Publications

Publications

2024

• Vázquez-López, M., Ramírez-Barrera, S. M., Terrones-Ramírez, A. K., Robles-Bello, S. M., de Oca, A. N. M., Ruegg, K., & Hernández-Baños, B. E.  2024.  Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys, 1188, 169-195.

2023

• Jen Tinsman, C. Gruppi, C. Bosssu…..K. Ruegg, T.C. Bonebrake, and T.B. Smith. 2023. Genomic and network analysis uncover the illegal pangolin trade between Africa and Asia. Science: 382, 1282-1286. DOI: 10.1126/science.adi5066                                              

• DeSaix, Matthew, M. Rodriguez, K. Ruegg, and E. Anderson. in press. Population assignment from genotype likelihoods for low-coverage whole-genome sequencing data.  Methods in Ecology and Evolution.

• Caitlin Miller, C. Bossu, J. Sarraco, D. Toews, C. Rushing, A. Roberto-Charron, J.A. Tremblay, R. Chandler, M. DeSaix, C. Fiss, J. Larkin, S. Haché, S. Nebel, K. Ruegg.  2023. Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird. Molecular Ecology. DOI: 10.1111/mec.17199

• Kelly Barr, C. Bossu, R.Bay, E. Anderson, J. Belthoff, L. Trulio, D. Chromczak, C. Wisinski, T. Smith, K.C. Ruegg.  2023.  Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evolutionary Applications. DOI: https://doi.org/10.1111/eva.13600

• Ryan Harrigan, J. Rajbhandary, C. Bossu, P. Sanzenbacher, T. Dietsch, C. Gruppi, T.E. Katzner, T.B. Smith, K. Ruegg. in press. Utilizing High-Resolution Genetic Markers to Track Population-Level Exposure of Migratory Birds to Renewable Energy Development. PLOS Sustainability and Transformation.

• Matthew G. DeSaix, E.C. Anderson, C.M. Bossu, C.E. Rayne, T.M. Schweizer, N.J. Bayly, D.S. Narang, J.C. Hagelin, H.L. Gibbs, J. F. Saracco, T.W. Sherry, M.S. Webster, T.B. Smith, P.P. Marra, K.C. Ruegg. 2023.  Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla).  Molecular Ecology.  32:5528–5540. DOI: 10.1111/mec.17137

•  Lynne A. Trulio, D.A. Chromczak, P. Higgins, S. Menzel, C. Bossu, and K.C. Ruegg. 2023..  Implications of Migratory Behavior for a Declining Population of Western Burrowing Owls in Northern California. Conservation Genetics. DOI: 10.1007/s10592-023-01578-3

• Sheela P. Turbek, C. Bossu, C. Rayne, C. Gruppi, B.E. Kus, M. Whitfield, T.B. Smith, E.H. Paxton, R.A. Bay, and K.C. Ruegg.  2023. Historical DNA reveals climate adaptation in an endangered songbird.  Nature Climate Change. 377(6613):1384-1385. DOI: 10.1126/science.add0007

• Christen M. Bossu, M. Rodriguez, C. Rayne, D.A. Chromczak , P.G. Higgins, L.A. Trulio, and K.C. Ruegg. 2023.  Genomic approaches to mitigating genetic diversity loss in declining populations. Molecular Ecology. 2023;00:1–13. DOI: 10.1111/mec.17109

• Cristian Gruppi, P. Sanzenbacher, K. Balekjian, R. Hagar, S. Hagen, C. Rayne, T. Schweizer, Daniel Cooper, T, Dietch, T.B Smith, K.C. Ruegg, Ryan J Harrigan.  2023.  An Identification Pipeline for Samples of Avian Origin Recovered from Alternative Energy Installations. PLOS ONE. DOI: 10.1371/journal.pone.0289949

• Ying Zhen, M.A.K. Dongmo, R.J. Harrigan, K.C. Ruegg, R. Hanna, T.C. Bonebrake, T.B. Smith.  2023.  Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly. Evolution.   77(6): 1430–1443. DOI: 10.1093/evolut/qpad052

• Nicole E. Adams, R.R. Bandivadekar, CJ Battey, M.W. Clark, K. Epperly, J. Klicka, K. Ruegg, L.A. Tell, R.A. Bay.  2023. Widespread gene flow following range expansion in Anna's hummingbird. Molecular Ecology.  DOI: 10.22541/au.166505052.20953845/v1

• Sheela P. Turbek, W.C. Funk, and K.C. Ruegg. 2023. Where to draw the line?  Expanding the delineation of conservation units to highly mobile taxa.  Journal of Heredity. 114(4): 300–311. DOI: 10.1093/jhered/esad011

• Brenna R. Forester, C.C. Day, K.C. Ruegg, E.L. Landguth.  2023.  Evolutionary potential mitigates extinction risk under climate change in the endangered southwestern willow flycatcher.  Journal of Heredity. 114(4): 341–353.  DOI: 10.1093/jhered/esac067

• Abigail A. Kimmitt, T.M. Pegan, A.W. Jones, C.L. Brennan J. Hudon, J. Kirchman, K.C. Ruegg, B.W. Benz, R. Herman and B.M. Winger. 2023. Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum. Proceedings of the Royal Society: Series B. 290(1991), 20221334.  DOI: 10.1098/rspb.2022.1334

• Andrea Contina, C.M. Bossu, D. Allen, M. Wunder and K.C. Ruegg.  2023. The genetic and ecological drivers of molting behavior in a migratory bird.  Scientific Reports. 13(1), 814.  DOI: 10.1038/s41598-022-26973-7

• Rafael Rueda-Hernández, C. Bossu, A. Contina, R.C. Castillo, K. Ruegg, B.E. Hernández-Baños. 2023. Winter connectivity and leap-frog migration in a migratory bird, the Painted Bunting.  Ecology and Evolution. DOI: 10.1002/ece3.9769

2022

• Kristen C. Ruegg. and S. Turbek.  2022. Perspective: Estimating Global Genetic Diversity Loss - A Mathematical Framework May Help Inform Conservation Efforts.  Science. 22 (377): 1384-1385. DOI: 10.1126/science.add0007

•  Matthew G. DeSaix, T.L. George, A.E. Seglund, G.M. Spellman, E.S. Zavaleta, K.C. Ruegg.  2022. Contrasting models of genomic offset and habitat suitability reveal the importance of considering novel climates. Diversity and Distributions. 2022: 1-16. DOI: 10.1111/ddi.13628

• Erik R. Funk, G.M. Spellman, K. Winker, J.J. Withrow, K.C. Ruegg, Scott A. Taylor.  2022.  The genetic basis of plumage coloration and elevation adaptation in recently diverged alpine and arctic songbirds. Evolution. https://doi.org/10.1093/evolut/qpac064

• William J. Smith, A.T. Sendell-Price, A. Fayet, T. Schweizer, M.T. Jezierski, B.C. Sheldon, K. Ruegg, S.K., Lindsay A. Turnbull and S.M. Clegg. 2022.  Limited domestic introgression in final refuge of the wild pigeon.  iScience. 25(7): 104620. https://doi.org/10.1016/j.isci.2022.104620

• Allison H. Alvarado,  C.M. Bossu, R.J.Harrigan, R.A. Bay, A.R. Nelson, T.B. Smith, and K.C. Ruegg.  2022. The Link Between Genome and Environment is Consistent Across Spatial Scales in a North American Songbird. Evolutionary Applications. 15: 1390-1407.  https://doi.org/10.1111/eva.13444

• C.M. Bossu, J.A. Heath, K.C. Ruegg. 2022. Clock-linked genes underlie seasonal migratory timing in a diurnal raptor.  Proceedings of the Royal Society of London: Series B. https://doi.org/10.1098/rspb.2021.2507

• D.S. Baetscher, J. Beck, E.C. Anderson, K. Ruegg, A. Ramey, S. Hatch, H. Nevins, S.M. Fitzgerald, J.C. Garza.  2022. Genetic assignment of fisheries bycatch reveals disproportionate mortality among Alaskan Northern Fulmar breeding colonies. Evolutionary Applications.  https://doi.org/10.1111/eva.13357

2021

• Marius Somveille, R. A. Bay, T. B. Smith, P. P. Marra, K.C. Ruegg. 2021. A general theory of migratory connectivity. Ecology Letters.  https://doi.org/10.1111/ele.13817

• Ruegg, K. C., E. C. Anderson, R. A. Bay, M. Whitefield, E. H. Paxton, T. B. Smith. 2021.  Linking climate niches across seasons to assess population vulnerability in a migratory bird.  Global Change Biology. ttps://doi.org/10.1111/gcb.15639

• Brenda Larison, A.R. Lindsay, C. Bossu, M.D. Sorenson, J.D. Kaplan, D.C. Evers, J. Paruk, J.M. DaCosa, T.B. Smith, K. Ruegg. 2021. Leveraging Genomics to Understand Threats in a Migratory Waterbird. Evolutionary Applications. https://doi.org/10.1111/eva.13231

• Ashley T. Sendell-Price, K.C. Ruegg, Bruce C. Robertson, Sonya. M. Clegg.  in press. The idiosyncratic nature of genomic divergence following population founding.  Molecular Ecology.

• R.A. Bay, D.S. Karp, J.F. Saracco, W.R.L. Anderegg, L. Frishkoff, D. Wiedenfeld, T.B. Smith, K.C. Ruegg.  2021. Genetic variation reveals individual-level climate tracking across the full annual cycle of a migratory bird.  Ecology Letters.  24(4): 819 - 828.  http://dx.doi.org/10.1111/ele.13706

• Thomas B. Smith, T.L. Fuller, Y. Zhen, V. Zaunbrecher, H.A. Thomassen, K. Njabo, N.M. Anthony, M.K. Gonder, W. Buermann, K. Ruegg, Ryan J. Harrigan.  2021. Genomic vulnerability and socio-economic threats in an African rainforest bird under future climate change.  Evolutionary Applications.  00: 1-9.  https://doi.org/10.1111/eva.13193

• Vázquez-López, Melisa, N. Córtes-Rodríguez, S.M. Robles-Bello, A. Bueno-Hernández, L.E. Zamudio-Beltrán, K. Ruegg, B. E. Hernandez-Banos.  2021.  Phylogeography and morphometric variation in the Cinnamon Hummingbird complex: Amazilia rutila (Aves: Trochilidae). Avian Research. https://doi.org/10.1186/s40657-021-00295-0

2020

• Kelly Barr*,  Beichman, A, Kalhori, P., Rajbhandary, J., Bay, R.**, Ruegg, K., and Smith, T. 2020.  Persistent Panmixia Despite Extreme Habitat Loss and Population Decline in the Threatened Tricolored Blackbird (Agelaius tricolor). Evolutionary Applications.

• Funk, Erik R., G.M. Spellman, K. Winker, J.J. Withrow, K.C. Ruegg, E. Zavaleta, S.A. Taylor.  2020.  Phylogenomic data reveal widespread introgression across continental islands in an alpine specialist.  Systematic Biology.

• Ashley T. Sendell-Price, K.C. Ruegg, E.C. Anderson, C.S. Quilodrán, B.M. Van Doren, V.L. Underwood, T. Coulson & S.M. Clegg.  2020. The Genomic Landscape of Divergence Across the Speciation Continuum in an Island-colonising Bird. G3: Genes, Genomes, Genetics. 10 (9): 3147-3163.

• Morgan, K., J.F. Mboumba, S. Ntie, P. Mickala, C.A. Miller, Y. Zhen, Ryan J. Harrigan, V.L. Underwood, K.C. Ruegg, P.R.S. Clee, T. Fuller, N.M. Anthony.  2020.  Predicting capacity to respond to climate change using geospatial modeling of genomic and craniometric data from a Central African forest mouse. Proceedings of the Royal Society of London: Series B. 287(1930): 20200449.

• K. C. Ruegg, Michaela Brinkmeyer*, Christen M. Bossu**, Racheal Bay**, Eric C. Anderson, Clint W. Boal, Russell D. Dawson, Amber Eschenbauch, Christopher JW McClure, Karl E. Miller, Lance Morrow, Jill Morrow, M. David Oleyar, Bill Ralph, Sarah Schulwitz, Ted Swem, Jean-Francois Therrien, Thomas B. Smith, Julie A. Heath. 2020. The American Kestrel Genoscape (Falco sparverius):  Implications for Monitoring, Management, and Subspecies Boundaries.  Ornithology. 138: (??)

• K. C. Ruegg, Ryan J. Harrigan, James F. Saracco, Thomas B. Smith, Caz M. Taylor. 2020. A genoscape-network model for conservation prioritization in a migratory bird.  Conservation Biology. 34(6), 1482-1491.  doi: 10.1111/cobi.13536.

• Ashley T. Sendell-Price, K.C. Ruegg, S.M. Clegg. 2020.  Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection.  Journal of Heredity. 124: 535-549.

     **Selected for the Heredity readers choice award.

• Quilodrán, C.S., T. Coulson, E. Anderson, K. Ruegg, A.T. Sendell-Price, S. Clegg.  2020.  The multiple population genetic and demographic routes to islands of genomic divergence.  Methods in Ecology and Evolution. 11(1): 6-21.

2019

• Contina, A., R.A. Bay**, V. L. Underwood, T. Smith, J. Kelly, E. Bridge, K.C. Ruegg. 2019. Characterization of SNP markers for the Painted Bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies. Conservation Genetics Resources. 11(1): 5-10.

• Contina, A., J. L. Alcantara, E. Bridge, J. D. Ross, W. F. Oakley, J. Kelly, K.C. Ruegg. 2019. Genetic structure of the Painted Bunting and its implications for conservation of migratory populations. IBIS.  161(2): 372-386.

2018

• vonHoldt, B.M., R.Y. Kartzinel, C.D. Huber, V.L. Underwood, Y. Zhen, K. Ruegg, K.E. Lohmueller, T.B. Smith.  2018.  Genetic variation at insulin-like growth factor 1 is associated with the bill size polymorphism in an African finch (Pyrenestes ostrinus).  Nature Ecology and Evolution, 9(1):4855, DOI:10.1038/s41467-018-07374-9

• Bay, R. A., R. J. Harrigan, W. Beurmann, V. L. Underwood, H. L. Gibbs, T. B. Smith, and K. C. Ruegg.  2018. Response to comment on “Genomic signals of selection predict climate-driven population declines.”  Science  

• Ruegg, K. C., R. A. Bay, E. C. Anderson, J. Saracco, R. J. Harrigan, M. Whitefield, E. H. Paxton, T. B. Smith. 2018.  Ecological genomics predicts climate vulnerability in an endangered southwestern songbird.  Ecology Letters, 21(7): 1085 – 1096.  

• Bay, R. A., R. J. Harrigan, V. L. Underwood, H. L. Gibbs, T. B. Smith, and K. C. Ruegg.  2018. Genomic signals of selection predict climate-driven population declines.  Science, 359: 83-86. 

• Contina, A., R.A. Bay, V. L. Underwood, T. Smith, J. Kelly, E. Bridge, K.C. Ruegg. 2018. Characterization of SNP markers for the Painted Bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies. Conservation Genetics Resources, 1-6.

• Contina, A., J. L. Alcantara, E. Bridge, J. D. Ross, W. F. Oakley, J. Kelly, K.C. Ruegg. 2018. Genetic structure of the Painted Bunting and its implications for conservation of migratory populations. IBIS.

• Albert, Steven, K. Ruegg, R. Siegel.  2018. El uso de marcadores intrinsecos y extrinsecos para enlazar poblaciones de aves a traves de las Americas. Zeledonia: Boletin de la Asociacion Ornithologica de Costa Rica, 22:1: 8 – 20.

2017

• Ruegg, K. C., Anderson, E. C., Harrigan, R. J., Paxton, K. L., Kelly, J. F., Moore, F. and Smith, T. B.  2017. Genetic assignment with isotopes and habitat suitability (gaiah), a migratory bird case study. Methods in Ecology and Evolution, 8(10): 1241-1252, http://doi:10.1111/2041-210X.12800

• Bay, R. A. and K. C. Ruegg. 2017. Genomic islands of divergence or opportunities for adaptive introgression. Proceedings of the Royal Society of London: Series B, 284(1850): 20162414, doi: 10.1098/rspb.2016.2414

• Zhen, Y., R. J. Harrigan, K. C. Ruegg, E. C. Anderson, T. Ng, S. Lao, K. E. Lohmueller, T. B. Smith. 2017. Genomic divergence across ecological gradients in a Central African songbird (Andropadus virens). Molecular Ecology, 26(19): 4966-4977, doi: 10.1111/mec.14270

Earlier Publications

• Frick, Winifred, J. Kelly, J. R. Shipley and K. C. Ruegg. 2016. University of California, Santa Cruz. Analytic Tools to Assess and Monitor Impacts of Existing and Future Energy Facilities on Aerial Faunas in California. California Energy Commission. Publication Number: CEC-500-2016-071.  

• Ruegg, K. C., E. C. Anderson, K. L. Paxton, *V. Apkenas, S. Lao, R. B. Siegel, D. F. DeSante, F. Moore and T. B. Smith. 2014.  Mapping migration in a songbird using high-resolution genetic tags.  Molecular Ecology, 23(23): 5726-5739. DOI: 10.1111/mec.12977. 

• Ruegg, K. C., E. C. Anderson, J. Boone, **J. Pouls, and T.B. Smith. 2014. A role for migration-linked genes and genomic islands in divergence of a songbird. Molecular Ecology, 23(19); 4757-4769. doi: 10.1111/mec.12842.

• Rundel, C., M. B. Wunder, A. H. Alvarado, K. C. Ruegg, R. Harrigan, A. Schuh, J. F. Kelly, R. B. Siegel, D. F. Desante, T. B. Smith, J. Novembre. 2013.  Novel statistical methods for integrating genetic and isotopic methods to study migratory connectivity. Molecular Ecology, 22(16):4163-76.

• Ruegg, K. C., H. C. Rosenbaum, E. C. Anderson, M. Engel, A. Rothschild, S. C. Baker, and S. R. Palumbi.  2013. Long-term population size of the North Atlantic humpback whale within the context of the worldwide population structure.  Conservation Genetics, 14(1): 103-114.

• Ruegg, K. C., E. C. Anderson, H. Slabbekoorn.  2012. Differences in the timing of migration and response to sexual signaling drive asymmetric hybridization across a migratory divide. Journal of Evolutionary Biology, 25(9): 1741-50.

• Hare, M.P., L. Nunney, M.K. Schwartz, D.E. Ruzzante, M. Burford, R.S. Waples, K. C. Ruegg, and F. Palstra.  2011.  Understanding and estimating effective population size for practical application in marine species management.  Conservation Biology, 25(3): 438-49 

• Ruegg, K. C., E. C. Anderson, S. C. Baker, M. Vant, J. Jackson and S. R. Palumbi. 2010.  Are Antarctic Minke whales unusually abundant because of 20th century whaling?  Molecular Ecology, 19: 281-291.

• Ruegg, K. 2008. Genetic, morphological and ecological characterization of a hybrid zone that spans a migratory divide. Evolution, 62(2): 452-466.

•  Ruegg, K.  2007. Divergence between subspecies groups of Swainson's thrush (Catharus ustulatus ustulatus and C. u. swainsoni). Ornithological Monographs, 63: 67-77.

• *Svensson, L. M. E., K. C. Ruegg, C. H. Sekercioglu, R. N. M. Sehgal.  2007. Widespread and sturctured distributions of blood parasite haplotypes across a migratory divide of the Swainson's thrush (Catharus ustulatus).  Journal of Parasitology, 93(6): 1488-1495.

• Ruegg, K., H. Slabbekoorn, S. Clegg and T.B. Smith.  2006.  Divergence in mating signals correlates with ecology in a migratory songbird the Swainson’s thrush, Catharus ustulatus. Molecular Ecology, 15: 3147-3156.  

•  Ruegg, K., R. Hijmans, and C. Moritz.  2006.  Climate change and the origin of migratory pathways in the Swainson’s thrush, Catharus ustulatus. Journal of Biogeography, 33: 1172 - 1182.

• Kelly, J., K. Ruegg and T.B. Smith.  2005.  Combining isotopic and genetic probes to examine breeding origins of a long-distance migrant.  Ecological Applications, 15(5): 1487-1494.

• Smith, T. B., S. M. Clegg, M. Kimura, K. Ruegg, B. Mila and I. Lovette.  2005. Molecular genetic approaches to linking breeding and overwintering areas in five Neotropical migrant passerines, edited by P. Marra and R. Greenberg.  Smithsonian Press. 

• Ruegg, K. and T.B. Smith.  2002.  Not as the crow flies:  an historical explanation for circuitous migration in the Swainson’s Thrush (Catharus ustulatus).  Proceedings of the Royal Society of London: Series B, 269: 1375-1381.  

• Armbruster, P., ***K. Ruegg, W. E. Bradshaw and C. M. Holzapfel.  2001. Geographic variation and the evolution of reproductive allocation in the pitcher-plant mosquito, Wyeomyia smithii.  Evolution, 55(2): 432-444. 

Photo Credit: Cszmurlo