Preprints
45. Langdon, Q., Groh, J., Aguillon, S., Powell, D.L., Gunn, T., Payne, C., Baczenas, J.J., Donny, A., Dodge, T.O., Du, K., Schartl, M., Ríos-Cárdenas, O., Gutiérrez, C., Morris, M., Schumer, M. (2023). Genome evolution is surprisingly predictable after initial hybridization. bioRxiv. doi: https://doi.org/10.1101/2023.12.21.572897.
44. Payne, C., Ly, D., Rodriguez-Soto, R., Powell, D.L., Robles, N., Gunn, T.R., Baczenas, J.J., Bergman, A., Delclos, P., Pollock, A., Moran, B., Baker, J., Reznick, D., Schumer, M. (2023). Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails. bioRxiv. doi: https://doi.org/10.1101/2023.12.15.571831.
43. Du, K., Lu, Y., Garcia-Olazabal, M., Walter, R.B., Warren, W.C., Dodge, T., Schumer, M., Park, H., Meyer, A., Schartl, M. (2023). Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus) highlights hybridization precedes speciation. bioRxiv. doi: https://doi.org/10.1101/2023.12.30.573732.
42. Preising, G.A., Gunn, T.R., Baczenas, J.J., Pollock, A., Powell, D.L., Dodge, T., Machin Kairuz, J.A., Savage, M., Lu, Y., Cummings, M., Thakur, S., Ríos-Cardenas, O., Morris, M., Schumer, M. (2022). Recurrent evolution of small body size and loss of the sword ornament in Northern Swordtail fish. bioRxiv. doi: https://doi.org/10.1101/2022.12.24.521833.
Published
41. Hoge, C.R., de Manuel, M., Mahgoub, M., Okami, N., Fuller, Z.L., Banerjee, S., Baker, Z., Mcnulty, M., Andolfatto, P., Macfarlan, T.S., Schumer, M., Tzika, A.C., Przeworski, M. (2024). Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features. Science, in press.
40. Moran, B.M., Payne, C.Y., Powell, D.L., Iverson, E.N.K., Donny, A.E., Banerjee, S.M., Langdon, Q.K., Gunn, T., Rodriguez-Soto, R.A., Madero, A., Baczenas, J.J., Kleczko, K.M., Liu, F., Matney, R., Singhal, K., Leib, R.D., Hernandez-Perez, O., Corbett-Detig, R., Frydman, J., Gifford, C., Schartl, M., Havird, J.D., Schumer, M. (2024). A Lethal Mitonuclear Incompatibility in Complex I of Natural Hybrids. Nature. doi: https://doi.org/10.1038/s41586-023-06895-8.
Nature Briefing: Deadly mismatch between nuclear and mitochondrial genes in swordtail fish hybrids.
Stanford Report article.
39. Thompson, K.A., Brandvain, Y., Coughlan, J.M., Delmore, K.E., Justen, H., Linnen, C.E., Ortiz-Barrientos, D., Schneemann, H., Schumer, M., Stelkens, R. (2024). The ecology of hybrid incompatibilities. Cold Spring Harbor Perspectives on Speciation. doi: 0.1101/cshperspect.a041440.
38. Zhang, J., Preising, G.A., Schumer, M., Palacios J.A. (2023). CRP-Tree: A phylogenetic association test for binary traits. Journal of the Royal Statistical Society: Series C. doi: https://doi.org/10.1093/jrsssc/qlad098.
37. Price, S., Schumer, M., Wang, S., Young, R., Cummings, M. (2023). Individual variation in preference and affiliative behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference. Ecology and Evolution. doi: https://doi.org/10.1002/ece3.10323.
36. Dodge, T.O., Farquharson, K.A., Ford, C., Cavanagh, L., Schumer, M., Belov, K., Hogg, C.J. (2023). Reference genomes of two extinct-in-the-wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Molecular Ecology Resources. doi: https://doi.org/10.1111/1755-0998.13780.
35. Banerjee, S.M., Powell, D.L., Moran, B.M., Ramírez-Duarte, W.F., Langdon, Q.K., Gunn, T.R. Vazquez, G., Rochman, C., Schumer, M. (2023). Complex hybridization between deeply diverged fish species in a disturbed ecosystem. Evolution. doi: https://doi.org/10.1093/evolut/qpad019.
34. Aguillon, S.M., Dodge, T.O., Preising, G.A., Schumer, M. (2022). Primer: Introgression. Current Biology. doi: https://doi.org/10.1016/j.cub.2022.07.004.
33. Payne, C., Bovio, S., Powell, D., Gunn, T., Banerjee, S.M., Grant, V., Rosenthal, G.G., Schumer, M. (2022). Genomic insights into variation in thermotolerance between hybridizing swordtail fishes. Molecular Ecology. doi: https://doi.org/10.1111/mec.16489
32. Li, J., Schumer, M., Bank, C. (2022). Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities. PLoS Genetics. doi: 10.1371/journal.pgen.1010120
31. Alves Cavassim, M.I., Baker, Z., Hoge, C., Schierup, M., Schumer, M., Przeworski, M. (2022). PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. PNAS. doi: https://doi.org/10.1073/pnas.2114401119
30. Thompson, K.A., Peichel, C.L., Rennison, D.J., McGee, M.D., Albert, A.Y.K., Vines, T.H., Greenwood, A.K., Wark, A.R., Brandvain, Y., Schumer, M., Schluter, D. (2021). Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback. PLoS Biology. doi: https://doi.org/10.1371/journal.pbio.3001469.
Perspective piece by Jenn Coughlan
29. Langdon, Q.K., Powell, D.L., Kim, B., Banerjee, S.M., Payne, C., Dodge, T.O., Moran, B., Fascinetto-Zago, P., Schumer, M. (2021). Predictability and parallelism in the contemporary evolution of hybrid genomes. PLoS Genetics. doi: https://doi.org/10.1371/journal.pgen.1009914.
28. Powell, D., Moran, B., Kim, B., Banerjee, S.M., Aguillon, S.M., Fascinetto-Zago, P., Langdon, Q., Schumer, M. (2021). Two new hybrid zones expand the swordtail hybridization model system. Evolution doi: https://doi.org/10.1111/evo.14337.
27. Moran, B.*, Payne, C.*, Langdon, Q., Powell, D., Brandvain, Y., Schumer, M. (2021). The genomic consequences of hybridization. eLife doi: 10.7554/eLife.69016. *co-first authorship
26. Powell, D., Payne, C.Y., Banerjee, S.M., Keegan, M., Cui, R., Andolfatto, P., Rosenthal, G.*, Schumer, M.* (2021). The genetic architecture of the sexually selected sword ornament. Current Biology doi: https://doi.org/10.1016/j.cub.2020.12.049. *co-supervised
Current Biology Digest by Florian Maderspacher
25. Powell, D.L., Garcia, M., Keegan, M., Reilly, P., Du, K., Díaz-Loyo, A.P., Banerjee, S., Blakkan, D., Reich, D., Andolfatto, P., Rosenthal, G.G., Schartl, M., Schumer, M. (2020). Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science doi: 10.1126/science.aba5216.
Perspective piece by Dagilis & Matute
Featured in Stanford News
24. Schumer, M., Powell, D., Corbett-Detig, R. (2020). Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer. Molecular Ecology Resources doi: https://doi.org/10.1111/1755-0998.13175.
23. Mateos, M., Kang, D., Klopp, C., Parrinello, H., Garcia, M., Schumer, M., Jue, N., Guiguen, Y., Schartl, M. (2019). Draft genome assembly and annotation of the Gila topminnow Poeciliopsis occidentalis. Frontiers in Ecology and Evolution.
22. Schumer, M., Xu, C., Powell, D., Durvasula, A., Skov, L., Holland, D., Blazier, J.C., Sankararaman, S., Andolfatto, P., Rosenthal, G.G.R, Przeworski, M. (2018). Natural selection and local recombination rates shape the genome evolution of swordtail hybrids. Science doi: 10.1126/science.aar3684.
21. Rosenthal, G.G.R, Schumer, M., Andolfatto, P. (2018). Letter: How the manakin got its crown: A novel trait that is unlikely to cause speciation. PNAS doi: 10.1073/pnas.1804061115.
20. Schumer, M., Rosenthal, G.G.R., Andolfatto, P. (2018) What do we mean when we talk about hybrid speciation? Heredity doi:10.1038/s41437-017-0036-z.
2018 editor’s choice
19. Schumer, M., Powell, D., Cui, R., Delclos, P., Squire, M., Andolfatto, P., Rosenthal, G. (2017). Assortative mating and persistent reproductive isolation in hybrids. PNAS doi: 10.1073/pnas.1711238114.
18. Baker, Z.*, Schumer, M.*, Haba, Y., Holland, C., Rosenthal, G., Przeworski, M. (2017). Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife. *co-first authorship
17. Cui, R., Delclos, P., Schumer, M., Rosenthal, G. (2017). Early social learning triggers neurogenomic expression changes in a swordtail fish. Proceedings Royal Society B.
16. Schumer, M., Brandvain, Y. (2016). Determining epistatic selection in admixed populations. Molecular Ecology doi: 10.1111/mec.13641.
15. Schumer, M., Cui, R., Powell, D., Rosenthal, G., Andolfatto, P. (2016). Ancient hybridization and genomic stabilization in a swordtail fish. Molecular Ecology doi: 10.1111/mec.13602.
14. Cui, R., Schumer, M., Rosenthal, G. (2016). Admix’em: A flexible framework for forward-time simulations of hybrid populations with selection and mate choice. Bioinformatics doi: 10.1093/bioinformatics/btv700.
13. Schumer, M.*, Cui, R.*, Rosenthal, G., Andolfatto, P. (2015). simMSG: an experimental design tool for high-throughput genotyping of hybrids. Molecular Ecology Resources doi: 10.1111/1755-0998.12434. *co-first authorship
12. Ghosh, R., Bloom, J.S., Mohammadi, A., Schumer, M., Andolfatto, P., Ryu, W., Kruglyak, L. (2015). Genetics of Intra-Species Variation in Avoidance Behavior Induced by a Thermal Stimulus in Caenorhabditis elegans. Genetics doi:10.1534/genetics.115.178491.
11. Schumer, M., Cui, R., Rosenthal, G., Andolfatto, P. (2015). Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genetics doi:10.1371/journal.pgen.1005041.
10. Schumer, M., Cui, R., Powell, D., Dresner, R., Rosenthal, G., Andolfatto, P. (2014). High-resolution Mapping Reveals Hundreds of Genetic Incompatibilities in Hybridizing Fish Species. eLife doi: http://dx.doi.org/10.7554/eLife.02535.
Featured in: Science News; The Naked Scientists podcast
9. Schumer, M., Rosenthal, G., Andolfatto, P. (2014). How common is homoploid hybrid speciation? Evolution doi:10.1111/evo.12399.
8. Culumber, Z. W., Schumer M., Monks S., Tobler M. (2014). Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population. Evolution doi: 10.1111/evo.12574.
7. Cui, R., Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., Rosenthal, G. (2013). Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution 67:2166-2179.
6. Renn, S.C.P. and Schumer, M. (2013). Genetic accommodation and behavioral evolution: insights from genomic studies. Animal Behavior 85: 1012-1022.
F1000 recommended article
5. Schumer, M., Cui, R., Boussau, B., Walter, W., Rosenthal, G., Andolfatto, P. (2012). An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 67: 1155-1168.
4. Zhen, Y., Aardema, M.L., Medina, E.M., Schumer, M., Andolfatto, P. (2012). Parallel molecular evolution in a herbivore community. Science 337:1634-1637.
3. Schumer, M.*, Birger, R.*, Tantipathananandh, C., Aurisano, J., Maggioni, M., Mwangi, P. (2012). Infestation by a Common Parasite is Correlated with Ant Symbiont Identity in a Plant-Ant Mutualism. Biotropica 45: 276-279. *co-first authorship
2. Schumer, M., Krishnakant, K., and Renn, S.C.P. (2011). Comparative gene expression profiles for highly similar aggressive phenotypes in male and female cichlid fishes (Julidochromis). Journal of Experimental Biology 214:3269-3278.
1. Spengler, M., Kuropatwinski, K., Schumer, M. and Antoch, M. (2009). A serine cluster mediates BMAL1-dependent CLOCK phosphorylation and degradation. Cell Cycle 8:24, 4138-4146.
Schumer lab 