Gene and host phylogenies are congruent
Evolution predicts that genetic change drives evolutionary change. Genetic changes that confer improved fitness are more likely to be selected and passed on. All of this means that evolutionary trees based on comparisons of genes should be similar, or congruent, with evolutionary trees based on comparisons of the entire species. Simply put, gene trees and species trees should be congruent. But while this has often been claimed to be a successful prediction, it is now known to be false. As one study explained, “Perhaps most unexpected of all is the substantial decoupling, now known in most, although not all, branches of organismal life, between the phylogenetic histories of individual gene families and what has generally been accepted to be the history of genomes and/or their cellular or organismal host lineages.” (Ragan, McInerney and Lake)
The molecular and the visible (morphological) features often indicate “strikingly different” evolutionary trees that cannot be explained as due to different methods being used. (Lockhart and Cameron) Making sense of these differences between the molecular and the morphological features has become a major task, (Gura) so common that it now has its own name: reconciliation. (Stolzer, et. al.) The growing gap between molecular analyses and the fossil record, concluded one researcher, “is astounding.” (Feduccia) Instead of a single evolutionary tree emerging from the data, there is a wealth of competing evolutionary trees. (de Jong) And while the inconsistencies between molecular and fossil data were, if anything, expected to be worse with the more ancient, lower, parts of the evolutionary tree, the opposite pattern is observed. As one study explained, “discord between molecular divergence estimates and the fossil record is pervasive across clades and of consistently higher magnitude for younger clades.” (Ksepka, Ware and Lamm) One interesting example is the Orangutans which share many similarities with humans. These “people of the forest,” as they have been called, have more in common with humans than do the other great apes. This includes features of anatomy, reproductive biology and behavior. But there is one feature in which orangutans are not the closest species to humans: the genome. The chimpanzee has the closest genome to the human genome, so it is thought to be our closest relative. The molecular and morphological comparisons point to incongruent phylogenies. As one paper concluded: There remains, however, a paradoxical problem lurking within the wealth of DNA data: our morphology and physiology have very little, if anything, uniquely in common with chimpanzees to corroborate a unique common ancestor. Most of the characters we do share with chimpanzees also occur in other primates, and in sexual biology and reproduction we could hardly be more different. It would be an understatement to think of this as an evolutionary puzzle. (Grehan) If it weren’t for DNA, it would be the orangutan rather than the chimp pictured next to the human in the evolutionary tree. References de Jong, W. 1998. “Molecules remodel the mammalian tree.”Trends in Ecology & Evolution, 13:270-275. Feduccia, A. 2003. “‘Big bang’ for tertiary birds?.” Trends in Ecology & Evolution 18:175. Gura, T. 2000. “Bones, molecules...or both?.” Nature 406:230-233. Grehan J. 2006. “Mona Lisa smile: the morphological enigma of human and great ape evolution.” The Anatomical Record Part B: The New Anatomist 289B:139-157. Ksepka, D. T., J. L. Ware, K. S. Lamm. 2014. “Flying rocks and flying clocks: disparity in fossil and molecular dates for birds.” Proceedings of the Royal Society B 281: 20140677. Lockhart, P., S. Cameron. 2001 “Trees for bees.” Trends in Ecology and Evolution 16:84-88. Ragan, M., J. McInerney, J. Lake. 2009. “The network of life: genome beginnings and evolution.” Philosophical Transactions of the Royal Society B 364:2169-2175.
Stolzer, M., et. al. 2012. “Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.” Bioinformatics 28 ECCB:i409–i415.
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