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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.

Species limits in the genus Plectrophenax have been difficult to assess. McKay's Buntings (Plectrophenax hyperboreus) are very similar both morphologically and behaviorally to Snow Buntings (P. nivalis). However, their breeding ranges are allopatric, and there is limited evidence of gene flow. The juvenal plumage of McKay's Buntings has never been described as different from that of Snow Buntings. Comparison of a series of McKay's Buntings in juvenal plumage with a series of Snow Buntings in juvenal plumage showed clear differences between the two forms. We used color spectrophotometry to quantify the differences between the two taxa in two areas of the body that appeared to be consistently different, the throat and back. The relative magnitude of the difference between McKay's and Snow buntings was greater than homologous differences between two subspecies of Snow Bunting (P. n. nivalis and P. n. townsendi). Four out of six variables were significantly different between McKay's and Snow buntings, whereas none of the variables were significantly different between the two subspecies of Snow Bunting. Bonferroni corrected t-tests of sexual dimorphism and regression of the variables against year of collection showed that these factors were not associated with these differences. Discriminant analysis accurately separated 100% of the specimens into their respective groups. These differences are notable given the evolutionarily conservative nature of juvenal plumage. Our results support continued recognition of McKay's Bunting as a species and reconfirm the use of juvenal plumage to help determine species limits. Received 7 December 2005, accepted 25 July 2006. Key words: discriminant analysis, juvenal plumage, Plectrophenax, reflectance spectrophotometry, species limits. Los limites entre especies del genero Plectrophenax han sido dificiles de establecer. Plectrophenax hyperboreus es muy similar en morfologia y comportamienento a P. nivalis. Sin embargo, sus rangos de cria son alopatricos y la evidencia de flujo genetico es limitada. El plumaje juvenil de P. hyperboreus nunca ha sido descrito como diferente del de P. nivalis. Una comparacion de series de especimenes de P. hyperboreus y P. nivalis en plumaje juvenil mostro claramente que existen diferencias entre las dos formas. Utilizamos espectrofotometria de color para cuantificar las diferencias entre los dos taxones en dos regiones del cuerpo que parecian diferir consistentemente, la garganta y la espalda. La magnitud relativa de la diferencia entre P. hyperboreus y P. nivalis fue mayor que la de diferencias homologas observadas entre dos subespecies de P. nivalis (P. n. nivalis y P. n. townsendi). Cuatro de seis variables fueron significativamente diferentes entre P. hyperboreus y P. nivalis, mientras que ninguna de las variables fue significativamente diferente entre las dos subespecies de P. nivalis. Pruebas de t corregidas mediante Bonferroni para evaluar dimorfismo sexual y analisis de regresion de las variables contra el ano de coleccion, mostraron que esos factores no estan asociados con las diferencias. Analisis discriminantes separaron el 100% de los especimenes con exactitud en sus grupos respectivos. Estas diferencias son notables dada la naturaleza evolutivamente conservada del plumaje juvenil. Nuestros resultados apoyan el reconocimiento continuado de P. hyperboreus como una especie, y reconfirman el uso del plumaje juvenil para ayudar a determinar los limites entre especies.

Next‐generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol–chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol–chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol–chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol–chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols. [ABSTRACT FROM AUTHOR]

The highlands of Mesoamerica harbour some of the highest biodiversity in the world, especially in cloud forests, but the landscape drivers of this diversification are not well known. Taxonomy in this region has been challenging owing to a lack of consensus about how to test species limits. We apply integrative taxonomy to an emblematic species of the Mesoamerican cloud forests, the unicolored jay (Aphelocoma unicolor). We assess divergence along three complementary axes (genetics, phenotype and ecological niche), finding evidence for differentiation among five lineages, currently described as subspecies, in isolated forest patches. DNA suggests that these lineages have long histories of divergence. Multivariate analysis of phenotype, along with an objective method for detecting phenotypic clusters, suggest that at least four of the five lineages are diagnosable. There was also a pattern of increasing ecological divergence through time. The divergence observed among lineages is comparable to other species-level divergences in the genus, arguing for elevation of at least two, and as many as four, lineages within A. unicolor to species rank. According to our time tree, cloud forest patches became isolated starting in the Pliocene and continuing into the Pleistocene, suggesting glacial cycles as the main drivers of speciation. [ABSTRACT FROM AUTHOR]

The Elegant Quail (Callipepla douglasii) is restricted to western mainland Mexico from Sonora south to Jalisco. It comprises five subspecies, described primarily on the basis of differences in plumage color and patterns. To assess patterns of differentiation in the Elegant Quail, we examined 114 specimens representing these five subspecies in the Moore Laboratory of Zoology. We measured wing chord, tail length, exposed culmen, and tarsus length, finding that males were significantly larger than females but that the only significant size difference between subspecies was that nominate douglasii has a tail longer than in the other four. Thus size is a minor component of the Elegant Quail's geographic variation in comparison to that in plumage color and pattern. We examined the plumage of specimens from southern Sonora and northern Sinaloa and found that several appeared to be intergrades between C. d. douglasii and C. d. bensoni and between C. d. bensoni and C. d. languens. [ABSTRACT FROM AUTHOR]

We present a new software package ( hzar) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium cline models using the Metropolis-Hastings Markov chain Monte Carlo ( MCMC) algorithm. The software applies likelihood functions appropriate for different types of data, including diploid and haploid genetic markers and quantitative morphological traits. The modular design allows flexibility in fitting cline models of varying complexity. To facilitate hypothesis testing, an autofit function is included that allows automated model selection from a set of nested cline models. Cline parameter values, such as cline centre and cline width, are estimated and may be compared statistically across clines. The package is written in the R language and is available through the Comprehensive R Archive Network ( CRAN; ). Here, we describe hzar and demonstrate its use with a sample data set from a well-studied hybrid zone in western Panama between white-collared ( Manacus candei) and golden-collared manakins ( M. vitellinus). Comparisons of our results with previously published results for this hybrid zone validate the hzar software. We extend analysis of this hybrid zone by fitting additional models to molecular data where appropriate. [ABSTRACT FROM AUTHOR]

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High-latitude diversification is a process characterized by speciation and extinction due to climatically driven vicariance and dispersal events. McKay’s buntings ( Plectrophenax hyperboreus) are high-latitude island endemic songbirds, and their global range is restricted to Beringia. Snow buntings ( P. nivalis), their closest relatives, are distributed throughout the Holarctic, breeding in available habitat surrounding the island range of McKay’s buntings. We sequenced 1123 base pairs of mitochondrial DNA for 40 individuals of each species and analysed a total of 913 AFLPs for 57 individuals. Both marker types suggested weak but significant genetic differentiation. Analysis of sequence data indicated divergence occurring when the current breeding range of McKay’s buntings was a hill on the Beringian steppe (∼18 400 to ∼73 700 years before present), suggesting that snow buntings were restricted to lower latitudes by ice sheets. Ancestral effective population size estimates indicate a founder event in McKay’s buntings followed by an expansion and then a reduction in effective size. Rising sea levels and asymmetric hybridization from McKay’s buntings into the postglacially-colonizing population of snow buntings could account for this reduction. Reproductive isolation is likely maintained through differential arrival dates on breeding grounds and the high breeding density of McKay’s buntings. This recent, high-latitude divergence best fits a model of founder event speciation driven by vicariance and oscillations in habitat due to climate change. [ABSTRACT FROM AUTHOR]

The article refutes the nesting status of the Pacific Wren in Wyoming as data on the migration schedule of the species in the region is still lacking and requires further study and confirmation. It informs that the only actual confirmation of nesting in the region is a single specimen taken in Wyoming in the year 1897 but which was later identified as a juvenile House Wren. It describes the close examination of the specimen which was found to lack the adult and immature Pacific Wren's rich cinnamon coloration with shorter bill, wing and tail lengths. Furthermore, it found that the plumage and measurements of the specimen were very similar to a juvenile House Wren.