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Center for Indigenous Science: Publications

Minhas, B. F., Beck, E. A., Cheng-De Vries, C-H. C., & Catchen, J. (2023). Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Scientific reports, 13(1), [6939].

Aqil, A., Gill, S., Gokcumen, O., Malhi, R. S., Reese, E. A., Smith, J. L., Heaton, T. T., & Lindqvist, C. (2023). A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience, 26(5), [106581].

Bader, A. C., Carbaugh, A. E., Davis, J. L., Krupa, K., & Malhi, R. S. (2023). Biological samples taken from Native American Ancestors are human remains under NAGPRA. American Journal of Biological Anthropology.

Kowal, E., Weyrich, L. S., Argüelles, J. M., Bader, A. C., Colwell, C., Cortez, A. D., Davis, J. L., Figueiro, G., Fox, K., Malhi, R. S., Matisoo-Smith, E., Nayak, A., Nelson, E. A., Nicholas, G., Nieves-Colón, M. A., Russell, L., Ulm, S., Vergara-Silva, F., Villanea, F. A., ... Tsosie, K. S. (2023). Community partnerships are fundamental to ethical ancient DNA research. Human Genetics and Genomics Advances, 4(2), [100161].

de Flamingh, A., Rivera-Colón, A. G., Gnoske, T. P., Kerbis Peterhans, J. C., Catchen, J., Malhi, R. S., & Roca, A. L. (2023). Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera. Journal of Heredity, 114(2), 120-130. [esac065].

Smalls, K. A., & Davis, J. L. (2023). Language and Racism. In A. Duranti, R. George, & R. C. Riner (Eds.), A New Companion to Linguistic Anthropology (pp. 560-576). (Wiley Blackwell Companions to Anthropology). Wiley-Blackwell.

Rivera-Colón, A. G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K. T., Yoon, V., Hüne, M., Gregory, S., Cheng, C-H. C., & Catchen, J. M. (2023). Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular biology and evolution, 40(3), [msad029].

de Flamingh, A., Ishida, Y., Pečnerová, P., Vilchis, S., Siegismund, H. R., Van aarde, R. J., Malhi, R. S., & Roca, A. L. (2023). Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Frontiers in Genetics, 13, [1021004].

Garland, C. J., Ritchison, B. T., Tucker, B., & Thompson, V. D. (2023). A preliminary consideration of craft production and settlement expansion on Ossabaw Island, Georgia, USA. Journal of Island and Coastal Archaeology, 18(2), 350-367.

Cheng, C-H. C., Rivera-Colón, A. G., Minhas, B. F., Wilson, L., Rayamajhi, N., Vargas-Chacoff, L., & Catchen, J. M. (2023). Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus—The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes, 14(6).

Thomas, G., Rusman, Q., Morrison, W. R., Magalhães, D. M., Dowell, J. A., Ngumbi, E., Osei-Owusu, J., Kansman, J., Gaffke, A., Pagadala Damodaram, K. J., Kim, S. J., & Tabanca, N. (2023). Deciphering Plant-Insect-Microorganism Signals for Sustainable Crop Production. Biomolecules, 13(6).

Cortez, A. D., Lippert, D., Davis, J. L., Nicholas, G., Malhi, R. S., Weyrich, L. S., Claw, K. G., Bader, A. C., & Colwell, C. (Accepted/In press). Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. American Journal of Biological Anthropology.

Rochette, N. C., Rivera-Colón, A. G., Walsh, J., Sanger, T. J., Campbell-Staton, S. C., & Catchen, J. M. (Accepted/In press). On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity. Molecular ecology resources.

Traniello, I. M., Bukhari, S. A., Dibaeinia, P., Serrano, G., Avalos, A., Ahmed, A. C., Sankey, A. L., Hernaez, M., Sinha, S., Zhao, S. D., Catchen, J., & Robinson, G. E. (Accepted/In press). Single-cell dissection of aggression in honeybee colonies. Nature Ecology and Evolution.

Ngumbi, E., Dady, E., & Calla, B. (2022). Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties. BMC Plant Biology, 22(1), [536].

Cerca, J., Petersen, B., Lazaro-Guevara, J. M., Rivera-Colón, A., Birkeland, S., Vizueta, J., Li, S., Li, Q., Loureiro, J., Kosawang, C., Díaz, P. J., Rivas-Torres, G., Fernández-Mazuecos, M., Vargas, P., McCauley, R. A., Petersen, G., Santos-Bay, L., Wales, N., Catchen, J. M., ... Martin, M. D. (2022). The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature communications, 13(1), [3729].

Rayamajhi, N., Cheng, C-H. C., & Catchen, J. M. (2022). Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki. G3 Genes|Genomes|Genetics, 12(11), [jkac192].

Cramb, J., Ritchison, B. T., Hadden, C. S., Zhang, Q., Alarcón-Tinajero, E., Chen, X., Jones, K. C., Jones, T., Napora, K., Veres, M., & Thompson, V. D. (2022). The Changing Profile of Tenure-Track Faculty in Archaeology. Advances in Archaeological Practice, 10(4), 371-381.

Small, C. M., Healey, H. M., Currey, M. C., Beck, E. A., Catchen, J., Lin, A. S. P., Cresko, W. A., & Bassham, S. (2022). Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proceedings of the National Academy of Sciences of the United States of America, 119(26), [e2119602119].

Raglin, S. S., Kent, A. D., & Ngumbi, E. N. (2022). Herbivory Protection via Volatile Organic Compounds Is Influenced by Maize Genotype, Not Bacillus altitudinis-Enriched Bacterial Communities. Frontiers in Microbiology, 13, [826635].

Severson, A. L., Byrd, B. F., Mallott, E. K., Owings, A. C., DeGiorgio, M., de Flamingh, A., Nijmeh, C., Arellano, M. V., Leventhal, A., Rosenberg, N. A., & Malhi, R. S. (2022). Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences, 119(13), e2111533119. [e2111533119].

Davis, J. L., & Krupa, K. (2022). Toward a Language of Possibility in Curation and Consultation Practices. Collections: A Journal for Museum and Archives Professionals, 18(1), 18-27.

Capel, S. L. R., Bouzat, J. L., Catchen, J. M., Johnson, J. A., Dunn, P. O., & Paige, K. N. (2022). Evaluating the genome-wide impacts of species translocations: the greater prairie-chicken as a case study. Conservation Genetics, 23(1), 179-191.

Davis, J. L. (2022). Trickster Academy. (Sun Tracks). University of Arizona Press.

Ritchison, B. T., & Anderson, D. G. (2022). “Vacant Quarters” and Population Movements: Legacy Data and the Investigation of a Large-Scale Emigration Event from the Savannah River Valley to the Georgia Coast. In Following the Mississippian Spread: Climate Change and Migration in the Eastern US (ca. AD 1000-1600) (pp. 257-299). Springer.

Davis, J. L. (2022). "Anadromous". Humana Obscura, (4), 39.

Potter, B. A., Chatters, J. C., Prentiss, A. M., Fiedel, S. J., Haynes, G., Kelly, R. L., Kilby, J. D., Lanoë, F., Holland-Lulewicz, J., Miller, D. S., Morrow, J. E., Perri, A. R., Rademaker, K. M., Reuther, J. D., Ritchison, B. T., Sanchez, G., Sánchez-Morales, I., Spivey-Faulkner, S. M., Tune, J. W., & Haynes, C. V. (2022). Current Understanding of the Earliest Human Occupations in the Americas: Evaluation of Becerra-Valdivia and Higham (2020). PaleoAmerica, 8(1), 62-76.

Chatters, J. C., Potter, B. A., Prentiss, A. M., Fiedel, S. J., Haynes, G., Kelly, R. L., Kilby, J. D., Lanoë, F., Holland-Lulewicz, J., Miller, D. S., Morrow, J. E., Perri, A. R., Rademaker, K. M., Reuther, J. D., Ritchison, B. T., Sanchez, G., Sánchez-Morales, I., Spivey-Faulkner, S. M., Tune, J. W., & Haynes, C. V. (2022). Evaluating Claims of Early Human Occupation at Chiquihuite Cave, Mexico. PaleoAmerica, 8(1), 1-16.

Yarlagadda, K., Zachwieja, A. J., de Flamingh, A., Phungviwatnikul, T., Rivera-Colón, A. G., Roseman, C., Shackelford, L., Swanson, K. S., & Malhi, R. S. (2022). Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proceedings of the Royal Society B: Biological Sciences, 289(1974), [20220052].

Rivera-Colón, A. G., & Catchen, J. (2022). Population Genomics Analysis with RAD, Reprised: Stacks 2. In Methods in Molecular Biology (pp. 99-149). (Methods in Molecular Biology; Vol. 2498). Humana Press Inc..

Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Author Correction: Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet (Scientific Reports, (2021), 11, 1, (3113), 10.1038/s41598-021-82362-6). Scientific reports, 11(1), [11445].

Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet. Scientific reports, 11(1), [3113].

Holland-Lulewicz, J., & Ritchison, B. T. (2021). How Many Dates Do I Need? Using Simulations to Determine Robust Age Estimations of Archaeological Contexts. Advances in Archaeological Practice, 9(4), 272-287.

Yarlagadda, K., Razik, I., Malhi, R. S., & Carter, G. G. (2021). Social convergence of gut microbiomes in vampire bats. Biology Letters, 17(11), 20210389. [20210389].

Davis, J. L., & Smalls, K. A. (2021). Dis/possession Afoot: American (Anthropological) Traditions of Anti‐Blackness and Coloniality. Journal of Linguistic Anthropology, 31(2), 275-282.

Lesure, R. G., Sinensky, R. J., Schachner, G., Wake, T. A., & Bishop, K. J. (2021). Large-Scale Patterns in the Agricultural Demographic Transition of Mesoamerica and Southwestern North America. American Antiquity, 86(3), 593-612.

Marciniak, S., Mughal, M. R., Godfrey, L. R., Bankoff, R. J., Randrianatoandro, H., Crowley, B. E., Bergey, C. M., Muldoon, K. M., Randrianasy, J., Raharivololona, B. M., Schuster, S. C., Malhi, R. S., Yoder, A. D., Louis, E. E., Kistler, L., & Perry, G. H. (2021). Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemur Megaladapis edwardsi. Proceedings of the National Academy of Sciences, 118(26), [117118].

Ngumbi, E. N., & Ugarte, C. M. (Accepted/In press). Flooding and Herbivory Interact to Alter Volatile Organic Compound Emissions in Two Maize Hybrids. Journal of Chemical Ecology, 47(7), 707-718.

Chang, C. H., Catchen, J., Moran, R. L., Rivera-Colón, A. G., Wang, Y. C., & Fuller, R. C. (2021). Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei). Journal of Heredity, 112(4), 357-366.

Ritchison, B. T., Thompson, V. D., Lulewicz, I., Tucker, B., & Turck, J. A. (2021). Climate change, resilience, and the Native American Fisher-hunter-gatherers of the late Holocene on the Georgia coast, USA. Quaternary International, 584, 82-92.

Cerca, J., Maurstad, M. F., Rochette, N. C., Rivera-Colón, A. G., Rayamajhi, N., Catchen, J. M., & Struck, T. H. (2021). Removing the bad apples: A simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms. Methods in Ecology and Evolution, 12(5), 805-817.

Capodiferro, M. R., Aram, B., Raveane, A., Rambaldi Migliore, N., Colombo, G., Ongaro, L., Rivera, J., Mendizábal, T., Hernández-Mora, I., Tribaldos, M., Perego, U. A., Li, H., Scheib, C. L., Modi, A., Gòmez-Carballa, A., Grugni, V., Lombardo, G., Hellenthal, G., Pascale, J. M., ... Achilli, A. (2021). Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell, 184(7), 1706-1723.e24.

Davis, J. L., & Hall, K. (2021). Ethnography and the Shifting Semiotics of Gender and Sexuality: Practice, Ideology, Theory. In J. Angouri, & J. Baxter (Eds.), The Routledge Handbook of Language, Gender and Sexuality (pp. 93-107). (Routledge Handbooks in Applied Linguistics). Routledge.

Davis, J. L. (2021). Famous Last Speakers: Celebrity and Erasure in Media Coverage of Language Endangerment. In J. Adese, & R. A. Innes (Eds.), Indigenous Celebrity: Entanglements with Fame University of Manitoba.

Schartl, M., Kneitz, S., Ormanns, J., Schmidt, C., Anderson, J. L., Amores, A., Catchen, J., Wilson, C., Geiger, D., Du, K., Garcia-Olazábal, M., Sudaram, S., Winkler, C., Hedrich, R., Warren, W. C., Walter, R., Meyer, A., & Postlethwait, J. H. (2021). The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. Current Biology, 31(5), 911-922.e4.

Monani, S., Burchfield, R. R., Medak-Saltzman, D., & Lempert, W. (2021). Indigenous Media: Dialogic Resistance to Climate Disruption. In T. J. Demos, E. E. Scott, & S. Banerjee (Eds.), The Routledge Companion to Contemporary Art, Visual Culture, and Climate Change (pp. 182-193). (Routledge Art History and Visual Studies Companions). Routledge.

Perri, A. R., Feuerborn, T. R., Frantz, L. A. F., Larson, G., Malhi, R. S., Meltzer, D. J., & Witt, K. E. (2021). Dog domestication and the dual dispersal of people and dogs into the Americas. Proceedings of the National Academy of Sciences of the United States of America, 118(6), [e2010083118].

Cerca, J., Colon, A. G. R., Ferreira, M. S., Ravinet, M., Nowak, M. D., Catchen, J. M., & Struck, T. H. (2021). Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ, 9, [e10896].

de Flamingh, A., Coutu, A., Sealy, J., Chirikure, S., Bastos, A. D. S., Libanda-Mubusisi, N. M., Malhi, R. S., & Roca, A. L. (2021). Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck. Current Biology, 31(3), 621-628.e4.

Rivera-Colón, A. G., Rochette, N. C., & Catchen, J. M. (2021). Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Molecular ecology resources, 21(2), 363-378.

Demkovich, M. R., Calla, B., Ngumbi, E., Higbee, B. S., Siegel, J. P., & Berenbaum, M. R. (2021). Differential regulation of cytochrome P450 genes associated with biosynthesis and detoxification in bifenthrin-resistant populations of navel orangewom (Amyelois transitella). PloS one, 16(1 January), [e0245803].

Davis, J. L. (2021). Honor Song for Tulsa: May 31, 2021. West Trestle Review, (Nov.-Dec. ).