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In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.

How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g. pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise. [ABSTRACT FROM AUTHOR]

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

Abstract Background Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.

We describe Laniarius willardi, a new species of boubou shrike (Malaconotidae) from the Albertine Rift of Africa. The most conspicuous, distinguishing morphological feature of the species is a gray to blue-gray iris. This and external morphometric data indicate that L. willardi is diagnosable from other black or sooty boubous. Further, L. willardi is genetically diagnosable, and its closest relative is the Mountain Sooty Boubou (L. poensis camerunensis) from Cameroon. The Crimson-breasted Bush-shrike (L. atrococcineus) and the Lowland Sooty Boubou (L. leucorhynchus) ate together the sister clade to L. willardi-L.p. camerunensis. Laniarius willardi and the geographically codistributed L. p. holomelas differ by 11.5% in uncorrected sequence divergence, and elevational data taken from museum specimens suggest the possibility of elevational segregation of the species at ~2,000 m, with L. willardi occurring at lower elevations. Our broad sampling of black and sooty boubou taxa indicate that (1) races of Mountain Sooty Boubou (L. poensis) do not form a monophyletic clade; (2) L. p. camerunensis may represent multiple, nonsister lineages; and (3) at least one race of Fulleborn's Black Boubou (L. fuelleborni usambaricus) is genetically distinct from other races of that species. Received 16 June 2009, accepted 12 December 2009. Key words: Africa, boubou, Laniarius, Malaconotidae, shrikes. Nous decrivons ici Laniarius willardi, une nouvelle espece de la famille des Malaconotidae vivant au Rift Albertine, en Afrique. Le caractere morphologique le plus remarquable de cette espece est un iris gris a bleu-gris. Ceci et des donnees morphometriques externes indiquent que L. willardi est different des autres Laniarius. De plus, L. willardi est genetiquement different et son plus proche parent est L. poensis camerunensis, au Cameroun. L. atrococcineus et L. leucorhynchus forment le clade saeur de L. willardi-L.p. camerunensis. L. willardi et L. p. holomelas, dont la repartition geographique est similaire, different de 11,5 % en ce qui concerne la divergence de la sequence corrigee. Les donnees altitudinales recoltees sur des specimens de musee suggerent qu'il existe une possibilite de segregation altitudinale des especes a ~2 000 m, L. willardi etant present h des altitudes plus faibles. Notre vaste echantillonnage de ce taxon indique que (1) les races L. poensis he forment pas un clade monophyletique, (2) L. p. camerunensis peut representer des lignees multiples qui ne sont pas saeurs et (3) au moins une race de L. fuelleborni usambaricus est genetiquement distincte des autres races de cette espece. DOI: 10.1525/auk.2010.09014

The double-collared sunbirds of the Eastern Arc Mountains of Tanzania and southeastern Kenya are characterized by regional variation in morphology and plumage. That variation has resulted in considerable dispute over their taxonomic status and delineation of range boundaries. It has been suggested that Moreau's Sunbird (Nectarinia moreaui) is an atypical phenotype that has arisen from a hybridization event between the more widely distributed Eastern Double-collared Sunbird (N. mediocris) and the narrowly distributed Loveridge's Sunbird (N. loveridgei). A discriminant analysis of six standard morphological characters indicates that Moreau's Sunbird is intermediate in shape and size between the Eastern Double-collared and Loveridge's sunbirds. There is greater overlap between female Moreau's and Eastern Double-collared sunbirds than between males; Loveridge's Sunbird shows little overlap with the other taxa. Discrete plumage characters separate all three taxa. Molecular analyses of 728 base pairs of mitochondrial DNA (NADH3 and control region) suggest that Moreau's Sunbird is a valid taxon and the sister species to Loveridge's Sunbird. Eastern Double-collared Sunbird haplotypes can be divided into three distinct clades, separated from each other by substantial genetic divergence (approximately 8-10% sequence divergence). We propose species status for each of those clades and suggest the following three taxa: N. mediocris Shelley 1855, N. usambarica Grote 1922, and N. fuelleborni Reichenow 1899. Finally, we propose a biogeographical hypothesis of speciation events within the N. mediocris species complex.

We studied relationships of five extant members of the endemic Malagasy family Brachypteraciidae, the ground rollers, using several mitochondrial genes (cytochrome-b, NADH dehydrogenase 2, 12S ribosomal RNA, and cytochrome oxidase I). As out-groups, we used other coraciiforms including the Cuckoo Roller (Family Leptosomatidae, Leptosomus discolor), several true rollers (Corcaciidae) and a tody (Todidae). Partial sequences of the Long-tailed Ground Roller (Uratelornis chimaera) were obtained from toe pad samples taken off museum specimens. For a combined data set of all genes, Kimura two-parameter distances between sequences of the five ground roller species were high, averaging 11% divergence. For several species, samples were available from widely separated geographic regions and intraspecific sequence divergence was low ([less than or equal to] 0.8%). Unweighted and weighted parsimony and maximum-likelihood analyses consistently recovered monophyly of the family, a sister relationship between Brachypteraciidae and Coraciidae, and monophyly of one of three currently recognized ground roller genera (Atelornis). At the base of the Brachypteraciidae clade, we could not fully resolve relationships between Uratelornis and two species currently placed in Brachypteracias. Because of the uncertainty of basal nodes in our phylogenetic reconstructions, we recommend returning B. squamigera to the monotypic genus Geobiastes. High levels of divergence among ground rollers are similar to levels found in other avian groups endemic to Madagascar. However, we suggest that molecular divergences appear far too low to be consistent with mid-Eocene fossils attributed to the family. Received 3 August 2000, accepted 28 February 2001.

Abstract Background Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.