@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{zhou_soghigian_xiang_2022, title={A New Pipeline for Removing Paralogs in Target Enrichment Data}, volume={71}, ISSN={["1076-836X"]}, DOI={10.1093/sysbio/syab044}, abstractNote={Abstract}, number={2}, journal={SYSTEMATIC BIOLOGY}, author={Zhou, Wenbin and Soghigian, John and Xiang, Qiu-Yun Jenny}, year={2022}, month={Feb}, pages={410–425} }
 @article{winkler_kirk-spriggs_bayless_soghigian_meier_pape_yeates_carvalho_copeland_wiegmann_2022, title={Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0274292}, abstractNote={The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to “orphaned” taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae–the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.}, number={10}, journal={PLOS ONE}, author={Winkler, Isaac S. and Kirk-Spriggs, Ashley H. and Bayless, Keith M. and Soghigian, John and Meier, Rudolf and Pape, Thomas and Yeates, David K. and Carvalho, A. Bernardo and Copeland, Robert S. and Wiegmann, Brian M.}, year={2022}, month={Oct} }
 @article{soghigian_livdahl_2021, title={Field Evidence of Mosquito Population Regulation by a Gregarine Parasite}, volume={58}, ISSN={["1938-2928"]}, DOI={10.1093/jme/tjab009}, abstractNote={Abstract}, number={3}, journal={JOURNAL OF MEDICAL ENTOMOLOGY}, author={Soghigian, John and Livdahl, Todd}, year={2021}, month={May}, pages={1188–1196} }
 @article{justi_soghigian_pecor_caicedo-quiroga_rutvisuttinunt_li_stevens_dorn_wiegmann_linton_2021, title={From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae)}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0247068}, abstractNote={Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.}, number={2}, journal={PLOS ONE}, author={Justi, Silvia Andrade and Soghigian, John and Pecor, David B. and Caicedo-Quiroga, Laura and Rutvisuttinunt, Wiriya and Li, Tao and Stevens, Lori and Dorn, Patricia L. and Wiegmann, Brian and Linton, Yvonne-Marie}, year={2021}, month={Feb} }
 @article{soghigian_gloria-soria_robert_le goff_failloux_powell_2020, title={Genetic evidence for the origin ofAedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean}, volume={29}, ISSN={["1365-294X"]}, DOI={10.1111/mec.15590}, abstractNote={Abstract}, number={19}, journal={MOLECULAR ECOLOGY}, author={Soghigian, John and Gloria-Soria, Andrea and Robert, Vincent and Le Goff, Gilbert and Failloux, Anna-Bella and Powell, Jeffrey R.}, year={2020}, month={Oct}, pages={3593–3606} }
 @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} }
 @article{gloria-soria_soghigian_kellner_powell_2019, title={Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti}, volume={13}, ISSN={["1935-2735"]}, DOI={10.1371/journal.pntd.0007930}, abstractNote={The yellow fever mosquito (Aedes aegypti), is the primary vector of dengue, Zika, and chikungunya fever, among other arboviral diseases. It is also a popular laboratory model in vector biology due to its ease of rearing and manipulation in the lab. Established laboratory strains have been used worldwide in thousands of studies for decades. Laboratory evolution of reference strains and contamination among strains are potential severe problems that could dramatically change experimental outcomes and thus is a concern in vector biology. We analyzed laboratory and field colonies of Ae. aegypti and an Ae. aegypti-derived cell line (Aag2) using 12 microsatellites and ~20,000 SNPs to determine the extent of divergence among laboratory strains and relationships to their wild relatives. We found that 1) laboratory populations are less genetically variable than their field counterparts; 2) colonies bearing the same name obtained from different laboratories may be highly divergent; 3) present genetic composition of the LVP strain used as the genome reference is incompatible with its presumed origin; 4) we document changes in two wild caught colonies over ~16 generations of colonization; and 5) the Aag2 Ae. aegypti cell line has experienced minimal genetic changes within and across laboratories. These results illustrate the degree of variability within and among strains of Ae. aegypti, with implications for cross-study comparisons, and highlight the need of a common mosquito repository and the implementation of strain validation tools.}, number={12}, journal={PLOS NEGLECTED TROPICAL DISEASES}, author={Gloria-Soria, Andrea and Soghigian, John and Kellner, David and Powell, Jeffrey R.}, year={2019}, month={Dec} }
 @article{bova_soghigian_paulson_2019, title={The Prediapause Stage of Aedes japonicus japonicus and the Evolution of Embryonic Diapause in Aedini}, volume={10}, ISSN={["2075-4450"]}, DOI={10.3390/insects10080222}, abstractNote={The genus Aedes is well known for its desiccation-resistant eggs, which frequently serve as an overwintering mechanism through diapause. Despite this, relatively little is known about the diapause and overwintering biology of most Aedes species including Aedes japonicus japonicus, an invasive mosquito in the United States. The importance of this mosquito in disease systems like La Crosse virus remain uncertain. Embryonic diapause is used by Ae. j. japonicus to survive temperate winters, and the persistence of this species in the Appalachian region is a result of overwintering, which has important implications for the transmission of this virus to humans. The objective of this study was to identify the prediapause stage, or the stage sensitive to environmental cues needed to induce diapause in this mosquito. By exposing each Ae. j. japonicus life stage independently to short-day photoperiods, we determined that the adult maternal life stage is the prediapause stage. Using the most recent phylogeny and prior literature on the prediapause stages in the genus Aedes, we were able to infer the evolutionary history of the prediapause stages of Aedes mosquitoes that overwinter or aestivate as eggs. This initial ancestral state reconstruction allowed us to hypothesize that Aedini mosquitoes that undergo obligate diapause may have evolved from those utilizing the embryonic prediapause stage, and that the ancestral prediapause state of Aedini appears to be maternally controlled.}, number={8}, journal={INSECTS}, author={Bova, Jake and Soghigian, John and Paulson, Sally}, year={2019}, month={Aug} }