Saturday, 1 August 2015

A criticism of Stephen Palmer's talks at the Coventry Creation Day - 8

Peppered moths, speciation, and mechanisms of evolutionary change

We’ve seen that the evidence for common descent just from comparative genomics is beyond reasonable doubt. Evolution as fact is no longer a question in science, any more than heliocentrism is. The mechanism of evolutionary change, evolution as theory, is however a separate issue and one that is still an area of active research. This does not mean that we are in the dark on how evolution occurs. Even though selection acting on random mutation is not the sole mechanism of evolutionary change,[1] its utility and power can hardly be underestimated.[2]

Perhaps the classic example of how evolutionary change occurs is that of the peppered moth Biston betularia. Prior to the mid-19th century, the dominant form of the peppered moth in Manchester was its light coloured variant. By the end of the 19th century, this had reversed, with the black form far outnumbering the white form. This was interpreted as reflected the considerable industrial pollution which blackened tree surfaces, providing camouflage for the melanic form and exposing the white form to predation.

Allegations of scientific fraud with respect to the studies investigating this hypothesis, coupled with considerable special creationist disinformation carried out to explain away a powerful example of evolution caused a temporary eclipse in the power of this example of evolution, but these doubts were ably answered by the late Michael Majerus – who was arguably one of the leading experts on this subject – who in his review paper pointed out:
Here, the main elements of the case are outlined and the reasons that the peppered moth case became the most cited example of Darwinian evolution in action are described. Four categories of criticism of the case are then evaluated. Criticisms of experimental work in the 1950s that centered on lack of knowledge of the behavior and ecology of the moth, poor experimental procedure, or artificiality in experiments have been addressed in subsequent work. Some criticisms of the work are shown to be the result of lack of understanding of evolutionary genetics and ecological entomology on the part of the critics. Accusations of data fudging and scientific fraud in the case are found to be vacuous. The conclusion from this analysis of criticisms of the case is that industrial melanism in the peppered moth is still one of the clearest and most easily understood examples of Darwinian evolution in action and that it should be taught as such in biology classes. [3] (Emphasis mine)
Majerus died before he could publish the results of his research into peppered moth colour variation, designed to address weaknesses in earlier studies. In 2012, his data was published in Biology Letters, showing not just the evidence for selection pressure against coloured moths, but that its status as an icon of evolution is well justified:
The lifespan of wild moths is several days, so the approximately 9 per cent reduction in daily survival of melanics is sufficient in magnitude and direction to explain their long-term local decline; the decline rate suggests a selection pressure against melanics of s ≈ 0.1–0.2 per generation. Majerus was able to see predation events from his window, involving nine species of local insectivorous birds. Clearly melanics disappeared faster than non-melanics in this experiment, and Majerus was able to confirm by direct observation that about one-quarter of the disappearances were owing to bird predation.
Factors other than predation have often been argued to play a substantial role in the rise and subsequent post-industrial fall of melanism in Biston. Nonetheless, with this new evidence added to the existing data, it is virtually impossible to escape the previously accepted conclusion that visual predation by birds is the major cause of rapid changes in frequency of melanic peppered moths. These new data answer criticisms of earlier work and validate the methodology employed in many previous predation experiments that used tree trunks as resting sites. The new data, coupled with the weight of previously existing data convincingly show that ‘industrial melanism in the peppered moth is still one of the clearest and most easily understood examples of Darwinian evolution in action’.[4] (Emphasis mine)
Attempts by special creationists to dismiss this because they are ‘still moths’ ignore the point that this example is an example of evolution in action – selection acting on mutation – and assumes without proof the special creationist claim that there is a ‘limit to evolution’, or selection acting on mutation is incapable of creating significant morphological change.

The discovery that animals share a group of 'tool kit genes' involved in the development of organs and body parts during embryogenesis not only has been one of the major breakthrough in developmental biology in recent years, but has shown us how mutations in that 'relatively short period' can result in developmental repatterning and large-scale evolutionary change. Developmental biologists and geneticist Sean Carroll gives a splendid example of how this happens:
The three-spine stickleback fish occurs in two forms in many lakes in North America—a shallow-water, bottom-dwelling, reduced-spined form and an open-water, full-spines form...The pelvic spines are actually part of the fishes’ pelvic fin skeleton, and the pelvic and pectoral fins are repeated structures. Pelvic spine length is under selection pressure from predators. In the open water, longer spines help protect the fish from being swallowed by larger predators. But, on the lake bottom, long pelvic spines are a liability. Dragonfly larvae seize and feed on young sticklebacks by grabbing them by their spines. 

The evolution of these stickleback populations is very recent. The lakes they inhabit were formed by receding glaciers in the last ice age, approximately 10,000 years ago and each lake was colonized by oceanic sticklebacks that then rapidly and repeatedly diverged into the short-and long-spined populations. Exceptional fossil records of stickleback evolution have been uncovered that document their rapid evolution.  
Because the two populations are so recently evolved, they can still mate together and produce offspring. This allows geneticists to trace the genetic changes that underlie the divergence of body forms. Recently, David Kingsley, Dolph Schluter, and their collaborators at Stanford University and the University of British Columbia have been able to pinpoint genes responsible for the evolution of different traits in sticklebacks. The evolution of one trait, the pelvic spines, reveals how the formation of a repeated structure evolves through changes in the way a tool-kit gene is used.  
The reduction of pelvic spines in bottom-dwelling populations is due to a reduction in the development of the pelvic fin bud. The major gene responsible for the reduction of the pelvic skeleton was recently identified as a tool-kit gene called Pitx1. This is a typical tool-kit gene—it has several jobs in the development of the fish, it acts by controlling other genes, and has counterparts in other animals, such as the mouse. In the mouse, Pitx1 helps make the hindlimb different from the forelimb (limbs are another repeated structure).  
We know from the fossil record that the pelvic fin was the evolutionary forerunner of the hindlimb of four-legged animals. The use of Pitx1 in the development of the pelvic fins in fish and in mammal hindlimbs is a very nice, independent piece of evidence supporting that history. But the main point I want to make here is how the fishes’ pelvic skeleton gets reduced by changes at the Pitx1 gene without affecting other body parts where Pitx1 also functions.  
The big clue comes from comparing the Pitx1 proteins of the pelvic-reduced and full pelvic forms. There is not a single difference in the protein sequence.  
But, wait, didn’t I say that changes at Pitx1 made the pelvic skeleton different? Yes, I did. The apparent paradox is resolved by understanding that, in addition to the coding part of a gene, every gene also contains noncoding DNA sequences that are regulatory. Embedded in this regulatory DNA are switchlike devices that determine where and when each gene is or is not used. Tool-kit genes can have many separate switches, with each switch controlling the way a gene is used in a different body part. The function of switches depends on their DNA sequence, and changes in their sequence can alter how they work. A critical property of these switches is that changes in one switch will not affect the function of the other switches. And therein lies a huge insight into how form evolves. That is, the use of a tool-kit gene can be fine-tuned in one structure without affecting any other structures.  
In the pelvic-reduced stickleback, the Pitx1 gene is, in fact, not used in pelvic fin development. Changes in the switch that govern its use in the hindlimb have enabled the selective reduction of this part of the fishes’ skeleton...The power of this example lies in its demonstration of how, at the fundamental level of DNA, a major change in body anatomy can rapidly evolve.[5] (Emphasis mine)

Two forms of stickleback fish occur in many lakes, the bottom-dwelling form has a reduced pelvic skeleton. The reduction of the skeleton is due to a change in the function of a genetic switch controlling the use of the Pitx1 gene in the developing pelvic fin (X). Drawing by Leanne Olds.

Finally, we have plenty of documented examples of speciation, which strictly speaking is macroevolution given that it refers to evolutionary change resulting in speciation, and not just ‘variation within species’. Speciation has been observed repeatedly in the natural world:

1. Homoploid hybrid speciation in plants has been documented[6] in eight cases: 
  • Helianthus anomalus
  • Helianthus deserticola
  • Helianthus paradoxus
  • Iris nelsonii
  • Peaonia emodi
  • Peaonia species group
  • Pinus densata
  • Stephanomeria diagensis
2. Incipient speciation has been documented in yeast via divergent adaptation and antagonistic epistasis. This was shown in an experimental population of the yeast Saccharomyces cerevisiae:
Unlike natural species, our experimental populations have an evolutionary history that is known with certainty. We can therefore conclude that divergent adaptation caused the reproductive isolation observed in this investigation. Experimental evolution of reproductive isolation has been studied in a few eukaryotes (mainly Drosophila) with mixed results. Previous research has focused mostly on prezygotic isolation, and we are aware of only a single study that reported successful evolution of postzygotic isolation by means of divergent selection. We present the most striking example of experimental evolution of postzygotic isolation observed in any organism, and the first for the fungal kingdom.  
Although the isolation that evolved de novo in our short-term experiment is partial, it represents incipient speciation. Given more time, complete reproductive isolation is likely to evolve.[7]
3. Incipient speciation in populations of Drosophila melanogaster via sexual isolation has been documented.[8] The authors note that “The results shed light on the population genetic processes underlying the formation of nascent species, as well as modes of speciation.”

4. Seehausen et al demonstrated[9] speciation within island populations of cichlid fish in Lake Victoria. The mechanism for this speciation is female preference for different male colouring, with differences in the light gradients in the lake being important in effecting speciation. As the authors note, this also explains why cichlid fish species collapsed during human-induced eutrophication.

5. The Rhagoletis apple fly provides an example of sympatric speciation occurring in the context of a shift from its native host to an introduced apple species.[10]

Examples could be readily multiplied, but the point has been made. Speciation has been repeatedly observed. We have seen examples both of microevolution - change within species - and macroevolution - change outside the species level.

[1] Genetic drift, for example.
[2] The field of evolutionary computation shows how using an electronic version of selection acting on mutation can effect elegant design which surpasses that of intelligent human designers.
[5] Carrol S.B. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution (2006: W. W. Norton & Company) p 205-207
[6] Rieseberg L.H. “Hybrid Origins of Plant SpeciesAnnu. Rev. Ecol. Syst. 1997. 28:359–89
[8] Ching C, Takahashi A, Wu C “Incipient speciation by sexual isolation in Drosophila: Concurrent evolution at multiple lociProc. Natl. Acad. Sci. USA (2001) 98:6709-6713
[9] Seehausen O et al “Speciation through sensory drive in cichlid fishNature (2008) 455:620-627
[10] Bush G.L., Smith J.L. “The Genetics and Ecology of Sympatric Speciation: A Case StudyRes. Popul. Ecol. (1998) 40(2):175-187