@article{naranjo_sither_conant_2024, title={Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa}, volume={196}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2024.108087}, abstractNote={Polyploidy, or whole-genome duplication, is expected to confound the inference of species trees with phylogenetic methods for two reasons. First, the presence of retained duplicated genes requires the reconciliation of the inferred gene trees to a proposed species tree. Second, even if the analyses are restricted to shared single copy genes, the occurrence of reciprocal gene loss, where the surviving genes in different species are paralogs from the polyploidy rather than orthologs, will mean that such genes will not have evolved under the corresponding species tree and may not produce gene trees that allow inference of that species tree. Here we analyze three different ancient polyploidy events, using synteny-based inferences of orthology and paralogy to infer gene trees from nearly 17,000 sets of homologous genes. We find that the simple use of single copy genes from polyploid organisms provides reasonably robust phylogenetic signals, despite the presence of reciprocal gene losses. Such gene trees are also most often in accord with the inferred species relationships inferred from maximum likelihood models of gene loss after polyploidy: a completely distinct phylogenetic signal present in these genomes. As seen in other studies, however, we find that methods for inferring phylogenetic confidence yield high support values even in cases where the underlying data suggest meaningful conflict in the phylogenetic signals.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Naranjo, Jaells G. and Sither, Charles B. and Conant, Gavin C.}, year={2024}, month={Jul} }
 @article{soghigian_sither_justi_morinaga_cassel_vitek_livdahl_xia_gloria-soria_powell_et al._2023, title={Phylogenomics reveals the history of host use in mosquitoes}, volume={14}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-023-41764-y}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Soghigian, John and Sither, Charles and Justi, Silvia Andrade and Morinaga, Gen and Cassel, Brian K. and Vitek, Christopher J. and Livdahl, Todd and Xia, Siyang and Gloria-Soria, Andrea and Powell, Jeffrey R. and et al.}, year={2023}, month={Oct} }
 @article{fish_tesh_guzman_rosa_balta_underwood_sither_vasilakis_2021, title={Emergence potential of mosquito-borne arboviruses from the Florida Everglades}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0259419}, abstractNote={The Greater Everglades Region of South Florida is one of the largest natural wetlands and the only subtropical ecosystem found in the continental United States. Mosquitoes are seasonally abundant in the Everglades where several potentially pathogenic mosquito-borne arboviruses are maintained in natural transmission cycles involving vector-competent mosquitoes and reservoir-competent vertebrate hosts. The fragile nature of this ecosystem is vulnerable to many sources of environmental change, including a wetlands restoration project, climate change, invasive species and residential development. In this study, we obtained baseline data on the distribution and abundance of both mosquitos and arboviruses occurring in the southern Everglades region during the summer months of 2013, when water levels were high, and in 2014, when water levels were low. A total of 367,060 mosquitoes were collected with CO2-baited CDC light traps at 105 collection sites stratified among the major landscape features found in Everglades National Park, Big Cypress National Preserve, Fakahatchee State Park Preserve and Picayune State Forest, an area already undergoing restoration. A total of 2,010 pools of taxonomically identified mosquitoes were cultured for arbovirus isolation and identification. Seven vertebrate arboviruses were isolated: Everglades virus, Tensaw virus, Shark River virus, Gumbo Limbo virus, Mahogany Hammock virus, Keystone virus, and St. Louis encephalitis virus. Except for Tensaw virus, which was absent in 2013, the remaining viruses were found to be most prevalent in hardwood hammocks and in Fakahatchee, less prevalent in mangroves and pinelands, and absent in cypress and sawgrass. In contrast, in the summer of 2014 when water levels were lower, these arboviruses were far less prevalent and only found in hardwood hammocks, but Tensaw virus was present in cypress, sawgrass, pinelands, and a recently burned site. Major environmental changes are anticipated in the Everglades, many of which will result in increased water levels. How these might lead to the emergence of arboviruses potentially pathogenic to both humans and wildlife is discussed.}, number={11}, journal={PLOS ONE}, author={Fish, Durland and Tesh, Robert B. and Guzman, Hilda and Rosa, Amelia P. A. Travassos and Balta, Victoria and Underwood, James and Sither, Charles and Vasilakis, Nikos}, year={2021}, month={Nov} }
 @article{seger_drummond_delgado_day_sither_soghigian_wiegmann_reiskind_ellis_byrd_2019, title={FIRST RECORD OF MANSONIA DYARI FROM SAINT CROIX, UNITED STATES VIRGIN ISLANDS}, volume={35}, ISSN={["1943-6270"]}, DOI={10.2987/19-6859.1}, abstractNote={ABSTRACT}, number={3}, journal={JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION}, author={Seger, Krystal R. and Drummond, Aubrey, II and Delgado, David and Day, Corey A. and Sither, Charles B. and Soghigian, John and Wiegmann, Brian M. and Reiskind, Michael H. and Ellis, Brett R. and Byrd, Brian D.}, year={2019}, month={Sep}, pages={214–216} }