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This study investigates the evolution of locomotory morphology and migratory behavior in nightingale-thrushes (genus Catharus ), a clade of songbirds with diverse migratory strategies. With large datasets of molecular and morphometric characters, we resolve phylogenetic relationships, identify and model migration-related morphological characters, and estimate ancestral states of those characters to infer evolutionary transitions in the migratory phenotype. While acknowledging that unknown factors (e.g., differential extinction) may confound interpretation, our results suggest that (1) migratory behavior and its functional morphology are fundamentally linked; (2) short-distance or elevational migration (not long-distance) was the ancestral state of Catharus ; (3) short-distance migration was the evolutionary precursor of long-distance migration; and (4) the short-distance migrant, Hermit Thrush ( C. guttatus ), may be in relative phenotypic (ecological) stasis. This potentially explains the ecological incumbency of C. guttatus in temperate North America during winter, and offers a new framework for interpreting the evolutionary sequence that produced long-distance migration in this model system.

South Texas is a highly variable region encompassing multiple habitat types and harboring a wide diversity of organisms. However, the parasite fauna in this region is poorly known, especially for avian ectoparasites such as lice. To better understand avian louse diversity and host associations in South Texas, we examined a total of 507 birds for chewing lice. Lice were morphologically identified to genus and phylogenetic analysis was performed using one mitochondrial (COI) and two nuclear (18S rRNA and EF-1α) genes. Of the birds examined, 69 (13.5%) were parasitized by lice resulting in a total of 63 host associations across 45 bird species, 29 of which were previously unrecorded. The predominant taxa encountered during this study included two of the most diverse louse genera, Myrsidea and Brueelia. Molecular analyses revealed 21 distinct genetic lineages, 17 of which are associated with novel host associations and may represent new species. This study represents the first extensive examination of avian louse host associations and relationships in Texas and reveals that there is still much to be learned about ectoparasite diversity in the New World.

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.

Unlike most bird species, individual kingfisher species (Aves: Alcedinidae) are typically parasitized by only a single genus of louse (Alcedoffula, Alcedoecus, or Emersoniella). These louse genera are typically specific to a particular kingfisher subfamily. Specifically, Alcedoecus and Emersoniella parasitize Halcyoninae, whereas Alcedoffula parasitizes Alcedininae and Cerylinae. Although Emersoniella is geographically restricted to the Indo-Pacific region, Alcedoecus and Alcedoffula are geographically widespread. We used DNA sequences from two genes, the mitochondrial COI and nuclear EF-1α genes, to infer phylogenies for the two geographically widespread genera of kingfisher lice, Alcedoffula and Alcedoecus. These phylogenies included 47 kingfisher lice sampled from 11 of the 19 currently recognized genera of kingfishers. We compared louse phylogenies to host phylogenies to reconstruct their cophylogenetic history. Two distinct clades occur within Alcedoffula, one that infests Alcedininae and a second that infests Cerylinae. All species of Alcedoecus were found only on host species of the subfamily Halcyoninae. Cophylogenetic analysis indicated that Alcedoecus, as well as the clade of Alcedoffula occurring on Alcedininae, do not show evidence of cospeciation. In contrast, the clade of Alcedoffula occurring on Cerylinae showed strong evidence of cospeciation.

Aim The use of intuitive or explicit biogeographical reconstruction techniques to estimate the timing of species radiations on the Hawaiian Islands, while often incorporating evidence on the timing of island formation, may be misleading if the effects of extinction are overlooked. Using phylogenies of the bark louse genus Ptycta (Psocidae), we compared results from biogeographical character mapping with those from molecular dating analyses. These results were used to evaluate the 'progression model', which predicts an oldest-to-youngest pattern of island colonization. Location The main Hawaiian Islands (Kauai, Oahu, Maui, Lanai, Molokai and Hawaii). Methods With a data set including 101 Hawaiian Ptycta specimens and 18 outgroup species, we constructed molecular phylogenies based on sequences of the nuclear gene wingless and mitochondrial genes 12S, 16S and cytochrome c oxidase subunit I (COI). Maximum-likelihood, maximum-parsimony and Bayesian phylogenetic analyses were used. We used BEAST to estimate a time-calibrated tree under a relaxed clock model. Results Our analyses suggested a single colonization event, followed by extensive movement of Ptycta among islands and species radiations within and between islands. This monophyletic radiation is composed of two well-supported clades that are also supported by two synapomorphic characters of the male genitalia. Main conclusions Very different biogeographical patterns are inferred by molecular dating versus approaches based on character mapping. Simple biogeographical reconstruction over the molecular phylogeny supports a pattern of youngest-to-oldest island colonization, the reverse of that predicted by the 'progression model', and implies that this radiation could be as young as the most recent islands of Maui (1.4 Ma) or Hawaii (0.5 Ma). Molecular dating, however, infers a pattern consistent with oldest-to-youngest island colonization, and suggests a lineage age of 7.1 Ma. Extinction on the oldest island of Kauai may account for the differences in results between the two analyses.

The diversity of permanent ectoparasites is likely underestimated due to the difficulty of collecting samples. Lice (Insecta: Phthiraptera) are permanent ectoparasites of birds and mammals; there are approximately 5,000 species described and many more undescribed, particularly in the Neotropics. We document the louse genera collected from birds sampled in Peru (2006–2007) and Colombia (2009–2016), from 22 localities across a variety of ecosystems, ranging from lowland tropical forest and Llanos to high elevation cloud forest. We identified 35 louse genera from a total of 210 bird species belonging to 37 avian families and 13 orders. These genera belong to two suborders and three families of lice: Amblycera, families Menoponidae (present on 131 bird species) and Ricinidae (39 bird species); and Ischnocera, family Philopteridae (119 bird species). We compared our bird-louse associations with data in Price et al. (2003) and recently published Neotropical studies. The majority of bird-louse associations (51.9%) were new, with most of these coming from Passeriformes, the most diverse avian order, with the most poorly known louse fauna. Finally, we found geographical variation in louse infestation and prevalence rates. With this study, we report the first comprehensive documentation of bird-louse associations for Colombia and substantially increase the known associations documented for Peru.

Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species’ common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.

Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genus Accipiter) are not monophyletic. Here, we combine a new large dataset obtained from Ultraconserved Elements (UCEs), generated from whole genome sequencing (WGS) of 120 species, with publicly available legacy markers (i.e., a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 236 extant or recently extinct species. Our densely-sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly of Accipiter and provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups.