Perhaps the strongest support for evolution lies in the fact that evidence from completely independent sources matches up in similar predictions of common descent. We have gone over some strong examples of this below.

A formal test of Universal Common Ancestry

In a 2010 paper written for the prestigious journal Nature, scientist Douglas Theobald performed a statistical formal test of common ancestry. His analysis compared the differences between taxa in 23 different proteins which are found in almost all known life today. By comparing sequence differences, he was able to compute a phylogenetic tree for the taxa from each protein independently. The clear consensus results from the analysis supported a single common ancestor for all of life; the same tree of common ancestry was clearly supported by the data. The chance of this occurring randomly was calculated by the author to be 1 in 10^2680!

Phylogenetic Results in Laboratories shown successful

As a large amount of the evidence presented on this page deals with phylogenetic trees constructed from molecular data, we will first give some examples of laboratory experiments in which phylogenetic methods successfully reconstructed already known trees of relationship. The below quote is from the evolution website TalkOrigins:

Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).
In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).

We can conclude that phylogenetic techniques are verifiably accurate and represent quality evidence of relationship and common descent.

The Number of Possible Phylogenetic trees

The total number of phylogenetic trees it is possible to arrange simply from the 30 major taxa is 10^38. Thus, the chance of two unrelated phylogenic trees of these taxa matching up perfectly by coincidence is 1 in 10^38, yet we see several dozen different trees consistently match. TalkOrigins created an excellent program which calculates the total number of possible phylogenetic trees with n number of taxa. For example, the chance of just two independent phylogenetic methods coincidentally finding identical trees of these seven loose primate taxa we take a look at below is 1 in 10,395. Thus, the chance of three independent methods coincidentally finding identical trees of these primate taxa is (1/10,395)*(1/10,395), or (1/108,056,025), yet, we find that several different methods add up to the same tree. Without common descent, we are at a complete loss to explain the matchup of phylogenetic trees.

Sources for the data above:
Fossil Record: See our page on the fossil record.
ERV Data: See (Lebedev et al., 2000)
Hemoglobin Data: See Figure 1 in (Genji, 1985) .
Protein Sequence Data: See Table 3 in (Glazko, et al., 2005)
DNA Data: See the tree created in (Koop et al., 1989).
Cytochrome C Data: Data from http://www.ncbi.nlm.nih.gov/. Simply search the Protein database for "CYCS" and the scientific name of the organism. We then took the protein sequences from the database and plugged them into the ClustalW2 sequence alignment program to create a phylogram. This is such a simple process that anyone can independently verify these results. Note that orangutans, gorillas, chimpanzees, and humans all have identical cytochrome C sequences and thus the cytochrome c data does not extend to that end of the chart.

Independent protein sequences show similar relationships among organisms

Examining three largely unrelated, random protein sequences from a variety of diverse organisms leads one to three nearly identical cladograms. The number of taxa below is 16, and thus it is a 1 in 6,190,283,353,629,375 chance that just two of these trees would show identical results, as all three cladograms below very nearly do. (See the TalkOrigins calculator discussed above for statistic details) The results of this are shown below.

Source: The data above was taken from the HomoloGene database at http://www.ncbi.nlm.nih.gov/. Simply type in the name of the protein to get the specific sequences for a large number of organisms. The sequences were plugged into the ClustalW2 sequence alignment program to create the cladograms above.

Evolutionary predictions tend to be confirmed by the primate fossil record

You've heard it before: sinister evolutionists have to completely change their story about prehistory each time a new fossil comes up which proves their last "missing link" was not in fact a missing link. That is, this would be true if one were to believe creationist websites such as AnswersInGenesis.

Of course, that's entirely wrong, for several reasons. The idea of "missing links" only exists today as a misinterpretation of evolutionary paleobiology in the mainstream media; individual fossil finds aren't interpreted to be direct ancestors of modern species, only ancestral relatives who were extremely closely related to the actual direct ancestors of their time.

Secondly, science is a self-correcting process. As new evidence is uncovered, prevailing views explaining the evidence should change. There is nothing mischievous or sinister about changing one's ideas to fit the evidence; rather, that is a good scientific practice.

Finally: the premise of the original statement is also false, according to Tarver, Donoghue, and Benton 2010.

In fact, Tarver et al. found that on the contrary, new primate fossil finds far more often confirm existing evolutionary predictions than contradict them. They used the data from fossil primate species collected over the past 200 years, and found that the primate phylogeny has stayed relatively constant as new finds have been uncovered, demonstrating the predictive power of evolution.

Independent protein sequences show similar relationships

A scientific study of 5 random protein sequences in a variety of mammals concluded that all phylogenetic trees created using each of the 5 sequences reached a very similar consensus tree. (Penny et al. 1982)

Independent Phylogenies confirm the Tree of Life

Sanderson 2008 reported that 14,289 independent phylogenies, built from a grand total of 2.6 million different genetic sequences, confirmed a strong phylogenetic trend. In other words, all of the independent analyses converged on a highly similar tree of life. The probability of such a strong indication is extraordinarily low without taking into account common descent.

Diverse fossil data and molecular data reach the same evolutionary conclusion

Scientists estimate that 80 million years ago fermentable fruits became prominent. This is supported by evidence from the yeast genome, which suggests that yeast obtained its ability to ferment glucose around that time. It is also supported by the fossil record, which shows that fruit also became widespread around that time. Molecular clocks also suggest that major changes occurred in the genomes of fruiting plants and fruit flies around that time. Quite simply, with all of this evidence converging, one must admit that 80 million years ago fermentable fruits did, in fact, become prominent. There is no other satisfactory explanation. (Benner et al. 2002)

Phylogeny of the Metazoa Based on Morphological and 18S Ribosomal DNA Evidence

By examining morphological data, developmental data, ultrastructural data, and ribosomal DNA evidence, scientists were able to produce a strong consensus tree of relationship for the higher taxa of metazoa. (Zrzavy et al. 2005)

Cetaceans: Atavism, Comparative Anatomy, Developmental Biology, Genetics, and Fossil evidence

In whales and dolphins we also see extraodinary evidence of common descent. First and most obviously, cetaceans, unlike most other sea creatures, are mammalian: they care for their youth, they are warm-blooded, and they exhibit other mammalian characteristics.(More Information) This in itself is odd (excluding common descent), as mammalian characteristics are not well suited for an organism which spends its life completely in the water. We also observe that cetaceans, unlike fish and other sea creatures, require a constant supply of air to regularly breathe, which again, is a trait that is is ill suited for a creature which spends its life underwater. These characteristics imply that cetaceans were not created recently by an intelligent force, but are instead the evolutionary descendants of terrestrial mammals which have taken to the water.

Next, we find that the fossil record exhibits a gradual and slow transition of a group of mammals to an aquatic lifestyle. These mammals are anatomically similar to modern cetaceans.

Next, we observe that several atavisms occur in cetaceans, specifically the rare emergence of fully formed atavistic hind legs which are virtually indistinguishable from terrestrial tetrapod limbs. An image of the bones from one specimen is to the left below(Andrews 1921). (The image is also from this source)

To add to this considerable evidence, we see rudimentary hindlegs form in the embryo stage of most cetaceans, which almost completely disappear in later development. A picture of these hindlegs can be seen to the right (Sedmera et al. 1997).(The image is also from this source)

The last piece of the puzzle is the evidence from genetics. Dolphins in particular have a large number of genes identified as identical to those which control the sense of smell in terrestrial mammals, except these vestigial genes are turned off and have no function in the dolphin(Freitag et al. 1998).

All of this evidence converges to the basic fact that modern cetaceans evolved from a terrestrial ancestor. There simply is no way to put the evidence together without common descent. Read more about the evolution of whales at TalkOrigins.

Molecular clocks confirm paleontological estimates of metazoa phyla origins

Analyzing several genes in a variety of metazoa, Ayala et al. 1998 found that their molecular clock approximations of the origins of the animal phyla corresponds to physical data from the fossil record.

Sources

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