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Aim: Palaeoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of paleoceanographic changes on the diversification and speciation in these highly mobile pelagic seabirds. We investigate shearwater biogeography and the evolution of a key phenotypic trait, body size, and we assess the validity of the current taxonomy of the group. Location: Worldwide. Taxa: Shearwaters (Order Procellariiformes, Family Procellariidae, Genera Ardenna, Calonectris and Puffinus). Methods: We generated genomic data (double-digest restriction site-associated DNA) for almost all extant shearwater species to infer a time-calibrated species tree. We estimated ancestral ranges and evaluated the roles of founder events, vicariance and surface ocean currents in driving shearwater diversification. We performed phylogenetic generalized least squares to identify potential predictors of variability in body size along the phylogeny. To assess the validity of the current taxonomy of the group, we analysed genomic patterns of recent shared ancestry and differentiation among shearwater taxa. Results: We identified a period of high dispersal and rapid speciation during the Late Pliocene - early Pleistocene. Species dispersal appears to be favoured by surface ocean currents, and biogeographic reconstructions support founder events as the main mode of speciation in these highly mobile pelagic seabirds. Body mass shows significant associations with life strategies and local conditions. The current taxonomy shows some incongruences with the patterns of genomic divergence. Main Conclusions: A reduction of neritic areas during the Pliocene seems to have driven global extinctions of shearwater species, followed by a subsequent burst of speciation and dispersal probably promoted by Plio-Pleistocene climatic shifts. Our findings extend our understanding on the drivers of speciation and dispersal of highly mobile pelagic seabirds and shed new light on the important role of paleoceanographic events.

Diversity does not drive speciation The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments relative to the tropics. Thus, for this group of birds, diversification in temperate to Arctic regions followed by the movement and retention of species in the tropics results in their higher local levels of species diversity. Science , this issue p. 1343 ; see also p. 1268

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.

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Significance Our understanding of the factors that affected the diversification of passerines, the most diverse and widespread bird order (Passeriformes), is limited. Here, we reconstruct passerine evolutionary history and produce the most comprehensive time-calibrated phylogenetic hypothesis of the group using extensive sampling of the genome, complete sampling of all passerine families, and a number of vetted fossil calibration points. Our phylogenetic results refine our knowledge of passerine diversity and yield divergence dates that are consistent with the fossil record, and our macroevolutionary analyses suggest that singular events in Earth history, such as increases in Cenozoic global temperature or the colonization of new continents, were not the primary forces driving passerine diversification., 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.

Summary 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 analyzed 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, it 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. This article is protected by copyright. All rights reserved.

We studied the influence of glacial oscillations on the genetic structure of seven species of white-headed gull that breed at high latitudes (Larus argentatus, L. canus, L. glaucescens, L. glaucoides, L. hyperboreus, L. schistisagus, and L. thayeri). We evaluated localities hypothesized as ice-free areas or glacial refugia in other Arctic vertebrates using molecular data from 11 microsatellite loci, mitochondrial DNA (mtDNA) control region, and six nuclear introns for 32 populations across the Holarctic. Moderate levels of genetic structure were observed for microsatellites (FST= 0.129), introns (ΦST= 0.185), and mtDNA control region (ΦST= 0.461), with among-group variation maximized when populations were grouped based on subspecific classification. Two haplotype and at least two allele groups were observed across all loci. However, no haplotype/allele group was composed solely of individuals of a single species, a pattern consistent with recent divergence. Furthermore, northernmost populations were not well differentiated and among-group variation was maximized when L. argentatus and L. hyberboreus populations were grouped by locality rather than species, indicating recent hybridization. Four populations are located in putative Pleistocene glacial refugia and had larger τ estimates than the other 28 populations. However, we were unable to substantiate these putative refugia using coalescent theory, as all populations had genetic signatures of stability based on mtDNA. The extent of haplotype and allele sharing among Arctic white-headed gull species is noteworthy. Studies of other Arctic taxa have generally revealed species-specific clusters as well as genetic structure within species, usually correlated with geography. Aspects of white-headed gull behavioral biology, such as colonization ability and propensity to hybridize, as well as their recent evolutionary history, have likely played a large role in the limited genetic structure observed.

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.

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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. Fil: Sanín, Camilo. National Museum of Natural History; Estados Unidos. Universidad de los Andes; Colombia Fil: Cadena, Carlos Daniel. Universidad de los Andes; Colombia Fil: Maley, James M.. State University of Louisiana; Estados Unidos Fil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Chesser, R. Terry. National Museum of Natural History; Estados Unidos

The white-browed woodswallow Artamus superciliosus and masked woodswallow A. personatus (Passeriformes: Artamidae) are members of Australia's diverse arid- and semi-arid zone avifauna. Widely sympatric and among Australia's relatively few obligate long-distance temperate-tropical migrants, the two are well differentiated morphologically but not ecologically and vocally. They are pair breeders unlike other Artamus species, which are at least facultative cooperative breeders. For these reasons they are an excellent case in which to use molecular data in integrative study of their evolution from ecological and biogeographical perspectives. We used mitochondrial DNA (mtDNA) to test whether they are each other's closest relatives, whether they evolved migration independently, whether they have molecular signatures of population expansions like some other Australian arid zone birds, and to estimate the timing of any inferred population expansions. Their mtDNAs are monophyletic with respect to other species of Artamus but polyphyletic with respect to each other. The two species appear not to have evolved migration independently of each other but their morphological and mtDNA evolution have been strongly decoupled. Some level of hybridization and introgression cannot be dismissed outright as being involved in their mtDNA polyphyly but incomplete sorting of their most recent common ancestor's mtDNA is a simpler explanation consistent with their ecology. Bayesian phylogenetic inference and analyses of diversity within the two species (n=77) with conventional diversity statistics, statistical parsimony, and tests for population expansion vs stability (Tajima's D, Fu's Fs and Ramos-Onsin and Rozas's R2) all favour recent population increases. However, a non-starlike network suggests expansion(s) relatively early in the Pleistocene. Repeated population bottlenecks corresponding with multiple peaks of Pleistocene aridity could explain our findings, which add a new dimension to accruing data on the effects of Pleistocene aridity on the Australian biota.

Phylogenetic relationships within the genus Muscisaxicola, a primarily Andean group of tyrant-flycatchers, were studied using complete sequences of the mitochondrial genes COII and ND3. Relationships among Muscisaxicola species were found to differ substantially from those of previous views, suggesting convergence in traditional avian taxonomic characters within the genus. The 11 species of large, gray, “typical” Muscisaxicola flycatchers (including M. grisea, newly restored to species status) formed a distinct clade, consisting of two major groups: a clade of 6 species breeding primarily in the central Andes and a clade of 5 species breeding primarily in the southern Andes. The other 2 species traditionally placed in this genus, M. fluviatilis, an Amazonian species, and M. maculirostris, were both rather divergent genetically from the typical species, although M. maculirostris may be the sister taxon to the typical clade. The patterns of sympatry exhibited by Muscisaxicola species in the high Andes appear to be the consequence of speciation and secondary contact within regions of the Andes, rather than a result of dispersal between regions. Diversification of the typical Muscisaxicola species appears to have occurred during the middle and late Pleistocene, suggesting generally that taxa of the high Andes and Patagonia may have been greatly influenced by mid-to-late Pleistocene events. There were likely several independent developments of migration within this genus, but migration is probably ancestral in the southern clade, with subsequent loss of migration in two taxa.

Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America, is described. Species included in the new genus, formerly placed in Upucerthia, are T. certhioides and T. harterti.

SummaryAustral migrants are species that breed in temperate areas of South America and migrate north, towards or into Amazonia, for the southern winter. Migrations among these species are the most extensive of Southern Hemisphere migrations, and the austral system represents a third major migration system, in the sense that the term has been applied to Northern Hemisphere temperate-tropical migration. The geography of South America greatly influences the austral system. Lack of east-west geographical barriers and the shape of the continent promote a pattern of partially overlapping breeding and wintering ranges. The suboscine family Tyrannidae, the tyrant-flycatchers, is the largest group of austral migrants, with other major families including Emberizidae, Anatidae, Furnariidae, Accipitridae and Hirundinidae. Tyrant-flycatchers constitute more than one-half of the passerine austral migrants and roughly one-third of total austral migrants, a taxonomic domination seen in no other global migration system. Parallels exist, however, between austral migration and the Nearctic and Palearctic systems. Many of the same families, including Hirundinidae, Anatidae and Charadriidae, exhibit similarly high degrees of migratory behavi-our in each system. Passerine migration in the austral system is similar in numbers to that of the Nearctic-Neotropical system, but species migrate shorter distances and breed in more open and scrubby habitats. Possible differences in year-round resource availability between South American and North American temperate forests, in addition to differing availability of these habitats, may contribute to the low numbers of forest-dwelling austral migrants.

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats. Citation: Aplin KP, Suzuki H, Chinen AA, Chesser RT, ten Have J, et al. (2011) Multiple Geographic Origins of Commensalism and Complex Dispersal History of

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.

solely or additionally in canopy or secondary habitats Temperate-tropical migrants are integral parts of tropical were all migratory to some degree. In addition, families bird communities (e.g., Keast and Morton 1980) and primarily consisting of exclusively insectivorous species their ecological attributes in the tropics may have influwere found, with one exception, to contain neither enced the evolution of their migratory behavior (Rappole shortnor long-distance (i.e., Nearctic) migrants, where1995). An earlier article (Levey and Stiles 1992), for exas families with frugivorous species were found in six ample, proposed that a continuum of seasonal moveof eight cases to have evolved Neotropical-Nearctic miments exists among Neotropical birds in response to regration. source fluctuations and that the evolutionary end point Although these results were consistent with the evoluof this continuum is Neotropical-Nearctic migration. tionary precursor hypothesis, the earlier analysis (Levey Most Neotropical resident species that engage in smalland Stiles 1992) had two shortcomings. First, it did not scale movements are frugivores or nectarivores of edge, provide a true test of the hypothesis because the data canopy, or open habitats—traits that entail reliance were not independent of the Central American bird obon variable resources (e.g., Croat 1975; Levey 1988; servations that initially generated the hypothesis. Second, Blake and Loiselle 1991). Avian taxa that undertake the use of the comparative method did not incorporate seasonal migrations out of the Neotropics were hypothphylogeny in a way that transitions between character esized to have most likely been drawn from lineages states could be inferred and evaluated, and likely violated with these dietary and habitat characteristics because statistical independence (Felsenstein 1985; Harvey and of their predisposition for tracking highly variable Pagel 1991). resources across space and time (Levey and Stiles 1992). Here we explore further the relationship among diet, Thus, a nonrandom group of Neotropical lineages— habitat, and migration, improving on the earlier apthose with at least partially frugivorous or nectarivorproach (Levey and Stiles 1992) through examination of ous species of edge, canopy, and open habitat—were a separate migratory system—austral migration in South hypothesized to be most likely to contain NeotropAmerica—and by incorporating the avian phylogeny of

Phylogenetic relationships within the genus Cinclodes, a group of South American furnariids, were studied using complete sequences of the mitochondrial genes COII and ND3. The 13 species of Cinclodes formed a monophyletic group consisting of three major lineages: (1) the southeastern Brazilian isolate C. pabsti, which was sister to the rest of the genus; (2) a clade of five primarily Patagonian or central Argentine highlands species; and (3) a clade of seven primarily north-central Andean or Pacific species. Biogeographic structure in the Patagonian-Andean taxa was consistent with the deep Patagonian and north-central Andean division previously noted in the similarly distributed genus Muscisaxicola. Evolutionary relationships among Cinclodes species were partially consistent with expectations based on plumage, behavior, and ecology. The phenotypically distinctive C. antarcticus was found to be sister to the widespread C. fuscus in the primarily Patagonian-Argentine clade, and the distinctive C. p...

Stomach contents of five syntopic, obligate army-ant-following birds (Gymnopithys salvini, Rhegmatorhina melanosticta, Myrmeciza fortis, Phlegopsis nigromaculata, and Dendrocincla merula) from a site in depto. Pando, Bolivia, were studied. The species studied are highly intra- and interspecifically aggressive and are similar in foraging behavior. Diet composition and prey size differed little among species and were in general unrelated to trophic morphological characters or dominance status. Stomachs of dominant species, however, had greater numbers of prey items than stomachs of subdominants; this was the major dietary difference discovered within this obligate ant-following assemblage. The opportunistic resource-use pattern of these species is similar to that of other groups of species, such as some carrion or fruit-eaters, or temperate-zone insectivores during resource flushes, that rely on temporally or spatially superabundant resources. It differs from predictions based on bill length or body size.