Origin of Life and the Fossil Record

ORIGIN OF LIFE AND THE FOSSIL RECORD

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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)

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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

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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

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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

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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.

Biogeography

BIOGEOGRAPHY

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We have referred to pattern and process throughout different sections of this course. These concepts are central to the study of biogeography which, in turn, incorporates many of the topics in evolutionary biology. Biogeography often leads us to infer process from pattern.
Biogeography is the study of the distributions of organisms in space and time. It can be studied with a focus on ecological factors that shape the distribution of organisms, or with a focus on the historical factors that have shaped the current distributions. Certain regions of the world have "Mediterranean climates" where ocean current and wind patterns hit the west coast of N and S continents (Medit. region, California coast, Chile coast, SW Africa coast). Similar climate has lead toconvergent , but unrelated (by definition) types of plants. To make sense of these types of ecological patterns we require a phylogenetic (historical) perspective: we need to focus on monophyletic groups.
The importance of a geographic scale was certainly appreciated by Darwin: the Galapagos finches were morphologically distinct and geographically distinct and there must be a connection. Moreover, the general view that speciation is a central phenomenon in evolution, and that most speciation is allopatric speciation assumes that geography plays a central role: some geographic feature divides a species range in two or more parts and over time speciation is achieved (details in later lectures).
These sorts of observations were made by early biogeographers who recognized certain types of distributions of organisms. Some species are restricted to a certain region and are referred to as endemic species. Endemism needs to be defined with relation to the taxonomic group: all life forms we know are endemic to the planet earth; the genus Geospiza (Darwin's finches) are restricted to the Galapagos islands; Geospiza fortis is endemic to specific islands; the spotted owl is endemic to the old-growth forests of the pacific northwest. Cosmopolitan species have a world wide distribution. They may be restricted to specific habitats, but occur on most continents.
In addition to endemism, another important pattern that needed to be explained were examples of disjunct distributions where clearly related species (or even the same species) are found in different areas. Marsupials are found in Australia and South America. Ratite birds (Ostrich, Emu&Cassowary, Rhea) are found in Africa, Australia and South America, respectively.
Alfred Russell Wallace noticed that different regions of the world had congruent patterns of endemic species and he drew up six biogeographic realms (see fig. 18.2, pg. 510; nearctic, neotropical, holarctic, ethiopian, oriental and australian). Wallace worked primarily in Malaysian region and had noticed a clear break between Australian fauna and the fauna on the islands to the northwest. This break has come to be known as Wallace's line (also a line between the Australian and the Asian biogeographic zones). These patterns described long before continental drift was an issue.
Different biogeographic areas can be quantified for levels of similarity in their biota (biota=general term for flora+fauna, includes microbes). N₁ = number of species (or other taxonomic unit) in one region, N₂ = number in another region (N₁ < N₂) and C = number of same species. Index of Similarity = C/N₁. For Australia: New Guinea, I.S. = 0.93 (93%), while Australia: Philippines, I.S. = 0.50 (50%). See table 18.1, pg 511. This provides a simple quantification of Wallace's Line.
How do we account for these patterns? Early biogeographers tended to invoke dispersal (prior to knowledge about continental drift). Potential problems: ad hoc, could pull dispersal out of a hat whenever you needed to explain a peculiar distribution. Leads to many wild scenarios of "gravid females" (pregnant, or inseminated females carrying eggs) making there way to distant regions. Muddyfooted duck carrying propagules in its feet; land bridges invoked connecting disjunct regions. Criticized by many as unscientific: cannot falsify the dispersal hypothesis because it is something we'll never know for sure, thus is of no explanatory power.
Nevertheless, all these types of events probably have occurred at some point. The Bering land bridge is well documented as an avenue of dispersal; the Opossum (a marsupial) in North America clearly dispersed here from South America via the Isthmus of Panama (see below); oceanic islands have life on them and it must have gotten there by dispersal. Several modes of dispersal can be described: Corridors between two regions on the same land mass, Filter bridges as selective connections between two areas, Sweepstakes as rare chance events (e.g. muddyfooted duck).
Dispersal hypotheses often associated with arguments about centers of origin: those regions with the greatest species (or higher rank) diversity. Greater diversity should be due to presence in that region longer (more time for speciation), hence should be the region where the group originated and from which dispersal events took place. Assumes that extant diversity has not moved from origin of diversity. Possible, but not guaranteed for all taxa.
Alternative to Centers of Origin and subsequent Dispersal as a way to explain the current distribution of species is vicariance where some barrier to genetic exchange causes the separation of the related taxa. With the acceptance of continental drift, vicariance biogeography became a discipline in which one could test hypotheses (see below). See models in fig. 18.6, 18.8 and 18.9, pgs. 518-521.
As with most dichotomies in science: often need to invoke Both vicariance and dispersal to account for distributions (not always in the same instance). Example: Galapagos finches had to have dispersed to the archipelago from the mainland and in so doing imposed a vicariance event on themselves. South American land bridge when sea levels dropped in the Pliocene the isthmus of Panama rose and served as an avenue of dispersal for terrestrial mammals (the "Great American Interchange" where unique N.American mammals dispersed to S. America and unique S. Amer. mammals moved north, 3 mil. years ago; see fig. 18.14, tables, 18.2, 18.3, pgs. 528-529), but served as a vicariance event for marine life that was distributed in the region. Lead to the formation of Geminate species (species pairs on either side of the isthmus who are each other's closest relative and were probably one species before the sea level dropped).
Pleistocene refugia nicely illustrate how vicariance and dispersal may need to be invoked to explain current distributions. Glacial ice sheet forced species to new distributions (vicariance event), after glacial retreat, the separated forms dispersed to previous regions (or wider distribution). Relative roles of dispersal and vicariance in determining species distributions can vary widely with a given species dispersal abilities (see fig. 18.3, 18.4 pg. 514-515). Essential to realize that dispersal has two components: the ability to move and the ability to become established. These two properties may not be "optimized" in the same organism.
Continental Drift as source of vicariance events. Evidence for continental drift provided by disjunct fossil specimens: Mesosaurus in South America and Africa. Illustrates the space and time component of biogeography since the strata reflect the same time (old) but are widely separated in space. Continents must have moved. (Fig. 18.5, pg. 517).
Major stages of the split-up of continents: Pangaea formed in Permian (> 250 MyBP) and began to break up in the Triassic (200 MyBP). Laurasia andGondwana separated at the Tethys seaway (135 MyBP). Tropical corals, sea grasses and mangroves are related in Americas and old world tropics reflecting earlier Tethyan distribution. Gondwana began to break up about 80 MyBP and the major continents were separated by late Cretaceous (65 MyBP). India smashed into Asia crating the Himalayas. As the continents separated vicariance events abounded and the fauna of various continents became increasingly Provincialized. The South American mammals had many unique forms with respect to the North American Fauna. Marsupials in Australian zone are distinct form of mammal.
Testing biogeographic hypotheses with cladistic analysis. Brundin's midges (fig. 18.7, 18.8, pg. 519-520) a classic in vicariance biogeography. Sibley and Ahlquist's Ratites and the Gondwana breakup. Testing hypotheses about the sequence of vicariance events with cladograms from several species. Validity of biogeographic hypothesis can be supported by congruence of independent cladograms from unrelated species (see Cracraft, 1983, American Scientist vol. 71: pg273). By considering the relationships of organisms and their geographic distributions, the most parsimonious combination of the species cladograms can lead to an hypothesis of vicariance events, a so-called area cladogram which presents the sequence of splitting events.
Using cladistic methods, one can test biogeographic hypotheses by asking whether area cladograms for other, unrelated taxa are congruent. If different taxa all have similar area cladograms (i.e., are "congruent"), then the sequence of vicariance events is supported. If one taxon is represented in a region where none of the other taxa are found, then one might be forced to invoke dispersal to account for the disjunct distribution. The strength of this approach is that hypotheses are testable and one need not resort to ad hoc explanations that should be taken on faith. Biogeography can be practiced in a scientific manner despite its historical nature.

Conservation Genetics

CONSERVATION GENETICS

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Conservation biology is a rapidly growing discipline of cology and evolutionary biology. In many ways the issues surrounding the conservation of endangered or threatened species have rejuvenated aspects of population genetics and systematics that were often viewed as "academic." Indeed, may aspects of conservation biology can be view as "applied" ecology and evolutionary biology.
We will consider two different approaches to conservation genetics: 1) population genetic issues relating to the maintenance of genetic variability, and 2) systematics issues relating to the description of biodiversity and the recognition of evolutionary "units" for preservation.
Due to the rapid destruction of habitat there are many species that are going extinct. One estimate is in the neighborhood of 100 species per day! Habitat destruction is generally attributable to human impact, but the causes of extinction are varied: environmental variability, natural catastrophes, demographic variability (stochasticity), genetic stochasticity, etc. Faced with this problem, biologist set out to determine a Minimum Viable Population Size (MVP): a population size that ensure the persistence of a species for specified period of time. One description is a 99% chance of persistence of 1000 years.
Theoretical population genetics simulations have lead to some predictions. There should be a positive relation between population carrying capacity (population size the (local) environment can sustain) and the average time to population extinction. Moreover, extinction times are exponentially distributed so a large proportion of populations will go extinct in a period of time less than the mean time to extinction.

The implication from these simulation results is that Larger Populations are Better: it will take longer for a larger population to go extinct, and larger populations will lower the extinction curve. If environmental stochasticity is added to these models, theory suggests that MVP should be 500 - 1000. If demographic stochasticity (randomly fluctuating birth and death rates, i.e., random population growth rates), MVP needs to be sustained at higher values (1000 - 5000). If this system is placed in the context of an interwoven ecosystem, the MVP should probably be higher.
MVP and Genetic variation Population genetic theory indicates that inbreeding depression will be likely with an effective population size of N_e < 50. To avoid the possibility of inbreeding, a lower limit of MVP = 500. These numbers may seem like obscure conclusions from a series of complex Populus simulations, but they are the working numbers for policy issues : N = 50 defines the critical list; N = 500 defines the endangered list.
The values for MVP and "critical" versus "endangered" lists stem from some basic issues relating to effective population size. N_e refers to the effective number of breeders in the population, and can be affected greatly by variance in reproductive success A focus here is the ratio of effective size to census size N_e/N ratio. Observations from field and laboratory experiments indicate that N_e/N ratios are about 0.25 (range = 0.05 to 1.0). This means that either some individuals are breeding and others are not, or that some individuals have different degrees reproductive success that others. It is possible that a substantial proportion of the population does reproduce, but that a small number of individuals produce most of offspring reducing the genetic pool from which alleles are drawn. This reduces the N_e/N ratio and hence brings the population closer to the demographic danger zone.
With a N_e/N ratio of 0.25, the census size should be 4 times higher than the simple numbers predicted by "critical" and "endangered" estimates. Now add population size fluctuations: bottlenecks in census size affect N_e more severely. Recall: = (1/N_e) = (1/t) (1/N_e)
The net effect of these factors is that MVP should be 5X to 10X N_e.
Given a finite amount of space for a nature preserve, do you establish a Single Large or Several Small (SLOSS) system. The answer depends on the likely causes of extinction in the particular system of concern. If the species is subject to demographic fluctuations, it would be better to maintain one large system, since the plot above suggests that extinction is more likely in small populations. In systems of species where environmental stochasticity is a general problem , the Several Small approach is probably better: many sub-reserves will reduce the chances of losing the entire system.
The SLOSS debate is closely related to the dynamics of Metapopulations. The maintenance of genetic diversity can be enhanced by structuring in a metapopulation system. Alleles that might be lost in one deme can be fixed in another, and the average of the metapopulation system may maintain more heterozygosity than a simple population of similar total population size. The solution to this is not general since metapopulation systems may have varying degrees of migration between demes (at some level of migration, metapopulations become 'systems of subpopulations' since in the strict sense the demes of a metapopulation experience little gene flow.)
Metapopulations can also contribute to the purging of deleterious recessive alleles. With some level of inbreeding in demes, deleterious recessives will be selected against. With limited amounts of gene flow, the system can effectively purge these alleles that might not be expressed in a large random mating population. One approach is to have semi- isolated subpopulations with corridors for dispersal.

There is no one solution to all these problems. The answers depend on 1) the species and ecosystem in question, 2) the demographic issues (constant or variable) and 3) the existing levels of genetic variation.
Many issues in conservation genetics have been centered around Zoo Biology. Most zoos maintain rare or endangered species and are involved in captive breeding programs with such species. Again, a central issue is the maintenance of genetic variation. A number of recent studies have addressed the captive breeding protocol to determine how mating systems affect the maintenance of genetic variation.
Using Drosophila, several studies have shown that populations maintained with equal founder size (EFS) retain more genetic variation that populations maintained by random mating. EFS approaches equalize the number of founders that contribute to the "captive" population each generation. Similarly, equal founder representation (EFR) studies retain slightly more genetic variation than randomly mating populations. EFR populations are maintained with a controlled pedigree where the parentage of each contributing female and male is known. These types of studies use allozyme electrophoresis to study directly the levels of heterozygosity in experimental (EFS, EFR) and randomly mating control populations over time. In addition, fitness studies can be performed by competing experimental flies against tester stocks to determine if a higher fitness is maintained. The conclusion from these studies is that controlled mating schemes can make a difference in retailing genetic variation and attaining higher levels of fitness. The next step is how do you translate these findings into captive breeding of Panda Bears??
Phylogenetic approaches to conservation biology have received a lot of attention. This follows directly from the general concern about Biodiversity. To properly appreciate and understand biodiversity, we must have a sense of phylogenetic structure of the taxa involved. This applies to broad levels of organization (soil bacteria, plants, animals) as well as to smaller taxonomic units (populations within species). Molecular systematic approaches have been of great use since many new techniques can be applied without harming wild individuals, and can even be applied to museum skins for historical comparisons. In the context of the Endangered Species Act several important issues come up: What is the phylogenetic relationship of the endangered species? How much and what type of genetic variation (gene trees)? What do we preserve? What IS a species? Any genetically distinct entity has evolutionary potential.
Two case studies: The Dusky seaside sparrow: The species declined in the 1960's; by 1980 only 6 birds remained that were all male. A captive breeding program was initiated and captive Scott's seaside sparrow was chosen as the females. When the last male Dusky died Avise & Nelson analyzed its mitochondrial DNA (mtDNA) and found that the Dusky and Scott's seaside sparrows were members of different clades on the phylogeny of these sparrows. The implication is that more detailed phylogenetic knowledge of the endangered species would have lead to different management decisions in handling this captive breeding program (choosing a different species to mate to the Dusky)
The red wolf was placed into a captive breeding program in 1974. By 1975 it was extinct in the wild. Early data suggested that red wolves hybridized with coyotes. Since coyote populations do well in human-disturbed habitats, hybridization may have affected the survival of the red wolf. Wayne & Jenks studied the mitochondrial DNA from captive red wolves and from 77 animals collected from the wild during the capture program. They also used the polymerase chain reaction (PCR) to sequence mitochondrial DNA from museum skins ("ancient DNA techniques") collected before hybridization between red wolves and coyotes is thought to have begun. They found that red wolves have either a gray wolf or a coyote mtDNA, indicating that the red wolf "species" is entirely a hybrid. Other researchers disagree about the species "status" of the red wolf. Nevertheless, this raises the question: What should we protect? If the species isn't really a clear entity phylogenetically, does it deserve a conservation/captive breeding effort? Wayne & Jenks argue that their data should not be used to advocate the discontinuation of the conservation effort of the red wolf.
These examples illustrate why the recognition of Evolutionarily Significant Units (ESU) is an issue of great concern in conservation genetics. ESUs are defined various ways, but they are recognized as populations with independent evolutionary histories. Fixed allelic differences or strong phylogenetic support such as multiplesynapomorphies distinguishing one population from another are good grounds for the recognition of distinct ESUs. Hence, a full understanding of how to do molecular systematics is very important in molecular conservation genetics.
It should be emphasized that mitochondrial DNA markers are maternally inherited and may not reflect the true evolutionary history of the entire populations. Hence it is advisable to have additional nuclear markers for ESU recognition such as allozymes, RAPDs or microsatellites. RAPDs are Randomly Amplified Polymorphic DNA. This method uses the polymerase chain reaction to amplify random regions of the genome with short random 10-base primers. Microsatellites are regions of the genome that vary in the number of tandemly repeated sequences. The repeats are short (2-4 base pair repeat unit), but there may be many of them in a row. Individuals differ in the number of repeat units they have and this difference can be determined by gel electrophoresis.
Another relevant level of concern is a Management Unit (MU). These are defined as populations that have different frequencies of alleles, but do not necessarily show fixed differences between populations. Hence several MUs may exist within an ESU. The figures below illustrate the difference. The general lesson is that molecular approaches to conservation biology are potentially highly informative since many overt phenotypic characteristics cannot reveal important differences that distinguish populations. Since conserving endangered species is inherently a "genetic" endeavor, to the extent that we recognize species as discrete reservoirs of historically unique genetic material, the molecular approaches are very useful.