QE: Can Next Generation Sequencing help with obtaining ecological information about endangered species? (Amrita Srivathsan, 9 Dec 2011: 10.00am)

Department of Biological Sciences, NUS
Qualifying Examination

Speaker:     Amrita Srivathsan  (Graduate Student, Dept.of Biological Sciences, NUS)
Date:          9 December 2011, Friday
Time:         10am
Supervisor:  Prof Meier, Rudolf


When an endangered species is elusive and rare, obtaining ecological data by field observations can be difficult and time consuming. However, this information can be supplemented by evaluating fecal samples that contain the DNA of the endangered species (from shed cells from the gut lining), food items (incompletely digested by the consumer), parasites, and microbes (residing in the intestine). Using next generation sequencing, one can thus simultaneously obtain information on the feeding ecology, population genetics, parasites, and the gut microbiome of the endangered species. I propose to use this approach to study fecal samples from the critically endangered Singapore population of the banded leaf monkey (Presbytis femoralis).

My study started by testing existing techniques that are used for species identification based on DNA barcodes and I am currently developing new alignment-free methods. I then tested the suitability of different genes to deliver species-level identifications for plants. Currently, I am generating a DNA barcode database for ca. 250 species of trees and lianas in the habitat of the banded leaf monkeys. My study will conclude with next generation sequencing runs for the fecal samples and the analysis of the data. The data will provide new insights into the diet of banded leaf monkeys. I will also be able to use these data for developing microsatellite markers and understanding the parasite and microbial communities of this endangered population.


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