Phylogenetic tree of life

Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species

Emese Meglécz, Gabriel Nève, Ed Biffin, Michael G. Gardner


Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

Phylogenetic Classification and the Universal Tree

W. Ford Doolittle
Science 25 June 1999:


From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a “universal tree of life,” taking it as the basis for a “natural” hierarchical classification of all living things. Although confidence in some of the tree’s early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If “chimerism” or “lateral gene transfer” cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Genetic Archaeology Finds Parts of Human Genome More Closely Related to Orangutans Than Chimps

ScienceDaily (Jan. 26, 2011) — In a study published online in Genome Research, in coordination with the publication of the orangutan genome sequence, scientists have presented the surprising finding that although orangutans and humans are more distantly related, some regions of our genomes are more alike than those of our closest living relative, the chimpanzee.

The Phylogenetic Tree Topples
2006, American Scientist, Lynn Margulis

What is “evolution?” If evolutionary theory (like the law of gravity or the periodic table of chemical elements) stems from accepted scientific knowledge, why is its teaching controversial? We seek here the source of the controversy: where evidence ends and dogma begins. No honest, rigorous and logical scientist appreciative of hard-earned data from nature disagrees about evolution’s incontrovertible core. Then why are so many who celebrate science as a most, if not the most, effective way of knowing about the world confused by lack of scientific unanimity? None doubts that gravity is the force that accelerates falling bodies, nor are statistics required to predict gas behavior when oxygen and hydrogen are sparked in a closed volume!
Why isn’t everyone convinced that “evolution is a fact, not just a theory” when biologists feel evolution of life from past life is as well established as gravity or the explosive chemical reaction of H2 and O2 to form water? Professionals in geology, biology and especially biochemistry concur: Evolutionary phenomena proffer crucial organizing principles. So what’s the problem? Evolutionary biologists act certain that they know how new life forms originate and complexify. But they don’t.
Evolution, no single fact, depends on four observable processes. First, life requires the incessant flow of energy and matter to survive. Second, a species-specific biotic potential, a measurable quantity, is assignable: the number of offspring that, in principle, can be produced per generation. A human couple has 20 children maximum. A single E. coli bacterial cell that doubles in 20 minutes potentially reaches a population size the weight of the Earth in less than a week! Third, all populations grow at rates more rapid than their immediate environment sustains. What Darwin called natural selection is simply this fact of elimination: Never do 100 percent of the offspring survive to reproduce 100 percent. Finally, offspring are not identical to their parent(s); observable inherited (genetic) change is easily measured.
From these facts Darwin correctly inferred that life “descended with modification” from common ancestors. Overwhelming evidence for this fact (and none against) comes from, e.g., animal behavior, biochemistry, comparative anatomy, ecology, genetics, geochronology, microbiology, physiology, paleobotany, sedimentary geology, virology and zoology, amplifying Darwin’s insight. More than 30 million kinds of life, placed unambiguously into five huge groups—bacteria, protoctists (including 50 phyla of ciliates, diatoms, red and brown seaweeds, slime molds, water molds), fungi, animals and plants—evolved during the past 3,500 million years from our small common ancestors: bacteria. Study of long-chain molecules such as chitin, DNA, lignin, protein, yields spectacular evidence for the shared ancestry of all living matter. Watery cell metabolism (chemical transformation by salt balance, synthesis of proteins and other metabolites always bounded by cell membranes) is incessant whether in aardvark or zoogloea.
But many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern! “No!” I say. Then how did one species evolve into another? This profound research question is assiduously undermined by the hegemony who flaunt their “correct” solution. Especially dogmatic are those molecular modelers of the “tree of life” who, ignorant of alternative topologies (such as webs), don’t study ancestors. Victims of a Whiteheadian “fallacy of misplaced concreteness,” they correlate computer code with names given by “authorities” to organisms they never see! Our zealous research, ever faithful to the god who dwells in the details, openly challenges such dogmatic certainty. This is science.



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