@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
               Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As the teleost genome duplication occurred after teleosts diverged from holosteans, holosteans have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome-sequenced to date, and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50 of 116.61 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.12% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar and bowfin to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements, and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.}, 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={AbstractFollowing the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.}, 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={AbstractHistorical records from museums or government agencies are of tremendous utility for illuminating the factors that shape the spatial distribution of the planet’s biodiversity. However, these data were often collected under heterogeneous and opportunistic sampling designs and therefore likely contain significant sampling biases that change over time. Understanding historical biases is particularly important for aquatic vertebrates, where no studies of changes in sampling effort have yet been conducted. Here, we use a dataset of 276,138 records that span all freshwater fishes known to occur in North Carolina as a case study from which to highlight major shifts in collection trends that cause sample biases in datasets that aggregate historical records. We found evidence for three distinct phases of sampling over the last two centuries: (1) early sampling in the late 19th and early 20th century that was largely dominated by the research interests of a few “mega‐collectors”; (2) a mid‐20th century shift toward more widespread sampling; and (3) a major surge of sampling that corresponds to the rise of major environmental movements. We find each period possesses distinct phylogenetic and spatial biases. Moreover, these phases mirror trends in other spatial datasets that aggregate historical records spanning plants to terrestrial vertebrates, thereby suggesting that historical contingency and a temporal bias toward recent records are likely hallmarks of compiled historical datasets. Given that the pace of spatial data sampling continues to grow, our results strongly caution that the continued development of new models and methods to mitigate against bias‐driven statistical artifacts will be critical to effectively harnessing the power of historical data.}, 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={AbstractHemidactylus mabouia is one of the most successful, widespread invasive reptile species and has become ubiquitous across tropical urban settings in the Western Hemisphere. Its ability to thrive in close proximity to humans has been linked to the rapid disappearance of native geckos. However, aspects of Hemidactylus mabouia natural history and ecomorphology, often assumed to be linked with this effect on native populations, remain understudied or untested. Here, we combine data from ∂15N and ∂13C stable isotopes, stomach contents, and morphometric analyses of traits associated with feeding and locomotion to test alternate hypotheses of displacement between H. mabouia and a native gecko, Phyllodactylus martini, on the island of Curaçao. We demonstrate substantial overlap of invertebrate prey resources between the species, with H. mabouia stomachs containing larger arthropod prey as well as vertebrate prey. We additionally show that H. mabouia possesses several morphological advantages, including larger sizes in feeding‐associated traits and limb proportions that could offer a propulsive locomotor advantage on vertical surfaces. Together, these findings provide the first support for the hypotheses that invasive H. mabouia and native P. martini overlap in prey resources and that H. mabouia possess ecomorphological advantages over P. martini. This work provides critical context for follow‐up studies of H. mabouia and P. martini natural history and direct behavioral experiments that may ultimately illuminate the mechanisms underlying displacement on this island and act as a potential model for other systems with Hemidactylus mabouia invasions.}, 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={AbstractThe bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era.}, 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} }