Darwin noticed that changes occurred in living things. We now know that these changes are caused by mutations in DNA bases. In his theory of evolution he ascribed changes to living organisms as being caused by these mutations. The slow, steady changing of a species has been studied in great detail, including in a recent book, Speciation, by Coyne and Orr.
Darwin assumed that the same process has produced all the changes seen in the fossil record. However, the fossil changes seem to work differently. While the slow changes we can track in living things make gradual changes in organisms, the changes seen in the fossil record seem to be much greater. A species in a fossil record seems to remain the same for a million years or more, then become something that may be measurebly different from the original. There are several studies that show this process, including a chart near the end of Speciation.
The above points seem to describe two different processes for speciation. Listed here are some basic points that we now know about the speciation process in the fossil record.
Several studies have looked at persistence of fossil species. Most last a million years, and several last many millions. A chart near the back of the book, Speciation, shows this process.
Even in continuous sedimentary beds, very few fossil speciations leave any record at all, so no minimum time for speciation can be calculated. (Proposed by Ernst Mayr)
S. Dorus et al. (2004). Accelerated evolution of nervous system genes in the origin of Homo sapiens, Cell, 119: 1027-1040.
K.S. Pollard et al. (2006). An RNA gene expressed during cortical development evolved rapidly in humans, Nature, 443: 167-172
K.S. Pollard et al. (2006). Forces shaping the fastest evolving regions in the human genome, PLoS Genetics, 2(10) Published Oct 2, 2006
The human MHC has many versions of proteins involved in identification of 'self' that date back to chimp and beyond, which would have been lost in a bottleneck.
The charts showing persistence of fossil species often include such species as Stickleback and Cichlid fish, neither of which are different species. The Stickleback changes by dominant and recessive genes, or by relative frequency of genes, according to selective pressure. The cichlid fish get much of the difference in appearance by a hormone wash during development that determines how large the mouth part become.Fossil speciation requires thousands of DNA base changes.
One of the authors in the Cell article commented in an interview that we now know that speciation requires thousands of DNA base changes. His study looked at about 200 genes involved in structure of the brain, that had not changed over millions of years but changed in Homo. The other studies lead by Dr Pollard looked at small control sections for genes which changed for Homo but not before. These seem to be mostly the same genes that Dr Dorus covered. With 200 genes and 200 control sections changing by several bases each, that makes well over 1000 changes just dealing with the Homo brain.No bottleneck can have occurred in the Homo lineage
It has been estimated that it would take 1500 individuals speciating together to transmit the known number of variations of the MHC proteins. These individuals would also probably have to include individuals from all the separate tribes in the entire pro-human family.Any proposed method of fossil speciation has to allow for these points.
It has been about 7 million years since Chimp and Homo diverged. Some have supposed that the long time period would give time for all the speciations needed to implement the changes analyzed by Dr Dorus and Dr Pollard. However, fossils of homo ancestors show much less time for the changes in brain size. While not all changes were made at once, changes seem to have included large subsets of the total changes noted. And thousands of DNA base changes divided into a few events still give hundreds of base changes for each speciation. Contrast that with the 'requirement' as stated by Dr Dawkins for very few changes per speciation.
The short sections of DNA studied by Dr Pollard were labeled HARs - Human Accelerated Regions - presumably because is was assumed that something in the evolution of humans caused an acceleration of the random mutation rate. However, the noted changes had to happen in a short time, and were confined to specific sections of the genome - the brain genes and the associated control sections. Random changes seldom work that way, particularly when hundreds or thousands of changes are confined to a very small part - 200 out of 20,000 genes - of the human genome.
The changes seen from chimp to homo did not occur in the 60 million years preceeding that change. It appears that changes to any single gene could not occur. Also, in order to keep the genes viable, it took several changes in each gene, with simultaneous changes in the control sections. That many changes at once would seem to be beyond the capability of evolution. A recent study reported in the October 2011 Discover magazine (p24) had a human version of one of the brain genes implanted in a mouse. There were just a few differences between the chimp and homo genes, but the effect was that some neurons grew longer axons with the homo gene than with the mouse. However, there was no corresponding change to the other neurons so that the axons had no place to go to. If that had happened to the mouse, or other species before the homo evolution, the gene would easily have mutated back to where the unusable axons were not called for.
The change from knuckle walking to upright walking requires changes to the feet, ankles, knees, hips, spine, and location of head attachment. Some small subsets of the total package could be implemented separately, but several parts are required to go together. The picture illustrated in many books, showing a stooping chimp in several iterations becoming more straight legged along with other gradual changes, would not work. A chimp waddling upright on bent legs could not withstand better adapted predators, and would have difficulty seeing forward until the neck was placed correctly. Recent finds have shown adapability, with, for example, a foot very similar to ours but with the 'thumb toe' separate, so that tree dwelling would allow grasping limbs with feet as well as hand.
There are other details bearing on this speciation as well. I would like an in-depth discussion of this proposal. I will add relevant E-Mails to this site.