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Unicellular Organisms

Evolution: Muatation of Gene(s), Natural Selection, and Time

The essence of Darwinian evolution is that natural selection for incremental variation forged the great diversity of life from its beginning as a simple ancestor (or what was re-phrased later as "the survival of the fittest."). Darwin's process of evolution involved three key components - variation, selection, and time. He had been struggling ever since to explain the idea to skeptical audience how slight variations would be selected for and accumulate over a period of time that was beyond human experience. It seems as if the human brain were specifically designed to misunderstand Darwinism, and to find it hard to believe. It wasn't until some fifty years after "The Origin of Species" that biologists finally appreciated the interplay of chance, selection, and time in concrete terms. It turns out that a little bit of everyday mathematics, the kind we use to calculate probabilities in a casino or in a lottery, and to calculate interest on savings and loans (see formula for natural selection in Figure 11-36m, where the selection coefficient s is similar to the interest rate in the more humdrum circumstance), finally convinced them that natural selection was, at least in theory, strong enough and fast enough to account for evolution.

Now, after 150 years, we can do even better by looking at the DNA in the genes and genomes, in which records are preserved for each step in the evolution. The ability to see into the machinery of evolution transforms how we look at the process. For more than a century, we were largely restricted to look only at the outside of evolution. We observed external change in the fossil record and assessed differences in anatomy.
Mutations However, we had no concrete knowledge of the mechanism of variation. In other word, we did not know how the fittest are made. It turns out that the slight variations are small mutation in the genes. If such change is useful it will be passed onto future generations, otherwise it would be rooted out - the essence of natural selection. Any gene that is not useful will accumulate errors and become obsolete (fossilized). Figure 11-36h shows the types of DNA mutations that introduce trait variations. Table 11-03 lists mutations on specific gene(s) and the consequences.

Figure 11-36h DNA Mutations [view large image]

Species Gene(s) Function Mutation Selection for MYA
Bacterium Genes coding FlgL and homologues Locomotion Duplication and divergence Flagellar components (rod, hook, filament) >3000
Fish Actinodin Making fins' rigid fibres Deletion Walking on land ~ 365
Giant Panda T1R1 Digesting protein Insertion in the 3rd & deletion in the 6th exon Change of diet to eating bamboo ~ 75
Old world primates Opsin Colour vision Duplication, fine tuning Trichromatic vision 30-40
Human V1r olfactory receptor gene Smell 50% fossilized Decreasing sense of smell 30-40
Icefish Globin gene Making globin in hemoglobin Fossilized and eroded adaptation to cold water 10-14
Antarctic fish Gene for an enzyme Anti-freeze 3 repeating amino acids Living in cold water 10-14
Colobus Monkey Ribonuclease gene for pancreatic enzyme Breaking down RNA Triple duplication and modification Ruminating stomach for fermented leaves ~ 6
Human Switch for the AR gene Facial whiskers and penile spines Lost Emotional Bonds (?) ~ 5
Human Switch for the GADD45G gene Suppressing the development of cortex Lost Permiting the development of cortex ~ 5
S. kudriavzevii 7 galactose genes Utilization of galactose Lost Living on decaying leaves ~ 3
West Eurasian SLC24A5 Skin color Single-nucleotide polymorphisms (SNP) Lighter skin color for vitamin D absorption in reduced sunlight 0.025
Stickleback fish Genes coding armor plates Protection in ocean Reduction of gene number Greater body flexibility in lake 0.01
Stickleback fish Switch for controlling Pitx1 gene expression Making pelvic fin Changed Reduced pelvic skeleton 0.01
Lactose-tolerant Populations Intestinal lactase gene Digest milk sugar lactose Single base-pair change in regulatory sequence Digest milk in adulthood 0.009
Tibetans HIF-2 Red blood cell production Single-nucleotide polymorphisms (SNP) Adoption to hypoxia environment 0.003
Nigerian LARGE Response to infection Single-nucleotide polymorphisms (SNP) Lassa fever virus resistance Recent
Pupfish Thyroid hormones from the thyroid gland Morphologic changes Thyroid suppression Environmental adoption 5 years
Blind cave fish Pigmentation gene Body colour Deletion of DNA text Albinism On-going
Birds and mammals MC1R Coloration of body Single letter change Camouflage On-going
Pea plant Gene for gibberellin oxidase Growth-stimulating hormone Single letter substitution, G A Mendel's Experiment on height of plants Man-made

Table 11-03 Evolution: Mutation of Gene(s), and Natural Selection

Note: MYA - million years ago when the selection process started.

The core of the Standard Evolutionary Theory (SET) consists of five elements :
Evolutionary Theory (a) Mutation - Change in the sequence of one or more nucleotides in DNA (the mutation) would alter the structure of proteins or its production regulator generating a change of certain trait(s). As shown in Figure 11-36i(a), insertion of a 800-base-pair in the gene changes the skin of the pea from smooth to winkled (see evolution in colour vision).

Figure 11-36i Evolutionary Theory [view large image]

(b) Natural Selection - The change in trait(s) can exert a positive or negative influence on survival and reproduction depending mainly by the environment. For example, giraffe's long neck and legs are selected for getting more food (Figure 11-36i(b), also see evolution in action).

(c) Gene Flow - Composition of a population is altered by the migration of other species into its territory. Figure 11-36i(c) shows the change in population characteristics as the result of the arrival of brown beetles.

(d) Genetic Drift - This is the change in population characteristics by chance, e.g., the birds prefer green beetles resulting in decimation of this kind as shown in Figure 11-36i(d).

(e) Recombination - This refers to the mixing of DNA (inherited from the parents) in the process of meiosis as shown in a much simplified diagram in Figure 11-36i(e). The end product are gametes (sperm or egg) with its own characteristics.

Lately in the 21st century, some researchers advocate the Extended Evolutionary Synthesis (EES), which includes more processes into the theory. The five main additions are summarized in the followings.

Extended Evolutionary Synthesis (1) Developmental Bias - Constraint for variation can be imposed by the inherently developmental processes within the organism. The processes may generate certain forms more readily than others. For example, the cichlid fishes in two different lakes have strikingly similar body shapes (Figure 11-36j(1)).

(2) Phenotypic plasticity - It is the ability of an organism to change its phenotype in response to changes in the environment. Figure 11-36j(2) shows the change of colour in commodore butterflies during dry (left) and wet seasons.

Figure 11-36j EES
[view large image]

(3) Inclusive Inheritance - Extra-genetic inheritance occurs outside genetic expression, e.g., epigenetic changes, social behaviors, ecological constraints, etc. Figure 11-36j(3) shows a rodent maternal behavior transmitted through epigenetic changes; in this case it is the expression of genes by sexual hormones.
(4) Niche Construction - It is the process in which an organism alters its own environment with evolutionary or ecological consequence. The sponges in Figure 11-36j(4) appear to have added oxygen to the deep ocean creating an enivronment where more mobile, major oxygen-using animals could have evolved.

(5) Contribution by viruses - It is suggested that viruses play an important role in the evolution of cellular organisms by integrating their genes into the host DNA. The evolution of mammalian placenta, and the adaptive immunity in vertebrates are just some of the examples in which evolutionary changes are not the results of random error (mutation) but of viral infection events.

In response to this criticism of neglecting key processes in evolution, the SET establishment maintains that such phenomena have been integrated into their consideration already, actually dating back to Darwin himself (see "Does Evolutionary Theory Need a Rethink ?").

To see the evolution in action, let's consider our colour vision in detail. Colour vision of vertebrates depends on the pigments in the cone cells. It turns out that birds, as well as reptiles, and many fish, have four types of cone pigments, whereas most mammals have only two types (Figure 11-36k). Mammals lost two of the pigments during their early evolution, very likely because these animals were nocturnal and cones are not needed for vision in dim light. After the dinosaurs died out, mammals began to diversify, and the lineage that gave rise to the Old World primates of today reclaimed a third cone through duplication of the opsin gene and subsequent mutation. The
Colour Visions Opsin Gene evolutionary changes have been located at three amino acid sites following the duplication. The mutations are retained because they appeared to have imparted a substantial advantage on the species (the old world primates) that bored them (see Figure 11-36l). The diagram shows those amino acid positions at 180, 277, and 285 within the opsin protein, which is bound to the light sensitive retinal. These differences are enough to shift the maximal light absorption from 560 nm for the red opsin to 530 nm for the green opsin. Note that mutation occurs with equal probability on all sites in the DNA; however, only those offering an advantage in survival will be retained.

Figure 11-36k Natural Selection

Figure 11-36l Mutation of Gene
[view large image]

Tangible evolutionary change occurs in time scale of million years although some adaptations such as the peppered moth to the environment becomes obvious in the order of fifty years or least (Figure 11-36m). Million years is an immense amount of time to us. However, it is short in
Moth geological scale, which offers ample time, many times over, for selection to shape a trait considering our ancestors' brains doubled in size in 1 million years (about 50,000 generations). Since change in the gene only becomes effective after passing onto the progeny, ultimately it is the number of generations that contributes to the speed of evolution with time serving only as an indicator. The evolution of simpler life appears to run faster because it can produce many generations within one year. It is crucial to appreciate that selection and mutation operate in nature every day. Every environment impacts continually upon the species that inhabit and reproduce within it. Evolution is an ongoing process. Selection acts only in the present, within a given environment. It cannot act on what a species no longer needs or uses. And it cannot act on what is not yet needed. Thus, fittest is a relative, transient status, not an absolute or permanent state.

Figure 11-36m Evolution Time Scale [view large image]

Note: For decades, the peppered moth was the textbook example of evolution in action. In the late 1990s a problem cropped up with the method of data gathering. It was seized by anti-evolution organizations as proof that the Darwinian theory is hopelessly flawed. A more rigour experiment few years later has finally restored the peppered moth as the well-understood example of evolution by natural selection.

Peppered Moth Evolution The mechanism to induce the change in coloration of the peppered moth had not been identified until 2016 when one research detects the insertion of jumping genes into the cortex gene of the melanic moth (Figure 11-36n,a). Usually, the cortex gene is expressed to cleanup redundant proteins in cell cycle and has nothing to do with coloration. The relationship becomes clearer when another research on butterfly colors reveals that a version of the cortex gene is involved in the development of size, density and surface properties (including coloring) of the wing scales (Figure 11-36n,b,c).

Figure 11-36n Peppered Moth Evolution [view large image]

Darwin's notion of evolutionary via gradual mutation had a long history of controversy even in Victorian times. It has come under fresh challenge with recent knowledge that many evolutionary advances were relatively abrupt, and there are "missing links" in the fossil record. It is pointed out that most fossil species share two features; first, they enter the record abruptly; second, they do not change in any marked way during the entire course of their existence. An explanation without the baggage of "intelligent design" involves both information theory and junk DNA. In information theory, novelty is related to the number of possibilities in the message source. In living organisms, these possibilities may exist as unused information in the genes (the junk DNA). Evolutionary innovation, the creation of new organs with new functions, would then be accomplished by making the possibilities actual (through mutation in the junk DNA). Usually, a gene copy, as an extra page, is ignored by natural selection, even when accumulating mutations, as long as the "original page" of which it was a duplicate continues to serve its beneficial function. The copy is free to change in ways, which would not be tolerated in the original. Once the new gene acquires a useful meaning it may then come under the protection of natural selection and be preserved. It is noticed that major new steps in evolution were not usually taken by the most advanced member of a class of animals, which has gone into a blind alley (too much specialization). It is the more "primitive" member, which is most likely to take advantage of the copies of junk DNA - much like a sheet of white paper ready to be written upon. It is argued that explosions of gene duplication took place many times in history with sudden evolutionary advances to follow.

In case there is still lingering doubt about our evolutionary past, further supporting evidences can be found in many of our ailments that can be traced back to the shark and even microbe. Table 11-04 presents a short list of some ailments arisen from the incompatibility between the modern lifestyle or body structure and the remnant of the evolutionary past. Our body is literally jerry-rigged into a shape produced by natural selection without giving much thought to minor inconveniences.

Ailment(s) Body Part(s) Modern Modification Past Existence
Obesity Body fat Sedentary lifestyle Active lifestyle in primates
Hemorrhoids Rectum Sitting for long hours Lot of walking in primates
Back Pain Lower back Bipedalism Body’s full weight was borne on four legs rather than two
Sleep apnea Throat Throat becomes flexible for the ability to talk Throat is not flexible for most mammals or reptiles
Hiccups Phrenic nerve Phrenic nerve takes long path to control breathing in human, its interference can cause a spasm Phrenic nerve takes shorter path from brain stem to gills in fish
Hernias Abdominal cavity The gonads in the fetus of mammals migrate from upper to lower part of the body creating weak spot in body wall around the groin area The gonads are located in the upper part of the body in fish and shark
Mitochondrial diseases An organelle In every cell Many human mitochondrial diseases are related to gene change that interrupts the normal metabolic function Diseases of such gene mutation in mitochondria can be duplicated in bacterium

Table 11-04 Ailments Related to Evolutionary Past

Note: Hernias is a condition in which part of an internal organ projects abnormally through the wall of the abdominal cavity.

July 2008 Update - The asymmetry of flatfish is an exceptional morphological specialization that arises in development:
Flatfish starting from a symmetrical larva/juvenile, the skull is remodelled so that one eye migrates over the top of the skull to sit next to its other eye. Such change seems to mirror in the form of many living species with the pair of eyes in varying degree of togetherness. The lack of any intermediate specimen has led to attacks on natural selection and arguments for saltatory (leaping as opposite to gradual) change. The discovery of 47 million year old fossils (in 2008) of the Amphistium with its migrating eye never gets further than the dorsal midline, even in fully adult fishes has finally settled the dispute and confirmed that evolution of

Figure 11-36o Morphological Change in Flatfish [large image]

the specialized flatfish bodyplan was a gradual process induced by bottom-dwelling lifestyle (see Figure 11-36o, a - d for the transition of morphology in flatfish).

Since "Darwinian Evolution" is just a theory (same as all the other concepts suggested by human), it should be validated by empirical evidences as all the other theories. A theory is believable if no contradiction is perceived. A theory has to be modified or discarded if it fails the test. There is also the degree of acceptance depending on the number of evidences available. The Nature Magazine has kindly provided 15 examples in a document on its website for everyone to judge whether the Darwinian Theory is a valid one.

For many people the appearance of a new trait (phenotype - such as a horn on the head of the rhino) as the result of evolution is very difficult to
Ecoli Evolution imagine. The process has now been demonstrated conclusively by an experiment starting way back in 1988 on an E. Coli population. A new trait finally emerges after 24 years or about 30000 generations. The new trait is the use of citrate (a salt of citric acid such as in lemon juice) as a nutrient in the presence of oxygen (labeled as cit+ in Figure 11-36p). In the beginning of the trial, the citrate can be absorbed as nutrient only in the absence of oxygen (labeled as cit- in Figure 11-36p). It is through the re-arrangement of a few DNA sequence and many duplications of such mutation that allows the new trait to establish itself in the E. Coli population. Figure 11-36p shows many dead ends until the condition is right for actualization (of the new

Figure 11-36p Ecoli Evolution [large image]

trait) and finally its refinement (maturity) after 40000 generations. This is Darwinian evolution in action albeit for small bacteria and only about one single trait.

Radiolaria Diatoms It is noticed that some single cell organisms do not constrain by the rule of natural selection. They don't have complex organization, which requires a processing sequence to develop. Any unfavorable mutation that occurs during such process will likely be eliminated by internal selection. Thus, single cell organisms such as radiolaria (Figure 11-36q) and diatoms (Figure 11-36r) can exhibit 100 thousands different forms by random mutation without being culled by natural selection.

Figure 11-36q Radiolaria
[view large image]

Figure 11-36r Diatoms
[view large image]

Darwin himself had mentioned this possibility but had forgotten to add a qualifier about small or simple. BTW, the holes in radiolaria are for the extrusion of the pseudopods, while it is for filtering in diatoms.

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