Speciation genomics   

Major insights into the genetics of speciation is crucial for understanding the origins of biodiversity. Speciation is usually a gradual process that can occur despite widespread hybridization between the emerging species. As a result, the genomic architecture of speciation is generally very complex, with the patterns of genetic divergence and the genealogical relationships in a group of species differing from one part of the genome to another. Given recent high-throughput sequencing and computational advances that allow genome-wide analyses, we aim to understand: 1) the relative roles of selection, introgression, drift, demographic processes, recombination and the genome structure in shaping heterogeneous patterns of diversity and divergence within and between recently diverged species. 2) the consequences of both ancient and contemporary hybridization events, and how does natural selection shape introgression across the genome between the emerging species.

Genetic basis of adaptive evolution     

Understanding the molecular mechanisms underpinning rapid phenotypic responses to environmental changes is central to evolutionary biology. Many perennial plants, such as forest trees, have wide geographic distributions and are thus exposed to a broad range of abiotic and biotic stresses, making adaptation to diverse environmental and climate conditions crucial in these species. By integrating field experiments, phenotypic measurements, population genomic approaches, and molecular work, we seek to understand: 1) How frequent is adaptive evolution? How natural selection shape neutral variations in natural populations over time? 2) Does adaptation generally involve mutations of large or small phenotypic effect? Does rapid adaptation tend to involve new mutation or use standing genetic variations? 3) Are adaptive mutations typically coding or mostly regulatory? How natural epigenetic variation (e.g. DNA methylation) interplay with genetic variation (e.g. transposable elements) to impact patterns of gene expression and thus phenotype? And how important is epigenetic variation for rapid adaptation to the environmental changes?

Genome evolution     

The advent of next- (short-read) and third-generation (long-read) sequencing technologies can generate de novo genome assemblies of many species with unprecedented quality and affordable cost. By generating and comparing high-quality reference genome assemblies from several recently and distantly diverged species in a phylogenetic framework, a long-term goal is to test for the evolutionary forces that drive evolution of the genome itself. Particular interests include: 1) Discover both conserved and novel loci likely to be responsible for core biological functions, phenotypic differences, environmental adaptations, and many other lineage-specific characteristics. 2) As transposable elements (TEs) typically make up a large proportion of eukaryotic genome, we are interested to test how TEs drive genome evolution ranging from small-scale structural changes to large-scale karyotype differences between lineages of closely related species, whether different families and classes of TEs have variable activity across lineages, and how TEs associated with epigenetic modifications rewire the gene regulatory network through evolutionary time. 3) Investigate how do newly evolved genes originate (e.g. de novo, duplication or horizontal gene transfer), spread, and contributed to adaptive evolutionary innovation, how do these new genes acquire regulatory sequences for proper spatial and temporal expression, and what genetic and evolutionary mechanism govern these processes.