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  1. "Dolphins and porpoises form a sister group to CF bats in a phylogenetic analysis of prestin sequences.", "dolphins and porpoises share at least 14 derived amino acid sites in prestin with echolocating bats",Molecular Evolution: Gene Convergence in Echolocating Mammals, 2010
  2. "Our algorithm found identical sequences of DNA located at completely different places on multiple plant genomes", A DNA INSIGHT Better analysis may result in new medicines and improved crops, April 2012
  3. Figure 1 shows 1,110*.23=255 complex, non-syntenic (not occurring at the same place) sequences of 100+ bp that could not be explained by any known mechanisms. Long identical multispecies elements in plant and animal genomes, PNAS, March 2012
  4. "The platypus genome encodes each of the four proteins of the human zona pellucida as well as two ZPAX genes that previously were observed only in birds, amphibians and fish." (but not mammals or reptiles), and "duplications in each of the b-defensin, C-type natriuretic peptide and nerve growth factor gene families have also occurred independently in reptiles during the evolution of their venom.", Genome analysis of the platypus reveals unique signatures of evolution, Nature, May 2008(http://www.pbs.org/wgbh/evolution/library/01/4/pdf/l_014_02.pdf) (see chart on last page).
  5. In snake and lizard genomes, "Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions (primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny.", Evidence for an ancient adaptive episode of convergent molecular evolution, PNAS, June 2009
  6. In dinoflagellates and euglenozoa, "the molecular processes associated with the nucleus, plastid and mitochondrion also reflect high levels of convergent evolution.", "they are also evolving strikingly similar mechanisms for achieving these essential biological functions.", "Euglenids and dinof lagellates also possess cytoskeletal elements that are not found in any other group of eukaryotes", and "both euglenids and dinof lagellates independently acquired photosynthesis", which is remarkable since they're on opposite sides of the tree of life--"Both euglenozoans and alveolates have a reputation for 'doing things their own way,’ they have developed seemingly unique ways to build important cellular structures or carry out molecular tasks critical for their survival.", Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates, PNAS, June 2009
  7. "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.", Molecules remodel the mammalian tree, Trends in Ecology and Evolution, July 1997
  8. "Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. 'Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,' Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen, Why Darwin was wrong about the tree of life, NewScientist, 2009
  9. "Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism. Comparative genome analysis shows not only a substantial level of plasticity in the gene repertoire, but also provides evidence that nearly all genes, including ribosomal genes, have been exchanged or recombined at some point in time. Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree." and " Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created through gene fusion, degradation, or other events, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.", The post-Darwinist rhizome of life, 2010
  10. "my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs.", "genes essential to the very survival of cells traded hands frequently", "[genes] that are arguably as critical to cell survival as are transcription and translation", Uprooting the Tree of Lilfe, Scientific American, 2000
  11. "We conclude that we simply cannot determine if a large portion of the genes have a common history.", and "Our phylogenetic analyses do not support tree-thinking. ... We argue that representations other than a tree should be investigated", Do orthologous gene phylogenies really support tree-thinking?
  12. "Since embracing Darwin’s tree-like representation of evolution and pondering over the universal Tree of Life, the field has moved on. ... the Tree of Life turns out to be more like a 'forest'", Methods in Molecular Biology, 2012
  13. "Conflicting [phylogenic] topologies are likely to become the norm", and listed as an outstanding question, "For data sets with high levels of gene tree conflict, how can researchers determine whether an AGT is likely? How often do AGTs arise in real data sets?" Gene tree discordance, phylogenetic inference and the multispecies coalescent, Cell, 2009
  14. Evolutionary biologist Eric Bapteste: "We have no evidence at all that the tree of life is a reality" and evolutionary biologist Michael Rose: "The tree of life is being politely buried", Charles Darwin wrong about tree of life, The Guardian, January 2009
  15. "No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.", The Universal Ancestor, PNAS, 1998
  16. "I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like, 'remarkable', 'striking', 'extraordinary', or even 'astonishing' and 'uncanny' are common place...the frequency of adjectival surprise associated with descriptions of convergence suggests there is almost a feeling of unease in these similarities. Indeed, I strongly suspect that some of these biologists sense the ghost of teleology looking over their shoulders.", Simon Conway Morris, Life's Solution: Inevitable Humans, pp. 127-128, 2003
  17. Retrivruses have been found in cimpanzees and gorillas but the human genome contains intact DNA at the same spot: "We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus.", A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans, 2001
  18. Another ERV has been found in old world monkeys and African apes, but missing from humans and Asian apes: "Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes.", and "Second, the PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates, suggesting a horizontal transmission as opposed to a vertical transmission from a common ape ancestor. An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists.", Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans, 2005
  19. Guinea pigs and humans share strong molecular convergence in the vitamin GULO (vitamin C) pseudogene, which contradicts random genetic drift: "The same substitutions from rats to both humans and guinea pigs occurred at 47 nucleotide positions among the 129 positions where substitutions occurred in the human sequences", and "Assuming an equal chance of substitution throughout the sequences, the probability of the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84x10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences.", The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon
  20. Widespread convergence of placental and marsupial mammals (See chart on last page).