Biodiversity Genomics Research Theme
Since 2006, our group (have) coordinate(d) >150 de novo sequenced genomes of non-model animals, including many mammals, birds, reptiles, amphibians, fishes, and insects. Particularly, our group initiated the comparative bird 10K (B10K) genome project aiming to collect and integrate genomic, ecological, life-historical, and morphological data for all 10500 extant bird species (b10k.genomics.cn). This initiation was built on the success of the avian phylogenomic project was published as a special issue (8 papers) of the journal Science on 12th December 2014, and another 34 papers elsewhere (avian.genomics.cn/en). Recently, together with other international researchers, we launched another large-scale genomics project, the Global Ant Genomics Alliance (GAGA), which has the ambition to genome- sequence representative species of every ant genus worldwide (antgenomics.dk)
- Genome-scale tree-of-life reconstructions
The reconstruction of phylogenetic relationships is most fundamental for understanding the evolution of phenotypic diversity. However, the traditional phylogenetic methods based on morphological data or partial genomic sequences often produce incongruent tree topologies, which mainly due to the incomplete lineage sorting (ILS), hybridization after speciation, nucleotide base composition biases, or insufficient data. The availability of full genome sequences for multiple species allows us to study the evolutionary history of species at an unprecedented scale of resolution. Our group has successfully applied this phylogenomic approach to bats (Science 2013), turtles (Nature Genetics 2013), and tree shrews (Nature Communications 2013) and we recently completed an analysis of the deep evolutionary relationships in birds based on 48 genomes, representing all major avian lineages (Science 2014). We propose that the phylogenomic approach with full genome data should be considered as a golden standard for future tree-of-life construction.
- Unraveling associations between genomic variation, life history adaptations, and ecological niches
An important goal of eco-evo-devo is to address the genetic basis underlying life-history responses of organisms to their natural environment. The B10K and GAGA projects, which focus on birds and ants, representing two of the most successful animal lineages worldwide that occupy all the major ecological niches on land, provide an unprecedented opportunity to address this fundamental question. We have now completed the genome sequencing for over 300 bird species covering all families in the avian class and are making rapid progress with next level to cover the genomes for all 2250 bird genera in the coming three years. The GAGA consortium has been initiated this year and will generate the genomes for at least 300 ant species covering all ant genera. Substantial life-histories and ecological databases have already been collected by key collaborators for both these lineages, offering unique opportunities for examining correlations between genomic evolution and ecological and life-history traits at the global level.
The new phylogenetic trees based on near complete genomes will serve as a backbone to remap the distribution of key phenotypic traits across the branches. Together with the wealth of biological data, it will allow us to draw on state of the art comparative genomic analyses that can accurately identify the typical genotypes associated with major life-historical traits, examine the genomic regions that respond to natural selection, and to explore the mutations underlying convergent evolution of widely distributed phenotypic traits that mediate adaptation to extreme environments. The full genome sequences will also allow us to obtain whole genome heterozygosity information and use that for inferring the demographic history for each species throughout the most recent 0.5-1 million years. This will enable us to add novel angles to understanding interrelations between environmental change and overall biodiversity and distribution patterns of birds or ants, which will facilitate predicting the effects of ongoing climate change, the spread and impact of invasive species, and habitat alteration.
- Global patterns of animal-microbiome symbiosis
All multicellular life is dependent on microbial symbionts in the guts and often also in other organs, which has led to the so-called ‘holobiont’ concept, referring to the combined genotypes of an animal host and its associated microbes. While food-processing functions of gut microbes are increasingly documented, there are likely to be other key symbiotic microbes essential to social and sexual behavior, implying that the holobiont might be a fundamental unit of co-evolutionary change. Recent breakthrough metagenomic studies have profoundly enriched our functional knowledge of the microbial diversity of humans and a few other model organisms, but systematic attempts to study animal-microbe symbioses at a global comparative phylogenomic scale are still lacking.
Due to their global distribution and recent discoveries of food-induced microbiome specialization, the ants are excellent models for examining host-symbiont interactions. The GAGA consortium provides an excellent platform for my collaborators and me to obtain world-wide ant samples to address the generality of such patterns. The high throughput sequencing data for the ant genomes will also allow us to uncover the diversity of the microbes associated with ants. We will exploit these data and start drawing the first phylogenetic landscapes of taxonomic composition of microbes across the ant genera.
- Genome evolution and animal adaptation
In addition to resolving macroevolutionary tree-of-life patterns of genomic evolution, structural genomes are also important for obtaining insight in fundamental mechanisms of animal adaptation to specific environment. My group has used high-throughput genome sequencing methods in biodiversity studies, often targeting species with unique biology to explore the degree to which key adaptations and their evolutionary history could be understood via genome-wide scans for signatures of selection on specific genes. For instance, by comparing the genomes of two distantly related bats with those of other mammals, we revealed that DNA damage checkpoints and NF-κB pathways have been under strong positive selection, possibly related to the origin of flight in bats and the need for strong immune systems (Science 2013). We also genome sequenced conservation icons (giant panda, polar bear, African lion, etc) and addressed domestication histories (e.g. rice and pigeon) with genomic tools. This has produced 40 publications so far, mostly in high profile journals such as Nature or Science. This type of work does not remain limited to genomic comparisons at the DNA level, but also routinely uses transcriptome and epigenomic profiling techniques to study the dynamics of gene-expression and regulation to understand how environmental factors affect the genetic pathways.