(including preprints)

48). Benowitz, K. M., Allan, C. W., Jaworski, C. C., Sanderson, M. J., Diaz, F., Chen, X., and Matzkin, L. M. (in review). Chromosome-length genome assemblies of cactophilic Drosophila illuminate links between structural and sequence evolution. bioRxiv. doi:10.1101/2022.10.16.512445. In review at Genome Research.

47). Moreyra, N. N., Almeida, F. C., Carson, C. W., Frankel, N, Matzkin, L. M. and Hasson, E. (Accepted). Phylogenomics provides insights into the evolution of cactophily and host plant shifts adaptation in Drosophila. bioRxiv. doi:10.1101/2022.04.29.490106. Molecular Phylogenetics and Evolution.

46). Shaible, T. M. and Matzkin, L. M. (2022). Physiological and life history changes associated with seasonal adaptation in the cactophilic Drosophila mojavensis. Biology Open. 11 (10): bio059610. doi.org/10.1242/bio.059610

45). Hurtado, J., Revale, S., and Matzkin, L. M. (2022). Propagation of seminal toxins through binary expression gene drives can suppress polyandrous populations. Scientific Reports. 12:6332. doi: 10.1038/s41598-022-10327-4

44). Benowitz, K. M., Allan, C. W., Degain, B. A., Li, X., Fabrick, J. A., Tabashnik, B., Carriere, Y, Matzkin, L.M.  (2022). Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea. Genetics. 221:1. doi.org/10.1093/genetics/iyac037

43). Diaz, F., Allan, C. W., Chen, X., Coleman, J. M., Bono, J. M. and Matzkin, L. M. (2022). Divergent evolutionary trajectories shape the postmating transcriptional profiles of conspecifically and heterospecifically mated cactophilic Drosophila females. Communications Biology. 5:842. doi.org/10.1038/s42003-022-03758-2

42). Diaz, F., Allan, C. W., Markow, T.A., Bono, J. M. and Matzkin, L. M. (2021). Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation. BMC Genomics. 22:359. doi:10.1186/s12864-021-07669-0.

41). Diaz, F., Kuijper, B., Hoyle, R. B., Coleman, J. M., Talamantes, N. and Matzkin, L. M. (2021). Environmental predictability drives adaptive within- and transgenerational plasticity of heat tolerance across life stages and climatic regions. Functional Ecology. 35:153-166. doi:10.1111/1365-2435.13704.

40). Benowitz K. M., Coleman, J. M., Allan, C. W. and Matzkin, L. M. (2020). Gene expression in the Drosophila mojavensis brain reveals tissue specific cis-regulatory and compensatory evolution across populations. Genome Biology and Evolution. 12(8):1407-1418. doi.org/10.1093/gbe/evaa145

39). Khallaf, M.A., Auer, T.O., Grabe, V., Depetris-Chauvin, A. Ammagarahalli, B., Zhang, D., Lavista-Llanos, S., Kaftan, F., Weibflog, J., Matzkin L. M., Rollmann, S.M., Lofstedt, C., Svatos, A., Dweck, H.K.M., Sachse, S., Benton, R., Hansson, B.S., and Knaden, M. (2020). A male pheromone promotes incipient isolation through conserved peripheral sensory pathways. Science Advances. 6(25):eaba5279. doi: 10.1126/sciadv.aba5279

38). Jaworski, C. C., Allan, C. W. and Matzkin, L. M. (2020). Chromosome-level hybrid de novo genome assemblies as an attainable option for non-model organisms. Molecular Ecology Resources. 20:1277-1293. doi:10.1111/1755-0998.13176

37). Allan, C. W. and Matzkin, L. M.  (2019).  Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis. BMC Genomics. 20(1):732. doi:10.1186/s12864-019-6097-z

36). Benowitz, K. M., Coleman, J. M. and Matzkin, L. M. (2019).  Assessing the architecture of Drosophila mojavensis locomotor evolution with bulk segregant analysis. G3. https://doi.org/10.1534/g3.119.400036

35). Diaz, F., Allan, C. W. and Matzkin, L. M (2018). Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila. BMC Evolutionary Biology. 18:144. doi: 10.1186/s12862-018-1250-x.

34). Coleman, J. M., Benowitz, K. M., Jost, A. G., and Matzkin, L. M. (2018). Behavioral evolution accompanying host shifts in cactophilic Drosophila larvae. Ecology and Evolution. 8:6921-6931. doi: 10.1002/ece3.4209.

33). Hoang, K., Matzkin, L. M.,Bono J. (2015).  Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri. Molecular Ecology. 24:5186-5199. doi: 10.1111/mec.13388

32). Bono, J., Killian, E. O., Matzkin, L. M. (2015). Connecting genotypes, phenotypes, and fitness: Harnessing the power of CRISPR/Cas9 genome editing. Molecular Ecology. 24:3810-3822.

31). Bono, J.*, Matzkin, L. M*, Hoang, K., and Brandsmeier, L. (2015). Molecular evolution of genes involved in post-mating pre-zygotic isolation in cactophilic Drosophila. Journal of Evolutionary Biology. (*Authors contributed equally). 28:403-414. doi: 10.1111/jeb.12574

30). Matzkin, L. M.  (2014). Ecological genomics of host shifts in Drosophila mojavensis. Advances in Experimental Medicine and Biology. 781:233-247. doi: 10.1007/978-94-007-7347-9_12

29). Matzkin, L. M., Johnson, S., Paight, C., and Markow, T. A. (2013). Preadult parental diet affects offspring development and metabolism in Drosophila melanogaster. PLoS ONE. 8:e59350. doi:10.1371/journal.pone.0059530

28). Matzkin, L. M. and Markow, T.A. (2013). Transcriptional differentiation across the four cactus host races of Drosophila mojavensis. In Speciation: Natural Processes, Genetics and Biodiversity. (Editor Michalak, P), pp 119-135. Nova Science Publishers Inc., New York.

27). Lang, M., Murat, S., Clark, A. G. Gouppil, G., Blais, C., Matzkin, L. M., Guittard, E., Yoshiyama-Ynagawa, T., Kataoka, H., Niwa, R., Lafont, R., Dauphin-Villemant, C., and Orgogozo, V. (2012). Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species. Science. 337:1658-1661.

26). Matzkin, L. M. (2012). Population transcriptomics of cactus host shifts in Drosophila mojavensis. Molecular Ecology. 21:2428-2439.

25). Bono, J. M.*, Matzkin, L. M.*, Kelleher, E. S., Markow, T. A. (2011). Postmating transcriptional changes in reproductive tracts of con- and heterospecifically-mated Drosophila mojavensis females. Proceedings of the National Academy of Sciences. 108:7878-7883. (*Authors contributed equally).

24). Matzkin, L. M., Johnson, S., Paight, C., Bozinovic, G. and Markow, T.A. (2011). Diet, development and metabolic pools in ecologically diverse Drosophila. Journal of Nutrition. 141:1127-1133.

23). Song, X. et al. (Matzkin, L. M. co-author). (2011). The 19 Genomes of Drosophila: A BAC Library Resource for Genus-wide and Genome Scale Comparative Evolutionary Research. Genetics. 187:1023-1030.

22). Matzkin, L. M., Mutsaka, K., Johnson, S., and Markow T. A. (2009). Metabolic pool differences among ecologically diverse Drosophila species. Journal of Insect Physiology. 55:1149-1150.

21). Matzkin, L. M., and Markow, T. A.  (2009). Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis. Genetics. 182:1279-1288.

20). Pfeiler, E., Bitler, B. G., Castrezana, S., Matzkin, L. M., and Markow T. A. (2009). Genetic diversification and demographic history of the cactophilic pseudoscorpion Dinocheirus arizonensis from the Sonoran Desert. Molecular Phylogenetics and Evolution. 52:133-141.

19). Matzkin, L. M., Watts, T. D., and Markow, T. A.  (2009). Evolution of stress resistance in Drosophila: Interspecific variation in tolerance to desiccation and starvation. Functional Ecology. 23:521-527.

18). Markow, T. A., Beall, S., Matzkin, L. M. (2009). Egg size, embryonic development time and ovoviparity in Drosophila species. Journal of Evolutionary Biology. 22:430-434.

17). Schaeffer, S. W., Bhutkar, A., McAllister, B. F., Matsuda, M., Matzkin, L. M., et al. (2008).  Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics. 179:1601-1655.

16). Bono, J., Matzkin, L. M., Castrezana, S. and Markow, T. A. (2008). Molecular evolution and population genetics of two Drosophila mettleri cytochrome P450 genes involved in host plant adaptation. Molecular Ecology. 17:3211-3221.

15). Matzkin, L. M. (2008). The molecular basis of host adaptation in cactophilic Drosophila: Molecular evolution of Glutathione S-transferase (GstD1) in Drosophila mojavensis. Genetics. 178:1073-1083.

14). Matzkin, L. M., Watts, T. D., and Markow, T. A.  (2007). Desiccation resistance in four Drosophila species: Sex and population effects. Fly. 1:268-273.

13). Drosophila 12 Genomes Consortium (Matzkin, L. M. co-author).  (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450:203-218.

12). Flowers, J. M., Sezgin, E., Kumagai, S., Duvernell, D. D., Matzkin, L. M., Schmidt, P. S., and Eanes, W. F.  (2007). Adaptive evolution of metabolic pathways in Drosophila. Molecular Biology and Evolution. 24: 1347-1354.

11). Machado, C. A., Matzkin, L. M. , Reed, L. K., and Markow T. A. (2007). Multilocus nuclear sequences reveal intra- and interspecific relationships among chromosomally polymorphic species of cactophilic Drosophila. Molecular Ecology. 16:3009-3024.

10). Matzkin, L. M. , Watts , T. D., Bitler B. G., Machado, C. A. and Markow, T. A. (2006). Functional genomics of cactus host shifts in Drosophila mojavensis. Molecular Ecology. 15:4635-4643.

9). Schmidt, P. S., Matzkin, L. M. , Ippollito, M. and W. F. Eanes. (2005). Geographic variation in diapause incidence, life history traits, and climatic adaptation in Drosophila melanogaster. Evolution. 59:1721-1732.

8). Matzkin, L. M.   (2005). Activity variation in alcohol dehydrogenase paralogs is associated with adaptation to cactus host use in cactophilic Drosophila. Molecular Ecology. 14:2223-2231.

7). Matzkin, L. M. , Merritt, T., Zhu, and W. F. Eanes. (2005). The structure and population genetics of the breakpoints associated with cosmopolitan inversion In(3R)Payne in Drosophila melanogaster. Genetics. 170:1143-1152.

6). Sezgin, E., W. F., Duvernell, D. D., Matzkin L. M. , Duan, Y., Zhu, C.T., Verrelli B. C., and W. F. Eanes. (2004). Single-locus latitudinal clines and their relationship to temperate adaptation in metabolic genes and derived alleles in Drosophila melanogaster. Genetics. 168:923-931.

5). Deckert-Cruz. D. J., Matzkin, L. M. , Graves Jr., J. L., and M. R. Rose. (2004). Electrophoretic analysis of methuselah flies from multiple species. Pp 237-248 in Methuselah flies: A case study in the evolution of aging. Edited by Rose, M.R., Passananti, H.B., and M. Matos. World Scientific Publishing Co.

4). Matzkin, L. M.   (2004). Population genetics and geographic variation of alcohol dehydrogenase (Adh) paralogs and glucose-6-phosphate dehydrogenase (G6pd) in Drosophila mojavensis. Molecular Biology and Evolution. 21:276-285.

3). Matzkin, L. M. and Eanes, W. F.  (2003).  Sequence variation of alcohol dehydrogenase (ADH) paralogs in cactophilic Drosophila. Genetics. 163:181-194.

2). Gibbs, A. G., Fukuzato, F. and Matzkin, L. M. (2003). Evolution of water conservation mechanisms in Drosophila. Journal of Experimental Biology. 203: 1183-1192.

1). Gibbs, A. G. and Matzkin, L. M. (2001).  Evolution of water balance in the genus Drosophila. Journal of Experimental Biology. 204 :2331-2338.

Manuscripts in review:

Million, K. M., Stallsmith, B. W., Brandsmeir, L. A., and Matzkin, L. M. Phylogenetic analysis of monogenean gill parasites (Genus Aethycteron) infecting darter (Etheostoma). Ichthyology & Herpetology.

Yanahan, A, L. M. Matzkin, and W. Moore. Impacts of Pleistocene climate oscillations on the phylogeography of Synuchus dubius (Coleoptera: Carabidae) in the U.S. Southwest. Ecology and Evolution.

Wang, X., Yang, L., Deng, Z., Gu, S., Gao, X., Zhang, Y., Ni, X., Matzkin, L. M. and Li, X. (in review). Transcriptomic divergences of larval labial salivary glands facilitate host-plant range oscillations between specialist and generalist Helicoverpa species. GigaScience.

Manuscripts in preparation:

Diaz, F. and Matzkin, L. M. Plasticity and transgenerational effects are regulated by transcriptional modulation.  (in prep). For submission to Genetics.

Shaible, T. M. and Matzkin, L. M.  Transcriptional responses of Drosophila mojavensis to the seasonal fluctuations of the Sonoran Desert. (in prep). For submission to Ecology and Evolution.