TAXONOMY, PHYLOGENY AND THE FOSSIL RECORD The Theory of Evolution in Modern Biology Science traffics in theories but the term "theory" should not be misunderstood. A scientific theory is not simply a best guess with a high level of uncertainty attached to it; rather, it represents the dogma of its day and is considered to be a fact. Consequently, theories guide our thinking about how the world operates and serve as paradigms for interpreting observations. Remember that to be scientific, a theory must always be falsifiable and so cannot be proven; hence, major scientific "truths" which enjoy wide acceptance are still called theories because future evidence might falsify them or cause them to be substantially modified. We still talk about the atomic theory of matter and the gene theory of heredity but no scientist doubts that matter consists of atoms and that inheritance is based on the transmission between generations of genes. The same holds true of the theory of evolution: it is considered to be a fact and it enjoys the highest level of certitude that can be afforded by science. What is the theory of evolution? Simply stated it is that existing species are the product of change in past species so that contemporary organic diversity is the result of "descent with modification" (to use Darwin's phrase) from pre-existing species. The theory of evolution is one of the two major building blocks of modern biology, the other being the cell theory. Together these two theories unify the science of biology. The cell theory explains why living beings are similar; the theory of evolution why they are diverse. The cell theory states that all living organisms are composed of cells and this concept provides a common structural basis for life. It is an inductive generalization based on a long history of observing living beings. In all cases so far observed living organisms have a cellular basis for their structure. For this reason, viruses which share many properties with living organisms, e.g., protein and nucleic acid composition, are not considered to be alive. Appended to the cell theory (which was promulgated independently in 1839 by a botanist named Schleiden and a zoologist named Schwann) is another idea developed by Virchow in 1858, namely, the theory of biogenesis or cell lineage which states that all cells come from pre-existing cells. This theory is also an inductive generalization based on observation of cell origin through the process of cell division (mitosis), although in Virchow's time it was simply an assumption. The modern version of the cell theory links these two concepts by stating that ALL LIVING ORGANISMS ARE COMPOSED OF CELLS AND ALL CELLS COME FROM PRE- EXISTING CELLS. If this statement is true, why is it that cells and species are different? Shouldn't they all be the same? Enter the theory of evolution which explains variation at all levels of biological organization. In the history of life cells changed and so the lineage of cells from the dawn of biological history to the present is characterized by descent with modification. Consequently, the cell theory and the theory of evolution provide a basis for unification of all the diverse phenomena studied in the field of biology. Destroy either of these ideas and biology would be reduced to a mere cataloging of independent observations with no way of relating information gained from the study of one species to others. The fact that the study of one species can serve as the basis of principles applicable to all other species, including ourselves, is made possible by the two major biological generalizations of the cell theory and the theory of evolution. Assumptions of the theory of evolution As with any theory, the theory of evolution rests on assumptions. The first being the validity of the cell theory and the second being that life arose only once on this planet. A third assumption is that species are real biological entities capable of change and not merely mental constructs due to our ability to abstract and generalize. A fourth assumption is that the Earth is very old and so sufficient time has existed for change to produce the diversity in species we observe today. Finally, a fifth assumption is that the rates of evolution within separate lineages are unequal so that some species have diverged little from a distant common ancestor while others have departed greatly in form. This last assumption is the basis for the principle of sequences - a method of reconstructing the past from analysis of contemporary diversity. Let's now examine each of these assumptions in more detail. If the cell theory is not valid (assumption 1) then there exists no continuity over time in living organisms; hence, there could be no evolution or descent with modification. No continuity means no line of descent. If life arose more than once (see assumption 2), then there would be as many lines of descent as their were independent origins of life, and there would exist no essential relationship between these different lines of descent. Taken to an extreme, as the biblical creation story does with each species being created separately, we are left with no historical integrity among species. Each species is an entity unto itself with no genetic connection to others. Thus, whatever is learned about the biology of one species cannot be legitimately generalized to apply to others and biology becomes reduced to a catalog of attributes of each separate book of life. Other than analogy, there would exist no logical basis for generalizing results. No progress in evolutionary thinking was possible when biologists denied that species were real, natural entities (see assumption 3) and considered them only to be generalized abstractions from observation of individuals. If species do not exist, they cannot change through biological process, and again there would exist no continuity to life which links the present with the past. In the 1650's James Ussher, The Irish Archbishop of Armagh, published a chronology based on information in the Bible and estimated that the Earth was created in 4004 B.C. If the Earth is only about six thousand years old (see assumption 4), then there simply would not be enough time for change to produce organic diversity. The observations of James Hutton and other geologists who posited a very old Earth and the subsequent validation of this viewpoint by radiometric dating have produced a time frame which allows for evolutionary process, slow as it is, to produce the level of organic diversity observed today. Finally, if rates of evolution were equal (see assumption 5), there would be much less variation among species alive today and all extant species would possess characters advanced over those found in extinct ancestral species. Comparison of fossil and contemporary species would show much less similarity thus making it very difficult to establish lines of continuity (phylogenetic relationships). Deductions of the theory of evolution Creation and evolution offer two entirely different explanations for the origin of organic diversity, but unlike the creation story, the theory of evolution makes a number of predictions which are deductive corollaries of the idea that species are the product of change through a long history of ancestral-descendant relationship. Among these deductions are the following. 1. That all species existing today are related through sharing a common ancestor at some time in the past. 2. That species which inhabited this planet in the past were different from those living today. The further back in time one looks, the greater will be the difference between species existing then and now. 3. That the longer a geographic area has been isolated, the more unique will be its related fauna and flora. 4. That the more recent the divergence between species, the greater will be their similarity genetically. We will examine the first two points now and discuss points three and four in subsequent classes. Evolutionary History and Phylogenetic Relationship According to an evolutionary perspective all species existing today are the product of change from previously existing species and if life arose only once, all of these species must be descendants of the first life form. Hence the history of life represents an unbroken ancestral- descendant lineage which had numerous branchings as new species were formed by the process of speciation. This history, called phylogeny, appears as a branching bush with all living species representing the terminal twigs. By tracing these twigs backwards to the point where they join branches which lead to other twigs, we can see the common ancestors which gave rise to current organic diversity. Upon what basis can we compare different species and so attempt to reconstruct phylogeny according to the branching bush metaphor? The answer is through comparative anatomy or morphology which forms the basis of classical taxonomy. We are all aware of a relationship between physical appearance (structure, anatomy or morphology) and genetics. Certainly offspring resemble parents and we have all heard people comment upon the arrival of a newborn as to which parent the child most closely resembles. For even more distant relatives we talk about a family resemblance. Hence, even common sense reinforces the linkage between structural similarity and genetic relationship. But biological classification need not be based on anatomy. We could use a number of other criteria for grouping different species. Aristotle, the first biologist, classified different animal species on the basis of locomotion. Habitat, other elements of behavior, and even biochemistry could serve as a basis of classification. Anatomy, however, has one distinct advantage over all other criteria and that is universality of application. Species can be described and classified from both living and dead specimens using the naked eye as the only instrument for observation. The same cannot be said for behavioral, ecological and biochemical criteria. The science of taxonomy Taxonomy is a specialized branch of biology which studies the rules and procedures used in describing, naming and classifying species. The modern system of classification is the hierarchical system proposed in the eighteenth century by Carl von Linne (also known by his Latin name Carolus Linnaeus) . Linnaeus grouped species into successively inclusive categories based on the morphological characters they shared with other species. Similar species, for example, would be grouped into the same genus which separated them from dissimilar species assigned to other genera (the plural form of genus). This process is continued until each species is included in each of the seven obligatory taxonomic categories which comprise the modern system. Five of these categories were recognized by Linnaeus (species, genus, order, class and kingdom) with two others (family and phylum) later added by Ernst Haeckel. The purpose of the Linnaean system is to order organic diversity to facilitate communication among biologists and make research results intelligible globally. Before this system was developed, research was communicated using the common name of the species in the native language of the scientist publishing the results. This practice resulted in considerable ambiguity and confusion. To alleviate this problem Linnaeus also proposed a binomial system of nomenclature wherein each species was given a name consisting of two components: the name of its genus and a specific epithet. Thus, our species is named Homo sapiens after the genus to which we belong (Homo) and a specific epithet (sapiens) which distinguishes us from other members of this same genus. Note that the scientific name of a species (derived either from Latin or Greek words) is always written with the first letter of the genus capitalized and all other letters written as lower case letters. Also, the name must be either italicized or underlined. Failure to follow these two conventions is a sign of scientific illiteracy! A problem with the original Linnaean system was that it contained too few categories to handle biological diversity. Consequently, taxonomists had to used a number of additional categories to account for all the similarities and differences between species they observed in nature. The full list of taxonomic categories used today is included below with the seven obligatory categories printed in capital letters. Any real group of organisms described and included in this classification system is called a taxon (plural,taxa) and the rank of the taxon is the rank of the category to which it is assigned. Thus, all birds constitute a taxon distinct from mammals and this distinction between the two taxa (birds and mammals) is one of class (the rank of each taxon). Species-specific differences refer only to differences between congeneric species, i.e., species belonging to the same genus. Thus, any difference between a human and a sugar maple tree would not constitute a species-specific difference even though the two items compared are separate species. This difference could be kingdom- specific. KINGDOM PHYLUM Subphylum Superclass CLASS Subclass Infraclass Cohort Superorder ORDER Suborder Infraorder Superfamily FAMILY Subfamily Tribe Subtribe GENUS Subgenus Superspecies SPECIES Subspecies The reason for all these categories is to handle the amount of diversity observed in nature. The nonobligatory or optional categories are only used when the number of different species within a taxon warrants their use to accommodate the similarities and differences which exist among them. The less the diversity within a taxon, the fewer categories needed to describe this diversity. The assignment of species to these various taxonomic categories is arbitrary and depends upon the evaluation of criteria chosen by the taxonomists doing the classifying. There exist no intrinsic definitions for categories except the species category (defined on the basis of reproduction among members as we will discuss later in the course). Furthermore, taxonomic characters chosen to delimit genera in one class could be used to define families in another class. This arbitrariness in character selection has given rise to a difference in procedure used by taxonomists with major implications for the usefulness of taxonomy as supportive of the theory of evolution. Taxonomic vs phylogenetic relationships. Species are classified in the Linnaean system on the basis of an evaluation of their anatomical similarities and differences. Anatomically similar species are grouped together in a common taxonomic category and separated from those that are anatomically different. Therefore, taxonomic relationship is based on degree of structural similarity. To what extent does the taxonomic relationship among living species reflect their evolutionary history? Should taxonomy attempt to reflect phylogeny? Considerable debate exists on these points. The original taxonomists (including Linnaeus himself) were creationists and so classified species without any consideration of phylogeny. Some taxonomists argue that phylogeny will never be known due to the incompleteness of the fossil record and so taxonomy should have no phylogenetic implications. For them, taxonomy is simply a way of ordering species for the purpose of facilitating communication among biologists of all specializations. These taxonomists, called phenetic taxonomists, subscribe to the view that all morphological features are of equal importance and must be used in determining taxonomic relationships among species. Phylogenetic taxonomists disagree and attempt to base their classification on phylogenetic relationships. Consequently, phylogenetic taxonomists are selective in what characters they use in classifying species and weight characters based on a scale of primitive to advanced (generalized to specialized). Phenetic taxonomists claim that this selectivity introduces too much subjectivity into taxonomy and opt for the greater objectivity of their approach. In either case the method of classifying species, once the characters to be used have been selected, is the same for both phenetic and phylogenetic taxonomists. They construct a dendogram, often with the aid of a computer, and then assign the branches of this tree-like diagram to the various Linnaean taxonomic categories. Phylogenetic taxonomy If not all structural characters of species can serve as taxonomic characters indicating phylogenetic relationships, what criterion should guide the choice of characters for constructing a phylogenetic classification? The answer is homology. Only homologous structures should be used and variations in these should be assigned different weight based on their degree of specialization. Homologous structures are structures shared by different species precisely because they are genetically related. Structures can be recognized as being homologous if they share a common developmental origin and have components which are similar in organizational plan and structural detail. Analogous structures, on the other hand, are nonhomologous and present a superficial similarity only. They possess neither a common developmental origin nor overall organizational ground plan. Their similarity derives simply from functional equivalence, hence, analogous structures do not indicate genetic affinity and should not be used to infer phylogeny. The difference between homology and analogy can be seen in comparing the wings of bats and butterflies with the human arm. Bat and butterfly wings are analogous structures which are similar in outward appearance because they have a common function, but fail to agree in structural detail and embryological origin. The bat wing and human arm are homologous because they arise from the same embryological precursor and possess the same bones arranged in the same overall organizational plan. Thus, bats and humans are more closely related to each other than either is to the butterfly based on their shared homologies. The concept of homology is not restricted to gross morphology (structures observable with the unaided eye) but extends equally well to microanatomical and molecular structures. At the molecular level enzymes and other proteins having the same basic sequence of amino acids are homologous and the degree of similarity in amino acid composition can provide an index of phylogenetic relationship. The greater the similarity in amino acid sequencing, the closer the genetic relationship between the different species compared. Molecular studies involving comparison of proteins and DNA molecules have indicated a remarkable degree of genetic relationship between ourselves and the chimpanzee. In fact, such studies have suggested that the chimpanzee may be more closely related to humans than to the gorilla, another great ape also found in Africa. Evolutionary vs. cladistic taxonomy. Phylogenetic taxonomists differ in the basis used to assign taxa to Linnaean categories. Evolutionary taxonomists believe that taxa should be grouped according to degree of morphological similarity (grade) even if this grouping includes species which do not share the same immediate common ancestor. Cladistic taxonomists believe that taxa should be grouped solely on phylogenetic affinity (clade) without regard for differences in morphology, i.e., all taxa in the same category should have the same common ancestor. Cladists therefore use phylogeny as the basis for their classification; evolutionary taxonomists simply require that their classification be consistent with phylogeny even if it doesn't depict it exactly. The difference between cladists and evolutionary taxonomists can be illustrated by how each handles the classification of birds and crocodilians. Traditional evolutionary taxonomy separates birds (Class Aves) and crocodilians (Class Reptilia) on the basis of overall morphology despite the fact that they have the same common ancestor, a thecodont reptile. Thecodonts were primitive reptiles which gave rise to dinosaurs and pterosaurs (flying reptiles) in addition to crocodilians and birds. Cladists would place all four derived taxa into the same higher taxonomic category since they share the same common ancestor. Evolutionary taxonomists do not deny the phylogentic affinity of birds to these other reptiles, but place them in a separate class because they have reached a new structural grade by possessing feathers. Like birds, and as far as we know unlike pterosaurs and dinosaurs, crocodilians have a four-chambered heart and so appear to be more closely related to birds than to the other thecodont descendants, but this similarity would be dismissed by evolutionary taxonomists in assigning crocodilians to the Class Reptilia. Based on strict cladistic analysis, however, crocodiles should be included in the same class with birds. Creationist vs Evolutionary Interpretations According to Ernst Mayr, a noted Harvard systematist, species constitute the fundamental discontinuity of life. Each species is unique and the morphological gap between species permits recognition of them as distinct entities. The early taxonomists, including Linnaeus, were creationists imbued with the idea that species were fixed, immutable and specially created by God. The similarities which enabled these taxonomists to group species into higher taxonomic categories were interpreted as basic ground plans or archetypes used by the creator in designing species. Hence, by studying organic diversity biologists could learn something of the divine plan. So skillful were these taxonomists in recognizing relationships based on structural similarity and difference that the shift from a creationist to an evolutionist interpretation of the origin of organic diversity had little effect on taxonomy. The morphological relationships between species did not change, only the interpretation of their significance changed. The shift in paradigm from creationism to evolution simply resulted in the notion of archetype being replaced by that of common ancestor. One major difference in interpretation did result, however, and that was regarding the position of human beings in the universe. A survey of life reveals a trend from simple to complex which was interpreted by the ancient Greeks as the Great Chain of Being or Scala Naturae. This ladder of life placed the simplest of living forms on the bottom rung and the most complex of all (ourselves) on the top rung. This idea was even extended later to include angels above humans and nonliving entities below the lowest forms of life. The evolutionary interpretation depicted organic diversity as a branching bush rather than a ladder of life. This bush treats all living species equally as regards success in surviving. According to this model, we are no longer considered the pinnacle of creation, but only one of many species which are endpoints of the evolutionary process. No doubt we are unique, but the same can be said for every other species. The shift from a creationist to an evolutionary paradigm further displaced us from central importance in the broad scheme of nature and demands that we rethink our position relative to other species in terms of the dynamic worldview which has replaced the static worldview of creationism - a topic we will discuss near the end of this course. The Fossil Record Paleontology as evidence for evolution Paleontology is the study of past life as revealed in fossils. As such it offers the only direct evidence of variation in the level of organic diversity over time. Despite this advantage, the fossil record studied by paleontologists has severe limitations. First of all, except for specimens trapped in amber, fossils are only fragments of entire organisms and so do not provide a complete picture of the specimen from which they were formed. Most fossils are hard parts, such as bones, shells or tree trunks in which the organic matter of the plant has been replaced by minerals. Some fossils are casts or molds formed when the organism is covered by sediment or volcanic lava. After being covered the body decomposes leaving an impression of its form (a mold) which might later be filled with sediment to produce a cast. In this way soft bodied species might be fossilized as well as tracks and artifacts, e.g., nests and burrows. Rarely is an entire skeleton fossilized or recovered so that most fossil species are represented by fragments. How valid these fragments are as indicators of species status is a matter of interpretation. The fossil record is biased and notoriously incomplete as a record of phylogeny. To be fossilized an individual must be covered quickly upon its death so that it is not destroyed by scavangers and erosive forces. For this reason most fossils are of aquatic organisms which get quickly buried in sediment. Terrestrial organisms might be fossilized if they live near water and their bodies end up in sediment. Species which inhabit forests, mountainous regions or deserts are unlikely to leave any fossil trace. Of the three types of rock (sedimentary, igneous and metamorphic) only sedimentary rocks commonly contain fossils. Igneous rocks formed from cooled magma would destroy organisms upon contact, and any fossils existing in metamorphic rock (igneous or sedimentary rock modified by great pressure and/or heat) would be destroyed by the process of metamorphism. Unfortunately, neither sedimentary rock nor the fossils contained therein can be accurately dated because they form slowly through deposition and mineralization, respectively. Consequently, strata and fossils must be dated by extrapolation from the nearest horizons of igneous rock which can be dated. A subtle bias in paleontology stems from the efforts of paleontologists themselves. The relative abundance of taxa described in the fossil record says more about the collecting interests of paleontologists than it does about the species collected. Since different sampling techniques are used for different types of fossils, one method of collecting would overlook or even possibly destroy fossils collected by a different method. For example, in the past paleontologists interested in collecting large dinosaurs would not sift through soil carefully - a technique required for sampling birds and mammals. Hence, collecting expeditions may not discover all of the fossil material in the area sampled. The fossil record must be evaluated very carefully because it: (1) overestimates marine and aquatic species and underestimates terrestrial ones due to the likelihood of an organism being fossilized, (2) variously represents species which can be fossilized based on the interests and collecting methods used by paleontologists, and (3) is subject to much interpretation because entire organisms are not recovered. Clever interpretation of fossil evidence (relying mostly on the principle of uniformitarianism) can shed much light on past species including their behavior and ecology, but the evidence (and its limitations) upon which such inferences are drawn must be clearly understood. Evolutionary vs creationist interpretations Despite these limitations the fossil record does demonstrate the following: (1) not all species known to have inhabited our planet existed at the same time, (2) more advanced forms of life appear later in the fossil record than more primitive forms, and (3) the abundance of species within taxonomic groups has varied over time, sometimes increasing and sometimes decreasing - even to the point of extinction. The fossil history of vertebrates provides the most compelling evidence for evolution. Creationists argue that since all major phyla are represented in the Cambrian rocks, the fossil record supports the biblical version of creation. They ignore the existence of preCambrian fossil invertebrates (rare because they are soft- bodied), the discovery of 3.5 billion year old unicellular, bacteria-like forms, and the sequence of vertebrate species from fish to mammals and birds. Note than no vertebrates exist in the Cambrian; the Phylum Chordata to which they belong was at this time represented by a primitive chordate species which was not a vertebrate. The existence of unicellular and invertebrate species before the Cambrian and a sequence of vertebrate species after the Cambrian following a scheme of simple to complex is quite consistent with an evolutionary interpretation of the history of life and quite inconsistent with the biblical account of species origin. A note of caution: the fossil record reveals pattern, not process. The sequence of bony fish, amphibians, reptiles, and then birds and mammals suggests but does not prove species origin by evolution. A sequence of successive creation events could also account for this same pattern. The process which produced this pattern is not evident in the record itself and so must be inferred in the form of an hypothesis which provides a logical interpretation of the pattern. If the pattern was produced by a mechanism of "descent with modification", then one would predict the existence of intermediary forms between the major taxonomic groups. Examples of such transitional forms have been found between most vertebrate classes, e.g., Eusthenopteron and Elpistostege between bony fish and amphibians, Seymouria between amphibians and reptiles, Archaeopteryx between reptiles and birds, and Diarthrognathus betwen reptiles and mammals. Furthermore, the various stages in a hypothetical transition between mammal-like reptiles (therapsids) and mammals is well documented in the fossil record. Such missing links would be expected if evolution were the reason for the origin of different vertebrate classes, but would not be necessary if they arose by creation. As a picture of the past, the fossil record portrays a dynamic Earth in terms of biotic composition. Select any point in time as seen in a particular geological stratum and then move vertically from this layer in either direction. What will be observed is a gradual deviation in fossil structure with each successive layer with the greatest differences found among fossils sampled from the extreme ends of the sequence. Darwin was well aware of this phenomenon and noted that the South American fossils he found on his global journey differed from the contemporary species he observed, but were not so different that he could not find a resemblance between fossil and extant species. Additional patterns supportive of evolution can be found in analysis of biogeography, comparative anatomy and embryology. These patterns will be discussed next.