DNA barcoding of the maritime shrew, Sorex maritimensis Smith: using DNA sequence of the cytochrome oxidase subunit 1 gene in taxonomic and field studies of a Canadian endemic mammal.

In 2002, the maritime shrew was elevated from a subspecies, Sorex arcticus maritimensis, to a distinct species, Sorex maritimensis Smith, based on sequence divergence for the mitochondrial cytochrome b gene. The maritime shrew is a Canadian endemic found only in Nova Scotia and New Brunswick. It has been identified as one of the most susceptible vertebrate species in Nova Scotia to the effects of global warming. The first part of this thesis tests the hypothesis that Sorex maritimensis is a distinct species by employing DNA barcoding theory and cytochrome oxidase subunit 1 (cox1) gene sequences. A variety of tree- and distance-based approaches are used including recently developed methods to delineate species from DNA sequence data such as the Poisson Tree Processes (PTP) method, the Automatic Barcode Gap Discovery (ABGD) method, the Assemble Species by Automatic Partitioning (ASAP) method, the General Mixed Yule Coalescent (GMYC) method, as well as multi-rate Poisson Tree Processes (mPTP), and Bayesian Poisson Tree Processes (bPTP). All analyses except mPTP and bPTP support the hypothesis that S. maritimensis is a distinct species. In addition, the rate of divergence for cox1 vs. cyt b was examined for eleven species of Sorex shrews which showed an atypically low rate of divergence for the cox1 gene between S. maritimensis and S. arcticus. The second part of this thesis is an optimization of a non-invasive method to identify shrew species from fecal samples using shrew-specific primers to amplify a short, ~120 base pair section of the cox1 gene. This approach uses feeding tubes baited with dead insect larvae to collect shrew feces, which are a source of DNA for species identification. This technique holds promise for more precisely mapping the distribution of this relatively rare shrew in Nova Scotia and surrounding regions.