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14 results on '"Martinez Cruzado, Juan Carlos"'

1. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno-Estrada, Andres, Byrnes, Jake K, Muzzio, Marina, Rodriguez-Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K, Ruiz-Linares, Andres, Burchard, Esteban G, Martinez-Cruzado, Juan Carlos, Bustamante, Carlos D., and Project, The 1000 Genomes

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics, 92D25
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Ta\'ino people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe., Comment: 30 pages, inludes supplement. v2 contains clarifications, extra analyses, and a change in the language classification scheme used

Published
2013

2. Reconstructing the Population Genetic History of the Caribbean

Author

Moreno-Estrada, Andres, Gravel, Simon, Zakharia, Fouad, McCauley, Jacob L., Byrnes, Jake K., Gignoux, Christopher R., Ortiz-Tello, Patricia A., Martinez, Ricardo J., Hedges, Dale J., Morris, Richard W., Eng, Celeste, Sandoval, Karla, Acevedo-Acevedo, Suehelay, Martinez-Cruzado, Juan Carlos, Norman, Paul J., Layrisse, Zulay, Parham, Peter, Burchard, Esteban Gonzalez, Cuccaro, Michael L., Martin, Eden R., and Bustamante, Carlos D.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean., Comment: 26 pages, 6 figures, and supporting information

Published
2013

3. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Shaffer, Christopher D, Alvarez, Consuelo J, Bednarski, April E, Dunbar, David, Goodman, Anya L, Reinke, Catherine, Rosenwald, Anne G, Wolyniak, Michael J, Bailey, Cheryl, Barnard, Daron, Bazinet, Christopher, Beach, Dale L, Bedard, James EJ, Bhalla, Satish, Braverman, John, Burg, Martin, Chandrasekaran, Vidya, Chung, Hui-Min, Clase, Kari, DeJong, Randall J, DiAngelo, Justin R, Du, Chunguang, Eckdahl, Todd T, Eisler, Heather, Emerson, Julia A, Frary, Amy, Frohlich, Donald, Gosser, Yuying, Govind, Shubha, Haberman, Adam, Hark, Amy T, Hauser, Charles, Hoogewerf, Arlene, Hoopes, Laura LM, Howell, Carina E, Johnson, Diana, Jones, Christopher J, Kadlec, Lisa, Kaehler, Marian, Key, S Catherine Silver, Kleinschmit, Adam, Kokan, Nighat P, Kopp, Olga, Kuleck, Gary, Leatherman, Judith, Lopilato, Jane, MacKinnon, Christy, Martinez-Cruzado, Juan Carlos, McNeil, Gerard, Mel, Stephanie, Mistry, Hemlata, Nagengast, Alexis, Overvoorde, Paul, Paetkau, Don W, Parrish, Susan, Peterson, Celeste N, Preuss, Mary, Reed, Laura K, Revie, Dennis, Robic, Srebrenka, Roecklein-Canfield, Jennifer, Rubin, Michael R, Saville, Kenneth, Schroeder, Stephanie, Sharif, Karim, Shaw, Mary, Skuse, Gary, Smith, Christopher D, Smith, Mary A, Smith, Sheryl T, Spana, Eric, Spratt, Mary, Sreenivasan, Aparna, Stamm, Joyce, Szauter, Paul, Thompson, Jeffrey S, Wawersik, Matthew, Youngblom, James, Zhou, Leming, Mardis, Elaine R, Buhler, Jeremy, Leung, Wilson, Lopatto, David, and Elgin, Sarah CR

Subjects
Attitude, Biology, Cooperative Behavior, Curriculum, Data Collection, Faculty, Genome, Genomics, Humans, Knowledge, Learning, Molecular Sequence Annotation, Program Evaluation, Research, Research Personnel, Self Report, Surveys and Questionnaires, Time Factors, Curriculum and Pedagogy, Education
Abstract

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014

4. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Shaffer, Christopher D., Alvarez, Consuelo J., Bednarski, April E., Dunbar, David, Goodman, Anya L., Reinke, Catherine, Rosenwald, Anne G., Wolyniak, Michael J., Bailey, Cheryl, Barnard, Daron, Bazinet, Christopher, Beach, Dale L., Bedard, James E. J., Bhalla, Satish, Braverman, John, Burg, Martin, Chandrasekaran, Vidya, Chung, Hui-Min, Clase, Kari, DeJong, Randall J., DiAngelo, Justin R., Du, Chunguang, Eckdahl, Todd T., Eisler, Heather, Emerson, Julia A., Frary, Amy, Frohlich, Donald, Gosser, Yuying, Govind, Shubha, Haberman, Adam, Hark, Amy T., Hauser, Charles, Hoogewerf, Arlene, Hoopes, Laura L. M., Howell, Carina E., Johnson, Diana, Jones, Christopher J., Kadlec, Lisa, Kaehler, Marian, Key, S. Catherine Silver, Kleinschmit, Adam, Kokan, Nighat P., Kopp, Olga, Kuleck, Gary, Leatherman, Judith, Lopilato, Jane, MacKinnon, Christy, Martinez-Cruzado, Juan Carlos, McNeil, Gerard, Mel, Stephanie, Mistry, Hemlata, Nagengast, Alexis, Overvoorde, Paul, Paetkau, Don W., Parrish, Susan, Peterson, Celeste N., Preuss, Mary, Reed, Laura K., Revie, Dennis, Robic, Srebrenka, Roecklein-Canfield, Jennifer, Rubin, Michael R., Saville, Kenneth, Schroeder, Stephanie, Sharif, Karim, Shaw, Mary, Skuse, Gary, Smith, Christopher D., Smith, Mary A., Smith, Sheryl T., Spana, Eric, Spratt, Mary, Sreenivasan, Aparna, Stamm, Joyce, Szauter, Paul, Thompson, Jeffrey S., Wawersik, Matthew, Youngblom, James, Zhou, Leming, Mardis, Elaine R., Buhler, Jeremy, Leung, Wilson, Lopatto, David, and Elgin, Sarah C. R.

Abstract

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit. [Contains 82 pages of Supplemental Material, which can be found at: http://www.lifescied.org/content/suppl/2014/02/12/13.1.111.DC1.html.]

Published
2014
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5. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles

Author

Kolchanova, Sofiia, primary, Komissarov, Alexey, additional, Kliver, Sergei, additional, Mazo-Vargas, Anyi, additional, Afanador, Yashira, additional, Velez-Valentín, Jafet, additional, de la Rosa, Ricardo Valentín, additional, Castro-Marquez, Stephanie, additional, Rivera-Colon, Israel, additional, Majeske, Audrey J., additional, Wolfsberger, Walter W., additional, Hains, Taylor, additional, Corvelo, André, additional, Martinez-Cruzado, Juan-Carlos, additional, Glenn, Travis C., additional, Robinson, Orlando, additional, Koepfli, Klaus-Peter, additional, and Oleksyk, Taras K., additional

Published
2021
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7. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

Author

Oleksyk Taras K, Pombert Jean-Francois, Siu Daniel, Mazo-Vargas Anyimilehidi, Ramos Brian, Guiblet Wilfried, Afanador Yashira, Ruiz-Rodriguez Christina T, Nickerson Michael L, Logue David M, Dean Michael, Figueroa Luis, Valentin Ricardo, and Martinez-Cruzado Juan-Carlos

Subjects
Amazona vittata, Puerto rican parrot, Genome sequence, Annotation, Assembly, Local funding, Education, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

Published
2012
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8. Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangeredSolenodon paradoxusfrom the island of Hispaniola

Author

Grigorev, Kirill, primary, Kliver, Sergey, additional, Dobrynin, Pavel, additional, Komissarov, Aleksey, additional, Wolfsberger, Walter, additional, Krasheninnikova, Ksenia, additional, Afanador-Hernández, Yashira M., additional, Paulino, Liz A., additional, Carreras, Rosanna, additional, Rodríguez, Luis E., additional, Núñez, Adrell, additional, Silva, Filipe, additional, Hernández-Martich, J. David, additional, Majeske, Audrey J., additional, Antunes, Agostinho, additional, Roca, Alfred L., additional, O’Brien, Stephen J., additional, Martinez-Cruzado, Juan Carlos, additional, and Oleksyk, Taras K., additional

Published
2017
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9. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

Author

Leung, Wilson, primary, Shaffer, Christopher D, additional, Reed, Laura K, additional, Smith, Sheryl T, additional, Barshop, William, additional, Dirkes, William, additional, Dothager, Matthew, additional, Lee, Paul, additional, Wong, Jeannette, additional, Xiong, David, additional, Yuan, Han, additional, Bedard, James E J, additional, Machone, Joshua F, additional, Patterson, Seantay D, additional, Price, Amber L, additional, Turner, Bryce A, additional, Robic, Srebrenka, additional, Luippold, Erin K, additional, McCartha, Shannon R, additional, Walji, Tezin A, additional, Walker, Chelsea A, additional, Saville, Kenneth, additional, Abrams, Marita K, additional, Armstrong, Andrew R, additional, Armstrong, William, additional, Bailey, Robert J, additional, Barberi, Chelsea R, additional, Beck, Lauren R, additional, Blaker, Amanda L, additional, Blunden, Christopher E, additional, Brand, Jordan P, additional, Brock, Ethan J, additional, Brooks, Dana W, additional, Brown, Marie, additional, Butzler, Sarah C, additional, Clark, Eric M, additional, Clark, Nicole B, additional, Collins, Ashley A, additional, Cotteleer, Rebecca J, additional, Cullimore, Peterson R, additional, Dawson, Seth G, additional, Docking, Carter T, additional, Dorsett, Sasha L, additional, Dougherty, Grace A, additional, Downey, Kaitlyn A, additional, Drake, Andrew P, additional, Earl, Erica K, additional, Floyd, Trevor G, additional, Forsyth, Joshua D, additional, Foust, Jonathan D, additional, Franchi, Spencer L, additional, Geary, James F, additional, Hanson, Cynthia K, additional, Harding, Taylor S, additional, Harris, Cameron B, additional, Heckman, Jonathan M, additional, Holderness, Heather L, additional, Howey, Nicole A, additional, Jacobs, Dontae A, additional, Jewell, Elizabeth S, additional, Kaisler, Maria, additional, Karaska, Elizabeth A, additional, Kehoe, James L, additional, Koaches, Hannah C, additional, Koehler, Jessica, additional, Koenig, Dana, additional, Kujawski, Alexander J, additional, Kus, Jordan E, additional, Lammers, Jennifer A, additional, Leads, Rachel R, additional, Leatherman, Emily C, additional, Lippert, Rachel N, additional, Messenger, Gregory S, additional, Morrow, Adam T, additional, Newcomb, Victoria, additional, Plasman, Haley J, additional, Potocny, Stephanie J, additional, Powers, Michelle K, additional, Reem, Rachel M, additional, Rennhack, Jonathan P, additional, Reynolds, Katherine R, additional, Reynolds, Lyndsey A, additional, Rhee, Dong K, additional, Rivard, Allyson B, additional, Ronk, Adam J, additional, Rooney, Meghan B, additional, Rubin, Lainey S, additional, Salbert, Luke R, additional, Saluja, Rasleen K, additional, Schauder, Taylor, additional, Schneiter, Allison R, additional, Schulz, Robert W, additional, Smith, Karl E, additional, Spencer, Sarah, additional, Swanson, Bryant R, additional, Tache, Melissa A, additional, Tewilliager, Ashley A, additional, Tilot, Amanda K, additional, VanEck, Eve, additional, Villerot, Matthew M, additional, Vylonis, Megan B, additional, Watson, David T, additional, Wurzler, Juliana A, additional, Wysocki, Lauren M, additional, Yalamanchili, Monica, additional, Zaborowicz, Matthew A, additional, Emerson, Julia A, additional, Ortiz, Carlos, additional, Deuschle, Frederic J, additional, DiLorenzo, Lauren A, additional, Goeller, Katie L, additional, Macchi, Christopher R, additional, Muller, Sarah E, additional, Pasierb, Brittany D, additional, Sable, Joseph E, additional, Tucci, Jessica M, additional, Tynon, Marykathryn, additional, Dunbar, David A, additional, Beken, Levent H, additional, Conturso, Alaina C, additional, Danner, Benjamin L, additional, DeMichele, Gabriella A, additional, Gonzales, Justin A, additional, Hammond, Maureen S, additional, Kelley, Colleen V, additional, Kelly, Elisabeth A, additional, Kulich, Danielle, additional, Mageeney, Catherine M, additional, McCabe, Nikie L, additional, Newman, Alyssa M, additional, Spaeder, Lindsay A, additional, Tumminello, Richard A, additional, Revie, Dennis, additional, Benson, Jonathon M, additional, Cristostomo, Michael C, additional, DaSilva, Paolo A, additional, Harker, Katherine S, additional, Jarrell, Jenifer N, additional, Jimenez, Luis A, additional, Katz, Brandon M, additional, Kennedy, William R, additional, Kolibas, Kimberly S, additional, LeBlanc, Mark T, additional, Nguyen, Trung T, additional, Nicolas, Daniel S, additional, Patao, Melissa D, additional, Patao, Shane M, additional, Rupley, Bryan J, additional, Sessions, Bridget J, additional, Weaver, Jennifer A, additional, Goodman, Anya L, additional, Alvendia, Erica L, additional, Baldassari, Shana M, additional, Brown, Ashley S, additional, Chase, Ian O, additional, Chen, Maida, additional, Chiang, Scott, additional, Cromwell, Avery B, additional, Custer, Ashley F, additional, DiTommaso, Tia M, additional, El-Adaimi, Jad, additional, Goscinski, Nora C, additional, Grove, Ryan A, additional, Gutierrez, Nestor, additional, Harnoto, Raechel S, additional, Hedeen, Heather, additional, Hong, Emily L, additional, Hopkins, Barbara L, additional, Huerta, Vilma F, additional, Khoshabian, Colin, additional, LaForge, Kristin M, additional, Lee, Cassidy T, additional, Lewis, Benjamin M, additional, Lydon, Anniken M, additional, Maniaci, Brian J, additional, Mitchell, Ryan D, additional, Morlock, Elaine V, additional, Morris, William M, additional, Naik, Priyanka, additional, Olson, Nicole C, additional, Osterloh, Jeannette M, additional, Perez, Marcos A, additional, Presley, Jonathan D, additional, Randazzo, Matt J, additional, Regan, Melanie K, additional, Rossi, Franca G, additional, Smith, Melanie A, additional, Soliterman, Eugenia A, additional, Sparks, Ciani J, additional, Tran, Danny L, additional, Wan, Tiffany, additional, Welker, Anne A, additional, Wong, Jeremy N, additional, Sreenivasan, Aparna, additional, Youngblom, Jim, additional, Adams, Andrew, additional, Alldredge, Justin, additional, Bryant, Ashley, additional, Carranza, David, additional, Cifelli, Alyssa, additional, Coulson, Kevin, additional, Debow, Calise, additional, Delacruz, Noelle, additional, Emerson, Charlene, additional, Farrar, Cassandra, additional, Foret, Don, additional, Garibay, Edgar, additional, Gooch, John, additional, Heslop, Michelle, additional, Kaur, Sukhjit, additional, Khan, Ambreen, additional, Kim, Van, additional, Lamb, Travis, additional, Lindbeck, Peter, additional, Lucas, Gabi, additional, Macias, Elizabeth, additional, Martiniuc, Daniela, additional, Mayorga, Lissett, additional, Medina, Joseph, additional, Membreno, Nelson, additional, Messiah, Shady, additional, Neufeld, Lacey, additional, Nguyen, San Francisco, additional, Nichols, Zachary, additional, Odisho, George, additional, Peterson, Daymon, additional, Rodela, Laura, additional, Rodriguez, Priscilla, additional, Rodriguez, Vanessa, additional, Ruiz, Jorge, additional, Sherrill, Will, additional, Silva, Valeria, additional, Sparks, Jeri, additional, Statton, Geeta, additional, Townsend, Ashley, additional, Valdez, Isabel, additional, Waters, Mary, additional, Westphal, Kyle, additional, Winkler, Stacey, additional, Zumkehr, Joannee, additional, DeJong, Randall J, additional, Hoogewerf, Arlene J, additional, Ackerman, Cheri M, additional, Armistead, Isaac O, additional, Baatenburg, Lara, additional, Borr, Matthew J, additional, Brouwer, Lindsay K, additional, Burkhart, Brandon J, additional, Bushhouse, Kelsey T, additional, Cesko, Lejla, additional, Choi, Tiffany Y Y, additional, Cohen, Heather, additional, Damsteegt, Amanda M, additional, Darusz, Jess M, additional, Dauphin, Cory M, additional, Davis, Yelena P, additional, Diekema, Emily J, additional, Drewry, Melissa, additional, Eisen, Michelle E M, additional, Faber, Hayley M, additional, Faber, Katherine J, additional, Feenstra, Elizabeth, additional, Felzer-Kim, Isabella T, additional, Hammond, Brandy L, additional, Hendriksma, Jesse, additional, Herrold, Milton R, additional, Hilbrands, Julia A, additional, Howell, Emily J, additional, Jelgerhuis, Sarah A, additional, Jelsema, Timothy R, additional, Johnson, Benjamin K, additional, Jones, Kelly K, additional, Kim, Anna, additional, Kooienga, Ross D, additional, Menyes, Erika E, additional, Nollet, Eric A, additional, Plescher, Brittany E, additional, Rios, Lindsay, additional, Rose, Jenny L, additional, Schepers, Allison J, additional, Scott, Geoff, additional, Smith, Joshua R, additional, Sterling, Allison M, additional, Tenney, Jenna C, additional, Uitvlugt, Chris, additional, VanDyken, Rachel E, additional, VanderVennen, Marielle, additional, Vue, Samantha, additional, Kokan, Nighat P, additional, Agbley, Kwabea, additional, Boham, Sampson K, additional, Broomfield, Daniel, additional, Chapman, Kayla, additional, Dobbe, Ali, additional, Dobbe, Ian, additional, Harrington, William, additional, Ibrahem, Marwan, additional, Kennedy, Andre, additional, Koplinsky, Chad A, additional, Kubricky, Cassandra, additional, Ladzekpo, Danielle, additional, Pattison, Claire, additional, Ramirez, Roman E, additional, Wande, Lucia, additional, Woehlke, Sarah, additional, Wawersik, Matthew, additional, Kiernan, Elizabeth, additional, Thompson, Jeffrey S, additional, Banker, Roxanne, additional, Bartling, Justina R, additional, Bhatiya, Chinmoy I, additional, Boudoures, Anna L, additional, Christiansen, Lena, additional, Fosselman, Daniel S, additional, French, Kristin M, additional, Gill, Ishwar S, additional, Havill, Jessen T, additional, Johnson, Jaelyn L, additional, Keny, Lauren J, additional, Kerber, John M, additional, Klett, Bethany M, additional, Kufel, Christina N, additional, May, Francis J, additional, Mecoli, Jonathan P, additional, Merry, Callie R, additional, Meyer, Lauren R, additional, Miller, Emily G, additional, Mullen, Gregory J, additional, Palozola, Katherine C, additional, Pfeil, Jacob J, additional, Thomas, Jessica G, additional, Verbofsky, Evan M, additional, Spana, Eric P, additional, Agarwalla, Anant, additional, Chapman, Julia, additional, Chlebina, Ben, additional, Chong, Insun, additional, Falk, I N, additional, Fitzgibbons, John D, additional, Friedman, Harrison, additional, Ighile, Osagie, additional, Kim, Andrew J, additional, Knouse, Kristin A, additional, Kung, Faith, additional, Mammo, Danny, additional, Ng, Chun Leung, additional, Nikam, Vinayak S, additional, Norton, Diana, additional, Pham, Philip, additional, Polk, Jessica W, additional, Prasad, Shreya, additional, Rankin, Helen, additional, Ratliff, Camille D, additional, Scala, Victoria, additional, Schwartz, Nicholas U, additional, Shuen, Jessica A, additional, Xu, Amy, additional, Xu, Thomas Q, additional, Zhang, Yi, additional, Rosenwald, Anne G, additional, Burg, Martin G, additional, Adams, Stephanie J, additional, Baker, Morgan, additional, Botsford, Bobbi, additional, Brinkley, Briana, additional, Brown, Carter, additional, Emiah, Shadie, additional, Enoch, Erica, additional, Gier, Chad, additional, Greenwell, Alyson, additional, Hoogenboom, Lindsay, additional, Matthews, Jordan E, additional, McDonald, Mitchell, additional, Mercer, Amanda, additional, Monsma, Nicholaus, additional, Ostby, Kristine, additional, Ramic, Alen, additional, Shallman, Devon, additional, Simon, Matthew, additional, Spencer, Eric, additional, Tomkins, Trisha, additional, Wendland, Pete, additional, Wylie, Anna, additional, Wolyniak, Michael J, additional, Robertson, Gregory M, additional, Smith, Samuel I, additional, DiAngelo, Justin R, additional, Sassu, Eric D, additional, Bhalla, Satish C, additional, Sharif, Karim A, additional, Choeying, Tenzin, additional, Macias, Jason S, additional, Sanusi, Fareed, additional, Torchon, Karvyn, additional, Bednarski, April E, additional, Alvarez, Consuelo J, additional, Davis, Kristen C, additional, Dunham, Carrie A, additional, Grantham, Alaina J, additional, Hare, Amber N, additional, Schottler, Jennifer, additional, Scott, Zackary W, additional, Kuleck, Gary A, additional, Yu, Nicole S, additional, Kaehler, Marian M, additional, Jipp, Jacob, additional, Overvoorde, Paul J, additional, Shoop, Elizabeth, additional, Cyrankowski, Olivia, additional, Hoover, Betsy, additional, Kusner, Matt, additional, Lin, Devry, additional, Martinov, Tijana, additional, Misch, Jonathan, additional, Salzman, Garrett, additional, Schiedermayer, Holly, additional, Snavely, Michael, additional, Zarrasola, Stephanie, additional, Parrish, Susan, additional, Baker, Atlee, additional, Beckett, Alissa, additional, Belella, Carissa, additional, Bryant, Julie, additional, Conrad, Turner, additional, Fearnow, Adam, additional, Gomez, Carolina, additional, Herbstsomer, Robert A, additional, Hirsch, Sarah, additional, Johnson, Christen, additional, Jones, Melissa, additional, Kabaso, Rita, additional, Lemmon, Eric, additional, Vieira, Carolina Marques dos Santos, additional, McFarland, Darryl, additional, McLaughlin, Christopher, additional, Morgan, Abbie, additional, Musokotwane, Sepo, additional, Neutzling, William, additional, Nietmann, Jana, additional, Paluskievicz, Christina, additional, Penn, Jessica, additional, Peoples, Emily, additional, Pozmanter, Caitlin, additional, Reed, Emily, additional, Rigby, Nichole, additional, Schmidt, Lasse, additional, Shelton, Micah, additional, Shuford, Rebecca, additional, Tirasawasdichai, Tiara, additional, Undem, Blair, additional, Urick, Damian, additional, Vondy, Kayla, additional, Yarrington, Bryan, additional, Eckdahl, Todd T, additional, Poet, Jeffrey L, additional, Allen, Alica B, additional, Anderson, John E, additional, Barnett, Jason M, additional, Baumgardner, Jordan S, additional, Brown, Adam D, additional, Carney, Jordan E, additional, Chavez, Ramiro A, additional, Christgen, Shelbi L, additional, Christie, Jordan S, additional, Clary, Andrea N, additional, Conn, Michel A, additional, Cooper, Kristen M, additional, Crowley, Matt J, additional, Crowley, Samuel T, additional, Doty, Jennifer S, additional, Dow, Brian A, additional, Edwards, Curtis R, additional, Elder, Darcie D, additional, Fanning, John P, additional, Janssen, Bridget M, additional, Lambright, Anthony K, additional, Lane, Curtiss E, additional, Limle, Austin B, additional, Mazur, Tammy, additional, McCracken, Marly R, additional, McDonough, Alexa M, additional, Melton, Amy D, additional, Minnick, Phillip J, additional, Musick, Adam E, additional, Newhart, William H, additional, Noynaert, Joseph W, additional, Ogden, Bradley J, additional, Sandusky, Michael W, additional, Schmuecker, Samantha M, additional, Shipman, Anna L, additional, Smith, Anna L, additional, Thomsen, Kristen M, additional, Unzicker, Matthew R, additional, Vernon, William B, additional, Winn, Wesley W, additional, Woyski, Dustin S, additional, Zhu, Xiao, additional, Du, Chunguang, additional, Ament, Caitlin, additional, Aso, Soham, additional, Bisogno, Laura Simone, additional, Caronna, Jason, additional, Fefelova, Nadezhda, additional, Lopez, Lenin, additional, Malkowitz, Lorraine, additional, Marra, Jonathan, additional, Menillo, Daniella, additional, Obiorah, Ifeanyi, additional, Onsarigo, Eric Nyabeta, additional, Primus, Shekerah, additional, Soos, Mahdi, additional, Tare, Archana, additional, Zidan, Ameer, additional, Jones, Christopher J, additional, Aronhalt, Todd, additional, Bellush, James M, additional, Burke, Christa, additional, DeFazio, Steve, additional, Does, Benjamin R, additional, Johnson, Todd D, additional, Keysock, Nicholas, additional, Knudsen, Nelson H, additional, Messler, James, additional, Myirski, Kevin, additional, Rekai, Jade Lea, additional, Rempe, Ryan Michael, additional, Salgado, Michael S, additional, Stagaard, Erica, additional, Starcher, Justin R, additional, Waggoner, Andrew W, additional, Yemelyanova, Anastasia K, additional, Hark, Amy T, additional, Bertolet, Anne, additional, Kuschner, Cyrus E, additional, Parry, Kesley, additional, Quach, Michael, additional, Shantzer, Lindsey, additional, Shaw, Mary E, additional, Smith, Mary A, additional, Glenn, Omolara, additional, Mason, Portia, additional, Williams, Charlotte, additional, Key, S Catherine Silver, additional, Henry, Tyneshia C P, additional, Johnson, Ashlee G, additional, White, Jackie X, additional, Haberman, Adam, additional, Asinof, Sam, additional, Drumm, Kelly, additional, Freeburg, Trip, additional, Safa, Nadia, additional, Schultz, Darrin, additional, Shevin, Yakov, additional, Svoronos, Petros, additional, Vuong, Tam, additional, Wellinghoff, Jules, additional, Hoopes, Laura L M, additional, Chau, Kim M, additional, Ward, Alyssa, additional, Regisford, E Gloria C, additional, Augustine, LaJerald, additional, Davis-Reyes, Brionna, additional, Echendu, Vivienne, additional, Hales, Jasmine, additional, Ibarra, Sharon, additional, Johnson, Lauriaun, additional, Ovu, Steven, additional, Braverman, John M, additional, Bahr, Thomas J, additional, Caesar, Nicole M, additional, Campana, Christopher, additional, Cassidy, Daniel W, additional, Cognetti, Peter A, additional, English, Johnathan D, additional, Fadus, Matthew C, additional, Fick, Cameron N, additional, Freda, Philip J, additional, Hennessy, Bryan M, additional, Hockenberger, Kelsey, additional, Jones, Jennifer K, additional, King, Jessica E, additional, Knob, Christopher R, additional, Kraftmann, Karen J, additional, Li, Linghui, additional, Lupey, Lena N, additional, Minniti, Carl J, additional, Minton, Thomas F, additional, Moran, Joseph V, additional, Mudumbi, Krishna, additional, Nordman, Elizabeth C, additional, Puetz, William J, additional, Robinson, Lauren M, additional, Rose, Thomas J, additional, Sweeney, Edward P, additional, Timko, Ashley S, additional, Paetkau, Don W, additional, Eisler, Heather L, additional, Aldrup, Megan E, additional, Bodenberg, Jessica M, additional, Cole, Mara G, additional, Deranek, Kelly M, additional, DeShetler, Megan, additional, Dowd, Rose M, additional, Eckardt, Alexandra K, additional, Ehret, Sharon C, additional, Fese, Jessica, additional, Garrett, Amanda D, additional, Kammrath, Anna, additional, Kappes, Michelle L, additional, Light, Morgan R, additional, Meier, Anne C, additional, O’Rouke, Allison, additional, Perella, Mallory, additional, Ramsey, Kimberley, additional, Ramthun, Jennifer R, additional, Reilly, Mary T, additional, Robinett, Deirdre, additional, Rossi, Nadine L, additional, Schueler, Mary Grace, additional, Shoemaker, Emma, additional, Starkey, Kristin M, additional, Vetor, Ashley, additional, Vrable, Abby, additional, Chandrasekaran, Vidya, additional, Beck, Christopher, additional, Hatfield, Kristen R, additional, Herrick, Douglas A, additional, Khoury, Christopher B, additional, Lea, Charlotte, additional, Louie, Christopher A, additional, Lowell, Shannon M, additional, Reynolds, Thomas J, additional, Schibler, Jeanine, additional, Scoma, Alexandra H, additional, Smith-Gee, Maxwell T, additional, Tuberty, Sarah, additional, Smith, Christopher D, additional, Lopilato, Jane E, additional, Hauke, Jeanette, additional, Roecklein-Canfield, Jennifer A, additional, Corrielus, Maureen, additional, Gilman, Hannah, additional, Intriago, Stephanie, additional, Maffa, Amanda, additional, Rauf, Sabya A, additional, Thistle, Katrina, additional, Trieu, Melissa, additional, Winters, Jenifer, additional, Yang, Bib, additional, Hauser, Charles R, additional, Abusheikh, Tariq, additional, Ashrawi, Yara, additional, Benitez, Pedro, additional, Boudreaux, Lauren R, additional, Bourland, Megan, additional, Chavez, Miranda, additional, Cruz, Samantha, additional, Elliott, GiNell, additional, Farek, Jesse R, additional, Flohr, Sarah, additional, Flores, Amanda H, additional, Friedrichs, Chelsey, additional, Fusco, Zach, additional, Goodwin, Zane, additional, Helmreich, Eric, additional, Kiley, John, additional, Knepper, John Mark, additional, Langner, Christine, additional, Martinez, Megan, additional, Mendoza, Carlos, additional, Naik, Monal, additional, Ochoa, Andrea, additional, Ragland, Nicolas, additional, Raimey, England, additional, Rathore, Sunil, additional, Reza, Evangelina, additional, Sadovsky, Griffin, additional, Seydoux, Marie-Isabelle B, additional, Smith, Jonathan E, additional, Unruh, Anna K, additional, Velasquez, Vicente, additional, Wolski, Matthew W, additional, Gosser, Yuying, additional, Govind, Shubha, additional, Clarke-Medley, Nicole, additional, Guadron, Leslie, additional, Lau, Dawn, additional, Lu, Alvin, additional, Mazzeo, Cheryl, additional, Meghdari, Mariam, additional, Ng, Simon, additional, Pamnani, Brad, additional, Plante, Olivia, additional, Shum, Yuki Kwan Wa, additional, Song, Roy, additional, Johnson, Diana E, additional, Abdelnabi, Mai, additional, Archambault, Alexi, additional, Chamma, Norma, additional, Gaur, Shailly, additional, Hammett, Deborah, additional, Kandahari, Adrese, additional, Khayrullina, Guzal, additional, Kumar, Sonali, additional, Lawrence, Samantha, additional, Madden, Nigel, additional, Mandelbaum, Max, additional, Milnthorp, Heather, additional, Mohini, Shiv, additional, Patel, Roshni, additional, Peacock, Sarah J, additional, Perling, Emily, additional, Quintana, Amber, additional, Rahimi, Michael, additional, Ramirez, Kristen, additional, Singhal, Rishi, additional, Weeks, Corinne, additional, Wong, Tiffany, additional, Gillis, Aubree T, additional, Moore, Zachary D, additional, Savell, Christopher D, additional, Watson, Reece, additional, Mel, Stephanie F, additional, Anilkumar, Arjun A, additional, Bilinski, Paul, additional, Castillo, Rostislav, additional, Closser, Michael, additional, Cruz, Nathalia M, additional, Dai, Tiffany, additional, Garbagnati, Giancarlo F, additional, Horton, Lanor S, additional, Kim, Dongyeon, additional, Lau, Joyce H, additional, Liu, James Z, additional, Mach, Sandy D, additional, Phan, Thu A, additional, Ren, Yi, additional, Stapleton, Kenneth E, additional, Strelitz, Jean M, additional, Sunjed, Ray, additional, Stamm, Joyce, additional, Anderson, Morgan C, additional, Bonifield, Bethany Grace, additional, Coomes, Daniel, additional, Dillman, Adam, additional, Durchholz, Elaine J, additional, Fafara-Thompson, Antoinette E, additional, Gross, Meleah J, additional, Gygi, Amber M, additional, Jackson, Lesley E, additional, Johnson, Amy, additional, Kocsisova, Zuzana, additional, Manghelli, Joshua L, additional, McNeil, Kylie, additional, Murillo, Michael, additional, Naylor, Kierstin L, additional, Neely, Jessica, additional, Ogawa, Emmy E, additional, Rich, Ashley, additional, Rogers, Anna, additional, Spencer, J Devin, additional, Stemler, Kristina M, additional, Throm, Allison A, additional, Van Camp, Matt, additional, Weihbrecht, Katie, additional, Wiles, T Aaron, additional, Williams, Mallory A, additional, Williams, Matthew, additional, Zoll, Kyle, additional, Bailey, Cheryl, additional, Zhou, Leming, additional, Balthaser, Darla M, additional, Bashiri, Azita, additional, Bower, Mindy E, additional, Florian, Kayla A, additional, Ghavam, Nazanin, additional, Greiner-Sosanko, Elizabeth S, additional, Karim, Helmet, additional, Mullen, Victor W, additional, Pelchen, Carly E, additional, Yenerall, Paul M, additional, Zhang, Jiayu, additional, Rubin, Michael R, additional, Arias-Mejias, Suzette M, additional, Bermudez-Capo, Armando G, additional, Bernal-Vega, Gabriela V, additional, Colon-Vazquez, Mariela, additional, Flores-Vazquez, Arelys, additional, Gines-Rosario, Mariela, additional, Llavona-Cartagena, Ivan G, additional, Martinez-Rodriguez, Javier O, additional, Ortiz-Fuentes, Lionel, additional, Perez-Colomba, Eliezer O, additional, Perez-Otero, Joseph, additional, Rivera, Elisandra, additional, Rodriguez-Giron, Luke J, additional, Santiago-Sanabria, Arnaldo J, additional, Senquiz-Gonzalez, Andrea M, additional, delValle, Frank R Soto, additional, Vargas-Franco, Dorianmarie, additional, Velázquez-Soto, Karla I, additional, Zambrana-Burgos, Joan D, additional, Martinez-Cruzado, Juan Carlos, additional, Asencio-Zayas, Lillyann, additional, Babilonia-Figueroa, Kevin, additional, Beauchamp-Pérez, Francis D, additional, Belén-Rodríguez, Juliana, additional, Bracero-Quiñones, Luciann, additional, Burgos-Bula, Andrea P, additional, Collado-Méndez, Xavier A, additional, Colón-Cruz, Luis R, additional, Correa-Muller, Ana I, additional, Crooke-Rosado, Jonathan L, additional, Cruz-García, José M, additional, Defendini-Ávila, Marianna, additional, Delgado-Peraza, Francheska M, additional, Feliciano-Cancela, Alex J, additional, Gónzalez-Pérez, Valerie M, additional, Guiblet, Wilfried, additional, Heredia-Negrón, Aldo, additional, Hernández-Muñiz, Jennifer, additional, Irizarry-González, Lourdes N, additional, Laboy-Corales, Ángel L, additional, Llaurador-Caraballo, Gabriela A, additional, Marín-Maldonado, Frances, additional, Marrero-Llerena, Ulises, additional, Martell-Martínez, Héctor A, additional, Martínez-Traverso, Idaliz M, additional, Medina-Ortega, Kiara N, additional, Méndez-Castellanos, Sonya G, additional, Menéndez-Serrano, Krizia C, additional, Morales-Caraballo, Carol I, additional, Ortiz-DeChoudens, Saryleine, additional, Ortiz-Ortiz, Patricia, additional, Pagán-Torres, Hendrick, additional, Pérez-Afanador, Diana, additional, Quintana-Torres, Enid M, additional, Ramírez-Aponte, Edwin G, additional, Riascos-Cuero, Carolina, additional, Rivera-Llovet, Michelle S, additional, Rivera-Pagán, Ingrid T, additional, Rivera-Vicéns, Ramón E, additional, Robles-Juarbe, Fabiola, additional, Rodríguez-Bonilla, Lorraine, additional, Rodríguez-Echevarría, Brian O, additional, Rodríguez-García, Priscila M, additional, Rodríguez-Laboy, Abneris E, additional, Rodríguez-Santiago, Susana, additional, Rojas-Vargas, Michael L, additional, Rubio-Marrero, Eva N, additional, Santiago-Colón, Albeliz, additional, Santiago-Ortiz, Jorge L, additional, Santos-Ramos, Carlos E, additional, Serrano-González, Joseline, additional, Tamayo-Figueroa, Alina M, additional, Tascón-Peñaranda, Edna P, additional, Torres-Castillo, José L, additional, Valentín-Feliciano, Nelson A, additional, Valentín-Feliciano, Yashira M, additional, Vargas-Barreto, Nadyan M, additional, Vélez-Vázquez, Miguel, additional, Vilanova-Vélez, Luis R, additional, Zambrana-Echevarría, Cristina, additional, MacKinnon, Christy, additional, Chung, Hui-Min, additional, Kay, Chris, additional, Pinto, Anthony, additional, Kopp, Olga R, additional, Burkhardt, Joshua, additional, Harward, Chris, additional, Allen, Robert, additional, Bhat, Pavan, additional, Chang, Jimmy Hsiang-Chun, additional, Chen, York, additional, Chesley, Christopher, additional, Cohn, Dara, additional, DuPuis, David, additional, Fasano, Michael, additional, Fazzio, Nicholas, additional, Gavinski, Katherine, additional, Gebreyesus, Heran, additional, Giarla, Thomas, additional, Gostelow, Marcus, additional, Greenstein, Rachel, additional, Gunasinghe, Hashini, additional, Hanson, Casey, additional, Hay, Amanda, additional, He, Tao Jian, additional, Homa, Katie, additional, Howe, Ruth, additional, Howenstein, Jeff, additional, Huang, Henry, additional, Khatri, Aaditya, additional, Kim, Young Lu, additional, Knowles, Olivia, additional, Kong, Sarah, additional, Krock, Rebecca, additional, Kroll, Matt, additional, Kuhn, Julia, additional, Kwong, Matthew, additional, Lee, Brandon, additional, Lee, Ryan, additional, Levine, Kevin, additional, Li, Yedda, additional, Liu, Bo, additional, Liu, Lucy, additional, Liu, Max, additional, Lousararian, Adam, additional, Ma, Jimmy, additional, Mallya, Allyson, additional, Manchee, Charlie, additional, Marcus, Joseph, additional, McDaniel, Stephen, additional, Miller, Michelle L, additional, Molleston, Jerome M, additional, Diez, Cristina Montero, additional, Ng, Patrick, additional, Ngai, Natalie, additional, Nguyen, Hien, additional, Nylander, Andrew, additional, Pollack, Jason, additional, Rastogi, Suchita, additional, Reddy, Himabindu, additional, Regenold, Nathaniel, additional, Sarezky, Jon, additional, Schultz, Michael, additional, Shim, Jien, additional, Skorupa, Tara, additional, Smith, Kenneth, additional, Spencer, Sarah J, additional, Srikanth, Priya, additional, Stancu, Gabriel, additional, Stein, Andrew P, additional, Strother, Marshall, additional, Sudmeier, Lisa, additional, Sun, Mengyang, additional, Sundaram, Varun, additional, Tazudeen, Noor, additional, Tseng, Alan, additional, Tzeng, Albert, additional, Venkat, Rohit, additional, Venkataram, Sandeep, additional, Waldman, Leah, additional, Wang, Tracy, additional, Yang, Hao, additional, Yu, Jack Y, additional, Zheng, Yin, additional, Preuss, Mary L, additional, Garcia, Angelica, additional, Juergens, Matt, additional, Morris, Robert W, additional, Nagengast, Alexis A, additional, Azarewicz, Julie, additional, Carr, Thomas J, additional, Chichearo, Nicole, additional, Colgan, Mike, additional, Donegan, Megan, additional, Gardner, Bob, additional, Kolba, Nik, additional, Krumm, Janice L, additional, Lytle, Stacey, additional, MacMillian, Laurell, additional, Miller, Mary, additional, Montgomery, Andrew, additional, Moretti, Alysha, additional, Offenbacker, Brittney, additional, Polen, Mike, additional, Toth, John, additional, Woytanowski, John, additional, Kadlec, Lisa, additional, Crawford, Justin, additional, Spratt, Mary L, additional, Adams, Ashley L, additional, Barnard, Brianna K, additional, Cheramie, Martin N, additional, Eime, Anne M, additional, Golden, Kathryn L, additional, Hawkins, Allyson P, additional, Hill, Jessica E, additional, Kampmeier, Jessica A, additional, Kern, Cody D, additional, Magnuson, Emily E, additional, Miller, Ashley R, additional, Morrow, Cody M, additional, Peairs, Julia C, additional, Pickett, Gentry L, additional, Popelka, Sarah A, additional, Scott, Alexis J, additional, Teepe, Emily J, additional, TerMeer, Katie A, additional, Watchinski, Carmen A, additional, Watson, Lucas A, additional, Weber, Rachel E, additional, Woodard, Kate A, additional, Barnard, Daron C, additional, Appiah, Isaac, additional, Giddens, Michelle M, additional, McNeil, Gerard P, additional, Adebayo, Adeola, additional, Bagaeva, Kate, additional, Chinwong, Justina, additional, Dol, Chrystel, additional, George, Eunice, additional, Haltaufderhyde, Kirk, additional, Haye, Joanna, additional, Kaur, Manpreet, additional, Semon, Max, additional, Serjanov, Dmitri, additional, Toorie, Anika, additional, Wilson, Christopher, additional, Riddle, Nicole C, additional, Buhler, Jeremy, additional, Mardis, Elaine R, additional, and Elgin, Sarah C R, additional

Published
2015
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10. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

Author

Oleksyk, Taras K., Pombert, Jean-Francois, Siu, Daniel, Mazo-Vargas, Anyimilehidi, Ramos, Brian, Guiblet, Wilfried, Afanador, Yashira, Ruiz-Rodriguez, Christina T., Nickerson, Michael L., Logue, David M., Dean, Michael, Figueroa, Luis, Valentin, Ricardo, Martinez-Cruzado, Juan-Carlos, Oleksyk, Taras K., Pombert, Jean-Francois, Siu, Daniel, Mazo-Vargas, Anyimilehidi, Ramos, Brian, Guiblet, Wilfried, Afanador, Yashira, Ruiz-Rodriguez, Christina T., Nickerson, Michael L., Logue, David M., Dean, Michael, Figueroa, Luis, Valentin, Ricardo, and Martinez-Cruzado, Juan-Carlos

Abstract

Background: Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings: In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50=6,983 bp, longest=75,003 bp), which was further scaffolded into 148,255 fragments (N50=19,470, longest=206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions: The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

Published
2012

13. Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

Author

Leung W, Shaffer CD, Reed LK, Smith ST, Barshop W, Dirkes W, Dothager M, Lee P, Wong J, Xiong D, Yuan H, Bedard JE, Machone JF, Patterson SD, Price AL, Turner BA, Robic S, Luippold EK, McCartha SR, Walji TA, Walker CA, Saville K, Abrams MK, Armstrong AR, Armstrong W, Bailey RJ, Barberi CR, Beck LR, Blaker AL, Blunden CE, Brand JP, Brock EJ, Brooks DW, Brown M, Butzler SC, Clark EM, Clark NB, Collins AA, Cotteleer RJ, Cullimore PR, Dawson SG, Docking CT, Dorsett SL, Dougherty GA, Downey KA, Drake AP, Earl EK, Floyd TG, Forsyth JD, Foust JD, Franchi SL, Geary JF, Hanson CK, Harding TS, Harris CB, Heckman JM, Holderness HL, Howey NA, Jacobs DA, Jewell ES, Kaisler M, Karaska EA, Kehoe JL, Koaches HC, Koehler J, Koenig D, Kujawski AJ, Kus JE, Lammers JA, Leads RR, Leatherman EC, Lippert RN, Messenger GS, Morrow AT, Newcomb V, Plasman HJ, Potocny SJ, Powers MK, Reem RM, Rennhack JP, Reynolds KR, Reynolds LA, Rhee DK, Rivard AB, Ronk AJ, Rooney MB, Rubin LS, Salbert LR, Saluja RK, Schauder T, Schneiter AR, Schulz RW, Smith KE, Spencer S, Swanson BR, Tache MA, Tewilliager AA, Tilot AK, VanEck E, Villerot MM, Vylonis MB, Watson DT, Wurzler JA, Wysocki LM, Yalamanchili M, Zaborowicz MA, Emerson JA, Ortiz C, Deuschle FJ, DiLorenzo LA, Goeller KL, Macchi CR, Muller SE, Pasierb BD, Sable JE, Tucci JM, Tynon M, Dunbar DA, Beken LH, Conturso AC, Danner BL, DeMichele GA, Gonzales JA, Hammond MS, Kelley CV, Kelly EA, Kulich D, Mageeney CM, McCabe NL, Newman AM, Spaeder LA, Tumminello RA, Revie D, Benson JM, Cristostomo MC, DaSilva PA, Harker KS, Jarrell JN, Jimenez LA, Katz BM, Kennedy WR, Kolibas KS, LeBlanc MT, Nguyen TT, Nicolas DS, Patao MD, Patao SM, Rupley BJ, Sessions BJ, Weaver JA, Goodman AL, Alvendia EL, Baldassari SM, Brown AS, Chase IO, Chen M, Chiang S, Cromwell AB, Custer AF, DiTommaso TM, El-Adaimi J, Goscinski NC, Grove RA, Gutierrez N, Harnoto RS, Hedeen H, Hong EL, Hopkins BL, Huerta VF, Khoshabian C, LaForge KM, Lee CT, Lewis BM, Lydon AM, Maniaci BJ, Mitchell RD, Morlock EV, Morris WM, Naik P, Olson NC, Osterloh JM, Perez MA, Presley JD, Randazzo MJ, Regan MK, Rossi FG, Smith MA, Soliterman EA, Sparks CJ, Tran DL, Wan T, Welker AA, Wong JN, Sreenivasan A, Youngblom J, Adams A, Alldredge J, Bryant A, Carranza D, Cifelli A, Coulson K, Debow C, Delacruz N, Emerson C, Farrar C, Foret D, Garibay E, Gooch J, Heslop M, Kaur S, Khan A, Kim V, Lamb T, Lindbeck P, Lucas G, Macias E, Martiniuc D, Mayorga L, Medina J, Membreno N, Messiah S, Neufeld L, Nguyen SF, Nichols Z, Odisho G, Peterson D, Rodela L, Rodriguez P, Rodriguez V, Ruiz J, Sherrill W, Silva V, Sparks J, Statton G, Townsend A, Valdez I, Waters M, Westphal K, Winkler S, Zumkehr J, DeJong RJ, Hoogewerf AJ, Ackerman CM, Armistead IO, Baatenburg L, Borr MJ, Brouwer LK, Burkhart BJ, Bushhouse KT, Cesko L, Choi TY, Cohen H, Damsteegt AM, Darusz JM, Dauphin CM, Davis YP, Diekema EJ, Drewry M, Eisen ME, Faber HM, Faber KJ, Feenstra E, Felzer-Kim IT, Hammond BL, Hendriksma J, Herrold MR, Hilbrands JA, Howell EJ, Jelgerhuis SA, Jelsema TR, Johnson BK, Jones KK, Kim A, Kooienga RD, Menyes EE, Nollet EA, Plescher BE, Rios L, Rose JL, Schepers AJ, Scott G, Smith JR, Sterling AM, Tenney JC, Uitvlugt C, VanDyken RE, VanderVennen M, Vue S, Kokan NP, Agbley K, Boham SK, Broomfield D, Chapman K, Dobbe A, Dobbe I, Harrington W, Ibrahem M, Kennedy A, Koplinsky CA, Kubricky C, Ladzekpo D, Pattison C, Ramirez RE Jr, Wande L, Woehlke S, Wawersik M, Kiernan E, Thompson JS, Banker R, Bartling JR, Bhatiya CI, Boudoures AL, Christiansen L, Fosselman DS, French KM, Gill IS, Havill JT, Johnson JL, Keny LJ, Kerber JM, Klett BM, Kufel CN, May FJ, Mecoli JP, Merry CR, Meyer LR, Miller EG, Mullen GJ, Palozola KC, Pfeil JJ, Thomas JG, Verbofsky EM, Spana EP, Agarwalla A, Chapman J, Chlebina B, Chong I, Falk IN, Fitzgibbons JD, Friedman H, Ighile O, Kim AJ, Knouse KA, Kung F, Mammo D, Ng CL, Nikam VS, Norton D, Pham P, Polk JW, Prasad S, Rankin H, Ratliff CD, Scala V, Schwartz NU, Shuen JA, Xu A, Xu TQ, Zhang Y, Rosenwald AG, Burg MG, Adams SJ, Baker M, Botsford B, Brinkley B, Brown C, Emiah S, Enoch E, Gier C, Greenwell A, Hoogenboom L, Matthews JE, McDonald M, Mercer A, Monsma N, Ostby K, Ramic A, Shallman D, Simon M, Spencer E, Tomkins T, Wendland P, Wylie A, Wolyniak MJ, Robertson GM, Smith SI, DiAngelo JR, Sassu ED, Bhalla SC, Sharif KA, Choeying T, Macias JS, Sanusi F, Torchon K, Bednarski AE, Alvarez CJ, Davis KC, Dunham CA, Grantham AJ, Hare AN, Schottler J, Scott ZW, Kuleck GA, Yu NS, Kaehler MM, Jipp J, Overvoorde PJ, Shoop E, Cyrankowski O, Hoover B, Kusner M, Lin D, Martinov T, Misch J, Salzman G, Schiedermayer H, Snavely M, Zarrasola S, Parrish S, Baker A, Beckett A, Belella C, Bryant J, Conrad T, Fearnow A, Gomez C, Herbstsomer RA, Hirsch S, Johnson C, Jones M, Kabaso R, Lemmon E, Vieira CM, McFarland D, McLaughlin C, Morgan A, Musokotwane S, Neutzling W, Nietmann J, Paluskievicz C, Penn J, Peoples E, Pozmanter C, Reed E, Rigby N, Schmidt L, Shelton M, Shuford R, Tirasawasdichai T, Undem B, Urick D, Vondy K, Yarrington B, Eckdahl TT, Poet JL, Allen AB, Anderson JE, Barnett JM, Baumgardner JS, Brown AD, Carney JE, Chavez RA, Christgen SL, Christie JS, Clary AN, Conn MA, Cooper KM, Crowley MJ, Crowley ST, Doty JS, Dow BA, Edwards CR, Elder DD, Fanning JP, Janssen BM, Lambright AK, Lane CE, Limle AB, Mazur T, McCracken MR, McDonough AM, Melton AD, Minnick PJ, Musick AE, Newhart WH, Noynaert JW, Ogden BJ, Sandusky MW, Schmuecker SM, Shipman AL, Smith AL, Thomsen KM, Unzicker MR, Vernon WB, Winn WW, Woyski DS, Zhu X, Du C, Ament C, Aso S, Bisogno LS, Caronna J, Fefelova N, Lopez L, Malkowitz L, Marra J, Menillo D, Obiorah I, Onsarigo EN, Primus S, Soos M, Tare A, Zidan A, Jones CJ, Aronhalt T, Bellush JM, Burke C, DeFazio S, Does BR, Johnson TD, Keysock N, Knudsen NH, Messler J, Myirski K, Rekai JL, Rempe RM, Salgado MS, Stagaard E, Starcher JR, Waggoner AW, Yemelyanova AK, Hark AT, Bertolet A, Kuschner CE, Parry K, Quach M, Shantzer L, Shaw ME, Smith MA, Glenn O, Mason P, Williams C, Key SC, Henry TC, Johnson AG, White JX, Haberman A, Asinof S, Drumm K, Freeburg T, Safa N, Schultz D, Shevin Y, Svoronos P, Vuong T, Wellinghoff J, Hoopes LL, Chau KM, Ward A, Regisford EG, Augustine L, Davis-Reyes B, Echendu V, Hales J, Ibarra S, Johnson L, Ovu S, Braverman JM, Bahr TJ, Caesar NM, Campana C, Cassidy DW, Cognetti PA, English JD, Fadus MC, Fick CN, Freda PJ, Hennessy BM, Hockenberger K, Jones JK, King JE, Knob CR, Kraftmann KJ, Li L, Lupey LN, Minniti CJ, Minton TF, Moran JV, Mudumbi K, Nordman EC, Puetz WJ, Robinson LM, Rose TJ, Sweeney EP, Timko AS, Paetkau DW, Eisler HL, Aldrup ME, Bodenberg JM, Cole MG, Deranek KM, DeShetler M, Dowd RM, Eckardt AK, Ehret SC, Fese J, Garrett AD, Kammrath A, Kappes ML, Light MR, Meier AC, O'Rouke A, Perella M, Ramsey K, Ramthun JR, Reilly MT, Robinett D, Rossi NL, Schueler MG, Shoemaker E, Starkey KM, Vetor A, Vrable A, Chandrasekaran V, Beck C, Hatfield KR, Herrick DA, Khoury CB, Lea C, Louie CA, Lowell SM, Reynolds TJ, Schibler J, Scoma AH, Smith-Gee MT, Tuberty S, Smith CD, Lopilato JE, Hauke J, Roecklein-Canfield JA, Corrielus M, Gilman H, Intriago S, Maffa A, Rauf SA, Thistle K, Trieu M, Winters J, Yang B, Hauser CR, Abusheikh T, Ashrawi Y, Benitez P, Boudreaux LR, Bourland M, Chavez M, Cruz S, Elliott G, Farek JR, Flohr S, Flores AH, Friedrichs C, Fusco Z, Goodwin Z, Helmreich E, Kiley J, Knepper JM, Langner C, Martinez M, Mendoza C, Naik M, Ochoa A, Ragland N, Raimey E, Rathore S, Reza E, Sadovsky G, Seydoux MI, Smith JE, Unruh AK, Velasquez V, Wolski MW, Gosser Y, Govind S, Clarke-Medley N, Guadron L, Lau D, Lu A, Mazzeo C, Meghdari M, Ng S, Pamnani B, Plante O, Shum YK, Song R, Johnson DE, Abdelnabi M, Archambault A, Chamma N, Gaur S, Hammett D, Kandahari A, Khayrullina G, Kumar S, Lawrence S, Madden N, Mandelbaum M, Milnthorp H, Mohini S, Patel R, Peacock SJ, Perling E, Quintana A, Rahimi M, Ramirez K, Singhal R, Weeks C, Wong T, Gillis AT, Moore ZD, Savell CD, Watson R, Mel SF, Anilkumar AA, Bilinski P, Castillo R, Closser M, Cruz NM, Dai T, Garbagnati GF, Horton LS, Kim D, Lau JH, Liu JZ, Mach SD, Phan TA, Ren Y, Stapleton KE, Strelitz JM, Sunjed R, Stamm J, Anderson MC, Bonifield BG, Coomes D, Dillman A, Durchholz EJ, Fafara-Thompson AE, Gross MJ, Gygi AM, Jackson LE, Johnson A, Kocsisova Z, Manghelli JL, McNeil K, Murillo M, Naylor KL, Neely J, Ogawa EE, Rich A, Rogers A, Spencer JD, Stemler KM, Throm AA, Van Camp M, Weihbrecht K, Wiles TA, Williams MA, Williams M, Zoll K, Bailey C, Zhou L, Balthaser DM, Bashiri A, Bower ME, Florian KA, Ghavam N, Greiner-Sosanko ES, Karim H, Mullen VW, Pelchen CE, Yenerall PM, Zhang J, Rubin MR, Arias-Mejias SM, Bermudez-Capo AG, Bernal-Vega GV, Colon-Vazquez M, Flores-Vazquez A, Gines-Rosario M, Llavona-Cartagena IG, Martinez-Rodriguez JO, Ortiz-Fuentes L, Perez-Colomba EO, Perez-Otero J, Rivera E, Rodriguez-Giron LJ, Santiago-Sanabria AJ, Senquiz-Gonzalez AM, delValle FR, Vargas-Franco D, Velázquez-Soto KI, Zambrana-Burgos JD, Martinez-Cruzado JC, Asencio-Zayas L, Babilonia-Figueroa K, Beauchamp-Pérez FD, Belén-Rodríguez J, Bracero-Quiñones L, Burgos-Bula AP, Collado-Méndez XA, Colón-Cruz LR, Correa-Muller AI, Crooke-Rosado JL, Cruz-García JM, Defendini-Ávila M, Delgado-Peraza FM, Feliciano-Cancela AJ, Gónzalez-Pérez VM, Guiblet W, Heredia-Negrón A, Hernández-Muñiz J, Irizarry-González LN, Laboy-Corales ÁL, Llaurador-Caraballo GA, Marín-Maldonado F, Marrero-Llerena U, Martell-Martínez HA, Martínez-Traverso IM, Medina-Ortega KN, Méndez-Castellanos SG, Menéndez-Serrano KC, Morales-Caraballo CI, Ortiz-DeChoudens S, Ortiz-Ortiz P, Pagán-Torres H, Pérez-Afanador D, Quintana-Torres EM, Ramírez-Aponte EG, Riascos-Cuero C, Rivera-Llovet MS, Rivera-Pagán IT, Rivera-Vicéns RE, Robles-Juarbe F, Rodríguez-Bonilla L, Rodríguez-Echevarría BO, Rodríguez-García PM, Rodríguez-Laboy AE, Rodríguez-Santiago S, Rojas-Vargas ML, Rubio-Marrero EN, Santiago-Colón A, Santiago-Ortiz JL, Santos-Ramos CE, Serrano-González J, Tamayo-Figueroa AM, Tascón-Peñaranda EP, Torres-Castillo JL, Valentín-Feliciano NA, Valentín-Feliciano YM, Vargas-Barreto NM, Vélez-Vázquez M, Vilanova-Vélez LR, Zambrana-Echevarría C, MacKinnon C, Chung HM, Kay C, Pinto A, Kopp OR, Burkhardt J, Harward C, Allen R, Bhat P, Chang JH, Chen Y, Chesley C, Cohn D, DuPuis D, Fasano M, Fazzio N, Gavinski K, Gebreyesus H, Giarla T, Gostelow M, Greenstein R, Gunasinghe H, Hanson C, Hay A, He TJ, Homa K, Howe R, Howenstein J, Huang H, Khatri A, Kim YL, Knowles O, Kong S, Krock R, Kroll M, Kuhn J, Kwong M, Lee B, Lee R, Levine K, Li Y, Liu B, Liu L, Liu M, Lousararian A, Ma J, Mallya A, Manchee C, Marcus J, McDaniel S, Miller ML, Molleston JM, Diez CM, Ng P, Ngai N, Nguyen H, Nylander A, Pollack J, Rastogi S, Reddy H, Regenold N, Sarezky J, Schultz M, Shim J, Skorupa T, Smith K, Spencer SJ, Srikanth P, Stancu G, Stein AP, Strother M, Sudmeier L, Sun M, Sundaram V, Tazudeen N, Tseng A, Tzeng A, Venkat R, Venkataram S, Waldman L, Wang T, Yang H, Yu JY, Zheng Y, Preuss ML, Garcia A, Juergens M, Morris RW, Nagengast AA, Azarewicz J, Carr TJ, Chichearo N, Colgan M, Donegan M, Gardner B, Kolba N, Krumm JL, Lytle S, MacMillian L, Miller M, Montgomery A, Moretti A, Offenbacker B, Polen M, Toth J, Woytanowski J, Kadlec L, Crawford J, Spratt ML, Adams AL, Barnard BK, Cheramie MN, Eime AM, Golden KL, Hawkins AP, Hill JE, Kampmeier JA, Kern CD, Magnuson EE, Miller AR, Morrow CM, Peairs JC, Pickett GL, Popelka SA, Scott AJ, Teepe EJ, TerMeer KA, Watchinski CA, Watson LA, Weber RE, Woodard KA, Barnard DC, Appiah I, Giddens MM, McNeil GP, Adebayo A, Bagaeva K, Chinwong J, Dol C, George E, Haltaufderhyde K, Haye J, Kaur M, Semon M, Serjanov D, Toorie A, Wilson C, Riddle NC, Buhler J, Mardis ER, and Elgin SC

Subjects
Animals, Codon, Computational Biology, DNA Transposable Elements, Drosophila melanogaster genetics, Exons, Gene Rearrangement, Heterochromatin, Introns, Molecular Sequence Annotation, Polytene Chromosomes, Repetitive Sequences, Nucleic Acid, Selection, Genetic, Species Specificity, Drosophila genetics, Drosophila Proteins genetics, Evolution, Molecular, Genome, Genomics
Abstract

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu., (Copyright © 2015 Leung et al.)

Published
2015
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14. Reconstructing Native American migrations from whole-genome and whole-exome data.

Author

Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, and Bustamante CD

Subjects
Black People genetics, Chromosome Mapping, Exome, Genome, Human, Hispanic or Latino genetics, Human Genome Project, Humans, Mexican Americans genetics, Mexico, Puerto Rico, Racial Groups genetics, White People genetics, Gene Frequency genetics, Genetics, Population, Human Migration, Indians, North American genetics
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations., Competing Interests: The authors have declared that no competing interests exist.

Published
2013
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