Understanding the evolutionary patterns in wild drosophila populations: insights from haplotype analysis over two decades

• Grant number: 23/09079-0
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: October 01, 2023
• End date: March 31, 2024
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Rodrigo Cogni
• Grantee: Vitória Horvath Miranda
• Supervisor: John Pool
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of Wisconsin-Madison (UW-Madison), United States
• Associated to the scholarship: 22/12549-6 - Long-Term Stability in Genomic Clines in Natural Populations of Drosophila melanogaster, BP.MS

Abstract

A major open question in evolutionary biology is how species will adapt to climate change. Drosophila melanogaster has proven to be a useful model in understanding evolutionary responses to climate change because of its short generation time and ease of manipulation. However, the majority of studies use pool-seq approaches, which cannot be phased easily. With phased data, we can get haplotype information which can be used to get clearer evidence regarding selection and demographic history of populations. Some examples include the detection of selective sweeps and the inference of local ancestries. Obtaining phased data by sequencing individual diploid flies would require high sample sizes and coverage depths, which could be quite expensive. There are two alternative strategies to gain haplotype information in D. melanogaster: sequencing inbred lines and sequencing haploid embryos. Sequencing inbred lines is not ideal, as even extensively inbred lines can show high levels of heterozygosity. We were able to get haploid embryos by crossing mutant male flies, capable of initiating haploid embryo development, with wild-type sampled females. By sequencing those embryos, we will be able to obtain phased data even with low coverage. We applied this procedure to two new collections made in 2022 in the northern United States. With this data, we will look for selective sweeps and infer local ancestry. With those new analyses, we expect to gather an additional set of robust evidence of recent directional selection that could be linked to climate change. (AU)