As a follow up to my last post on Kleptoplasty in Elysia chlorotica, I want to point out some updates to some of our ideas about the early evolution of life.
Most of us who have ever taken a course in Biology, or even read something on the topic are familiar with the concept of the Tree of Life. The three separate branches or Kingdoms of life that exist today branch separately off of a separate trunk. These three branches are the Bacteria and Archaea—single celled organisms that have different enough biochemistry to list them as different Kingdoms—and the Eucaryota, organisms whose cells contain complex structures enclosed within membranes.
Larry Moran has a series where he discusses the demise of the concept of a tree and the movement toward a more weblike structure of life.
In one of his essays, he quotes a presentation from Proceedings of the National Academy of Sciences (USA) on a 2008 paper.
Evolving Views on the Tree of Life
Next to life itself, the origin of complex cells is one of the most fundamental, and intractable, problems in evolutionary biology. Progress in this area relies heavily on an understanding of the relationships between present-day organisms, yet despite tremendous advances over the last half-century scientists remain firmly divided on how to best classify cellular life. Many adhere to the textbook concept of 2 basic types of cells, prokaryotes and eukaryotes, as championed by Stanier and van Niel. Others posit that at its deepest level life is not a dichotomy but a trichotomy comprised of cells belonging to the domains Bacteria, Archaea, and Eukarya, each monophyletic and sufficiently distinct from one another to warrant equal status. The conceptual and practical challenges associated with establishing a genealogy-based classification scheme for microbes have been fiercely debated for decades, and the literature is rich in philosophy and rhetoric.
The genomics revolution of the 1990s brought tremendous optimism to the field of microbial systematics: if enough genomes from diverse organisms could be sequenced and compared, definitive answers to questions about evolutionary relationships within and between eubacteria, archaebacteria, and eukaryotes would surely emerge. More specifically, it should be possible to discern how eukaryotes evolved from prokaryotes (if indeed that is what happened), and perhaps even who among modern-day prokaryotic lineages is our closest ancestor. Unfortunately, with the sequences of hundreds of eubacterial, archaebacterial, and eukaryotic genomes has come the realization that the number of universally distributed genes suitable for global phylogenetic analysis is frustratingly small. Lateral (or horizontal) gene transfer has shown itself to be a pervasive force in the evolution of both prokaryotic and eukaryotic genomes, and even if a “core” set of genes can be identified (and there is much debate on this issue), how confident are we that the phylogenetic signal in these genes reflects the vertical history of cells? How meaningful are sequence alignment-independent, gene content-based approaches to resolving the “tree of life” ? To what extent is a “net of life” a more accurate and useful metaphor for describing the full spectrum of life on Earth?
In simple terms, the newer concept, based upon genetic analysis, proposes multiple cells as origins of life, and frequent lateral genetic transfer over time. Thus a “Web of Life” supports the genetic data more accurately than the traditional tree.