Part 1 Outline
According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.
If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.
The structures that all known organisms use to perform these four basic processes are all quite similar, in spite of the odds. All known living things use polymers to perform these four basic functions. Organic chemists have synthesized hundreds of different polymers, yet the only ones used by life, irrespective of species, are polynucleotides, polypeptides, and polysaccharides. Regardless of the species, the DNA, RNA and proteins used in known living systems all have the same chirality, even though there are at least two chemically equivalent choices of chirality for each of these molecules. For example, RNA has four chiral centers in its ribose ring, which means that it has 16 possible stereoisomers—but only one of these stereoisomers is found in the RNA of known living organisms.
Ten years after the publication of The Origin of Species, nucleic acids were first isolated by Friedrich Miescher in 1869. It took another 75 years after this discovery before DNA was identified as the genetic material of life (Avery et al. 1944). It is quite conceivable that we could have found a different genetic material for each species. In fact, it is still possible that newly identified species might have unknown genetic materials. However, all known life uses the same polymer, polynucleotide (DNA or RNA), for storing species specific information. All known organisms base replication on the duplication of this molecule. The DNA used by living organisms is synthesized using only four nucleosides (deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine) out of the dozens known (at least 99 occur naturally and many more have been artificially synthesized) (Rozenski et al. 1999; Voet and Voet 1995, p. 969).
In order to perform the functions necessary for life, organisms must catalyze chemical reactions. In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules (and in relatively rare, yet important, cases by RNA molecules). There are over 320 naturally occurring amino acids known (Voet and Voet 1995, p. 69; Garavelli et al. 2001); however, the protein molecules used by all known living organisms are constructed with the same subset of 22 amino acids.
There must be a mechanism for transmitting information from the genetic material to the catalytic material; all known organisms, with extremely rare exceptions, use the same genetic code for this. The few known exceptions are, nevertheless, simple and minor variations from the "universal" genetic code (see Figure 1.1.1) (Lehman 2001; Voet and Voet 1995, p. 967), exactly as predicted by evolutionary biologists, if common descent were correct, years before the genetic code was solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).
All known organisms use extremely similar, if not the same, metabolic pathways and metabolic enzymes in processing energy-containing molecules. For example, the fundamental metabolic systems in living organisms are glycolysis, the citric acid cycle, and oxidative phosphorylation. In all eukaryotes and in the majority of prokaryotes, glycolysis is performed in the same ten steps, in the same order, using the same ten enzymes (Voet and Voet 1995, p. 445). In addition, the most basic unit of energy storage, the adenosine triphosphate molecule (ATP), is the same in all species that have been studied.
Thousands of new species are discovered yearly, and new DNA and protein sequences are determined daily from previously unexamined species (Wilson 1992, Ch. 8). At the current rate, which is increasing exponentially, over 20,000 new sequences are deposited at GenBank every day, amounting to over 34 million new bases sequenced every day. Each and every one is a test of the theory of common descent. When I first wrote these words in 1999, the rate was less than one tenth what it is today (in 2004), and we now have 20 times the amount of DNA sequenced.
Based solely on the theory of common descent and the genetics of known organisms, we strongly predict that we will never find any modern species from known phyla on this Earth with a foreign, non-nucleic acid genetic material. We also make the strong prediction that all newly discovered species that belong to the known phyla will use the "standard genetic code" or a close derivative thereof. For example, according to the theory, none of the thousands of new and previously unknown insects that are constantly being discovered in the Brazilian rainforest will have non-nucleic acid genomes. Nor will these yet undiscovered species of insects have genetic codes which are not close derivatives of the standard genetic code. In the absence of the theory of common descent, it is quite possible that every species could have a very different genetic code, specific to it only, since there are 1.4 x 1070 informationally equivalent genetic codes, all of which use the same codons and amino acids as the standard genetic code (Yockey 1992). This possibility could be extremely useful for organisms, as it would preclude interspecific viral infections. However, this has not been observed, and the theory of common descent effectively prohibits such an observation.
As another example, nine new lemur and two marmoset species (all primates) were discovered in the forests of Madagascar and Brazil in 2000 (Groves 2000; Rasoloarison et al. 2000; Thalmann and Geissmann 2000). Ten new monkey species have been discovered in Brazil alone since 1990 (Van Roosmalen et al. 2000). Nothing in biology prevents these various species from having a hitherto unknown genetic material or a previously unused genetic code—nothing, that is, except for the theory of common descent. However, we now know definitively that the new lemurs use DNA with the standard genetic code (Yoder et al. 2000); the marmosets have yet to be tested.
Furthermore, each species could use a different polymer for catalysis. The polymers that are used could still be chemically identical yet have different chiralities in different species. There are thousands of thermodynamically equivalent glycolysis pathways (even using the same ten reaction steps but in different orders), so it is possible that every species could have its own specific glycolysis pathway, tailored to its own unique needs. The same reasoning applies to other core metabolic pathways, such as the citric acid cycle and oxidative phosphorylation.
Finally, many molecules besides ATP could serve equally well as the common
currency for energy in various species (CTP, TTP, UTP, ITP, or any ATP-like
molecule with one of the 293 known amino acids or one of the dozens of other
bases replacing the adenosine moiety immediately come to mind). Discovering any
new animals or plants that contained any of the anomalous examples proffered
above would be potential falsifications of common ancestry, but they have not
As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as "groups within groups", otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.
The nested hierarchical organization of species contrasts sharply with other possible biological patterns, such as the continuum of "the great chain of being" and the continuums predicted by Lamarck's theory of organic progression (Darwin 1872, pp. 552-553; Futuyma 1998, pp. 88-92). Mere similarity between organisms is not enough to support macroevolution; the nested classification pattern required by a gradual evolutionary process, such as universal common descent, is much more specific than simple similarity. Real world examples that cannot be objectively classified in nested hierarchies are the elementary particles (which are described by quantum chromodynamics), the elements (whose organization is described by quantum mechanics and illustrated by the periodic table), the planets in our Solar System, books in a library, or specially designed objects like buildings, furniture, cars, etc.
Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically—perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.
The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.
Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution. Slowly evolving characters let us see farther back into time; faster evolving characters restrict that view to more recent events. If the rate of evolution for a certain character is extremely slow, a nested hierarchy will be observed for that character only for very distantly related taxa. However, "rate of evolution" vs. "time since divergence" is relative; if common descent is true, then in some time frame we will always be able to observe a nested hierarchy for any given character. Furthermore, we know empirically that different characters evolve at different rates (e.g. some genes have higher background mutation rates than others). Thus, if common descent is true, we should observe nested hierarchies over a broad range of time at various biological levels.
Therefore, since common descent is a genealogical process, common descent should produce organisms that can be organized into objective nested hierarchies. Equivalently, we predict that, in general, cladistic analyses of organisms should produce phylogenies that have large, statistically significant values of hierarchical structure (in standard scientific practice, a result with "high statistical significance" is a result that has a 1% probability or less of occurring by chance [P < 0.01]). As a representation of universal common descent, the universal tree of life should have very high, very significant hierarchical structure and phylogenetic signal.
Most existing species can be organized rather easily in a nested hierarchical classification. This is evident in the use of the Linnaean classification scheme. Based on shared derived characters, closely related organisms can be placed in one group (such as a genus), several genera can be grouped together into one family, several families can be grouped together into an order, etc.
As a specific example (see Figure 1), plants can be classified as vascular and nonvascular (i.e. they have or lack xylem and phloem). Nested within the vascular group, there are two divisions, seed and non-seed plants. Further nested within the seed plants are two more groups, the angiosperms (which have enclosed, protected seeds) and the gymnosperms (having non-enclosed seeds). Within the angiosperm group are the monocotyledons and the dicotyledons.
Most importantly, the standard phylogenetic tree and nearly all less inclusive evolutionary phylogenies have statistically significant, high values of hierarchical structure (Baldauf et al. 2000; Brown et al. 2001; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991).
It would be very problematic if many species were found that combined characteristics of different nested groupings. Proceeding with the previous example, some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems. Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals. A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies. Unlike organisms, cars do have a mix and match of characters, and this is precisely why a nested hierarchy does not flow naturally from classification of cars.
If it were impossible, or very problematic, to place species in an objective nested classification scheme (as it is for the car, chair, book, atomic element, and elementary particle examples mentioned above), macroevolution would be effectively disproven. More precisely, if the phylogenetic tree of all life gave statistically significant low values of phylogenetic signal (hierarchical structure), common descent would be resolutely falsified.
In fact, it is possible to have a "reciprocal" pattern from nested hierarchies. Mathematically, a nested hierarchy is the result of specific correlations between certain characters of organisms. When evolutionary rates are fast, characters become randomly distributed with respect to one another, and the correlations are weakened. However, the characters can also be anti-correlated—it is possible for them to be correlated in the opposite direction from what produces nested hierarchies (Archie 1989; Faith and Cranston 1991; Hillis 1991; Hillis and Huelsenbeck 1992; Klassen et al. 1991). The observation of such an anti-correlated pattern would be a strong falsification of common descent, regardless of evolutionary rates.
One widely used measure of cladistic hierarchical structure is the consistency index (CI). The statistical properties of the CI measure were investigated in a frequently cited paper by Klassen et al. (Klassen et al. 1991; see Figure 1.2.1). The exact CI value is dependent upon the number of taxa in the phylogenetic tree under consideration. In this paper, the authors calculated what values of CI were statistically significant for various numbers of taxa. Higher values of CI indicate a greater degree of hierarchical structure.
As an example, a CI of 0.2 is expected from random data for 20 taxa. A value of 0.3 is, however, highly statistically significant. Most interesting for the present point is the fact that a CI of 0.1 for 20 taxa is also highly statistically significant, but it is too low—it is indicative of anti-cladistic structure. Klassen et al. took 75 CI values from published cladograms in 1989 (combined from three papers) and noted how they fared in terms of statistical significance. The cladograms used from 5 to 49 different taxa (i.e. different species). Three of the 75 cladograms fell within the 95% confidence limits for random data, which means that they were indistinguishable from random data. All the rest exhibited highly statistically significant values of CI. None exhibited significant low values; none displayed an anti-correlated, anti-hierarchical pattern.
Note, this study was performed before there were measures of statistical significance which would allow researchers to "weed out" the bad cladograms. Predictably, the three "bad" data sets considered under ten taxa—it is of course more difficult to determine statistical significance with very little data. Seventy-five independent studies from different researchers, on different organisms and genes, with high values of CI (P < 0.01) is an incredible confirmation with an astronomical degree of combined statistical significance (P << 10-300, Bailey and Gribskov 1998; Fisher 1990). If the reverse were true—if studies such as this gave statistically significant values of CI (i.e. cladistic hierarchical structure) which were lower than that expected from random data—common descent would have been firmly falsified.
Keep in mind that about 1.5 million species are known currently, and that the
majority of these species has been discovered since Darwin first stated his
hypothesis of common ancestry. Even so, they all have fit the correct
hierarchical pattern within the error of our methods. Furthermore, it is
estimated that only 1 to 10% of all living species has even been catalogued, let
alone studied in detail. New species discoveries pour in daily, and each one is
a test of the theory of common descent (Wilson
1992, Ch. 8).
Here we commence to beat Pauling's poor 40-year dead horse. If there is one historical phylogenetic tree which unites all species in an objective genealogy, all separate lines of evidence should converge on the same tree (Penny et al. 1982; Penny et al. 1991; Zuckerkandl and Pauling 1965). Independently derived phylogenetic trees of all organisms should match each other with a high degree of statistical significance.
Well-determined phylogenetic trees inferred from the independent evidence of morphology and molecular sequences match with an extremely high degree of statistical significance. Many genes with very basic cellular functions are ubiquitous—they occur in the genomes of most or all organisms. An oft-cited example is the cytochrome c gene. Since all eukaryotes contain the gene for this essential protein, neither its presence nor its function correlates with organismal morphology. Additionally, because of the fact of DNA coding redundancy, parts of certain DNA sequences have absolutely no correlation with phenotype (e.g. certain introns or the four-fold degenerate third-base position of most DNA codons). Due to these two aspects of certain DNA sequences, ubiquity and redundancy, DNA sequences can be carefully chosen that constitute completely independent data from morphology. (See point 17 and 18 for more background about the molecular sequence evidence and for more detail about how it is independent of morphology.) The degree of phylogenetic congruence between these independent data sets is nothing short of incredible.
In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in science—all we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are "When comparing two measurements, how much of a discrepancy does it take to be a problem?" and "How close must the measurements be in order to give a strong confirmation?" Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 1038 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the "twin nested hierarchy". This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.
When two independently determined trees mismatch by some branches, they are called "incongruent". In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see "Statistics of Incongruent Phylogenetic Trees".
The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:
For a more realistic universal phylogenetic tree with dozens of taxa including all known phyla, the accuracy is better by many orders of magnitude. To put the significance of this incredible confirmation in perspective, consider the modern theory of gravity. Both Newton's Theory of Universal Gravitation and Einstein's General Theory of Relativity rely upon a fundamental physical constant, G, the gravitational constant. If these theories of gravity are correct, independent methods should determine similar values for G. However, to date, very precise independent measurements of the gravitational constant G disagree by nearly 1% (Kestenbaum 1998; Quinn 2000). Here is how David Kestenbaum describes the current scientific status of the theory of gravity, as reported in the prestigious journal Science:
Over two years later, the same Terry Quinn (of the International Bureau of Weights and Measures [BIPM] in Sèvres, France) summarized the situation in a review for the journal Nature:
Nevertheless, a precision of just under 1% is still pretty good; it is not enough, at this point, to cause us to cast much doubt upon the validity and usefulness of modern theories of gravity. However, if tests of the theory of common descent performed that poorly, different phylogenetic trees, as shown in Figure 1, would have to differ by 18 of the 30 branches! In their quest for scientific perfection, some biologists are rightly rankled at the obvious discrepancies between some phylogenetic trees (Gura 2000; Patterson et al. 1993; Maley and Marshall 1998). However, as illustrated in Figure 1, the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants. For comparison, the charge of the electron is known to only seven decimal places, the Planck constant is known to only eight decimal places, the mass of the neutron, proton, and electron are all known to only nine decimal places, and the universal gravitational constant has been determined to only three decimal places.
Furthermore, if common descent is true, we expect that including more data in phylogenetic analyses will increase the correspondence between phylogenetic trees. As explained in the phylogenetic caveats sidebar, gene trees are not equivalent to species trees (Avise and Wollenberg 1997; Fitch 1970; Hudson 1992; Nichols 2001; Wu 1991). Genetics and heredity are stochastic (i.e. probabilistic) processes, and consequently we expect that phylogenies constructed with single genes will be partially incongruent. However, including multiple independent genes in a phylogenetic analysis should circumvent this difficulty; in general more than five independent genes are needed to accurately reconstruct a species phylogeny (Wu 1991). Phylogenetic trees constructed with multiple genes should thus be more accurate than those constructed with single genes, and indeed combined gene trees are more congruent (Baldauf et al. 2000; Hedges 1994; Hedges and Poling 1999; Penny et al. 1982).
When it became possible to sequence biological molecules, the realization of a markedly different tree based on the independent molecular evidence would have been a fatal blow to the theory of evolution, even though that is by far the most likely result. More precisely, the common descent hypothesis would have been falsified if the universal phylogenetic trees determined from the independent molecular and morphological evidence did not match with statistical significance. Furthermore, we are now in a position to begin construction of phylogenetic trees based on other independent lines of data, such as chromosomal organization. In a very general sense, chromosome number and length and the chromosomal position of genes are all causally independent of both morphology and of sequence identity. Phylogenies constructed from these data should recapitulate the standard phylogenetic tree as well (Hillis et al. 1996; Li 1997).
One common objection is the assertion that anatomy is not independent of biochemistry, and thus anatomically similar organisms are likely to be similar biochemically (e.g. in their molecular sequences) simply for functional reasons. According to this argument, then, we should expect phylogenies based on molecular sequences to be similar to phylogenies based on morphology even if organisms are not related by common descent. This argument is very wrong. There is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry. Though this logic may seem quite reasonable initially, all of molecular biology refutes this "common sense" correlation. In general, similar DNA and biochemistry give similar morphology and function, but the converse is not true—similar morphology and function is not necessarily the result of similar DNA or biochemistry. The reason is easily understood once explained; many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies (see predictions 4.1 and 4.2 for a detailed explanation).
As a close analogy, consider computer programs. Netscape works essentially the same on a Macintosh, an IBM, or a Unix machine, but the binary code for each program is quite different. Computer programs that perform the same functions can be written in most any computer language—Basic, Fortran, C, C++, Java, Pascal, etc. and identical programs can be compiled into binary code many different ways. Furthermore, even using the same computer language, there are many different ways to write any specific computer program, even using the same algorithms and subroutines. In the end, there is no reason to suspect that similar computer programs are written with similar code, based solely on the function of the program. This is the reason why software companies keep their source code secret, but they don't care that competitors can use their programs—it is essentially impossible to deduce the program code from the function and operation of the software. The same conclusion applies to biological organisms, for very similar reasons.
To reiterate, although similar genotypes (e.g. molecular sequences) often
give similar phenotypes (e.g. morphological characters), similar phenotypes are
not necessarily the result of similar genotypes. Thus, it is entirely possible
that phylogenetic trees constructed from genotypic data could be radically
different from phylogenetic trees constructed from phenotypic data. In fact, in
the absence of common descent or any other reason to suppose that these two
types of trees should be similar, the most likely result by far is that they
will be radically different. This is precisely why it is possible to falsify the
macroevolutionary prediction that independently derived phylogenies should be
Prediction 1.4: Intermediate and transitional forms: the possible morphologies of predicted common ancestors
All fossilized animals found should conform to the standard phylogenetic tree. If all organisms are united by descent from a common ancestor, then there is one single true historical phylogeny for all organisms. Similarly, there is one single true historical genealogy for any individual human. It directly follows that if there is a unique universal phylogeny, then all organisms, both past and present, fit in that phylogeny uniquely. Since the standard phylogenetic tree is the best approximation of the true historical phylogeny, we expect that all fossilized animals should conform to the standard phylogenetic tree within the error of our scientific methods.
Every node shared between two branches in a phylogeny or cladogram represents a predicted common ancestor; thus there are ~29 common ancestors predicted from the tree shown in Figure 1. Our standard tree shows that the bird grouping is most closely related to the reptilian grouping, with a node linking the two (A in Figure 1); thus we predict the possibility of finding fossil intermediates between birds and reptiles. The same reasoning applies to mammals and reptiles (B in Figure 1). However, we predict that we should never find fossil intermediates between birds and mammals.
It should be pointed out that there is no requirement for intermediate organisms to go extinct. In fact, all living organisms can be thought of as intermediate between adjacent taxa in a phylogenetic tree. For instance, modern reptiles are intermediate between amphibians and mammals, and reptiles are also intermediate between amphibians and birds. As far as macroevolutionary predictions of morphology are concerned, this point is trivial, as it is essentially just a restatement of the concept of a nested hierarchy.
However, a phylogenetic tree does make significant predictions about the morphology of intermediates which no longer exist or which have yet to be discovered. Each predicted common ancestor has a set of explicitly specified morphological characteristics, based on each of the most common derived characters of its descendants and based upon the transitions that must have occurred to transform one taxa into another (Cunningham et al. 1998; Futuyma 1998, pp. 107-108). From the knowledge of avian and reptilian morphology, it is possible to predict some of the characteristics that a reptile-bird intermediate should have, if found. Therefore, we expect the possibility of finding reptile-like fossils with feathers, bird-like fossils with teeth, or bird-like fossils with long reptilian tails. However, we do not expect transitional fossils between birds and mammals, like mammalian fossils with feathers or bird-like fossils with mammalian-style middle ear bones.
Example 1: bird-reptiles
In the case just mentioned, we have found a quite complete set of dinosaur-to-bird transitional fossils with no morphological "gaps" (Sereno 1999), represented by Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus, Sinornithosaurus, Microraptor, Archaeopteryx, Rahonavis, Confuciusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba, among many others (Carroll 1997, pp. 306-323; Norell and Clarke 2001; Sereno 1999; Xu et al. 1999; Xu et al. 2000; Xu et al. 2002). All have the expected possible morphologies (see Figure 3.1.1 from Prediction 3.1 for a few examples), including organisms such as Protarchaeopteryx, Caudipteryx, and the famous "BPM 1 3-13" (an unnamed dromaeosaur from China) which are flightless bipedal dinosaurs with modern-style feathers (Chen et al.1998 ; Qiang et al. 1998; Norell et al. 2002). Additionally, several similar flightless dinosaurs have been found covered with nascent evolutionary precursors to modern feathers (branched feather-like integument indistinguishable from the contour feathers of true birds), including Sinornithosaurus ("Bambiraptor"), Sinosauropteryx, Beipiaosaurus, Microraptor, and an unnamed dromaeosaur specimen, NGMC 91, informally called "Dave" (Ji et al. 2001). The All About Archaeopteryx FAQ gives a detailed listing of the various characters of Archaeopteryx which are intermediate between reptiles and modern birds.
Example 2: reptile-mammals
We also have an exquisitely complete series of fossils for the reptile-mammal intermediates, ranging from the pelycosauria, therapsida, cynodonta, up to primitive mammalia (Carroll 1988, pp. 392-396; Futuyma 1998, pp. 146-151; Gould 1990; Kardong 2002, pp. 255-275). As mentioned above, the standard phylogenetic tree indicates that mammals gradually evolved from a reptile-like ancestor, and that transitional species must have existed which were morphologically intermediate between reptiles and mammals—even though none are found living today. However, there are significant morphological differences between modern reptiles and modern mammals. Bones, of course, are what fossilize most readily, and that is where we look for transitional species from the past. Osteologically, two major striking differences exist between reptiles and mammals: (1) reptiles have at least four bones in the lower jaw (e.g. the dentary, articular, angular, surangular, and coronoid), while mammals have only one (the dentary), and (2) reptiles have only one middle ear bone (the stapes), while mammals have three (the hammer, anvil, and stapes) (see Figure 1.4.1).
Early in the 20th century, developmental biologists discovered something that further complicates the picture. In the reptilian fetus, two developing bones from the head eventually form two bones in the reptilian lower jaw, the quadrate and the articular (see the Pelycosaur in Figure 1.4.1). Surprisingly, the corresponding developing bones in the mammalian fetus eventually form the anvil and hammer of the unique mammalian middle ear (also known more formally as the incus and malleus, respectively; see Figure 1.4.2) (Gilbert 1997, pp. 894-896). These facts strongly indicated that the hammer and anvil had evolved from these reptilian jawbones—that is, if common descent was in fact true. This result was so striking, and the required intermediates so outlandish, that many anatomists had extreme trouble imagining how transitional forms bridging these morphologies could have existed while retaining function. Young-earth creationist Duane Gish stated the problem this way:
Gish was incorrect in stating that there were no transitional fossil forms, and he has been corrected on this gaff numerous times since he wrote these words. However, Gish's statements nicely delineate the morphological conundrum at hand. Let's review the required evolutionary conclusion. During their evolution, two mammalian middle ear bones (the hammer and anvil, aka malleus and incus) were derived from two reptilian jawbones. Thus there was a major evolutionary transition in which several reptilian jawbones (the quadrate, articular, and angular) were extensively reduced and modified gradually to form the modern mammalian middle ear. At the same time, the dentary bone, a part of the reptilian jaw, was expanded to form the major mammalian lower jawbone. During the course of this change, the bones that form the hinge joint of the jaw changed identity. Importantly, the reptilian jaw joint is formed at the intersection of the quadrate and articular whereas the mammalian jaw joint is formed at the intersection of the squamosal and dentary (see Figure 1.4.1).
How could hearing and jaw articulation be preserved during this transition? As clearly shown from the many transitional fossils that have been found (see Figure 1.4.3), the bones that transfer sound in the reptilian and mammalian ear were in contact with each other throughout the evolution of this transition. In reptiles, the stapes contacts the quadrate, which in turn contacts the articular. In mammals, the stapes contacts the incus, which in turn contacts the malleus (see Figure 1.4.2). Since the quadrate evolved into the incus, and the articular evolved into the malleus, these three bones were in constant contact during this impressive evolutionary change. Furthermore, a functional jaw joint was maintained by redundancy—several of the intermediate fossils have both a reptilian jaw joint (from the quadrate and articular) and a mammalian jaw joint (from the dentary and squamosal). Several late cynodonts and Morganucodon clearly have a double-jointed jaw. In this way, the reptilian-style jaw joint was freed to evolve a new specialized function in the middle ear. It is worthy of note that some modern species of snakes have a double-jointed jaw involving different bones, so such a mechanical arrangement is certainly possible and functional.
Since Figure 1.4.3 was made, several important intermediate fossils have been discovered that fit between Morganucodon and the earliest mammals. These new discoveries include a complete skull of Hadrocodium wui (Luo et al. 2001) and cranial and jaw material from Repenomamus and Gobiconodon (Wang et al. 2001). These new fossil finds clarify exactly when and how the malleus, incus, and angular completely detached from the lower jaw and became solely auditory ear ossicles.
Recall that Gish stated: "There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones" (Gish 1978, p. 80). Gish simply does not understand how gradual transitions happen (something he should understand, obviously, if he intends to criticize evolutionary theory). These fossil intermediates illustrate why Gish's statement is a gross mischaracterization of how a transitional form should look. In several of the known intermediates, the bones have overlapping functions, and one bone can be called both an ear bone and a jaw bone; these bones serve two functions. Thus, there is no reason to expect transitional forms with intermediate numbers of jaw bones or ear bones. For example, in Morganucodon, the quadrate (anvil) and the articular (hammer) serve as mammalian-style ear bones and reptilian jaw bones simultaneously. In fact, even in modern reptiles the quadrate and articular serve to transmit sound to the stapes and the inner ear (see Figure 1.4.2). The relevant transition, then, is a process where the ear bones, initially located in the lower jaw, become specialized in function by eventually detaching from the lower jaw and moving closer to the inner ear.
Example 3: human-apes
One of the most celebrated examples of transitional fossils is our collection of fossil hominids (see Figure 1.4.4 below). Based upon the consensus of numerous phylogenetic analyses, Pan troglodytes (the chimpanzee) is the closest living relative of humans. Thus, we expect that organisms lived in the past which were intermediate in morphology between humans and chimpanzees. Over the past century, many spectacular paleontological finds have identified such transitional hominid fossils.
Example 4: legged fossil whales
Another impressive example of incontrovertible transitional forms predicted to exist by evolutionary biologists is the collection of land mammal-to-whale fossil intermediates. Whales, of course, are sea animals with flippers, lacking external hindlimbs. Since they are also mammals, the consensus phylogeny indicates that whales and dolphins evolved from land mammals with legs. In recent years, we have found several transitional forms of whales with legs, both capable and incapable of terrestrial locomotion (Bajpai and Gingerich 1998; Gingerich et al. 1983; Gingerich et al. 1990; Gingerich et al. 1994; Gingerich et al. 2001; Thewissen et al. 2001).
Example 5: legged seacows
Seacows (manatees and dugongs) are fully aquatic mammals with flippers for forelimbs and no hindlimbs. Evolutionary theory predicts that seacows evolved from terrestrial ancestors with legs, and that thus we could find seacow intermediates with legs. Recently, a new transitional fossil has been found in Jamaica, a seacow with four legs (Domning 2001).
There are many other examples such as these—most can be found in the excellent Transitional Vertebrate Fossils FAQ.
Any finding of a striking half-mammal, half-bird intermediate would be highly inconsistent with common descent. Many other examples of prohibited intermediates can be thought of, based on the standard tree (Kemp 1982; Stanley 1993; Carroll 1997; Chaterjee 1997).
A subtle, yet important point is that a strict cladistic evolutionary
interpretation precludes the possibility of identifying true ancestors; only
intermediates or transitionals can be positively identified. (For the purposes
of this article, transitionals and intermediates are considered synonymous.) The
only incontrovertible evidence for an ancestor-descendant relationship is the
observation of a birth; obviously this is normally rather improbable in the
fossil record. Intermediates are not necessarily the same as the exact predicted
ancestors; in fact, it is rather unlikely that they would be the same. Simply
due to probability considerations, the intermediates that we find will most
likely not be the true ancestors of any modern species, but will be closely
related to a predicted common ancestor. Therefore, the intermediates we do find
will likely have additional derived characters besides the characters that
identified them as intermediates. Because of these considerations, when a new
and important intermediate fossil species is discovered, careful paleontologists
will often note that the transitional species under study is probably not an
ancestor, but rather is "representative of a common ancestor" or is an
evolutionary "side-branch". The fewer extra dervied characters that an
intermediate fossil has, the higher the probability that an intermediate fossil
is an actual ancestor. For further clarification see prediction
Fossilized intermediates should appear in the correct general chronological order based on the standard tree. Any phylogenetic tree predicts a relative chronological order of the evolution of hypothetical common ancestors and intermediates between these ancestors. For instance, in our current example, the reptile-mammal common ancestor (B) and intermediates should be older than the reptile-bird common ancestor (A) and intermediates.
Note, however, that there is some "play" within the temporal constraints demanded by any phylogeny, for two primary reasons: (1) the statistical confidence (or conversely, the error) associated with a phylogeny and its specific internal branches, and (2) the inherent resolution of the fossil record (ultimately stemming from the vagaries of the fossilization process). As mentioned earlier, most phylogenetic trees have some branches with high confidence, because they are well-supported by the data, and other branches in which we have less confidence, because they are statistically less significant and poorly supported by the data. See also the caveats associated with phylogenetic analysis.
When evaluating the geological order of fossils, remember that once a transitional species appears there is no reason why it must become extinct and be replaced. For instance, some organisms have undergone little change in as much as 100 to 200 million years in rare cases. Some familiar examples are the "living fossils", such as the coelacanth, which has persisted for approximately 80 million years; the bat, which has not changed much in the past 50 million years; and even the modern tree squirrel, which has not changed in 35 million years. In fact, paleontological studies indicate the average longevity of 21 living families of vertebrates is approximately 70 million years (Carroll 1997, p. 167).
Furthermore, the fossil record is demonstrably incomplete; species appear in the fossil record, then disappear, then reappear later. An exceptional instance is the coelacanth, which last appeared in the fossil record 80 million years ago, yet it is alive today. During the Cretaceous (a critical time in bird evolution), there is a 50 million-year gap in the diplodocoidean record, greater than a 40 million-year gap in the pachycephalosaurian record, greater than a 20 million-year gap in the trodontidiae, and about a 15 million-year gap in the oviraptosaurian fossil record (both of these last two orders of dinosaurs are maniraptoran coelurosaurian theropods, which figure significantly in the evolution of birds). During the Jurassic, there is a 40 million-year gap in the fossil record of the heterodontosauridae (Sereno 1999). Most organisms do not fossilize, and there is no reason why a representative of some species must be found in the fossil record. As every graduate student in scientific research knows (or eventually learns, perhaps the hard way), arguments based upon negative evidence are very weak scientific arguments, especially in the absence of proper positive controls. Thus, based on the fossil remains of modern species and the known gaps in the current paleontological records of extinct species, the observation of transitional species "out of order" by 40 million years should be fairly common. This degree of "play" in the fossil record is actually rather minor, considering that the fossil record of life spans between 2 to 3.8 billion years and that of multicellular organisms encompasses a total of ~660 million years. An uncertainty of 40 million years is equivalent to about a 1% or 6% relative error, respectively—rather small overall.
The reptile-bird intermediates mentioned above date from the Upper Jurassic and Lower Cretaceous (about 150 million years ago), whereas pelycosauria and therapsida (reptile-mammal intermediates) are older and date from the Carboniferous and the Permian (about 250 to 350 million years ago, see the Geological Time Scale). This is precisely what should be observed if the fossil record matches the standard phylogenetic tree.
The most scientifically rigorous method of confirming this prediction is to demonstrate a positive corellation between phylogeny and stratigraphy, i.e. a positive corellation between the order of taxa in a phylogenetic tree and the geological order in which those taxa first appear and last appear (whether for living or extinct intermediates). For instance, within the error inherent in the fossil record, prokaryotes should appear first, followed by simple multicellular animals like sponges and starfish, then lampreys, fish, amphibians, reptiles, mammals, etc., as shown in Figure 1. Contrary to the erroneous (and unreferenced) opinions of some anti-evolutionists (e.g. Wise 1994, p. 225-226), studies from the past ten years addressing this very issue have confirmed that there is indeed a positive corellation between phylogeny and stratigraphy, with statistical significance (Benton 1998; Benton and Hitchin 1996; Benton and Hitchin 1997; Benton et al. 1999; Benton et al. 2000; Benton and Storrs 1994; Clyde and Fisher 1997; Hitchin and Benton 1997; Huelsenbeck 1994; Norell and Novacek 1992a; Norell and Novacek 1992b; Wills 1999). Using three different measures of phylogeny-stratigraphy correlation [the RCI, GER, and SCI (Ghosts 2.4 software, Wills 1999)], a high positive correlation was found between the standard phylogenetic tree portrayed in Figure 1 and the stratigraphic range of the same taxa, with very high statistical significance (P < 0.0001) (this work, Ghosts input file available upon request).
As another specific example, an early analysis published in Science by Mark Norell and Michael Novacek (Norell and Novacek 1992b) examined 24 different taxa of vertebrates (teleosts, amniotes, reptiles, synapsids, diapsids, lepidosaurs, squamates, two orders of dinosaurs, two orders of hadrosaurs, pachycephalosaurs, higher mammals, primates, rodents, ungulates, artiodactyls, ruminants, elephantiformes, brontotheres, tapiroids, chalicotheres, Chalicotheriinae, and equids). For each taxa, the phylogenetic position of known fossils was compared with the stratigraphic position of the same fossils. A positive correlation was found for all of the 24 taxa, 18 of which were statistically significant. Note that the correlation theoretically could have been negative. A statistically significant negative correlation would indicate that, in general, organisms rooted deeply in the phylogeny are found in more recent strata—a strong macroevolutionary inconsistency. However, no negative correlations were observed.
As a third example, Michael Benton and Rebecca Hitchin published a more recent, greatly expanded, and detailed stratigraphic analysis of 384 published cladograms of various multicellular organisms (Benton and Hitchin 1997). Using the three measures of congruence between the fossil record and phylogeny mentioned above (the RCI, GER, and SCI), these researchers observed values "skewed so far from a normal distribution [i.e. randomness] that they provide evidence for strong congruence of the two datasets [fossils and cladograms]." Furthermore, Benton and Hitchin's analysis was extremely conservative, since they made no effort to exclude cladograms with poor resolution or to exclude cladograms with very small numbers of taxa. Including both of these types of cladograms will add confounding random elements to the analysis and will decrease the apparent concordance between stratigraphy and cladograms. Even so, the results were overall extremely statistically significant (P < 0.0005). As the authors comment in their discussion:
Additionally, if the correlation between phylogeny and stratigraphy is due to common descent, we would expect the correlation to improve over longer geological time frames (since the relative error associated with the fossil record decreases). This is in fact observed (Benton et al. 1999). We also would expect the correlation to improve, not to get worse, as more fossils are discovered, and this has also been observed (Benton and Storrs 1994).
It would be highly inconsistent if the chronological order were reversed in the reptile-bird and reptile-mammal example. More generally, the strongest falsification of this prediction would be the finding that there was a negative correlation between stratigraphy and the phylogenetic tree that describes the genealogical relatedness of all living organisms. Even the finding that there was no overall correlation, neither positive nor negative, between stratigraphy and the consensus phylogeny of the major taxa would be very problematic for the theory of common descent. In addition, the observed correlation could decrease over longer time frames or as we acquire more paleontological data—but neither is the case (Benton et al. 1999; Benton and Storrs 1994).
Based on the high confidence in certain branches of phylogenetic trees, some temporal constraints are extremely rigid. For example, we should never find mammalian or avian fossils in or before Devonian deposits, before reptiles had diverged from the amphibian tetrapod line. This excludes Precambrian, Cambrian, Ordovician, and Silurian deposits, encompassing 92% of the earth's geological history and 65% of the biological history of multicellular organisms. Even one incontrovertible find of any pre-Devonian mammal, bird, or flower would shatter the theory of common descent (Kemp 1982; Carroll 1988; Stanley 1993; Chaterjee 1997).
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