@article{mallik_carlson_wcisel_fisk_yoder_dornburg_2023, title={A chromosome-level genome assembly of longnose gar, Lepisosteus osseus}, volume={4}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkad095}, DOI={10.1093/g3journal/jkad095}, abstractNote={Abstract}, journal={G3-GENES GENOMES GENETICS}, author={Mallik, Rittika and Carlson, Kara B. and Wcisel, Dustin J. and Fisk, Michael and Yoder, Jeffrey A. and Dornburg, Alex}, editor={Whiteman, NEditor}, year={2023}, month={Apr} }
 @article{carlson_nguyen_wcisel_yoder_dornburg_2023, title={Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution}, volume={8}, ISSN={["1432-1211"]}, url={https://doi.org/10.1007/s00251-023-01315-7}, DOI={10.1007/s00251-023-01315-7}, abstractNote={Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.}, journal={IMMUNOGENETICS}, author={Carlson, Kara B. and Nguyen, Cameron and Wcisel, Dustin J. and Yoder, Jeffrey A. and Dornburg, Alex}, year={2023}, month={Aug} }
 @article{wcisel_dornburg_mcconnell_hernandez_andrade_jong_litman_yoder_2022, title={A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors}, volume={7}, ISSN={["1432-1211"]}, url={https://doi.org/10.1007/s00251-022-01270-9}, DOI={10.1007/s00251-022-01270-9}, abstractNote={Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3-Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation, and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.}, journal={IMMUNOGENETICS}, author={Wcisel, Dustin J. and Dornburg, Alex and McConnell, Sean C. and Hernandez, Kyle M. and Andrade, Jorge and Jong, Jill L. O. and Litman, Gary W. and Yoder, Jeffrey A.}, year={2022}, month={Jul} }
 @article{dornburg_yoder_2022, title={On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity}, volume={74}, ISSN={["1432-1211"]}, url={https://doi.org/10.1007/s00251-021-01232-7}, DOI={10.1007/s00251-021-01232-7}, abstractNote={For over half a century, deciphering the origins of the genomic loci that form the jawed vertebrate adaptive immune response has been a major topic in comparative immunogenetics. Vertebrate adaptive immunity relies on an extensive and highly diverse repertoire of tandem arrays of variable (V), diversity (D), and joining (J) gene segments that recombine to produce different immunoglobulin (Ig) and T cell receptor (TCR) genes. The current consensus is that a recombination-activating gene (RAG)-like transposon invaded an exon of an ancient innate immune VJ-bearing receptor, giving rise to the extant diversity of Ig and TCR loci across jawed vertebrates. However, a model for the evolutionary relationships between extant non-recombining innate immune receptors and the V(D)J receptors of the jawed vertebrate adaptive immune system has only recently begun to come into focus. In this review, we provide an overview of non-recombining VJ genes, including CD8β, CD79b, natural cytotoxicity receptor 3 (NCR3/NKp30), putative remnants of an antigen receptor precursor (PRARPs), and the multigene family of signal-regulatory proteins (SIRPs), that play a wide range of roles in immune function. We then focus in detail on the VJ-containing novel immune-type receptors (NITRs) from ray-finned fishes, as recent work has indicated that these genes are at least 50 million years older than originally thought. We conclude by providing a conceptual model of the evolutionary origins and phylogenetic distribution of known VJ-containing innate immune receptors, highlighting opportunities for future comparative research that are empowered by this emerging evolutionary perspective.}, number={1}, journal={IMMUNOGENETICS}, publisher={Springer Science and Business Media LLC}, author={Dornburg, Alex and Yoder, Jeffrey A.}, year={2022}, month={Jan} }
 @misc{dornburg_mallik_wang_bernal_thompson_bruford_nebert_vasiliou_yohe_yoder_et al._2022, title={Placing human gene families into their evolutionary context}, volume={16}, ISSN={["1479-7364"]}, DOI={10.1186/s40246-022-00429-5}, abstractNote={Abstract}, number={1}, journal={HUMAN GENOMICS}, author={Dornburg, Alex and Mallik, Rittika and Wang, Zheng and Bernal, Moises A. and Thompson, Brian and Bruford, Elspeth A. and Nebert, Daniel W. and Vasiliou, Vasilis and Yohe, Laurel R. and Yoder, Jeffrey A. and et al.}, year={2022}, month={Nov} }
 @article{carlson_wcisel_ackerman_romanet_christiansen_niemuth_williams_breen_stoskopf_dornburg_et al._2022, title={Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri}, volume={4}, ISSN={["1572-9737"]}, url={https://doi.org/10.1007/s10592-022-01444-8}, DOI={10.1007/s10592-022-01444-8}, abstractNote={Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.}, journal={CONSERVATION GENETICS}, author={Carlson, Kara B. and Wcisel, Dustin J. and Ackerman, Hayley D. and Romanet, Jessica and Christiansen, Emily F. and Niemuth, Jennifer N. and Williams, Christina and Breen, Matthew and Stoskopf, Michael K. and Dornburg, Alex and et al.}, year={2022}, month={Apr} }
 @article{sigler_warren_tracy_forrestel_hogue_dornburg_2021, title={Assessing temporal biases across aggregated historical spatial data: a case study of North Carolina's freshwater fishes}, volume={12}, ISSN={["2150-8925"]}, DOI={10.1002/ecs2.3878}, abstractNote={Abstract}, number={12}, journal={ECOSPHERE}, author={Sigler, Kyra and Warren, Dan and Tracy, Bryn and Forrestel, Elisabeth and Hogue, Gabriela and Dornburg, Alex}, year={2021}, month={Dec} }
 @article{lamb_lippi_watkins-colwell_jones_warren_iglesias_brandley_dornburg_2021, title={Comparing the dietary niche overlap and ecomorphological differences between invasive Hemidactylus mabouia geckos and a native gecko competitor}, ISSN={["2045-7758"]}, DOI={10.1002/ece3.8401}, abstractNote={Abstract}, journal={ECOLOGY AND EVOLUTION}, author={Lamb, April D. and Lippi, Catherine A. and Watkins-Colwell, Gregory J. and Jones, Andrew and Warren, Dan L. and Iglesias, Teresa L. and Brandley, Matthew C. and Dornburg, Alex}, year={2021}, month={Dec} }
 @article{thompson_hawkins_parey_wcisel_ota_kawasaki_funk_losilla_fitch_pan_et al._2021, title={The bowfin genome illuminates the developmental evolution of ray-finned fishes}, volume={8}, ISSN={["1546-1718"]}, DOI={10.1038/s41588-021-00914-y}, abstractNote={Abstract}, journal={NATURE GENETICS}, author={Thompson, Andrew W. and Hawkins, M. Brent and Parey, Elise and Wcisel, Dustin J. and Ota, Tatsuya and Kawasaki, Kazuhiko and Funk, Emily and Losilla, Mauricio and Fitch, Olivia E. and Pan, Qiaowei and et al.}, year={2021}, month={Aug} }
 @article{dornburg_lamb_warren_watkins-colwell_lewbart_flowers_2019, title={Are Geckos Paratenic Hosts for Caribbean Island Acanthocephalans? Evidence from Gonatodes antillensis and a Global Review of Squamate Reptiles Acting as Transport Hosts}, volume={60}, ISSN={["2162-4135"]}, DOI={10.3374/014.060.0103}, abstractNote={Abstract It is well known that reptiles can act as paratenic hosts for parasites that use mammals as their definitive hosts. However, studies of potential paratenic hosts in the Caribbean have been temporally restricted to only diurnal species of lizards, thereby neglecting a dominant component of the nocturnal reptilian community: geckos. Many gecko species are human commensals with activity periods that overlap temporally with those of domestic cats, making them prime candidates as potential transport hosts for cat parasites. However, no studies have reported geckos as paratenic hosts for felid parasites on any Caribbean island. Here we report the first records of subcutaneous oligacanthorhynchid cystacanths on the Venezuelan Coastal Clawed Gecko (Gonatodes antillensis) based on specimens collected in Curaçao and Bonaire. The cysts were identified as belonging to the genus Oncicola, likely those of Oncicola venezuelensis. This study reports these geckos as a new host record for oligacanthorhynchid cystacanths, as well as Curaçao and Bonaire as new geographic locales for these acanthocephalan parasites. We additionally provide a review of saurian cystacanths, comparing the restricted taxonomic focus of transport hosts in Caribbean islands to the distribution of paratenic squamate hosts both in the Neotropics and globally. We find evidence that the ability of squamate reptiles to act as transport hosts is a pervasive feature across their Tree of Life, suggesting that these animals may serve as important vectors for transporting parasites between intermediate and definitive hosts.}, number={1}, journal={BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY}, author={Dornburg, Alex and Lamb, April D. and Warren, Dan and Watkins-Colwell, Gregory J. and Lewbart, Gregory A. and Flowers, James}, year={2019}, month={Apr}, pages={55–79} }