The order Passeriformes (''perching birds'') comprises extant species diversity comparable to that of living mammals. For over a decade, a single phylogenetic hypothesis based on DNA-DNA hybridization has provided the primary framework for numerous comparative analyses of passerine ecological and behavioral evolution and for tests of the causal factors accounting for rapid radiations within the group. We report here a strongly supported phylogenetic tree based on two single-copy nuclear gene sequences for the most complete sampling of passerine families to date. This tree is incongruent with that derived from DNA-DNA hybridization, with half of the nodes from the latter in conflict and over a third of the conflicts significant as assessed under maximum likelihood. Our historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. The revised history implied by these data will require reassessment of comparative analyses of passerine diversification and adaptation.M ajor lineages of the Ϸ5,739 species of passerine birds (1) have diversified on all continents and now occupy nearly all terrestrial ecosystems. The songbirds (oscines, suborder Passeri) alone comprise nearly half of all extant avian species and represent the largest identifiable radiation of birds (2), encompassing a staggering ecological and behavioral diversity. The foundation for understanding passerine diversification and for integrating the spatial, ecological, and temporal history of the group is a comprehensive and robust phylogenetic hypothesis. A decade ago, in a pioneering work, Sibley and Ahlquist (3) used DNA-DNA hybridization to produce the first large-scale phylogenetic hypothesis for passerine birds and suggested a specific temporal history for passerine diversification. Despite oftenvoiced concerns about the robustness of this phylogeny (colloquially termed the ''Tapestry'' after its appearance on the wall at an ornithological meeting), it has provided a framework for numerous historical analyses of passerine ecology (4), behavior (5), and diversification (6, 7), and continues to fuel the search for explanations of passerine diversity (8).Recently, studies have begun to contradict aspects of the DNA hybridization hypothesis for passerines (ref. 9; citations in ref. 10). These investigations, however, used relatively short gene sequences and, more importantly, limited taxon sampling across passerines; thus the phylogenetic, biogeographic, and temporal interpretations of the radiation were incomplete, and broad tests of the DNA hybridization tree were not possible. Here we analyze 4,126 aligned positions of the nuclear genes RAG-1 and -2 from 144 passerine species in 45 families, including representatives of all but one family recognized by current taxonomy (1). We find substantial support for many portions of the passerine tree, as well as quantitative evidence for the re...
Pleistocene climate fluctuations shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Late Pleistocene for East Asia, a region of great topographical complexity and presumably milder historical climate, remains poorly understood. We analysed 3.86 kb of the mitochondrial genome of 186 Chinese Hwamei birds, Leucodioptron canorum canorum, and found that contrary to the conventional expectation of population decline during cold periods (stadials), the demographic history of this species shows continuous population growth since the penultimate glacial period (about 170,000 years ago). Refugia were identified in the south, coastal regions, and northern inland areas, implying that topographic complexity played a substantial role in providing suitable habitats for the Chinese Hwamei during cold periods. Intermittent gene flow between these refugia during the warmer periods (interstadials) might have resulted in a large effective population of this bird through the last glacial period.
Sequences from complete mitochondrial cytochrome b genes of 34 tigers support the hypothesis that Sumatran tigers are diagnostically distinct from mainland populations. None of the latter, including Bengals, Siberians, or Indochinese tigers, were found to have fixed diagnostic characters. Phylogenetic analysis of these sequences confirms these results. Within the framework of a phylogenetic species concept, current evidence thus supports the recognition of two distinct taxa, and within the context of this definition they could be ranked at the species level. This paper also documents a previously unrecognized nuclear insert of mitochondrial DNA that includes, minimally, mitochondrial homologues of a control region that lacks the feline mitochondrial repeat sequences, a complete cytochrome b gene, and complete tRNA Thr and tRNA Pro genes. In a phylogenetic analysis of the nuclear cytochrome b-like sequences and various feline mitochondrial sequences, the nuclear insert clusters with lion mitochondrial cytochrome b sequences, which suggests the insert is at least as old as the split between lions and tigers. The results of this study emphasize the importance of doing more to conserve Sumatran tigers. Because they are underrepresented in zoos relative to Bengals and Siberians, an effort should be made to increase captive breeding stocks of Sumatrans. That Sumatrans are a distinct taxonomic entity relative to mainland populations can be used in educational programs to increase conservation efforts within Indonesia.
The cnemophiline`birds of paradise' (Cnemophilinae) and Macgregor's`bird of paradise' (Macgregoria) have traditionally been included in the Paradisaeidae although their relationships within the group have been enigmatic and subject to repeated discussion in the literature. Here we use sequences from two mitochondrial genes, cytochrome b and cytochrome oxidase I, along with a suite of morphological characters, to investigate their relationships to paradisaeids and other members of the passerine Parvorder Corvida. The combined data strongly support the removal of both groups from the birds of paradise: the cnemophilines are basal members of the Corvoidea and Macgregoria is a member of the Meliphagoidea and embedded in the honeyeaters (Meliphagidae) close to the genus Melipotes. The amount of sequence divergence among basal passeriforms and members of the Corvida, as well as available fossil evidence for Australian corvidans, suggest that cnemophilines represent an ancient lineage within the corvoid radiation. Because cnemophilines and Macgregoria have been placed at the base of the paradisaeid tree, hypotheses of morphological, behavioural and ecological character-state transformations within the family will require reanalysis.
Wolbachia spp. are obligate maternally inherited endosymbiotic bacteria that infect diverse arthropods and filarial nematodes. Previous microscopic and molecular studies have identified Wolbachia in several bed bug species (Cimicidae), but little is known about how widespread Wolbachia infections are among the Cimicidae. Because cimicids of non-medical importance are not commonly collected, we hypothesized that preserved museum specimens could be assayed for Wolbachia infections. For the screening of museum specimens, we designed a set of primers that specifically amplify small diagnostic fragments (130 to 240 bp) of the Wolbachia 16S rRNA gene. Using these and other previously published primers, we screened 39 cimicid species (spanning 16 genera and all 6 recognized subfamilies) and 2 species of the sister family Polyctenidae for Wolbachia infections using museum and wild-caught material. Amplified fragments were sequenced to confirm that our primers were amplifying Wolbachia DNA. We identified 10 infections, 8 of which were previously undescribed. Infections in the F supergroup were common in the subfamily Cimicinae, while infections in the A supergroup were identified in the subfamilies Afrocimicinae and Haematosiphoninae. Even though specimens were degraded, we detected infections in over 23% of cimicid species. Our results indicate that Wolbachia infections may be common among cimicids and that archived museum material is a useful untapped resource for invertebrate endosymbiont surveys. The new screening primers listed in this report will be useful for other researchers conducting Wolbachia surveys with specimens with less-than-optimum DNA quality.
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