Evolution is not progress. The popular notion that evolution can be represented as a series of improvements from simple cells, through more complex life forms, to humans (the pinnacle of evolution), can be traced to the concept of the scale of nature. This view is incorrect.
All species have descended from a common ancestor. As time went on, different lineages of organisms were modified with descent to adapt to their environments. Thus, evolution is best viewed as a branching tree or bush, with the tips of each branch representing currently living species.
No living organisms today are our ancestors. Every living species is as fully modern as we are with its own unique evolutionary history. No extant species are “lower life forms,” atavistic stepping stones paving the road to humanity.
A related, and common, fallacy about evolution is that humans evolved from some living species of ape. This is not the case—humans and apes share a common ancestor.
Both humans and living apes are fully modern species; the ancestor we evolved from was an ape, but it is now extinct and was not the same as present day apes (or humans for that matter). If it were not for the vanity of human beings, we would be classified as an ape. Our closest relatives are, collectively, the chimpanzee and the pygmy chimp. Our next nearest relative is the gorilla.
Microevolution can be studied directly. Macroevolution cannot. Macroevolution is studied by examining patterns in biological populations and groups of related organisms and inferring process from pattern. Given the observation of microevolution and the knowledge that the earth is billions of years old — macroevolution could be postulated. But this extrapolation, in and of itself, does not provide a compelling explanation of the patterns of biological diversity we see today.
Evidence for macroevolution, or common ancestry and modification with descent, comes from following fields of study:
i. Comparative biochemical and genetic studies.
ii. Comparative developmental biology.
iii. Patterns of biogeography.
iv. Comparative morphology and anatomy and the fossil record.
Closely related species (as determined by morphologists) have similar gene sequences. Overall sequence similarity is not the whole story, however. The pattern of differences we see in closely related genomes is worth examining.
All living organisms use DNA as their genetic material, although some viruses use RNA. DNA is composed of strings of nucleotides. There are four different kinds of nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). Genes are sequences of nucleotides that code for proteins. Within a gene, each block of three nucleotides is called a codon. Each codon designates an amino acid (the subunits of proteins).
The three letter code is the same for all organisms (with a few exceptions). There are 64 codons, but only 20 amino acids to code for; so, most amino acids are coded for by several codons. In many cases the first two nucleotides in the codon designate the amino acid. The third position can have any of the four nucleotides and not affect how the code is translated.
A gene, when in use, is transcribed into RNA — a nucleic acid similar to DNA. (RNA, like DNA, is made up of nucleotides although the nucleotide uracil (U) is used in place of thymine (T). The RNA transcribed from a gene is called messenger RNA.
Messenger RNA is then translated via cellular machinery called ribosomes into a string of amino acids—a protein. Some proteins function as enzymes, catalysts that speed the chemical reactions in cells. Others are structural or involved in regulating development.
Gene sequences in closely related species are very similar. Often, the same codon specifies a given amino acid in two related species, even though alternate codons could serve functionally as well. But, some differences do exist in gene sequences. Most often, differences are in third codon positions, where changes in the DNA sequence would not disrupt the sequence of the protein.
There are other sites in the genome where nucleotide differences do not effect protein sequences. The genome of eukaryotes is loaded with ‘dead genes’ called pseudogenes. Pseudogenes are copies of working genes that have been inactivated by mutation. Most pseudogenes do not produce full proteins.
They may be transcribed, but not translated. Or, they may be translated, but only a truncated protein is produced. Pseudogenes evolve much faster than their working counterparts. Mutations in them do not get incorporated into proteins, so they have no effect on the fitness of an organism.
Introns are sequences of DNA that interrupt a gene, but do not code for anything. The coding portions of a gene are called exons. Introns are spliced out of the messenger RNA prior to translation, so they do not contribute information needed to make the protein. They are sometimes, however, involved in regulation of the gene. Like pseudogenes, introns (in general) evolve faster than coding portions of a gene.
Nucleotide positions that can be changed without changing the sequence of a protein are called silent sites. Sites where changes result in an amino acid substitution are called replacement sites. Silent sites are expected to be more polymorphic within a population and show more differences between populations.
Although both silent and replacement sites receive the same amount of mutations, natural selection only infrequently allows changes at replacement sites. Silent sites, however, are not as constrained.
Kreitman was the first to demonstrate that silent sites were more variable than coding sites. Shortly after the methods of DNA sequencing were discovered, he sequenced 11 alleles of the enzyme alcohol dehydrogenase (AdH). Of the 43 polymorphic nucleotide sites he found, only one resulted in a change in the amino acid sequence of the protein.
Silent sites may not be entirely selectively neutral. Some DNA sequences are involved with regulation of genes, changes in these sites may be deleterious. Likewise, although several codons code for a single amino acid, an organism may have a preferred codon for each amino acid. This is called codon bias.
If two species shared a recent common ancestor one would expect genetic information, even information such as redundant nucleotides and the position of introns or pseudogenes, to be similar. Both species would have inherited this information from their common ancestor.
The degree of similarity in nucleotide sequence is a function of divergence time. If two populations had recently separated, few differences would have built up between them. If they separated long ago, each population would have evolved numerous differences from their common ancestor (and each other).
The degree of similarity would also be a function of silent versus replacement sites. Li and Graur, in their molecular evolution text, give the rates of evolution for silent vs. replacement rates. The rates were estimated from sequence comparisons of 30 genes from humans and rodents, which diverged about 80 million years ago.
Silent sites evolved at an average rate of 4.61 nucleotide substitution per 109 years. Replacement sites evolved much slower at an average rate of 0.85 nucleotide substitutions per 109 years.
Groups of related organisms are ‘variations on a theme’ — the same set of bones is used to construct all vertebrates. The bones of the human hand grow out of the same tissue as the bones of a bat’s wing or a whale’s flipper; and, they share many identifying features such as muscle insertion points and ridges. The only difference is that they are scaled differently. Evolutionary biologists say this indicates that all mammals are modified descendants of a common ancestor which had the same set of bones.
Closely related organisms share similar developmental pathways. The differences in development are most evident at the end. As organisms evolve, their developmental pathway gets modified. An alteration near the end of a developmental pathway is less likely to be deleterious than changes in early development.
Changes early on may have a cascading effect. Thus most evolutionary changes in development are expected to take place at the periphery of development, or in early aspects of development that have no later repercussions. For a change in early development to be propagated, the benefit of the early alteration must outweigh the consequences to later development.
Because they have evolved this way, organisms pass through the early stages of development that their ancestors passed through up to the point of divergence. So, an organism’s development mimics its ancestors although it doesn’t recreate it exactly. Development of the flatfish, Pleuronectes, illustrates this point.
Early on, Pleuronectes develops a tail that comes to a point. In the next developmental stage, the top lobe of the tail is larger than the bottom lobe (as in sharks). When development is complete, the upper and lower lobes are equally sized. This developmental pattern mirrors the evolutionary transitions it has undergone.
Natural selection can modify any stage of a life cycle, so some differences are seen in early development. Thus, evolution does not always recapitulate ancestral forms — butterflies did not evolve from ancestral caterpillars, for example. There are differences in the appearance of early vertebrate embryos.
Amphibians rapidly form a ball of cells in early development. Birds, reptiles and mammals form a disk. The shape of the early embryo is a result of different yolk concentrations in the eggs. Birds’ and reptiles’ eggs are heavily yolked. Their eggs develop similarly to amphibians except the yolk has deformed the shape of the embryo.
The ball is stretched out and lying atop the yolk. Mammals have no yolk, but still form a disk early. This is because they have descended from reptiles. Mammals lost their yolky eggs, but retained the early pattern of development. In all these vertebrates, the pattern of cell movements is similar despite superficial differences in appearance. In addition, all types quickly converge upon a primitive, fish-like stage within a few days. From there, development diverges.
Traces of an organism’s ancestry sometimes remain even when an organism’s development is complete. These are called vestigial structures. Many snakes have rudimentary pelvic bones retained from their walking ancestors. Vestigial does not mean useless, it means the structure is clearly a vestige of a structure inherited from ancestral organisms. Vestigial structures may acquire new functions. In humans, the appendix now houses some immune system cells.
Closely related organisms are usually found in close geographic proximity; this is especially true of organisms with limited dispersal opportunities. The mammalian fauna of Australia is often cited as an example of this; marsupial mammals fill most of the equivalent niches that placentals fill in other ecosystems.
If all organisms descended from a common ancestor, species distribution across the planet would be a function of site of origination, potential for dispersal, distribution of suitable habitat, and time since origination. In the case of Australian mammals, their, physical separation from sources of placentals means potential niches were filled by a marsupial radiation rather than a placental radiation or invasion.
Natural selection can only mold available genetically based variation. In addition, natural selection provides no mechanism for advance planning. If selection can only tinker with the available genetic variation, we should expect to see examples of jury-rigged design in living species. This is indeed the case. In lizards of the genus Cnemodophorus, females reproduce parthenogenetically.
Fertility in these lizards is increased when a female mounts another female and simulates copulation. These lizards evolved from sexual lizards whose hormones were aroused by sexual behaviour. Now, although the sexual mode of reproduction has been lost, the means of getting aroused (and hence fertile) has been retained.
Fossils show hard structures of organisms less and less similar to modern organisms in progressively older rocks. In addition, patterns of biogeography apply to fossils as well as extant organisms. When combined with plate tectonics, fossils provide evidence of distributions and dispersals of ancient species.
For example, South America had a very distinct marsupial mammalian fauna until the land bridge formed between North and South America. After that marsupials started disappearing and placentals took their place. This is commonly interpreted as the placentals wiping out the marsupials, but this may be an over simplification.
Transitional fossils between groups have been found. One of the most impressive transitional series is the ancient reptile to modern mammal transition. Mammals and reptiles differ in skeletal details, especially in their skulls. Reptilian jaws have four bones. The foremost is called the dentary.
In mammals, the dentary bone is the only bone in the lower jaw. The other bones are part of the middle ear. Reptiles have a weak jaw and a mouthful of undifferentiated teeth. Their jaw is closed by three muscles- the external, posterior and internal adductor. Each reptile tooth is single cusped.
Mammals have powerful jaws with differentiated teeth. Many of these teeth, such as the molars, are multi- cusped. The temporalis and masseter muscles, derived from the external adductor, close the mammalian jaw. Mammals have a secondary palate, a bony structure separating their nostril passages and throat, so most can swallow and breathe simultaneously. Reptiles lack this.
The evolution of these traits can be seen in a series of fossils. Procynosuchus shows an increase in size of the dentary bone and the beginnings of a palate. Thrinaxodon has a reduced number of incisors, a precursor to tooth differentiation. Cynognathus (a doglike carnivore) shows a further increase in size of the dentary bone.
The other three bones are located inside the back portion of the jaw. Some teeth are multicusped and the teeth fit together tightly. Diademodon (a plant eater) shows a more advanced degree of occlusion (teeth fitting tightly). Probelesodon has developed a double joint in the jaw. The jaw could hinge off two points with the upper skull.
The front hinge was probably the actual hinge while the rear hinge was an alignment guide. The forward movement of a hinge point allowed for the precursor to the modern masseter muscle to anchor further forward in the jaw. This allowed for a more powerful bite.
The first true mammal was Morgonucudon, a rodent-like insectivore from the late Triassic. It had all the traits common to modern mammals. These species were not from a single, unbranched lineage. Each is an example from a group of organisms along the main line of mammalian ancestry.
The strongest evidence for macroevolution comes from the fact that suites of traits in biological entities fall into a nested pattern. For example, plants can be divided into two broad categories- nonvascular (ex. mosses) and vascular. Vascular plants can be divided into seedless (ex. ferns) and seeded.
Vascular seeded plants can be divided into gymnosperms (ex. pines) and flowering plants (angiosperms). Angiosperms can be divided into monocots and dicots. Each of these types of plants has several characters that distinguish them from other plants. Traits are not mixed and matched in groups of organisms.
For example, flowers are only seen in plants that carry several other characters that distinguish them as angiosperms. This is the expected pattern of common descent. All the species in a group will share traits they inherited from their common ancestor. But, each subgroup will have evolved unique traits of its own. Similarities bind groups together. Differences show how they are subdivided.
The real test of any scientific theory is its ability to generate testable predictions and, of course, have the predictions borne out. Evolution easily meets this criterion. In several of the above examples I stated, closely related organisms share X. If I define closely related as sharing X, this is an empty statement.
It does however, provide a prediction. If two organisms share a similar anatomy, one would then predict that their gene sequences would be more similar than a morphologically distinct organism.
This has been spectacularly borne out by the recent flood of gene sequences — the correspondence to trees drawn by morphological data is very high. The discrepancies are never too great and usually confined to cases where the pattern of relationship was debated.