The promise of genomics for a “next generation” of advances in higher-level legume molecular systematics

Abstract

The years since the first International Legume Conference in 1978 have seen a veritable revolution in molecular phylogenetics. The first two volumes of Advances in Legume Systematics series, which were based on that conference, contained no information on DNA-level variation. The next volume in the series, in 1987, had a chapter on the potential of DNA approaches and results of some early studies that used restriction enzyme mapping. The 1990s saw the application of chloroplast gene sequencing to family-level phylogenetic problems that culminated in the studies from the first decade of the present century that have provided the working phylogenetic hypotheses for the family. The first full legume nuclear genome sequences have appeared more recently, and, fueled by the advent of “next-generation” sequencing in the late 2000s, there is now a flood of genomic and transcriptomic data that is again revolutionizing biology in the way that the molecular revolution did previously. How to take advantage of this opportunity is a key question for legume systematists, particularly its own “next generation”. The mere availability of massive amounts of data does not guarantee that all phylogenetic problems in legumes will be resolved once and for all; “megadata” is not a panacea, and the apparent rapid radiation of the family and its constituent clades represents a serious technical challenge. Moreover, major analytical controversies are simmering, notably between proponents of concatenation – the conventional way to analyze genome-scale data – and those who favor a coalescent-based species tree approach. Assuming that a stable, well-resolved phylogeny based on the nuclear genome is eventually produced, it will be useful not only for classification, but also for addressing questions involving homoplasy, such as the potential multiple origins of nodulation in the family. The rich legacy of the International Legume Conferences, embodied in the Advances in Legume Systematics, is that the increasing refinement of phylogenetic hypotheses serves the full range of comparative studies on the myriad facets of this huge, diverse, and fascinating family.