Reconstructing the avian tree of life has become one of the major goals in ornithology. The use of genomic tools seemed a promising approach to reach this goal, but, instead, phylogenetic analyses of large numbers of genes uncovered high levels of incongruence between the resulting gene trees. This incongruence can be caused by several biological processes, such as recombination, hybridization, and rapid speciation (which can lead to incomplete lineage sorting). These processes directly or indirectly amount to deviations from tree-like patterns, thereby thwarting the use of phylogenetic trees. Phylogenetic networks provide an ideal tool to deal with these difficulties. We illustrate the usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches. With the increasing amount of genomic data in avian phylogenetic studies, capturing the evolutionary history of a set of taxa in a phylogenetic tree will become increasingly difficult. Moreover, given the widespread occurrence of hybridization and the numerous adaptive radiations in birds, phylogenetic networks provide a powerful tool to display and analyse the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

The study of feather-degrading microorganisms in avian plumage is steadily growing, but it is still a poorly understood field. Feather-degrading microorganisms were first isolated from chicken feathers in 1992, and their presence in wild birds was first described in 1997. The bulk of research in this area has focused on the possible selection pressures generated by these organisms. Yet we still lack detailed knowledge about the pattern of distribution among species of birds, ecological associations of the birds and feather-degrading microbes, and the effects of these bacteria and fungi on live wild birds. We sampled 3,548 birds representing 154 species for a group of 3 closely related bacilli that are well known to degrade feathers. We found these bacilli to be widespread among birds, occurring in the plumage of 39% of sampled individuals. Furthermore, these bacteria occur in most, if not all, avian taxa at similar frequencies, though variation exists. We found that ground-foraging species had a higher prevalence of feather-degrading bacilli, and tree-probing and nectivorous species had a lower prevalence. Additionally, fly-catching and foliage-gleaning birds were more likely to have feather-degrading bacilli than tree-probing species. Furthermore, the presence of feather-degrading bacilli, but not the abundance of bacteria in general, was correlated with our measure of plumage condition. A correlation cannot separate cause from effect, but it suggests that the presence of these bacteria is related to degradation of feathers in wild birds. This relationship implies that these bacteria may indeed constitute an important selection pressure that broadly influences the evolution of color, timing of molt, and behaviors such as preening and other maintenance activities in birds.

The Willet (Tringa semipalmata; Scolopacidae) is composed of 2 morphologically and vocally distinct subspecies with broadly disjunct breeding distributions in North America. Nominate T. s. semipalmata breeds in coastal salt and brackish marshes along the Atlantic and Gulf coasts of eastern North America and the West Indies, and T. s. inornata breeds in wet grasslands and prairies in the northwestern interior of North America. To assess divergence and test for hybridization between the 2 subspecies, we sampled breeding and wintering populations and collected morphological data, mitochondrial DNA sequences from the ND2 locus, and nuclear DNA sequences from genomic libraries enriched for ultraconserved elements (UCEs). Mitochondrial haplotypes were reciprocally monophyletic between the 2 subspecies and indicated divergence approximately 700,000 yr ago. The UCE dataset included 4,635 loci containing 19,322 single nucleotide polymorphisms (SNPs), and, based on these data, individuals clustered by subspecies with no evidence of admixture between them and no substructure within subspecies. We identified 42 nuclear loci that contained SNPs fixed for alternate alleles between the 2 subspecies. Of the 42 loci with fixed differences, a statistically disproportional 17 were Z-linked, indicating a role for sexual selection in the divergence of the 2 subspecies. Genetic, morphological, ecological, and behavioral differences suggest that the 2 Willet subspecies may merit treatment as separate species. Further studies are needed to determine the presence of pre- or post-mating reproductive isolation.

Neogene fossils of Old World vultures (Aegypiinae and Gypaetinae) are known from both Old World and New World records. There are no extant Old World vultures in the Americas today, although a large diversity of Gypaetinae is known from Miocene to late Pleistocene records. Despite a comparatively large number of North American gypaetine fossils, complete specimens have rarely been reported from Eurasia and Africa. We describe the exceptional skeleton of a new gypaetine vulture from the late Miocene deposits of the Linxia Basin in northwestern China. The specimen is the oldest record of Gypaetinae from Eurasia or Africa. A reexamination of the geographic and temporal distribution of most Old World vultures from Neogene deposits indicates a diverse radiation, coincident with early- to mid-Miocene grassland expansion for Gypaetinae. Although the diversification of Aegypiinae has been linked to the transition from C₃ to C₄ grassland, Gypaetinae diversification predates that transition in both North America and Asia. A shift in the known latitudinal distribution is also noted. Neogene records of Old World vultures are found primarily in mid- and high-latitude regions of North America and Eurasia as well as in the middle and low latitudes of Eurasia and Africa. With very few records in the middle to late Miocene, a latitudinal distribution similar to that of extant species is first seen in the early Pliocene. The new fossil provides further temporal constraints on avian subclade diversification. It is also consistent with an emerging pattern of profound recent shifts in avian diversity and distribution more generally.

Vast improvements in sequencing technology have made it practical to simultaneously sequence millions of nucleotides distributed across the genome, opening the door for genomic studies in virtually any species. Ornithological research stands to benefit in three substantial ways. First, genomic methods enhance our ability to parse and simultaneously analyze both neutral and non-neutral genomic regions, thus providing insight into adaptive evolution and divergence. Second, the sheer quantity of sequence data generated by current sequencing platforms allows increased precision and resolution in analyses. Third, high-throughput sequencing can benefit applications that focus on a small number of loci that are otherwise prohibitively expensive, time-consuming, and technically difficult using traditional sequencing methods. These advances have improved our ability to understand evolutionary processes like speciation and local adaptation, but they also offer many practical applications in the fields of population ecology, migration tracking, conservation planning, diet analyses, and disease ecology. This review provides a guide for field ornithologists interested in incorporating genomic approaches into their research program, with an emphasis on techniques related to ecology and conservation. We present a general overview of contemporary genomic approaches and methods, as well as important considerations when selecting a genomic technique. We also discuss research questions that are likely to benefit from utilizing high-throughput sequencing instruments, highlighting select examples from recent avian studies.

For birds, a migratory lifestyle confers several benefits including avoidance of harsh winters and increased access to food resources during the breeding season. However, migration is energetically costly and elevates oxidative stress, which may contribute to increased mortality during migration. Oxidative stress is known to shorten telomeres, which are protective DNA regions on the ends of chromosomes. Thus, one consequence of migration may be accelerated telomere attrition. A migratory lifestyle may also increase telomere shortening via reduced investment into self-maintenance, as high mortality during migration may cause migrants to invest more in reproduction than residents. We therefore hypothesized that greater telomere attrition may reflect a long-term cost of a migratory life history strategy. We predicted that, among individuals of the same age, migrants would have shorter telomeres as compared to residents. We compared first-year individuals in an overwintering population of Slate-colored Dark-eyed Juncos (Junco hyemalis) that included both a migratory (J. h. hyemalis) and resident (J. h. carolinensis) subspecies in western Virginia. As predicted, first-year migrants had shorter telomeres than first-year residents. Since members of both subspecies experienced the same winter conditions and had not yet bred, differences in telomere lengths are likely due to migration-related costs as this was the only energetically expensive life history stage that differed between subspecies. Telomere length differences between subspecies could also be due to differences in initial telomere lengths or loss during growth, which could reflect relative investment into self-maintenance. These results are consistent with the idea that accelerated telomere shortening is a potential cost of a migratory life history strategy. This consequence could be the result of direct metabolic costs of migration and/or a life history strategy that places less emphasis on self-maintenance.

The reproductive biology of living birds differs dramatically from that of other extant vertebrates. Although some attributes of modern avian reproduction had their origin within theropod dinosaurs like oviraptors and troodontids, even the most derived non-avian theropods lack key features of modern birds. We review the current knowledge of reproduction in Mesozoic birds and 3 lines of evidence that contribute to our understanding of the evolution of the modern avian reproductive mode: (1) efforts to define the ancestral reproductive condition on the basis of extant birds, (2) the fossil record of non-avian theropod dinosaurs, and (3) the fossil record of reproduction in primitive Mesozoic birds (e.g., Enantiornithes).

The fossil evidence from Mesozoic birds and non-avian theropods suggests that reproduction passed through 5 stages from basal theropods to neornithines: (1) pre-maniraptoran theropods, (2) oviraptor-grade maniraptorans, (3) troodontid-grade paravians, (4) Enantiornithes, and (5) basal Neornithes. Major changes occurred incrementally in egg size, shape, and microstructure; in nest form; in incubation method; and in parental care. Reproduction in troodontid theropods concurs with this clade representing the sister taxon to birds. Reproduction in enantiornithine birds included sequential ovulation from a single ovary and oviduct, eggs planted upright within sediments, and incubation by a combination of sediment and attendant adult or eggs fully buried with superprecocial young. Incubation modes of derived non-avian theropods and enantiornithines may have favored paternal care.

Significant changes between enantiornithines and neornithines include an additional increase in relative egg size and sediment-free incubation. The latter permitted greater adult–egg contact and likely more efficient incubation. Associated changes also included improved egg shape, egg rotation, and chalazae—the albumin chords that suspend the yolk and facilitate proper embryonic development during rotation. Neornithes are the only Mesozoic clade of Dinosauria to nest completely free of sediment, and this may have played a crucial role in their surviving the K–Pg mass extinction event.

Seasonal fluctuations in food availability can affect diets of consumers, which in turn may influence the physiological state of individuals and shape intra- and inter-specific patterns of resource use. High-elevation ecosystems often exhibit a pronounced seasonal “pulse” in productivity, although few studies document how resource use and energetic condition by avian consumers change in relation to food-resource availability in these ecosystems. We tested the hypothesis that seasonal increases (pulses) in food resources in high-elevation sagebrush ecosystems result in 2 changes after the pulse, relative to the before-pulse period: (1) reduced diet breadth of, and overlap between, 2 sympatric sparrow species; and (2) enhanced energetic condition in both species. We tracked breeding-season diets using stable isotopes and energetic condition using plasma metabolites of Brewer's Sparrows (Spizella breweri), Vesper Sparrows (Pooecetes gramineus), and their food resources during 2011, and of only Brewer's Sparrows and their food resources during 2013. We quantify diet breadth and overlap between both species, along with coincident physiological consequences of temporal changes in resource use. After invertebrate biomass increased following periods of rainfall in 2011, dietary breadth decreased by 35% in Brewer's Sparrows and by 48% in Vesper Sparrows, while dietary overlap decreased by 88%. Energetic condition of both species increased when dietary overlap was lower and diet breadth decreased, after the rapid rise of food-resource availability. However, energetic condition of Brewer's Sparrows remained constant in 2013, a year with low precipitation and lack of a strong pulse in food resources, even though the species' dietary breadth again decreased that year. Our results indicate that diet breadth and overlap in these sparrow species inhabiting sagebrush ecosystems generally varied as predicted in relation to intra- and interannual changes in food resources, and this difference in diet was associated with improved energetic condition of sparrows at least in one year.

Populations that have experienced long periods of geographic isolation will diverge over time. The application of high-throughput sequencing technologies to study the genomes of related taxa now allows us to quantify, at a fine scale, the consequences of this divergence across the genome. Throughout a number of studies, a notable pattern has emerged. In many cases, estimates of differentiation across the genome are strongly heterogeneous; however, the evolutionary processes driving this striking pattern are still unclear. Here we quantified genomic variation across several groups within the Yellow-rumped Warbler species complex (Setophaga spp.), a group of North and Central American wood warblers. We showed that genomic variation is highly heterogeneous between some taxa and that these regions of high differentiation are relatively small compared to those in other study systems. We found that the clusters of highly differentiated markers between taxa occur in gene-rich regions of the genome and exhibit low within-population diversity. We suggest these patterns are consistent with selection, shaping genomic divergence in similar genomic regions across the different populations. Our study also confirms previous results relying on fewer genetic markers that several of the phenotypically distinct groups in the system are also genomically highly differentiated, likely to the point of full species status.

Physical characteristics of nest sites are thought to influence their use by birds and the outcome of breeding attempts. The presence of preexisting nesting structures can also be an important factor influencing reuse patterns and reproductive success. We examined the relationships between nest-site physical characteristics, patterns of nest reuse, and reproductive output in Rough-legged Hawks (Buteo lagopus) breeding in the Canadian High Arctic. Because this species is a rodent specialist, we also examined the effect of variation in lemming density, their primary prey, on reproductive output. We monitored 109 nesting attempts over a 9 yr period and sampled physical characteristics of 87 known nesting sites in 53 territories on Bylot Island, Nunavut, Canada. The probability that a nest was used by a breeding pair increased with the distance to the nearest breeding conspecific, for nests sheltered by an overhang, and with lemming density. Hawk nests inaccessible to foxes and facing away from the north were associated with high reproductive success. Reproductive success was also positively related to summer lemming density and negatively related to rainfall. Our results suggest that nest-site physical characteristics that offer a favorable microclimate and protection from weather and predators provide the highest-quality sites. We observed a high level of reuse of preexisting nests and previously occupied territories, which is indicative of site fidelity by individuals. Hawks that bred in a newly built nest had similar clutch size and hatching date compared to those that used preexisting nests, which suggests that building a new nest entailed no short-term reproductive costs. Reproductive success was nonetheless reduced for birds breeding in new nests located in newly occupied territories compared to those nesting in previously occupied ones, which suggests that a high proportion of pairs in new territories were young birds or that some of these sites were of low quality.

Supplementary materials (SM) are a relatively new addition to published research. The volume of SM has been increasing over time for many journals, and in a few cases SM appear to be replacing appendices. We review the costs and benefits of SM to authors, reviewers, production teams, and readers. We conclude that SM can have value but that they place additional demands on all participants. Given the difficulty of recruiting reviewers for journal submissions and the added effort required by all participants, this may lead to incomplete vetting that may undermine the reliability of SM in some instances.

Birds that winter in cold northern climates experience harsh conditions, including reduced food availability and increased energy demands. In raptors, the ability to forage and maintain body condition may be related to age (hunting experience) or the ability to defend good-quality territories (dominance). We examined the effects of age and sex on body condition and various sources of mortality in wintering Snowy Owls (Bubo scandiacus) on the Canadian prairies. Because of reversed sexual size dimorphism, we predicted that females, the dominant sex, would be in better condition than males and that adults would be in better condition than juveniles. Consistent with these predictions, data from 537 live Snowy Owls trapped over 18 winter field seasons showed that adults were heavier than juveniles for a given body size and carried more fat reserves. We found that 56% of males lacked furcular and wing-pit fat, whereas only 31% of females lacked such fat; and females, but not males, tended to put on fat during the winter months. A comparison of the sex ratio of starving Snowy Owls turned in to rehabilitation centers (63% male) and that of living Snowy Owls observed in the wild (45% male) showed a male bias in starving and diseased individuals. Although most of the wild-trapped birds were above the starvation threshold, the proximate mechanisms by which sex-biased competitive dominance is manifested in differences in body condition and survival warrant further study.

We examined social behavior and documented cooperative breeding in Kalij Pheasants (Lophura leucomelanos) in an introduced population in Hawaii, only the third reported instance of cooperative breeding in Phasianidae. Birds in 31 distinct social groups occupied overlapping home ranges, and group composition remained relatively constant over the 3-yr study period. Each social group contained 1 breeding female and 1 to 6 males. One male was socially dominant in each multiple-male group. Age was the only factor found to determine within-group dominance, suggesting that subordinate males may gain dominance and breeding status by staying in the group. All adults exhibited cooperative behavior, including caring for chicks, agonistic behaviors against conspecific intruders, and vigilance against predators. Average population density was high (3.21 residents per ha), which may lead to habitat saturation in this population. The adult sex ratio was male-biased, with an average M:F ratio of 2.1:1.0. Genetic sex identification of egg samples revealed unbiased primary and secondary sex ratios, which suggests that the bias in adult sex ratio may be caused by differential survival and/or dispersal. Paternity analysis of 13 broods revealed that ~68% of offspring were fathered by the dominant male of the social group, while ~17% were fathered by subordinate males in the group, suggesting that helpers gained some direct benefit by sharing reproduction. We suggest that cooperative breeding may be more common in precocial species than conventionally recognized.

Migrating birds make strategic decisions at multiple temporal and spatial scales. They must select flight altitudes, speeds, and orientations in order to maintain preferred directions of movement and to minimize energy expenditure and risk. Spring flights follow a rapid phenology, but how this rapid transit translates to in-flight decisions is not clear. We described flight strategies of nocturnally migrating landbirds using 6 weather surveillance radars during spring (2013–2015) and fall (2013–2014) migratory periods in the eastern United States to investigate seasonal decision-making patterns and how climate change may influence these trends. During spring, we found groundspeed and airspeed of migrants to be significantly higher than those of fall migrants; compensation for wind drift was also significantly greater during spring. Our results indicate that birds make more rapid and precise flights in spring that are only partially explained by meteorological phenomena. Future applications at greater spatial scales will allow direct comparisons of in-flight behaviors with predictions from migration theory.

Temperature and water availability affect the survival, reproductive success, and behavior of all animals; thus, traits that influence thermoregulation and water balance should be under strong selection. Avian bills can dissipate excess body heat through convection and radiation. We hypothesized that in hot, dry locations, bill size would be selected for its value in thermoregulation: males with larger bills would shed excess heat more efficiently, allowing greater activity levels during thermally challenging periods of the breeding season. We predicted that thermoregulatory challenges would require Melospiza melodia atlantica, which breeds in hot, dry sand dunes, to trade off between behaviors associated with breeding (song output) and behaviors related to thermoregulation, and that in the hot environment occupied by our study population, males with larger bills would sing at higher rates. We captured, measured, and marked individual birds and then observed singing behavior, microclimate, and microhabitat use to assess thermoregulatory challenges. Ambient weather indicated thermally challenging conditions, and birds displayed thermoregulatory behaviors, including reducing their song rates at higher temperatures. Birds with larger bills sang at higher rates than birds with smaller bills, and males with the largest bills in the population sang almost twice as many songs per minute than birds with the smallest bills. These results are consistent with the hypothesis that climate influences selection on the bill as a thermoregulatory organ.

Transparency regarding methods, data, and results is essential to scientific progress. However, in ecological, evolutionary, and ornithological research, transparency is often insufficient, and the distribution of published results may often be biased. To address this issue, we advocate adoption of editorial policies that explicitly promote transparency. We hope that The Auk, as a leading ornithological journal, will lead the way in promoting transparency in the study of birds.

The evolution of morphology in a population reflects several factors, including the influence of environmental variability on natural selection. We estimated natural selection on, and heritability of, 4 individual morphological traits (bill length, bill depth, flipper length, and foot length) and 2 multivariate morphological traits in adult Magellanic Penguins (Spheniscus magellanicus) at Punta Tombo, Argentina, from 1983 to 2010. We estimated heritability of morphology with parent–offspring regression and animal models, conditioning on sex because the species is sexually dimorphic. For the analysis of selection on each trait, we estimated both linear and quadratic selection gradients, based on the number of fledglings produced, for breeding males and females in each year. Estimates from animal models indicated that all 6 traits were heritable; in parent–offspring regressions, corresponding heritabilities were significantly higher in sons than in daughters in 100% of tests. Over 28 yr, we detected no selection in 21 yr for males and in 21 yr for females. For the years in which we did detect selection, the direction and intensity of selection on traits varied, being especially variable for females. We detected selection on primarily multivariate body size but also on male bill sizes and female bill and foot lengths. Selection on male flipper and foot lengths and on female bill depth was detectable only in relation to selection on body size. When there was selection in males, selection on body and bill sizes was mainly toward larger sizes and occurred in 4 of 6 yr with high chick starvation. The absence of detectable selection on morphology in most years suggests that it is not tightly linked to fitness and that the dynamic environment where Magellanic Penguins live helps maintain morphological variation. The temporal variability in selection likely fosters stability of morphology through time, a pattern that might not be evident in short-term studies.