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)

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.
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.