Search Results - "Catchen, Julian M"

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics by Rochette, Nicolas C., Rivera‐Colón, Angel G., Catchen, Julian M.

“…For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing,…”
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Lost in parameter space: a road map for stacks by Paris, Josephine R., Stevens, Jamie R., Catchen, Julian M., Johnston, Susan

“…Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms…”
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Stacks: building and genotyping Loci de novo from short-read sequences by Catchen, Julian M, Amores, Angel, Hohenlohe, Paul, Cresko, William, Postlethwait, John H

“…Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the…”
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Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout by HOHENLOHE, PAUL A, AMISH, STEPHEN J, CATCHEN, JULIAN M, ALLENDORF, FRED W, LUIKART, GORDON

“…The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions…”
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Resolving postglacial phylogeography using high-throughput sequencing by Emerson, Kevin J., Merz, Clayton R., Catchen, Julian M., Hohenlohe, Paul A., Cresko, William A., Bradshaw, William E., Holzapfel, Christina M.

“…The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being…”
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Automated identification of conserved synteny after whole-genome duplication by Catchen, Julian M, Conery, John S, Postlethwait, John H

“…An important objective for inferring the evolutionary history of gene families is the determination of orthologies and paralogies. Lineage-specific paralog…”
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Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance by Moran, Rachel L., Zhou, Muchu, Catchen, Julian M., Fuller, Rebecca C.

“…Determining which reproductive isolating barriers arise first between geographically isolated lineages is critical to understanding allopatric speciation. We…”
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Retinoic acid metabolic genes, meiosis, and gonadal sex differentiation in zebrafish by Rodríguez-Marí, Adriana, Cañestro, Cristian, BreMiller, Ruth A, Catchen, Julian M, Yan, Yi-Lin, Postlethwait, John H

“…To help understand the elusive mechanisms of zebrafish sex determination, we studied the genetic machinery regulating production and breakdown of retinoic acid…”
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The genomic basis of the plant island syndrome in Darwin’s giant daisies by Cerca, José, Petersen, Bent, Lazaro-Guevara, José Miguel, Rivera-Colón, Angel, Birkeland, Siri, Vizueta, Joel, Li, Siyu, Li, Qionghou, Loureiro, João, Kosawang, Chatchai, Díaz, Patricia Jaramillo, Rivas-Torres, Gonzalo, Fernández-Mazuecos, Mario, Vargas, Pablo, McCauley, Ross A., Petersen, Gitte, Santos-Bay, Luisa, Wales, Nathan, Catchen, Julian M., Machado, Daniel, Nowak, Michael D., Suh, Alexander, Sinha, Neelima R., Nielsen, Lene R., Seberg, Ole, Gilbert, M. Thomas P., Leebens-Mack, James H., Rieseberg, Loren H., Martin, Michael D.

“…The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in…”
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Deriving genotypes from RAD-seq short-read data using Stacks by Rochette, Nicolas C, Catchen, Julian M

“…In this protocol, the authors provide a strategy and set of methods to analyze restriction-site-associated DNA-sequencing (RAD-seq) data using Stacks, enabling…”
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Evolution of a new function by degenerative mutation in cephalochordate steroid receptors by Bridgham, Jamie T, Brown, Justine E, Rodríguez-Marí, Adriana, Catchen, Julian M, Thornton, Joseph W

“…Gene duplication is the predominant mechanism for the evolution of new genes. Major existing models of this process assume that duplicate genes are redundant;…”
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Antarctic blackfin icefish genome reveals adaptations to extreme environments by Kim, Bo-Mi, Amores, Angel, Kang, Seunghyun, Ahn, Do-Hwan, Kim, Jin-Hyoung, Kim, Il-Chan, Lee, Jun Hyuck, Lee, Sung Gu, Lee, Hyoungseok, Lee, Jungeun, Kim, Han-Woo, Desvignes, Thomas, Batzel, Peter, Sydes, Jason, Titus, Tom, Wilson, Catherine A., Catchen, Julian M., Warren, Wesley C., Schartl, Manfred, Detrich, H. William, Postlethwait, John H., Park, Hyun

“…Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we…”
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Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species by Cerca, José, Rivera-Colón, Angel G, Ferreira, Mafalda S, Ravinet, Mark, Nowak, Michael D, Catchen, Julian M, Struck, Torsten H

“…Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis…”
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Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery by Zhang, GuangJun, Hoersch, Sebastian, Amsterdam, Adam, Whittaker, Charles A, Beert, Eline, Catchen, Julian M, Farrington, Sarah, Postlethwait, John H, Legius, Eric, Hopkins, Nancy, Lees, Jacqueline A

“…The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging…”
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Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes by Cañestro, Cristian, Catchen, Julian M, Rodríguez-Marí, Adriana, Yokoi, Hayato, Postlethwait, John H

“…Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the…”
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Replicate phylogenies and post-glacial range expansion of the pitcher-plant mosquito, Wyeomyia smithii, in North America by Merz, Clayton, Catchen, Julian M, Hanson-Smith, Victor, Emerson, Kevin J, Bradshaw, William E, Holzapfel, Christina M

“…Herein we tested the repeatability of phylogenetic inference based on high throughput sequencing by increased taxon sampling using our previously published…”
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UDP xylose synthase 1 is required for morphogenesis and histogenesis of the craniofacial skeleton by Eames, B. Frank, Singer, Amy, Smith, Gabriel A., Wood, Zachary A., Yan, Yi-Lin, He, Xinjun, Polizzi, Samuel J., Catchen, Julian M., Rodriguez-Mari, Adriana, Linbo, Tor, Raible, David W., Postlethwait, John H.

“…UDP-xylose synthase (Uxs1) is strongly conserved from bacteria to humans, but because no mutation has been studied in any animal, we do not understand its…”
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Genome-wide genetic marker discovery and genotyping using next-generation sequencing by Davey, John W, Hohenlohe, Paul A, Etter, Paul D, Boone, Jason Q, Catchen, Julian M, Blaxter, Mark L

“…Key Points New methods that make use of high-throughput sequencing are enabling the simultaneous discovery and sequencing of thousands of genetic markers…”
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Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations by Catchen, Julian M., Hohenlohe, Paul A., Bernatchez, Louis, Funk, W. Chris, Andrews, Kimberly R., Allendorf, Fred W.

“…Recently, Lowry et al. addressed the ability of RADseq approaches to detect loci under selection in genome scans. While the authors raise important…”
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Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation by Moran, Rachel L, Catchen, Julian M, Fuller, Rebecca C

“…Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have…”
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