Tree of Life

Western religion adopted the concept of a “Great Chain of Being”, which was borrowed from the ancient Greek Neoplatonists, in particular from Aristotle. The concept held that everything was part of a divinely orchestrated hierarchical order with God above all, followed by angels, humans, lower animals, plants, and so on down to inanimate objects. This notion persisted through the works of 17th and 18th century philosophers. 16th century illustration of "Great Chain of Being" concept From Didacus Valades, Rhetorica Christiana (1579).

Almost all later philosophers and scientists abandoned the notion in the face of a greater understanding of the nature of matter based upon empirical evidence. However, remnants of the concept persist in theology and in creationism. Scientific evidence supports the view that life inheres self-replication, and that living and extinct organisms are interrelated on a branching “Tree of Life”.

Tree of Life Project
"One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved."

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Tree of Life or Fuzzy Bush of Life

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Peter Gogarten is a professor of molecular and cell biology at the University of Connecticut. During his presentation at the World Summit on Evolution, he asked 'Is the 'Tree of Life' a Tree?'

Horizontal gene transfer between organisms allows us to understand genealogical relationships in prokaryote evolution. 'Over long periods of time gene transfer makes organisms existing in the same environment more similar to one another. This is most clearly seen in the case of organisms that live in environments that are otherwise inhabited by distant relatives only.' Thus, Gogarten concluded, 'the boundaries between prokaryotic species are fuzzy. Therefore the principles of population genetics need to be broadened so that they can be applied to higher taxonomic categories.'

See also: Genomes and the Tree of Life Tree of Life Horizontal Gene Transfer in Prokayotes

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Comparing Gene Trees and Genome Trees: A Cobweb of Life?

PLoS Biology: Comparing Gene Trees and Genome Trees: A Cobweb of Life?: "The tree of life has long served as a useful tool for describing the history and relationships of organisms over evolutionary time. One species is represented as a branching point, or node, on the tree, and the branches represent paths of descent from a parental node. The tree diagram carries an implicit assumption that genes are transferred vertically, from parent to child, and that all the genes in a new species come from the ancestral species. In theory, one should be able to trace the origin of each gene in a species back to its ancestor. In practice, however, the ancestral gene is rarely available, so researchers look for the gene in a closely related species. (These similar genes, which diverge slightly after a speciation event, are called orthologs.)

But as the tools of genome analysis became more refined, searches for similar genes sometimes turned up sequences that belonged to a species on a different branch of the evolutionary tree. Clearly, vertical gene transfer was not the only mechanism of genetic transmission. Organisms, it turns out, can acquire genes from non-ancestral species through a mechanism called horizontal gene transfer (HGT).

Such genetic exchanges, most common among bacteria and other microbes, are not represented in the tree of life—no single branch connects the two unrelated species. Initial studies suggested that HGT events were extremely common, prompting some to say it was time to replace the tree with a netlike diagram. Other studies have since suggested that methods used to calculate HGT overestimated its frequency: researchers detect HGT events by finding inconsistencies between gene trees and organism, or whole-genome, trees, but statistical errors can artificially increase the number of HGT events."
(2005) Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3(10): e347

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Genomes and the Tree of Life

EVOLUTION: GENOMES AND THE TREE OF LIFE: "Although we have not yet counted the total number of species on our planet, biologists in the field of systematics are assembling the 'Tree of Life' (1,2). The Tree of Life aims to define the phylogenetic relationships of all organisms on Earth.

Computer simulation studies (5) recently showed that, contrary to the prevailing view, phylogenetic accuracy depends more on having sufficient characters (such as amino acids) than on whether data are missing. Clearly, building a super-tree allows for an abundance of characters even though there are many missing entries in the resulting matrix." K.A. Crandall and J.E. Buhay (Science 2004 306:1144)

5. J. Wiens, Syst. Biol. 52, 528 (2003)

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