Tiny shelled protists called foraminifera have been claimed to “perfectly illustrate” evolution, as long as you redefine evolution.
Foraminifera (“hole bearers”), or forams for short, are abundant in the sea. Some live on the sea floor (benthic), and some float as plankton. Since the Jurassic the calcium carbonate shells of these creatures have settled on the bottom of the ocean, providing a lengthy record of their evolution. This creates perfect conditions to test Darwin’s theory: a long, undisturbed record of evolutionary progress, innovation, and positive selection.
The European foraminifera study site, foraminifera.eu, seems reputable enough to speak on the subject. It has a lengthy list of scientists on its roster, and plenty of specimens in its catalog. So when it speaks on the value of forams for evolutionary theory, we should perk up:

“Nothing in biology makes sense except in the light of evolution.” Theodosius Dobzhansky, 1973

Foraminifera may perfectly illustrate evolution at work. As single celled organisms with a short life-cycle foraminifera and the composition of a specific foraminiferal fauna adopt rapidly to even small environmental changes. The great abundance of foraminifera in marine space and time in the long fossil record may be used to perfectly illustrate evolution.

A paper in Nature this week describes the evolutionary record of foraminifera, but one would be hard pressed to find any indication of really significant evolution. There’s diversification, for sure; slight changes in the size and shape of the “tests” or rock shells of the forams. But they’re still forams. Even the most ardent Young Earth Creationists accept that kind of “evolution.”
Let’s see if the Nature paper can describe the kind of evolution Darwin preached: increases in information, new organs and structures, the gradual emergence of whole new types of organisms by natural selection.

Here we test the long-standing hypothesis that changes in the physiochemical state of the ocean have exerted a dominant influence on the long-term macroevolution of planktonic foraminifera. To do so, we compare patterns of taxonomic diversity and rates of extinction and origination to analogous macrostratigraphic quantities that describe spatiotemporal patterns of sedimentation in the deep sea.

The focus of the paper, though, is not so much on the emergence of new, wondrous creatures evolving from simple to complex; it’s about extinction. In “Oceanographic controls on the diversity and extinction of planktonic foraminifera,” three geoscientists concluded that extinction has “common cause” with environmental factors:

Here we use macrostratigraphic data from the Atlantic Ocean basin to show that changes in global species diversity and rates of extinction among planktonic foraminifera have been linked to tectonically and climatically forced changes in ocean circulation and chemistry from the Jurassic period to the present.

The extinction signal is strong, but it gets more difficult to see new species originating:

Rates of species origination, by contrast, are not correlated with corresponding macrostratigraphic quantities, indicating that physiochemical changes in the ocean-atmosphere system affect evolution principally by driving the synchronous extinction of lineages that originated owing to more protracted and complex interactions between biological and environmental factors.

Now they have a problem. They can watch environmental factors lead to extinction, but the same factors that are supposed to create reproductive barriers leading to the “origin of species” don’t seem to work:

The ability of macrostratigraphy to predict the extinction of planktonic foraminifera better than origination is difficult to explain under the hypothesis of sampling bias, but it is readily interpretable as a biological signal. The discovery that most extant morphospecies of planktonic foraminifera consist of multiple genotypes with an extraordinary capacity to disperse, challenges the view that tectonic and hydrographic barriers facilitate speciation by isolating reproductive populations. Instead, the genetic and zoogeographic evidence suggest that the evolution of new planktonic foraminiferal species may be limited by their ability to maintain populations in areas where unfavourable ecological conditions exist rather than by an inability to disperse beyond tectonic and hydrographic barriers. An important corollary of this finding is that biotic processes such as competitive exclusion between sibling species, establishment of symbiotic relationships, differences in trophic behaviour, and divergent reproductive strategies may have a more prominent role in the origination of new species than the tectonic and climatic perturbations that consistently drive synchronous changes in the physiochemical structure of the ocean, the distribution and extent of deep-sea sedimentation, and species extinction.

Translation: we can see extinction patterns in the stratigraphy, but the “origin of species” may have to do with “biotic processes,” not with the environment. Conclusion: “reproductive isolation” as a cause of speciation is falsified, at least in the case of forams, those creatures that “perfectly illustrate” evolution.
But do they give any examples of origination that truly show macroevolution? Do they show any new kinds of animals emerging by natural selection? No; it’s all diversification — minor changes in shell shape. They’re still forams.
The researchers mention macroevolution several times, but in the Methods section of the paper, they admit that their “macroevolutionary quantities” can be imprecise due to errors of taxonomic practice (deciding what is a new species) and correlation (deciding what species fits with what strata). Both of those, they say, are “random effects” in their analysis. In short, they don’t show any evolutionary progress from bottom strata to top.
Steven M. Holland, analyzing this paper in the same issue of Nature, agrees:

On page 398 of this issue, Peters et al. make a convincing case that the number of species of a major group of single-celled marine organisms is closely linked to historical changes in the physical and chemical properties of the ocean and atmosphere. Extinctions seem also to have mostly resulted from these environmental factors, but species origination does not, suggesting that speciation is primarily controlled by organismal interactions.

Neither article mentions “innovation” or “progress.” The only macroevolution evident is a kind of oscillating measure of species number (that’s why Holland titled his article, “Evolution: A history of give and take”). In fact, the paper raises more questions than answers about evolution, as Holland states:

The finding of a strong coupling between deep-sea sedimentation and extinctions suggests that extinction is driven primarily by environmental perturbations. However, the lack of a link between sedimentation and species origination suggests that origination is governed more by species interactions.
This intriguing conclusion raises many questions that other palaeobiologists will surely address. One set of questions relates to macroevolutionary processes — those that occur at or above the level of species. For example, why do environmental perturbations drive extinction but apparently have little effect on origination? Might this indicate that origination takes longer than extinction, which would weaken its apparent correlation with the rock record? And what are the specific mechanisms that link environmental change and extinction?

Perceptive critics of neo-Darwinism will see embarrassing admissions here: environment doesn’t affect speciation, and the fossil record does not correlate with macroevolution. Strike two! To keep from striking out, the Darwinists have to hold a time out, asking themselves what kind of theoretical processes of species interactions might rescue macroevolution from the evidence.
Going back to the European foraminifera website, let’s see what they have to say about evolution. The page was last updated August 2012. There’s a brief section on “What Evolution Is” that avoids all mention of progress or innovation: “Biological evolution is simply seen as a change in the frequency of genes through time.” Then they explain the major role of the environment in natural selection:

In a group of organisms the environmental conditions will favor some individuals while others will not reproduce as well. If heritable characters are the cause a shift in their frequency within a population will occur. This process is called natural selection.

A second section discusses how forams survive in various habitats. Again, there is nothing about progress or innovation.
Then we come to the meat of the article, where the European foram experts will really show that nothing makes sense except in the light of evolution. What does the reader find?

Mutation and Variation
under construction
Natural Selection
under construction

So there you have it: the perfect illustration of Darwinian evolution and its power to generate biological innovation. Watch this space.
Image: Ammonia beccarii/Wikipedia.