Conservation Mitochondrial Genomics of the Gopher Snake on the Northern Channel Islands

Abstract

Island populations often experience accelerated evolutionary divergence due to reduced gene flow as a result of geographic isolation and strong genetic drift, resulting in high levels of island endemism, relative to mainland populations. However, these same forces, combined with habitat loss and human disturbance, may also lead to greater threats of extinction compared to mainland populations. The Channel Islands are an archipelago off the coast of California, home to over 100 endemic species, and were subject to intense agricultural disturbance in the late 1800s. Despite the conservation importance of the Channel Islands, the evolutionary history and effects of human disturbance on many island endemic populations remain unknown. Here, I aim to understand the genetic conservation status and genetic divergence of one Channel Islands endemic, the “dwarf” Santa Cruz Island gopher snake (Pituophis catenifer pumilus). Using whole mitochondrial genomes, I compare demography between two Northern Channel Islands populations (Santa Cruz Island and Santa Rosa Island) and two mainland California relatives, the San Diego gopher snake (Pituophis catenifer annectens) and the Pacific gopher snake (Pituophis catenifer catenifer). Haplotype network analyses show that individuals cluster into location-specific haplogroups. Principal component analyses, estimates of divergence, patterns of genetic diversity, and unique amino acid changes indicate (1) P. c. annectens colonized the islands, (2) each island was an independent colonization, and (3) Santa Cruz Island had multiple colonization events by different P. c. annectens lineages. While genetic diversity on Santa Cruz Island is comparable to the mainland subspecies, diversity on Santa Rosa Island is much lower, potentially reducing adaptive potential of this population. These results highlight the distinct evolutionary trajectories of the Santa Cruz Island gopher snake and the need for island-specific management strategies. Future work will include analysis of the nuclear genome to further resolve the tempo of colonization, as well as tests for signatures of selection in correlation with the evolution of insular dwarfism.