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We are interested in understanding the general pattern and evolutionary history of biodiversity. Insects are major players in various ecosystems, acting as herbivores, predators, parasitoids, and pollinators. They also serve as hosts, harboring a well fortune of microbial diversity, which can be essential to the survival of the insects or bringing massive damage to crops and forests. By studying how these systems interact and evolve, we hope to learn some of the most intriguing questions in evolutionary biology and to contribute to the improvement of human's well-bing. 

Evolution of insects
Biodiversity genomics

Phylogenomics: As one of the most diverse groups of metazoan organisms, insects play a pivotal role in most non-marine ecosystems and many insect species are of enormous economical and medical importance. Unraveling the evolution history of insects is essential for understanding how organisms in terrestrial and limnic environments have evolved. We are interested in deep-level phylogenies of insects, with a special focus on Trichoptera (caddisflies). Nuclear orthologous genes at the whole-genome level, which are generated by transcriptomic and hybrid-enrichment methods, are used to reconstruct the backbone phylogeny of insects (inter-ordinal and superfamily levels). Mitochondrial DNA barcodes (COI) and nuclear rDNA (28S) are employed to add leaves to the Tree of Insects.

Evolution of complex traits: Insects are among the most successful groups, occupying nearly all available ecological niches. Many of their adaptive features are related to complex traits, e.g., ability to fly, secondary adaptation to freshwater. Yet the genomic mechanisms associated with these adaptive features remain largely unknown. The 1KITE, as well as many on-going insect phylogenetic studies, is elucidating the evolutionary history (topology and time) for the insects and creates an enormous gene database, many of which are associated with functions. We are particularly interested in learning how did these functional genes evolve during major adaptation events within insects. Genes generated from transcriptomic and genomic studies are used in comparative genomic analyses.

Host-microbiota network

Bee-microbe system: microbial communities associated with hosts have been proven critical for many essential functions of the host, e.g. general health, basic nutritional efficacy, resilience to external stress, etc. The honeybee-gut microbe system provides an ideal model for the understanding of host-microbe interactions. The bee gut contains a much simplified (compared to human) but conservative microbial community that is inherited across generations via their fascinating social network, a mechanism that none of the current model systems possess. On the other hand, the bees provide critical pollination services to various ecosystems and are facing massive threats globally. Understanding how members of this network interact will likely improve the health of the host and contribute to bee conservation and management, as well as the understanding of more complexed gut systems. 

Metabarcoding: As the result of successful adaptations, insects account for more than 60% of all described species. The distribution and dynamics of insect diversity are critical components in ecology and biodiversity studies. On practical fronts, these features also provide important evidence for assessing habitat quality and management efficacy, e.g., bio-monitoring, bio-assessment. My team has been developing new methodologies based on high-throughput sequencing and bioinformatics, with a goal to characterize biodiversity in a rapid, accurate, and cost effective way. In particular, we have made breakthroughs in applying mitochondrial metagenomics using a PCR-free approach, which effectively reduces taxonomic biases introduced by target gene amplifications. Our current research involves biodiversity assessment using “insect soups” and construction of pollination networks using pollen metabarcoding.

DNA barcoding, the use of standard, short DNA fragments in species identification, provides an alternative approach in characterizing biodiversity. The International Barcode of Life (iBOL) project has constructed comprehensive DNA barcode libraries for many organismal groups. In 2007, Zhou and collaborators initiated the Trichoptera Barcode of Life project, which now has barcode coverage for nearly 1/3 of known caddisfly species (15,000 globally), covering all extant families and 2/3 genera. This collaborative project contains barcode references for many common caddisfly species of the world, facilitating species identification where morphology proves difficult (immature, female). As part of integrative evidence, DNA barcodes have revealed many cases of cryptic diversity in Trichoptera and accelerated larval identification and description.

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