@article{dye_muga_mwangi_hoyer_ly_rosado_sharpee_mware_wambugu_labadie_et al._2023, title={Cassava begomovirus species diversity changes during plant vegetative cycles}, volume={14}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2023.1163566}, DOI={10.3389/fmicb.2023.1163566}, abstractNote={Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dye, Anna E. and Muga, Brenda and Mwangi, Jenniffer and Hoyer, J. Steen and Ly, Vanessa and Rosado, Yamilex and Sharpee, William and Mware, Benard and Wambugu, Mary and Labadie, Paul and et al.}, year={2023}, month={May} }
 @article{catto_labadie_jacobson_kennedy_srinivasan_hunt_2023, title={Pest status, molecular evolution, and epigenetic factors derived from the genome assembly of Frankliniella fusca, a thysanopteran phytovirus vector}, volume={24}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-023-09375-5}, DOI={10.1186/s12864-023-09375-5}, abstractNote={The tobacco thrips (Frankliniella fusca Hinds; family Thripidae; order Thysanoptera) is an important pest that can transmit viruses such as the tomato spotted wilt orthotospovirus to numerous economically important agricultural row crops and vegetables. The structural and functional genomics within the order Thysanoptera has only begun to be explored. Within the > 7000 known thysanopteran species, the melon thrips (Thrips palmi Karny) and the western flower thrips (Frankliniella occidentalis Pergrande) are the only two thysanopteran species with assembled genomes.A genome of F. fusca was assembled by long-read sequencing of DNA from an inbred line. The final assembly size was 370 Mb with a single copy ortholog completeness of ~ 99% with respect to Insecta. The annotated genome of F. fusca was compared with the genome of its congener, F. occidentalis. Results revealed many instances of lineage-specific differences in gene content. Analyses of sequence divergence between the two Frankliniella species' genomes revealed substitution patterns consistent with positive selection in ~ 5% of the protein-coding genes with 1:1 orthologs. Further, gene content related to its pest status, such as xenobiotic detoxification and response to an ambisense-tripartite RNA virus (orthotospovirus) infection was compared with F. occidentalis. Several F. fusca genes related to virus infection possessed signatures of positive selection. Estimation of CpG depletion, a mutational consequence of DNA methylation, revealed that F. fusca genes that were downregulated and alternatively spliced in response to virus infection were preferentially targeted by DNA methylation. As in many other insects, DNA methylation was enriched in exons in Frankliniella, but gene copies with homology to DNA methyltransferase 3 were numerous and fragmented. This phenomenon seems to be relatively unique to thrips among other insect groups.The F. fusca genome assembly provides an important resource for comparative genomic analyses of thysanopterans. This genomic foundation allows for insights into molecular evolution, gene regulation, and loci important to agricultural pest status.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Catto, Michael A. and Labadie, Paul E. and Jacobson, Alana L. and Kennedy, George G. and Srinivasan, Rajagopalbabu and Hunt, Brendan G.}, year={2023}, month={Jun} }
 @article{burford reiskind_labadie_bargielowski_lounibos_reiskind_2018, title={Rapid evolution and the genomic consequences of selection against interspecific mating}, volume={27}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/mec.14821}, DOI={10.1111/mec.14821}, abstractNote={While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the United States in the mid‐1980s, resulting in the displacement of A. aegypti in much of the south‐eastern United States. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called “satyrization.” The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double‐digest restriction enzyme DNA sequencing (ddRADseq) to analyse outlier loci between selected and control lines of laboratory‐reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either “resisted” or “mated with” A. albopictus males via mating trials of wild‐derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and nonmated A. aegypti females in the laboratory and wild‐derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behaviour, and specifically in avoiding interspecific mating choices.}, number={18}, journal={Molecular Ecology}, publisher={Wiley}, author={Burford Reiskind, Martha O. and Labadie, Paul and Bargielowski, Irka and Lounibos, L. Philip and Reiskind, Michael H.}, year={2018}, month={Aug}, pages={3641–3654} }
 @article{jones_vargo_keefer_labadie_scherer_gallagher_gold_2017, title={Efficacy of Chlorantraniliprole in Controlling Structural Infestations of the Eastern Subterranean Termite in the USA}, volume={8}, ISSN={["2075-4450"]}, DOI={10.3390/insects8030092}, abstractNote={Subterranean termites are the most economically important structural pests in the USA, and the eastern subterranean termite, Reticulitermes flavipes (Kollar) (Dictyoptera: Rhinotermitidae) is the most widely distributed species. Soil treatment with a liquid termiticide is a widely used method for controlling subterranean termites in structures. We assessed the efficacy of a nonrepellent termiticide, Altriset® (active ingredient: chlorantraniliprole), in controlling structural infestations of R. flavipes in Texas, North Carolina, and Ohio and determined the post-treatment fate of termite colonies in and around the structures. In all three states, microsatellite markers indicated that only one R. flavipes colony was infesting each structure. A single chlorantraniliprole treatment provided effective structural protection as there was no further evidence of termite activity in and on the majority of structures from approximately 1 month to 2 years post-treatment when the study concluded. Additionally, the treatment appeared to either severely reduce the infesting colony’s footprint at monitors in the landscape or eliminate colony members from these monitors. A supplemental spot-treatment was conducted at one house each in Texas and North Carolina at 5 and 6 months post-treatment, respectively; no termites were observed thereafter in these structures and associated landscaping. The number of colonies found exclusively in the landscape (not attacking the structure) varied among the states, with the largest number of colonies in Texas (0–4) and North Carolina (0–5) as compared to 0–1 in Ohio, the most northern state.}, number={3}, journal={INSECTS}, author={Jones, Susan C. and Vargo, Edward L. and Keefer, T. Chris and Labadie, Paul and Scherer, Clay W. and Gallagher, Nicola T. and Gold, Roger E.}, year={2017}, month={Sep} }
 @article{burford reiskind_coyle_daniels_labadie_reiskind_roberts_roberts_schaff_vargo_2016, title={Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa}, volume={16}, ISSN={1755-098X}, url={http://dx.doi.org/10.1111/1755-0998.12527}, DOI={10.1111/1755-0998.12527}, abstractNote={The generation of genome‐scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome‐scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high‐throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double‐digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence‐able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired‐end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.}, number={6}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Burford Reiskind, M. O. and Coyle, K. and Daniels, H. V. and Labadie, P. and Reiskind, M. H. and Roberts, N. B. and Roberts, R. B. and Schaff, J. and Vargo, E. L.}, year={2016}, month={May}, pages={1303–1314} }
 @article{haifig_vargo_labadie_costa-leonardo_2016, title={Unrelated secondary reproductives in the neotropical termite Silvestritermes euamignathus (Isoptera: Termitidae)}, volume={103}, ISSN={["1432-1904"]}, DOI={10.1007/s00114-015-1325-0}, abstractNote={A termite colony is usually founded by a pair of alates, the primary reproductives, which produce all the nestmates. In some species, secondary reproductives appear to either replace the primaries or supplement colony reproduction. In termites, secondary reproductives are generally ergatoids derived from workers or nymphoids derived from nymphs. Silvestritermes euamignathus is a termite species that forms multiple nymphoid reproductives, and to date it was hypothesized that these secondary reproductives were the progeny of the primary founding reproductives. We developed markers for 12 microsatellite loci and used COI mitochondrial DNA (mtDNA) to genotype 59 nymphoid neotenics found in a colony of S. euamignathus to test this hypothesis. Our results showed that nymphoids of S. euamignathus are not all siblings. The microsatellite analysis suggests that the secondary reproductives derived from a minimum of four different pairs of reproductives belonging to at least two different matrilines. This is the first record of non-sibling secondary reproductives occupying the same nest in a higher termite. These unrelated reproductives might be the result of either pleometrotic colony foundation or colony fusion.}, number={1-2}, journal={SCIENCE OF NATURE}, author={Haifig, Ives and Vargo, Edward L. and Labadie, Paul and Costa-Leonardo, Ana Maria}, year={2016}, month={Feb} }
 @misc{perdereau_bagneres_vargo_baudouin_xu_labadie_dupont_dedeine_2015, title={Relationship between invasion success and colony breeding structure in a subterranean termite}, volume={24}, ISSN={["1365-294X"]}, DOI={10.1111/mec.13094}, abstractNote={Factors promoting the establishment and colonization success of introduced populations in new environments constitute an important issue in biological invasions. In this context, the respective role of pre‐adaptation and evolutionary changes during the invasion process is a key question that requires particular attention. This study compared the colony breeding structure (i.e. number and relatedness among reproductives within colonies) in native and introduced populations of the subterranean pest termite, Reticulitermes flavipes. We generated and analysed a data set of both microsatellite and mtDNA loci on termite samples collected in three introduced populations, one in France and two in Chile, and in the putative source population of French and Chilean infestations that has recently been identified in New Orleans, LA. We also provided a synthesis combining our results with those of previous studies to obtain a global picture of the variation in breeding structure in this species. Whereas most native US populations are mainly composed of colonies headed by monogamous pairs of primary reproductives, all introduced populations exhibit a particular colony breeding structure that is characterized by hundreds of inbreeding reproductives (neotenics) and by a propensity of colonies to fuse, a pattern shared uniquely with the population of New Orleans. These characteristics are comparable to those of many invasive ants and are discussed to play an important role during the invasion process. Our finding that the New Orleans population exhibits the same breeding structure as its related introduced populations suggests that this native population is pre‐adapted to invade new ranges.}, number={9}, journal={MOLECULAR ECOLOGY}, author={Perdereau, E. and Bagneres, A. -G. and Vargo, E. L. and Baudouin, G. and Xu, Y. and Labadie, P. and Dupont, S. and Dedeine, F.}, year={2015}, month={May}, pages={2125–2142} }
 @article{vargo_labadie_matsuura_2012, title={Asexual queen succession in the subterranean termite Reticulitermes virginicus}, volume={279}, DOI={10.1098/rspb.2011.1030}, abstractNote={
            Termite colonies are founded by a pair of primary reproductives. In many species, including subterranean termites (family Rhinotermitidae), the primary king and queen can be succeeded by neotenic reproductives that are produced from workers or nymphs within the colony. It is generally believed that these neotenics inbreed within the colony, sometimes for many generations. Here, we show that primary queens of the North American subterranean termite,
            Reticulitermes virginicus
            , are replaced by numerous parthenogenetically produced female neotenics. We collected functional female neotenics from five colonies of
            R. virginicus
            in North Carolina and Texas, USA. Genetic analysis at eight microsatellite loci showed that 91–100% of the neotenics present within a colony were homozygous at all loci, indicating that they were produced through automictic parthenogenesis with terminal fusion. In contrast, workers, soldiers and alates were almost exclusively sexually produced by mating between the female neotenics and a single king. This is the second termite species shown to undergo asexual queen succession, a system first described in the Japanese species,
            Reticulitermes speratus
            . Thus, the conditional use of sexual and asexual reproduction to produce members of different castes may be widespread within
            Reticulitermes
            and possibly other subterranean termites.
          }, number={1729}, journal={Proceedings of the Royal Society of London. Series B}, author={Vargo, E. L. and Labadie, P. E. and Matsuura, K.}, year={2012}, pages={813–819} }
 @article{brightwell_labadie_silverman_2010, title={Northward Expansion of the Invasive Linepithema humile (Hymenoptera: Formicidae) in the Eastern United States is Constrained by Winter Soil Temperatures}, volume={39}, ISSN={["0046-225X"]}, DOI={10.1603/en09345}, abstractNote={ARSTRACT 
 The invasive Argentine ant, Linepithema humile (Mayr) (Hymenoptera: Formicidae) has been evident in the North Carolina Piedmont, United States for 90 yr but has failed to spread further north. We investigated the mechanisms preventing this expansion. The Argentine ant ceases foraging at temperatures below 5°C and we hypothesized that winter soil temperatures at higher latitudes restricted foraging long enough to cause colony starvation. We tested if the Argentine ant could successfully feed at temperatures below 5°C and found that colonies would starve. We subjected Argentine ant nests to a range of sub- and above-freezing temperatures and measured worker mortality at various time intervals. We found that Argentine ant colonies will collapse after 8.5 d at 5°C Argentine ants can escape ambient cold temperatures by moving nests into the soil column. We tested how deeply into the soil Argentine ant queens and workers need to move to survive winter in North Carolina. Soil temperatures in the North Carolina Piedmont do not fall below 5°C for longer than nine consecutive days; therefore, Argentine ant colonies need only to retreat a few centimeters into the soil column to escape unsuitable temperatures. Winter soil temperature data from four climate stations situated from latitudes 35°, the current Eastern United States latitudinal limit for Argentine ant population expansion, to 39° were searched for periods where soil temperatures would have led to colony extirpation. North of their current distributions, extended periods of soil temperatures below 5°C regularly occur, preventing Argentine ant colonies from persisting.}, number={5}, journal={ENVIRONMENTAL ENTOMOLOGY}, author={Brightwell, R. J. and Labadie, P. E. and Silverman, J.}, year={2010}, month={Oct}, pages={1659–1665} }
 @article{matsuura_vargo_kawatsu_labadie_nakano_yashiro_tsuji_2009, title={Queen Succession Through Asexual Reproduction in Termites}, volume={323}, ISSN={["0036-8075"]}, DOI={10.1126/science.1169702}, abstractNote={The evolution and maintenance of sexual reproduction may involve important tradeoffs because asexual reproduction can double an individual's contribution to the gene pool but reduces diversity. Moreover, in social insects the maintenance of genetic diversity among workers may be important for colony growth and survival. We identified a previously unknown termite breeding system in which both parthenogenesis and sexual reproduction are conditionally used. Queens produce their replacements asexually but use normal sexual reproduction to produce other colony members. These findings show how eusociality can lead to extraordinary reproductive systems and provide important insights into the advantages and disadvantages of sex.}, number={5922}, journal={SCIENCE}, author={Matsuura, Kenji and Vargo, Edward L. and Kawatsu, Kazutaka and Labadie, Paul E. and Nakano, Hiroko and Yashiro, Toshihisa and Tsuji, Kazuki}, year={2009}, month={Mar}, pages={1687–1687} }