Evolution 1: How Does Life Change?

I. The Growth of Biological Thought

A. Darwin's Contributions: The Origin of Species (1859)

1. Observations

a. The Earth is old: James Hutton (1726-1797): Hutton was the first great british geologist. He compared Hadrian's wall - which looks new but was 1600 years old (122 AD) - with natural rock outcrops that were strongly weathered. Hutton concluded that the natural outcrops must be 100's of times older. He also examined an important formation at Siccar Point, where one series of nearly vertical strata is overlain by another series of horizontal strata. This is now called an 'unconformity', and Hutton explained it as follows. Based on Steno's laws of superposition, the bottom vertical sediments must have been laid down first, and they must have been laid down horizontally. Ages must have passed between each deposit, as each turned to rock. Then, uplifts must have occurred to bend them into a vertical aspect. Long periods of erosion must take place to wear that uplift flat, followed by the long intervals of time needed to deposit the second horizontal series. Also, if erosion and deposition acted slowly (as current observations show), then it must have taken a really long time to erode mountains or build up marine deposits (White Cliffs of Dover). He concluded that this slow, 'uniformitarian' cycle of deposition, uplift, erosion, and deposition meant that the Earth was unfathomably old. Indeed, the cycle may mean that it's age might not be discoverable. In short, Hutton concludes, the Earth has "no vestige of a beginning, no prospect of an end."

b. Paleontology: Fossils show Patterns

Paleontology provided a variety of interesting patterns. First, there were extinct forms that were different from the species alive today. Although some earlier natural philosophers suggested that the creatures might still exist in some unexplored corner of the globe, that was a less satisfying hypothesis in the mid-1800's... most areas of the globe had been visited by Europeans. Also, the idea of extinction was repugnant to some people on theological grounds. If God had created a perfect world, then extinction renders that creation imperfect. Also, if species could go extinct since the creation, could species also come into existence since the creation? Just how dynamic was this system?

Darwin was impressed by two major patterns in the fossil record.

1. The major groups of animals accumulate in an orderly manner'. Everything is not represented at the beginning. In vertebrates, for instance, the fishes appear first, and exist throughout the rest of the record. Amphibians appear next, followed by reptiles, mammals, and birds. So it is not everything at the beginning, and it is not a replacement. Where did mammals come from? Spontaneous generation had been refuted, so Darwin knew that mammals had to come from other pre-existing animals. But the only completely terrestrial vertebrates before mammals were reptiles.

2. A second major pattern occurred within some lineages of similar organisms. Within some lineages, we seen orderly change in the size or characteristics of species in a geological sequence. For instance, consider the morphological patterns in a particular taxon (horses). Fossils in a stratigraphic sequence are similar, but often have traits that form a continuum...like the progressive loss of digits on the horse limb. And, with each innovation, there are often radiations - a "spurt" in the number of species that show this new trait. And finally, these species in recent strat are more similar to living ('extant') species than the species found in deeper, older strata. So, many of these transitional sequences terminate in living representatives.

c. Comparative Anatomy shows patterns realted to the environment:

Homologous Structures
    Although having a different outward "look" and although used for different purposes, they have an underlying similarity in structure - forelimbs of vertebrates all have one long upper arm bone, two lower arm bones, a bunch of wrist bones, and five digits. Darwin saw the similarity in structure as important. An engineer builds different things for different purposes - cars, boats, and airplanes are structurally DIFFERENT. Here, however, it seemed as if one basic structure was modified for different uses. Darwin knew why siblings in a family were similar - they had the same parents (ancestors). He reasoned that these structural similarities in different species might be due to the same principle - common ancestry. Also, he observed a correlation: Different uses correlated with different environments. Could this correlation be causal?

Analogous Structures
    Organisms in the same environment often have a similar outward structure or body plan. For example, flying animals all have an aerodynamic wing that is wider at the front than at the rear. However, the wings of differnt animals are differnt in underlying structure. Bats have fingers that support the membraneous wing, whereas birds lack fingers and the body of the wing consists of feathers. Insect wings don't involve the limbs at all (even though they have 6!). Again, Darwin observed this correlation with the environment: similar use (and outward structure) in similar environments. Could this correlation be causal?

Vestigial Organs
   These are organs that have no function in one organism (where they are 'vestigial') but they do function in other organisms. So, some whales have hip bones, but no legs. Why do they have these bones? Darwin was struck by the IMPERFECTIONS in nature, as much as the adaptations. Why do men have nipples? Why do we have muscles that wiggle our ears? Why do we have strong muscles in the front of our stomach, which are not "load-bearing", and weak muscles at the base of our abdomen (which rupture in a hernia)? This is a reasonable relationship in a quadraped, but not in a biped. Why do we have tail bones, but no external tail? Again, these are NOT well-designed features. In fact, attributing these imperfect designs to a perfect creator could be interpreted as heretical.  However, when we see them working in OTHER species, it suggests that maybe we inherited them from common ancestors where they DID serve a function. As a scientist, Darwin was trying to explain ALL the data (adaptations and imperfections), he was not simply bringing forward only the data that supported a preferred position (design).

d. Species distributions show patterns realtd to the environment:
    Under similar environmental conditions, we find different species filling similar ecological niches.  Outward 'form' correlates with ecological niche (role) across entire communities. So, in Australia, marsupials fill the role of dog-like predator, cat-like predator, burrowing animal, ant-eater, etc. These same roles are filled by outwardly similar placental mammals in South America. However, the similarity between a wolf (placental) and a Thylacine (marsupial - the 'tasmanian wolf') are strictly ANALOGIES. Their underlying structure shows them to be quite different - a wolf is more similar to a ground hog (both placentals) in underlying structure than to a thylacine.

    Islands often have fewer species than a mainland - even a patch of mainland the same size. As such, the patterns and interactions are often simpler to describe and understand. For both Darwin and Alfred Russel Wallace (the other independent author of the theory of evolution by natural selection), the study of islands was critical in to the development of their ideas.

1. Distance correlates with the uniqueness of the inhabitants: the animals on the Fauklands are the same species as on the mainland, but the Galapagos fauna is composed of unique species, found nowhere else:

"The natural history of these islands is eminently curious, and well deserves attention. Most of the organic productions are aboriginal creations, found nowhere else; there is even a difference between the inhabitants of the different islands; yet all show a marked relationship with those of America, though separated from that continent by an open space of ocean, between 500 and 600 miles in width. The archipelago is a little world within itself, or rather a satellite attached to America, whence it has derived a few stray colonists, and has received the general character of its indigenous productions. Considering the small size of the islands, we feel the more astonished at the number of their aboriginal beings, and at their confined range. Seeing every height crowned with its crater, and the boundaries of most of the lava- streams still distinct, we are led to believe that within a period geologically recent the unbroken ocean was here spread out. Hence, both in space and time, we seem to be brought somewhat near to that great fact -- that mystery of mysteries -- the first appearance of new beings on this earth."  The Voyage of the Beagle - Darwin (1839).

    2. The Galapagos fauna:
        - It was related to american fauna, yet different: the types of animals are new world animals.... there are iguanas like the green iguana of Central and South America, but the iguanas are different species. So, darwin describe it as " a world within itself, or rather, a satellite of the Americas" .... it was different, but more like the American fauna than any other...(no chameleons, for instance, which are old world lizards...)

        - It was dominated by dispersive forms. This is critical. The communities are dominated by reptiles, birds, and marine mammals. All of these organisms could MIGRATE to the islands from the mainland. (Terrestrial mammals don't migrate as well as terrestrial reptiles over open ocean. Throw a reptile in cold salty water, and: 1) its metabolism slows down (its cold), so 2) its demand for food and water decline; and 3) its scales protect it against water loss... which is why reptiles do well in the desert, too. Throw a mammal in cold salt water, and it's going to have a VERY tought time: 1) the temperature gradient between its warm body and the cold ocean is very large - in order to maintain its high body temperature against this gradient, it's metabolism has to INCREASE (to produce more heat to compensate for the heat lost to the environment). This increased metabolic demand will INCREASE the need for food and water... that's probably in pretty short supply in the open ocean; and 2) water is lost quickly from the skin to the salty ocean once the fur is wet... so, mammals are more likely to starve or die of exposure than reptiles.

       - So, the islands are dominated by dispersive forms, and this suggests they came from America. But if they came from America, WHY ARE THEY DIFFERENT SPECIES THAN THOSE IN AMERICA? They must have changed since their arrival.

- There are even differences between species on different islands. On the 14 species of finches - "Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends." The Voyage of the Beagle - Darwin (1839) VIDEO

2. Argument For Evolution as a Historical Fact:

Premise 1: Species that are alive today are different from those that have lived previously.
Premise 2: Spontaneous Generation is refuted, so organisms only come from other organisms.
Conclusion 1: Thus, the organisms alive today must have come from those pre-existing, yet different, species.
Conclusion 2: There must have been change through time (evolution).
Conclusion 3: The fossil record, vestigial organs, and homologies are all suggestive of descent from common ancestors.

Below, the figure from The Origin of Species that shows Darwin's idea of descent from common ancestors.

So, if species do change over time (evolve), the next question is "How?" How does this change occur?

3. How does change occur? Natural Selection

(Know this.  Understand it.  You WILL be asked to outline NS in this very form.)

P1: Populations over-reproduce (Malthus)

P2: resources are finite (Malthus)

C1: Eventually, a population will grow until it becomes limited by its resources. At that time, their will be a "struggle for existence" and most offspring produced will die. (Malthus)

P3: Individuals in a population vary, and some of this variation is heritable (Darwin - observations and animal/plant breeding)

C2: Variations will not have the same probability of survival and reproduction in a particular environment; those well-suited to the environment will be more likely to survive and reproduce than others, passing on the genes for these adapted traits. There will be "Differential Reproductive Success" (Observations, breeding).

C3: Over time, adaptive traits will accumulate and the characteristics in a population will change. This is lineage evolution. (Like change in horse toes in a sequence of fossil species, or like the change in the chihuahua lineage from the ancestral wolves).

Corollary: Two sub-populations, separated in different environments, would be selected for different traits and may subsequently lose the capacity to interbreed. At this point, they are different biological species. This is Speciation and Radiational Evolution. (like the production of different Finches, mockingbirds, etc. on different islands in the galapagos, and like the radiation of St. Bernards AND chihuahua's, which diverged from one another over time).
 

Darwin here provides a natural explanation for why purposeful structures and behaviors occurs in nature. Through some process unknown to him, variation arises in natural populations. These varieties differ in terms of functional efficiency in a common environment; so some improving an organisms probability of surviving and mating than others. Organisms with these beneficial traits will leave more offspring, and the frequencies of these beneficial characteristics will increase through time - much as humans select for smaller and smaller dogs. He ends The Origin of Species (1859) like this:

"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved". - The Origin of Species (Darwin 1859).

II. Testing Darwin's Theories

A. The Fossil Evidence

1. Radioactive Decay and Geological Clocks

Darwin had guessed that the earth had to be at least 300 million years old to explain the evolution of life through the stately process of natural selection.  W. Thompson ("Lord Kelvin") was a physicist who demonstrated that the Earth could be no more than 24 million years old.  He did this by calculating how long it would take for a molten object with the Earth's mass to cool to the current temperature of the Earth.  However, he made his predictions before Becquerel and the Curies discovered radioactivity - a process that releases heat and keeps the Earth warmer than it "should be" (based on Thompson's inference). After the Curies discovered  radium and studied radiactivity (1898), Ernst Rutherford realized that the regular rate of decay could be used to age rocks.

a. Principle:
                   - measure amt of parent and daughter isotopes = total initial parental
                   - with the measureable1/2 life, determine time needed to decay this fraction
                   - K40-Ar40  suppose 1/2 of total is Ar40 = 1.3by                

(Now, you might say "be real"! How can we measure something that is this slow?)

Well, 40 grams of Potassium (K) contains:
6.0 x 10²³ atoms (Avogadro's number, remember that little chemistry tid-bit?).  So, For 1/2 of them to change, that would be:
3.0 x 10²³ atoms in 1.3 billion years (1.3 x 10⁹)
So, divide 3.0 x 10²³ by 1.3 x 10⁹ = 2.3 X 10¹⁴ atoms/year.
Then, divide 2.3 x 10¹⁴ by 365 (3.65 x 10²) days per year = 0.62 x 10¹² atoms per day ( shift decimal = 6.2 x 10¹¹)
Then, divide 6.2 x 10¹¹ by 24*60*60 = 86,400 seconds/day: (= 8.64 x 10⁴) = 0.7 x 10⁷ atoms per second
0.7 x 10⁷ = 7 x 10⁶ = 7 million atoms changing from Potassium to Argon every second!!!

This 'decay' gives off energy - radiation that is detectible and measureable by Geiger counters and similar instruments. It is actually an easily measured rate.  And you can come back and measure it again tomorrow, next week, next year, or in 50 years; and it has always been the same.

b. Different Clocks

The K-Ar clock is ok for measuring things that happened billions of years ago, but it is not a good clock for things happening hundreds or thousands of years ago because the rate of change is so slow. It would be like measuring an olympic 100m sprint (which last less than 10 seconds these days) with a 2-minute hour-glass egg timer. After ten seconds, only a few grains of sand will have fallen. For measuring anything, you need a gauge with the correct level of resolution. For an olympic 100m sprint, an electronic 'stopwatch' measuring to the thousandths of a second is needed. For measuring the marathon, you don't want that type of resolution; an analog clock that measures hours, minutes, and seconds is probably appropriate. Of course, when you measure the same event with different types of clocks, they should all give roughly the same answer, even if the answers differ in precision. Luckily, there are different isotopic series that give resolution at different time scales:

C14 - decays to C12 with a half-life of 5730 years
Longer periods - use different elements with longer half-lives
- K40 decays to Ar40 at a rate of 50%/1.3 b years
- U238 - Pb208 = 4.5 by
- Rb87 - St87 = 47 by
- U238 - Thorium 230 = 80,000
- U235 - Protactinium231 = 34,000       

c. Tests of Corroboration

We gain greater confidence in a conclusion if it is supported by multiple, independent pieces of evidence. One eyewitness to a crime is ok, but three different people who all tell the same story are far more convincing.   Because the decay process in one element present in rock has no effect on the way other elements decay, the decay series are independent of one another. So, one rock could be aged using the K-Ar clock, the Rb-St clock, and the U-Pb clock. If we get roughly the same age using these three different clocks, we would be more confident in that age. There are other corroborating methods, too, that don't involve decay, at all. For example, we can carbon-date material from Pompeii, which we know from historical record should date to 79ACE. Indeed, they do, corroborating the use of radiocarbon dating. One of the most dramatic corroborations involves predictions from astronomers. Astronomers have postulated that, because of tidal friction between the water in the ocean and the earth, the rotation of the Earth has been slowing down over time. In fact, astronomers have calculated that, based on the masses of the oceans and the Earth, and the frictional coefficient of water against land, that the length of an Earth's rotation (a day) has slowed at a rate of 2 seconds every 100,000 years. (So days were SHORTER in the past and have SLOWED to the current 24 period).  This process would not affect the time it takes the Earth to orbit the sun, however. So, it would take a year for the Earth to orbit the sun, but the Earth would be spinning on its axis more rapidly in the past. This means that a year in the past would have MORE days  than it does now.  Indeed, astrophysicists predict that, based on tidal friction, a year 380 million years ago would have contained 400 days. Wow... crazy. Well, corals lay down a layer of calcium carbonate 'shell' every day.  There are seasonal changes in the thickness of the layers, so years can be distinguished, too.  Some corals have been dated by radioactive decay to be 380 million years old. If this age based on decay is correct, and if the astrophysicists are correct, then they should have 400 daily layers of growth within each yearly band.  They do. So, we can use basic physics to predict the "age" of a coral.  And when we compare that "age" to the "age" determined by radioactive decay, the ages are the same. So, either they are both true, or they are both wrong in the same way.  It is unlikely that we have such basic physics wrong.  Very unlikely.  So, the Earth is, indeed, very very old. Radioactive decay is constant; if it wasn't, or if it hadn't been in the past, none of these comparisons would work.  period.  But they DO work, and so it is irrational to conclude that the Earth is young, or that radioactive dating doesn't work or is somehow "dubious".  Again, our ability to harness the power of radioactive decay in nuclear reactors is powerful testimony to the degree of confidence we have in our knowledge and understanding of the decay process. And thus, we have great confidence in the great age of the Earth.

2. 'Transitional' fossils

One of Darwin's dilemmas was the lack of continuous sequences of fossils that preserve a complete record of evolutionary change. In 1859, the fossil record was best described as 'discontinuous' for most lineages. Of particular interest to Darwin's model of common descent was the absence of 'transitional' fossils - fossils that showed the nascent beginnings of a major new type of organism evolving from more primitive stock. In the last 150 years, paleontology has unearthed millions of fossils and many have been placed in very complete sequences. They provide a solution to Darwin's dilemma and also allow us to reconstruct phylogenies. We will take a look at some of the more remarkable transitional sequences that have been documented in the evolution of vertebrates.

Transitional fossils are important in two ways. First, they contain a complement of traits that makes them hard to pigeonhole into one group of organisms or another. In other words, they have a combination of traits from two separate groups (an intermediate morphology).

But this is not all.  I mean, there are alot of crazy organisms out there.  The existence of a weird combination of traits does not mean the organism is necessarily a transitional form, nor does this support common ancestry in and of itself. Evolution does something more than simply predict the existence of transitional forms - if predicts WHEN these forms should exist. Let's apply these ideas to some real fossils.

a. Ichthyostega spp. and the evolution of tetrapods               

Darwin hypothesized that amphibians evolved from fish. This created a few important problems - how did lungs and feet evolve? In 1929, several species with a mix of fish and amphibain characters were discovered in Greenland and placed within the genus Ichthyostega. These animals had lungs and gills - an obviously intermediate morphology. And they had tails with cartilagineous rays in the fin, like a fish tail. But these animals also had feet. The legs were probably not strong enough to bear the entire weight of the animal, but it was a true tetrapod. So, it had a suite of fish and amphibian traits. However, that is not enough. To be a transitional fossil and to truly test the hypothesis that this animal is an ancestor of amphibians and a descendant of fish, it must come after true fish and before true amphibians. Indeed, that is right where it is.

This transition between fish and land animals was one of the most important evolutionary transitions in the history of life. Since 1929, many fossils have been found that form a very complete transitional sequence, linking lobe-finned fish like Panderichthyes to proto-amphibians like Ichthyostega and Acanthostega. In 2004, an exceptional fossil was found in Northern Canada that was intermediate between Panderichthyes and Ichthyostega. Tiktaalik rosae was such a beautiful transitional form that it was dubbed the "fish-o-pod". The animal has short bony forelimbs that terminate in fins, not feet. However, the limbs are able to support weight, and have a wrist-like joint that allows the limb to pivot and propel the animal forward. It has a decidedly fish-like body, but an Ichthyostegan head and intermediate limbs.

Ichthyostega was one of the first fossils that bridged the gap between fish and amphibians	Now, a series of intermediates shows the transition from ancestral, lobe-finned fishes, through limbed fishes like the "fish-a-pod" Tiktaalik, to amphibians

b. Archeopteryx lithographica and the evolution of birds               

Archeopteryx has an intermediate morphology containing reptilian and avian characteristics. It has fingers, teeth, and a bony tail like reptiles (and unlike birds), but it has feathers like birds (and unlike modern reptiles). So, it had a combination of traits from two major groups.  No birds today have teeth or fingers, and no reptiles have feathers. So, it is intermediate in morphology.  But evolution PREDICTS something else about this organism.  IF it was a biological link between reptiles and birds, then it would have to have lived after other reptiles (who were its ancestors) and BEFORE all true birds (who might be its descendants).                 

It is.  The hypothesis has been tested by evidence from the physical world. Evolution is a testable, supported theory. Indeed, since 1861, further paleontological evidence suggests that birds didn't evolve from just any reptile, but from a specific group called the Maniraptoriformes. This group diverged from the Tyrannosauroidea, which includes Tyrannosaurus rex. Within the maniraptoriformes, we see a wide variety of feathered reptiles discoverd in China since 1990. However, the feathers are not only on the limbs and they are definitely not used for flight. In fact, in the oldest fossils of feathered dinosaurs, the protofeathers are only on the head and spine. A likely scenario is that feathers were first used for attracting mates. Selection for increased feather distribution provided the additional benefit of insulation and homeothermy. Finally, large feathers on the limbs might provide lift while climbing, running, or gliding, and selection could favor the acquisition of flight. This provides a nice example of how a complex trait - flight feathers - might NOT have evolved for that purpose intially.

Archaeopteryx was the first intermediate discovered between reptiles and birds.	Now, paleonotologists have found numberous lineages of 'feathered dinosaurs', showing that the lineage leading to Archaeopteryx and modern birds was only one branch of ancestral, feathered animals.

c. Therapsids and the evolution of mammals

The transition from reptiles to mammals is one of the most well-document transitions in the fossil record. Indeed, there is such a nice sequence that it is difficult to specify where the most important or instructive transition occurs. For our purposes, we will look at a group of organisms called the therapsids. Like reptiles, therapsids have several bones in their lower jaw, and one inner ear bone. Like mammals, they had specialized detition with incisor-like teeth at the front,and larger canines. Also like mammals, they walked with their legs underneath them, rather than out to the side like ancestral reptiles. Through the therapsid lineages, we have a very clear sequence of transitions that show how several of the lower jaw bones of reptiles became reduced and were eventually used as inner ear bones in the mammals. And of course, the therapsids fill the temporal gap between one group of ancestral reptiles and the more modern mammals - just as evolutionary theory and common ancestry predict.

Therapsids were a group of reptiles that dominated during the Permian Period, 250 million years ago.	The evolution of the mammalian middle ear bones is beautifully preserved in the fossil record. The three middle ear bones in mammals (blue, yellow, pink) are homologous and descended from lower jaw bones of reptiles that became reduced in size and took on another function as their role in reptilian jaw function was assumed by the dentary bone (white).

d. Australopithecines and the evolution of humans

Even Linnaeus recognized the morphological similarity between humans and apes (chimpanzees, gorillas, and orangutans). When we look at these species, the things that set humans apart are our upright stance and bipedal locomotion, our large heads, and our relatively short forelimbs. Ever since the first neanderthal fossil was found in 1856 and after Darwin wrote The Descent of Man in 1871, we have been reconstructing the phylogeny of our own species. There are many fossil species that form an excellent transitional sequence between ancestral primates and modern humans, again making it difficult to pick just one group. However, The Australopithecines provide a good and historically important group. In 1924, Raymond Dart discovered a very small skull of a juvenile primate that he named Australopithecus africanus, meaning "southern man-ape from Africa". Like other australopithecine fossils to follow, it had a short but ape-like snout with reduced canines. Dart suggested that the presence of this fossil in Africa, and the presence of chimps and gorillas in Africa, confirmed Darwin's hypothesis of an African origin of humans. This was highly debated by other anthropologists who believed that humans evolved in Europe or Asia. The discoveries of the Leakey's in Olduvai Gorge in the 1950's and 1960's, and the discovery of Australopithecus afarensis in the 1970's by Donald Johanson, supported the African origins model. The most complete single fossil of A. afarensis, known as the 'Lucy" fossil, shows the combination of traits expected in an intermediate, transitional species. The hip and the articulation of the femur and tibia show that the organism walked erect - a characteristic that is distinctly human. However, the cranial volume is very small - only 25% the volume of modern humans and equal to the volume of chimpanzees. However, other facial features are intermediate; the snout is shorter than in chimps and gorillas, but the canines are much larger than in humans. And again, these fossils fall before more human species and after more primitive primates; just as common ancestry and evolution would predict.

Yes, this is redundant; but it is redundant for a reason.  There aren't just one or two fossils that 'conform' to the expectations of evolutionary theory.  There are 100's of intermediates that provide tests and confirmation of evolutionary theory. One of the most frequent claims of creationists is that "there are no intermediate fossils". Well, you've seen quite a few, linking the major types of vertebrates.  Darwin's theory of common ancestry predicted their existence, and scientists have tested this prediction by looking for physical evidence that could test this hypothesis.  Although only Archeopteryx and neanderthals were discovered in his lifetime, we now have intermediates linking all major groups of vertebrates, confirming these hypotheses.  It makes you wonder why these claims continue to be made, in the face of such overwhelming physical evidence.

When discovered in 1974, Australopithecus afarensis was the oldest fossil of a bipedal hominid.	Since then, several more primitive bipedal species have been discovered. The fossil history of the hominid lineage has been very well described.

C. Genetic Evidence

1. Gross Chromosomal Similarities

The most definitive tests of biological relatedness come by examining DNA. Why?  Because the only place an organism gets its DNA is from its parents, their parents, their great-grand parents, and their ancestors. Barring the rare events of lateral gene transfer that can occur in some organisms, the only reason two organisms would have similar DNA is that they are biologically related. So, If I am accused of fathering a child, and my DNA is similar to that child's DNA, then I can be "convicted" of being related to that child.  That is the only reason two organisms will share DNA - because they are biologically related.  This pattern is reinforced by our understanding of meiosis and sexual reproduction, which explain why these patterns of relatedness occur. Now, when we see similarities among species in DNA structure, logical consistency demands that we propose the same hypothesis for the same pattern. In the figure at right, you see the chromosomes from a human, a chimp, a gorilla, and an orangutan. The most striking thing is the similarity in banding patterns across these chromosomes. Remember what those bands signify? The dark areas are heterochromatin, that have a low concentration of coding sequences. The lighter areas are euchromatin, where most of the genes are. So, we are looking at similarities in the large scale architecture of the genomes from these organisms. Evolutionary theory predicted that humans would have similar DNA to apes, and they do - even at the level of gross chromosomal structure. However, there is a major difference here; humans have n=23 while the other species have n=24. How can evolutionary biology explain this difference in chromosome number? Well, even the exception here proves the rule. The long #2 chromosome in humans - the first chromosome in thes econd set of chromosomes in the upper left corner of the figure - is banded like two of the chromosomes in other primates (shown next to it). A simple hypothesis would be that, at some point in the human lineage after divergence with chimp-like ancestors, these two chromosomes fused and became inherited as one unit. Can you remember an instance where chromosomes get stuck together and inherited as a single unit? It happens in translocation events, like in translocation Downs. And of course, this is not always deleterious to the organism - carriers for the translocation chromosome are phenotypically normal. A mating between two carriers could produce an offspring with the correct DNA content, but with two fewer chromosomes. Apparently, just such a modification may have occurred in the human lineage after divergence for the common ancestor we share with chimpanzees.

2. Mutational clocks

Mutations occur over time; the longer populations diverge from one another, the more mutational differences should accumulate between them. Many mutations have little effect on the phenotype - indeed, mutations in the non-coding intron regions of a gene, or in non-coding sequences between genes, have no effect on the phenotype. These mutations will be selectively neutral - and they should accumulate at a steady rate over time. If we can measure the mutation rate, then we can use this rate like a 'clock': we can count the number of mutational differences there are between the DNA from differnt populations, and then compute how long they must have diverged from one another to account for the genetic difference that we see.

3. Genetic Phylogenies

Because DNA comes from ancestors, similarity in DNA implies common ancestry. The greater the similarity, the less time since their common ancestor; in other words, the more "recent" their common ancestry. For example, human DNA and chimp DNA is 98.4% similar in nucleotide sequence, so they share a more recent common ancestor than either species shares with gorillas - which are similar to both humans and chimps at a rate of 95%.  Now, some might claim that these similarities are analogous, representing similarities between organisms that function in a similar way (but are not biologically related).  But, only 10% of the genome is a recipe for protein.  Even the 90% that does not code for protein, that is random sequence, still shows this similarity.  Even non-functional DNA is similar, so functional similarity (ie., ANALOGY) can't be the answer... the similarity must be HOMOLOGOUS - the result of common ancestry. Genetic phylogenies have been a powerful tool for reconstructing the evolutionary relationships among broad categories of organisms that are very different or similar morphologically. So, for instance, biologists had long believed that all prokaryotes were closely related to one another, and not closely related to the eukaryotes. Genetic analyses revealed, however, that the Archaeans were more closely related to eukaryotes than to the other prokaryotic group, the eubacteria. Likewise, genetic analyses show that fungi are more similar to animals than they are to plants, and green algae is more similar to plants than they are to other forms of algae. These relationships can be understood in an evolutionary context. The eukaryotes evolved from a type of prokaryote - and so should be more similar genetically, to this parental stock of prokaryotes (the archaeans) than other prokaryotes (eubacteria). Green algae gave rise to terrestrial plants, and so should be more similar, genetically, to this closely related group (plants) than to other algal groups. This new, more realistic view of the history of life is reflected in a new way to classify organisms - based on common ancestry rather than common morphology, alone. For example, as described above, some reptile groups are more similar to birds than to other reptiles, and some reptile groups (though extinct) are more similar to mammals than other reptiles. The new classification scheme takes a more systematic approach, and groups organisms based on their phylogenetic relationships (grouping crocodilians with their close relatives the birds, for instance), rather than grouping organisms based on shared primitive characteristics (grouping crocodiles with turtles, snakes, and lizards in "the reptilia" because they have scales and lay shelled eggs). We will take a look at this later in the course.

D. Concordant Phylogenies

Both the fossil record and the pattern of genetic similarity among living species are presented as evidence of evolution and descent from common ancestors. If BOTH patterns due to the same phenomenon (common descent), then their patterns should be the same.  In short, there should only be one tree of life, and both patterns should reveal that same tree. Indeed, we should be able to test the theory of evolution yet again, in a most remarkable way: we should be able to use the degree of genetic divergence to predict where (really "when"), in the sedimentary strata of the earth's crust, the common ancestor of two groups should be. Then, we should be able to go to that strata and find that common ancestral species.

Let's see an example of this type of test. All vertebrates have many of the same proteins, but these proteins can differ in specific amino acid sequence. In this case, the amino acid sequences for the same 7 proteins were sampled from 17 mammals.  For each possible pair of species, the minimum number of nucleotide substitutions in the DNA, needed to explain the differences in the amino acid sequences, were determined. For example, suppose humans have an argenine as the third amino acid in collagen, while cows have lucine. Argenine is encoded by the codons CGU, CGG, CGC, and CGA. Leucine is eoncoded by the codons CUU, CUG, CUC, and CUA. So, although a two-base change could be responsibile (from CGU to CUA), the minimum number of substitutions would be 1 - with just a change in the second position (CGU to CUU). So, the minimum number of substitution mutations necessary to explain all the sequence differerences between every pair of species is computed, and then species are linked together based on sequence similarity. The number at each "node" refers to the order of the clustering. So, the most similar pair of species, of all the possible pair-wise combinations among these 17 mammals (255 pairwise combinations) is humans and chimps - they are linked at 'node 1'.  Then, gorillas are more similar to humans and chimps than any other pair of taxa, so gorillas link to humans and chimps at node 2.  Then, the next most similar pair of taxa are Rhesus monkeys and Aethiops monkeys, linked at node 3, and so forth.  All placental mammals link together with one another before any link to the sole marsupial, the kangaroo.
          Now, this is just a clustering procedure.  It could be done on cars, nuts and bolts, anything.  But since it is done on life forms, we can test an evolutionary prediction.  Evolution suggests that organisms are similar because of common descent from shared ancestors - represetned by these nodes.  Species that are more similar, genetically, should have a more recent ancestor than organisms that are more different, genetically.  So, there should be a relationship between 'time since divergence' and 'genetic difference', as we explained above (mutational clocks). Well, using the group of organisms that we have, we can describe what evolution predicts that relationship should be:        

IF: the oldest mammal in the fossil record is ancestral to all more recent mammals, and
IF: the most different groups of mammals today (placentals and marsupials) are descended from that ancestor, and
IF: the accumulation of genetic differences (mutations) occur at a constant rate,        

THEN: We can plot 'node 16' based on the age of the oldest mammal fossil (120 mya) and the genetic difference measured between marsupials and placentals (98 substitutions in DNA).        

AND:   if mutation rate is assumed to be constant, we can draw a straight line from 'node 16' to the origin.  This is the predicted relationship between genetic similarity and time - predicted by the theory of evolution by common descent and the assumption of a constant mutation rate. So, evolutionary theory predicts that, if two mammals differ by 50 substitutions in these seven proteins, then it must have taken 58-60 million years for these differences to accumulate.  In other words, their common ancestor should have lived 58-60 million years ago.

Well, rabbits and rodents differ by 50 substitutions in the DNA.  Our model predicts that the common ancestor should live 58-60 million years ago.  Well, where ARE the presumed ancestors in the fossil record?  They are in strata that date to 58-60 million years old - just where the genetic analysis of LIVING species predicts they should be (see node 12, below).        

Now lets consider where all the ancestral fossils are (figure to the right). The intermediate fossils that link these taxa, and represent these numbered nodes, are pretty much where our genetic analysis of existing species predicts they should be - very close to the line.  There is some variation - not all points are exactly on the line - but our assumption of a constant mutation rate is probably not explicitly correct for all genes, and probably introduces some slight source of error.  None the less, the data is strongly supportive of our hypothesis - our evolutionary prediction has been confirmed by the data.        

So, as we have seen before, evolution not only predicts the existence of common ancestors, but genetic analyses of living species can predict WHEN, millions to hundreds of millions of years ago, these different, extinct, ancestral species lived.  (Remember those intermediate fossils?  It's not just that they have a combination of traits, but they existed at the right time.  Now we see genetics showing the same thing, in a PREDICTIVE way, like an good scientific theory should).                

The only rational explanation that explains our ability to do this is evolution from common ancestors.  This wouldn't work if evolution was false, radiaoctive dating was false, or genetic analyses did not reflect biological relatedness.  All these hypotheses are confirmed by these experiments. Evolution is a predictive, explanatory model for how the universe works.  It has been tested and supported in an extraordinary variety of ways. 

Study Questions:

1. What observations did Hutton make, and what did he conclude from these observations?

2. What two patterns occur in the fossil record that impress Darwin regarding the hypothesis of evolution and common descent?

3. What are homologous structures?  What correlations occurs with the environment?

4. What are analogous structures?  What correlation occurs with the environment?

5. How did Darwin explain the existence of 'convergent communities"?

6. The Galapagos are dominated by many unique species of reptiles, birds, and marine mammals. What did this non-random assemblage suggest to Darwin about their origin, and how was evolution implied?

7. Why were the mockingbirds so critical to Darwin's ideas about the production of new species?

8. How did Darwin use the comparative method and observations of 'artificial selection' to produce the theory of 'natural selection'?

9. How were Malthus's observations and conclusion rlevant to the development of Darwin's theory?

10. Outline the theory of natural selection as an argument, with three premises, 3 conclusions, and a corollary.

11. If a rock has a ratio of Ar:K of 7:1, how old is it?

12. What are the two key characteristics of transitional fossils?

13. Why is Ichthyostega considered to be an intermediate fossil?

14. What characteristics make Archaeopteryx an intermediate fossil?

15. What characteristics do therapsids have that make them intermediate fossils?

16. What characteristics do Australopithecines have that make them intermediate fossils?

17. Explain the logic of using genetic differences and mutational clocks to determine the time since a common ancestor.

 Study Questions:

11.  What are the five assumptions of the Hardy-Weinberg Equilibrium Model?

12.  Consider the following population:

• - calculate the genotypic frequencies.
• - calculate the gene frequencies
• - calculate the HARDY WEINBERG EQUILIBRIUM frequencies.

13. If the HWE model does not describe any real population, how can it be useful?