Out of Gondwanaland; the evolutionary history of cooperative breeding and social behaviour among crows, magpies, jays and allies

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri)

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

Social behavior mediates the use of social and personal information in wild jays

The factors favoring the evolution of certain cognitive abilities in animals remain unclear. Social learning is a cognitive ability that reduces the cost of acquiring personal information and forms the foundation for cultural behavior. Theory predicts the evolutionary pressures to evolve social learning should be greater in more social species. However, research testing this theory has primarily occurred in captivity, where artificial environments can affect performance and yield conflicting results. We compared the use of social and personal information, and the social learning mechanisms used by wild, asocial California scrub-jays and social Mexican jays. We trained demonstrators to solve one door on a multi-door task, then measured the behavior of naïve conspecifics towards the task. If social learning occurs, observations of demonstrators will change the rate that naïve individuals interact with each door. We found both species socially learned, though personal information had a much greater effect on behavior in the asocial species while social information was more important for the social species. Additionally, both species used social information to avoid, rather than copy, conspecifics. Our findings demonstrate that while complex social group structures may be unnecessary for the evolution of social learning, it does affect the use of social versus personal information.

Maternal feeding benefits of allomaternal care in black-and-white colobus (Colobus guereza)

Caring for infants involves lactation, protection, provisioning, and carrying-all energetically taxing states for primate mothers. Holding and carrying clinging infants often constrains mothers from moving and traveling, potentially reducing their food and energy intake; however, when separated from its mother an infant is at risk of predation. This separation therefore requires that mothers be vigilant, further deterring them from feeding. Allomaternal care (AMC) is hypothesized to allow mothers to safely detach from their infants to feed, permitting them to increase energy intake, which is particularly needed for lactation. We examined the nutritional benefits of AMC in black-and-white colobus monkeys (Colobus guereza) by estimating energy intake by lactating mothers during AMC versus non-AMC. We studied seven mother-infant dyads in three groups of C. guereza during six months in Kibale National Park, Uganda. Immature group members handled infants more often than adults, and females handled infants more often than males. An infant's distance to its mother and its nearest neighbor's age and sex best predicted the occurrence of AMC. Lactating mothers fed more often, fed and rested for longer durations, and consumed more metabolizable energy during AMC compared to when they were caring for their infants. These results demonstrate that AMC in C. guereza provides mothers with feeding opportunities that increase their energy intake.

Extended parenting and the evolution of cognition

Traditional attempts to understand the evolution of human cognition compare humans with other primates. This research showed that relative brain size covaries with cognitive skills, while adaptations that buffer the developmental and energetic costs of large brains (e.g. allomaternal care), and ecological or social benefits of cognitive abilities, are critical for their evolution. To understand the drivers of cognitive adaptations, it is profitable to consider distant lineages with convergently evolved cognitions. Here, we examine the facilitators of cognitive evolution in corvid birds, where some species display cultural learning, with an emphasis on family life. We propose that extended parenting (protracted parent-offspring association) is pivotal in the evolution of cognition: it combines critical life-history, social and ecological conditions allowing for the development and maintenance of cognitive skillsets that confer fitness benefits to individuals. This novel hypothesis complements the extended childhood idea by considering the parents' role in juvenile development. Using phylogenetic comparative analyses, we show that corvids have larger body sizes, longer development times, extended parenting and larger relative brain sizes than other passerines. Case studies from two corvid species with different ecologies and social systems highlight the critical role of life-history features on juveniles' cognitive development: extended parenting provides a safe haven, access to tolerant role models, reliable learning opportunities and food, resulting in higher survival. The benefits of extended juvenile learning periods, over evolutionary time, lead to selection for expanded cognitive skillsets. Similarly, in our ancestors, cooperative breeding and increased group sizes facilitated learning and teaching. Our analyses highlight the critical role of life-history, ecological and social factors that underlie both extended parenting and expanded cognitive skillsets. This article is part of the theme issue 'Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.

Prospects for sociogenomics in avian cooperative breeding and parental care

For the last 40 years, the study of cooperative breeding (CB) in birds has proceeded primarily in the context of discovering the ecological, geographical, and behavioral drivers of helping. The advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped, in some cases, confirming predictions of kin selection theory. Methods for genome-wide analysis of sequence variation, gene expression, and epigenetics promise to add new dimensions to our understanding of avian CB, primarily in the area of molecular and developmental correlates of delayed breeding and dispersal, as well as the ontogeny of achieving parental status in nature. Here, we outline key ways in which modern -omics approaches, in particular genome sequencing, transcriptomics, and epigenetic profiling such as ATAC-seq, can be used to add a new level of analysis of avian CB. Building on recent and ongoing studies of avian social behavior and sociogenomics, we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream, context-dependent destructive and non-destructive sampling of specific tissues or physiological states in the field for analysis of gene expression and epigenetics. -Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time, but real-time analyses of behavioral interactions in the field or lab. Sociogenomics of birds represents a new branch in the network of methods used to study CB, and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.

Habitat Saturation Results in Joint-Nesting Female Coalitions in a Social Bird

Joint nesting by females and cooperative polyandry-cooperatively breeding groups with a male-biased breeder sex ratio-are little-understood, rare breeding systems. We tested alternative hypotheses of factors potentially driving these phenomena in a population of joint-nesting acorn woodpeckers (Melanerpes formicivorus). During periods of high population density and thus low independent breeding opportunities, acorn woodpecker females formed joint-nesting coalitions with close kin. Coalitions were typically associated with groups with a male bias. We found strong evidence for both inter- and intrasexual conflict, as joint nesting conferred a fitness benefit to some males, a significant fitness cost to females, and no gain in per capita reproductive output for either sex. Such conflict, particularly the cost to females, may be an important reason why joint nesting is rare among cooperatively breeding taxa.

What constitutes "social complexity" and "social intelligence" in birds? Lessons from ravens

In the last decades, the assumption that complex social life is cognitively challenging, and thus can drive mental evolution, has received much support from empirical studies in nonhuman primates. While extending the scope to other mammals and birds, different views have been adopted on what constitutes social complexity and which specific cognitive skills are selected for. Notably, many avian species form "open" groups as non-breeders (i.e., seasonally and before sexual maturity) that have been largely ignored as potential sources of social complexity. Reviewing 30 years of research on ravens, we illustrate the socio-ecological conditions faced by these birds as non-breeders and discuss how these relate to their socio-cognitive skills. We argue that the non-breeding period is key to understand raven social life and, to a larger extent, avian social life in general. We furthermore emphasize how the combination of the large-scale perspective (defining social system components: e.g., social organization, mating system) and the individual-scale perspective on social systems allows to better capture the complete set of social challenges experienced by individuals throughout their life, ultimately resulting on a more comprehensive understanding of species' social complexity.

The ecology of cooperative breeding behaviour

Ecology is a fundamental driving force for the evolutionary transition from solitary living to breeding cooperatively in groups. However, the fact that both benign and harsh, as well as stable and fluctuating, environments can favour the evolution of cooperative breeding behaviour constitutes a paradox of environmental quality and sociality. Here, we propose a new model - the dual benefits framework - for resolving this paradox. Our framework distinguishes between two categories of grouping benefits - resource defence benefits that derive from group-defended critical resources and collective action benefits that result from social cooperation among group members - and uses insider-outsider conflict theory to simultaneously consider the interests of current group members (insiders) and potential joiners (outsiders) in determining optimal group size. We argue that the different grouping benefits realised from resource defence and collective action profoundly affect insider-outsider conflict resolution, resulting in predictable differences in the per capita productivity, stable group size, kin structure and stability of the social group. We also suggest that different types of environmental variation (spatial vs. temporal) select for societies that form because of the different grouping benefits, thus helping to resolve the paradox of why cooperative breeding evolves in such different types of environments.

DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes)

DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.

Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations

A key characteristic of MHC genes is the persistence of allelic lineages over macroevolutionary periods, often through multiple speciation events. This phenomenon, known as trans-species polymorphism (TSP), is well documented in several major taxonomic groups, but has less frequently been observed in birds. The order Passeriformes is arguably the most successful terrestrial vertebrate order in terms of diversity of species and ecological range, but the reasons for this success remain unclear. Passerines exhibit the most highly duplicated MHC genes of any major vertebrate taxonomic group, which may generate increased immune response relative to other avian orders with fewer MHC loci. Here, we describe phylogenetic patterns of the MHC IIB in the passerine family Corvidae. Our results indicate wide-spread TSP within this family, with at least four supported MHC IIB allelic lineages that predate speciation by many millions of years. Markov chain Monte Carlo simulations indicate that divergence of these lineages occurred near the time of the divergence of the Passeriformes and other avian orders. We suggest that the current MHC diversity observed in passerines is due in part to the multiple duplication of a single MHC locus, DAB1, early in passerine evolution and that subsequent duplications of these paralogues have contributed to the enormous success of this order by increasing their ability to recognize and mount immune responses to novel pathogens.

Acoustic profiling in a complexly social species, the American crow: caws encode information on caller sex, identity, and behavioural context

Previous research on inter-individual variation in the calls of corvids has largely been restricted to single call types, such as alarm or contact calls, and has rarely considered the effects of age on call structure. This study explores structural variation in a contextually diverse set of "caw" calls of the American crow (Corvus brachyrhynchos), including alarm, foraging recruitment and territorial calls, and searches for structural features that may be associated with behavioural context and caller sex, age, and identity. Automated pitch detection algorithms are used to generate 23 pitch-related and spectral parameters for a collection of caws from 18 wild, marked crows. Using principal component analysis and mixed models, we identify independent axes of acoustic variation associated with behavioural context and with caller sex, respectively. We also have moderate success predicting caller sex and identity from call structure. However, we do not find significant acoustic variation with respect to caller age.

Evolutionary routes to non-kin cooperative breeding in birds

Cooperatively breeding animals live in social groups in which some individuals help to raise the offspring of others, often at the expense of their own reproduction. Kin selection--when individuals increase their inclusive fitness by aiding genetic relatives--is a powerful explanation for the evolution of cooperative breeding, particularly because most groups consist of family members. However, recent molecular studies have revealed that many cooperative groups also contain unrelated immigrants, and the processes responsible for the formation and maintenance of non-kin coalitions are receiving increasing attention. Here, I provide the first systematic review of group structure for all 213 species of cooperatively breeding birds for which data are available. Although the majority of species (55%) nest in nuclear family groups, cooperative breeding by unrelated individuals is more common than previously recognized: 30% nest in mixed groups of relatives and non-relatives, and 15% nest primarily with non-relatives. Obligate cooperative breeders are far more likely to breed with non-kin than are facultative cooperators, indicating that when constraints on independent breeding are sufficiently severe, the direct benefits of group membership can substitute for potential kin-selected benefits. I review three patterns of dispersal that give rise to social groups with low genetic relatedness, and I discuss the selective pressures that favour the formation of such groups. Although kin selection has undoubtedly been crucial to the origin of most avian social systems, direct benefits have subsequently come to play a predominant role in some societies, allowing cooperation to persist despite low genetic relatedness.

Environmental stability and the evolution of cooperative breeding in hornbills

Reproductive cooperation in social animals has been the focus of intensive research, yet the role of environmental factors in promoting such cooperation remains uncertain. A recent global analysis suggested that cooperative breeding in birds is a 'bet-hedging' strategy associated with climatic uncertainty, but it is unclear whether this mechanism applies generally or is restricted to the insectivorous passerines that predominate as cooperative breeders at the global scale. Here, we use a phylogenetic framework to assess the effect of climate on the evolution of cooperation in hornbills (Bucerotidae), an avian family characterized by frugivory and carnivory. We show that, in contrast to the global pattern, cooperative reproduction is positively associated with both inter- and intra-annual climatic stability. This reversed relationship implies that hornbills are relatively insensitive to climatic fluctuations, perhaps because of their dietary niche or increased body mass, both of which may remove the need for bet-hedging. We conclude that the relationship between climatic variability and cooperative breeding is inconsistent across taxa, and potentially mediated by life-history variation. These findings help to explain the mixed results of previous studies and highlight the likely shortcomings of global datasets inherently biased towards particular categories.

Tests of inferential reasoning by exclusion in Clark's nutcrackers (Nucifraga columbiana)

We examined inferential reasoning by exclusion in the Clark's nutcracker (Nucifraga columbiana) using two-way object-choice procedures. While other social scatter-hoarding corvids appear capable of engaging in inferential reasoning, it remains unclear if the relatively less social nutcracker is able to do so. In an initial experiment, food was hidden in one of two opaque containers. All of the birds immediately selected the baited container when shown only the empty container during testing. We subsequently examined the nutcrackers in two follow-up experiments using a task that may have been less likely to be solved by associative processes. The birds were trained that two distinctive objects were always found hidden in opaque containers that were always positioned at the same two locations. During testing, one of the two objects was found in a transparent "trash bin" and was unavailable. The birds were required to infer that if one of the objects was in the "trash," then the other object should still be available in its hidden location. Five out of six birds were unable to make this inference, suggesting that associative mechanisms likely accounted for our earlier results. However, one bird consistently chose the object that was not seen in the "trash," demonstrating that nutcrackers may have the ability to use inferential reasoning by exclusion to solve inference tasks. The role of scatter hoarding and social organization is discussed as factors in the ability of corvid birds to reason.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Cooperative breeding: a question of climate?

In some species, including humans, parents receive help with offspring care. A new comparative study suggests that birds breed cooperatively when environmental conditions vary. Further empirical and theoretical work will be required to understand the evolutionary significance of this insight.

Environmental uncertainty and the global biogeography of cooperative breeding in birds

Understanding why organisms as different as amoebas, ants, and birds cooperate remains an important question in evolutionary biology. Although ecology can influence cooperation and conflict within animal societies and has been implicated in species differences in sociality, the environmental predictors of sociality across broad geographic and taxonomic scales remain poorly understood. In particular, the importance of temporal variation in selection pressure has been underestimated in most evolutionary studies. Environmental uncertainty resulting from climatic variation is likely to be an important driver of temporal variation in selection pressure and therefore is expected to impact the evolution of behavioral, morphological, and physiological traits, including cooperation. Using a data set of over 95% of the world's birds, we examine the global geography and environmental, biotic, and historical biogeographic predictors of avian social behavior. We find dramatic spatial variation in social behavior for which environmental and biotic factors--namely, among-year environmental variability in precipitation--are important predictors. Although the clear global biogeographic structure in avian social behavior carries a strong signal of evolutionary history, environmental uncertainty plays an additional key role in explaining the incidence and distribution of avian cooperative breeding behavior.

First evidence for heritable variation in cooperative breeding behaviour

Understanding the evolution of complex social behaviours, such as cooperative breeding, is a fundamental problem in evolutionary biology, which has attracted much theoretical and empirical interest. Variation within and between species in the frequency of helping behaviour has been typically associated with variation in direct costs and benefits due to ecological constraints, or with indirect fitness payoffs (i.e. kin selection). Here, we provide the first evidence that individual variation in cooperative behaviour within a natural population also has a heritable component. Using a seven-generation pedigree in a wild population of western bluebirds (Sialia mexicana), we show significant heritable variation for the propensity to help rather than breed, as well as for the probability of having a helper at the nest. We also document a strong positive relationship between a bird's lifespan and its prospect of receiving help when breeding, in accordance with earlier comparative studies across species. These findings provide useful insights into the possible mechanisms which have led to the evolution of cooperative breeding and other social systems.

Prevalence of avian influenza and host ecology

Waterfowl and shorebirds are common reservoirs of the low pathogenic subtypes of avian influenza (LPAI), which are easily transmitted to poultry and become highly pathogenic. As the risk of virus transmission depends on the prevalence of LPAI in host-reservoir systems, there is an urgent need for understanding how host ecology, life history and behaviour can affect virus prevalence in the wild. To test for the most important ecological correlates of LPAI virus prevalence at the interspecific level, we applied a comparative analysis by using quantitative data on 30 bird species. We controlled for similarity among species due to common descent, differences in study effort and for covariance among ecological variables. We found that LPAI prevalence is a species-specific attribute and is a consequence of virus susceptibility, as it was negatively associated with the relative size of the bursa of Fabricius, an estimate of juvenile immune function. Species that migrate long distances have elevated prevalence of LPAI independent of phylogeny and other confounding factors. There was also a positive interspecific relationship between the frequency of surface feeding and virus prevalence, but this was sensitive to phylogenetic relatedness of species. Feeding in marine habitats is apparently associated with lower virus prevalence, but the effect of water salinity is likely to be indirect and affected by phylogeny. Our results imply that virus transmission via surface waters and frequent intra- and interspecific contacts during long migration are the major risk factors of avian influenza in the wild. However, the link between exploitation of surface waters and LPAI prevalence appears to be weaker than previously thought. This is the first interspecific study that provides statistical evidence that host ecology, immunity and phylogeny have important consequence for virus prevalence.

Temporal Environmental Variability Drives the Evolution of Cooperative Breeding in Birds

Many vertebrates breed in cooperative groups in which more than two members provide care for young. Studies of cooperative breeding behavior within species have long highlighted the importance of environmental factors in mediating the paradox of why some such individuals delay independent breeding to help raise the offspring of others. In contrast, studies involving comparisons among species have not shown a similarly clear evolutionary-scale relationship between the interspecific incidence of cooperative breeding and any environmental factors. Here, we use a phylogenetically controlled comparative analysis of a complete, socially diverse group of birds-45 species of African starlings-to show that cooperative breeding is positively associated with living in semiarid savanna habitats and with temporal variability in rainfall. Savanna habitats are not only highly seasonal, but also temporally variable and unpredictable, and this temporal variability directly influences individual reproductive decisions in starlings and helps explain interspecific patterns of sociality. Cooperative breeding is likely to be adaptive in temporally variable environments because it allows for both reproduction in harsh years and sustained breeding during benign years. This "temporal variability" hypothesis might help explain the phylogenetic and geographic concentrations of cooperatively breeding vertebrates in savanna-like habitats and other temporally variable environments worldwide.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.