Molecular Clock Problems

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) pp 9-11:

As is apparent from the above discussion of the work by Cann et al. (1987), molecular methods rely on knowledge of the mutation rate of DNA across time and between species. The molecular clock hypothesis is a consequence of the neutral theory of evolution (Kimura, 1968) and implies an approximately constant rate of mutation, so long as the DNA sequence retains its original function. If this is the case, then the degree of difference between sequences being compared is simply proportional to the time since the sequences diverged. By incorporating fossil evidence, the clock can be calibrated, and thus divergence times can be attached to a molecular phylogeny.  

In fact, particular DNA sequences and proteins can mutate at vastly different rates at different times and in different lineages, and although there may be some local validity of the molecular clock hypothesis, in general there is global failure (Avise, 2000; Gibbons, 1998; Ruvolo, 1996; Strauss, 1999; Wills, 1995). The fast-mutating microsatellite loci, i.e. short repetitive sections of DNA that lie between genes, have been used to construct an alternative method for timing lineages that does not rely on external calibration of the rate of molecular evolution (Goldstein et al., 1995). However, because of mutational saturation, nuclear microsatellites are only useful for timing relatively recent events. In particular, the deepest split in the human phylogeny can be recovered with such a method, but saturation will occur in less time than the five million years or more back to the human–chimpanzee common ancestor (Jorde et al., 1998).

This situation also affects substantially the common ancestor calculations described above. For example, Wills (1995) includes a variable mutation rate across mtDNA sites and obtains a range of 436 000 to 800 000 years ago for the mitochondrial common ancestor, depending on the date used for the human–chimpanzee common ancestor.

 In general, the molecular data seem to support the replacement hypothesis, but when all the aforementioned caveats are considered, it remains far from conclusive. The dates vary widely, depending on the method and assumptions employed. Furthermore, a recent African origin has difficulty with the observed continuity of regional morphological traits, especially outside of Europe, whereas the multiregional hypothesis has difficulty with the amount of gene flow required for its support, as well as with a number of aspects of the molecular data. Perhaps the only thing that is truly clear is that population size, breeding patterns, local geographic events, migrations and reproductive barriers present a severe challenge when it comes to interpreting these results (Lahr and Foley, 1998). So long as positions at both extremes in this debate consider themselves equally well supported by the same data, be it fossil or molecular, substantial further study into the basis of all these methods is obviously of great importance.

Species Tree vs. Gene Tree

Wessen-Simulating-human-origin-evo.pdf
Simulating Human Origins and Evolution by Ken Wessen (2005) p 9:

It must be remembered that a species tree is actually a combination of several individual gene trees, and the overall picture may only be recoverable through the study of several of these individual genes (Moore, 1995). The three species shown in Figure 1.2 contain a gene whose form in species C is older than the form in species A and B (the B–C species ancestor being polymorphic). Sampling this particular gene would incorrectly imply a closer relationship between species A and B than between B and C. (Analogously, in a morphological study, many independent morphological characters may be needed for accurate resolution of a species tree.)

History of Simulating Evolution

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 12:

Raup et al. (1973) studied the generation of species lineages by modelling speciation as an equilibrium process of random lineage branching. All lineages stem from a common ancestor, and may continue in time, become extinct, or produce a new lineage by branching, with a probability based on the difference between the existing diversity and a predetermined equilibrium value. An algorithm for the automatic identification of clades was included, allowing study of the taxonomy of the resulting phylogeny. The simulations produced quite a variety of clade shapes, which were then compared with actual clades for the Reptilia. An important fact demonstrated by this work is that differences in evolutionary pattern do not necessarily imply an inherent difference in the associated taxonomic groups: simulated groups evolving under identical constraints can behave very differently. Sepkoski and Kendrick (1993) used a similar model to simulate phylogenies. Employing exponential, logistic and mass-extinction diversification profiles, the resulting phylogenies were degraded in various ways (to model the effects of fossilisation, for example) and the information content remaining was analysed with respect to the ‘true’ phylogeny. Both these models can be generalised to allow the study of higher taxa, e.g. genus, family, etc. Nee et al. (1994) also used a similar approach to study the reconstruction of phylogenies, looking particularly at the role of lineages that become extinct.

Coalescent theory is a probabilistic framework

Wessen-Simulating-human-origin-evo.pdf Simulating Human Origins and Evolution by Ken Wessen (2005) pp 13: The study of a population is generally retrospective in nature, starting with a sample from an existing population and then attempting to describe the observed features in terms of the population’s prior evolution. Results are then generalised from the sample to the entire population. Coalescent theory (Kingman, 1982b; Hudson, 1990) provides a probabilistic framework perfectly suited to this approach, and has therefore become an extremely important tool in population genetics over the past 20 years. In brief, coalescent theory describes the merging of lineages from a sample of a population as one goes backwards in time, to the point where only a single lineage remains, i.e. the common ancestor. It is particularly well suited to molecular data, and although the usual formulation is based on the neutral model (Kimura, 1968) and a single, randomly mating population of constant size, extensions to cover recombination (Hudson, 1983), population growth (Kuhner et al., 1998), population subdivision (Hudson, 1990; Donnelly and Tavaré, 1995) and selection (Neuhauser and Krone, 1997) are well developed and are the subject of much ongoing research. A good review may be found in Fu and Li (1999).

Sarich and Wilson, 1967

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 3:

Sarich and Wilson employed an immunological technique, measuring the cross-reaction of antigens and antibodies from different hominoid species, as a method of comparing amino acid sequences, the degree of cross-reaction being a measure of similarity. The immune system is obviously highly important in natural selection, and therefore the results obtained by using this method are strongly correlated with the evolution of the species being studied. Results from this new research revealed the fact that humans, chimpanzees and gorillas are in fact more closely related to each other than any of them is to orangutans, so a more accurate phylogeny groups humans, gorillas and chimpanzees (the African apes) together, with orangutans as a sister taxon (see Figure 1.1). The ground-breaking aspect of this work was the imposition of a time scale, leading to an estimate of the time of the human–chimpanzee common ancestor of around 5 million years ago, far more recent than was being indicated by other work at the time.

Biological species vs. Phylogenetic species

Biological species concept: a group of organisms is a species if it consists of actually or potentially interbreeding individuals, and is reproductively isolated from other such groups (Mayr, 1969). Phylogenetic species concept: a group of organisms is a species if it is the least inclusive monophyletic group definable by at least one autapomorphy (i.e. a derived character state exclusive to a particular taxon) (Mishler and Donoghue, 1982). Closely related to this is the diagnostic species concept (Cracraft, 1983), where the classification is based on character states that are fixed and not necessarily autapomorphic. In practical terms, these two definitions are not as different as they at first seem. Both of them attempt to define a species essentially as an evolutionarily independent unit; in genetic terms, the biological species concept implies that gene flow can occur, whereas the phylogenetic species concept implies that gene flow has occurred. However, both concepts have limitations. The biological species concept is unable to classify asexual species, and neither can it be applied to fossil species; it tends to be overly lumpy and results in groups larger than perhaps are desired; and it can also be argued that, because the ability to interbreed is a primitive trait, the biological species concept may result in grouping of species that are not actually closest genetic relatives. The phylogenetic species concept is limited in ways that are in many respects the flip-side of the above problems. It tends to be overly splitting, resulting in groups smaller than desirable; organisms may be grouped on characteristics of unclear biological relevance; and different species (according to this definition) may interbreed, leading to interspecies gene flow.

Grade vs. Clade

Wessen-Simulating-human-origin-evo.pdf Simulating Human Origins and Evolution by Ken Wessen (2005) p 19: Any group of species may be classified according to the phylogenetic relationships of its members. A group that contains its most recent common ancestor and all its descendants is said to be monophyletic. If some, but not all, descendants are contained, it is a paraphyletic group. If the most recent common ancestor is not in the group, it is said to be polyphyletic. Traditionally, classification has been based on the concept of a grade, i.e. a grouping determined on the basis of overall morphological similarity. Such groupings often do not reflect the precise genetic relationships between the species, and are frequently paraphyletic or polyphyletic groups. The alternative is a clade-based classification, determined on the basis of common genetic origin, or monophyly. Because both morphological similarity and genetic relatedness between species are such primary concerns, both grades and clades remain important for taxonomy (Cronquist, 1987; Sokal, 1985). On the basis of the computer simulations mentioned in Section 1.3, Sepkoski and Kendrick (1993) found that, for incomplete data, polyphyletic groups may be just as useful ‘systematically’ as are clades (monophyletic groups). The species simulations in this book employ both techniques (see Section 3.1).