Research
My research focuses on how genome evolution contribute to the phenotypic evolution and diversification of eukaryotes. The aims of my ongoing and future research are to investigate (1) the genomic basis of evolutionary innovations; (2) the processes of duplicate gene retention and loss; (3) Why polyploidy (genome duplication) is rarer in animals relative to plants.
Genomic Basis of Evolutionary Innovations
Key innovations are novel traits that permit a lineage to occupy new niches and diversify; Examples include wings in insects and flowers in angiosperms. How these novelties evolve remains a fundamental question in evolutionary biology. My recent postdoctoral research was focused on understanding the molecular basis of an evolutionary innovation in leafhoppers called brochosomes (Li et al. 2022, Mol. Biol. Evol.). By generating a chromosome-level genome assembly of a leafhopper, and analyzing transcriptomes and proteomes of organs that produce brochosomes, I found candidate genes that are likely important for brochosome production. Overall, my research explores how evolutionary novelties arise in leafhoppers, with evidence for a combination of novel gene evolution, tandem duplication, and horizontal gene transfer.
Duplicate Gene Retention and Loss
Gene and genome duplication is recognized as a significant source of genetic novelty in eukaryotes and important for their ecological and evolutionary diversification. But whether duplicate genes, called paralogs, contribute to evolution and diversification of life depends on whether the paralogs persist in the face of ongoing mutations. Although some paralogs are lost very quickly, others persist for millions of years. Multiple hypotheses such as Dosage Balance Hypothesis and neo/subfunctionalization have been proposed to explain duplicate gene retention. In contrast, how genes are deleted in the genome is understudied. In a review paper (Li et al. 2021, Annu. Rev. Plant Biol. ), I highlighted major knowledge gaps in this research area. I aim to continue understanding the differences in gene detection mechanisms and rate of gene loss between major lineages of vascular plants and between plants and animals.
Polyploid Incidence
Theodosius Dobzhansky stated that the rarity of polyploidy in animals compared to plants constituted the biggest known difference between the evolutionary patterns in these two kingdoms. Polyploidy is common in plants, with nearly 15% and 31% of speciation events in flowering plants and ferns, respectively, being attributed to recent WGDs. Although polyploidy has been found in some animal lineages, it has long been observed that polyploidy is much rarer in animals than in plants. During my PhD, I studied the incidence of polyploidy in land plants and hexapods, two of the most diverse groups of eukaryotes. These studies set the stage for future analyses to test hypotheses about the difference in incidence of polyploidy between plants and animals. In collaboration with Dr. Mike Barker's lab at the University of Arizona, I plan to enhance our understanding of reason(s) why polyploidy is rarer in animals compared to plants.
Genomic Basis of Evolutionary Innovations
Key innovations are novel traits that permit a lineage to occupy new niches and diversify; Examples include wings in insects and flowers in angiosperms. How these novelties evolve remains a fundamental question in evolutionary biology. My recent postdoctoral research was focused on understanding the molecular basis of an evolutionary innovation in leafhoppers called brochosomes (Li et al. 2022, Mol. Biol. Evol.). By generating a chromosome-level genome assembly of a leafhopper, and analyzing transcriptomes and proteomes of organs that produce brochosomes, I found candidate genes that are likely important for brochosome production. Overall, my research explores how evolutionary novelties arise in leafhoppers, with evidence for a combination of novel gene evolution, tandem duplication, and horizontal gene transfer.
Duplicate Gene Retention and Loss
Gene and genome duplication is recognized as a significant source of genetic novelty in eukaryotes and important for their ecological and evolutionary diversification. But whether duplicate genes, called paralogs, contribute to evolution and diversification of life depends on whether the paralogs persist in the face of ongoing mutations. Although some paralogs are lost very quickly, others persist for millions of years. Multiple hypotheses such as Dosage Balance Hypothesis and neo/subfunctionalization have been proposed to explain duplicate gene retention. In contrast, how genes are deleted in the genome is understudied. In a review paper (Li et al. 2021, Annu. Rev. Plant Biol. ), I highlighted major knowledge gaps in this research area. I aim to continue understanding the differences in gene detection mechanisms and rate of gene loss between major lineages of vascular plants and between plants and animals.
Polyploid Incidence
Theodosius Dobzhansky stated that the rarity of polyploidy in animals compared to plants constituted the biggest known difference between the evolutionary patterns in these two kingdoms. Polyploidy is common in plants, with nearly 15% and 31% of speciation events in flowering plants and ferns, respectively, being attributed to recent WGDs. Although polyploidy has been found in some animal lineages, it has long been observed that polyploidy is much rarer in animals than in plants. During my PhD, I studied the incidence of polyploidy in land plants and hexapods, two of the most diverse groups of eukaryotes. These studies set the stage for future analyses to test hypotheses about the difference in incidence of polyploidy between plants and animals. In collaboration with Dr. Mike Barker's lab at the University of Arizona, I plan to enhance our understanding of reason(s) why polyploidy is rarer in animals compared to plants.