Hot off the volcano

The Mexican volcano mouse (Neotomodon alstoni, Merriam 1898), is the only species within the monotypic genus Neotomodon, and is endemic to the Transverse Neovolcanic Ridge of central Mexico. Its geographic range spans high-elevation Sacaton grasslands of seven Mexican states (Michoacán, Hidalgo, Tlaxcala, Morelos, Puebla, Veracruz, and Estado de México), with different mountain tops hosting morphologically distinct geographic races.

Neotomodon alstoni by aguilargm, via, [CC-BY-NC]

Similar to some of their deer mouse relatives (genus Peromyscus), Mexican volcano mice are monogamous and have been used as models to better understand the molecular and physiological underpinnings of both monogamy and paternal care (Luis et al. 2000; Luis et al. 2017). The species is also an emerging biomedical model for studies of both obesity and circadian biology (Miranda-Anaya et al. 2019).

Morphologically intermediate to deer mice (Peromyscus) and voles (Microtus), the genus Neotomodon is named for their morphologically distinct teeth which resemble those of wood rats in the genus Neotoma. Genetically however, Neotomodon are more closely allied with deer mice (Peromyscus) and Florida mice (Podomys) (Bradley et al. 2007; Miller and Engstrom 2008; Platt et al. 2015), with a long history of systematic uncertainty.

Today, we share a chromosome-length genome assembly for the Mexican volcano mouse, Neotomodon alstoni (see also the contact map for the 24 chromosomes below). This assembly has a contig N50 of 45 KB and a scaffold N50 of 92 MB. The individual sequenced here was collected by David Ribble and Victor Sanchez-Cordero near Cuernavaca, Mexico in Morelos. The chromosome-length genome assembly was created in collaboration with the MacManes lab, University of New Hampshire. The draft assembly was generated using 10X data and was scaffolded using Oxford Nanopore data. The resulting assembly was misjoin-corrected, ordered and oriented into chromosomes using Hi-C data. See Methods for more details!

Interested in more mice genomes? Check out these blog posts on the cactus mouse and the Northern rock mouse, also created in collaboration with between the MacManes Lab and the DNA Zoo!


R. D. Bradley, N. D. Durish, D. S. Rogers, J. R. Miller, M. D. Engstrom, C. W. Kilpatrick. Toward a molecular phylogeny for Peromyscus: Evidence from mitochondrial cytochrome-b sequences. J. Mamm., 88(5) (2007), pp. 1146-1159.

O. Dudchenko, M. S. Shamim, S. S. Batra, N. C. Durand, N. T. Musial, R. Mostofa, M. Pham, B. Glenn St. Hilaire, W. Yao, E. Stamenova, M. Hoeger, S. K. Nyquist, V. Jorchina, K. Pletch, J. P. Flanagan, A. Tomaszewicz, D. McAloose, C. Pérez Estrada, B. J. Novak, A. D. Omer, E. L. Aiden. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. 2018. Biorxiv: https://dio,org/10.1101/254797.

J. Luis, A. Carmona, J. Delgado, F. Cervantes, R. Cardenas. Paternal Behavior of the Volcano Mouse, *Neotomodon alstoni* (Rodentia: Muridae), in Captivity. J. Mammal., 81 (2) (2000), pp. 600-605

J. Luis, G. Ramos, M. Martínez-Torres, A. Carmona, B. Cedillo, J. Delgado. Testosterone induces paternal behavior in sexually inexperienced males of Neotomodon alstoni (Rodentia: Muridae). Revista de Biologia Tropical, 65 (4) (2017), pp. 1419-1427

J. R. Miller, M. D. Engstrom. The relationship of major lineages within Peromyscine rodents: a molecular phylogenetic hypothesis and systematic reappraisal. J. Mamm., 89 (2008), 1279-1295.

M. Miranda-Anaya, M. Pérez-Mendoza, C. R. Juárez-Tapia, A. Carmona-Castro. The volcano mouse Neotomodon alstoni of central Mexico, a biological model in the study of breeding, obesity, and circadian rhythms. General and Comparative Endocrinology, 273 (2019), 61-66.

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