Patterns of Diversity

PATTERNS OF DIVERSITY

---

To appreciate the temporal scale of the phenomena that we will discuss, we should review the geologic time scale and the major eras (Paleozoic, Mesosoic, Cenozoic) and periods (Cam Or Sil Dev Car Per Tri Jur Cre Ter Quat) and epochs (Pal Eo Oli Mio Plio Pleisto Holo). The point here is that there has been immense amounts of time in earth history (recall our 15 second moment of silence in class as one frame of reference). Each of these geologic time periods is defined on sedimentary evidence, much of which is comprised of fossils characteristic of each time period.
On ridiculously simple terms, there has been a dramatic increase in species diversity from the origin of life to the present. But the patterns of species diversity are much more complex when viewed in the fossil record. There are periods of rapid increase in diversity, periods of rapid loss of diversity (mass extinction events) and subsequent periods of increased diversity. These patterns beg a variety of questions about the dynamics of the history of species diversity and what forces might regulate this diversity: are there equilibria of diversity?, does diversity increase without limit?, are the patterns of diversity random patterns?
We will first consider some simple models of diversity. Two general processes that affect standing diversity are origination and extinction. These processes are in turn going to depend on the number of taxa, N present at any one time. Thus the change in the number of taxa per unit time, dN/dt can be described as follows:
The rate of origination = O = # new taxa arising / existing taxon / unit time
The rate of extinction = E = probability of extinction during period dt.
thus, change in diversity = dN/dt = ON - EN = N(O-E)
Diversity will be constant if O = E, diversity will increase if O > E (speciation rates exceed extinction rates) and decrease if O<E. Diversity might be maintained at a constant level if an increase in O was matched with an increase in E: is there an equilibrium diversity? This could only be achieved if there was some feedbackbetween N, O and E to keep O and E in approximate balance. Consider a graphical model where the equilibrium number of species depends on the effect of N on the values of E and O (see figure).
These models just provide ways of thinking about the history of diversity on earth. What might such diversity dependent forces/phenomena be? Do they exist?
What do the data tell us? First, how do we get the data? Simple on one hand: count the number of taxa present in each time interval. Complicating issues: species concept = typological (morphospecies) any "reasonably" different forms will be classified as a different species. If these morphospecies co-occur in time and space then they are probably "good" species and should be counted as separate entities. Many fossil series show temporal gradations of morphology from one form into another. These chronospecies introduce error into estimates of diversity since the end of one name and the beginning of another name look like extinction and origination, or pseudoextinction and pseudoorigination. Moreover, the taxononic level under consideration will alter one's estimate of the patterns of diversity since lower taxa (species, genus) might vary in diversity more than higher taxa (family, order). Also, differences in the identification of taxa will alter estimates of patterns (see figure 20.12, pg.577).

In the literature it is difficult to tell which extinction/speciation events represent real events and not "chrono" events. We can avoid this problem by tabulating higher taxa. It is unlikely that all representatives of a genus will evolve simultaneously into a new genus, but what is a genus (or a family)? is it a real unit of diversity?
Additional biases in quantifying diversity: thickness of sediments different sediments deposit at different rates so that the resolution is quite different among sediments (affecting the rate (dt) component of the dN/dt calculations). Area of exposed sediments are not always representative of the temporal and spatial scales one might want to sample/represent in a fossil assemblage.
Additional artifact of the age of the rocks known as "the pull of the recent" Young rocks are less likely to be destroyed by the forces of time than are old rocks. This means that last occurrences of a fossil are more likely to be better recorded than first appearances (actual first "appearance" might have been exposed, eroded, reworked, etc. moving the observed first appearance up in time). Thus the duration of lineages will be "pulled" toward the recent (pulled implies an artifact of increased likelihood of a fossil to be recorded in younger rocks). Similarly, and extant group with a single fossil occurrence has a temporal range from its fossil date through to the present, but and extinct group with a single fossil occurrence has only that single date as a temporal range, even if it lived for a long time but was not deposited as a fossil.
Biases aside, what does the record tell us? Does diversity increase with time? The Cambrian Explosion ("sudden" appearance of many invertebrate phyla in the early Precambrian) shows a clear patterns of increase in diversity from the known forms present in Pre-Cambrian strata. Were there some physical triggers of diversity increase such as geologic activity inducing major changes in the physical environment?. Or were there some biological triggers that allowed the rapid evolution of new forms? These might consist of the evolution of a key innovation (a unique new trait that allows a species/taxon to exploit a new way of life)? This idea invokes the concept of the adaptive zone, a new set of ecological niches utilized/exploited by a group of related species in which this group might radiate (speciate) extensively and increase in diversity.
The diversity of marine invertebrates in the Phanerozoic (period of visible life) is the best example. Increase from Cambrian to Ordovician, then mass extinction;increase to plateau through the Paleozoic (major extinction events in middle of plateau); continuous increase from Triassic through Tertiary (see figure below).
Patterns of increase of diversity indicate three evolutionary faunas: 1) Cambrian, 2) Paleozoic and 3) Modern (work of J. Sepkoski). Despite the major patterns, different taxa have very different profiles: there are examples of extinction and reradiation, maintenance of diversity and continuous diversification all spanning the same time frame (compare fig. below with other taxa: fig. 21.11 - 21.16. pp. 602-607). This suggests that if there are biological forces/pressures regulating diversity, they may be acting quite differently in different taxa.
Increases in diversity were measured by Bambach in a slightly different way: he classified organisms into guilds (groups of organisms with similar ways of life) and examined the increase in taxonomic diversity from the perspective of guilds. Conclusion: increase in diversity through the Phanerozoic achieved more by the increase in number of guilds rather than increasing number of species within each guild. This suggests that "ecospace" becomes more tightly packed through the Phanerozoic. Ecospace is represented by three axes and different species would "fill" different regions of the "cube" of ecospace.

All these observations again beg the question: is diversity regulated, or put another way, can we treat the patterns of diversity in the fossil record as we might treat an ecological system? There are inferences that support both answers to this question. Computer models where the rates of extinction and origination (speciation) fluctuated randomly. One constraint was that the mean probability of a taxon going extinct equaled the mean probability of it speciating. Thus, diversity would fluctuate but hover about some "equilibrium" value. Results produced patterns of diversity within clades very similar to those observed in the fossil record (see below).
Data supporting the notion of regulation is the observation that rates of extinction and rates of origination are correlated. This suggests that when speciation increases diversity, extinction rates increase and bring diversity back down; similarly if extinction rates increased, speciation rates would increase and bring diversity back up (beware of using a teleological argument; these changes are effects of changes in diversity presumably occurring due to ecological pressures at the time, not for the purpose of restoring diversity). Observation of correlation of extinction and speciation rates suggest diversity dependent effects or feedback in an ecological sense.
Can also model patterns of increase in diversity as one would model exponential growth in ecology N_t = N₀e^rt where r = birth rate - death rate (or in our case, origination rate - extinction rate). N₀ = 1 species (beginning of group) and t = time since first fossil
The data from Cambrian fit this relationship fairly well. Diversity during the Paleozoic fit a Logistic growth curve quite well (logistic curve has a feedback where number if individuals [taxa] levels off with increasing density; sigmoid curves in figure below)
One can extend this analogy even further and treat Sepkoski's three evolutionary faunas as one might treat competing species. The patterns fit models of species competition. But: the observation is a pattern in the fossil record and we do not know whether the process of competition existed between the two major faunas. This pattern can be seen on a lower taxonomic level also: rodents increase in diversity as the multituberculates (rodent-like mammals) decrease to extinction. Shortly after the brachiopods (clam-like marine invertebrates) bite the dust, the bivalves (e.g., clams) diversify extensively. The patterns look like what one might expect from competitive exclusion, and is referred to as ecological replacement since one group with a similar set of key innovations replaces another group (see figure below).
Re analysis of the brachiopod/bivalve replacement has suggested that there has been no interaction between the "competing" forms and that they are best though of as "ships that pass in the night". This does not mean that all ecological replacements in the fossil record do not involve competition, just that it is hard to say. A nice way to compare the possibility of interaction, or the lack of i

Cloning Dinosaurs

CLONING DINOSAURS

---

What is a Dinosaur? 1) occured from the mid-late Triassic to the end of the Cretaceous (220 mil. years ago, mya to 65 mya) 2) they are "reptiles", (but as we know this is not a natural group), 3) they were terrestrial (excludes marine plesiosaurs, ichthyosaurs, mososaurs, 4) Upright pillared legs (an obvious structural "necessity" given their weight. Only the latter is a good "defining" character, cladistically, since there are plenty of other organisms that fit descriptions 1-3 that are not dinosaurs. Moreover, some mammals and birds have pillared legs.
There are two general groups of dinosaurs based on hip morphology The Saurischia (reptile-hipped) and the Ornithischia (bird-hipped). In both groups the iliumand the ischium have relatively similar forms, but in the Ornithiscia, the pubis has a narrow rod-shaped extension running ventrally and posteriorly along the ventral side of the ischium. In the Saurischia, the pubis extends ventrally and anteriorly and only articulates with the ischium (and ilium) to form the hip "socket". Most of the Ornithischia also have a horn covered beak and bony rods and vertebral spines.
Within each of these two major groups there are further distinct types. Within the Saurischia there are two major groups the Therapods (beast-foot) and theSauropods. Typical Therapods are Tyrannosaurus rex, Deinonychus. These are carnivorous, have bird-like feet, bodies are balanced at the hip with a long powerful tail. Within the Sauropods are the huge species such as Apatosaurus (~Brontosaurus) and Brachiosaurus. These walked on all fours, had long whip-like tails and were herbivorous.
Within the Ornithischia there are five major groups:
Ornithopods e.g. Hadrosaurs, duck-billed dinosaurs
Ceratopians e.g., horned and frilled dinos such as Triceratops
Pachycephalosaurs with large bone-filled heads
Stegosaurs (e.g., Stegosaurus) with large dorsal spines of disputed use in thermoregulation
Ankylosaurs heavily armored and abundant in late Cretaceous
The only living relatives of Dinosaurs are Birds. From the names of the two groups one might expect that the birds descended from the Ornithischians. This is not the case. Birds are related to Therapod dinosaurs. The living sister taxon to birds are Crocodylians; how do they fit in? You probably think of Pterosaurs as dinosaurs, too, but they are not. Below is a simplified cladogram of relationships.





Cloning Dinosaurs - Can it be done?
What do we need to do? What are the "parts" needed?

• DNA, in the form of an entire Genome
• Cell
• Technology for putting these together

With the right combination of DNA and cell, it could work
BUT: a genome and a cell are remarkably complex "parts"
However, if you wanted to do it, Crichton's (Poinar/Wilson) approach is a plausible one
Technology:
Dinosaur DNA from fossil bones and cells of dinosaurs in the bodies of blood sucking insects trapped in amber
DNA extraction - remove tissue from amber with sterile tools, grind tissue in sterile homogenizing buffer, dehydrate and then dissolve in buffer solution.
Vector Cloning: cut DNA into pieces, splice fragments into a cloning vector, introduce vector+DNA into bacterial cells where many copies are made in cell culture
Remove Dino DNA from vector and reassemble DNA fragments by splicing (ligation)
Assemble complete chromosomes by filling gaps with frog DNA
PCR (Polymerase Chain Reaction): Amplify random fragments of DNA, then clone
Genome: If we do get DNA:
A. what species of DNA is it? = A molecular systematics problem
identify DNA by its affiliation to putative extant relatives
characters, shared derived character states, group membership
Could be different parts of different taxa: DNA extracted could be a mixed bag of different dinosaur species and other vertebrate taxa different. Probably not enough taxonomic resolution to determine the species identity of the DNA sequence. This is important: how do you tell whether a chunk of DNA is Tyrannosaurus or Stegosaurus simply based on phylogeny of these sequences if there are no living members of either linage to provide a basis for discrimination
Here's where bones are key: species (at least genus?) identify available AND the DNA for the same sample.
B. What part and percent of the genome is it?
Coding DNA and Genome Size, C-value paradox, Numerology:

• Genome Size: 1 - 10 x 109 base pairs in a sperm or egg cell (twice that in "diploid" cell)
• Number of genes: 50,000
• Average gene length: 1,000 base pairs
• Genome is mostly "Junk DNA": 50,000 x 1,000 = 50,000,000
• Coding DNA = "2% of the total genome
• Largest fragment recovered: " 300 base pairs of only two kinds of genes
• Percent of genome recovered: 1 / 10,000,000th of the genome in base pairs
• Percent Coding DNA recovered: 1 / 166,667 Actually less since there are introns

Cell: Which species of cell?
How do the proteins and other molecules of one species interact with the DNA/genes of another species (will Dino+frog DNA function properly in modified crocodile eggs??)
DNA as a generative program: does the DNA alone cary the info. to tell any old cell how to make a dinosaur? Development involved many important tissue inductive events.
Tissue specific gene expression: Liver cells express liver genes, blood cells express blood genes
De-differentiation: easy in plants; rare in animals. Mitotic arrest: who says the cells will keep on dividing? These are Big problems; it will be some time before we clone dinos.
Of all the problems, the Phylogenetic problem of knowing the species identity of any cell from an insect's gut is as serious as the technical problem of getting the DNA in the first place! A reconstructd dinosaur might well wind up as part Ceratopian, part Sauropod and part Therapod (assuming mosquitos were not super host-specific).

Origin of Life and the Fossil Record

ORIGIN OF LIFE AND THE FOSSIL RECORD

---

A brief review of salient points regarding the origin of life:
Cosmic calendar: Earth formed 4.6 billion years ago; there has been a long time for life to evolve. It took about a billion years to get through the early stages of chemical evolution such that there is some form of self-replicating system (e.g., a primitive living thing in its simplest definition). Miller experiments lead to formation of amino acids under lab conditions simulating a primitive earth atmosphere. Subsequent reactions could produce short polymers of the amino acids. When polymers are heated to 130°C to 180°C and then cooled in water to 25°C - 0°C proteinoid microspheres form. These provide evidence that simple cells could have formed from some of the earliest compounds.
Progress has also been made on the synthesis of nucleic acids. One significant bit of evidence, much further down the line, was the discovery of catalytic RNAs that performed enzyme like functions. This, and other evidence, suggested that RNA may be ancestral and DNA is a derived molecule for the storage of genetic material.
By 3.2 billion years ago, first procaryotes (Bacteria, blue green algae). By 2.5 - 2.0 billion years ago, communities of procaryotes emerge. e.g. Stromatolites as colonies of Blue green algae, formed biosedimentary domes of calcium carbonate = some of the earliest fossils. Photosynthetic bacteria have significant effect on the earth's atmosphere and the subsequent evolution of life. Blue green algae are photosynthetic and produce oxygen as a waste product. This was initially a poisonous molecule (as environment was an anoxic one) Lead to the production of an oxidizing atmosphere.
Large amounts of Oxygen oxidize the vast quantities of dissolved iron in the oceans: i.e., the oceans "rust." This counteracts the poisonous atmosphere problem, but only until the reservoir of iron is depleted and the iron settles out as the banded ironstone formation = layers of iron which form iron ore deposits. Ultimately, with the absence of iron to oxidize, the oxygen builds in the atmosphere and produces an ozone layer. This is a singular event which eukaryotes will ultimately take advantage of in the form of oxidative respiration. Subsequent cellular (at this time = organismal) evolution is contingent on this singular event. If we started earth over again, would this event re-occur? at the same time?, if not would we have evolved???
1.5 Billion years ago, a diverse flora of Eukaryotes present as asexual species. 1.4 By eukaryotic algae present. First metazoans seen in the Ediacara fauna for Australia (680 MyrBP).
Before considering the diversity of fossils we need to think about how representative the fossils are of past life which is largely a function of what gets preservedand where it might get preserved.
What gets preserved? Hard parts, and other parts that can be mineralized. Sequence of events from death to scavenging to decay to covering with soil. Example from heard of elephants: "wet" stage = two weeks (too much tissue for vultures so many invertebrates helped out). By the end of the third week, Dermestid beetles had removed all the skin and sinew from the bones. Within five weeks the temperature fluctuations caused the bones to crack and flake. Within one year the skeletons were completely disarticulated. Within two years many bones were covered with soil. Current day events can shed light on the fossilization process.
Fossilization: percolation of mineral grains (e.g. calcium carbonate) into interstitial spaces of hard part tissue. In bone the mineral is calcium phosphate which can incorporate fluorine, present in minute amounts in water, into the Calcium Phosphate to produce a crystal more resistant to erosion.
Death assemblage: become fossils at a site away from their actual habitat due to death and transport to an area. Life assemblage: organisms preserved in their natural habitat. Obvious example: If large mammal bones were found scattered among fossil fish, one presumably would not invoke the existence of primitive mammals that walked on lake or ocean floors!
Environments: fossils are generally restricted to areas of deposition. Upland areas less likely to preserve fossils: more erosion. In deserts material is covered by sand and has a good chance of being fossilized. In shallow seas sediment is being deposited and can cover skeletons. Some of the best fossil assemblages are from shallow sea deposits, lake beds, outwash plains from periodic river floodings, etc.
Ediacara fauna (640 MyBP) Many forms that bear some resemblance to modern phyla. Appears as if it were a major "evolutionary experiment" that did not work as it appears that none of their representatives made it into the Cambrian.
Burgess shale (530 MyBP, British Columbian rockies) Discovered in 1909 by Charles Doolittle Walcott: remarkable diversity of many different forms. Some of these are represented today many others are not (about 15-20 distinct, and now extinct, phyla). e.g. Hallucigenia, Opabinia, Yohoia, Pikaia (first chordate), etc. Nicely illustrate the nature of Contingency (see S. J. Gould, Wonderful Life, 1989, Norton). The "iconography of the cone" led Walcott to erroneous pigeonholing of the Burgess shale organisms into "known" groups. The more appropriate image is "decimation" where only some organisms get through alive and those that do may be simply lucky. Harry Whittington in the 1960s and 1970s with Simon Conway Morris in the mid to late 1970s reanalyzed Walcott's collections. Concluded that there were many unique morphologies so new that they deserve the status of new phyla!. Many of Walcott's classifications were wrong. What would have happened if Pikaia had not made it through the "decimation"? (would you be here reading this? Another example of contingency).
Other important points in interpreting the fossil record: Dating fossils requires radiometric dating of associated igneous rock. (sedimentary rock is of highly mixed origin). Moreover, fossils and the bed in which they lay have been reworked and redeposited. Careful stratigraphy and analyses of surrounding strata must be done to provide meaningful data about the relative and absolute ages of fossils. Gaps in the record. The nature of the fossilization process almost assures that there will be gaps in the fossil record. We have to live with it.
What do we know about fossil organisms? Certain associated information allows informed speculation about the biology of fossil organisms. Large dinosaurs that left tracks without tail dragging marks suggest an active lifestyle? (other fossil remains do show clear evidence of tail dragging and footprints). Other assemblages show fossil bones of adults associated with nest sites and eggs: suggests parental care? Simple footprints may seem like a cute form of fossil evidence. Actually a lot can be learned about the organisms: one can corroborate estimates of the animal's size; one can measure distance between prints and obtain information about gait, travel speeds, etc.; these interpretations further dictate a host of different physiological processes that might be able to sustain such a manner of locomotion. These types of issues are the main point of this lecture: from a small amount of fossil information, certain biological interpretations are implied simply by the necessary biological attributes that go along with a given footprint size, shape, etc.
Fossils can help define ancestral character states and thus help clarify relationships of extant organisms. However, this cannot be done without the extant organism's character states (i.e. fossils alone aren't much help. Is Archaeopteryx birdlike enough to be considered a bird ancestor?

Earth History

EARTH HISTORY (NOTE: this material covered in lecture on Origin of Life & Fossil Record)

---

Much of evolutionary biology involves the history of organic diversity. Organic diversity has been shaped and affected by the origin and history of planet earth. To appreciate this history we need to acquire some knowledge of the geological processes that have shaped the earth. One general theme to consider in this and the next lecture is: if we were to start the history of earth over again from the "primeval soup" would the results be the same? Almost certainly not (see Gould, 1989.Wonderful Life for a detailed discussion). History is unique and events are contingent on what has occurred previously. Much of the contingency of organic evolution is dependent on the unique series of events that shaped the earth, this is why we need to understand some basic geology.

How was the planet formed? What is its relationship to other matter in the universe? A popular hypothesis for the formation of the earth is the nebular hypothesis. This idea dates back to the philosopher Immanuel Kant (1755) and Laplace (1796) and has been modified as empirical evidence and theory mount. Recent incarnations (chemical -condensation-sequence model) start with the solar system forming from a rotating, diffuse cloud of dust and gasses (a nebula). As the nebula cooled the matter condensed into "planetesimals", near the sun where temperatures were highest elements with the highest melting points (metals and heavy minerals) condensed first. Lower melting temperature elements and compounds (water, methane, ammonia) condensed more readily in the cooler areas further from the sun. This helps to explain the density gradient in the solar system, the closest planets to the sun are terrestrial while those further away are gaseous.
How did the earth form in the condensing nebula? The earth may have formed through the accretion of many planetesimals and as the mass increased through gravitational attraction and compression (overhead). The earth was probably initially a homogeneous ball that heated from three sources: 1) energy of planetesimal impacts, 2) gravitational compression lowered potential energy releasing heat, and 3) heat from radioactive disintegration (20 cals is released for 1 cm3 of granite over 500 million years). As the earth heated it began to differentiate into various zones of matter with different properties (overhead). Differentiation was possible because molten material could rise or sink depending on density, be moved by convective currents, and localize due to chemical zonation (overhead). As the earth cooled outgassing of the mantle released compounds (water vapor, carbon dioxide, hydrogen, nitrogen) into a primitive atmosphere.
Early geologists tried to determine how old the earth was from observations about the features of the earth. Age = Thickness of sedimentary rock/rate of sedimentation. Old (<1.5 billion years) but not old enough. Age = salinity of sea/rate of salt deposition in seas. Again old, but not old enough. Lord Kelvin (of absolute zero fame) calculated the age of earth from its temperature, assuming it was molten at its formation. Gave 100 million years (and gave Darwin a bit of a problem: was this enough time?? Radioisotopes cleared things up (see below)
We can divide the processes that alter the earth's surface into two categories: 1) igneous processes (volcanism and mountain building) construct features by increasing the average elevation of the land, 2) Sedimentary and erosive processes (deposition and weathering) act as forces wearing down features created by volcanoes and creating new horizontal features (e.g. river delta). The theory of Plate tectonics provides a synthetic model for understanding how the dynamics of the earth work. The plates move around, collide, move over or under one another. Divergent boundaries are where plates move apart, convergent boundaries are where plates move toward one another, transform boundaries (e.g. San Andreas fault) are where plates move by each other. The continental plates (lithosphere) float on molten inner layer (asthenosphere). Where plates meet there can be uplifting or subduction. Uplifting results in mountain building through igneous activity and at the boundaries between plates and actual scraping off of material from the subducted plate. Subduction results in plates being forced downward and is seen is formations such as ocean trenches.
The rock material of continental plates can be viewed as going through a rock cycle that can be related to plate tectonics. Magma (molten rock) e.g., released from volcanoes, crystallizes and forms igneous rocks ("fire formed rocks"). Through weathering and transport sediment is formed which by lithification become sedimentary rock. Through exposure to high temperatures and pressure, sedimentary rock (or any rock) can be changed into metamorphic rocks. If this rock is exposed to extreme temperatures it can become molten again and form magma, and if released through volcanic activity be reintroduced as igneous rock.
In what kind of rock would we expect to find fossils? Sedimentary rocks. Their structure can tell us a lot about earth history. Laid down in strata of sedimentary layers. Bedding planes generally mark the boundary between the end of one sediment and the beginning of another.
Several logical rules can be used to determine the sequence of events: Relative dating. generally one follows several principles: superposition the older rock is below and the younger rock is above; original horizontality: the strata are laid down originally in a horizontal position (gravity is what lays them down). Thus nonhorizontality must have occurred after the deposition. The cross cutting relationship states that the cut formation is older that the formation doing the cutting.
Another prominent feature is an unconformity which occurs when the rate of deposition has been interrupted, the sediments eroded and deposition renewed. A clear break in the sequence of events is apparent. One type of unconformity is an angular unconformity where strata with originally horizontal bedding planes now have bedding planes that intersect. Significant because it reflects a major episode of geologic change.
All well and good for a given formation, but one would like to be able to make general statements about larger regions. This can be done by correlation of strata from different formations separated by some distance. Stratum "X" may lie near the top of one formation and many miles away, X may be found near the bottom of a new formation, at the top of which is a different layer "Y". Several miles further on, "Y" may lie at the bottom of a third formation, and in this way one can link or correlate the different strata.
This may work for a large region but one would like to do this for the entire earth. It turns out that there are diagnostic fossils found in different formations around the world. These Index fossils help correlate different formations on each of the major land masses. This was recognized by William Smith (see lecture 2). The phenomenon is more pronounced than an occasional fossil here and there: entire biotas go through successive changes in sequential strata, illustrating the principle of faunal (biotic) succession. We thus have the "age of trilobites" seen early in the fossil record. Later the age of fishes, age of reptiles, age of mammals are clear in formations around the world indicating the comparable ages of formations separated on different continents.
These fossil beds lead to the formation of the Geologic time scale, the names of each period deriving from the locality where the characteristic formation was found. The major divisions (eons, eras) are defined by the presence or absence of fossils: proterozoic, phanerozoic (visible life or animals). Geological dating is often problematic because geologists use fossils to date rocks and biologists use rocks to date fossils. A measure independent of stratigraphy and fossil remains is necessary. With the discovery of radioactive decay it became apparent that one could use the ratio between the parent isotope and the daughter product (e.g., U238 decays through several steps to Pb206). By measuring the amount of isotope and daughter product and knowing the half life of the isotope one can estimate the absolute age of a rock formation. Problems: when the daughter material escapes and hence produces an inaccurate estimate. Additional tests with different isotopes can corroborate one another.

Plasticity and Norms

PHENOTYPIC PLASTICITY AND NORMS OF REACTION

---

Phenotypic plasticity is the ability of individuals to alter its physiology, morphology and/or behavior in response to a change in the environmental conditions. This is clearly demonstrated by the appearance of plants grown at different densities: crowded plants look spindly and lanky, uncrowded plants look healthy and robust. In the context of evolution, phenotypic plasticity demonstrates the two meanings of adaptation: the plastic response is itself an example of a physiological adaptation and it is widely held that the ability to be plastic is adaptive in the sense of increasing fitness.
In thinking about phenotypic plasticity as a evolutionary adaptation it is important to separate the trait in question from the plasticity for that trait. For example: growing taller in response to plant crowding is adaptive in the sense that it increases an individual's competitive ability for sunlight (lower fitness when shaded by other plants). The "normal" height for a plant (lets assume there is such a thing) may have evolved in response to pressures to allocate resources to growth versus reproduction in a particular way. Thus there is a genetic basis for plasticity of plant height, and a genetic basis for plant height itself. The point is that different genesprobably control these processes so the trait and its plasticity can (as opposed to must) evolve independently.
Now consider the environment: certain physical properties of the environment can be described by the mean (average) value or the range of values (highest - lowest). Which aspect of an organism (the trait itself or the plasticity for that trait) will evolve in response to which measure? It may be that the plasticity for a trait will evolve in response to the range of values the environment throws at an organism (e.g., coldest - hottest, driest-wettest days), whereas the trait itself (e.g., thickness of fur) will evolve in response to the mean. This is not a rule! but would be an interesting thing to test and/or think about.
The idea of plasticity is interwoven with the notion of canalization. In light of the ball rolling down the trough of a developmental pathway (previous lecture), one can consider the width of the trough as an indication of the amount of plasticity "tolerated" in the organism in question. A highly canalized organism (or developmental program) would have low plasticity.
Another variant form of the plasticity issue is that some organisms may exhibit threshold effects where there is not a clear gradual transition between forms, but a stepwise change of phenotype in response to a gradual environmental change. See fig. 9.11, pg. 242, but note that these graphs do not have an environmental axis, so a distinct from a norm of reaction. One example of this are plants that have distinctly different growth forms in different environments. Question: is there an "environment" that is half way in between air and water?, and if so would these plants exhibit a graded response to such an environmental gradient?
A concept that places phenotypic plasticity in the context of a genotype-specific response is the norm of reaction. A norm of reaction is an array of phenotypes that will be developed by a genotype over an array of environments. The quantification of a norm of reaction is conceptually quite simple: one obtains a number of different genotypes (clonal pants are great for this) and grows each one in a variety of different environments (e.g., different nutrient, light, water conditions). After a period of growth one measures the desired trait(s) from each individual and plots the data out as shown in figure below; this case for Drosophila bristles. Each line represents the data for a different genotype. If all lines are perfectly horizontal and on top of one another there is no effect of environment (E) or genotype (G) in case 1 below (each genotype is x, y or z). If all lines are not horizontal but on top of each other there is an environmental effect, but no genotype effect (case 2). If all lines are horizontal but at different positions there is no effect of environment but there is an effect of genotype (case 3 below). If lines not horizontal but are parallel there is an effect of environment and genotype, but there is no genotype x environment interaction (figure and case 4 below). If the lines are anything other than horizontal, there is an effect of environment. If the lines are neither horizontal nor parallel there is an effect of I) environment (nonhorizontality), ii) genotype (lines not on top of each other) and iii) genotype x environment interaction (not parallel; case 5 below).


The interesting case comes when the norms of reaction lines cross. Then there is a range of environments where genotype 1 is "bigger" than genotype 2, where both genotypes are about the same and where genotype 2 is "bigger" than the genotype 1 (see figure below). Thus determining what is the "best" genotype, or the "fittest" genotype depends on the environment.

Genes and Form

EVOLUTION AND DEVELOPMENT II: GENES AND MORPHOLOGY

---

Documenting allometry and patterns of size and shape changes in evolution are helpful as descriptive approaches to the evolution of development. But these phenomena are themselves the result of developmental mechanisms at the molecular and cellular level. We can often say without reservation that there has been a change in development during evolution, but how that change in development was achieved is yet another question. We improve the description somewhat by saying that changes in development result from changes in the: 1) spatial organization of cells, 2) timing of gene action and tissue differentiation and 3) geometry of tissues and organs. But how are these changes mediated?
Consider the comparison between humans and chimps: the adult morphology is obviously distinct, but at the genetic level we are extremely close to chimps: >99% similar at the genetic level. This is less genetic divergence that seen between sibling species (can't tell them apart) of Drosophila and some mammals These observations indicate that morphological evolution has proceeded faster than molecular evolution suggesting that regulatory evolution has proceeded faster than DNA sequence evolution. Where are the important mutations (short arrows)? in the coding sequences of genes or in the regulatory sequences upstream from them? May depend on how the product of a gene interacts with other genes (longer arrows).

Thus perhaps the key to understanding the evolution of development is the study the evolution of the genetic regulatory mechanisms that control development. Now the question becomes: what do we know about genetic regulation of development?
A fair amount is known in Drosophila. The exciting point here is that in recent years there have been increasing numbers of papers describing the existence ofgradients across the egg or early embryo in the concentration of specific proteins encoded by a handful of loci. These proteins can be thought of as morphogens("form creators"), molecules that, for years, were postulated to exist by embryologists. With a gradient across the embryo of such a morphogen, there is the possibility the other proteins that might interact with such a morphogen can obtain position information from the gradient such that high concentration means "anterior" (or "limb end" in vertebrate limb bud) and low concentration means "posterior" (or "limb base").
The significant point in all this is that Drosophila geneticists have been able to identify specific developmental mutations (mutations in the genes that code for morphogens, or genes that code for molecules that interact with morphogens) that disrupt specific events in development. One such example is the bicoid gene: when this gene is mutated, its normal gradient is disrupted and the embryo has two tails (bi-caudal). The point is that there are specific genes that determine the major body axes and one can envision that evolution of major new developmental programs might proceed by naturally occurring mutations in these genes that would move/alter the gradient, or, equally as significant move/alter the cellular localization of the receptor of a morphogen.
On a more theoretical level, morphogens have been hypothesized to operate in a threshold-like manner in more localized examples of pattern formation such as the generation of additional bristles in Drosophila or specific patterns of striping in mammals (see figs. below). Specific molecules causing "prepattern" such as one sees in zebras have yet to be identified, in contrast to the major advances made in Drosophila, but mating zebras is a major undertaking.
There is solid support for such ideas in Drosophila development. The RNA encoded by the bicoid gene is localized in the anterior portion of the embryo. Theprotein translated from this localized RNA is distributed as a gradient from anterior to posterior across the embryo. The bicoid protein affects the distribution of the RNA of another gene, hunchback. This RNA (hunchback) is not distributed as a gradient but in a discrete way: present in the anterior, absent in the posterior. Thus there appears to be positional information in the concentration of bicoid which is read by hunchback as a threshold. One could imagine that a mutation that affected the localization of one morphogen could alter the localization of important thresholds of different morphogens, which would in turn lead to the development of new morphologies.
The genes controlling the early events in the development of Drosophila can be classified into three broad categories: Gap genes are a set of genes that act to define broad regions of the early embryo; these can regulate the expression and action of Pair rule genes which further define the broad regions into more numeroussegments; the pair rule genes can affect the expression and action of Segment polarity genes which will determine the fate of certain structure within each segment. As with the gradients of morphogens described above, one can envision mutations that alter the interactions between these broad classes of genes controlling the developmental fate of parts of the organism which, if established in the population, could lead to the evolution of new morphological "plans" (.g., a new Bauplan).
There is good evidence for such a supposition in another very important set of genes: the homeotic genes. Certain mutations in these genes result in homeotic mutations where one body part is transformed into the structure of another body part. The best examples are the Antennapedia complex and the Bithorax complex which are large regions of the chromosome containing several genes each. The positions of the genes on the chromosome have a remarkable correlation with the segment of the body in which they are active! (see figures below). The genes contain a region of DNA that codes for a highly conserved stretch of amino acids, known as the homeobox that generally are involved in the determination of body segments (but bicoid has a homeobox and it is more involved with anterior-posterior determination). While mutations that move a leg to the position of an antenna (in the Antennapedia complex) or transforms the balancing organs (halteres) into a pair of wings (in the Bithorax complex) is of dubious fitness value to the organism, it does show that modifications of the general body plan be achieved by mutations in one or a few genes, i.e., there is genetic evidence that Hopeful (hopeless?) Monsters could be produced.
These phenomena are compelling in light of the belief that arthropods (insects, crustaceans, etc.) evolved from annelids (segmented worms; see figure below). One can envision that sequential modification of body segments, through mutations such as those described above, might allow for the evolution of insects from a worm-like ancestor. Suggestive of this is the observation that when the Antennapedia complex and the Bithorax complex are mutated the larval stage of the fruit fly is transformed into a larva with many thoracic segments rather than the wild-type pattern of differentiation into maxillary, labial and abdominal segments (see fig.below). This "throw back" to the ancestral form (i.e., the middle segments of worms are relatively undifferentiated) is called an atavism.
In thinking about all possible morphologies one might be able to get with bizarre mutants in flies, and looking out at the incredible diversity of form in the natural world we might best think of this problem in terms of the question: why this and not that? Are there forbidden morphologies that development cannot produce?. There is some nice evidence that the different forms seen between species may be the result of the "playing out" of discretely different developmental programs. When the developing limb bud of one salamander is treated with an inhibitor of mitosis, the number and pattern of digits developing resembles that of another species (section reading). This suggests that there are developmental constraints, i.e., that development is constrained to proceed in a certain way. If different developmental programs are carried by different lineages of organisms as they diverge from one another, these developmental constraints become phylogenetic constraints: there is no chance that horses will sprout wings because the lineage of horses (and ungulates in general) are constrained to develop and use their forelimbs in very different ways than bats, lets say.
A conceptual model for this notion of constrains is to think of there being canalization of developmental programs. Waddington's model of development as a ball rolling down a landscape suggests that the program is canalized to follow a particular trough. Mutations and/or environmental fluctuations (next lecture) might knock the ball around in the trough, and if these perturbations were strong enough might throw the developmental program over into a new canalized ontogeny. In this model the location of the troughs suggests that events that perturb development early on are more likely to result in major changes in the developmental plan. Perhaps developmental programs become more "canalized" as they proceed through development. This is of particular significance in light of the network of genes described above that establish body plan during early embryogenesis.

Size and Shape

EVOLUTION AND DEVELOPMENT I: SIZE AND SHAPE

---

First, some general background to the study of development and evolution. Evolution of organisms involves a change in the developmental program, a change in a series of developmental processes. We often refer to evolution as "descent with modification" and the modification we often notice first is the overall appearance of the organism. This appearance is a result of the development of the organism, thus evolution is intricately involved with development.
Embryology played a major role in evolutionary theory in the 19th century, but was largely ignored in the 20th. Development never really became part of the modern synthesis. Some argue that this is due to the lack of communication between geneticists and developmental biologists. The geneticists were concerned with the rules of transmission of genetic material between generations and the developmentalists were concerned with cellular changes that led to the transformation of an egg into an adult organism. Mutations in adult phenotype were readily available for the study of genetics, but there were precious few "developmental mutants" that bridged the gap between development and genetics (such mutants were discovered in growing numbers during the formulation of the "Modern Synthesis", and many more discovered later).
The general approach is the same as we have taken with the evolution of other traits: development has a genetic basis, if there is genetic variation for the developmental program then development can evolve. We will first take a descriptive approach to evolution and development and next lecture look at some of the more genetic and cellular mechanisms of development.
Early embryologists noticed similarities between ontogeny (the development of an organism) and phylogeny (ancestor descendant relationships in a group). The common phrase "ontogeny recapitulates phylogeny" was put forward by Haeckel as his biogenetic law (see fig. 21.3, pg. 588). Haeckel held that descendants, during their ontogeny, passed through stages that resembled the adults of their ancestors. Before this, Cuvier (1812) held that there were four major classes of organisms: vertebrates, mollusks, articulates and radiates. Cuvier noticed that there was nothing in the ontogeny of a vertebrate that resembled the adult stages of, say, a mollusk. This is because evolution is a bush or a tree not a "ladder" of the great chain of beings. This "branch-like" pattern to phylogeny was apparent to Haeckel, but he still claimed there was "recapitulation".
von Baer made observations about ontogeny and phylogeny that seem obvious to us today, but they are important in development and evolution as they run counter to recapitulation: 1) more general characters appear early in development, 2) less general forms develop from the more general forms, 3) embryos do not pass through other forms they diverge from them, 4) embryos of higher forms only resemble embryos of other forms (human, calf, chick and fish look similar at embryo stage but diverge quickly). See section 17.8.2, and fig. 17.11, pgs. 478-479.
Putting these two views together, we see that there can be a sort of recapitulation within a lineage (i.e., within an evolutionary sequence of ontogenies) but there are many examples that refute the notion that phylogeny is reviewed during ontogeny.
First efforts to place development and evolution in a quantitative, descriptive context were provided by d'Arcy Thompson in On Growth and Form. Using simple rules of geometric transformation he showed that one could obtain the varied forms of organisms by "warping" or "bending" the relative positions of their body parts (see fig. 21.10, pg. 599). These types of diagrams are helpful in identifying what changes of form have taken place, but they do not identify how developmentalmechanisms have evolved (the same criticism might be leveled towards Raup's computer snails (see figures 13.7 and 13.8, pgs. 356-357), but mechanism was not the intention of these approaches).
One thing Thompson and Raup's diagrams did contribute was to focus attention on the notion of size and shape. These two very simple words are deceptively complex in the context of the evolution of development. A general paleontological pattern is Cope's rule which states that the body sizes of species in a lineage of organisms tend to get bigger through time. Horse evolution is a classic example. But what happens when you get bigger? In most cases body parts do not grow at the same rate, thus we have allometry.
Allometric growth is the differential rates of growth of two measurable traits of an organism (often it is described as size-correlated changes in shape). It is quantified as y = bxa where x is the measure of one trait, b is a constant, a is the allometric coefficient and y is the other trait. In this form it describes a logarithmic relationship. It can be made into a linear relationship by taking the logs of the values measured for each trait (or by plotting on log x log graph paper):
log y = log b + a log x. This is the equation for a strait line with a being the slope of the line. When a<1 we have negative allometry which means that as x gets bigger, y gets bigger at a smaller rate. When a >1 we have positive allometry which means that as x gets bigger, y gets bigger at a faster rate. When a=1 we haveisometry (or isometric growth) which means that there is no change in shape (i.e., the relative sizes of body parts) during growth. See fig. 21.9, pg. 597.
We can describe different kinds of allometry: 1) interspecific allometry where traits of individuals of the same age (usually adults) are compared between different species, 2) intraspecific allometry where a) traits of individuals of all ages are compared within a species (also called ontogenetic allometry), or b) traits of individuals of the same age are compared within a species (also called static allometry).
Some examples: interspecific=the Irish elk example (more below), intraspecific (static)=measurements of body height and arm length in class, intraspecific (ontogenetic)=measurements of body height and arm length with my daughter's day-care measurements included. See figure demonstrating ontogenetic and interspecific allometry of brain and body weight in the same graph.
Intraspecific allometry just describes growth, and alone is not an evolutionary comparison. It is of interest that the allometric coefficient of Bio 48 males and females is ~ 1.0, but if the toddler data are included the allometric coefficient goes up to ~ 1.3. This means that as adults we have about the same proportions (a=1) but as we grow from infant to adult, our arms get proportionally longer (a=1.3).
Allometry is useful in describing the evolution of size and shape. Different species attain different morphologies by virtue of different timing of various developmental processes. This change in timing is called heterochrony. Figures 21.5 - 21.8 and table 21.1, pgs. 590-594 review some of the typical examples of heterochrony. Using the figure below, we can group these into two general classes: in figs B and C the ancestor (dotted) and descendant (solid, but hard to see in C) have the same slope but the descendant stops growing (=adult) at a different time; in figure D and E, the descendant grows for the same amount of time (in these cases same amount of x but different amount of y) but at a different slope. Both are heterochronic changes because some aspect of timing (relative or absolute) has changed in evolution.
Notice that each axis of these graphs include both a measurement component and a time component simply because growth by definition is both a temporal and a dimensional phenomenon. Note that only one of these examples of different growth plans (graph B) demonstrates "ontogeny recapitulates phylogeny": hypermorphosis. Therefore, shape changes can be observed as 1) changes in the slope of an allometric relationship, or 2) changes in the y intercept of an allometric relationship. Recalling high school algebra, a change in the slope will change the intercept, but the intercept can be changed without changing the slope (keep the line parallel and move it up or down). All of these changes result in change in shape. Even with the same slope but different intercepts the relative sizes of x and y will be different so there will be a change in shape. The only case where there is a change in size with no change in shape is when the allometric slope = 1.0and growth continues (or retards) relative to the ancestor.
Classic examples of allometry are neoteny in human evolution: as adults we look like the juvenile stages of chimps; and neoteny in salamanders: the adult of descendant retains gills (a juvenile morphology in the ancestor). Peramorphosis in the evolution of deer: the "Irish elk" (actually a deer) has phenomenally large antlers and are "disproportionately" large because there is an allometric relationship between body size and antler size. In fact the Irish elk falls right on the line of allometry for other species in the family (interspecific allometry). Thus, the antlers are larger than usual, but they follow precisely the developmental program that seems to be a part of its phylogenetic group. Previous adaptive (and maladaptive) stories had been told about these huge antlers and how they probably drove the elk to extinction, thus a challenge for "adaptive" evolution, but the allometry shows that they are not really "abnormal" (probably went extinct due to climatic changes and hunting). See discussion on pg. 356-358 of adaptive, vs. non-adaptive explanations of morphology.
Allometry is also important in the context of the criticisms to the "adaptationist program". If you looked at a Titanothere with its bizarre horns pointing out of its snout, you might say "what are those things for" as if they evolved for some function. They may not be "for" anything but simply the result of a positive allometric relationship between body size and horn size during evolution. Now the question becomes: what causes Cope's rule? Since allometry is so common, changes in size will produce changes in shape.