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Marissa Kaminski, Joshua I. Brown, Sara R. Seibert, Flor Hernández, Melizar V. Duya, Ian Kendrich C. Fontanilla, David Roshier, Adam Miles, Leo Joseph, Jeffrey L. Peters, Philip Lavretsky

Courtney A. Miller, Geraud C. Tasse Taboue, Eric B. Fokam, Katy Morgan, Ying Zhen, Ryan J. Harrigan, Vinh Le Underwood, Kristen Ruegg, Paul R. Sesink Clee, Stephan Ntie, Patrick Mickala, Jean Francois Mboumba, Trevon Fuller, Breda M. Zimkus, Thomas B. Smith, Nicola M. Anthony

Jie Zhang, Francisco Pina‐Martins, Zu‐Shi Jin, Yong‐Peng Cha, Zu‐Yao Liu, Jun‐Chu Peng, Jian‐Li Zhao, Qing‐Jun Li

Xavier Dallaire, Raphael Bouchard, Philippe Hénault, Gabriela Ulmo-Diaz, Eric Normandeau, Claire Mérot, Louis Bernatchez, Jean-Sébastien Moore

Stuart B. Piertney, Marius Wenzel, Alan J. Jamieson

E. Anne Chambers, Rebecca D. Tarvin, Juan C. Santos, Santiago R. Ron, Mileidy Betancourth‐Cundar, David M. Hillis, Mikhail V. Matz, David C. Cannatella

Adam H. Freedman, Ryan J. Harrigan, Ying Zhen, Alison M. Hamilton, Thomas B. Smith

Amely Branquinho Martins, Mônica Mafra Valença-Montenegro, Marcela Guimarães Moreira Lima, Jessica W. Lynch, Walfrido Kühl Svoboda, José de Sousa e Silva-Júnior, Fábio Röhe, Jean Philippe Boubli, Anthony Di Fiore

Philipp Hühn, Markus S. Dillenberger, Michael Gerschwitz-Eidt, Elvira Hörandl, Jessica A. Los, Thibaud F.E. Messerschmid, Claudia Paetzold, Benjamin Rieger, Gudrun Kadereit

Benjamin M. Titus, Marymegan Daly

Jonatan Leo, Therése Bengtsson, Anders S. Carlsson, Jonathan Brassac, Roland von Bothmer

Marco Dorfner, Tankred Ott, Philipp Ott, Christoph Oberprieler

Roberta Gargiulo, Tiiu Kull, Michael F. Fay

Tristan Cumer, Charles Pouchon, Frédéric Boyer, Glenn Yannic, Delphine Rioux, Aurélie Bonin, Thibaut Capblancq

Cen Guo, Peng-Fei Ma, Guo-Qian Yang, Xia-Ying Ye, Ying Guo, Jing-Xia Liu, Yun-Long Liu, Deren A R Eaton, Zhen-Hua Guo, De-Zhu Li

Haw Chuan Lim, Subir B. Shakya, Michael G. Harvey, Robert G. Moyle, Robert C. Fleischer, Michael J. Braun, Frederick H. Sheldon

Thomas J. Devitt, April M. Wright, David C. Cannatella, David M. Hillis

Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, DePaul U. Foxworth, Donna L. Dittmann, Steven W. Cardiff, Robb T. Brumfield

Natalia Díaz-Arce, Naiara Rodríguez-Ezpeleta

Vladimir Salvador De Jesús-Bonilla, Rubi Nelsi Meza-Lázaro, Alejandro Zaldívar-Riverón

Sarah A. Sonsthagen, Robert E. Wilson, Philip Lavretsky, Sandra L. Talbot

Evan McCartney‐Melstad, Müge Gidiş, H. Bradley Shaffer

Jamie R. Oaks, Cameron D. Siler, Rafe M. Brown

Michael R Gemmell, Steven A Trewick, James S Crampton, Felix Vaux, Simon F K Hills, Elizabeth E Daly, Bruce A Marshall, Alan G Beu, Mary Morgan-Richards

Mario Fernández-Mazuecos, Greg Mellers, Beatriz Vigalondo, Llorenç Sáez, Pablo Vargas, Beverley J Glover

Yu-Long Li, Dong-Xiu Xue, Bai-Dong Zhang, Jin-Xian Liu

Lisa N Barrow, Alan R Lemmon, Emily Moriarty Lemmon

Glenn F. Seeholzer, Robb T. Brumfield

Praveen Nadukkalam Ravindran, Paul Bentzen, Ian R. Bradbury, Robert G. Beiko

Elizabeth J. Beckman, Phred M. Benham, Zachary A. Cheviron, Christopher C. Witt

Michael G. Harvey, Alexandre Aleixo, Camila C. Ribas, Robb T. Brumfield

Kin Onn Chan, Alana M. Alexander, L. Lee Grismer, Yong‐Chao Su, Jesse L. Grismer, Evan S. H. Quah, Rafe M. Brown

James L. Dimond, Sanoosh K. Gamblewood, Steven B. Roberts

Haw Chuan Lim, Dency F. Gawin, Subir B. Shakya, Michael G. Harvey, Mustafa A. Rahman, Frederick H. Sheldon

Adam D. Leaché, Jared A. Grummer, Rebecca B. Harris, Ian K. Breckheimer

Anna Papadopoulou, L. Lacey Knowles

Mercedes Burns, James Starrett, Shahan Derkarabetian, Casey H. Richart, Allan Cabrero, Marshal Hedin

Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C. Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez

Nicolas C Rochette, Julian M Catchen

Ying Zhen, Ryan J. Harrigan, Kristen C. Ruegg, Eric C. Anderson, Thomas C. Ng, Sirena Lao, Kirk E. Lohmueller, Thomas B. Smith

Cécile Berthouly-Salazar, Cédric Mariac, Marie Couderc, Juliette Pouzadoux, Jean-Baptiste Floc’h, Yves Vigouroux

Haw Chuan Lim, Michael J. Braun

Jeffrey M. DaCosta, Michael D. Sorenson

Naiara Rodríguez‐Ezpeleta, Ian R. Bradbury, Iñaki Mendibil, Paula Álvarez, Unai Cotano, Xabier Irigoien

David P. L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. McCormack, Kevin G. McCracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S. C. Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert C. Uy, Benjamin M. Winger

Michael G. Harvey, Brian Tilston Smith, Travis C. Glenn, Brant C. Faircloth, Robb T. Brumfield

Timothy C. Bray, Ladislav Bocak

Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, DePaul U. Foxworth, Steven W. Cardiff, Donna L. Dittmann, Libby C. Megna, Matthew D. Carling, Robb T. Brumfield

Philip Lavretsky, Jeffrey M. Dacosta, Blanca E. Hernández‐Baños, Andrew Engilis, Michael D. Sorenson, Jeffrey L. Peters

Elisa G. Dierickx, Allison J. Shultz, Fumio Sato, Takashi Hiraoka, Scott V. Edwards

Scott V. Edwards, Allison J. Shultz, Shane C. Campbell-Staton

2024	Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data Molecular Phylogenetics and Evolution Marissa Kaminski, Joshua I. Brown, Sara R. Seibert, Flor Hernández, Melizar V. Duya, Ian Kendrich C. Fontanilla, David Roshier, Adam Miles, Leo Joseph, Jeffrey L. Peters, Philip Lavretsky
2024	Environmental variation predicts patterns of genomic variation in an African tropical forest frog Frontiers in Conservation Science Courtney A. Miller, Geraud C. Tasse Taboue, Eric B. Fokam, Katy Morgan, Ying Zhen, Ryan J. Harrigan, Vinh Le Underwood, Kristen Ruegg, Paul R. Sesink Clee, Stephan Ntie, Patrick Mickala, Jean Francois Mboumba, Trevon Fuller, Breda M. Zimkus, Thomas B. Smith, Nicola M. Anthony
2023	Excessive and asymmetrical removal of heterozygous sites by maxSH biases downstream population genetic inference: Implications for hybridization between two primroses Journal of Systematics and Evolution Jie Zhang, Francisco Pina‐Martins, Zu‐Shi Jin, Yong‐Peng Cha, Zu‐Yao Liu, Jun‐Chu Peng, Jian‐Li Zhao, Qing‐Jun Li
2023	Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication Genome Biology and Evolution Xavier Dallaire, Raphael Bouchard, Philippe Hénault, Gabriela Ulmo-Diaz, Eric Normandeau, Claire Mérot, Louis Bernatchez, Jean-Sébastien Moore
2023	Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench Molecular Ecology Stuart B. Piertney, Marius Wenzel, Alan J. Jamieson
2023	2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics Ecology and Evolution E. Anne Chambers, Rebecca D. Tarvin, Juan C. Santos, Santiago R. Ron, Mileidy Betancourth‐Cundar, David M. Hillis, Mikhail V. Matz, David C. Cannatella
2023	Evidence for ecotone speciation across an African rainforest‐savanna gradient Molecular Ecology Adam H. Freedman, Ryan J. Harrigan, Ying Zhen, Alison M. Hamilton, Thomas B. Smith
2023	A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation Genes Amely Branquinho Martins, Mônica Mafra Valença-Montenegro, Marcela Guimarães Moreira Lima, Jessica W. Lynch, Walfrido Kühl Svoboda, José de Sousa e Silva-Júnior, Fábio Röhe, Jean Philippe Boubli, Anthony Di Fiore
2022	How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae) Molecular Phylogenetics and Evolution Philipp Hühn, Markus S. Dillenberger, Michael Gerschwitz-Eidt, Elvira Hörandl, Jessica A. Los, Thibaud F.E. Messerschmid, Claudia Paetzold, Benjamin Rieger, Gudrun Kadereit
2022	Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity Benjamin M. Titus, Marymegan Daly
2022	Population structure and phylogeography ofElymus mutabilisand its genetic relationships withE. transbaicalensis(Poaceae) Nordic Journal of Botany Jonatan Leo, Therése Bengtsson, Anders S. Carlsson, Jonathan Brassac, Roland von Bothmer
2022	Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping) Applications in Plant Sciences Marco Dorfner, Tankred Ott, Philipp Ott, Christoph Oberprieler
2021	Effective double‐digest RAD sequencing and genotyping despite large genome size Molecular Ecology Resources Roberta Gargiulo, Tiiu Kull, Michael F. Fay
2021	Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Molecular Genetics and Genomics Tristan Cumer, Charles Pouchon, Frédéric Boyer, Glenn Yannic, Delphine Rioux, Aurélie Bonin, Thibaut Capblancq
2021	Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos Systematic Biology Cen Guo, Peng-Fei Ma, Guo-Qian Yang, Xia-Ying Ye, Ying Guo, Jing-Xia Liu, Yun-Long Liu, Deren A R Eaton, Zhen-Hua Guo, De-Zhu Li
2020	Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA Ecology and Evolution Haw Chuan Lim, Subir B. Shakya, Michael G. Harvey, Robert G. Moyle, Robert C. Fleischer, Michael J. Braun, Frederick H. Sheldon
2019	Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation Proceedings of the National Academy of Sciences Thomas J. Devitt, April M. Wright, David C. Cannatella, David M. Hillis
2019	Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World Molecular Ecology Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, DePaul U. Foxworth, Donna L. Dittmann, Steven W. Cardiff, Robb T. Brumfield
2019	Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better? Frontiers in Genetics Natalia Díaz-Arce, Naiara Rodríguez-Ezpeleta
2019	Full Bayesian Comparative Phylogeography from Genomic Data Systematic Biology Jamie R Oaks
2019	3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae) Molecular Phylogenetics and Evolution Vladimir Salvador De Jesús-Bonilla, Rubi Nelsi Meza-Lázaro, Alejandro Zaldívar-Riverón
2019	Coast to coast: High genomic connectivity in North American scoters Ecology and Evolution Sarah A. Sonsthagen, Robert E. Wilson, Philip Lavretsky, Sandra L. Talbot
2019	An empirical pipeline for choosing the optimal clustering threshold in RADseq studies Molecular Ecology Resources Evan McCartney‐Melstad, Müge Gidiş, H. Bradley Shaffer
2019	The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate‐driven vicariant diversification across an island archipelago Evolution Jamie R. Oaks, Cameron D. Siler, Rafe M. Brown
2018	Genetic structure and shell shape variation within a rocky shore whelk suggest both diverging and constraining selection with gene flow Biological Journal of the Linnean Society Michael R Gemmell, Steven A Trewick, James S Crampton, Felix Vaux, Simon F K Hills, Elizabeth E Daly, Bruce A Marshall, Alan G Beu, Mary Morgan-Richards
2018	Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing Systematic Biology Mario Fernández-Mazuecos, Greg Mellers, Beatriz Vigalondo, Llorenç Sáez, Pablo Vargas, Beverley J Glover
2018	An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals Royal Society Open Science Yu-Long Li, Dong-Xiu Xue, Bai-Dong Zhang, Jin-Xian Liu
2018	Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data Systematic Biology Lisa N Barrow, Alan R Lemmon, Emily Moriarty Lemmon
2018	Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient Molecular Ecology Glenn F. Seeholzer, Robb T. Brumfield
2018	PMERGE: Computational filtering of paralogous sequences from RAD‐seq data Ecology and Evolution Praveen Nadukkalam Ravindran, Paul Bentzen, Ian R. Bradbury, Robert G. Beiko
2018	Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins Molecular Ecology Elizabeth J. Beckman, Phred M. Benham, Zachary A. Cheviron, Christopher C. Witt
2017	Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds The American Naturalist Michael G. Harvey, Alexandre Aleixo, Camila C. Ribas, Robb T. Brumfield
2017	Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs Molecular Ecology Kin Onn Chan, Alana M. Alexander, L. Lee Grismer, Yong‐Chao Su, Jesse L. Grismer, Evan S. H. Quah, Rafe M. Brown
2017	Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology James L. Dimond, Sanoosh K. Gamblewood, Steven B. Roberts
2017	Sundaland's east–west rain forest population structure: variable manifestations in four polytypic bird species examined using RAD‐Seq and plumage analyses Journal of Biogeography Haw Chuan Lim, Dency F. Gawin, Subir B. Shakya, Michael G. Harvey, Mustafa A. Rahman, Frederick H. Sheldon
2017	Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone Molecular Ecology Adam D. Leaché, Jared A. Grummer, Rebecca B. Harris, Ian K. Breckheimer
2017	Linking micro‐ and macroevolutionary perspectives to evaluate the role of Quaternary sea‐level oscillations in island diversification Evolution Anna Papadopoulou, L. Lacey Knowles
2017	Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages Molecular Ecology Resources Mercedes Burns, James Starrett, Shahan Derkarabetian, Casey H. Richart, Allan Cabrero, Marshal Hedin
2017	Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study Molecular Phylogenetics and Evolution Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C. Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
2017	Deriving genotypes from RAD-seq short-read data using Stacks Nature Protocols Nicolas C Rochette, Julian M Catchen
2017	Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens) Molecular Ecology Ying Zhen, Ryan J. Harrigan, Kristen C. Ruegg, Eric C. Anderson, Thomas C. Ng, Sirena Lao, Kirk E. Lohmueller, Thomas B. Smith
2016	Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy Frontiers in Plant Science Cécile Berthouly-Salazar, Cédric Mariac, Marie Couderc, Juliette Pouzadoux, Jean-Baptiste Floc’h, Yves Vigouroux
2016	High‐throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements Molecular Ecology Resources Haw Chuan Lim, Michael J. Braun
2016	ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories Molecular Phylogenetics and Evolution Jeffrey M. DaCosta, Michael D. Sorenson
2016	Population structure of Atlantic mackerel inferred from RAD‐seq‐derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection Molecular Ecology Resources Naiara Rodríguez‐Ezpeleta, Ian R. Bradbury, Iñaki Mendibil, Paula Álvarez, Unai Cotano, Xabier Irigoien
2016	Genomic approaches to understanding population divergence and speciation in birds The Auk David P. L. Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. McCormack, Kevin G. McCracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S. C. Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert C. Uy, Benjamin M. Winger
2016	Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics Systematic Biology Michael G. Harvey, Brian Tilston Smith, Travis C. Glenn, Brant C. Faircloth, Robb T. Brumfield
2016	Slowly dispersing neotenic beetles can speciate on a penny coin and generate space-limited diversity in the tropical mountains Scientific Reports Timothy C. Bray, Ladislav Bocak
2016	Willet be one species or two? A genomic view of the evolutionary history ofTringa semipalmata The Auk Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, DePaul U. Foxworth, Steven W. Cardiff, Donna L. Dittmann, Libby C. Megna, Matthew D. Carling, Robb T. Brumfield
2015	Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards Molecular Ecology Philip Lavretsky, Jeffrey M. Dacosta, Blanca E. Hernández‐Baños, Andrew Engilis, Michael D. Sorenson, Jeffrey L. Peters
2015	Morphological and genomic comparisons of Hawaiian and Japanese Black‐footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation Evolutionary Applications Elisa G. Dierickx, Allison J. Shultz, Fumio Sato, Takashi Hiraoka, Scott V. Edwards
2015	Next-generation sequencing and the expanding domain of phylogeography Folia Zoologica Scott V. Edwards, Allison J. Shultz, Shane C. Campbell-Staton
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