Genomic evidence of a previously undetected Peromyscus truei invasion on San Clemente Island, California

Abstract

Museum genomics (museomics) provide powerful tools for detecting cryptic diversity in natural history collections, including previously undetected invasions. We analyzed genomic and morphological data from 75 Peromyscus specimens collected during the Channel Islands Biological Survey (1939-1941), a series of expeditions on the California Channel Islands spearheaded by the Natural History Museum of Los Angeles County (LACM). Most of these specimens were confirmed as native Channel Island deer mice (P. gambelii subspp.), but two specimens from San Clemente Island (SCL) were re-identified as P. truei, a species never reported before on the Channel Islands. Using study skins, complete mitogenomes, and low coverage whole-genome data, we confirmed these identifications, and our phylogenetic analyses determined that these P. truei individuals are closely related to California mainland populations. We also placed these species within the subfamily Neotominae, including the first mitogenome of a native Channel Island deer mouse. Additional morphological data reveal several more likely P. truei specimens, indicating the existence of a substantial populations of this species in 1939. Combined with the presence of other non-native rodents on San Clemente Island (Reithrodontomys megalotis and Microtus californicus), these findings suggest a possible co-introduction from San Diego County during the 1930s via hay shipments. Our results have important implications for conservation management on San Clemente Island, and potentially Santa Rosa Island, where some specimens appear phenotypically inconsistent with P. gambelii. This study highlights the value of molecular tools for reassessing historic collections, especially in dynamic systems subject to high levels of anthropogenic modification.