Lay Summary center dot We use genetic data from across the genome and produce a robust family tree for herons, which clarifies the relationships among subfamilies and genera. center dot A comprehensive phylogeny of herons is lacking. As a result, their taxonomy is unstable and their evolutionary history is poorly known. center dot Several species were found to be incorrectly classified, and we recommend appropriate taxonomic revisions. center dot Comparisons of molecular evolution support previous studies. Bitterns have evolved comparatively faster, with some tiger herons and the Boat-billed Heron having evolved comparatively slower. Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees-that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.

Understanding a haplodiploid species' social structure and quantifying relatedness among individuals are both important when designing sampling schemes or identifying potential biases in population genetics studies. However, it is not always possible to accurately identify social structure of study species in the field, or to collect large numbers of individuals from a single colony to estimate relatedness with methods that rely on accurate estimation of allele frequencies. Here, we assessed the utility of allele-frequency-free inference of relationships in haplodiploid ant colonies, while using limited sample sizes. Using genome-wide single-nucleotide polymorphism data, we measured intracolony relatedness and kinship estimates consistent with full-sister relationships among workers in three Nearctic species: Camponotus herculeanus, C. laevissimus, and C. modoc. Notably, the allele-frequency-free inference of relationships clearly demonstrated these full-sister relationships without ambiguity; this result suggests the utility of these methods for identifying closely related individuals in population genetics studies of haplodiploid organisms. We additionally performed a literature review of relatedness estimates in the subfamily Formicinae both as a compiled resource and to place our results in context within this larger clade of ants. Our results suggestive of Camponotus colonies founded by a lone singly mated queen are consistent with previously published relatedness estimates in the genus Camponotus that have generally shown high intracolony relatedness.

In this study, we infer genus-level relationships within shrikes (Laniidae), crows (Corvidae), and their allies using ultraconserved elements (UCEs). We confirm previous results of the Crested Shrikejay (Platylophus galericulatus) as comprising its own taxonomic family and find strong support for its sister relationship to laniid shrikes. We also find strong support that the African-endemic genus Eurocephalus, which comprises two allopatric species (E. ruppelli and E. anguitimens), are not "true-shrikes." We propose elevating the white-crowned shrikes to their own family, Eurocephalidae. center dot Understanding how species are related (systematics) and classified (taxonomy) is important to the study of the world's biodiversity.center dot Recent work has raised doubt about the phylogenetic placement of the Crested Shrikejay (Platylophus galericulatus) and Eurocephalus, the white-crowned shrike genus, traditionally considered within the crow and jay family, Corvidae, and the shrike family, Laniidae, respectively.center dot We collected a genome-wide dataset for all genera of shrikes, crows, and jays to determine their evolutionary histories with phylogenetic methods.center dot We confirm that the Crested Shrikejay constitutes a family-level lineage most closely related to Laniidae, not Corvidae. We show for the first time that Eurocephalus also represents a family-level lineage separate from shrikes and more closely related to crows and jays.center dot We propose a new avian family, Eurocephalidae, the white-crowned shrikes, for these two African-endemic birds. Graphical Abstract Dans cette etude, nous inferons les relations a l'echelle du genre chez les Laniidae, les Corvidae et leurs allies a l'aide d'elements ultraconserves (EUC). Nous confirmons les resultats anterieurs concernant Platylophus galericulatus comme constituant sa propre famille taxonomique et nous trouvons un fort soutien de sa relation de s oe ur des Laniidae. Nous trouvons egalement un soutien solide que le genre endemique africain Eurocephalus, qui comprend deux especes allopatriques (E. ruppelli et E. anguitimens), n'est pas compose de << vraies pies-grieches >>. Nous proposons d'elever ces especes au rang de leur propre famille, les Eurocephalidae.

Abstract Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole‐genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole‐genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome‐wide estimates of genetic drift and number of genes with relaxed selection pressures.

The northern flicker, Colaptes auratus , is a widely distributed North American woodpecker and a long-standing focal species for the study of ecology, behavior, phenotypic differentiation, and hybridization. We present here a highly contiguous de novo genome assembly of C. auratus, the first such assembly for the species and the first published chromosome-level assembly for woodpeckers (Picidae). The assembly was generated using a combination of short-read Chromium 10x and long-read PacBio sequencing, and further scaffolded with chromatin conformation capture (Hi-C) reads. The resulting genome assembly is 1.378 Gb in size, with a scaffold N50 of 43.948 Mb and a scaffold L50 of 11. This assembly contains 87.4 % - 91.7 % of genes present across four sets of universal single-copy orthologs found in tetrapods and birds. We annotated the assembly both for genes and repetitive content, identifying 18,745 genes and a prevalence of ~ 28.0 % repetitive elements. Lastly, we used four-fold degenerate sites from neutrally evolving genes to estimate a mutation rate for C. auratus , which we estimated to be 4.007 × 10−9 substitutions / site / year, about 1.5x times faster than an earlier mutation rate estimate of the family. The highly contiguous assembly and annotations we report will serve as a resource for future studies on the genomics of C. auratus and comparative evolution of woodpeckers.

Mutualism discernibly connects the evolution of two or more interacting taxa. Endosymbioses, especially those that are obligate, are an intimate mutualism that link the evolution of host and endosymbiont. In these instances, we may expect codiversification of hosts and endosymbionts as well as host demography discernibly affecting the course of endosymbiont evolution. While many studies have demonstrated cospeciation of hosts and endosymbionts, detailed investigations of the impact of host demography on endosymbiont molecular evolution are generally lacking. Here, we sequenced complete genomes of carpenter ants (Genus Camponotus) and their Blochmannia endosymbionts to investigate their codiversification and test hypotheses about how host demography impacts molecular evolution in endosymbionts. Using whole genome phylogenomics, we identified strong signatures of codiversification between carpenter ants and their endosymbionts. We found that endosymbiont genes have evolved rapidly, at a pace of ~30x that of their hosts. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. We identified a positive relationship between host demography and shifts toward intensified selection in endosymbiont genes, but no relationship between host demography and shifts toward relaxed selection in endosymbiont genes. About 10% of the Blochmannia genes exhibited variable presence and absence across endosymbiont genomes. Of those, about half exhibited phylogenetic signal, indicating somewhat random patterns of gene loss in endosymbiont genomes. Lastly, we found no relationship between host demography and endosymbiont gene loss.

Basic natural history and behavioural data are lacking for the majority of broadbills and pittas (Eurylaimidae, Calyptomenidae and Pittidae). We present a series of observations on these birds made during two visits to Tawau Hills Park, Sabah, Malaysia. During this period, we detected changes in temporal presence, detectability or vocal behaviour in various species. We also found habitat overlap on one ridgeline among four species of pitta. We observed a Green Broadbill Calyptomena viridis respond to our imitation of a call with a wing display. We discuss the social behaviour of Black-and-yellow Eurylaimus ochromalus and Banded Broadbills E. javanicus, including wing displays, territoriality, and in the first-named species, social groups comprising multiple adults. We also describe various nesting behaviours in these two species, including nest-construction techniques, incubation behaviour, nest defence, and the first described Banded Broadbill nest on Borneo. We found Dusky Broadbills Corydon sumatranus to frequently be the most conspicuous members of mixed-species flocks otherwise dominated by Cuculidae and Picidae. We analysed Black-crowned Pitta Erythropitta ussheri home range size and density in a colour-banded population, and found a potential hybrid or backcross with Garnet Pitta E. granatina. We observed that Blue-banded Pitta E. arquata make non-vocal sonations by striking their closed wings on their flanks, and discuss the immature male plumage of Blue-headed Pitta Hydrornis baudii.

The natural history of the Sapayoa Sapayoa aenigma, the sole member of the Sapayoidae and the only New World representative of the ‘Old World suboscines’, is poorly known. Previously, we reported a pair of adult Sapayoas breeding with assistance from two immature males, but their kinship was unknown. Here, we use double-digest restriction site-associated DNA sequencing (ddRAD-seq) to conduct parentage and relatedness analyses among this group. We found that the members of the adult pair were unrelated, but all other dyads were probably first order (parent-offspring or full sibling). In addition, the helper males were very unlikely to have sired either of the chicks. We conclude that the group consisted of two unrelated adults and two offspring from a previous brood. These results provide important context for social behaviours observed within the group, which included mounting events; such behaviour may be involved in group cohesion.

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As natural history collections are enjoying a renaissance in their uses as referents for modern genomic studies, they are also expanding their scope by adding or linking to digital media on behavior, vocalizations, and anatomy. At the same time, a new generation of students, uncommonly well-versed in natural history and biodiversity, is hungering for demanding fieldwork in out-of-the-way localities. This combination of developments creates an historic opportunity for student-led expeditions to study taxa of phylogenetic interest by collecting "complete specimen packages," traditional museum specimens coupled with digital documentation of their behaviors and ecologies. This chapter summarizes our experiences with such expeditions, from the preparatory steps, through activities during the expedition, to the challenges of post-expedition work. We hope that our successes and failures can inform similar programs at other institutions.

The Sapayoa (Sapayoa aenigma), a low-density resident of Choco rainforests from Panama to Ecuador, has long perplexed ornithologists. It was originally described as a manakin (Pipridae), but molecular work has revealed its closest living relatives to be Old World suboscines (Eurylaimides) and supported its placement in the monotypic family of Sapayoidae. Despite such phylogenetic intrigue, little is known about the Sapayoa's general life history or reproductive biology; only one nest has been described. We present information on 2 actively attended and 13 inactive Sapayoa nests in Darien National Park, Panama. We provide the first detailed description of individual effort at an active nest, family group dynamics during the nesting period, the plumage of immature birds, and the range of vocalizations produced. We also present the first documentation of cooperative breeding and compile several recent nesting observations, extending the published Sapayoa breeding period by several months. Furthermore, we describe unusual behaviors among provisioning birds, including mounting between individuals of the same sex and mounting of a female by immature male helpers during chick provisioning. The receiving individual gave a conspicuous solicitation display before each mounting. Finally, we highlight elements of the Sapayoa's natural history that echo its Old World relatives and contrast with members of the New World Tyranni. For example, the Sapayoa resembles the eurylaimid broadbills-and differs starkly from the manakins-in diet, nest structure, breeding system, and mode of parental care.