Notes on Evolution

These notes are from my Biology 339 class (Evolution) from McNeese State University. [Textbook: "Evolutionary Analysis" by Scott Freeman and Jon C. Herron (University of Washington); Prentice-Hall, 1998]. These are not ALL of my notes, therefore this page is not in any way meant to be a complete outline of the course. This is only a brief overview of the main concepts reviewed in the class. Also, this text is presented in terms related to biological sciences. If you are unfamiliar with any of the terms, refer to a science book or dictionary.

Darwinism and the Fact of Evolution

I. The Fact of Evolution
Evidence from biology and geology was contradictory to creationism because it showed that species had changed through time and descended with modification from common ancestors, instead of each remaining unchanged since a special and independent origin. We review three types of data. Taken together, they were convincing enough to shake many scientists' belief in the Theory of Special Creation.

Homology---literally, the study of likeness---was a key concept in the new field of comparative anatomy. Homologous structures in adults develop from the same groups of cells in embryos. As a consequence, homology was defined as a similarity due to shared developmental pathways. But why should some organisms share developmental pathways? Darwin argued that descent from a common ancestor was the most logical explanation. He contended that the embryos in certain vertebrates (fish, salamander, tortoise, chicken, pig, cow, rabbit, human) are similar because all vertebrates evolved from a common ancestor, and because early developmental stages have remained unchanged as fish, ammmals, amphibians, and reptiles diversified. Darwin's recognition of relationship through shared descent was a conceptual breakthrough, and extended to other phenomena other than homology.

Change Through Time
One of the central tenets of the Theory of Special Creation was that species, once created, were immutable. Four lines of evidence challenged this claim.

An early eighteenth-century paleontologist named William Clift was the first to publish an observation later confirmed and expanded upon by Darwin (Eisely 1958). Fossil and living mammals in the same geographic region are related to each other, and distinctly different from faunas of other areas. Clift worked on the extinct marsupial fauna of Austrailia and noted its close relationship to forms alive today; Darwin analyzed the armadillos of Argentina and their relationship to the fossil glyptodonts he excavated there. This general result, termed the Law of Succession, provided strong documentation for evolution.

Darwin added another strong piece of evidence for change through time: the presence of vestigial structures in a wide variety of organisms. Some blind, cave-dwelling fish have eye sockets but no eyes; flightless birds and insects have reduced wings; humans have a nonfunctional appendix and reduced tailbone. We also have muscles that make our body hair stand on end when we are cold or excited. Erectile fur is found in many mammals, and is important in signaling alarm or agressive intent. In humans, the result is goosebumps.

The Age of the Earth
By the time Darwin first began working on "the species problem," data from the young science of geology had challenged a factor of the Theory of Special Creation. Special Creation stated that the earth was only about 6,000 years old. Geologists were finding evidence that proved that the earth was ancient; much older than 6,000 years.

James Hutton was the first to articulate a principle called uniformitarianism: geological processes taking place now operated similarly in the past. This assumption led Hutton and Charles Lyell to infer that the geological time scale was unimaginably long in human terms. Given the measurements these early geologists made of ongoing rock-forming processes like decomposition at beaches and river deltas and the accumulation of marine shells (the precursors of limestone), it was clear that vast stretches of time were required to produce the immense rock formation they were studying.

When Darwin began his work, Hutton and followers were already in the midst of a 50-year effort to put the major rock formations and fossil-bearing strata of Europe in a younger-to-older sequence. Their technique, called, relative dating, was based on the following:

Using these rules, geologists established the chronology known as the geologic time scale and created the concept of the geologic column. This is a history of the earth based on a composite, older-to-younger sequence of rock strata. Taken together with the principle of uniformitarianism, the geologic time scale and the geologic column furnished impressive evidence for an ancient earth.

II. Natural Selection: Darwin's 4 Potulates
Because homologies, extinction, and the law of succession were widely recognized in Western Europe, the idea of evolution had been in the air long before Darwin began his work. Several writers, including Darwin's grandfather Erasmus Darwin, had proposed that existing species are the modified descendants of forms that existed previously. But no one had yet proposed a satisfactory mechanism for how a population of organisms could change through time. Darwin's solution is the theory of evolution by natural selection. It can be stated concisely, as the logical outcome of four postulates:

  1. Individuals within species are variable.
  2. Some of these variations are passed on to offspring.
  3. In every generation, more offspring are produced than can survive.
  4. Survival and reproduction are not random: The individuals that survive and go on to reproduce, or who reproduce the most, are those with the most favorable variations. They are naturally selected.

Evolutionary change is an outcome of the process described by Darwin, which he called natural selection. The logic is clear: If there is variation among individuals in a population that can be passed on to offspring, and if there is differential success among those individuals in surviving and/or reproducing and thus is passing on those variations, then the characteristics of the population will change slightly with each succeeding generation.

III. The Nature of Natural Selection
Each generation is a product of selection by the nevironmental conditions that prvailed in the generation before. There is a common misconception, however, that organisms can be adapted to future conditions, or that selection can look ahead in the sense of anticipating environmental changes during future generations. This is impossible. Evolution is always a generation behind any changes in the environment.

Natural selection can select only from the variations that already exist in a population. Selection cannot, for example, instantly create a new and optimal characteristic that was not previously extant. Even though it only acts on existing traits, natural selection can be a creative process that leads to completely new characteristics. This seems paradoxical, but novel features can evolve because selection is able to "repurpose" existing behaviors, structures, or genes for new functions.

Evolution by natural selection is sometimes characterized as a random chance process, but nothing could be further from the truth. Evolution is both directed and purposeful: it is directed by the environment and purposeful in the sense of increasing adaptation to that environment. Although evolution has tended to increase the complexity, degree of organization, and specialization of organisms through time, it is not progressive in the everyday sense of leading toward some predetermined goal. Evolution makes organisms better only in the sense of increasing their adaptation to their environment. There is no inexorable trend toward higher forms of life.

One of the most pervasive misconceptions about natural selection, especially selection on animal behavior, is that individual organisms will do things for the good of the species. Self-sacrificing, or altruistic, acts do occur in nature: Prarie dogs will give warning calls when predators approach, and lionesses will nurse cubs that are not her own.

Mutation: The Origin of New Genes and Alleles

I. Where New Alleles Come From
Most new alleles are derived from already existing alleles, typically as a result of point mutation. Point mutations are single-based substitutions cause by one of two processes: random errors in DNA synthesis, or random errors in the repair of sites damaged by chemical mutagens or high-energy radiation. Both types of changes are caused by DNA polymerase.

If during normal synthesis or repair synthesis, DNA polymerase mistakenly substitues a purine (Adenine or Guanine) for another purine, or a pyrimidine (Thymine or Cytosine) for another pyrimidine, the point mutation is called a transition. If a purine is substituted for a pyrimidine, or vice versa, then the mutation is called a transversion. Of the two kinds of point mutations, transitions are far more common, because they are easier mistakes for polymerase to make and cause much less disruption in the DNA helix during synthesis.

Mutation Rates
How often are new alleles formed? Many of our best data on mutation rates are for loss-of-function mutations. In these types of mutations, the lack of normal protein product leads to an easily recognizable phenotype. The problem with this method is that loss-of-function mutations result from any process that inactivates a gene. Genes can be knocked out by base-pair substitutions that produce a chain-terminating codon or a dysfunctional amino acid sequence, frameshifts (additions or deletions of one or two base pairs that disrupt the reading sequence of codons), the insertion of a mobile genetic element, chromosome rearrangements, and so on. As a result, we have scant data on what is perhaps the most interesting type of mutation rate for evolutionary analyses: replacement substitutions per codon per generation.

Mutation rates are very low on a per-gene basis, but there are so many loci (approximately 100,000 in humans) that almost 10% of all gametes carry a phenotypically detectable mutation. It is probable that the majority of all offspring carry at least one new allele somewhere in their genome.

II. Where New Genes Come From
As with new alleles, several kinds of mutations can create new genes. Gene duplications are probably the most important source of new genes. Duplications result from a phenomenon known as unequal cross-over. Unequal cross-over is a chance mistake caused by the proteins involved in managing recombination (crossing over) during meiosis. One of the products of unequal cross-over is a redundant stretch of DNA. The genome now has an extra copy of the sequences located in the duplicated segment. Because the parent copy still produces a normal product, the redundant sequences are free to accumulate mutations without consequences to the phenotype. The new sequence may even change function over time, and become a new locus. Because it creates additional DNA, gene duplication is the first mechanism we have encountered that results in entirely new possibilities for gene function. Duplicated genes can (1)retain their original function and provide an additional copy of the parent locus, (2)gain a new function through mutation and selection, or (3)become functionless pseudogenes.

In addition to duplication, there are other mechanisms that can create new genes or radically new functions for duplicated genes. One example, called overprinting, results from point mutations that produce new start codons and new reading frames for translation. Evolution at the new locus is likely to be tightly constrained, because any mutation that improves the function of the overlapping protein would probably be deleterious to the function of the replicase protein. Overprinting has also been a common mechanism for creating new genes during viral evolution.

III. Chromosome Alterations
A wide variety of changes can occur in the gross morphology of chromosomes. Some of these mutations affect only gene order and organization; others produce duplications or deletions that affect the total amount of genetic material. Chromosomal alterations can involve the entire DNA molecule or just segments.

Inversions
Chromosome inversions involve much larger stretches of DNA than other mutation types. They also produce very different consequences. Inversions result from a multi-step process that starts when ionizing radiation causes two double-strand breaks in a chromosome. After breakage a chromosome segment can detatch, flip, and reanneal in its original location. Inversions affect a phenomenon known as genetic linkage. Linkage is the tendencey for alleles of different genes to assort together at meiosis. Genes on the same chromosome tend to be more tightly linked than genes on nonhomologous chromosomes. The closer together genes are on the same chromosome, the tighter the linkage. Crossing over at meiosis, on the other hand, breaks up allele combinations and reduces linkage.

The Origin of Life and Precambrian Evolution

I. The Most Recent Common Ancestor of All Living Things
The oldest fossils established as those of living organisms are 3.465 billion years old. These fossils, which come from a rock formation called the Apex chert in Western Austrailia, show simple cells growing in short filaments. Their discoverer, J. William Schopf (1993), believes these organisms belonged to the cyanobacteria family. This identification is tentative. The fossil record for times earlier than 2.5 billion years ago is too spotty to allow paleontologists to trace lines of evolutionary descent from present-day organisms back to the Apex chert fossils. As a result, we have no way of knowing whether the organisms recorded in the Apex chert represent extinct or living branches of the tree of life. If we want to discover the characteristics of the most recent common ancestor, we must use methods other than examination of the fossil record.

Finding the Common Ancestor Without Fossils
If we knew the phylogeny, or evolutionary tree, of all living things, we could use it to infer the characteristics of the cenancestor. The first attempts to construct such a phylogeny were based on the morphologies of organisms (see reviews in Woese 1991; Dolittle and Brown 1994). The morphological approach was productive for biologists interested in the branches of the tree of life that contain eukaryotes. Morphology was the basis of the phylogeny of tetrapods. The fact that monotremes, marsupials, and eutherians have hair, for example, indicates that these mammal groups are all more closely related to each other than any of them are related to any other tetrapod.

When biologists developed methods for reading the sequences of amino acids in proteins, and the sequences of nucleotides in DNA and RNA, a new technique for estimating phylogenies quickly became established (Zuckerkandl and Pauling, 1965). Imagine that we have a group of species, all carrying their genomes in a particular gene. We can read the sequence of nucleotides in this gene in each of the species, then compare the sequences. If the species are closely related, their sequences will be fairly similar. If the species occupy distant branches on the evolutionary tree, then their sequences are less similar. As a result, we can use the relative similarity of the sequences of the species to infer their evolutionary relationships.

The Earliest Possible Date for the Cenancestor
If we assume that the cenancestor lived on Earth, then the cenancestor could not have lived before the Earth existed and was inhabitable. The Earth is descended, along with the sun and other planets, from an interstellar dust cloud (Hughes 1989; Wetherill 1990). The cloud contained hydrogen and helium left over from the big bang, plus heavier elements ejected in the explosion of earlier generations of stars. These heavy elements were vital: They became major constituents of the Earth. As the spinning interstellar dust cloud condensed under the force of gravity, it formed countless small planetesimals in orbit around a central mass. The central mass became the sun; its thermonuclear furnace was ignited by heat generated during its gravitational collapse. The orbiting planetesimals collided with each other, forming the planets by gradual accretion. The process of planetary accretion has slowed dramatically, but it is not yet finished. Planetesimals---meteors---continue to collide with the Earth and other planets. Radioisotopic dating of meteorites yeilds an estimated age for the solar system, and hence the Earth, of 4.5 to 4.6 billion years (Badash 1989).

The newborn Earth remained uninhabitable for at least a few hundred million years. At first, it was simply much too hot. The collisions of the plantesimals that formed the Earth released enough heat to melt the entire planet (Wetherill 1990). Eventually the Earth's outer surface cooled and solidified to form the crust, and water vapor released from the planet's interior cooled and condensed to form the oceans. We know that at least some solid crust existed by about 4 billion years ago, because there are 3.96 billion-year-old rocks in Arctic Canada (Bowring 1989), and 4.2 to 4.3 billion-year-old zircon crystals embedded in younger sandstones in Austrailia (Myers and William 1985; Compston and Pidgeon 1986). We know that surface water existed by 3.85 billion years ago, because there are sedimentary rocks of that age at Akilia Island, Greenland, and sedimentary rocks that are 3.8 billion years old at nearby Isua, Greenland (Mojzsis 1996).

The oldest sedimentary rocks contain the oldest living evidence suggesting the presence of life. The rocks are of a type known as banded iron formations. Geological processes have exposed the rocks to high temperatures and pressures, which have compacted the rocks and crystallized many of the minerals they contain. This transformation would have destroyed any microfossils the rocks might have originally harbored. The rocks do contain apatite crystals, however. Apatites are calcium phosphate minerals. Apatites are produced by many microorganisms, and are also the main component of bones and teeth in vertebrates. Apatites can also be produced by non-biological processes.

Solid crust and oceans probably existed earlier than the 3.96 and 3.85 billion years ago demonstrated by the Canadian and Akilia Island rocks, but erosion, plate tectonics, and volcanic eruptions have obliterated all direct evidence. Even if crust and oceans did exist earlier, however, continued bombardment of the planet by large meteors probably would have prevented life from being established much earlier than 3.85 billion years ago. Large meteor impacts generate heat, create sun-blocking dust, and produce a blanket of debris. All of these effects, if intense enough, can kill organisms. The mass extinction at the end of the Cretaceous that killed off the non-avian dinosaurs may have been caused by a large meteor impact. As time passed, and the largest planetesmials got swept up by the Earth and other planets, the sizes of the largest impacts decreased. It is estimated that the last impact that had sufficient energy to vaporize the entire global ocean, and thereby kill any and all organisms then alive, probably happened between 4.44 and 3.8 billion years ago (Norman Sleep et. al. 1989).

Based on the Akilia sedimentary rocks, then, and on the history of large impacts, we can estimate that the earliest the cenancestor could possibly have lived was somewhere between 3.85 and about 4.4 billion years ago.

The Latest Possible Date for the Cenancestor The cenancestor could not have lived any more recently than the occurrence of any of the branch points above it on the universal phylogeny. The most definitive information about branching times comes from fossils. The fossils useful in this regard are those that can be confidently identified as belonging to a particular group of organisms. If we can place a fossil on the whole-life phylogeny, then we know that the cenancestor is older than the fossil.

The oldest known fossils that are probably those of eukaryotes are 2.1 billion years old. Found by Tsu-Ming Han and Bruce Runnegar (1992) at the Empire Mine in Michigan, these fossils show a spiral-shaped organism similar to a more recent fossil named Grypania spiralis. G. spiralis is known from fossils in Montana, China, and India that range in age from 1.1 to 1.4 billion years old (Han and Runnegar 1992). Because of its large size and structural complexity, paleontologists believe that Grypania was a eukaryote, probably an alga. Fossil cyanobacteria support a similar conclusion (Schopf 1994a). In a testament to the length of time that successful organisms can remain at least superficially unchanged, many fossil cyanobacteria are identifiable based on their structural similarity to extant forms. The extant cyanobacteria occupy a limb of the universal phylogeny that is, like those occupied by the extant algae, several branch points above the last common ancestor.

In summary, we can use the estimated universal phylogeny, along with geological and paleontological data, to bracket the time when the cenancestor could have lived. The earliest possible date is between 4.4 and 3.85 billion years ago; the most recent possible date is between 3.5 and 2 billion years ago.

II. Origin of the Cenancestor
The most recent common ancestor of all extant organisms was a descendant of the "one primordial form," the first self-replicating entity that could evolve by natural selection. The most compelling puzzles question what the primordial form was, and how it was created by nonbiological processes. We may never have direct fossil evidence of the nature of the first living thing (Schopf 1994b). The oldest known rocks from the inhabitable Earth contain evidence suggesting that life was already established by the time the rocks were formed. Even if we find rocks that date from the time of the primordial form, it is unlikely that they will contain any useful clues to the origin of life. The first self-replicating entity was probably chemical, not cellular, meaning that it had no cell walls to fossilize. Furthermore, the organic molecules that likely made up the primordial form are far too unstable to have remained preserved in rock for 4 billion years.

We will assume that the primordial form originated on Earth. We know that evolution before the cenancestor had to progress from a collection of nonliving chemicals to the primordial form to the cenancestor itself, and we know that the cenancestor was essentially a modern organism. Following the most widely accepted scenario, sometimes referred to as the Oparin-Haldane Theory (Lazcano and Miller 1996), we can break the spontaneous generation of the primordial form into a series of steps that occurred sequentially in the waters or moist clay of the young Earth:

  1. Nonbiological processes synthesized organic molecules, such as amino acids and nucleotides, that would later serve as the building blocks of life. The accumulation of these organic molecules in solution created what is known as the pre-biotic soup.
  2. The organic building blocks in the pre-biotic soup were assembled into biological polymers, such as proteins and nucleic acids.
  3. Some combination of biological polymers was assembled into a self-replicating organism that fed off the organic molecules in the pre-biotic soup.

Once the first self-replicating organism appeared, its descendants acquired cellular form and the metabolic ability to synthesize their own organic building blocks. The actual route of evolution may have been less direct than that, but with this outline at least we have a starting point.

Nonbiological Synthesis of the Building Blocks of Life The first step, the nonbiological synthesis of the building blocks of life, is fairly easy, at least under the right conditions. In 1953, Stanley L. Miller, then a graduate student reported a simple and elegant experiment. He built an apparatus that boiled water and circulated the hot vapor through an atmosphere of methane (CH4), ammonia (NH3), and hydrogen (H2), past an electric spark, and finally through a cooling jacket that condensed the vapor and directed it back into the bioling flask. Miller let the apparatus run for a week; the water inside turned deep red and cloudy. Using paper chromatography, Miller identified the cause of the red color as a mixture of organic molecules, most notably the amino acids glycine, alpha-alanine, and beta-alanine. Since 1953, chemists working on the pre-biotic synthesis of organic molecules have, in similar experiments, documented the formation of a tremendous diversity of organic molecules, includin amino acids, nucleotides, and sugars. Miller used methane, ammonia, and hydrogen as his atmosphere; at the time, this mixture was thought to model the atmosphere of a young Earth. The implication of Miller's result was that if lightning or UV radiation could have played the role that the spark did in his experiment, then the young Earth's oceans would have quickly become a rich pre-biotic soup.

Many atmospheric chemists now believe that the early atmosphere was dominated by carbon dioxide (CO2) rather than methane, and molecular nitrogen (N2) rather than ammonia (Kasting 1993). This conclusion is based on the mixture of gases released by contemporary volcanoes, and on improved knowledge of the chemical reactions that occur in the upper atmosphere.

Even if the early atmosphere did not allow the synthesis of organic molecules on Earth, there may have been another mechanism for the accumulation of a pre-biotic soup. We noted earlier that the young Earth experienced heavy bombardment by meteors and comets. Carbonaceous chondrite meteorites, believed to be fragments of asteroids, contain an abundance of organic molecules (Chyba 1990; Lazcano and Miller 1996). Thus, they very same bombardment of the young Earth that made early conditions uncomfortable for life may, ironically, have supplied the ingredients for the construction of the primordial form.

The Cambrian Explosion

I. The Nature of the Fossil Record

How Organic Remains Fossilize A fossil is any trace left by an organism that lived in the past. Fossils are enormously diverse, but four general categories can be defined by method of formation: