Gaughran Lab

Publications

You can also see a full list of publications and preprints at Stephen's Google Scholar page.

Please email Stephen to request PDFs of the below manuscripts.

2026

  1. A whale apart: further evidence for genetic isolation of Arabian Sea humpback whales from other recognised subspecies

    A. Rita Amaral, Stephen J. Gaughran, Melina I. Giakoumis, Andrew Willson, Gianna Minton, Robert Baldwin, Maia Sarrouf Willson, Suaad Al Harthi, Aida Al Jabri, Tim Collins, Koen Van Waerebeek, Howard C. Rosenbaum

    Frontiers in Marine Science 13, 1735173, 2026

  2. Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

    Alexander Ochoa, Stephen J. Gaughran, Rachel Gray, Nicole A. Fusco, Johanna N. J. Weston, Cyler Conrad, Nikos Poulakakis, Joshua M. Miller, Adalgisa Caccone, Evelyn L. Jensen

    Proceedings of the Royal Society B: Biological Sciences 293 (2075), 20260103, 2026

  3. Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity

    Bridgett M vonHoldt, Matt James, Stephen J. Gaughran, Alexandra L DeCandia, Klaus-Peter Koepfli, Dan Flores, Nucharin Songsasen, Kristin E Brzeski, Evelyn L Jensen

    Journal of Heredity, esag040, 2026

  4. Signatures of the Anthropocene: Population Genomic Structure Detected in Pennsylvania Coyotes

    Craig A. Marshall, Julia Halo, Kyle Van Why, Yeraldi Loera, Stavi R. Tennenbaum, Casey Burton, Ariana Di Landro, Dominic Dominguez, Daniel Duncan, Madison Machado, Catalina Posada, Stephen J. Gaughran, Madison Lichak, Kristin Brzeski, Elizabeth Heppenheimer, Bridgett vonHoldt

    Ecology and Evolution 16 (3), e73216, 2026

2025

  1. Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

    Stephen J. Gaughran, Rachel Gray, Alexander Ochoa, Menna Jones, Nicole Fusco, Joshua M Miller, Nikos Poulakakis, Kevin de Queiroz, Adalgisa Caccone, Evelyn L Jensen

    Evolution 79 (2), 296-308, 2025

2022

  1. Pleistocene parades of carnivores into North America

    Stephen J. Gaughran, Bridgett vonHoldt

    Molecular ecology 31 (24), 6387-6389, 2022

  2. Coyotes in New York City carry variable genomic dog ancestry and influence their interactions with humans

    Anthony Caragiulo, Stephen J. Gaughran, Neil Duncan, Christopher Nagy, Mark Weckel, Bridgett M. vonHoldt

    Genes 13 (9), 1661, 2022

  3. A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

    David W. Mohr, Stephen J. Gaughran, Justin Paschall, Ahmed Naguib, Andy Wing Chun Pang, Olga Dudchenko, Erez Lieberman Aiden, Deanna M. Church, Alan F. Scott

    Genes 13 (7), 1270, 2022

  4. The Galapagos giant tortoise Chelonoidis phantasticus is not extinct

    Evelyn L. Jensen, Stephen J. Gaughran, Nicole A. Fusco, Nikos Poulakakis, Washington Tapia, Christian Sevilla, Jeffreys Málaga, Carol Mariani, James P. Gibbs, Adalgisa Caccone

    Communications biology 5 (1), 546, 2022

2021

  1. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises

    Evelyn L. Jensen, Stephen J. Gaughran, Ryan C. Garrick, Michael A. Russello, Adalgisa Caccone

    Molecular Ecology 30 (23), 6325-6339, 2021

  2. Genetic and demographic history define a conservation strategy for earth’s most endangered pinniped, the Mediterranean monk seal Monachus monachus

    Alexandros A. Karamanlidis, Tomaž Skrbinšek, George Amato, Panagiotis Dendrinos, Stephen J. Gaughran, Panagiotis Kasapidis, Alexander Kopatz, Astrid Vik Stronen

    Scientific Reports 11 (1), 373, 2021

  3. Patterns of Adaptive and Purifying Selection in the Genomes of Phocid Seals

    Stephen J. Gaughran

    Yale University, 2021 Dissertation

2019

  1. Giant tortoise genomes provide insights into longevity and age-related disease

    Víctor Quesada, Sandra Freitas-Rodríguez, Joshua Miller, José G. Pérez-Silva, Zi-Feng Jiang, Washington Tapia, Olaya Santiago-Fernández, Diana Campos-Iglesias, Lukas F. K. Kuderna, Maud Quinzin, Miguel G. Álvarez, Dido Carrero, Luciano B. Beheregaray, James P. Gibbs, Ylenia Chiari, Scott Glaberman, Claudio Ciofi, Miguel Araujo-Voces, Pablo Mayoral, Javier R. Arango, Isaac Tamargo-Gómez, David Roiz-Valle, María Pascual-Torner, Benjamin R. Evans, Danielle L. Edwards, Ryan C. Garrick, Michael A. Russello, Nikos Poulakakis, Stephen J. Gaughran, Danny O. Rueda, Gabriel Bretones, Tomàs Marquès-Bonet, Kevin P. White, Adalgisa Caccone, Carlos López-Otín

    Nature ecology & evolution 3 (1), 87-95, 2019

2018

  1. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study

    Stephen J. Gaughran, Maud C. Quinzin, Joshua M. Miller, Ryan C. Garrick, Danielle L. Edwards, Michael A. Russello, Nikos Poulakakis, Claudio Ciofi, Luciano B. Beheregaray, Adalgisa Caccone

    Evolutionary Applications 11 (7), 1084-1093, 2018

2016

  1. How elephants beat cancer

    Stephen J. Gaughran, Evlyn Pless, Stephen C Stearns

    Elife 5, e21864, 2016

  2. A novel molecular method for noninvasive sex identification of order Carnivora

    Alexandra DeCandia, Stephen J. Gaughran, Anthony Caragiulo, George Amato

    Conservation Genetics Resources 8 (2), 119-121, 2016

  3. Potential bycatch impact on distinct sea turtle populations is dependent on fishing ground rather than gear type in the Mediterranean Sea

    Marcel Clusa, Carlos Carreras, Marta Pascual, Stephen J. Gaughran, Susanna Piovano, Diego Avolio, Gepi Ollano, Gloria Fernández, Jesús Tomás, Juan Antonio Raga, Alex Aguilar, Luis Cardona

    Marine Biology 163 (5), 122, 2016

  4. Shaping species conservation strategies using mtDNA analysis: The case of the elusive Mediterranean monk seal (Monachus monachus)

    Alexandros A. Karamanlidis, Stephen J. Gaughran, Alex Aguilar, Panagiotis Dendrinos, Djuro Huber, Rosa Pires, Jennifer Schultz, Tomaž Skrbinšek, George Amato

    Biological Conservation 193, 71-79, 2016

2014

  1. Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling

    Eugenia Naro-Maciel, Stephen J. Gaughran, Nathan F. Putman, George Amato, Felicity Arengo, Peter H. Dutton, Katherine W. McFadden, Erin C. Vintinner, Eleanor J. Sterling

    Journal of the Royal Society Interface 11 (93), 20130888, 2014

  2. Fine-scale distribution of juvenile Atlantic and Mediterranean loggerhead turtles (Caretta caretta) in the Mediterranean Sea

    Marcel Clusa, Carlos Carreras, Marta Pascual, Stephen J. Gaughran, Susanna Piovano, Cristina Giacoma, Gloria Fernández, Yaniv Levy, Jesús Tomás, Juan Antonio Raga, Fulvio Maffucci, Sandra Hochscheid, Alex Aguilar, Luis Cardona

    Marine biology 161 (3), 509-519, 2014