Species Identification in Forensic Casework using Proteomics

Title: Species Identification in Forensic Casework using Proteomics

This proposal develops and assesses tools for law enforcement to identify species from the hairs of processed furs using proteomic phylogenetics. Currently, recovery of amplifiable DNA for law enforcement species identification is limited for processed source materials, likely due to the extreme chemical conditions involved in fur manufacturing. Morphological analysis of hair shafts is limited by the restricted number of trained practitioners, sometimes poor species resolution, and controversial nature of microscopic comparisons. Here, we propose to use phylogenetic information in proteins to close this major enforcement gap. Protein is more stable than DNA, and thousands of protein sequences can be extracted from a single processed fur hair shaft, including sequences with phylogenetic sequence variants. With awareness of the growing and broader impact of wildlife crime, and its environmental impact on the environment, there is increased pressure on law enforcement. Development of robust forensic tools is required for full enforcement of the federal Endangered Species Act and imminent Californian Fur Ban. Therefore, this project will develop and assess proteomic methods to identify and resolve two groups of fur-bearing mammals: 1) Felidae fur species, a major trafficking target, and 2) commercially prominent fur-bearing mammals that comprise the national fur trade. Proteomic analysis will occur at three levels: identification of protein profiles using species-specific reference proteomes, development of a streamlined bioinformatic workflow using composite reference proteome databases, and mass spectrometry spectral comparison alone. To obtain necessary high-quality species-specific reference proteomes, nineteen existing twenty genomes will be annotated for protein sequences and the essential coyote genome will be obtained and assembled for annotation as well. Proteomic data will be collected from the fur hair of 44 species. The project phases will each contain performance assessments and result in submission of novel gene and protein sequences to publicly available national databases. The ultimate goal of this project is to develop protocols to identify legally-relevant species in casework where amplifiable DNA is not normally recovered, thus providing a template for expansion of proteomic phylogenetic technology to other species that require identification for law enforcement purposes.