Phylogenetic Trees Quote Collection

Welcome to our Phylogenetic Trees quote collection. Many of the quotes in our collections have been verified for accuracy, but not all have been verified. Thus, we present our quote-collections as a starting point for research, and suggest you verify any individual quote before using it.

If you have information about problems or inaccuracies in any quotes, we welcome corrections. Please send them to us at: info@ideacenter.org.

The Quotes:

"'For a long time the holy grail was to build a tree of life,' says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. 'We have no evidence at all that the tree of life is a reality,' says Bapteste." (Graham Lawton, "Why Darwin Was Wrong About the Tree of Life," New Scientist, (January 21, 2009).)
---."The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse."
---."More fundamentally, recent research suggests that the evolution of animals and plants isn't exactly tree-like either."
---."The problem was that different genes told contradictory evolutionary stories."
---."We've just annihilated the tree of life."

"Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species." (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats," Biological Reviews of the Cambridge Philosophical Society, Vol. 87: 991-1024 (2012).)
---."Phylogenetic conflict is common, and frequently the norm rather than the exception."
---."Phylogenetic conflict has become a more acute problem with the advent of genomescale data sets."

"As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology." (Patterson et al., "Congruence between Molecular and Morphological Phylogenies," Annual Review of Ecology and Systematics, Vol. 24: 179 (Nov. 24, 1993).)

"With respect to molecular evolution, more work on sequences and with more organisms is needed, as the number and branching patterns of the main branches of organisms are still in dispute" (Betsey D. Dyer and Robert A. Obar, Tracing the History of Eukaryotic Cells, (Columbia University Press, 1994).)

"New genome sequences are mystifying evolutionary biologists...on one front the study of evolution-the information pouring out in the genome sequences has so far proved more confusing than enlightening. Indeed, it threatens to overturn what researchers though they already knew about how microbes evolved and gave rise to higher organisms." (Science, Vol. 280: 672 (May 1, 1998).)

"Molecular systematics has not yet produced phylogenetic trees of broad phylum relationships more robust than those based on morphology." (J. M. Turbeville, J. R. Schulz, and R.A. Raff, "Deuterostome Phylogeny and the Sister Group of the Chordates: Evidence from Molecules and Morphology," Molecular Biological Evolution, Vol. 11: 648-655 (1994).)

"That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent." (Masami Hasegawa, Jun Adachi, and Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44: S117-S120 (Supplement 1, 1997).)

"[M]olecular phylogenists 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." (W. F. Doolittle, "Phylogenetic Classification and the Universal Tree," Science, Vol. 284: 2124-2128 (June 25, 1999).)

"A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome." (James H. Degnan and Noah A. Rosenberg, "Gene Tree Discordance, Phylogenetic Inference and the Multispecies Coalescent," Trends in Ecology and Evolution, Vol. 24: 6 (March, 2009).)

"[T]he 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." (Wilfried W. de Jong, "Molecules Remodel the Mammalian Tree," Trends in Ecology and Evolution, Vol. 13: 270-275, Issue 7 (July 1, 1998).)

“When biologists talk of the 'evolution wars', they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species' morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. (Trisha Gura, “Bones, Molecules or Both,” Nature, Vol. 406: 230-233 (2000).)

"[O]ur ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years" (M. A. Wills, "The Tree of Life and the Rock of Ages: Are We Getting Better at Estimating Phylogeny?," BioEssays, Vol. 24: 203-207 (2002) reporting on the findings of M. J. Benton, "Finding the Tree of Life: Matching Phylogenetic Trees to the Fossil Record Through the 20th Century," Proceedings of the Royal Society B, Vol. 268: 2123-2130 (2001).)
---."Despite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”

"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand." (Emile Zuckerkandl and Linus Pauling, "Evolutionary Divergence and Convergence in Proteins," Evolving Genes and Proteins: A Symposium Held at the Institute of Microbiology of Rutgers, With Support from the National Science Foundation, page 101 (Vernon Bryson and Henry J. Vogel, eds., New York: Academic Press, 1965).)

"[T]he mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting." (Michael S. Y. Lee, "Molecular Phylogenies Become Functional," Trends in Ecology and Evolution, Vol. 14(5): 177-178 (May, 1999).)

"[D]ifferent proteins generate different phylogenetic tree[s]" (Mushegian et al., "Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes," Genome Research, Vol. 8: 590-598 (1998).)

“Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate.“ (Degnan and Rosenberg, “Discordance of Species Trees with Their Most Likely Gene Trees,” Public Library of Science: Genetics, Vol. 2, Issue 5 (May, 2006).)
---."It is noteworthy that our theoretical results apply to known—rather than estimated—gene trees, and do not consider the effect of mutations on inference of gene trees. This issue is important, as mutational history is a key factor in determining when an empirical study might actually be misled by AGTs. As an illustration, in one human-chimp-gorilla study, a substantial fraction of loci—six of 45 considered—had no informative substitutions that could provide support to any particular phylogenetic grouping. That this many loci would not have any phylogenetic information in the human-chimp-gorilla clade suggests that for the smaller branch lengths typical of the anomaly zone, the fraction of uninformative loci could be much greater."

"The robust reconstruction of metazoan history has proven to be a difficult task." (Rokas et al., "Conflicting Phylogenetic Signals at the Base of the Metazoan Tree," Evolution and Development, Vol. 5(4): 346-359 (2003).)

"The phylogenetic relationships among most metazoan phyla remain uncertain." (Rokas et al., "Animal Evolution and the Molecular Signature of Radiations Compressed in Time," Science, Vol. 310: 1933-1938 (December 23, 2005).)
---."Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study employed the many-gene technique, and yet still found that '[a] 50-gene data matrix does not resolve relationships among most metazoan phyla.'"

"[N]on-coding" DNA contains a large quantity of information arranged in a coherent, structured and complex manner whose linguistic character (coding?) lead us to think some kind of biological function." (B. Cantu-Golan and E. Hernandez-Lemus, "Statistical Properties and Linguistic Coherence in Noncoding DNA Sequences," Revista Mexicana de Fisica E, Vol. 51(2): 118-125 (December, 2005).)

"[I]t is highly unlikely that large numbers of species of organisms will repeatedly evolve similar morphologies, over and over again in time, simply by chance. Yet that is precisely what we observe in the fossil record: the convergent evolution of form in many different groups of organisms, over and over again in time." (George R. McGhee, The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces, page 32 (Cambridge University Press, 2007).)

“The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous.” (Marketa Zvelebil and Jeremy O. Baum, Understanding Bioinformatics, page 239 (Garland Science, 2008).)

“Cladistics can run into difficulties in its application because not all character states are necessarily homologous. Certain resemblances are convergent -- that is, the result of independent evolution. We cannot always detect these convergences immediately, and their presence may contradict other similarities, ‘true homologies’ yet to be recognized. Thus, we are obliged to assume at first that, for each character, similar states are homologous, despite knowing that there may be convergence among them.” (Guillaume Lecointre & Hervé Le Guyader, The Tree of Life: A Phylogenetic Classification, page 16 (Harvard University Press, 2006).)



Source: Many of the quotes in our collection have been verified for accuracy, but not all have been verified. Thus, we present our quote-collections as a starting point for research, and suggest you verify any individual quote before using it.

If you have information about problems or inaccuracies in any quotes, we welcome corrections. Please send them to us at: info@ideacenter.org.

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