Pattern and timing of mitochondrial divergence of island spotted skunks on the California Channel Islands

Abstract

Island spotted skunks (Spilogale gracilis amphiala) are a rare subspecies endemic to the California Channel Islands, currently extant on Santa Cruz and Santa Rosa islands. How and when skunks arrived on the islands is unknown, hindering decision-making about their taxonomic status and conservation priority. We investigated these questions by sequencing the complete mitochondrial genomes of 55 skunks from the two islands and mainland (California and Arizona) and examining phylogenetic patterns and estimations of isolation times among populations. Island spotted skunks grouped in a single monophyletic clade distinct from mainland spotted skunks. A haplotype network analysis had the most recent common ancestral haplotype sampled from an individual on Santa Rosa, suggesting both islands were colonized by a single matriline. Additionally, no haplotypes were shared between skunk populations on the two islands. These patterns imply that both island populations were derived from a common ancestral population shortly after establishment and have remained isolated from each other ever since. Together with divergence estimates from three methods, this topology is consistent with colonization of the super-island, Santarosae, by a single ancestral population of spotted skunks in the early Holocene, followed by divergence as the sea level rose and split Santarosae into Santa Cruz and Santa Rosa islands 9,400–9,700 years ago. Such a scenario of colonization could be explained either by rafting or one-time transport by Native Americans. Given their distinct evolutionary history, high levels of endemism, and current population status, island spotted skunks may warrant management as distinct evolutionarily significant units.

Population Genetics of California Gray Foxes Clarify Origins of the Island Fox

“…Both species exhibit a single mitochondrial haplogroup endemic to the northern islands. In both cases, distributions of haplotypes and their nucleotide diversity were consistent with origins from a single maternal founder during the time sea level was low enough for the northern islands to form the single super-island, Santarosae, up to slightly <10 kya [ 3 , 39 ]. Thus, other than the missing mitochondrial link between the northern island haplogroup and modern gray foxes, there are no major conflicts in the evidence for the timing of colonization in the north.…”

“…The archaeological, cultural, and DNA evidence all agree in suggesting that foxes arrived on the northern Channel Islands approximately 13–7500 kya, long before they arrived in the southern islands, closer to 5.5 kya [ 3 , 8 , 10 , 11 , 12 , 16 , 17 ]. The mitochondrial pattern of the northern islands is similar to that of the island spotted skunk ( Spilogale gracilis amphialus ), which also inhabits two of the northern islands and was thought to have arrived around the same time as foxes [ 39 ]. Both species exhibit a single mitochondrial haplogroup endemic to the northern islands.…”

The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine‐scale differentiation across host species and island populations

“…This distinction may reflect the more specialized nature of island spotted skunk ecology, in contrast to the more generalist nature of island fox ecology. It may further reflect evolutionary processes operating during a longer period of separation between island spotted skunk populations, which diverged roughly 10,000 years ago, compared to island foxes, which colonized the islands roughly 7000 years ago (Bolas, Quinn, et al., 2022 ; Floyd et al., 2011 ; Hofman et al., 2015 ).…”

“…Counter to these ecological patterns, Channel Island foxes ( Urocyon littoralis santacruzae and U. l. santarosae ) and island spotted skunks ( Spilogale gracilis amphiala ) coexist on two islands off the coast of southern California: Santa Cruz Island and Santa Rosa Island (Figure 1 ). Both mesocarnivore taxa are endemic to the Channel Islands, where they have coexisted alongside one another for at least 7000 years (Bolas, Quinn, et al., 2022 ; Floyd et al., 2011 ; Hofman et al., 2015 ). While island foxes are found on six of eight islands in the archipelago, island spotted skunks are only found on the two largest islands.…”