@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={AbstractMosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188–250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.}, 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{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{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={AbstractTarget enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]}, number={2}, journal={SYSTEMATIC BIOLOGY}, author={Zhou, Wenbin and Soghigian, John and Xiang, Qiu-Yun Jenny}, year={2022}, month={Feb}, pages={410–425} }
 @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
               Although parasites are by definition costly to their host, demonstrating that a parasite is regulating its host abundance in the field can be difficult. Here we present an example of a gregarine parasite, Ascogregarina taiwanensis Lien and Levine (Apicomplexa: Lecudinidae), regulating its mosquito host, Aedes albopictus Skuse (Diptera: Culicidae), in Bermuda. We sampled larvae from container habitats over 2 yr, assessed parasite prevalence, and estimated host abundance from egg counts obtained in neighboring ovitraps. We regressed change in average egg count from 1 yr to the next on parasite prevalence and found a significant negative effect of parasite prevalence. We found no evidence of host density affecting parasite prevalence. Our results demonstrate that even for a parasite with moderate virulence, host regulation can occur in the field.}, 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={AbstractAedes aegypti is among the best‐studied mosquitoes due to its critical role as a vector of human pathogens and ease of laboratory rearing. Until now, this species was thought to have originated in continental Africa, and subsequently colonized much of the world following the establishment of global trade routes. However, populations of this mosquito on the islands in the southwestern Indian Ocean (SWIO), where the species occurs with its nearest relatives referred to as the Aegypti Group, have received little study. We re‐evaluated the evolutionary history of Ae. aegypti and these relatives, using three data sets: nucleotide sequence data, 18,489 SNPs and 12 microsatellites. We found that: (a) the Aegypti Group diverged 16 MYA (95% HPD: 7–28 MYA) from its nearest African/Asian ancestor; (b) SWIO populations of Ae. aegypti are basal to continental African populations; (c) after diverging 7 MYA (95% HPD: 4–15 MYA) from its nearest formally described relative (Ae. mascarensis), Ae. aegypti moved to continental Africa less than 85,000 years ago, where it recently (<1,000 years ago) split into two recognized subspecies Ae. aegypti formosus and a human commensal, Ae. aegypti aegypti; (d) the Madagascar samples form a clade more distant from all other Ae. aegypti than the named species Ae. mascarensis, implying that Madagascar may harbour a new cryptic species; and (e) there is evidence of introgression between Ae. mascarensis and Ae. aegypti on Réunion, and between the two subspecies elsewhere in the SWIO, a likely consequence of recent introductions of domestic Ae. aegypti aegypti from Asia.}, 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
               The first report of Mansonia dyari on Saint Croix, United States Virgin Islands (USVI), is confirmed. Adult and larval specimens were collected in 2018 and 2019 through adult surveillance and larval collections. Specimens were identified by microscopic methods, and a representative specimen was confirmed by DNA sequencing (mitochondrial cytochrome c oxidase subunit I). Morphological features are reviewed and compared with Mansonia flaveola, a species previously reported in the USVI. Notes are provided on the locations, collection methods, and mosquito associates found with Ma. dyari in the USVI.}, 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} }