Using and navigating the plant tree of life
Douglas E. Soltis Michael J. Moore Emily B. Sessa Stephen A. Smith Pamela S. Soltis
First published: 27 April 2018 https://doi.org/10.1002/ajb2.1071
Source/Fonte: One Zoom Tree of Life
Abstract
The “tree of life” has become a metaphor for the interconnectivity and breadth of all life on Earth. It also has come to symbolize the broad investigation of biodiversity, including both the reconstruction of phylogeny and the numerous downstream analyses that are possible with a firm phylogenetic underpinning. Only a few decades ago, the construction of large phylogenetic trees of hundreds of taxa (or more) was considered an impossible task due to the immense computational challenges posed by analyses of large data sets. And no wonder—the number of possible trees that can describe the relationships of just 200 species exceeds the number of atoms in the universe (Hillis, 1996). As a result, building the tree of all named life, including the green plant branch (Viridiplantae)—a major clade with perhaps 500,000 species—has long been considered a grand challenge in biology. However, a perfect storm of algorithm development, increases in computational power, and DNA sequencing improvements over the last decade has not only made the construction of large trees more feasible, but also allowed us to attain some far‐reaching goals—a noteworthy example being the recent publication of a first draft tree of all life (Hinchcliff et al., 2015).
In plant biology, the frequent reconstruction of large phylogenetic trees has had an immense impact on the field. Large trees have helped to resolve deep‐level relationships and resulted in the revision of classifications, including some of the most profound changes in our view of plant relationships over the past 200 years (e.g., reviewed in part by Gitzendanner et al., 2018, in this issue). Large trees have also ushered in a renaissance in the study of conservation, ecology, methods development, crop improvement, genome evolution, and much more. Building the plant tree of life has come to represent the biodiversity equivalent of the human genome project, with numerous and often unanticipated downstream outcomes.
Accompanying these exciting advances are equally significant challenges that remain for the construction of a better and more complete picture of the evolution of plant lineages. In addition to the computational challenges of larger data sets, these include conceptual and methodological barriers. For example, where it was once thought that simply increasing DNA sequence data would increase resolution of relationships, we now understand that increasing data leads to increasing analytical complexity. Furthermore, this complexity is not due solely to limitations in computational power and methodology, but in part reflects the underlying complexity of the evolutionary process and its impact on genomes. Nevertheless, current conceptual and computational limitations present fantastic opportunities for transformative developments in our understanding of plant evolution. In this special issue, we explore many of the uses and challenges of big trees and big data in plant biology. Diverse papers provide overviews of the current status of the green plant tree of life and describe some of the myriad applications of the knowledge of phylogenetic relationships as well as some of the challenges inherent in handling plant phylogenomic data.
FREE PDF GRATIS: American Journal of Botany
