CAREER: Reproductive mode and horizontal gene transfer in nematode worms: Training early career researchers in computational evolutionary biology

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An organism’s DNA comes from two sources: (a) inheritance from parents to offspring, and (b) lateral or horizontal gene transfer (HGT) from other organisms. The evolutionary significance of HGT in eukaryotes is a fundamental open question in biology. Prior to the advent of next-generation genome sequencing HGT was thought to be common in microbes but limited to eukaryotes with endosymbionts and parasites. Published findings over the last ten years have suggested that both ancient and recent horizontal transfer may be common in eukaryotes but pursuing these scientific questions has been hampered by contamination problems in assembled genome sequences and a lack of appropriate methods for identifying HGT across entire genomes. The most significant questions regarding HGT in eukaryotic evolution are now: (a) How does the likelihood of HGT depend on an organism’s ecology and life history?; and (b) What are the consequences of HGT for evolution? This project will develop the methods necessary to pursue these questions, and distribute freely available software packages that will enable other scientific researchers to use these methods to identify HGT. Reference genome sequences and gene annotations will be produced for 50 nematode species and these data will be made publicly available through WormBase and the National Center for Biotechnology Information Sequence Read Archive. This project will integrate research and education by training early career scientists in computational biology and scientific research through a new, innovative mentored summer research experience at the University of Alabama.The evolution of self-fertility and asexuality affects important aspects of a species genetics including levels of genetic variation. Sexual reproduction generates new genetic variants through recombination and affects every aspect of organismal evolution. Self-fertility and asexuality may therefore have consequences for HGT as these organisms may use HGT to generate variation. Conversely, outcrossing organisms with separate males and females may be subject to HGT due to endosymbionts and parasites. This project takes a unique, innovative approach to study the relationship between HGT and reproductive mode across Phylum Nematoda and will result in the development of a conceptual framework linking reproductive mode with HGT. These findings will advance understanding of the significance and role of HGT in eukaryotic evolution. HGT-derived genes will be studied in a functional context and these results will contribute to understanding the patterns of environmental selection shaping HGT-derived genes in eukaryotic genomes. This research will result in important discoveries regarding the ways in which reproductive mode and HGT have shaped genome evolution and contribute novel insights to the broader scientific understanding of how evolutionary processes shape genomic patterns. In order to achieve these objectives this project has four specific goals: (1) Develop bioinformatic methods for separating contaminants from true HGT in de novo sequencing projects; (2) Develop a probabilistic approach for identifying HGT in assembled genome sequences; (3) Utilize phylogenetic comparative methods to analyze HGT in outcrossing, self-fertile and asexual organisms; and (4) Develop a new, innovative summer research program for undergraduates, Computational Research Experience at the University of Alabama (CRE@UA).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.