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517 results on '"Fitzpatrick, John W."'

1. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
General Science & Technology
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021

2. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

4. Allele frequency dynamics in a pedigreed natural population

Author

Chen, Nancy, Juric, Ivan, Cosgrove, Elissa J, Bowman, Reed, Fitzpatrick, John W, Schoech, Stephan J, Clark, Andrew G, and Coop, Graham

Subjects
Biological Sciences, Ecology, Genetics, Human Genome, Algorithms, Animals, Birds, Gene Frequency, Genetic Variation, Genetics, Population, Models, Genetic, Pedigree, Population Dynamics, population genetics, pedigrees, fitness, gene flow, genetic drift
Abstract

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes-variation in individual survival, reproductive success, and movement-are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

Published
2019

5. Deconstructing isolation-by-distance: The genomic consequences of limited dispersal.

Author

Aguillon, Stepfanie M, Fitzpatrick, John W, Bowman, Reed, Schoech, Stephan J, Clark, Andrew G, Coop, Graham, and Chen, Nancy

Subjects
Animals, Passeriformes, Genetics, Population, Genomics, Population Density, Microsatellite Repeats, Genotype, Female, Male, Genetic Variation, Reproductive Isolation, Developmental Biology, Genetics
Abstract

Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance, commonly called isolation-by-distance. Despite the prevalence of isolation-by-distance in nature, to date few studies have empirically demonstrated the processes that generate this pattern, largely because few populations have direct measures of individual dispersal and pedigree information. Intensive, long-term demographic studies and exhaustive genomic surveys in the Florida Scrub-Jay (Aphelocoma coerulescens) provide an excellent opportunity to investigate the influence of dispersal on genetic structure. Here, we used a panel of genome-wide SNPs and extensive pedigree information to explore the role of limited dispersal in shaping patterns of isolation-by-distance in both sexes, and at an exceedingly fine spatial scale (within ~10 km). Isolation-by-distance patterns were stronger in male-male and male-female comparisons than in female-female comparisons, consistent with observed differences in dispersal propensity between the sexes. Using the pedigree, we demonstrated how various genealogical relationships contribute to fine-scale isolation-by-distance. Simulations using field-observed distributions of male and female natal dispersal distances showed good agreement with the distribution of geographic distances between breeding individuals of different pedigree relationship classes. Furthermore, we built coalescent simulations parameterized by the observed dispersal curve, population density, and immigration rate, and showed how incorporating these extensions to Malécot's theory of isolation-by-distance allows us to accurately reconstruct observed sex-specific isolation-by-distance patterns in autosomal and Z-linked SNPs. Therefore, patterns of fine-scale isolation-by-distance in the Florida Scrub-Jay can be well understood as a result of limited dispersal over contemporary timescales.

Published
2017

6. Correction: Batch-produced, GIS-informed range maps for birds based on provenanced, crowd-sourced data inform conservation assessments

Author

Huang, Ryan M., primary, Medina, Wilderson, additional, Brooks, Thomas M., additional, Butchart, Stuart H. M., additional, Fitzpatrick, John W., additional, Hermes, Claudia, additional, Jenkins, Clinton N., additional, Johnston, Alison, additional, Lebbin, Daniel J., additional, Li, Binbin V., additional, Ocampo-Peñuela, Natalia, additional, Parr, Mike, additional, Wheatley, Hannah, additional, Wiedenfeld, David A., additional, Wood, Christopher, additional, and Pimm, Stuart L., additional

Published
2023
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17. Preface

Author

Fitzpatrick, John W., primary and Woolfenden, Glen E., additional

Published
2020
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18. Proactive Conservation Management of an Island-endemic Bird Species in the Face of Global Change

Author

Morrison, Scott A., Sillett, T. Scott, Ghalambor, Cameron K., Fitzpatrick, John W., Graber, David M., Bakker, Victoria J., Bowman, Reed, Collins, Charles T., Collins, Paul W., Delaney, Kathleen Semple, Doak, Daniel F., Koenig, Walter D., Laughrin, Lyndal, Lieberman, Alan A., Marzluff, John M., Reynolds, Mark D., Scott, J. Michael, Stallcup, Jerre Ann, Vickers, Winston, and Boyce, Walter M.

Published
2011
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33. The structure and organisation of an Amazonian bird community remains little changed after nearly four decades in Manu National Park

Author

Martínez, Ari E., primary, Ponciano, José M., additional, Gomez, Juan P., additional, Valqui, Thomas, additional, Novoa, Jorge, additional, Antezana, Mariamercedes, additional, Biscarra, Gabriela, additional, Camerlenghi, Ettore, additional, Carnes, Blaine H., additional, Huayanca Munarriz, Renato, additional, Parra, Eliseo, additional, Plummer, Isabella M., additional, Fitzpatrick, John W., additional, Robinson, Scott K., additional, Socolar, Jacob B., additional, and Terborgh, John, additional

Published
2023
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36. Archiving Primary Data: Solutions for Long-Term Studies

Author

Mills, James A., Teplitsky, Céline, Arroyo, Beatriz, Charmantier, Anne, Becker, Peter. H., Birkhead, Tim R., Bize, Pierre, Blumstein, Daniel T., Bonenfant, Christophe, Boutin, Stan, Bushuev, Andrey, Cam, Emmanuelle, Cockburn, Andrew, Côté, Steeve D., Coulson, John C., Daunt, Francis, Dingemanse, Niels J., Doligez, Blandine, Drummond, Hugh, Espie, Richard H.M., Festa-Bianchet, Marco, Frentiu, Francesca, Fitzpatrick, John W., Furness, Robert W., Garant, Dany, Gauthier, Gilles, Grant, Peter R., Griesser, Michael, Gustafsson, Lars, Hansson, Bengt, Harris, Michael P., Jiguet, Frédéric, Kjellander, Petter, Korpimäki, Erkki, Krebs, Charles J., Lens, Luc, Linnell, John D.C., Low, Matthew, McAdam, Andrew, Margalida, Antoni, Merilä, Juha, Møller, Anders P., Nakagawa, Shinichi, Nilsson, Jan-Åke, Nisbet, Ian C.T., van Noordwijk, Arie J., Oro, Daniel, Pärt, Tomas, Pelletier, Fanie, Potti, Jaime, Pujol, Benoit, Réale, Denis, Rockwell, Robert F., Ropert-Coudert, Yan, Roulin, Alexandre, Sedinger, James S., Swenson, Jon E., Thébaud, Christophe, Visser, Marcel E., Wanless, Sarah, Westneat, David F., Wilson, Alastair J., and Zedrosser, Andreas

Published
2015
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