found that the role of migration in island colonization increases with the geographic isolation of islands. Furthermore, the success of speciation events depends in part on species biogeographic and ecological factors, here positively associated with greater range size and larger flock sizes. These results highlight the importance of shifts in migratory behaviour in the speciation process and calls for greater consideration of migratory drop-off in the biogeographic distribution of birds.

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.

Adaptive evolution and loss of a putative magnetoreceptor in passerines

Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magnetic sensitivity in vitro compared to Cry4a from resident species. We investigate Cry and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes and identifies different selection regimes in passerines. We show that Cry4a is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that are likely to have facilitated the evolution of an optimized sensory protein for night-time orientation in songbirds. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines), and thus identified a gene deletion, which might facilitate testing the function of Cry4a in birds. In contrast, the other avian Cry (Cry1 and Cry2) were highly conserved across all species, indicating basal, non-sensory functions. Our results support a specialization or functional differentiation of Cry4 in songbirds which could be magnetosensation.

Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis

Factors such as the Andean uplift, Isthmus of Panama, and climate changes have influenced bird diversity in the Neotropical region. Studying bird species that are widespread in Neotropical highlands and lowlands can help us understand the impact of these factors on taxa diversification. Our main objectives were to determine the biogeographic factors that contributed to the diversification of Euphoniinae and re-evaluate their phylogenetic relationships. The nextRAD and mitochondrial data were utilized to construct phylogenies. The ancestral distribution range was then estimated using a time-calibrated phylogeny, current species ranges, and neotropical regionalization. The phylogenies revealed two main Euphoniinae clades, Chlorophonia and Euphonia, similar to previous findings. Furthermore, each genus has distinctive subclades corresponding to morphology and geography. The biogeographic results suggest that the Andean uplift and the establishment of the western Amazon drove the vicariance of Chlorophonia and Euphonia during the Miocene. The Chlorophonia lineage originated in the Andes mountains and spread to Central America and the Mesoamerican highlands after the formation of the Isthmus of Panama. Meanwhile, the ancestral area of Euphonia was the Amazonas, from which it spread to trans-Andean areas during the Pliocene and Pleistocene due to the separation of the west lowlands from Amazonas due to the Northern Andean uplift. Chlorophonia and Euphonia species migrated to the Atlantic Forest during the Pleistocene through corridors from the East Andean Humid Forest and Amazonas. These two genera had Caribbean invasions with distinct geographic origins and ages. Finally, we suggested taxonomic changes in the genus Euphonia based on the study's phylogenetic, morphological, and biogeographic findings.

Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone

Background

The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.

Methods

We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge.

Results

Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.

Comparison of the Phenotypic Flexibility of Muscle and Body Condition of Migrant and Resident White-Crowned Sparrows

AbstractSeasonally breeding birds express variations of traits (phenotypic flexibility) throughout their life history stages that represent adaptations to environmental conditions. Changes of body condition during migration have been well studied, whereas alterations of skeletal and cardiac muscles, body mass, and fat scores have yet to be characterized throughout the spring or fall migratory stages. Additionally, we examined flexible patterns of muscle, body mass, and fat score in migrant white-crowned sparrows (Zonotrichia leucophrys gambelii) in comparison with those in a resident subspecies (Zonotrichia leucophrys nuttalli) during the stages they share to evaluate the influence of different life histories. Migrants showed hypertrophy of the pectoralis muscle fiber area on the wintering grounds in late prealternate molt, yet increased pectoralis muscle mass was not detected until birds readied for spring departure. While pectoralis profile and fat scores enlarged at predeparture in spring and fall, pectoralis, cardiac, and body masses were greater only in spring stages, suggesting seasonal differences for migratory preparation. Gastrocnemius mass showed little change throughout all stages, whereas gastrocnemius fiber area declined steadily but rebounded in fall on the wintering grounds, where migrants become more sedentary. In general, residents are heavier birds with larger leg structures, while migrants sport longer wings and greater heart mass. Phenotypic flexibility was most prominent among residents with peaks of pectoralis, gastrocnemius, and body masses during the winter stage, when local weather is most severe. Thus, the subspecies express specific patterns of phenotypic flexibility with peaks coinciding with the stages of heightened energy demands: the winter stage for residents and the spring stages for migrants.

Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum

Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.

Environmentally driven phenotypic convergence and niche conservatism accompany speciation in hoary bats

Species that are geographically widespread may exist across environmentally heterogeneous landscapes that could influence patterns of occupation and phylogeographic structure. Previous studies have suggested that geographic range size should be positively correlated with niche breadth, allowing widespread species to sustain viable populations over diverse environmental gradients. We examined the congruence of phenotypic and phylogenetic divergence with the environmental factors that help maintain species level diversity in the geographically widespread hoary bats (Lasiurus cinereus sensu lato) across their distribution. Genetic sequences were analyzed using multiple phylogenetic and species delimitation methods, and phenotypic data were analyzed using supervised and unsupervised machine learning approaches. Spatial data from environmental, geographic, and topographic features were analyzed in a multiple regression analysis to determine their relative effect on phenotypic diversity. Ecological niches of each hoary bat species were examined in environmental space to quantify niche overlap, equivalency, and the magnitude of niche differentiation. Phylogenetic and species delimitation analyses support existence of three geographically structured species of hoary bat, each of which is phenotypically distinct. However, the Hawaiian hoary bat is morphologically more similar to the South American species than to the North American species despite a closer phylogenetic relationship to the latter. Multiple regression and niche analyses revealed higher environmental similarities between the South American and Hawaiian species. Hoary bats thus exhibit a pattern of phenotypic variation that disagrees with well-supported genetic divergences, instead indicating phenotypic convergence driven by similar environmental features and relatively conserved niches occupied in tropical latitudes.

Evaluation of tropical-temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae

PREMISE

There has been a great increase in using climatic data in phylogenetic studies over the past decades. However, compiling the high-quality spatial data needed to perform accurate climatic reconstructions is time-consuming and can result in poor geographical coverage. Therefore, researchers often resort to qualitative approximations. Our aim was to evaluate the climatic characterization of the genera of the Asian Palmate Group (AsPG) of Araliaceae as an exemplar lineage of plants showing tropical-temperate transitions.

METHODS

We compiled a curated worldwide spatial database of the AsPG genera and created five raster layers representing bioclimatic regionalizations of the world. Then, we crossed the database with the layers to climatically characterize the AsPG genera.

RESULTS

We found large disagreement in the climatic characterization of genera among regionalizations and little support for the climatic nature of the tropical-temperate distribution of the AsPG. Both results are attributed to the complexity of delimiting tropical, subtropical, and temperate climates in the world and to the distribution of the study group in regions with transitional climatic conditions.

CONCLUSIONS

The complexity in the climatic classification of this example of the tropical-temperate transitions calls for a general climatic revision of other tropical-temperate lineages. In fact, we argue that, to properly evaluate tropical-temperate transitions across the tree of life, we cannot ignore the complexity of distribution ranges.

Niche dynamics suggest ecological factors influencing migration in an insectivorous owl

Seasonal migration is a widespread phenomenon undertaken by myriad organisms, including birds. Competing hypotheses about ultimate drivers of seasonal migration in birds contrast relative resource abundances at high latitudes ("southern home hypothesis") against avoidance of winter resource scarcity ("dispersal-migration hypothesis"). However, direct tests of these competing hypotheses have been rare and heretofore limited to historical biogeographic reconstructions. Here we derive novel predictions about the dynamics of individual niches from each hypothesis and provide a framework for evaluating support for these competing hypotheses using contemporary environmental and behavioral data. Using flammulated owls (Psiloscops flammeolus) as a model, we characterized year-round occupied niche dynamics using high resolution GPS tracking and remote-sensed environmental data. We also compared occupied niche dynamics to counterfactual niches using simulated alternative non-migratory strategies. Owls' occupied mean niche was conserved between seasons whereas niche variance was generally higher during migratory periods. Simulated year-round residents in Mexico would have experienced putatively more productive niches than migrants. These findings provide ecological support for the "dispersal-migration" hypothesis wherein winter resource scarcity is the primary driver of migration rather than summer resource abundances. This article is protected by copyright. All rights reserved.

Evolutionary and Ecological Explanations for the Elevational Flexibility of Several East African Bird Species Complexes

Africa’s montane areas are broken up into several large and small units, each isolated as forest-capped “sky islands” in a “sea” of dry lowland savanna. Many elements of their biota, including montane forest birds, are shared across several disjunct mountains, yet it has been difficult to rigorously define an Afromontane forest avifauna, or determine its evolutionary relationships with the birds of the surrounding lowland forests. In order to trace the historical relationship between lowland and highland avifaunas, we review cases of species or groups of closely related species with breeding populations at different elevations, and use phylogeographic methods to explore the historical connections between such populations within the biodiversity hotspot of East Africa. The study reveals several idiosyncratic patterns, but also a prominent number of cases of gene flow between populations in southern areas, mainly around the Malawi Rift, and mountains and coastal forests to the north, close to the equator. This may reflect more continuous past distributions through northern Mozambique and coastal Tanzania, or seasonal migrations between areas with different rainfall regimes. Over time, these distributional dynamics have resulted in a higher persistence of lineages, and an accumulation of forest-dependent lineages within the Eastern Arc Mountains of Tanzania and the northern part of the coastal forest mosaic.

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.

Geographic variation in dispersal of western burrowing owl (Athene cunicularia hypugaea) populations across North America

Dispersal is one of the key elements of species’ metapopulation dynamics and, hence, influences global conservation status. Furthermore, determining the geographic variation in magnitude and direction of dispersal throughout a species’ distribution may expand our understanding of the causes of population declines in species of conservation concern. For instance, western burrowing owl (Athene cunicularia hypugaea) populations have declined at the northern and eastern edge of their breeding distribution during the 20th century. In the same period, large areas of thornscrub that did not support breeding owls were converted to irrigated agriculture in the southern edge of the subspecies’ breeding distribution in northwestern Mexico. These farmlands now support some of the highest breeding densities of owls. We tested the hypothesis that owls that colonized this recently created habitat originated from declining migratory populations from the northern portion of the subspecies’ range. We used stable isotopes 2H, 13C, and 15N in owl feathers to infer breeding dispersal patterns throughout the subspecies’ breeding range. Populations near the northern edge of the subspecies’ breeding range had immigrants that dispersed over larger distances than immigrants at low and mid latitude populations. However, agricultural populations in northwestern Mexico disrupted this latitudinal pattern, attracting owls from more distant locations. We also found immigrants originated from further distances in declining populations than increasing populations. Stable isotopes provided no evidence of contemporaneous breeding dispersal from Canadian populations to northwestern Mexico but suggest that agricultural areas in the southern edge of the subspecies’ distribution have altered the continental dispersal pattern.

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.

A tale of two seasons: The link between seasonal migration and climatic niches in passerine birds

The question of whether migratory birds track a specific climatic niche by seasonal movements has important implications for understanding the evolution of migration, the factors affecting species' distributions, and the responses of migrants to climate change. Despite much research, previous studies of bird migration have produced mixed results. However, whether migrants track climate is only one half of the question, the other being why residents remain in the same geographic range year-round. We provide a literature overview and test the hypothesis of seasonal niche tracking by evaluating seasonal climatic niche overlap across 437 migratory and resident species from eight clades of passerine birds. Seasonal climatic niches were based on a new global dataset of breeding and nonbreeding ranges. Overlap between climatic niches was quantified using ordination methods. We compared niche overlap of migratory species to two null expectations, (a) a scenario in which they do not migrate and (b) in comparison with the overlap experienced by closely related resident species, while controlling for breeding location and range size. Partly in accordance with the hypothesis of niche tracking, we found that the overlap of breeding versus nonbreeding climatic conditions in migratory species was greater than the overlap they would experience if they did not migrate. However, this was only true for migrants breeding outside the tropics and only relative to the overlap species would experience if they stayed in the breeding range year-round. In contrast to the hypothesis of niche tracking, migratory species experienced lower seasonal climatic niche overlap than resident species, with significant differences between tropical and nontropical species. Our study suggests that in seasonal nontropical environments migration away from the breeding range may serve to avoid seasonally harsh climate; however, different factors may drive seasonal movements in the climatically more stable tropical regions.

Agriculture creates subtle genetic structure among migratory and nonmigratory populations of burrowing owls throughout North America

Population structure across a species distribution primarily reflects historical, ecological, and evolutionary processes. However, large-scale contemporaneous changes in land use have the potential to create changes in habitat quality and thereby cause changes in gene flow, population structure, and distributions. As such, land-use changes in one portion of a species range may explain declines in other portions of their range. For example, many burrowing owl populations have declined or become extirpated near the northern edge of the species' breeding distribution during the second half of the 20th century. In the same period, large extensions of thornscrub were converted to irrigated agriculture in northwestern Mexico. These irrigated areas may now support the highest densities of burrowing owls in North America. We tested the hypothesis that burrowing owls that colonized this recently created owl habitat in northwestern Mexico originated from declining migratory populations from the northern portion of the species' range (migration-driven breeding dispersal whereby long-distance migrants from Canada and the United States became year-round residents in the newly created irrigated agriculture areas in Mexico). We used 10 novel microsatellite markers to genotype 1,560 owls from 36 study locations in Canada, Mexico, and the United States. We found that burrowing owl populations are practically panmictic throughout the entire North American breeding range. However, an analysis of molecular variance provided some evidence that burrowing owl populations in northwestern Mexico and Canada together are more genetically differentiated from the rest of the populations in the breeding range, lending some support to our migration-driven breeding dispersal hypothesis. We found evidence of subtle genetic differentiation associated with irrigated agricultural areas in southern Sonora and Sinaloa in northwestern Mexico. Our results suggest that land use can produce location-specific population dynamics leading to subtle genetic structure even in the absence of dispersal barriers.

Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)

The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.

Simulation-based reconstruction of global bird migration over the past 50,000 years

Migration is a widespread response of birds to seasonally varying climates. As seasonality is particularly pronounced during interglacial periods, this raises the question of the significance of bird migration during past periods with different patterns of seasonality. Here, we apply a mechanistic model to climate reconstructions to simulate the past 50,000 years of bird migration worldwide, a period encompassing the transition between the last glacial period and the current interglacial. Our results indicate that bird migration was also a prevalent phenomenon during the last ice age, almost as much as today, suggesting that it has been continually important throughout the glacial cycles of recent Earth history. We find however regional variations, with increasing migratory activity in the Americas, which is not mirrored in the Old World. These results highlight the strong flexibility of the global bird migration system and offer a baseline in the context of on-going anthropogenic climate change.

It is unclear whether bird migration patterns are restricted to interglacial periods or are maintained during glacial maxima. Somveille et al. apply a global migration simulation model to climate reconstruction to show that the prevalence of this phenomenon has likely been largely maintained up to 50,000 years ago.

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae)

The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles' only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical-Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent 'reverse colonization' of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.

Metrics matter: the effect of parasite richness, intensity and prevalence on the evolution of host migration

Parasites have long been thought to influence the evolution of migration, but precisely determining the conditions under which this occurs by quantifying costs of infection remains a challenge. Here we developed a model that demonstrates how the metric used to describe infection (richness/diversity, prevalence or intensity) shapes the prediction of whether migration will evolve. The model shows that predictions based on minimizing richness yield opposite results compared to those based on minimizing prevalence, with migration only selected for when minimizing prevalence. Consistent with these findings, empirical studies that measure parasite diversity typically find that migrants are worse off than residents, while those measuring prevalence or intensity find the opposite. Our own empirical analysis of fish parasite data finds that migrants (of all types) have higher parasite richness than residents, but with no significant difference in either prevalence or intensity.

A long winter for the Red Queen: rethinking the evolution of seasonal migration

This paper advances an hypothesis that the primary adaptive driver of seasonal migration is maintenance of site fidelity to familiar breeding locations. We argue that seasonal migration is therefore principally an adaptation for geographic persistence when confronted with seasonality - analogous to hibernation, freeze tolerance, or other organismal adaptations to cyclically fluctuating environments. These ideas stand in contrast to traditional views that bird migration evolved as an adaptive dispersal strategy for exploiting new breeding areas and avoiding competitors. Our synthesis is supported by a large body of research on avian breeding biology that demonstrates the reproductive benefits of breeding-site fidelity. Conceptualizing migration as an adaptation for persistence places new emphasis on understanding the evolutionary trade-offs between migratory behaviour and other adaptations to fluctuating environments both within and across species. Seasonality-induced departures from breeding areas, coupled with the reproductive benefits of maintaining breeding-site fidelity, also provide a mechanism for explaining the evolution of migration that is agnostic to the geographic origin of migratory lineages (i.e. temperate or tropical). Thus, our framework reconciles much of the conflict in previous research on the historical biogeography of migratory species. Although migratory behaviour and geographic range change fluidly and rapidly in many populations, we argue that the loss of plasticity for migration via canalization is an overlooked aspect of the evolutionary dynamics of migration and helps explain the idiosyncratic distributions and migratory routes of long-distance migrants. Our synthesis, which revolves around the insight that migratory organisms travel long distances simply to stay in the same place, provides a necessary evolutionary context for understanding historical biogeographic patterns in migratory lineages as well as the ecological dynamics of migratory connectivity between breeding and non-breeding locations.

Population trends in Vermivora warblers are linked to strong migratory connectivity

Migratory species can experience limiting factors at different locations and during different periods of their annual cycle. In migratory birds, these factors may even occur in different hemispheres. Therefore, identifying the distribution of populations throughout their annual cycle (i.e., migratory connectivity) can reveal the complex ecological and evolutionary relationships that link species and ecosystems across the globe and illuminate where and how limiting factors influence population trends. A growing body of literature continues to identify species that exhibit weak connectivity wherein individuals from distinct breeding areas co-occur during the nonbreeding period. A detailed account of a broadly distributed species exhibiting strong migratory connectivity in which nonbreeding isolation of populations is associated with differential population trends remains undescribed. Here, we present a range-wide assessment of the nonbreeding distribution and migratory connectivity of two broadly dispersed Nearctic-Neotropical migratory songbirds. We used geolocators to track the movements of 70 Vermivora warblers from sites spanning their breeding distribution in eastern North America and identified links between breeding populations and nonbreeding areas. Unlike blue-winged warblers (Vermivora cyanoptera), breeding populations of golden-winged warblers (Vermivora chrysoptera) exhibited strong migratory connectivity, which was associated with historical trends in breeding populations: stable for populations that winter in Central America and declining for those that winter in northern South America.

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape. Widespread species (occurring on both islands and continents), and those that are migratory, exhibit wing morphologies better adapted to long-distance flight compared with sedentary continental or insular forms. Habitat preferences also strongly predict wing form, with species that occur in canopies and/or areas of sparse vegetation possessing dispersive morphologies. By contrast, we found no significant differences in diversification rates among either the migratory or habitat classifications, but species distributed in island settings diversify at higher rates than those found on continents. This latter finding may reflect the elevated dispersal capabilities of widespread taxa, facilitating the radiation of these lineages across insular areas. However, as the correlations between wing morphology and diversification rates were consistently weak throughout our dataset, this suggests that historical patterns of diversification are not particularly well reflected by present-day wing morphology.

Glaciation as a migratory switch

Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents. A smaller percentage of short-distance migrants (27%) experienced altered migratory behavior at the LGM, although the ranges of all species were shifted southward, as traditionally envisioned. We suggest that many species oscillate between sedentary and migratory strategies with each glacial cycle acting as an adaptive switch. Thus, range shifts occur more frequently than speciation events and are inadequately depicted by phylogenetic reconstructions. We suggest that reconstructing the evolutionary history of traits, such as migratory behavior, is best served by using ranges at glacial maxima. A phylogeny of warblers strongly predicted LGM, but not present distributions, and suggested that migration was re-expressed from three tropical centers of warbler diversity. Understanding of evolutionary history will be improved when reconstructions use distributions relevant to the time of character transitions.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino‐Himalayan Mountains or these mountains and Central Asia–Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid‐Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo‐/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials—contrary to the usual view that glacial periods resulted mainly in fragmentations.

The conquering of North America: dated phylogenetic and biogeographic inference of migratory behavior in bee hummingbirds

BACKGROUND

Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods.

RESULTS

All phylogenetic analyses confirmed monophyly of the Mellisugini and the inclusion of Atthis, Calothorax, Doricha, Eulidia, Mellisuga, Microstilbon, Myrmia, Tilmatura, and Thaumastura. Mellisugini consists of two clades: (1) South American species (including Tilmatura dupontii), and (2) species distributed in North and Central America and the Caribbean islands. The second clade consists of four subclades: Mexican (Calothorax, Doricha) and Caribbean (Archilochus, Calliphlox, Mellisuga) sheartails, Calypte, and Selasphorus (incl. Atthis). Coalescent-based dating places the origin of the Mellisugini in the mid-to-late Miocene, with crown ages of most subclades in the early Pliocene, and subsequent species splits in the Pleistocene. Bee hummingbirds reached western North America by the end of the Miocene and the ancestral mellisuginid (bee hummingbirds) was reconstructed as sedentary, with four independent gains of migratory behavior during the evolution of the Mellisugini.

CONCLUSIONS

Early colonization of North America and subsequent evolution of migration best explained biogeographic and diversification patterns within the Mellisugini. The repeated evolution of long-distance migration by different lineages was critical for the colonization of North America, contributing to the radiation of bee hummingbirds. Comparative phylogeography is needed to test whether the repeated evolution of migration resulted from northward expansion of southern sedentary populations.

Behavioral and physiological traits of migrant and resident White-crowned Sparrows: a common garden approach

To accommodate a migratory life history, migrants express a greater number of physiological and behavioral stages per annum than residents and are thus considered to have higher finite state diversity (FSD). To investigate the physiological mechanisms and constraints associated with migration, direct comparison of two subspecies of White-crowned Sparrow - migrant, Zonotrichia leucophrys gambelii and resident, Z.l.nuttalli - were made under common garden conditions of photoperiod and housing, as birds progressed from winter through the vernal life history stages. We tested the hypothesis that migrants (higher FSD) respond differently than residents (lower FSD) to the initial predictive cue, photoperiod, to initiate and integrate the progression of vernal stages of prenuptial molt, migration and development of breeding. If differences in vernal phenology were noted then the basis for the distinctions was considered genetic. Results: 1. residents had a lower threshold to vernal photoperiod with elevations of plasma androgen, growth and development of reproductive structures preceeding migrants, 2. only migrants displayed prenuptial molt, preparations for migration and migratory restlessness, 3. neither baseline nor stress-induced plasma corticosterone differed across subspecies suggesting energetic demands of the common garden were insufficient to induce a differential adrenocortical response in either subspecies highlighting the impact of environmental conditions on corticosterone secretion. Thus, in a common garden, Z.l.gambelii responds differently to the initial predictive cue, photoperiod, to initiate and execute the vernal stages of molt, migration and development of breeding in comparisons to the shared stage of breeding with Z.l.nuttalli confirming a genetic basis for the subspecies differences.

Clock gene polymorphism, migratory behaviour and geographic distribution: a comparative study of trans-Saharan migratory birds

Migratory behaviour is controlled by endogenous circannual rhythms that are synchronized by external cues, such as photoperiod. Investigations on the genetic basis of circannual rhythmicity in vertebrates have highlighted that variation at candidate 'circadian clock' genes may play a major role in regulating photoperiodic responses and timing of life cycle events, such as reproduction and migration. In this comparative study of 23 trans-Saharan migratory bird species, we investigated the relationships between species-level genetic variation at two candidate genes, Clock and Adcyap1, and species' traits related to migration and geographic distribution, including timing of spring migration across the Mediterranean Sea, migration distance and breeding latitude. Consistently with previous evidence showing latitudinal clines in 'circadian clock' genotype frequencies, Clock allele size increased with breeding latitude across species. However, early- and late-migrating species had similar Clock allele size. Species migrating over longer distances, showing delayed spring migration and smaller phenotypic variance in spring migration timing, had significantly reduced Clock (but not Adcyap1) gene diversity. Phylogenetic confirmatory path analysis suggested that migration date and distance were the most important variables directly affecting Clock gene diversity. Hence, our study supports the hypothesis that Clock allele size increases poleward as a consequence of adaptation to the photoperiodic regime of the breeding areas. Moreover, we show that long-distance migration is associated with lower Clock diversity, coherently with strong stabilizing selection acting on timing of life cycle events in long-distance migratory species, likely resulting from the time constraints imposed by late spring migration.

Minimal effects of latitude on present-day speciation rates in New World birds

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.

Departures from the Energy-Biodiversity Relationship in South African Passerines: Are the Legacies of Past Climates Mediated by Behavioral Constraints on Dispersal?

Legacies of paleoclimates in contemporary biodiversity patterns have mostly been investigated with global datasets, or with weakly dispersive organisms, and as a consequence been interpreted in terms of geographical or physical constraints. If paleoclimatic legacies also occurred at the regional scale in the distributions of vagile organisms within biomes, they would rather suggest behavioral constraints on dispersal, i.e., philopatric syndromes. We examined 1) the residuals of the regression between contemporary energy and passerine species richness in South African biomes and 2) phylogenetic dispersion of passerine assemblages, using occupancy models and quarter-degree resolution citizen science data. We found a northeast to southwest gradient within mesic biomes congruent with the location of Quaternary mesic refugia, overall suggesting that as distance from refugia increased, more clades were lacking from local assemblages. A similar but weaker pattern was detected in the arid Karoo Biomes. In mobile organisms such as birds, behavioral constraints on dispersal appear strong enough to influence species distributions thousands of years after historical range contractions.

Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes)

Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple nonbreeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited. Here, using data from a globally distributed group of corvoid birds in concordance with state-dependent speciation and extinction models, we suggest that pair breeding is associated with elevated speciation rates. Estimates of transition between breeding systems imply that cooperative lineages frequently evolve biparental care, whereas pair breeders rarely become cooperative. We further highlight that these groups have differences in their spatial distributions, with pair breeders overrepresented on islands, and cooperative breeders mainly found on continents. Finally, we find that speciation rates appear to be significantly higher on islands compared to continents. These results imply that the transition from cooperative breeding to pair breeding was likely a significant contributing factor facilitating dispersal across tropical archipelagos, and subsequent world-wide phylogenetic expansion among the core Corvoidea.

Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus)

Todiramphus chloris is the most widely distributed of the Pacific's 'great speciators'. Its 50 subspecies constitute a species complex that is distributed over 16 000 km from the Red Sea to Polynesia. We present, to our knowledge, the first comprehensive molecular phylogeny of this enigmatic radiation of kingfishers. Ten Pacific Todiramphus species are embedded within the T. chloris complex, rendering it paraphyletic. Among these is a radiation of five species from the remote islands of Eastern Polynesian, as well as the widespread migratory taxon, Todiramphus sanctus. Our results offer strong support that Pacific Todiramphus, including T. chloris, underwent an extensive range expansion and diversification less than 1 Ma. Multiple instances of secondary sympatry have accumulated in this group, despite its recent origin, including on Australia and oceanic islands in Palau, Vanuatu and the Solomon Islands. Significant ecomorphological and behavioural differences exist between secondarily sympatric lineages, which suggest that pre-mating isolating mechanisms were achieved rapidly during diversification. We found evidence for complex biogeographic patterns, including a novel phylogeographic break in the eastern Solomon Islands that separates a Northern Melanesian clade from Polynesian taxa. In light of our results, we discuss systematic relationships of Todiramphus and propose an updated taxonomy. This paper contributes to our understanding of avian diversification and assembly on islands, and to the systematics of a classically polytypic species complex.