Baja GeoGenomics consortium

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Baja GeoGenomics consortium

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Papers

preprints


Fellows SR, Araya-Donoso R, Davalos-Dehullu E, Khan R, Weisz D, Dudchenko O, Lieberman  AE, Munguia-Vega A, Dolby GA, Edwards DL, (preprint) A chromosome-length reference genome for the common side-blotched lizard Uta stansburiana and gene expression data reveals fast pace-of-life comes with environmental stability. preprint: https://doi.org/10.1101/2025.05.28.656178


Moore DG, Morales M, Walker SI, Dolby GA (preprint) The information signature of diverging lineages.  Prepint: https://doi.org/10.1101/2021.08.30.458276 


Maag G, Biddy AR, Stokes M, Dolby GA, (preprint) A river runs through it: Causal graphs capture rivers’ complex control on the genetic structure of populations. Preprint: link. 


     2025

Darin, MH, Dorsey, RJ, Niemi, TM, Salgado Muñoz, VO, Henry, MW, and Pecha, M, (2025) Depositional age of the Boleo Formation and marine flooding in the central Gulf of California Rift, Santa Rosalía basin, Baja California Sur, México, in Riggs, NR, Putirka, K, and Wakabayashi, J, eds, The Virtue of Fieldwork in Volcanology, Sedimentology, Structural Geology, and Tectonics – Celebrating the Career of Cathy Busby: Geological Society of America Special Paper 563, 23. p, https://doi.org/10.1130/2025.2563(13)


Gardner, KK, Dorsey, RJ (2025) Planform geometric classification of fluvial and tidal channels via machine learning. Earth Surface Processes and Landforms, 50(4), e70010, https://doi.org/10.1002/esp.70010 .


     2024

Araya-Donoso R, Biddy A, Munguia-Vega A, Lira-Noriega A, Dolby GA (2024), Habitat quality or quantity? Changes in niche marginality suggest adaptive pressure differences in 22 species of plants and animals Ecography. 9,  https://doiorg/101111/ecog07391


     2023

Davalos-Dehullu L, Baty SM, Fisher RN, Scott PA, Dolby GA, Munguia-Vega A, Cortez D, (2023) Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evad210


Vargas KL, Kraberger S, Custer JM, Paietta EN, Culver M, Dolby GA, Varsani A (2023) Identification of a novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae. Archives of Virology. https://doi.org/10.1007/s00705-023-05877-5  


     2022

Araya-Donoso R, Baty SM, Alonso-Alonso P, Sanín MJ, Wilder BT, Munguía-Vega A, Dolby GA (2022), Implications of barrier ephemerality and generation time in Geogenomic research. Journal of Biogeography. https://doi.org/10.1111/jbi.14487 


Dolby GA, Bennett SEK, Dorsey RJ, Stokes M, Riddle BR, Lira-Noriega A, Munguia-Vega A, Wilder B, (2022) Integrating Earth-life systems: A geogenomics approach. Trends in Ecology and Evolution (TREE). https://doi.org/10.1016/j.tree.2021.12.004


     2021

Dolby GA (2021) Towards a unified framework to study causality in Earth-life systems, Molecular Ecology, 30, 5628–5642. paper

Abstracts & Presentations

     2025

Bacteriophage diversity and biogeographic dynamics in wild rodents from Baja California peninsula link

Vargas et al, Mexico Arizona and New Mexico Chapters of The Wildlife Society and AZ/NM Chapter of the American Fisheries Society 58th Joint Annual Meeting, Albuquerque, NM 


Recent demographic history and climate-driven adaptations in a desert plant, Encelia farinosa

Andreev et al, Botany, Palm Springs, California


Genetic structure and natural selection of the Northern Baja Deer Mouse (Peromyscus fraterculus) 

Hein et al, 48th West Coast Biological Sciences Undergraduate Research Conference, San Marcos, California 


Genetic Structure and Natural Selection of the Northern Baja Deer Mouse (Peromyscus fraterculus) 

Hein et al, ENViSion conference, Tucson, Arizona 


Recent evolutionary history and current population structure of Peromyscus eremicus species complex from Baja California 

Andreev et al, 58th Joint Annual Meeting of the Arizona and New Mexico Chapters of the Wildlife Society, Albuquerque, New Mexico 


Using directed graphs to test the riverine barrier hypothesis with genetic data link

Dolby, Society for Integrative and Comparative Biology (SICB), Atlanta, Georgia.


Strong differential gene expression parallels clade divergence and ecological divergence in a Baja California endemic lizard (Urosaurus nigricaudus), link

Biddy  et al, Society for Integrative and Comparative Biology (SICB), Atlanta, Georgia.


Neogene volcano-tectonic evolution of the central Baja California Peninsula, Mexico, https://gsa.confex.com/gsa/2025CD/meetingapp.cgi/Paper/409916

Bennett et al, GSA Cordilleran Section Meeting, Sacramento, CA.


     2024

Bacteriophage diversity and biogeographic dynamics in wild rodents from Baja California peninsula, Mexico 

Vargas et al, Arizona Postdoctoral Research Conference, Tucson, Arizona


DNA viral diversity associated with Baja California wild rodents 

Vargas et al, Arizona and New Mexico Chapters of The Wildlife Society and AZ/NM Chapter of the American Fisheries Society 57th Joint Annual Meeting, Flagstaff, Arizona 


Population structure and demography of the Peromyscus eremicus species complex from Baja California

Andreev et al, Arizona Postdoctoral Research Conference, Tucson, Arizona 


Patterns of genetic differentiation in two Baja California species 

Andreev et al, 57th Joint Annual Meeting of the Arizona and New Mexico Chapters of the Wildlife Society, Flagstaff, Arizona


A new working model for co-evolution of plant and animal species on the Baja California peninsula from genomic and geologic data https://gsa.confex.com/gsa/2024AM/meetingapp.cgi/Paper/404092

Dolby et al, Geological Society of America, Anaheim, CA.


Differential gene expression is constrained by clade divergence and microclimate in a Baja California endemic lizard (Urosaurus nigricaudus)

Biddy et al, Society for the Study of Evolution (SSE), Montreal, Canada.


Comparative genomic analyses of two desert adapted shrub species, Encelia farinosa and E. californica, shows conservation of synteny and species-level gene duplications. 

Baty et al, Society for the Study of Evolution (SSE), Montreal, Canada.


Capturing the nuance of physiographic barriers: an example from rivers link

Dolby, North American Paleontological Convention, Ann Arbor, MI. 


Miocene tectonic evolution of the central Baja California peninsula and rapid marine flooding into the Gulf of California at ca. 6.3-6.4 Ma https://gsa.confex.com/gsa/2024AM/webprogram/Paper402328.html

Dorsey et al, Geological Society of America, Anaheim, CA.


Submarine emplacement of a late Miocene volcanic landslide complex, central Baja California Peninsula, Mexico https://gsa.confex.com/gsa/2024AM/webprogram/Paper401950.html

Gardner et al, Geological Society of America, Anaheim, CA


Geometric analysis and classification of tidal and fluvial channel planforms via machine learning algorithms. https://agu.confex.com/agu/agu24/meetingapp.cgi/Paper/1597518

Gardner and Dorsey, AGU Fall Meeting, Washington, D.C. 


Geología de la Sierra San Jorge, margen occidental de la rift del Golfo de California, peninsula central de Baja California, México. https://gsa.confex.com/gsa/2024AM/webprogram/Paper402193.html

Bennett et al, Geological Society of America, Anaheim, CA


     2023

Identification of novel polyomavirus in wild Sonoran Desert rodents 

Vargas KL et al, American Society for Virology 42nd Annual Meeting, Athens, Georgia


Identification of novel polyomavirus in wild Sonoran Desert rodents 

Vargas et al, Annual Meeting of the Arizona and Southern Nevada Branch of the American Society for Microbiology, Tucson, Arizona


Building explicit causal frameworks in evolutionary genomics: From concept to analysis. 

Dolby, Society for the Study of Evolution, Albuquerque, NM. 


Submarine emplacement of a late Miocene volcanic landslide complex, central Baja California peninsula, Mexico. https://gsa.confex.com/gsa/2023CD/webprogram/Paper387418.html

Gardner et al, GSA Cordilleran Section, Las Vegas, NV 


Geologic mapping and structural analysis of San Marcos Island, Baja California Sur, Mexico. https://gsa.confex.com/gsa/2023CD/webprogram/Paper387665.html

Morebeck et al, Geological Society of America, Pittsburgh, PA


     2022

Stratigraphy, Sedimentology, Age, And Tectonic Significance Of The Upper Miocene Boleo Formation In The Santa Rosalia Basin, Baja California Sur, Mexico https://gsa.confex.com/gsa/2022AM/webprogram/Paper381103.html

Dorsey et al, Geological Society of America, Denver, CO


New Observations About The Structural Architecture Of The Gulf Of California Rift Margin In Baja California Sur: Lessons Learned From Paul Umhoefer’s Legacy. https://gsa.confex.com/gsa/2022AM/webprogram/Paper381850.html

Bennett et al, Geological Society of America, Denver, CO


Miocene-Pliocene volcanism in the Sierra San Francisco, central Baja California peninsula, Mexico. https://gsa.confex.com/gsa/2022CD/webprogram/Paper374066.html

Grandy et al, GSA Cordilleran Section Meeting, Las Vegas 


Volcanic and topographic evolution of the Sierra San Francisco, Baja California Sur, Mexico https://gsa.confex.com/gsa/2022CD/webprogram/Paper373847.html

Hausback et al, GSA Cordilleran Section Meeting, Las Vegas, NV


The Baja Basins Program: Mentored undergraduate field and lab research integrating multidisciplinary geologic data to address the tectonic evolution of the Gulf of California rift of the east-central Baja Peninsula, México. https://gsa.confex.com/gsa/2022AM/webprogram/Paper380608.html

Niemi et al, Geological Society of America, Denver, CO


Stratigraphic analysis of the upper Miocene Boleo Formation at Arroyo Providencia, Baja California Sur, southwest margin of the paleo-Gulf of California. https://gsa.confex.com/gsa/2022AM/meetingapp.cgi/Paper/382039

Usher et al, GSA Annual Meeting, Denver, CO

 

     2021

On understanding causal relationships within the Earth-life sciences https://agu.confex.com/agu/fm21/meetingapp.cgi/Paper/918125

Dolby, American Geophysical Union annual meeting, New Orleans, LA


Geochronological constraints on the volcanic and topographic evolution of central Baja California, Mexico https://agu.confex.com/agu/fm21/meetingapp.cgi/Paper/966010

Hausback et al, American Geophysical Union annual meeting, New Orleans, LA


Geometric and spectral analysis of relict channel planforms in central Baja California, Mexico: A novel approach to paleo-sea level reconstruction and testing hypotheses for genetic divergence https://gsa.confex.com/gsa/2021AM/webprogram/Paper368437.html

Gardner et al, American Geophysical Union annual meeting, New Orleans, LA


Using channel planform geometries to identify tidal channels on relict landscapes: A novel approach to tracking sea level change. https://doi.org/10.1130/abs/2021AM-368437

Gardner and Dorsey, GSA Fall Meeting, Portland, OR


Genetic divergence and ephemeral barriers: Reconciling genetic and geological timescale within geogenomics https://agu.confex.com/agu/fm21/meetingapp.cgi/Paper/988278

Araya-Donoso et al, American Geophysical Union annual meeting, New Orleans, LA


Drivers of speciation using genomic analysis of two desert brittlebush species, Encelia farinosa and Encelia californica https://agu.confex.com/agu/fm21/meetingapp.cgi/Paper/976169

Baty et al., American Geophysical Union annual meeting, New Orleans, LA


Volcano-tectonic evolution of central Baja California peninsula, Mexico: Implications for speciation and barriers to gene flow. https://agu.confex.com/agu/fm21/meetingapp.cgi/Paper/986894

Bennett et al, American Geophysical Union annual meeting, New Orleans, LA


Genome annotations and analyses of two recently diverged brittlebush species, Encelia farinosa and Encelia californica

Baty et al, Society for the Study of Evolution, Virtual


Using genetic simulations and climatic niches to test plant and animal population divergence on the Baja California peninsula

Araya-Donoso et al, Society for the Study of Evolution, Virtual


The information signature of diverging populations: Using partial information decomposition to study speciation. 

Moore et al, Society for the Study of Evolution, Virtual


     2020

Genomic and ecological signatures of landscape change: a geologically constrained, simulation-based case study in the Baja California Peninsula. https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/713147

Araya-Donoso et al, AGU Fall Meeting, Virtual


The influence of Miocene to recent tectonics and landscape evolution on genetic diversity along the Central Baja California Peninsula. https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/712864

Bennett et al,  GSA Cordilleran Section Meeting, Pasadena, CA. 


Long-lived subduction and post-subduction volcanism and incision in the Sierra San Francisco, Central Baja California Peninsula, Mexico. https://gsa.confex.com/gsa/2020CD/meetingapp.cgi/Paper/347422

Hausback et al, GSA Cordilleran Section Meeting, Pasadena, CA. 


The influence of Miocene to recent tectonics and landscape evolution on genetic diversity along the central Baja California peninsula. https://gsa.confex.com/gsa/2020CD/webprogram/Paper347327.html

Bennett et al, GSA Cordilleran Section meeting, Pasadena, CA. 


Can we use causal theory to understand how Earth processes shape life? Examples from the Baja California peninsula, MX, https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/708008

Dolby et al, AGU Fall Meeting, Virtual


New Discovery of Pliocene Tidal Deposits Near the Crest of the Central Baja California Peninsula: A Key Constraint on Vertical Crustal Motions and Genetic Divergence https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/679330

Dorsey et al, AGU Fall Meeting, Virtual


Late Miocene-Pliocene Volcanism in the Sierra de San Francisco, Central Baja Peninsula https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/704184

Grandy et al, AGU Fall Meeting, Virtual 


Topographic and volcanic evolution of Central Baja California, Mexico: Constraints and evidence for a Pliocene marine embayment or trans-peninsular strait https://agu.confex.com/agu/fm20/meetingapp.cgi/Paper/713470

Hausback et al, AGU Fall Meeting, Virtual 

Workshops & Meetings

2025 - Synthesis workshop, Boulder, Colorado, June 2025.

2024 - geo-bio data share workshop, Newport, Oregon, June 2024.

2023 - geo-bio data share workshop, Virtual (zoom), July 2023.

2022 - geo-bio data share workshop, Virtual (zoom), July 2022.

2022 - geo-bio Mule field trip, Sierra San Pedro Màrtir, Mexico, March 21-31, 2022.

2021 - PI meeting, zoom, July 26, 2021

2020 - all hands annual meeting, zoom, December 12, 2020 

2020 - all hands data share workshop, zoom, July 21, 2020 

2019 - geo-bio field trip, Baja California, Mexico, November 2019

2019 - all hands annual meeting, Decision Theater, Phoenix, Arizona,  September 25, 2019

Copyright © 2025 Baja GeoGenomics consortium - All Rights Reserved.

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