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2. Homage to Felsenstein 1981, or why are there so few/many species?

Author

Butlin, Roger K., Servedio, Maria R., Smadja, Carole M., Bank, Claudia, Barton, Nicholas H., Flaxman, Samuel M., Giraud, Tatiana, Hopkins, Robin, Larson, Erica L., Maan, Martine E., Meier, Joana, Merrill, Richard, Noor, Mohamed A. F., Ortiz-Barrientos, Daniel, and Qvarnström, Anna

Published
2021

5. Synthesis and Scope of the Role of Postmating Prezygotic Isolation in Speciation

Author

Garlovsky, Martin D., primary, Whittington, Emma, additional, Albrecht, Tomas, additional, Arenas-Castro, Henry, additional, Castillo, Dean M., additional, Keais, Graeme L., additional, Larson, Erica L., additional, Moyle, Leonie C., additional, Plakke, Melissa, additional, Reifová, Radka, additional, Snook, Rhonda R., additional, Ålund, Murielle, additional, and Weber, Alexandra A.-T., additional

Published
2023
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8. Supplementary material 1 from: Byerly AR, Jenck C, Goetz ARB, Weissman DB, Gray DA, Ross CL, Maroja LS, Larson EL (2023) Geographic variation in phenotypic divergence between two hybridizing field cricket species. Journal of Orthoptera Research 32(2): 189-200. https://doi.org/10.3897/jor.32.90713

Author

Byerly, Amy R., primary, Jenck, Clara, additional, Goetz, Alexander R. B., additional, Weissman, David B., additional, Gray, David A., additional, Ross, Charles L., additional, Maroja, Luana S., additional, and Larson, Erica L., additional

Published
2023
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18. The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice (accepted)

Author

Kopania, Emily E K, Watson, Eleanor M, Rathje, Claudia C., Skinner, Benjamin M, Ellis, Peter J.I., Larson, Erica L., and Good, Jeffrey M.

Abstract

Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome-autosome interactions cause strong incompatibilities in Mus musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. Additionally, X-Y chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here we evaluated the contribution of X-Y lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of X-Y mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than X-Y gene copy number imbalance. Y-chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise non-hybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of X-Y conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice., Author's Accepted Manuscript

Published
2022
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19. Global urban environmental change drives adaptation in white clover

Author

Santangelo, James S., primary, Ness, Rob W., additional, Cohan, Beata, additional, Fitzpatrick, Connor R., additional, Innes, Simon G., additional, Koch, Sophie, additional, Miles, Lindsay S., additional, Munim, Samreen, additional, Peres-Neto, Pedro R., additional, Prashad, Cindy, additional, Tong, Alex T., additional, Aguirre, Windsor E., additional, Akinwole, Philips O., additional, Alberti, Marina, additional, Álvarez, Jackie, additional, Anderson, Jill T., additional, Anderson, Joseph J., additional, Ando, Yoshino, additional, Andrew, Nigel R., additional, Angeoletto, Fabio, additional, Anstett, Daniel N., additional, Anstett, Julia, additional, Aoki-Gonçalves, Felipe, additional, Arietta, A. Z. Andis, additional, Arroyo, Mary T. K., additional, Austen, Emily J., additional, Baena-Díaz, Fernanda, additional, Barker, Cory A., additional, Baylis, Howard A., additional, Beliz, Julia M., additional, Benitez-Mora, Alfonso, additional, Bickford, David, additional, Biedebach, Gabriela, additional, Blackburn, Gwylim S., additional, Boehm, Mannfred M. A., additional, Bonser, Stephen P., additional, Bonte, Dries, additional, Bragger, Jesse R., additional, Branquinho, Cristina, additional, Brans, Kristien I., additional, Bresciano, Jorge C., additional, Brom, Peta D., additional, Bucharova, Anna, additional, Burt, Briana, additional, Cahill, James F., additional, Campbell, Katelyn D., additional, Carlen, Elizabeth J., additional, Carmona, Diego, additional, Castellanos, Maria Clara, additional, Centenaro, Giada, additional, Chalen, Izan, additional, Chaves, Jaime A., additional, Chávez-Pesqueira, Mariana, additional, Chen, Xiao-Yong, additional, Chilton, Angela M., additional, Chomiak, Kristina M., additional, Cisneros-Heredia, Diego F., additional, Cisse, Ibrahim K., additional, Classen, Aimée T., additional, Comerford, Mattheau S., additional, Fradinger, Camila Cordoba, additional, Corney, Hannah, additional, Crawford, Andrew J., additional, Crawford, Kerri M., additional, Dahirel, Maxime, additional, David, Santiago, additional, De Haan, Robert, additional, Deacon, Nicholas J., additional, Dean, Clare, additional, del-Val, Ek, additional, Deligiannis, Eleftherios K., additional, Denney, Derek, additional, Dettlaff, Margarete A., additional, DiLeo, Michelle F., additional, Ding, Yuan-Yuan, additional, Domínguez-López, Moisés E., additional, Dominoni, Davide M., additional, Draud, Savannah L., additional, Dyson, Karen, additional, Ellers, Jacintha, additional, Espinosa, Carlos I., additional, Essi, Liliana, additional, Falahati-Anbaran, Mohsen, additional, Falcão, Jéssica C. F., additional, Fargo, Hayden T., additional, Fellowes, Mark D. E., additional, Fitzpatrick, Raina M., additional, Flaherty, Leah E., additional, Flood, Pádraic J., additional, Flores, María F., additional, Fornoni, Juan, additional, Foster, Amy G., additional, Frost, Christopher J., additional, Fuentes, Tracy L., additional, Fulkerson, Justin R., additional, Gagnon, Edeline, additional, Garbsch, Frauke, additional, Garroway, Colin J., additional, Gerstein, Aleeza C., additional, Giasson, Mischa M., additional, Girdler, E. Binney, additional, Gkelis, Spyros, additional, Godsoe, William, additional, Golemiec, Anneke M., additional, Golemiec, Mireille, additional, González-Lagos, César, additional, Gorton, Amanda J., additional, Gotanda, Kiyoko M., additional, Granath, Gustaf, additional, Greiner, Stephan, additional, Griffiths, Joanna S., additional, Grilo, Filipa, additional, Gundel, Pedro E., additional, Hamilton, Benjamin, additional, Hardin, Joyce M., additional, He, Tianhua, additional, Heard, Stephen B., additional, Henriques, André F., additional, Hernández-Poveda, Melissa, additional, Hetherington-Rauth, Molly C., additional, Hill, Sarah J., additional, Hochuli, Dieter F., additional, Hodgins, Kathryn A., additional, Hood, Glen R., additional, Hopkins, Gareth R., additional, Hovanes, Katherine A., additional, Howard, Ava R., additional, Hubbard, Sierra C., additional, Ibarra-Cerdeña, Carlos N., additional, Iñiguez-Armijos, Carlos, additional, Jara-Arancio, Paola, additional, Jarrett, Benjamin J. M., additional, Jeannot, Manon, additional, Jiménez-Lobato, Vania, additional, Johnson, Mae, additional, Johnson, Oscar, additional, Johnson, Philip P., additional, Johnson, Reagan, additional, Josephson, Matthew P., additional, Jung, Meen Chel, additional, Just, Michael G., additional, Kahilainen, Aapo, additional, Kailing, Otto S., additional, Kariñho-Betancourt, Eunice, additional, Karousou, Regina, additional, Kirn, Lauren A., additional, Kirschbaum, Anna, additional, Laine, Anna-Liisa, additional, LaMontagne, Jalene M., additional, Lampei, Christian, additional, Lara, Carlos, additional, Larson, Erica L., additional, Lázaro-Lobo, Adrián, additional, Le, Jennifer H., additional, Leandro, Deleon S., additional, Lee, Christopher, additional, Lei, Yunting, additional, León, Carolina A., additional, Lequerica Tamara, Manuel E., additional, Levesque, Danica C., additional, Liao, Wan-Jin, additional, Ljubotina, Megan, additional, Locke, Hannah, additional, Lockett, Martin T., additional, Longo, Tiffany C., additional, Lundholm, Jeremy T., additional, MacGillavry, Thomas, additional, Mackin, Christopher R., additional, Mahmoud, Alex R., additional, Manju, Isaac A., additional, Mariën, Janine, additional, Martínez, D. Nayeli, additional, Martínez-Bartolomé, Marina, additional, Meineke, Emily K., additional, Mendoza-Arroyo, Wendy, additional, Merritt, Thomas J. S., additional, Merritt, Lila Elizabeth L., additional, Migiani, Giuditta, additional, Minor, Emily S., additional, Mitchell, Nora, additional, Mohammadi Bazargani, Mitra, additional, Moles, Angela T., additional, Monk, Julia D., additional, Moore, Christopher M., additional, Morales-Morales, Paula A., additional, Moyers, Brook T., additional, Muñoz-Rojas, Miriam, additional, Munshi-South, Jason, additional, Murphy, Shannon M., additional, Murúa, Maureen M., additional, Neila, Melisa, additional, Nikolaidis, Ourania, additional, Njunjić, Iva, additional, Nosko, Peter, additional, Núñez-Farfán, Juan, additional, Ohgushi, Takayuki, additional, Olsen, Kenneth M., additional, Opedal, Øystein H., additional, Ornelas, Cristina, additional, Parachnowitsch, Amy L., additional, Paratore, Aaron S., additional, Parody-Merino, Angela M., additional, Paule, Juraj, additional, Paulo, Octávio S., additional, Pena, João Carlos, additional, Pfeiffer, Vera W., additional, Pinho, Pedro, additional, Piot, Anthony, additional, Porth, Ilga M., additional, Poulos, Nicholas, additional, Puentes, Adriana, additional, Qu, Jiao, additional, Quintero-Vallejo, Estela, additional, Raciti, Steve M., additional, Raeymaekers, Joost A. M., additional, Raveala, Krista M., additional, Rennison, Diana J., additional, Ribeiro, Milton C., additional, Richardson, Jonathan L., additional, Rivas-Torres, Gonzalo, additional, Rivera, Benjamin J., additional, Roddy, Adam B., additional, Rodriguez-Muñoz, Erika, additional, Román, José Raúl, additional, Rossi, Laura S., additional, Rowntree, Jennifer K., additional, Ryan, Travis J., additional, Salinas, Santiago, additional, Sanders, Nathan J., additional, Santiago-Rosario, Luis Y., additional, Savage, Amy M., additional, Scheepens, J.F., additional, Schilthuizen, Menno, additional, Schneider, Adam C., additional, Scholier, Tiffany, additional, Scott, Jared L., additional, Shaheed, Summer A., additional, Shefferson, Richard P., additional, Shepard, Caralee A., additional, Shykoff, Jacqui A., additional, Silveira, Georgianna, additional, Smith, Alexis D., additional, Solis-Gabriel, Lizet, additional, Soro, Antonella, additional, Spellman, Katie V., additional, Whitney, Kaitlin Stack, additional, Starke-Ottich, Indra, additional, Stephan, Jörg G., additional, Stephens, Jessica D., additional, Szulc, Justyna, additional, Szulkin, Marta, additional, Tack, Ayco J. M., additional, Tamburrino, Ítalo, additional, Tate, Tayler D., additional, Tergemina, Emmanuel, additional, Theodorou, Panagiotis, additional, Thompson, Ken A., additional, Threlfall, Caragh G., additional, Tinghitella, Robin M., additional, Toledo-Chelala, Lilibeth, additional, Tong, Xin, additional, Uroy, Léa, additional, Utsumi, Shunsuke, additional, Vandegehuchte, Martijn L., additional, VanWallendael, Acer, additional, Vidal, Paula M., additional, Wadgymar, Susana M., additional, Wang, Ai-Ying, additional, Wang, Nian, additional, Warbrick, Montana L., additional, Whitney, Kenneth D., additional, Wiesmeier, Miriam, additional, Wiles, J. Tristian, additional, Wu, Jianqiang, additional, Xirocostas, Zoe A., additional, Yan, Zhaogui, additional, Yao, Jiahe, additional, Yoder, Jeremy B., additional, Yoshida, Owen, additional, Zhang, Jingxiong, additional, Zhao, Zhigang, additional, Ziter, Carly D., additional, Zuellig, Matthew P., additional, Zufall, Rebecca A., additional, Zurita, Juan E., additional, Zytynska, Sharon E., additional, and Johnson, Marc T. J., additional

Published
2022
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32. Evolution of Widespread Recombination Suppression on the Dwarf Hamster (Phodopus) X Chromosome.

Author

Moore, Emily C., Thomas, Gregg W. C., Mortimer, Sebastian, Kopania, Emily E. K., Hunnicutt, Kelsie E., Clare-Salzler, Zachary J., Larson, Erica L., and Good, Jeffrey M.

Subjects
SEX chromosomes, CHROMOSOME structure, X chromosome, MOLECULAR evolution, HAMSTERS, GENE mapping
Abstract

The X chromosome of therian mammals shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across ∼65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. These data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, substantial changes in the recombination landscape have so far had relatively subtle influences on patterns of X-linked molecular evolution in these species. [ABSTRACT FROM AUTHOR]

Published
2022
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34. Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids.

Author

Larson, Erica L., Kopania, Emily E. K., Hunnicutt, Kelsie E., Vanderpool, Dan, Keeble, Sara, and Good, Jeffrey M.

Subjects
*X chromosome, *MICE, *SPERMATOGENESIS, *SEX chromosomes, *MALE sterility in plants, *GENETIC regulation
Abstract

Hybrid sterility is a complex phenotype that can result from the breakdown of spermatogenesis at multiple developmental stages. Here, we disentangle two proposed hybrid male sterility mechanisms in the house mice, Mus musculus domesticus and M. m. musculus, by comparing patterns of gene expression in sterile F1 hybrids from a reciprocal cross. We found that hybrid males from both cross directions showed disrupted X chromosome expression during prophase of meiosis I consistent with a loss of meiotic sex chromosome inactivation (MSCI) and Prdm9-associated sterility, but that the degree of disruption was greater in mice with an M. m. musculus X chromosome consistent with previous studies. During postmeiotic development, gene expression on the X chromosome was only disrupted in one cross direction, suggesting that misexpression at this later stage was genotype-specific and not a simple downstream consequence of MSCI disruption which was observed in both reciprocal crosses. Instead, disrupted postmeiotic expression may depend on the magnitude of earlier disrupted MSCI, or the disruption of particular X-linked genes or gene networks. Alternatively, only hybrids with a potential deficit of Sly copies, a Y-linked ampliconic gene family, showed overexpression in postmeiotic cells, consistent with a previously proposed model of antagonistic coevolution between the X- and Y-linked ampliconic genes contributing to disrupted expression late in spermatogenesis. The relative contributions of these two regulatory mechanisms and their impact on sterility phenotypes await further study. Our results further support the hypothesis that X-linked hybrid sterility in house mice has a variable genetic basis, and that genotype-specific disruption of gene regulation contributes to overexpression of the X chromosome at different stages of development. Overall, these findings underscore the critical role of epigenetic regulation of the X chromosome during spermatogenesis and suggest that these processes are prone to disruption in hybrids. [ABSTRACT FROM AUTHOR]

Published
2022
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39. The Evolution of Polymorphic Hybrid Incompatibilities in House Mice

Author

Larson, Erica L, primary, Vanderpool, Dan, additional, Sarver, Brice A J, additional, Callahan, Colin, additional, Keeble, Sara, additional, Provencio, Lorraine L, additional, Kessler, Michael D, additional, Stewart, Vanessa, additional, Nordquist, Erin, additional, Dean, Matthew D, additional, and Good, Jeffrey M, additional

Published
2018
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40. Microsatellites for Oenothera gayleana and O. hartwegii subsp. filifolia (Onagraceae), and their utility in section Calylophus1

Author

Lewis, Emily M., Fant, Jeremie B., Moore, Michael J., Hastings, Amy P., Larson, Erica L., Agrawal, Anurag A., and Skogen, Krissa A.

Subjects
Oenothera sect. Calylophus, population genetics, gypsum endemism, Primer Note, Onagraceae, microsatellites
Abstract

Premise of the study: Eleven nuclear and four plastid microsatellite markers were screened for two gypsum endemic species, Oenothera gayleana and O. hartwegii subsp. filifolia, and tested for cross-amplification in the remaining 11 taxa within Oenothera sect. Calylophus (Onagraceae). Methods and Results: Microsatellite markers were tested in two to three populations spanning the ranges of both O. gayleana and O. hartwegii subsp. filifolia. The nuclear microsatellite loci consisted of both di- and trinucleotide repeats with one to 17 alleles per population. Several loci showed significant deviation from Hardy–Weinberg equilibrium, which may be evidence of chromosomal rings. The plastid microsatellite markers identified one to seven haplotypes per population. The transferability of these markers was confirmed in all 11 taxa within Oenothera sect. Calylophus. Conclusions: The microsatellite loci characterized here are the first developed and tested in Oenothera sect. Calylophus. These markers will be used to assess whether pollinator foraging distance influences population genetic parameters in predictable ways.

Published
2016

45. The Composite Regulatory Basis of the Large X-Effect in Mouse Speciation.

Author

Larson, Erica L., Keeble, Sara, Vanderpool, Dan, Dean, Matthew D., and Good, Jeffrey M.

Abstract

The disruption of meiotic sex chromosome inactivation (MSCI) has been proposed to be a major developmental mechanism underlying the rapid evolution of hybrid male sterility. We tested this idea by analyzing cell-specific gene expression across spermatogenesis in two lineages of house mice and their sterile and fertile reciprocal hybrids. We found pervasive disruption of sex chromosome gene expression in sterile hybrids at every stage of spermatogenesis. Failure of MSCI was developmentally preceded by increased silencing of autosomal genes, supporting the hypothesis that divergence at the hybrid incompatibility gene, Prdm9, results in increased rates of autosomal asynapsis which in turn triggers widespread silencing of unsynapsed chromatin. We also detected opposite patterns of postmeiotic overexpression or hyper-repression of the sex chromosomes in reciprocal hybrids, supporting the hypothesis that genomic conflict has driven functional divergence that leads to deleterious X-Y dosage imbalances in hybrids. Our developmental timeline also exposed more subtle patterns of mitotic misregulation on the X chromosome, a previously undocumented stage of spermatogenic disruption in this cross. These results indicate that multiple hybrid incompatibilities have converged on a common regulatory phenotype, the disrupted expression of the sex chromosomes during spermatogenesis. Collectively, these data reveal a composite regulatory basis to hybrid male sterility in mice that helps resolve the mechanistic underpinnings of the well-documented large X-effect in mice speciation. We propose that the inherent sensitivity of spermatogenesis to X-linked regulatory disruption has the potential to be a major driver of reproductive isolation in species with chromosomal sex determination. [ABSTRACT FROM AUTHOR]

Published
2017
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