695 results on '"Winker, Kevin"'
Search Results
302. Sixty-fourth Supplement to the American Ornithological Society’s Check-list of North American Birds.
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Chesser, R. Terry, Billerman, Shawn M., Burns, Kevin J., Cicero, Carla, Dunn, Jon L., Hernández-Baños, Blanca E., Jiménez, Rosa Alicia, Kratter, Andrew W., Mason, Nicholas A., Rasmussen, Pamela C., Remsen, Jr. J. V., and Winker, Kevin
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BIRD classification , *BIRD phylogeny , *ORNITHOLOGISTS - Published
- 2023
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303. Brina Cattell Kessel, 1925–2016
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Winker, Kevin, Kessel, Quentin Cattell, and Gibson, Daniel D.
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- 2016
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304. Occurrence and taxonomy of Arctic Warblers (Phylloscopus borealis) sensu lato in North America
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Withrow, Jack J., Gibson, Daniel D., Gerasimov, Yuri, Gerasimov, Nickolay, Shestopalov, Alexander, and Winker, Kevin
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- 2016
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305. HBW AND BIRDLIFE INTERNATIONAL ILLUSTRATED CHECKLIST OF THE BIRDS OF THE WORLD.
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Winker, Kevin
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NONFICTION - Published
- 2015
306. High-Latitude Passerine Migrants Overlap Energetically Demanding Events in Autumn
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Benson, Anna-Marie and Winker, Kevin
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- 2015
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307. Fifty-sixth Supplement to the American Ornithologists' Union: Check-list of North American Birds
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Chesser, R. Terry, Banks, Richard C., Burns, Kevin J., Cicero, Carla, Dunn, Jon L., Kratter, Andrew W., Lovette, Irby J., Navarro-Sigüenza, Adolfo G., Rasmussen, Pamela C., Remsen, J. V., Rising, James D., Stotz, Douglas F., and Winker, Kevin
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- 2015
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308. Voucher specimens and quality control in avian molecular studies.
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Winker, Kevin, Braun, Michael J., and Graves, Gary R.
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- 1996
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309. Fifty-Fourth Supplement to the American Ornithologists' Union Check-list of North American Birds
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Chesser, R. Terry, Banks, Richard C., Barker, F. Keith, Cicero, Carla, Dunn, Jon L., Kratter, Andrew W., Lovette, Irby J., Rasmussen, Pamela C., Remsen, J. V., Rising, James D., Stotz, Douglas F., and Winker, Kevin
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- 2013
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310. Errata: Fifty-First Supplement to the American Ornithologists' Union Check-List of North American Birds
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Terry Chesser, R., Banks, Richard C., Keith Barker, F., Cicero, Carla, Dunn, Jon L., Kratter, Andrew W., Lovette, Irby J., Rasmussen, Pamela C., Remsen, J. V., Rising, James D., Stotz, Douglas F., and Winker, Kevin
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- 2010
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311. Fiftieth Supplement to the American Ornithologists' Union Check-List of North American Birds
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Terry Chesser, R., Banks, Richard C., Keith Barker, F., Cicero, Carla, Dunn, Jon L., Kratter, Andrew W., Lovette, Irby J., Rasmussen, Pamela C., Remsen, J. V., Rising, James D., Stotz, Douglas F., and Winker, Kevin
- Published
- 2009
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312. Molecular “Cuckoo Clock” Suggests Listing of Western Yellow-billed Cuckoos May Be Warranted
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Pruett, Christin L., Gibson, Daniel D., and Winker, Kevin
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- 2001
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313. Handbook of the Birds of the World, Volume 13.
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Winker, Kevin
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BIRDS ,NONFICTION - Abstract
The article reviews the book "Handbook of the Birds of the World: Penduline-tits to Shrikes," Volume 13, edited by J. del Hoyo, A. Elliott, and D. Christie.
- Published
- 2009
314. The autumn passage of yellow-bellied flycatchers in south Texas
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Rappole, John H. and Winker, Kevin
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POPULATION dynamics - Published
- 1992
315. Population dynamics of the wood thrush in southern Veracruz, Mexico
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Rappole, John H., Ramos, Mario A., and Winker, Kevin
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POPULATION dynamics - Published
- 1990
316. Intercontinental Spread of Asian-Origin H5N8 to North America through Beringia by Migratory Birds.
- Author
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Dong-Hun Lee, Mia Kim Torchetti, Winker, Kevin, Ip, Hon S., Chang-Seon Song, and Swayne, David E.
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AVIAN influenza A virus , *MIGRATORY birds , *PHYLOGENY , *AVIAN influenza , *MIGRATION flyways - 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. [ABSTRACT FROM AUTHOR]
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- 2015
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317. Measuring Birds (Vógel Vermissen).
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Winker, Kevin and Engstrom, R. Todd
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BIRDS , *ORNITHOLOGY , *NONFICTION - Abstract
The article reviews the book "Measuring Birds (Vógel Vermissen)," edited by Deutsche Ornithologen-Gesellshaft.
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- 2012
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318. HANDBOOK OF THE BIRDS OF THE WORLD, VOLUME 15. WEAVERS TO NEW WORLD WARBLERS.
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Winker, Kevin
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WOOD warblers ,NONFICTION - Abstract
The article reviews the book "Handbook of the Birds of the World: Weavers to New World Warblers," Volume 15, by J. del Hoyo, A. Elliott, and D. Christie.
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- 2010
319. HANDBOOK OF THE BIRDS OF THE WORLD, VOLUME 14. Bush-shrikes to Old World Sparrows.
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Winker, Kevin
- Subjects
SPARROWS ,NONFICTION - Abstract
The article reviews the book "Handbook of the Birds of the World: Volume 14: Bush-Shrikes to Old World Sparrows," edited by J. del Hoyo, A. Elliott, and D. Christie.
- Published
- 2010
320. Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex.
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Spaulding, Fern, McLaughlin, Jessica F., Cheek, Rebecca G., McCracken, Kevin G., Glenn, Travis C., and Winker, Kevin
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GENE flow , *VICARIANCE , *NUCLEAR DNA , *GENOMICS , *DUCKS , *PHYLOGENY , *GENETIC speciation - Abstract
[Display omitted] • Resolved uncertainty in the green-winged teal and the yellow-billed teal complex. • Ultraconserved elements were used to resolve phylogenic relationships. • Mitogenomic and nuclear DNA showed discordant phylogenetic relationships. • Divergence with gene flow was present in each pairwise demographic analyses. • Heteropatric, parapatric, and allopatric modes of speciation are likely to be involved. The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca , A. c. nimia , and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca , A. c. nimia , and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca , nimia , carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca , nimia)(carolinensis , flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca − nimia , crecca − carolinensis , and carolinensis − flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1–0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca − nimia), parapatric (crecca − carolinensis), and (mostly) allopatric (carolinensis − flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits. [ABSTRACT FROM AUTHOR]
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- 2023
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321. Clarifying the systematics of an enigmatic avian lineage: What is a bombycillid?
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Spellman, Garth M., Cibois, Alice, Moyle, Robert G., Winker, Kevin, and Keith Barker, F.
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- 2008
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322. Specimen collection is essential for modern science.
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Nachman MW, Beckman EJ, Bowie RC, Cicero C, Conroy CJ, Dudley R, Hayes TB, Koo MS, Lacey EA, Martin CH, McGuire JA, Patton JL, Spencer CL, Tarvin RD, Wake MH, Wang IJ, Achmadi A, Álvarez-Castañeda ST, Andersen MJ, Arroyave J, Austin CC, Barker FK, Barrow LN, Barrowclough GF, Bates J, Bauer AM, Bell KC, Bell RC, Bronson AW, Brown RM, Burbrink FT, Burns KJ, Cadena CD, Cannatella DC, Castoe TA, Chakrabarty P, Colella JP, Cook JA, Cracraft JL, Davis DR, Davis Rabosky AR, D'Elía G, Dumbacher JP, Dunnum JL, Edwards SV, Esselstyn JA, Faivovich J, Fjeldså J, Flores-Villela OA, Ford K, Fuchs J, Fujita MK, Good JM, Greenbaum E, Greene HW, Hackett S, Hamidy A, Hanken J, Haryoko T, Hawkins MT, Heaney LR, Hillis DM, Hollingsworth BD, Hornsby AD, Hosner PA, Irham M, Jansa S, Jiménez RA, Joseph L, Kirchman JJ, LaDuc TJ, Leaché AD, Lessa EP, López-Fernández H, Mason NA, McCormack JE, McMahan CD, Moyle RG, Ojeda RA, Olson LE, Kin Onn C, Parenti LR, Parra-Olea G, Patterson BD, Pauly GB, Pavan SE, Peterson AT, Poe S, Rabosky DL, Raxworthy CJ, Reddy S, Rico-Guevara A, Riyanto A, Rocha LA, Ron SR, Rovito SM, Rowe KC, Rowley J, Ruane S, Salazar-Valenzuela D, Shultz AJ, Sidlauskas B, Sikes DS, Simmons NB, Stiassny MLJ, Streicher JW, Stuart BL, Summers AP, Tavera J, Teta P, Thompson CW, Timm RM, Torres-Carvajal O, Voelker G, Voss RS, Winker K, Witt C, Wommack EA, and Zink RM
- Subjects
- Animals, Natural History, Museums, Specimen Handling
- Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
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- 2023
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323. Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule.
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Carbeck K, Arcese P, Lovette I, Pruett C, Winker K, and Walsh J
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- Animals, Body Size, Models, Biological, Climate, Temperature, Sparrows genetics
- Abstract
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species' capacity to adapt to change. To identify genes underlying Bergmann's Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 - 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann's Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species., (© 2023. The Author(s).)
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- 2023
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324. Beringia as a high-latitude engine of avian speciation.
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Winker K, Withrow JJ, Gibson DD, and Pruett CL
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- Animals, Phylogeny, Genetic Speciation, Biological Evolution, Passeriformes
- Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification., (© 2023 Cambridge Philosophical Society.)
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- 2023
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325. Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the variable seedeater (Sporophila corvina).
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Ocampo D, Winker K, Miller MJ, Sandoval L, and Uy JAC
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- Animals, Genetic Drift, Hybridization, Genetic, Gene Flow, Reproductive Isolation, Passeriformes genetics
- Abstract
After establishing secondary contact, recently diverged populations may remain reproductively isolated or may hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the variable seedeater (Sporophila corvina) to examine how coloration and genetic divergence shape patterns of hybridization. We found that differences in plumage coloration are probably maintained by divergent selection across contact zones; however, the degree of plumage differentiation does not match overall patterns of hybridization. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage), populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting frequent reproduction and high survivorship for hybrid individuals. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic structure between populations. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
- Published
- 2023
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326. Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow.
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Ocampo D, Winker K, Miller MJ, Sandoval L, and Uy JAC
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- Animals, Biological Evolution, DNA, Mitochondrial chemistry, DNA, Mitochondrial genetics, Phylogeny, Gene Flow, Passeriformes genetics
- Abstract
Disentangling the evolutionary relationships of rapidly radiating clades is often challenging because of low genetic differentiation and potentially high levels of gene flow among diverging taxa. The genus Sporophila consists of small Neotropical birds that show, in general, relatively low genetic divergence, but particularly high speciation rates and pronounced variation in secondary sexual traits (e.g., plumage color), which can be important in generating premating reproductive isolation. In cases like these, the use of genome-wide sequence data can increase the resolution to uncover a clade's evolutionary history. Here, we used a phylogenomic approach to study the evolutionary history and genetic structure of the Variable Seedeater superspecies complex, which includes S. corvina, S. intermedia, and S. americana. Using ∼25,000 genome-wide single nucleotide polymorphisms (SNPs), we confirmed that the Variable Seedeater superspecies complex is monophyletic. However, a phylogenetic reconstruction based on a mitochondrial marker (ND2) resulted in a discordant tree topology, particularly in the position of Wing-barred Seedeater S. americana, which might be due to a mitochondrial capture event. Our results suggest historical gene flow among lineages, particularly between species with conflicting topologies. Among the four phenotypically variable S. corvina subspecies, our structure analyses identified three main distinct genetic groups (K = 3), and that the entirely black subspecies, S. c. corvina, is derived from within a pied-colored clade. Further, we inferred widespread gene flow across the whole species' distribution, including between subspecies. However, gene flow was about 100 times lower at the geographic boundaries of the entirely black and the pied subspecies, suggesting an important role for plumage divergence in limiting gene flow. Overall, our findings suggest that the early diversification of the Sporophila genus occurred rapidly despite historical gene flow between lineages and that divergence in plumage color possibly influences the extent of gene flow among taxa., (Copyright © 2022 Elsevier Inc. All rights reserved.)
- Published
- 2022
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327. Adaptive introgression of the beta-globin cluster in two Andean waterfowl.
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Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, and McCracken KG
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- Animals, Carrier Proteins, Evolution, Molecular, Sequence Analysis, DNA, Altitude, beta-Globins genetics, beta-Globins metabolism
- Abstract
Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O
2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.- Published
- 2021
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328. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.
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Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, and Knight R
- Abstract
Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith's PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies. In addition, we provide a BSD-licensed QIIME2 plugin (https://github.com/biocore/q2-fragment-insertion) for SEPP and integration into the microbial study management platform QIITA. IMPORTANCE The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.
- Published
- 2018
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329. An examination of species limits in the Aulacorhynchus "prasinus" toucanet complex (Aves: Ramphastidae).
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Winker K
- Abstract
The number of species recognized in Aulacorhynchus toucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in the A. "prasinus" complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups of A. "prasinus" sensu lato are simply "cookie-cutter" (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial between A. "p." cyanolaemus and A. "p." atrogularis and nonexistent between other major groups, although from genetic evidence it is likely rare between A. "p." albivitta and A. "p." cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species: A. wagleri, prasinus, caeruleogularis, albivitta, and atrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study., Competing Interests: The author declares there are no competing interests.
- Published
- 2016
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330. Development and characterization of microsatellite loci for common raven (Corvus corax) and cross species amplification in other Corvidae.
- Author
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Pruett CL, Wan L, Li T, Spern C, Lance SL, Glenn T, Faircloth B, and Winker K
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- Alaska, Alleles, Animals, Crows classification, Gene Frequency, Genotype, Geography, Linkage Disequilibrium, Molecular Sequence Data, Polymorphism, Genetic, Songbirds classification, Species Specificity, Crows genetics, Genetic Loci genetics, Microsatellite Repeats genetics, Songbirds genetics
- Abstract
Background: A priority for conservation is the identification of endemic populations. We developed microsatellite markers for common raven (Corvus corax), a bird species with a Holarctic distribution, to identify and assess endemic populations in Alaska., Results: From a total of 50 microsatellite loci, we isolated and characterized 15 loci. Eight of these loci were polymorphic and readily scoreable. Eighteen to 20 common ravens from Fairbanks, Alaska were genotyped showing the following variability: 3-8 alleles per locus, 0.25-0.80 observed heterozygosity (Ho), and 0.30-0.80 expected heterozygosity (He). All loci were in Hardy-Weinberg equilibrium and linkage equilibrium and many loci amplified and were polymorphic in related taxa., Conclusions: These loci will be used to identify endemic populations of common raven and assess their genetic diversity and connectivity.
- Published
- 2015
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331. Intercontinental Spread of Asian-Origin H5N8 to North America through Beringia by Migratory Birds.
- Author
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Lee DH, Torchetti MK, Winker K, Ip HS, Song CS, and Swayne DE
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- Animals, Asia, Birds, Europe, Humans, Influenza in Birds transmission, Molecular Epidemiology, North America, Siberia, Animal Migration, Influenza A virus classification, Influenza A virus isolation & purification, Influenza in Birds epidemiology, Influenza in Birds virology
- 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., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)
- Published
- 2015
- Full Text
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332. Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas).
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Peters JL, Winker K, Millam KC, Lavretsky P, Kulikova I, Wilson RE, Zhuravlev YN, and McCracken KG
- Subjects
- Animals, Cell Nucleus genetics, DNA, Mitochondrial genetics, Ducks genetics, Haplotypes, Introns, Molecular Sequence Data, Phenotype, Sequence Analysis, DNA, Ducks classification, Gene Flow, Genetic Speciation, Genetics, Population
- Abstract
Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation., (© 2014 John Wiley & Sons Ltd.)
- Published
- 2014
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333. Heteropatric speciation in a duck, Anas crecca.
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Winker K, McCracken KG, Gibson DD, and Peters JL
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- Alaska, Animals, DNA, Mitochondrial genetics, Ducks classification, Genetic Variation, Introns, Models, Genetic, Molecular Sequence Data, Sequence Analysis, DNA, Sympatry, Ducks genetics, Gene Flow, Genetic Speciation, Genetics, Population
- Abstract
Heteropatric differentiation is a mode of speciation with gene flow in which divergence occurs between lineages that are in sympatry and allopatry at different times during cyclic spatial movements. Empirical evidence suggests that heteropatric differentiation may prove to be common among seasonally migratory organisms. We examined genetic differentiation between the sedentary Aleutian Islands population of green-winged teal (Anas crecca-nimia) and its close migratory relative, the Eurasian, or Old World (OW), Anas c. crecca population, a portion of which passes through the range of nimia during its seasonal migrations. We also examined its relationship with the parapatric North American, New World (NW), A. c. carolinensis population. Sequence data from eight nuclear introns and the mtDNA control region showed that the nimia-crecca divergence occurred much more recently than the deeper crecca-carolinensis split (~83 000 years vs. ~1.1 Myr). Despite considerable spatial overlap between crecca and nimia during seasonal migration, three key predictions of heteropatric differentiation are supported: significant genetic divergence (overall mean Φst = 0.07), low gene flow (2Ne m ~ 1.8), and an effective population size in nimia that is not especially low (Ne ~ 80 000 individuals). Similar levels of gene flow have come into nimia from carolinensis, but no detectable nuclear gene flow has gone out of nimia into either OW (crecca) or NW (carolinensis) populations. We infer that adaptations of these populations to local optima in different places (e.g. each matching their reproductive effort to different resource blooms) promote genetic isolation and divergence despite periods of sympatry between them, as the heteropatric model predicts., (© 2013 John Wiley & Sons Ltd.)
- Published
- 2013
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- View/download PDF
334. How migratory thrushes conquered northern North America: a comparative phylogeography approach.
- Author
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Topp CM, Pruett CL, McCracken KG, and Winker K
- Abstract
Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson's thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson's thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species' ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
- Published
- 2013
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335. Decadal changes and delayed avian species losses due to deforestation in the northern Neotropics.
- Author
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Shaw DW, Escalante P, Rappole JH, Ramos MA, Oehlenschlager RJ, Warner DW, and Winker K
- Abstract
How avifauna respond to the long-term loss and fragmentation of tropical forests is a critical issue in biodiversity management. We use data from over 30 years to gain insights into such changes in the northernmost Neotropical rainforest in the Sierra de Los Tuxtlas of southern Veracruz, Mexico. This region has been extensively deforested over the past half-century. The Estación de Biología Tropical Los Tuxtlas, of the Universidad Nacional Autónoma de México (UNAM), protects a 640 ha tract of lowland forest. It became relatively isolated from other forested tracts between 1975 and 1985, but it retains a corridor of forest to more extensive forests at higher elevations on Volcán San Martín. Most deforestation in this area occurred during the 1970s and early 1980s. Forest birds were sampled on the station and surrounding areas using mist nets during eight non-breeding seasons from 1973 to 2004 (though in some seasons netting extended into the local breeding season for some species). Our data suggested extirpations or declines in 12 species of birds subject to capture in mist nets. Six of the eight species no longer present were captured in 1992-95, but not in 2003-2004. Presence/absence data from netting and observational data suggested that another four low-density species also disappeared since sampling began. This indicates a substantial time lag between the loss of habitat and the apparent extirpation of these species. Delayed species loss and the heterogeneous nature of the species affected will be important factors in tropical forest management and conservation.
- Published
- 2013
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336. Natural history: Small collections make a big impact.
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Winker K and Withrow JJ
- Subjects
- Alaska, Animals, Natural History, Universities, Birds, Museums
- Published
- 2013
- Full Text
- View/download PDF
337. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.
- Author
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Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, and Glenn TC
- Subjects
- Animals, Bayes Theorem, Birds physiology, Computational Biology methods, Conserved Sequence, Databases, Factual, Evolution, Molecular, Gene Library, Genomics, MicroRNAs metabolism, Models, Statistical, Phylogeny, Sequence Analysis, DNA, Biological Evolution, Turtles physiology
- Abstract
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.
- Published
- 2012
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338. A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato).
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Peters JL, McCracken KG, Pruett CL, Rohwer S, Drovetski SV, Zhuravlev YN, Kulikova I, Gibson DD, and Winker K
- Subjects
- Animals, Arctic Regions, Breeding, Cell Nucleus genetics, Computer Simulation, DNA, Mitochondrial genetics, Evolution, Molecular, Genetics, Population, Haplotypes, Introns, Male, Molecular Sequence Data, Multilocus Sequence Typing, Population Density, Sequence Analysis, DNA, Ducks genetics, Gene Flow, Genetic Speciation
- Abstract
Speciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green-winged teal (Anas crecca carolinensis). These ducks come into contact in Beringia (north-eastern Asia and north-western North America) and have probably done so, perhaps cyclically, since the Pliocene-Pleistocene transition, ~2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (Φ(st) ≥ 0.35), but six loci were undifferentiated or only weakly structured (Φ(st) = 0.0-0.06). Gene flow between crecca and carolinensis was ~1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ~1 and ~20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion., (© 2012 Blackwell Publishing Ltd.)
- Published
- 2012
- Full Text
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339. Transcriptome analysis of a North American songbird, Melospiza melodia.
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Srivastava A, Winker K, Shaw TI, Jones KL, and Glenn TC
- Subjects
- Animals, Gene Expression Profiling, Genetic Markers, North America, Polymorphism, Single Nucleotide, Sparrows genetics, Transcriptome genetics
- Abstract
An effective way to understand the genomics of divergence in non-model organisms is to use the transcriptome to identify genes associated with divergence. We examine the transcriptome of the song sparrow (Melospiza melodia) and contrast it with the avian models zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). We aimed to (i) obtain a functional annotation of a substantial portion of the song sparrow transcriptome; (ii) compare transcript divergence; (iii) efficiently characterize single nucleotide polymorphism/indel markers possibly fixed between song sparrow subspecies; and (iv) identify the most common set of transcripts in birds using the zebra finch as a reference. Using two individuals from each of three populations, whole-body mRNA was normalized and sequenced (110 Mb total). The assembly yielded 38,539 contigs [N50 (the length-weighted median) = 482 bp]; 4574 were orthologous to both model genomes and 3680 are functionally annotated. This low-coverage scan of the song sparrow transcriptome revealed 29,982 SNPs/indels, 1402 fixed between populations and subspecies. Referencing zebra finch and chicken, we identified 43 and 5 fast-evolving genes, respectively. We also identified the most common set of transcripts present in birds with respect to zebra finch. This study provides new insight into songbird transcriptomes, and candidate markers identified here may help research in songbirds (oscine Passeriformes), a frequently studied group.
- Published
- 2012
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340. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.
- Author
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Peters JL, Roberts TE, Winker K, and McCracken KG
- Subjects
- Animals, Biodiversity, Cell Nucleus metabolism, Computational Biology methods, DNA genetics, Ducks, Gene Flow, Geography, Haplotypes, Models, Biological, Models, Theoretical, Probability, Selection, Genetic, Sequence Analysis, DNA, Genetic Variation, Genetics, Population
- Abstract
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.
- Published
- 2012
- Full Text
- View/download PDF
341. In scientific publishing at the article level, effort matters more than journal impact factors: hard work and co-authors overshadow journal venue in acquiring citations.
- Author
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Winker K
- Subjects
- Humans, Regression Analysis, Science, Authorship, Bibliometrics, Journal Impact Factor, Peer Review, Research standards, Periodicals as Topic standards, Workload
- Published
- 2011
- Full Text
- View/download PDF
342. Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds.
- Author
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Humphries EM and Winker K
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Animals, Anseriformes classification, Anseriformes genetics, Birds classification, Cell Nucleus genetics, Charadriiformes classification, Charadriiformes genetics, Genetic Variation, Genetics, Population, Genome, Mitochondria, Muscle genetics, Passeriformes classification, Passeriformes genetics, Phenotype, Sequence Analysis, DNA, Birds genetics, DNA genetics, DNA, Mitochondrial genetics, Evolution, Molecular, Genetic Speciation
- Abstract
Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits., (© 2010 Blackwell Publishing Ltd.)
- Published
- 2011
- Full Text
- View/download PDF
343. Short-term hurricane impacts on a neotropical community of marked birds and implications for early-stage community resilience.
- Author
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Johnson AB and Winker K
- Subjects
- Animals, Belize, Disasters, Population Dynamics, Species Specificity, Time Factors, Tropical Climate, Birds growth & development, Cyclonic Storms, Ecosystem, Trees growth & development
- Abstract
Populations in fragmented ecosystems risk extirpation through natural disasters, which must be endured rather than avoided. Managing communities for resilience is thus critical, but details are sketchy about the capacity for resilience and its associated properties in vertebrate communities. We studied short-term resilience in a community of individually marked birds, following this community through the catastrophic destruction of its forest habitat by Hurricane Iris in Belize, Central America. We sampled for 58 d immediately before the storm, 28 d beginning 11 d after Hurricane Iris, and for 69 d approximately one year later. Our data showed that the initial capacity for resilience was strong. Many banded individuals remained after the storm, although lower post-hurricane recapture rates revealed increased turnover among individuals. Changes occurred in community dynamics and in abundances among species and guilds. Survivors and immigrants both were critical components of resilience, but in a heterogeneous, species-specific manner. Delayed effects, including higher fat storage and increased species losses, were evident one year later.
- Published
- 2010
- Full Text
- View/download PDF
344. Neotropical birds show a humped distribution of within-population genetic diversity along a latitudinal transect.
- Author
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Miller MJ, Bermingham E, Klicka J, Escalante P, and Winker K
- Subjects
- Animals, Gene Flow, Species Specificity, Birds genetics, Genetic Variation, Tropical Climate
- Abstract
The latitudinal gradient in species richness is a nearly universal ecological phenomenon. Similarly, conspecific genetic diversity often increases towards the equator - usually explained as the consequence of post-glacial range expansion or due to the shared response of genetic diversity to processes that promote species richness. However, no study has yet examined the relationship between latitude and within-population genetic diversity in exclusively tropical species. We surveyed genetic variation in nine resident bird species co-occurring in tropical lowlands between southern Mexico and western Ecuador, where avian species richness increases with decreasing latitude. Within-population genetic variation was always highest at mid-range latitudes, and not in the most equatorial populations. Differences in demography and gene flow across species' ranges may explain some of our observations; however, much of the pattern may be due simply to geometric constraints. Our findings have implications for conservation planning and for understanding how biodiversity scales from genes to communities.
- Published
- 2010
- Full Text
- View/download PDF
345. The Asia-to-America influx of avian influenza wild bird hosts is large.
- Author
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Winker K and Gibson DD
- Subjects
- Alaska epidemiology, Animal Migration, Animals, Asia epidemiology, Population Surveillance, Animals, Wild, Birds, Influenza in Birds epidemiology
- Abstract
Recent literature has underestimated the number and taxonomic diversity of wild birds moving between Asia and North America. Our analyses of the major avian influenza (AI) host groups show that fully 33 species of waterfowl (Anatidae), 46 species of shorebirds (Charadriidae and Scolopacidae), and 15 species of gulls and terns (Laridae) are involved in movements from Asia to Alaska across northern oceans (Table 1). Our data suggest that about 1.5-2.9 million individuals in these important host groups move from Asia to Alaska annually. Among all of the host groups we consider most relevant for AI virus movement models in this region (waterfowl, shorebirds, and gulls and terns), it seems likely that thousands of AI-infectious birds may be involved in annual Asia-to-America migrations. Importantly, host availability in Alaska once these vectors arrive is also very high, representing at least 5-10 times more birds and infectious birds than the host populations moving from Asia to North America. Incorporating our data into a recent model of the global spread of the highly pathogenic H5N1 suggests that wild birds are a more likely source of this strain being brought into the United States than trade in domestic birds, although the latter remain a numerically more probable source of introduction into the New World. Our results should help in defining the key taxonomic, geographic, and seasonal factors involved in this complex intercontinental association of wild bird AI hosts. The next steps are to determine infection rates of low pathogenicity and highly pathogenic viruses among these hosts and to incorporate these into dynamic models.
- Published
- 2010
- Full Text
- View/download PDF
346. Diversification at high latitudes: speciation of buntings in the genus Plectrophenax inferred from mitochondrial and nuclear markers.
- Author
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Maley JM and Winker K
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Animals, Arctic Regions, Bayes Theorem, Cell Nucleus genetics, DNA, Mitochondrial genetics, Founder Effect, Gene Flow, Genetic Variation, Models, Genetic, Population Density, Sequence Analysis, DNA, Evolution, Molecular, Genetic Speciation, Genetics, Population, Songbirds genetics
- Abstract
High-latitude diversification is a process characterized by speciation and extinction due to climatically driven vicariance and dispersal events. McKay's buntings (Plectrophenax hyperboreus) are high-latitude island endemic songbirds, and their global range is restricted to Beringia. Snow buntings (P. nivalis), their closest relatives, are distributed throughout the Holarctic, breeding in available habitat surrounding the island range of McKay's buntings. We sequenced 1123 base pairs of mitochondrial DNA for 40 individuals of each species and analysed a total of 913 AFLPs for 57 individuals. Both marker types suggested weak but significant genetic differentiation. Analysis of sequence data indicated divergence occurring when the current breeding range of McKay's buntings was a hill on the Beringian steppe (approximately 18,400 to approximately 73,700 years before present), suggesting that snow buntings were restricted to lower latitudes by ice sheets. Ancestral effective population size estimates indicate a founder event in McKay's buntings followed by an expansion and then a reduction in effective size. Rising sea levels and asymmetric hybridization from McKay's buntings into the postglacially-colonizing population of snow buntings could account for this reduction. Reproductive isolation is likely maintained through differential arrival dates on breeding grounds and the high breeding density of McKay's buntings. This recent, high-latitude divergence best fits a model of founder event speciation driven by vicariance and oscillations in habitat due to climate change.
- Published
- 2010
- Full Text
- View/download PDF
347. Working through polytomies: auklets revisited.
- Author
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Humphries EM and Winker K
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Animals, Bayes Theorem, Charadriiformes classification, DNA, Mitochondrial genetics, Models, Genetic, NADH Dehydrogenase genetics, Sequence Analysis, DNA, Charadriiformes genetics, Evolution, Molecular, Phylogeny
- Abstract
Polytomies, or phylogenetic "bushes", are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7-9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.
- Published
- 2010
- Full Text
- View/download PDF
348. Signatures of high-altitude adaptation in the major hemoglobin of five species of andean dabbling ducks.
- Author
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McCracken KG, Barger CP, Bulgarella M, Johnson KP, Kuhner MK, Moore AV, Peters JL, Trucco J, Valqui TH, Winker K, and Wilson RE
- Subjects
- Amino Acid Substitution, Animal Migration, Animals, Ducks physiology, Gene Frequency, Genotype, Polymorphism, Genetic, Population Dynamics, Sequence Analysis, DNA, Sequence Analysis, Protein, South America, Adaptation, Biological genetics, Altitude, Ducks genetics, Evolution, Molecular, alpha-Globins genetics, beta-Globins genetics
- Abstract
Hypoxia is one of the most important factors affecting survival at high altitude, and the major hemoglobin protein is a likely target of selection. We compared population genetic structure in the alphaA and betaA hemoglobin subunits (HBA2 and HBB) of five paired lowland and highland populations of Andean dabbling ducks to unlinked reference loci. In the hemoglobin genes, parallel amino acid replacements were overrepresented in highland lineages, and one to five derived substitutions occurred at external solvent-accessible positions on the alpha and beta subunits, at alpha(1)beta(1) intersubunit contacts, or in close proximity to inositolpentaphosphate (IPP) binding sites. Coalescent analyses incorporating the stochasticity of drift and mutation indicated that hemoglobin alleles were less likely to be transferred between highland and lowland populations than unlinked alleles at five other loci. Amino acid replacements that were overrepresented in the highlands were rarely found within lowland populations, suggesting that alleles segregating at high frequency in the highlands may be maladaptive in the lowlands and vice versa. Most highland populations are probably nonmigratory and locally adapted to the Altiplano, but gene flow for several species may be sufficiently high to retard divergence at unlinked loci. Heterozygosity was elevated in the alphaA or betaA subunits of highland populations exhibiting high gene flow between the southern lowlands and the highlands and in highland species that disperse seasonally downslope to midelevation environments from the central Andean plateau. However, elevated heterozygosity occurred more frequently in the alphaA subunit but not simultaneously in both subunits, suggesting that selection may be more constrained by epistasis in the betaA subunit. Concordant patterns among multiple species with different evolutionary histories and depths of historical divergence and gene flow suggest that the major hemoglobin genes of these five dabbling duck species have evolved adaptively in response to high-altitude hypoxia in the Andes.
- Published
- 2009
- Full Text
- View/download PDF
349. Clarifying the systematics of an enigmatic avian lineage: what is a bombycillid?
- Author
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Spellman GM, Cibois A, Moyle RG, Winker K, and Keith Barker F
- Subjects
- Animals, Bayes Theorem, DNA, Mitochondrial genetics, Exons, Genes, Mitochondrial, Genes, RAG-1, Likelihood Functions, Markov Chains, Mitochondria genetics, Models, Genetic, Sequence Alignment, Sequence Analysis, DNA, Evolution, Molecular, Passeriformes classification, Passeriformes genetics, Phylogeny
- Published
- 2008
- Full Text
- View/download PDF
350. Rarity of influenza A virus in spring shorebirds, southern Alaska.
- Author
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Winker K, Spackman E, and Swayne DE
- Subjects
- Alaska epidemiology, Animals, Influenza in Birds epidemiology, Influenza in Birds virology, Prevalence, Charadriiformes virology, Influenza A virus isolation & purification
- Published
- 2008
- Full Text
- View/download PDF
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