Publications

* Undergraduate student

 

Starkie, M.L., S.L. Cameron, M.N. Krosch, M.J. Phillips, J.E. Royer, M.K. 

Schutze, F. Strutt, A.D. Sweet, M.P. Zalucki, and A.R. Clarke. 2022. A dated phylogeny of the Australian Dacini fruit flies (Diperta: Tephritidae). Molecular Phylogenetics and Evolution. Accepted.

Boyd, B.M., N.-P. Nguyen, J.M. Allen, R. Waterhouse, K.B. Vo, A.D. Sweet, D.H. Clayton, S.E. Bush, M.D. Shapiro, and K.P. Johnson. 2022. Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites. Proceedings of the Royal Society B. 289: 20220042. https://doi.org/10.1098/rspb.2022.0042.
 

Smith, A.D., M.J. Kamiński, K. Kanda, A.D. Sweet, J.L. Betancourt, C.A. Holmgren, E. Hempel, F. Alberti, M. Hofreiter. 2021. Recovery and analysis of ancient insect DNA from subfossil packrat middens using high-throughput sequencing. Scientific Reports. 11:12635. https://doi.org/10.1038/s41598-021-91896-8.

Sweet, A.D., K.P. Johnson, Y. Cao, R.S. de Moya, R.K. Skinner, M. Tan, S. Virrueta-Herrera, and S.L. Cameron. 2021. Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera. Gene. 768: 145312. https://doi.org/10.1016/j.gene.2020.145312.

de Moya, R.S., K. Yoshizawa, K.K.O. Walden, A.D. Sweet, C.H. Dietrich, and K.P. Johnson. 2021. Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): exploring compositional bias in Next Generation datasets. Systematic Biology. 70: 719-738. https://doi.org/10.1093/sysbio/syaa075.

Najer, T., I. Papousek, O. Sychra, A. Sweet, K. Johnson. 2021. Combining nuclear and mitochondrial loci provides phylogenetic information in the Philopterus complex of lice. Journal of Medical Entomology. 58: 252-260. https://doi.org/10.1093/jme/tjaa166.

Doña, J., A.D. Sweet, and K.P. Johnson. 2020. Comparing rates of introgression in parasitic feather lice with differing dispersal capabilities. Communications Biology. 3: 610. https://doi.org/10.1038/s42003-020-01345-x.

Sweet, A.D., R.E. Wilson, S.A. Sonsthagen, and K.P. Johnson. 2020. Lousy grouse: comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions. Ecology and Evolution. 10(15): 8379-8393. https://doi.org/10.1002/ece3.6545.

Sweet, A.D., K.P. Johnson, and S.L. Cameron. 2020. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice. PeerJ. 8: e8759. https://doi.org/10.7717/peerj.8759.

Virrueta-Herrera, S., A.D. Sweet, J.M. Allen, K.K.O. Walden, J.D. Weckstein, and K.P. Johnson. 2020. Extensive in situ radiation of feather lice on tinamous. Proceedings of the Royal Society B. 287: 20193005. http://dx.doi.org/10.1098/rspb.2019.3005.

Tyagi, K., R. Chakraborty, S.L. Cameron, A.D. Sweet, K. Chandra, and V. Kumar. 2020. So few thrips, so many mitochondrial genome rearrangements: Expanded sampling reveals extensive genomic evolution within Thysanoptera. Scientific Reports. 10: 695. https://doi.org/10.1038/s41598-020-57705-4.

Skinner, R.K., C.H. Dietrich, K.K.O. Walden, E. Gordon, A.D. Sweet, L. Podsiadlowski, M. Petersen, C. Simon, D.M. Takiya, and K.P. Johnson. 2019. Phylogenomics of Auchenorrhynca (Insecta: Hemiptera) using transcriptomes. Systematic Entomology. 45(1): 85-113. https://doi.org/10.1111/syen.12381.

de Moya, R.S., J.M. Allen, A.D. Sweet, K.K.O. Walden, R.L. Palma, V.S. Smith, S.L. Cameron, M.P. Valim, T.D. Galloway, J.D. Weckstein, and K.P. Johnson. 2019. Extensive host-switching of avian lice following the Cretaceous-Paleogene mass extinction. Communications Biology. 2: 445. https://doi.org/10.1038/s42003-019-0689-7.

de Moya, R.S., Weirauch, C., A.D. Sweet, R. Skinner, K.K.O. Walden, D.R. Swanson, C. Dietrich, and K.P. Johnson. 2019. Deep instability in the phylogenetic backbone of Heteroptera is only partly overcome by transcriptome-based phylogenomics. Insect Systematics and Diversity. 3: 7. https://doi.org/10.1093/isd/ixz020.

de Moya, R.S, J.K. Brown, A.D. Sweet, K.K.O. Walden, J.R. Paredes-Montero, R.M. Waterhouse, and K.P. Johnson. 2019. Nuclear orthologs derived from whole genome sequencing indicate cryptic diversity in the Bemisia tabaci (Insecta: Aleyrodidae) complex of whiteflies. Diversity. 11: 151. https://doi.org/10.3390/d11090151.

Nowak, J.E.*†, A.D. Sweet†, J.D. Weckstein, and K.P. Johnson. 2019. A molecular phylogenetic analysis of the genera of fruit doves and allies using dense taxonomic sampling. Illinois Natural History Survey Bulletin. 42: 2019001.
       † Contributed equally to the work

 

Leonardi, M.S., S. Virrueta Herrera, A. Sweet, J. Negrete, and K.P. Johnson. 2019. Phylogenomics and population genomics of seal lice. Systematic Entomology. 44(4): 699-708. https://doi.org/10.1111/syen.12350.

Catanach, T.A.†, A.D. Sweet†, N.D. Nguyen, R.M. Peery, A.H. Debevec, A.K. Thomer, A.C. Owings, B.M. Boyd, A.D. Katz, F.N. Soto-Adames, and J.M. Allen. 2019. Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ. 7:e6142. https://doi.org/10.7717/peerj.6142.

† Contributed equally to the work

Sweet, A.D. and K.P. Johnson. 2018. The role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales. Molecular Ecology. 27: 5104-5119. http://dx.doi.org/10.1111/mec.14937.

Johnson, K.P., N. Nguyen, A.D. Sweet, B.M. Boyd, T. Warnow, and J.M. Allen. 2018. Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biology Letters. 14(5). https://doi.org/10.1098/rsbl.2018.0141. 

Soto, J., G. Londono, K.P. Johnson, J.D. Weckstein, J.E. Avendano, J. Jankowski, T.A. Catanach, A.D. Sweet, and J.M. Allen. 2018. Composition and distribution of lice (Insecta: Phthiraptera) on Colombian and Peruvian birds: New data on host-louse association in the Neotropics. Biodiversity Data Journal. 6: e21635. https://doi.org/10.3897/BDJ.6.e21635.


Sangster, G., A.D. Sweet, and K.P. Johnson. 2018. Paraclaravis, a new genus for the Purple-winged and Maroon-chested Ground-doves (Aves: Columbidae). Zootaxa. 4461(1): 134-140. http://dx.doi.org/10.11646/zootaxa.4461.1.10.

Sweet, A.D., S.E. Bush, D.R. Gustafsson, J.M. Allen, E. DiBlasi, H.R. Skeen, J.D. Weckstein, and K.P. Johnson. 2018. Host and parasite morphology influence congruence between host and parasite phylogenies. International Journal for Parasitology. 48: 641-648. doi.org/10.1016/j.ijpara.2018.01.007.

Sweet, A.D., B.M. Boyd, J.M. Allen, S.M. Villa, M.P. Valim, J.L. Rivera-Parra, R.E. Wilson, and K.P. Johnson. 2018. Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution. Evolution. 72(1): 95-112. doi.org/10.1111/evo.13386/full.

 

Yoshizawa, K., K.P. Johnson, A.D. Sweet, I. Yao, R. Ferreira, and S. Cameron. Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea). 2017. Molecular Phylogenetics and Evolution. 119: 118-127. doi.org/10.1016/j.ympev.2017.10.014.

Dona, J., A.D. Sweet, K.P. Johnson, D. Serrano, S. Mironov, and R. Jovani. 2017. Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system. Molecular Phylogenetics and Evolution. 115: 190-196. doi.org/10.1016/j.ympev.2017.08.005.
 
Sweet, A.D., R.T. Chesser, and K.P. Johnson. 2017. Comparative cophylogenetics of Australian phabine pigeons and doves (Aves: Columbidae) and their feather lice (Insecta: Phthiraptera). International Journal for Parasitology. 47: 347-356. doi.org/10.1016/j.ijpara.2016.12.003.
 
Boyd, B.M., J.M. Allen., N. Nguyen, A.D. Sweet, T. Warnow, M.D. Shapiro, S.M. Villa, S.E. Bush, D.H. Clayton, and K.P. Johnson. Phylogenomics using target-restricted assembly resolves intra-generic relationships of parasitic lice (Phthiraptera: Columbicola). Systematic Biology. doi.org/10.1093/sysbio/syx027.
 
Sweet, A.D., J.D. Maddox, and K.P. Johnson. 2017. A complete molecular phylogeny of Claravis confirms its paraphyly within small New World ground-doves (Aves: Peristerinae) and implies multiple plumage state transitions. Journal of Avian Biology. 48: 459-464. doi.org/10.1111/jav.01077.
 
Sweet, A.D. and K.P. Johnson. 2016. Cophylogenetic analysis of New World ground-doves (Aves: Columbidae) and their parasitic wing lice (Insecta: Phthiraptera: Columbicola). Molecular Phylogenetics and Evolution. 103: 122-132. doi.org/10.1016/j.ympev.2016.07.018.
 
Boyd, B.M., J.M. Allen, R. Koga, T. Fukatsu, A.D. Sweet, K.P. Johnson, and D.L. Reed. 2016. Two bacteria, Sodalis and Rickettsia, associated with the seal louse Proechinophthirus fluctus (Phthiraptera: Anoplura). Applied and Environmental Microbiology. 82(11): 3185-3197. doi.org/10.1128/AEM.00282-16.
 
Sweet, A.D., B.M. Boyd, and K.P. Johnson. 2016. Cophylogenetic patterns are uncorrelated between two lineages of parasites on the same hosts. Biological Journal of the Linnean Society. 118(4): 813-828. doi.org/10.1111/bij.12771.
 
Escalante, G.C.*, A.D. Sweet, K.G. McCracken, D. Gustaffson, R. Wilson, and K.P. Johnson. 2016. Patterns of cryptic host specificity in duck lice based on molecular data. Medical and Veterinary Entomology. 30(2): 200-208. doi.org/10.1111/mve.12157.
 
Sweet, A.D. and K.P. Johnson. 2015. Patterns of diversification in small New World ground doves are consistent with major geologic events. The Auk. 132: 300-312. doi.org/10.1642/AUK-14-193.1.
 
Sweet, A.D., J.M. Allen, and K.P. Johnson. 2014. Novel primers from informative nuclear loci for louse molecular phylogenetics (Insecta: Phthiraptera). Journal of Medical Entomology. 51(6): 1122-1126. doi.org/10.1603/ME13218.

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