Kevin Winker

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.

Phylogenetic Diversity among Low-Virulence Newcastle Disease Viruses from Waterfowl and Shorebirds and Comparison of Genotype Distributions to Those of Poultry-Origin Isolates

ABSTRACT Low-virulence Newcastle disease viruses (loNDV) are frequently recovered from wild bird species, but little is known about their distribution, genetic diversity, or potential to cause disease in poultry. NDV isolates recovered from cloacal samples of apparently healthy waterfowl and shorebirds (WS) in the United States during 1986 to 2005 were examined for genomic diversity and their potential for virulence (n = 249). In addition 19 loNDV isolates from U.S. live bird markets (LBMs) were analyzed and found to be genetically distinct from NDV used in live vaccines but related to WS-origin NDV. Phylogenetic analysis of the fusion protein identified nine novel genotypes among the class I NDV, and new genomic subgroups were identified among genotypes I and II of the class II viruses. The WS-origin viruses exhibited broad genetic and antigenic diversity, and some WS genotypes displayed a closer phylogenetic relationship to LBM-origin NDV. All NDV were predicted to be lentogenic based upon sequencing of the fusion cleavage site, intracerebral pathogenicity index, or mean death time in embryo assays. The USDA real-time reverse transcription-PCR assay, which targets the matrix gene, identified nearly all of the class II NDV tested but failed to detect class I viruses from both LBM and WS. The close phylogenetic proximity of some WS and LBM loNDV suggests that viral transmission may occur among wild birds and poultry; however, these events may occur unnoticed due to the broad genetic diversity of loNDV, the lentogenic presentation in birds, and the limitations of current rapid diagnostic tools.

Intercontinental Spread of Asian-Origin H5N8 to North America through Beringia by Migratory Birds

ABSTRACT Phylogenetic network analysis and understanding of waterfowl migration patterns suggest that the Eurasian H5N8 clade 2.3.4.4 avian influenza virus emerged in late 2013 in China, spread in early 2014 to South Korea and Japan, and reached Siberia and Beringia by summer 2014 via migratory birds. Three genetically distinct subgroups emerged and subsequently spread along different flyways during fall 2014 into Europe, North America, and East Asia, respectively. All three subgroups reappeared in Japan, a wintering site for waterfowl from Eurasia and parts of North America.

Fifty-Second Supplement to the American Ornithologists' Union check-list of North American Birds

The Auk, Vol. 128, Number 3, pages 600−613. ISSN 0004-8038, electronic ISSN 1938-4254.  2011 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2011.128.3.600 R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11

Daily mass gains among woodland migrants at an inland stopover site

We investigated fat deposition in transient, nocturnal, long-distance migrants at a wooded stopover site that is not near an ecological barrier (e.g. desert, large water body). The changes in body mass of recaptured birds have traditionally been used as a measure of mass gains at stopover sites. This technique ignores the majority of transients, however, possibly hindering the ability to answer species-level questions regarding stopover mass gain. We compare an analysis of recaptures with a technique that considers all captures and their condition by time of day. Eleven woodland-associated migrant species were analyzed, as well as a resident species (Black-capped Chickadee, Parus atricapillus) for comparison. Based on recapture data alone, our study site appears to be primarily a location of mass loss, rather than one of fat deposition. Conversely, the examination of condition by time of day suggests that individuals of several species have net daily gains greatly exceeding those of recaptured individuals. During autumn, however, several species exhibited net daily losses. Although some of these losses may be related to molt, it seems unlikely that molt is the only contributing factor. Differences among species in mass gains at our site suggest that various fat-deposition patterns (and, thus, migration strategies) may occur among migrants that are not approaching ecological barriers. Received 10 December 1991, accepted 11 March 1992.

Movements of Birds and Avian Influenza from Asia into Alaska

Despite involvement of large numbers of birds, the delivery rate of Asian-origin viruses to North America through Alaska is apparently low.

Fifty-First Supplement to the American Ornithologists' Union Check-List of North American Birds

The Auk, Vol. 127, Number 3, pages 726−744. ISSN 0004-8038, electronic ISSN 1938-4254.  2010 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2010.127.3.726. R. TeRRy ChesseR,1,12,13 RiChaRd C. Banks,1 F. keiTh BaRkeR,2 CaRla CiCeRo,3 Jon l. dunn,4 andRew w. kRaTTeR,5 iRBy J. loveTTe,6 Pamela C. Rasmussen,7 J. v. Remsen, JR.,8 James d. Rising,9 douglas F. sToTz,10 and kevin winkeR11

Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.

Northwestern song sparrow populations show genetic effects of sequential colonization

Two genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single‐step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10 000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (HE = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence.

PHYLOGEOGRAPHY OF THE MALLARD (ANAS PLATYRHYNCHOS): HYBRIDIZATION, DISPERSAL, AND LINEAGE SORTING CONTRIBUTE TO COMPLEX GEOGRAPHIC STRUCTURE

Abstract Population genetic variation in Mallards (Anas platyrhynchos; n = 152) from Western Russia, North Asia, the Aleutian Islands, and mainland Alaska was investigated using 667 base pairs of the 5′-end of the mitochondrial DNA (mtDNA) control region. DNA sequencing revealed two clades that correspond to Avise et al.’s (1990) group A and B mtDNA haplotypes. Group A haplotypes (80.3%) were wide- spread in all localities from Western Russia to Alaska. Group B haplotypes (19.7%), by contrast, were found primarily in mainland Alaska, where they occurred at high frequency (77.4%), but they also occurred at low frequencies (declining east to west) in the Aleutian Islands (11.8%) and the Primorye region of North Asia (4.4%). Group B haplotypes were not observed in Western Russia or elsewhere in North Asia outside Primorye. Consequently, Mallards exhibited substantial genetic structure between Old World and New World (ΦST = 0.4112–0.4956) but possessed little genetic structure within the Old World continental area (ΦST = 0.0018). Nonetheless, when only group A haplotypes were included in the analysis, Mallards from the Aleutian Islands differed (albeit with low levels of divergence) from each of the other three sampled regions in the Old World and New World (ΦST = 0.0728–0.1461, P < 0.05). Mallards inhabit the Aleutian Islands year-round, so these insular populations may be isolated from Asian and North American populations that occur in the Aleutian Islands only during migration. Overall weak phylogeographic structure and low genetic differentiation within Asia, and between Asia and North America when only group A haplotypes were evaluated, is probably explained by large long-term population sizes and significant intra-continental dispersal. The coexistence and nonrandom distribution of two divergent mtDNA haplotype lineages in Alaska, the Aleutian Islands, and the Primorye region of North Asia, but not in Western Russia or elsewhere in North Asia, is consistent with historical and contemporary hybridization and incomplete sorting of A and B mtDNA haplotype lineages in Mallards and closely related species inhabiting the Old World and New World.