We may be in the middle of an insect mass extinction. The Rocky Mountain locust (Melanplus spretus), was once dominant in the North American ecosystem. It was found in western Canada and the United States until the end of the 19th century. It occurred in incredible masses. One sighting in 1875, is believed to be the biggest aggregation of insects on record with 12 trillion individuals. However, in 1902, the last alighting of this species was recorded in southern Canada. Questions have been raised about both the causes for its extinction and the status of the locust. My project involved genomic comparison of related extant locust species, to those generated from museum data. In particular, I aimed to identify bioinformatic artefacts inherent to museum samples, which may provide direct comparisons between the two data sets.
Due to the low coverage of the museum samples of the extinct species and draft genome for the present-day samples, I filtered and optimize the quality of the samples by vcftools. However, under the visualization under Geneious Prime, there is many potential misalignments present in the museum samples due to the short fragment. Then I genotyped the museum sanguinipes and spretus individuals using samtools based on the bam filed offered at all the markers in the reference. To further improve the quality of samples, I calculated the informativenss of each single nucleotide polymorphisms and selected the most informative loci at various standard which was used for the phylogenies tree generation. The draft phylogenies tree was generated by the package “SNPRelate”, which illustrated that the museum samples are grouped together, indicating that the artifacts are driving the data.
Apart from the finding of the research, I am grateful to Sasha’s suggestion and had an opportunity to attend the three-day SNPs in population- and phylo-genomics workshop in University of Canberra, which impressed me a lot about those excellent researchers in evolution field. I am immensely grateful to my supervisors, Sasha (Alexander) Mikheyev, who provided the patient guidance, encouragement during my research. I have been very lucky to have supervisors who cared so much about my work, and who responded to my questions so promptly, although I am extremely new in this area.