Median-Joining Network of Island and Mainland Mitochondrial DNA.

<p>A Median joining network using the variable sites of the mitochondrial genome was generated in the program Network v.4.612. The size of the circles and branch lengths are proportional to number of individuals represented and the number mutations between haplotypes (red), respectively. Hash marks indicate shortened branches. Santa Catalina and Santa Cruz are the only islands that share a haplotype, which is more closely related to the northern island haplotypes than the southern.</p

Bayesian phylogeny of mitogenomes of island and mainland foxes.

<p>The northern Channel Island foxes (San Miguel, Santa Rosa and Santa Cruz) diverged from the southern island foxes (Santa Catalina, San Clemente, and San Nicolas) ~7100 years BP (lineage bolded). Northern California (purple) and southern California (gray) foxes show patterns of climate-induced expansion. Divergence dates were calculated in BEAST v1.7.5 with node bars indicating height 95% highest posterior density. Nodes with * indicate greater than 0.99 posterior probability. Global surface temperature is overlaid in δ°C to show how climatic events may have impacted fox diversity [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118240#pone.0118240.ref055" target="_blank">55</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118240#pone.0118240.ref057" target="_blank">57</a>]. Local temperature curves were not used due to the geographic distance sampled and the short time scale of local curves.</p

Nonsynonymous and Synonymous Substitutions.

<p>Nonsynonymous and Synonymous Substitutions.</p

Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (<i>Urocyon littoralis</i>)

<div><p>Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (<i>Urocyon littoralis</i>), endemic to California’s Channel Islands, and mainland gray foxes (<i>U. cinereoargenteus</i>). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200–7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics.</p></div

Mitogenome Haplotype Summary.

<p>Mitogenome Haplotype Summary.</p

Sampled Localities of Island and Mainland Foxes.

<p>Mainland foxes were sampled from northern and southern California and island foxes were sampled from every island where they occur. The earliest directly AMS ¹⁴C dated island foxes are indicated. The two gray foxes most closely related to the island fox lineage in this study are enclosed in the gray box on the inset map.</p