Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds.

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.].

Earth history and the passerine superradiation.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae).

Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura. Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura. We recommend that C. viridipennis, currently generally treated as specifically distinct from C. chapmani, be returned to its former status as C. chapmani viridipennis, and that C. andrei, now generally regarded as synonymous with C. vauxi aphanes, again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa, C. egregia, and C. martinica. Geographically structured genetic variation within some other species of Chaetura, especially notable in C. cinereiventris, suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.

Isotopic niches support the resource breadth hypothesis.

Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the 'white-headed' gull (Larus sp.) complex.

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Testing founder effect speciation: divergence population genetics of the spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves).

Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10(-8)) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we discuss the potential importance of evolutionarily labile traits with significant fitness consequences, such as migratory behavior and habitat preference, in facilitating divergence of the spoonbills.

Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic.

Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.

Long-term isolation of a highly mobile seabird on the Galapagos.

The Galapagos Islands are renowned for their high degree of endemism. Marine taxa inhabiting the archipelago might be expected to be an exception, because of their utilization of pelagic habitats-the dispersal barrier for terrestrial taxa-as foraging grounds. Magnificent frigatebirds (Fregata magnificens) have a highly vagile lifestyle and wide geographical distribution around the South and Central American coasts. Given the potentially high levels of gene flow among populations, the species provides a good test of the effectiveness of the Galapagos ecosystem in isolating populations of highly dispersive marine species. We studied patterns of genetic (mitochondrial DNA, microsatellites and nuclear introns) and morphological variation across the distribution of magnificent frigatebirds. Concordant with predictions from life-history traits, we found signatures of extensive gene flow over most of the range, even across the Isthmus of Panama, which is a major barrier to gene flow in other tropical seabirds. In contrast, individuals from the Galapagos were strongly differentiated from all conspecifics, and have probably been isolated for several hundred thousand years. Our finding is a powerful testimony to the evolutionary uniqueness of the taxa inhabiting the Galapagos archipelago and its associated marine ecosystems.

No population genetic structure in a widespread aquatic songbird from the Neotropics.

Neotropical lowland organisms often show marked population genetic structure, suggesting restricted migration among populations. However, most phylogeographic studies have focused on species inhabiting humid forest interior. Little attention has been devoted to the study of species with ecologies conducive to dispersal, such as those of more open and variable environments associated with watercourses. Using mtDNA sequences, we examined patterns of genetic variation in a widely distributed Neotropical songbird of aquatic environments, the Yellow-hooded Blackbird (Icteridae, Chrysomus icterocephalus). In contrast to many forest species, Yellow-hooded Blackbirds showed no detectable genetic structure across their range, which includes lowland populations on both sides of the Andes, much of northeastern South America, Amazonia, as well as a phenotypically distinct highland population in Colombia. A coalescent-based analysis of the species indicated that its effective population size has increased considerably, suggesting a range expansion. Our results support the hypothesis that species occurring in open habitats and tracking temporally dynamic environments should show increased dispersal propensities (hence gene flow) relative to species from closed and more stable environments. The phenotypic and behavioral variation among populations of our study species appears to have arisen recently and perhaps in the face of gene flow.

Taxonomic evaluation of the Grallaria rufula (Rufous Antpitta) complex (Aves: Passeriformes: Grallariidae) distinguishes sixteen species.

Populations in the Rufous Antpitta (Grallaria rufula) complex occupy humid montane forests of the Andes from northern Colombia and adjacent Venezuela to central Bolivia. Their tawny to cinnamon-colored plumages are generally uniform, featuring subtle variation in hue and saturation across this range. In contrast to their conservative plumage, substantial vocal differences occur among geographically isolated or parapatric populations. Working within the framework of a comprehensive molecular phylogeny, we reexamined species limits in the G. rufula complex, basing taxonomic recommendations on diagnostic differences in vocalizations and considering identifiable differences in plumage where pertinent. We identified 16 populations for species designation, including seven populations previously described as subspecies and, remarkably, six new species described herein. Within one of these species, we identified less robust vocal differences between populations that we designate as subspecies. Geographic variation exists within another species, but its critical evaluation requires additional material. Taxonomic revisions of groups consisting of cryptic species, like the Grallaria rufula complex, are imperative for their conservation. Rather than widespread species as currently defined, these complexes can comprise many range-restricted taxa at higher risk of extinction given the continuing human pressures on their habitats.

The evolution of a tropical biodiversity hotspot.

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1283 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots.

Paraphyly of Cinclodes fuscus (Aves: Passeriformes: Furnariidae): implications for taxonomy and biogeography.

The Andes are a hotspot of global avian diversity, but studies on the historical diversification of Andean birds remain relatively scarce. Evolutionary studies on avian lineages with Andean-Patagonian distributions have focused on reconstructing species-level phylogenies, whereas no detailed phylogeographic studies on widespread species have been conducted. Here, we describe phylogeographic patterns in the Bar-winged Cinclodes (Cinclodes fuscus), a widespread and common species of ovenbird (Furnariidae) that breeds from Tierra del Fuego to the northern Andes. Traditionally, C. fuscus has been considered a single species composed of nine subspecies, but its long and narrow range suggests the possibility of considerable genetic variation among populations. Sequences of two mitochondrial genes revealed three discrete and geographically coherent groups of C. fuscus, occupying the southern, central, and northern Andes. Surprisingly, phylogenetic analyses indicated that these groups were more closely related to other species of Cinclodes than to each other. Relationships of the southern and northern C. fuscus clades to other species of Cinclodes were straightforward; in combination with available information on plumage, behavioral, and vocal variation, this suggests that each should be recognized as a distinct biological species. The central Andean group was paraphyletic with respect to C. oustaleti, and relationships among these taxa and C. olrogi were poorly resolved. We suggest that the central Andean C. fuscus should also be considered a different species, pending new information to clarify species limits in this group. These new phylogenetic data, along with recently developed methods, allowed us to review the biogeography of the genus, confirming southern South America and the central Andes as important areas for the diversification of these birds.

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: infraorder Furnariides).

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods.

Evidence for a duplicated mitochondrial region in Audubon's shearwater based on MinION sequencing.

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese.

Recent reviews identified the reliance on fecal or cloacal samples as a significant limitation hindering our understanding of the avian gastrointestinal (gut) microbiota and its function. We investigated the microbiota of the esophagus, duodenum, cecum, and colon of a wild urban population of Canada goose (Branta canadensis). From a population sample of 30 individuals, we sequenced the V4 region of the 16S SSU rRNA on an Illumina MiSeq and obtained 8,628,751 sequences with a median of 76,529 per sample. These sequences were assigned to 420 bacterial OTUs and a single archaeon. Firmicutes, Proteobacteria, and Bacteroidetes accounted for 90% of all sequences. Microbiotas from the four gut regions differed significantly in their richness, composition, and variability among individuals. Microbial communities of the esophagus were the most distinctive whereas those of the colon were the least distinctive, reflecting the physical downstream mixing of regional microbiotas. The downstream mixing of regional microbiotas was also responsible for the majority of observed co-occurrence patterns among microbial families. Our results indicate that fecal and cloacal samples inadequately represent the complex patterns of richness, composition, and variability of the gut microbiota and obscure patterns of co-occurrence of microbial lineages.

Publisher Correction: Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese.

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Comparative cophylogenetics of Australian phabine pigeons and doves (Aves: Columbidae) and their feather lice (Insecta: Phthiraptera).

Host-parasite coevolutionary histories can differ among multiple groups of parasites associated with the same group of hosts. For example, parasitic wing and body lice (Insecta: Phthiraptera) of New World pigeons and doves (Aves: Columbidae) differ in their cophylogenetic patterns, with body lice exhibiting higher phylogenetic congruence with their hosts than wing lice. In this study, we focus on the wing and body lice of Australian phabine pigeons and doves to determine whether the patterns in New World pigeons and doves are consistent with those of pigeons and doves from other regions. Using molecular sequence data for most phabine species and their lice, we estimated phylogenetic trees for all three groups (pigeons and doves, wing lice and body lice), and compared the phabine (host) tree with both parasite trees using multiple cophylogenetic methods. We found a pattern opposite to that found for New World pigeons and doves, with Australian wing lice showing congruence with their hosts, and body lice exhibiting a lack of congruence. There are no documented records of hippoboscid flies associated with Australian phabines, thus these lice may lack the opportunity to disperse among host species by attaching to hippoboscid flies (phoresis), which could explain these patterns. However, additional sampling for flies is needed to confirm this hypothesis. Large differences in body size among phabine pigeons and doves may also help to explain the congruence of the wing lice with their hosts. It may be more difficult for wing lice than body lice to switch among hosts that vary more dramatically in size. The results from this study highlight how host-parasite coevolutionary histories can vary by region, and how local factors can shape the relationship.

A replacement name for Asthenes wyatti perijanus Phelps 1977.

A recent near-complete phylogeny of the avian family Furnariidae (Derryberry et al. 2011) found a number of discrepancies between the phylogeny and the then-current taxonomy of the group, and several changes were proposed to reconcile the taxonomy of the family with the phylogeny. Among these was the merging of the genus Schizoeaca Cabanis 1873 into Asthenes Reichenbach 1853 (Derryberry et al. 2010). This change has now been generally adopted. The Committee on Classification and Nomenclature (South America) of the American Ornithologists' Union (Remsen et al. 2015) passed a proposal to merge the genera in 2010, and recent global reference works (e.g., Dickinson & Christidis 2014) have likewise adopted the lumping of these genera.