New name for evolution, "The Bacteria Diet"

I would like to add this paper to the mix:

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Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10254-60.

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Constructing primate phylogenies from ancient retrovirus sequences.
Johnson WE, Coffin JM.

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Department of Molecular Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA.

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Abstract
The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.

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Full paper here

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In this paper they demonstrate that ERV's establish shared ancestry between humans and other apes by testing this hypothesis:"Given the size of vertebrate genomes (>1 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). "So they look at the ERV placement in genomes and look at the species distribution of these ERV's. They find that they are found in the species and genomic positions that the theory of evolution predicts they should be in. So this paper first demonstrates shared ancestry.It then goes on to demonstrate the accumulation of random mutations in these ERV's by two different methods. First, it shows the divergence of the overall ERV sequence:"as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species."As expected, the divergence of provirus sequence matches the pattern of species distribution as the theory predicts.They then look at LTR divergence. Each provirus contains two repeat regions at either end of the genome. When the virus inserts it copies one of these repeat regions which results in two tandem repeat regions that are identical. The theory predicts that these two repeat regions will diverge over time within the same ERV, with the divergence dependent on the time spent in the genome. As stated in the paper:"Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. ​(Fig.11A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication."So this paper has some very nice pieces of evidence pointing to both common ancestry and the process of accumulating mutations over time. Oh, and no bacteria involved.

Other way around. Mutations can tell us how the fossils changed.

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Nature. 2004 Mar 25;428(6981):415-8.

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Myosin gene mutation correlates with anatomical changes in the human lineage.
Stedman HH, Kozyak BW, Nelson A, Thesier DM, Su LT, Low DW, Bridges CR, Shrager JB, Minugh-Purvis N, Mitchell MA.

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Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. hstedman@mail.med.upenn.edu

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Comment in:

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Nature. 2004 Mar 25;428(6981):373-4.

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Abstract
Powerful masticatory muscles are found in most primates, including chimpanzees and gorillas, and were part of a prominent adaptation of Australopithecus and Paranthropus, extinct genera of the family Hominidae. In contrast, masticatory muscles are considerably smaller in both modern and fossil members of Homo. The evolving hominid masticatory apparatus--traceable to a Late Miocene, chimpanzee-like morphology--shifted towards a pattern of gracilization nearly simultaneously with accelerated encephalization in early Homo. Here, we show that the gene encoding the predominant myosin heavy chain (MYH) expressed in these muscles was inactivated by a frameshifting mutation after the lineages leading to humans and chimpanzees diverged. Loss of this protein isoform is associated with marked size reductions in individual muscle fibres and entire masticatory muscles. Using the coding sequence for the myosin rod domains as a molecular clock, we estimate that this mutation appeared approximately 2.4 million years ago, predating the appearance of modern human body size and emigration of Homo from Africa. This represents the first proteomic distinction between humans and chimpanzees that can be correlated with a traceable anatomic imprint in the fossil record.

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A mutation in our MYH gene results in a weaker jaw muscle. A weaker jaw muscle requires less bone as an anchor. This allowed for both the gracilization of the human lower jaw and the expansion of the cranium.But just on a more general note, perhaps you could answer this question. Why are humans and chimps different? What explains this difference?Edited by Taq, : No reason given.

I provided that info in my earlier post on ERV's. These ancient retroviral insertions provide information on the accumulation of mutations and common ancestry.

Those phylogenies demonstrate the accumulation of random mutations over time, common ancestry, and sequence divergence. This is the very evidence you have been asking for. I don't see anthing in this paragraph to indicate that my conclusions are wrong. Care to explain?

Bolderdash,Why are humans different than chimps? Simple question.

Why? I am going to need more than your say so.We have clear cut evidence that mutations accumulate over time, and has done so amongst our ape family. We directly observe that differences between apes, including humans, is due to differences in DNA. It doesn't take a rocket scientist to put these two together.We observe that the accumulation of mutations in genes such as ERV's differs greatly than the accumulation of mutations in coding genes which is clear cut evidence for selection.All of the evidence you want is right there.

Playing it coy, are we?Why is human and chimp morphology different?

The evidence of what these mechanisms HAVE DONE is in our genomes, and in the genomes of other living species. I have already shown that shared ERV's in humans and other apes demonstrates a common ancestor. I have also shown that these same ERV's demonstrate the accumulation of random mutations over time. I have also shown that the rate of this accumulation differs between ERV's and coding genes, which demonstrates selection. We can even show a difference between exons and introns within a gene which also demonstrates selection of mutations within exons (the coding portion of a gene). We can also show a difference in the accumulation of mutations between coding genes and pseudogenes between species that are known to share a common ancestor (through such evidence as shared ERV's).Genomes are a record of random mutation and selection.