Publications - Angel G. Rivera-Colón

MKado: a toolkit for McDonald–Kreitman tests of natural selection

Angel G. Rivera-Colón, Clara T. Rehmann, Andrew D. Kern

G3: Genes, Genomes, Genetics 2026

[Paper] [Preprint]

MKado: a toolkit for McDonald–Kreitman tests of natural selection

Angel G. Rivera-Colón, Clara T. Rehmann, Andrew D. Kern

G3: Genes, Genomes, Genetics 2026

[Paper] [Preprint]

GPU accelerated population genetics statistics using pg_gpu

Nathaniel S. Pope, Angel G. Rivera-Colón, Ananya Kapoor, Kevin Korfmann, Murillo F. Rodrigues, Scott T. Small, Anastasia A. Teterina, Andrew D. Kern

bioRxiv 2026 Preprint

[Paper]

GPU accelerated population genetics statistics using pg_gpu

Nathaniel S. Pope, Angel G. Rivera-Colón, Ananya Kapoor, Kevin Korfmann, Murillo F. Rodrigues, Scott T. Small, Anastasia A. Teterina, Andrew D. Kern

bioRxiv 2026 Preprint

[Paper]

Ecotypes, Wolbachia, and urbanization shape Culex pipiens population structure in a West Nile virus hotspot

Sonia Cebrián-Camisón, Angel G. Rivera-Colón, Scott T. Small, Jordi Figuerola, Andrew D. Kern, Peter L. Ralph, Aureliano Bombarely, María José Ruiz-López

bioRxiv 2026 Preprint

[Paper]

Ecotypes, Wolbachia, and urbanization shape Culex pipiens population structure in a West Nile virus hotspot

Sonia Cebrián-Camisón, Angel G. Rivera-Colón, Scott T. Small, Jordi Figuerola, Andrew D. Kern, Peter L. Ralph, Aureliano Bombarely, María José Ruiz-López

bioRxiv 2026 Preprint

[Paper]

Large population sizes shape genome evolution in barnacles

Angel G. Rivera-Colón, Scott T. Small, Erin Jezuit, John P. Wares, Andrew D. Kern

bioRxiv 2026 Preprint

[Paper]

Large population sizes shape genome evolution in barnacles

Angel G. Rivera-Colón, Scott T. Small, Erin Jezuit, John P. Wares, Andrew D. Kern

bioRxiv 2026 Preprint

[Paper]

Hemoglobin-Gene Cluster Deletions in Antarctic White-Blooded Icefishes Facilitated by Transposable Elements

Thomas Desvignes, Angel G. Rivera-Colón, John H. Postlethwait

Genome Biology and Evolution 2025

[Paper]

Hemoglobin-Gene Cluster Deletions in Antarctic White-Blooded Icefishes Facilitated by Transposable Elements

Thomas Desvignes, Angel G. Rivera-Colón, John H. Postlethwait

Genome Biology and Evolution 2025

[Paper]

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

Niraj Rayamajhi, Angel G. Rivera-Colón, Bushra Fazal Minhas, C. H. Christina Cheng, Julian M. Catchen

G3: Genes, Genomes, Genetics 2025

[Paper] [Preprint]

The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

Niraj Rayamajhi, Angel G. Rivera-Colón, Bushra Fazal Minhas, C. H. Christina Cheng, Julian M. Catchen

G3: Genes, Genomes, Genetics 2025

[Paper] [Preprint]

High genetic connectivity and moderate diversity detected in the common octopus (Octopus vulgaris) in Puerto Rico through reduced-representation DNA sequencing

Omar Zayas-Cruz, Angel G. Rivera-Colón, Nikolaos V. Schizas

Journal of the Marine Biological Association of the United Kingdom 2025

[Paper]

High genetic connectivity and moderate diversity detected in the common octopus (Octopus vulgaris) in Puerto Rico through reduced-representation DNA sequencing

Omar Zayas-Cruz, Angel G. Rivera-Colón, Nikolaos V. Schizas

Journal of the Marine Biological Association of the United Kingdom 2025

[Paper]

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

Kira M. Long, Angel G. Rivera-Colón, Kevin F. P. Bennett, Julian M. Catchen, Michael J. Braun, Jeffrey D. Brawn

Evolution 2024

[Paper] [Preprint]

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

Kira M. Long, Angel G. Rivera-Colón, Kevin F. P. Bennett, Julian M. Catchen, Michael J. Braun, Jeffrey D. Brawn

Evolution 2024

[Paper] [Preprint]

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction

Alida de Flamingh, Thomas P. Gnoske, Angel G. Rivera-Colón, Velizar A. Simeonovski, Julian C. Kerbis Peterhans, Nobuyuki Yamaguchi, Kelsey E. Witt, Julian Catchen, Alfred L. Roca, Ripan Singh Malhi

Journal of Heredity 2024

[Paper] [Preprint]

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction

Alida de Flamingh, Thomas P. Gnoske, Angel G. Rivera-Colón, Velizar A. Simeonovski, Julian C. Kerbis Peterhans, Nobuyuki Yamaguchi, Kelsey E. Witt, Julian Catchen, Alfred L. Roca, Ripan Singh Malhi

Journal of Heredity 2024

[Paper] [Preprint]

Genomics and conservation: Guidance from training to analyses and applications

Lauren M. Schiebelhut, Annie S. Guillaume, Arianna Kuhn, Rena M. Schweizer, Ellie E. Armstrong, Mark A. Beaumont, Margaret Byrne, Ted Cosart, Brian K. Hand, Leif Howard, Steven M. Mussmann, Shawn R. Narum, Rita Rasteiro, Angel G. Rivera-Colón, Norah Saarman, Arun Sethuraman, Helen R. Taylor, Gregg W. C. Thomas, Maren Wellenreuther, Gordon Luikart

Molecular Ecology Resources 2024

[Paper]

Genomics and conservation: Guidance from training to analyses and applications

Lauren M. Schiebelhut, Annie S. Guillaume, Arianna Kuhn, Rena M. Schweizer, Ellie E. Armstrong, Mark A. Beaumont, Margaret Byrne, Ted Cosart, Brian K. Hand, Leif Howard, Steven M. Mussmann, Shawn R. Narum, Rita Rasteiro, Angel G. Rivera-Colón, Norah Saarman, Arun Sethuraman, Helen R. Taylor, Gregg W. C. Thomas, Maren Wellenreuther, Gordon Luikart

Molecular Ecology Resources 2024

[Paper]

On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity

Nicolas C. Rochette, Angel G. Rivera-Colón, Jessica Walsh, Thomas J. Sanger, Shane C. Campbell‐Staton, Julian M. Catchen

Molecular Ecology Resources 2023

[Paper] [Preprint]

On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity

Nicolas C. Rochette, Angel G. Rivera-Colón, Jessica Walsh, Thomas J. Sanger, Shane C. Campbell‐Staton, Julian M. Catchen

Molecular Ecology Resources 2023

[Paper] [Preprint]

Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus—The Closest Ancestral Proxy of Antarctic Cryonotothenioids

Chi-Hing Christina Cheng, Angel G. Rivera-Colón, Bushra Fazal Minhas, Loralee Wilson, Niraj Rayamajhi, Luis Vargas-Chacoff, Julian M. Catchen

Genes 2023

[Paper]

Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus—The Closest Ancestral Proxy of Antarctic Cryonotothenioids

Chi-Hing Christina Cheng, Angel G. Rivera-Colón, Bushra Fazal Minhas, Loralee Wilson, Niraj Rayamajhi, Luis Vargas-Chacoff, Julian M. Catchen

Genes 2023

[Paper]

Numt Parser: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Alida de Flamingh, Angel G. Rivera-Colón, Tom P. Gnoske, Julian C. Kerbis Peterhans, Julian Catchen, Ripan S. Malhi, Alfred L. Roca

Journal of Heredity 2023

[Paper] [Preprint]

Numt Parser: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Alida de Flamingh, Angel G. Rivera-Colón, Tom P. Gnoske, Julian C. Kerbis Peterhans, Julian Catchen, Ripan S. Malhi, Alfred L. Roca

Journal of Heredity 2023

[Paper] [Preprint]

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

Angel G. Rivera-Colón, Niraj Rayamajhi, Bushra Fazal Minhas, Giovanni Madrigal, Kevin T. Bilyk, Veronica Yoon, Mathias Hüne, Susan Gregory, C. H. Christina Cheng, Julian M. Catchen

Molecular Biology and Evolution 2023

[Paper] [Preprint]

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

Angel G. Rivera-Colón, Niraj Rayamajhi, Bushra Fazal Minhas, Giovanni Madrigal, Kevin T. Bilyk, Veronica Yoon, Mathias Hüne, Susan Gregory, C. H. Christina Cheng, Julian M. Catchen

Molecular Biology and Evolution 2023

[Paper] [Preprint]

The genomic basis of the plant island syndrome in Darwin’s giant daisies

José Cerca, Bent Petersen, José Miguel Lazaro-Guevara, Angel G. Rivera-Colón, Siri Birkeland, Joel Vizueta, Siyu Li, Qionghou Li, João Loureiro, Chatchai Kosawang, Patricia Jaramillo Díaz, Gonzalo Rivas-Torres, Mario Fernández-Mazuecos, Pablo Vargas, Ross A. McCauley, Gitte Petersen, Luisa Santos-Bay, Nathan Wales, Julian M. Catchen, Daniel Machado, Michael D. Nowak, Alexander Suh, Neelima R. Sinha, Lene R. Nielsen, Ole Seberg, M. Thomas P. Gilbert, James H. Leebens-Mack, Loren H. Rieseberg, Michael D. Martin

Nature Communications 2022

[Paper]

The genomic basis of the plant island syndrome in Darwin’s giant daisies

José Cerca, Bent Petersen, José Miguel Lazaro-Guevara, Angel G. Rivera-Colón, Siri Birkeland, Joel Vizueta, Siyu Li, Qionghou Li, João Loureiro, Chatchai Kosawang, Patricia Jaramillo Díaz, Gonzalo Rivas-Torres, Mario Fernández-Mazuecos, Pablo Vargas, Ross A. McCauley, Gitte Petersen, Luisa Santos-Bay, Nathan Wales, Julian M. Catchen, Daniel Machado, Michael D. Nowak, Alexander Suh, Neelima R. Sinha, Lene R. Nielsen, Ole Seberg, M. Thomas P. Gilbert, James H. Leebens-Mack, Loren H. Rieseberg, Michael D. Martin

Nature Communications 2022

[Paper]

Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes

K. Yarlagadda, A. J. Zachwieja, A. de Flamingh, T. Phungviwatnikul, Angel G. Rivera-Colón, C. Roseman, L. Shackelford, K. S. Swanson, R. S. Malhi

Proceedings of the Royal Society B: Biological Sciences 2022

[Paper]

Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes

K. Yarlagadda, A. J. Zachwieja, A. de Flamingh, T. Phungviwatnikul, Angel G. Rivera-Colón, C. Roseman, L. Shackelford, K. S. Swanson, R. S. Malhi

Proceedings of the Royal Society B: Biological Sciences 2022

[Paper]

Population Genomics Analysis with RAD, Reprised: Stacks 2

Angel G. Rivera-Colón, Julian Catchen

Marine Genomics 2022

[Paper]

Population Genomics Analysis with RAD, Reprised: Stacks 2

Angel G. Rivera-Colón, Julian Catchen

Marine Genomics 2022

[Paper]

Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei)

Chia-Hao Chang, Julian Catchen, Rachel L. Moran, Angel G. Rivera-Colón, Yu-Chun Wang, Rebecca C. Fuller

Journal of Heredity 2021

[Paper]

Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei)

Chia-Hao Chang, Julian Catchen, Rachel L. Moran, Angel G. Rivera-Colón, Yu-Chun Wang, Rebecca C. Fuller

Journal of Heredity 2021

[Paper]

Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

José Cerca, Marius F. Maurstad, Nicolas C. Rochette, Angel G. Rivera-Colón, Niraj Rayamajhi, Julian M. Catchen, Torsten H. Struck

Methods in Ecology and Evolution 2021

[Paper]

Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

José Cerca, Marius F. Maurstad, Nicolas C. Rochette, Angel G. Rivera-Colón, Niraj Rayamajhi, Julian M. Catchen, Torsten H. Struck

Methods in Ecology and Evolution 2021

[Paper]

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

José Cerca, Angel G. Rivera-Colón, Mafalda S. Ferreira, Mark Ravinet, Michael D. Nowak, Julian M. Catchen, Torsten H. Struck

PeerJ 2021

[Paper]

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

José Cerca, Angel G. Rivera-Colón, Mafalda S. Ferreira, Mark Ravinet, Michael D. Nowak, Julian M. Catchen, Torsten H. Struck

PeerJ 2021

[Paper]

Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

Angel G. Rivera-Colón, Nicolas C. Rochette, Julian M. Catchen

Molecular Ecology Resources 2021

[Paper]

Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

Angel G. Rivera-Colón, Nicolas C. Rochette, Julian M. Catchen

Molecular Ecology Resources 2021

[Paper]

Multiple Loci Control Eyespot Number Variation on the Hindwings of Bicyclus anynana Butterflies

Angel G. Rivera-Colón, Erica L. Westerman, Steven M. Van Belleghem, Antónia Monteiro, Riccardo Papa

Genetics 2020

[Paper]

Multiple Loci Control Eyespot Number Variation on the Hindwings of Bicyclus anynana Butterflies

Angel G. Rivera-Colón, Erica L. Westerman, Steven M. Van Belleghem, Antónia Monteiro, Riccardo Papa

Genetics 2020

[Paper]

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Nicolas C. Rochette, Angel G. Rivera-Colón, Julian M. Catchen

Molecular Ecology 2019

[Paper]

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Nicolas C. Rochette, Angel G. Rivera-Colón, Julian M. Catchen

Molecular Ecology 2019

[Paper]