Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population

Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity

Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.

Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus)

We provide a response to a recently published evaluation of the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus). The work we discuss used exon capture genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies, with recommendation that it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of this study, and explain in clearer terms how to interpret genomic analyses for applied management. We identify four broad conceptual issues that led to errant recommendations: (1) interpretation of subspecies and diagnosability, (2) inappropriate use of reciprocal monophyly as a criterion for subspecies, (3) importance of geographic isolation, and (4) error in hypothesis testing and misinterpretation of results. We conclude that the data from this genomic appraisal add to information from prior studies providing strong support for recognition of N. m. atristriatus as a subspecies. Our conclusions have important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.