The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)


Addressing the unresolved phylogeny of Leishmania: a next-gen and ancient DNA approach

KELLY M. HARKINS.

School of Human Evolution and Social Change, Arizona State University

Thursday 11:15-11:30, Ballroom A Add to calendar

Leishmania, a genus of parasites transmitted to human hosts and mammalian/reptilian reservoirs by a sandfly vector, is the causative agent of the human disease complex leishmaniasis. Despite the increasing availability of genome sequence data, evolutionary relationships within the genus Leishmania and its origins are the source of ongoing debate, reflected in unresolved phylogenetic and biogeographic reconstructions. Given recent epidemics and the global increase in disease incidence, sequence projects often focus on human pathogenic taxa. While invaluable for clinical research, this biased sampling strategy limits comprehensive examination on the genus level, creating obstacles for well-supported phylogenetic analyses. This project addresses the sampling bias by sequencing (Illumina HiSeq 2x100bp) thirteen new genomes, broadly representing poorly/unclassified taxa, those only found to infect reptiles and mammals, and new human pathogenic species. De-novo assembly (SOAPdenovo) is performed for four species too divergent from reference data. Coupled with previously available genomes, these new data are used in phylogenomic analyses to infer evolutionary relationships and test hypotheses about the origins and dispersal of leishmaniasis. Preliminary reconstructions using maximum likelihood and Bayesian methods with publicly available sequences indicate that missing data (species with few gene sequences) and an improper outgroup when inferring a genus-wide phylogeny contribute to poor tree resolution. Including loci on a genomic scale with a more representative sample creates higher support of the phylogenetic inferences. The observable genetic diversity also informs the design of a Leishmania-specific enrichment array, currently being used to target the parasite in archaeological remains from northern Chile.

This research was funded by the School of Human Evolution and Social Change Graduate Research Award and NSF DDIG 1232582.

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