Gene phylogenies are congruent:
Just as evolution predicts that gene trees and species trees should be congruent, it also predicts that different gene trees should be congruent. In 1982 David Penny and co-workers tested this prediction. They wrote that “The theory of evolution predicts that similar phylogenetic trees should be obtained from different sets of character data.” Their character data came from five different proteins and they concluded “there is strong support from these five sequences for the theory of evolution.” (Penny, Foulds and Hendy) But in later years, as more genetic data became available, it was clear that different genes led to very different evolutionary trees. As one study explained, the sequences of genes, “often disagree and can seldom be proven to agree.” (Doolittle and Bapteste) It is now well understood that “Gene and genome trees conflict at many levels” (Haggerty, et. al.) and that “Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era.” (Galtier and Daubin) For evolutionists this failed prediction will require more complicated models of evolutionary history. As Penny now writes, he is “not rejecting the tree per se but enriching the tree concept into a network.” (Penny)
References
Doolittle, W., E. Bapteste. 2007. “Pattern pluralism and the Tree of Life hypothesis.” Proceedings of the National Academy of Sciences 104:2043-2049.
Galtier, N., V. Daubin. 2008. “Dealing with incongruence in phylogenomic analyses.” Philosophical Transactions of the Royal Society B 363:4023-4029.
Haggerty, L., et. al. 2009. “Gene and genome trees conflict at many levels.” Philosophical Transactions of the Royal Society B 364:2209-2219.
Penny, D. 2011. “Darwin’s Theory of Descent with Modification, versus the Biblical Tree of Life.” PLoS Biol 9:e1001096.
Penny, D., L. Foulds, M. Hendy. 1982. “Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences.” Nature 297:197-200.
Just as evolution predicts that gene trees and species trees should be congruent, it also predicts that different gene trees should be congruent. In 1982 David Penny and co-workers tested this prediction. They wrote that “The theory of evolution predicts that similar phylogenetic trees should be obtained from different sets of character data.” Their character data came from five different proteins and they concluded “there is strong support from these five sequences for the theory of evolution.” (Penny, Foulds and Hendy) But in later years, as more genetic data became available, it was clear that different genes led to very different evolutionary trees. As one study explained, the sequences of genes, “often disagree and can seldom be proven to agree.” (Doolittle and Bapteste) It is now well understood that “Gene and genome trees conflict at many levels” (Haggerty, et. al.) and that “Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era.” (Galtier and Daubin) For evolutionists this failed prediction will require more complicated models of evolutionary history. As Penny now writes, he is “not rejecting the tree per se but enriching the tree concept into a network.” (Penny)
References
Doolittle, W., E. Bapteste. 2007. “Pattern pluralism and the Tree of Life hypothesis.” Proceedings of the National Academy of Sciences 104:2043-2049.
Galtier, N., V. Daubin. 2008. “Dealing with incongruence in phylogenomic analyses.” Philosophical Transactions of the Royal Society B 363:4023-4029.
Haggerty, L., et. al. 2009. “Gene and genome trees conflict at many levels.” Philosophical Transactions of the Royal Society B 364:2209-2219.
Penny, D. 2011. “Darwin’s Theory of Descent with Modification, versus the Biblical Tree of Life.” PLoS Biol 9:e1001096.
Penny, D., L. Foulds, M. Hendy. 1982. “Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences.” Nature 297:197-200.
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