Yin-Long Qiu

University of Massachusetts, Amherst

The research in my lab lies at the interface of organismal phylogenetics and evolutionary genomics. We employ molecular genetic techniques and bioinformatic tools to investigate evolution of genes and genomes, and use this information to infer phylogenetic history of organisms, in particular basal angiosperms and basal land plants.

Phylogeny of Basal Angiosperms. We have been analyzing DNA sequences of several genes located in mitochondrial, chloroplast, and nuclear genomes from a large number of basal angiosperms, to reconstruct the diversification patterns of early angiosperms. Our strategy is to boost the signal/noise ratio rather than to try to optimize a particular model for phylogenetic analysis, which typically involves a unpredictable number of poorly understood factors that generate homoplasy. Through a previously NSF-DOE-USDA funded coordinating project (Deep Green), we collaborated with Doug and Pam Soltis at Washington State University and Mark Chase at Royal Botanic Garden at Kew, and identified an assemblage of taxa dubbed ANITA (Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya) as the earliest living angiosperms. We are currently amassing an even larger data set, nine genes in total and approximately 16 kb from ~100 species, to resolve the remaining issues in basal angiosperm phylogeny, in particular, the origins of eudicots and monocots. With so much sequence data collected across all three genomes and from a diverse and dense taxonomic sampling of basal angiosperms, many of which exhibit disjunct distribution patterns with well dated geological separation, we are also exploring molecular clocks to estimate the time of origin of angiosperms.

Phylogeny of Pre- and Early Land Plants and Organellar Genome Evolution. The emergence of land plants (embryophytes) approximately 480 million years ago was one of the major events in the history of life, which led to major changes in the earth's environment (e.g. reduced atmospheric CO2 level and consequently lowered earth's surface temperature), initiated development of the entire terrestrial ecosystem, and set the stage for evolution of other terrestrial organisms, including ourselves. Yet, what represents the algal ancestor of land plants and how the extant basal land plant lineages (i.e. liverworts, mosses, hornworts, lycopods, Equisetum, Psilotaceae, ferns, and seed plants) are related to each other remain as unresolved issues. Here, we take a different approach than in the case of angiosperms to attack the problem - to search for rare events of genome structural evolution that occur on a larger scale than single nucleotide substitutions: gain and loss of introns, transposition of introns, change of intron splicing patterns, formation and disruption of gene clusters, and loss of genes. This strategy takes advantage of the unique evolutionary histories of the chloroplast and mitochondrial genomes, which experienced dramatic structural changes during pre- and early land plant evolution. Previously, we have identified three introns that are present (with losses) in all land plant lineages but entirely absent in liverworts and green and red algae. Thus, these data suggest that liverworts had already diverged when the introns were gained in the common ancestor of all other land plants, and consequently they represent the earliest land plants. Currently, we are sequencing the entire mitochondrial genome from the hornwort Anthoceros agrestis to identify whether many of the angiosperm specific introns are present at this early stage of land plant evolution. We are also interested in knowing whether many of the short repeat sequences, which are commonly found in angiosperm mitochondrial genomes and possibly related to retrotransposons, are present in the hornwort genome, as they may be implicated in causing rapid genome rearrangement in land plant mitochondrion. We are also trying to identify phylogenetic distribution patterns of the set of introns found in Marchantia mitochondrial genome. On the chloroplast side, we are investigating distribution of several gene clusters and their intron content in several species that represent major charophyte lineages. We hope that the data gathered here, in synergy with large scale DNA sequence analyses, will clarify diversification patterns before and after the emergence of land plants, and also help us to gain understanding of organellar genome evolution when plants invaded the land.