From Douglas E. Soltis, Michael J. Moore, Emily B. Sessa, Stephen A. Smith, and Pamela S. Soltis, Using and navigating the plant tree of life, at Amerian Journal of Botany 7 April 2018 https://doi.org/10.1002/ajb2.1071 (open access) :
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.
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.
Since the last American Journal of Botany Tree of Life issue in 2004 (Palmer et al., 2004), the rise of high throughput sequencing has both revolutionized our understanding of the processes that have generated plant diversity and, to a great extent, confounded our attempts to reconstruct phylogeny by unlocking the evolutionary history of the plant nuclear genome.More.
In short, unlocking the genome raised heck with the fabled Tree of Life. Look, it’s okay if things are a mess, as long as we admit it and confront honestly what wrong assumptions got us here and how to get out again. Or, in vulgar English: If we are in a hole, let’s stop digging and rethink.
See also: Monkey hybrids are monkeying with the biological species concept
The non-tree of life.