Publications

2024

Phred M Benham, Carla Cicero, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, Benjamin L King, W Kelley Thomas, Adrienne I Kovach, Michael W Nachman, Rauri C K Bowie, Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery, Genome Biology and Evolution, 2024;, evae067, https://doi.org/10.1093/gbe/evae067

Whitney L E Tsai, Merly Escalona, Kimball L Garrett, Ryan S Terrill, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, William Seligmann, Colin W Fairbairn, Ryan J Harrigan, John E McCormack, Michael E Alfaro, Thomas B Smith, Rachael A Bay, A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia), Journal of Heredity, 2024;, esae008, https://doi.org/10.1093/jhered/esae008

Samantha L R Capel, Natalie M Hamilton, Devaughn Fraser, Merly Escalona, Oanh Nguyen, Samuel Sacco, Ruta Sahasrabudhe, William Seligmann, Juan M Vazquez, Peter H Sudmant, Michael L Morrison, Robert K Wayne, Michael R Buchalski, Reference genome of Townsend’s big-eared bat, Corynorhinus townsendii, Journal of Heredity, Volume 115, Issue 2, March 2024, Pages 203–211, https://doi.org/10.1093/jhered/esad078

Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork, The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species, Journal of Heredity, Volume 115, Issue 2, March 2024, Pages 221–229, https://doi.org/10.1093/jhered/esae002

Cade D Mirchandani, Allison J Shultz, Gregg W C Thomas, Sara J Smith, Mara Baylis, Brian Arnold, Russ Corbett-Detig, Erik Enbody, Timothy B Sackton, A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics, Molecular Biology and Evolution, Volume 41, Issue 1, January 2024, msad270, https://doi.org/10.1093/molbev/msad270

Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman, A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris, Journal of Heredity, Volume 115, Issue 1, January 2024, Pages 130–138, https://doi.org/10.1093/jhered/esad060

Philip S Ward, Elizabeth I Cash, Kailey Ferger, Merly Escalona, Ruta Sahasrabudhe, Courtney Miller, Erin Toffelmier, Colin Fairbairn, William Seligmann, H Bradley Shaffer, Neil D Tsutsui, Reference genome of the bicolored carpenter ant, Camponotus vicinus, Journal of Heredity, Volume 115, Issue 1, January 2024, Pages 120–129, https://doi.org/10.1093/jhered/esad055

Joseph N Curti, Devaughn Fraser, Merly Escalona, Colin W Fairbairn, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, William Seligmann, Peter H Sudmant, Erin Toffelmier, Juan Manuel Vazquez, Robert Wayne, H Bradley Shaffer, Michael R Buchalski, A genome assembly of the Yuma myotis bat, Myotis yumanensis, Journal of Heredity, Volume 115, Issue 1, January 2024, Pages 139–148, https://doi.org/10.1093/jhered/esad053

2023

Keller AG, Dahlhoff EP, Bracewell R, Chatla K, Bachtrog D, Rank NE, Williams CM. Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle. Proc Biol Sci. 2023 Aug 30;290(2005):20230630. doi: 10.1098/rspb.2023.0630. Epub 2023 Aug 16. PMID: 37583321; PMCID: PMC10427825.

Chambers, E. A., Bishop, A. P., & Wang, I. J. (2023). Individual-based landscape genomics for conservation: An analysis pipeline. Molecular Ecology Resources, 00, 1–12. https://doi.org/10.1111/1755-0998.13884

Julia N Adams, Merly Escalona, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, William Seligmann, Oanh Nguyen, Noravit Chumchim, Jason E Stajich, The reference genome assembly of the bright cobblestone lichen, Acarospora socialis, Journal of Heredity, Volume 114, Issue 6, December 2023, Pages 707–714, https://doi.org/10.1093/jhered/esad052

Erin P Westeen, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Robert N Fisher, Erin Toffelmier, H Bradley Shaffer, Ian J Wang, A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus, Journal of Heredity, Volume 114, Issue 6, December 2023, Pages 690–697, https://doi.org/10.1093/jhered/esad051

Devon A DeRaad, Merly Escalona, Phred M Benham, Mohan P A Marimuthu, Ruta M Sahasrabudhe, Oanh Nguyen, Noravit Chumchim, Eric Beraut, Colin W Fairbairn, William Seligmann, Rauri C K Bowie, Carla Cicero, John E McCormack, Robert K Wayne, De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica, Journal of Heredity, Volume 114, Issue 6, December 2023, Pages 669–680, https://doi.org/10.1093/jhered/esad047

Erin P Westeen, Merly Escalona, Matthew L Holding, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ralph Perri, Robert N Fisher, Erin Toffelmier, H Bradley Shaffer, Ian J Wang, A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex, Journal of Heredity, Volume 114, Issue 6, December 2023, Pages 681–689, https://doi.org/10.1093/jhered/esad045

Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman, A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta, Journal of Heredity, Volume 114, Issue 6, December 2023, Pages 698–706, https://doi.org/10.1093/jhered/esad043

Phred M Benham, Carla Cicero, Devon A DeRaad, John E McCormack, Robert K Wayne, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Michael W Nachman, Rauri C K Bowie, A highly contiguous reference genome for the Steller’s jay (Cyanocitta stelleri), Journal of Heredity, Volume 114, Issue 5, September 2023, Pages 549–560, https://doi.org/10.1093/jhered/esad042

Anusha P Bishop, Erin P Westeen, Michael L Yuan, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Erin Toffelmier, Robert N Fisher, H. Bradley Shaffer, Ian J Wang, Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis, Journal of Heredity, Volume 114, Issue 5, September 2023, Pages 521–528, https://doi.org/10.1093/jhered/esad037

Sorel Fitz-Gibbon, Alayna Mead, Scott O’Donnell, Zhi-Zhong Li, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork, Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales, Journal of Heredity, Volume 114, Issue 5, September 2023, Pages 570–579, https://doi.org/10.1093/jhered/esad036

Jonathan Q Richmond, Jimmy A McGuire, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Robert N Fisher, Ian J Wang, H Bradley Shaffer, Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii, Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 410–417, https://doi.org/10.1093/jhered/esad032

Gregory F Grether, Joscha Beninde, Eric Beraut, Noravit Chumchim, Merly Escalona, Zachary G MacDonald, Courtney Miller, Ruta Sahasrabudhe, Andrew M Shedlock, Erin Toffelmier, H Bradley Shaffer, Reference genome for the American rubyspot damselfly, Hetaerina americana, Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 385–394, https://doi.org/10.1093/jhered/esad031

Laurie A Hall, Ian J Wang, Merly Escalona, Eric Beraut, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Steven R Beissinger, Reference genome of the Virginia rail, Rallus limicola, Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 428–435, https://doi.org/10.1093/jhered/esad026

Laurie A Hall, Ian J Wang, Merly Escalona, Eric Beraut, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Steven R Beissinger, Reference genome of the black rail, Laterallus jamaicensis, Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 436–443, https://doi.org/10.1093/jhered/esad025

Seira A Adams, Natalie R Graham, Anna J Holmquist, Monica M Sheffer, Emma C Steigerwald, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, Colin Fairbairn, Samuel Sacco, William Seligmann, Merly Escalona, H Bradley Shaffer, Erin Toffelmier, Rosemary G Gillespie, Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae), Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 395–403, https://doi.org/10.1093/jhered/esad013

Phred M Benham, Carla Cicero, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Michael W Nachman, Rauri C K Bowie, A highly contiguous genome assembly for the California quail (Callipepla californica), Journal of Heredity, Volume 114, Issue 4, July 2023, Pages 418–427, https://doi.org/10.1093/jhered/esad008

Bishop, A. P., Chambers, E. A., & Wang, I. J. (2023). Generating continuous maps of genetic diversity using moving windows. Methods in Ecology and Evolution, 00, 1– 7. https://doi.org/10.1111/2041-210X.14090

Shannon Rose Kieran Blair, Andrea Schreier, Merly Escalona, Amanda J Finger, Shannon E K Joslin, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Emily Reister Morris, Hayley Mangelson, Joshua Hull, A chromosome-level reference genome for the Versatile Fairy Shrimp, Branchinecta lindahli, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 74–80, https://doi.org/10.1093/jhered/esac057

Shannon Rose Kieran Blair, Andrea Schreier, Merly Escalona, Amanda J Finger, Shannon E K Joslin, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Emily Reister Morris, Hayley Mangelson, Joshua Hull, A draft reference genome of the Vernal Pool Fairy Shrimp, Branchinecta lynchi, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 81–87, https://doi.org/10.1093/jhered/esac056

Daniel B Wright, Merly Escalona, Mohan P A Marimuthu, Ruta Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Giacomo Bernardi, Reference genome of the Woolly Sculpin, Clinocottus analis, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 60–67, https://doi.org/10.1093/jhered/esac055

Daniel B Wright, Merly Escalona, Mohan P A Marimuthu, Ruta Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Giacomo Bernardi, Donovan P German, Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 52–59, https://doi.org/10.1093/jhered/esac054

Kimberly M Ballare, Merly Escalona, Kelly Barr, William Seligmann, Samuel Sacco, Ruta Madhusudan Sahasrabudhe, Oanh Nguyen, Christy Wyckoff, Thomas B Smith, Beth Shapiro, A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor, Journal of Heredity, Volume 114, Issue 1, January 2023, Pages 44–51, https://doi.org/10.1093/jhered/esac053

2022

Featured publication: H Bradley Shaffer, Erin Toffelmier, Russ B Corbett-Detig, Merly Escalona, Bjorn Erickson, Peggy Fiedler, Mark Gold, Ryan J Harrigan, Scott Hodges, Tara K Luckau, Courtney Miller, Daniel R Oliveira, Kevin E Shaffer, Beth Shapiro, Victoria L Sork, Ian J Wang, Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 577–588, https://doi.org/10.1093/jhered/esac020

Joscha Beninde, Erin Toffelmier, H Bradley Shaffer, A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 604–614, https://doi.org/10.1093/jhered/esac049Hvilsom, C., Segelbacher, G., Ekblom, R., Fischer, M.C., Laikre, L., Leus, K., O´Brien, D., Shaw, R. and Sork, V. (2022). Selecting species and populations for monitoring of genetic diversity. Gland, Switzerland: IUCN. https://doi.org/10.2305/IUCN.CH.2022.07.en

Yi Huang, Merly Escalona, Glen Morrison, Mohan P A Marimuthu, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Amy Litt, Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca), Journal of Heredity, Volume 113, Issue 2, March 2022, Pages 188–196, https://doi.org/10.1093/jhered/esab071

Ioana G Anghel, Sarah J Jacobs, Merly Escalona, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Felipe Zapata, Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 712–721, https://doi.org/10.1093/jhered/esac052

Shannon Rose Kieran Blair, Joshua Hull, Merly Escalona, Amanda Finger, Shannon E K Joslin, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Emily Reister Morris, Samantha Velazquez, Andrea Schreier, The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 706–711, https://doi.org/10.1093/jhered/esac051

Brendan H Cornwell, Eric Beraut, Colin Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Merly Escalona, Erin Toffelmier, Reference genome assembly of the sunburst anemone, Anthopleura sola, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 699–705, https://doi.org/10.1093/jhered/esac050

Joscha Beninde, Erin Toffelmier, H Bradley Shaffer, A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 604–614, https://doi.org/10.1093/jhered/esac049

Jesse L Grismer, Merly Escalona, Courtney Miller, Eric Beraut, Colin W Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Erin Toffelmier, Ian J Wang, H Bradley Shaffer, Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae), Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 641–648, https://doi.org/10.1093/jhered/esac048

Joanna S Griffiths, Ruta M Sahasrabudhe, Mohan P A Marimuthu, Noravit Chumchim, Oanh H Nguyen, Eric Beraut, Merly Escalona, Andrew Whitehead, A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 673–680, https://doi.org/10.1093/jhered/esac047

Peggy L Fiedler, Bjorn Erickson, Michael Esgro, Mark Gold, Joshua M Hull, Jennifer M Norris, Beth Shapiro, Michael Westphal, Erin Toffelmier, H Bradley Shaffer, Seizing the moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 589–596, https://doi.org/10.1093/jhered/esac046

Erin Toffelmier, Joscha Beninde, H Bradley Shaffer, The phylogeny of California, and how it informs setting multispecies conservation priorities, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 597–603, https://doi.org/10.1093/jhered/esac045

Melissa B DeBiasse, Lauren M Schiebelhut, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, Michael N Dawson, A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 689–698, https://doi.org/10.1093/jhered/esac044

Lisa X Paggeot, Melissa B DeBiasse, Merly Escalona, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, Michael N Dawson, Reference genome for the California ribbed mussel, Mytilus californianus, an ecosystem engineer, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 681–688, https://doi.org/10.1093/jhered/esac041

Dustin A Wood, Jonathan Q Richmond, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Michael Westphal, Robert N Fisher, Amy G Vandergast, Erin Toffelmier, Ian J Wang, H Bradley Shaffer, Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 632–640, https://doi.org/10.1093/jhered/esac040

Giacomo Bernardi, Jason A Toy, Merly Escalona, Mohan P A Marimuthu, Ruta Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Courtney Miller, H Bradley Shaffer, Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 657–664, https://doi.org/10.1093/jhered/esac034

Giacomo Bernardi, Melissa DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Courtney Miller, Erin Toffelmier, H Bradley Shaffer, Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 649–656, https://doi.org/10.1093/jhered/esac032

Meixi Lin, Merly Escalona, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, Michael R Buchalski, Robert K Wayne, A Reference Genome Assembly of the Bobcat, Lynx rufus, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 615–623, https://doi.org/10.1093/jhered/esac031

Chloé Orland, Merly Escalona, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Eric Beraut, Blythe Marshman, James Moore, Peter Raimondi, Beth Shapiro, A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 665–672, https://doi.org/10.1093/jhered/esac024

Brian D Todd, Thomas S Jenkinson, Merly Escalona, Eric Beraut, Oanh Nguyen, Ruta Sahasrabudhe, Peter A Scott, Erin Toffelmier, Ian J Wang, H Bradley Shaffer, Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata, Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 624–631, https://doi.org/10.1093/jhered/esac021