Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Assessing Population Structure, Facilitating Supportive Breeding, and Identifying Adaptive Potential

The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new microsatellite markers for use in population structure and kinship analyses. We also used DNA from natural mortalities to generate ~10,000 single nucleotide polymorphisms (SNPs), which were used to assess genomic diversity. Whole mitochondrial genomes were assembled, annotated, and used to infer a phylogeny with museum specimens of insulanus collected ~100 years ago from Vancouver Island and other members of the E. ausonides species complex. The results indicated that the population of American Camp, San Juan Island National Historical Park insulanus experiences low heterozygosity, a small effective population size (Ne), and low allelic diversity. High levels of inbreeding were found in some individuals, but inbreeding was uneven across the population. No population structure or partitioning by host plant was detected. The mitogenomes of extant insulanus were all identical and modern samples showed a loss of allelic diversity compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management decisions and genetic monitoring.