The general theme of our research is the study of evolutionary processes at the genomic level and the use of sequence information to investigate biodiversity, ecosystems, and environmental change. The work in our group spans from molecular evolutionary biology to technology development and bioinformatics.
Over the last two decades, taxonomic marker genes (e.g. DNA barcodes) have been sequenced from a wide range of organisms. For example, the International Barcode of Life Project (iBOL) generated over 5M sequence records from specimens collected across the globe. These efforts have largely been based on Sanger sequencing technology. Recent advances in High Throughput Sequencing (HTS) technologies have revolutionized genomics data generation. DNA Metasystematics (aka DNA metabarcoding, metagenetics, environmental barcoding) aims at gathering biodiversity information through the analysis of selected marker genes from bulk samples such as water, soil, and sediments. This information can be used in addressing a wide range of ecological/evolutionary questions or in applications such as environmental assessment and tracking harmful or endangered organisms. Our lab pioneered DNA metasystematics for the analysis of benthic macroinvertebrates used widely as bioindicators of aquatic ecosystems. We further developed this approach for the analysis of tropical insects and their associated microbes collected passively through Malaise traps. We are now developing and using DNA metasystematics in various ecological and environmental investigations from tropical soil to boreal wetlands.
Comparative transcriptomics provides tremendous potential for investigating how species respond to environmental change from individual physiological scale to ecological and evolutionary scales. Given recent advances in HTS technologies, RNA sequencing has become a feasible approach for large-scale analysis of transcripomes. Whole or targeted transcritpomics (e.g. genes involved in certain pathways) can be applied on large sample sizes across a broad phylogenetic spectrum. We are developing comparative transcritpome-based approaches mainly for non-model organisms (e.g. aquatic bioindicator species) to gain insights on evolution of transcriptomes as well as understanding molecular responses at ecological scale. For example, we recently developed a targeted transcritpomics approach to investigate exposure to polychlorinated biphenyls (PCBs) and tested this approach in mayflies.
Bioinformatic approaches for biodiversity genomics data
We have been involved in developing and testing taxonomic assignment approaches for various taxonomic groups and marker genes and a DNA metabarcoding sequences analysis pipeline, which integrates all aspects of NGS analysis from sample tracking to data interpretation through statistical and visualization tools. We have investigated and developed tools to enhance analysis of metabarcoding and biodiversity genomic data through machine-learning methods and refined analysis.