OMNAMO BIOLOGY CONCEPTS

Monday, 16 September 2013

HUMAN DIVERSITY

Modes of evolution Throughout course we have stressed that traits must have a genetic basis
WHY? for transmission to next generation. What do humans have that allows transmission to next generation without genetics?? CULTURAL transmission. This is a major distinction with other animals (although other animals do have "culture", it is not as "advanced" as humans) Cultural transmission can be vertical (between generations) or horizontal (within generation). Vertical cultural transmission is Lamarkian: what you acquire during your lifetime you can pass on to your offspring ("inheritance of acquired characteristics").
Some analogies with other evolutionary forces:

mutation ~ innovation, new behavior, skate boarding, rap music, pierced navels
selection ~ popularity, status: trait gets swept into high frequency
drift ~ random variation in culture, language, dialects (southerners, Maine hicks, etc.)
there can even be gene flow: yo!, like dude, my cousin in California pierced her navel!

Communication, and especially language, are further "key innovations" that may have lead humans into a new "adaptive zone". But literature (Lascaux cave paintings, National Inquirer; and now consider electronic transfer of literary info, e-mail, etc.) really sets us apart. Our rate of evolution is dramatic on all counts. While the beaver, in building its dam, alters the environment that surrounds it, it has evolved in this context of altering its environment in a predictable way for a long time. We are no where near "equilibrium" with respect to how we are evolving with the extensive alterations we are making to our environment. One hopes that we have the genetic wherewithal to "run fast enough just to stay in place" (as the Red Queen suggests we must).
All organisms vary and humans are quite good at recognizing nodes or clusters in that variation (demes, populations, species). The nodes or clusters within human phenotypic variation are quite pronounced and most of us would sort the ambassadors to the UN into more-or-less the same "groups". The question thus arises: how is the genetic variation within humans partitioned? This question was asked (and answered) by R. C. Lewontin in 1972 (The apportionment of human diversity. Evolutionary Biology vol. 6: pp. 381-398).
Lewontin collected data on the frequencies of different alleles at various nuclear loci in different human populations. These populations were nested into larger groups we know as races, and the various races can be nested further into the larger group we call the species Homo sapiens.

With data on allele frequencies in each population, Lewontin could ask how much additional variation is added to the unit in question by pooling together the data from all populations within races, or at one level up the hierarchy, by pooling all the data from within races to one large species sample.
To quantify what proportion of the total genetic variation within humans, a measure of "heterozygosity" was used similar to H = 2pq (or [1-

(allele frequency _i)²] for i different alleles; in the paper the very similar Shannon-Weaver index was used). The numbers obtained from this formula provide a measure of genetic diversity at each of the many loci tabulated by Lewontin. Four points are relevant in thinking about this measure of "diversity": 1) a locus with only one allele will have H = 0; 2) the greatest diversity will be when all alleles are equally frequent (p=q=0.5 for 2 alleles; p₁=p₂=p₃=p₄=0.25 for 4 alleles); 3) diversity will increase as the number of alleles increases (the 4 allele case above is more 'diverse' than the 2 allele case); 4) diversity is a convex function of allele frequency (a diversity measure from a pooled sample obtained by combining alleles from two different populations will be greater than the average of the two diversity measures from each population).
These H values can be tabulated for several different levels of the hierarchy described above: by considering a single population's p and q, or the average p and average q within a single race (averaged among all populations within that race = H_pop), or the average p and average q for all races (pooling all populations within a race to determine the p for that race, then averaging the p's for each of the races = H_race). H_species will be determined by pooling all populations irrespective of race to obtain a species-wide p, then calculating H = 2pq (or as above for the multiple allele case). Thus we can have an H_pop which will be less than H_race which, in turn, will be less than H_species.
These H values can then be partitioned or apportioned so that the total variation within humans can be attributed to the within population component or to thewithin race component or to the between race component. The simple expressions for these, and the data for each locus are presented below. The conclusions from the results are very clear. Of all the variation within humans, 85.4% of it lies within populations (i.e. is due to variation among individuals within populations). An additional 8.3% lies between populations within races. Only 6.3% of all the genetic variation within humans is due to differences between races!
Recent analyses with microsatellites in human populations give slightly different numbers, but the general conclusions are the same. Microsatellites are regions of the genome that generally show a repetition of a simple sequence, such as CA repeated over and over. In some instances the repeated units can be longer and these regions are called minisatellites. See figs. 10.9, 10.10, pg. 271-272 for an example. Such regions are very useful since the repeated sequence allows for the insertion and deletion of repeats. As a result, there can be many alleles in a population that differ in the number of repeated units in the specific region of the chromosome. This allows for the discrimination among individuals, based on whether they share, or do not share, alleles of similar length. This is determined by amplifying a person's DNA using specific primers in a PCR reaction, and running the two samples out on a gel. If bands are shared, the two individuals are related, if the band sizes do not match, the two are unrelated (or if you are an accused criminal, you might be convicted or let off the hook based on these sorts of DNA 'fingerprint' analyses). As with protein allele frequencies, one can still calculate the H values described above and partition the variation into different levels of a hierarchy.
Lewontin concludes that there is no genetic or taxonomic basis to racial distinction and classifications of this sort are of no social value. While you are free to agree or disagree with Lewontin's social interpretation of the data, the population genetic conclusions are clear: with the largest component due to variation among individuals within populations, each and every one of us matters.

Human Evolution

HUMAN EVOLUTION

Humans are too complex to be "understood" by any one field. Thus we will look at a few major steps in evolution and some of the things affecting human evolution.
Humans are members of the order Primates which consists of about 180 species (there are 17 different orders of mammals which diverged 80-65 million years ago). Primates are a relatively old order of mammals. Most of the synapomorphies of this order are associated with an arboreal way of life: flexible digits, forward facing eyes, vision as a primary sense. These traits may have played a role in the evolution of brain size in the lineage leading to humans. Humans are a member of the family Hominidae which is believed to have diverged about 5 million years before the present (mybp) from the other members of the Old world monkeys. At least 20 mybp the Hominoids split off from the other old world monkeys. The dates are rough and get changed now and then.

Relationship of humans to African apes (= chimps, gorillas) and orangutan DNA hybridization indicates that apes are our closest relatives. Human/chimp/gorilla relationships not proven but chimps are most likely our closest relatives. The molecular clock says ~ 5 million years ago the human-chimp line split.
While Chimp and gorilla have knuckle walking , the humans posses many traits associated with bipedality: vertebral column, shape of pelvis, angle of femur,foramen magnum at base of skull. Bipedality seems to be a major "innovation" which allowed humans to enter a new "adaptive zone". The first human (Australopithecus afarensis) seems to have an angle between the femur and tibia (Upper and lower leg) that is intermediate to that of humans and gorillas.
The evolution of modern humans from our hominid ancestor is commonly considered as having involved four major steps: evolving terrestriality, bipedalism, a large brain (encephalization) and civilization. There are (and have been) several competing hypotheses that have acknowledged these four steps, but put them in a different sequence during human evolution.
Origin of Homo sapiens: Australopithecus afarensis = first bipedal hominid, found in east Africa about 3.0-3.2 MYBP. Later forms became more slender (= "gracile"). Homo habilis and H. erectus (~1.5mybp) came later. The evolution of bipedalism may have freed the hands for us in other functions: carrying, tool use. The trends in the evolution of tool use (more types, more specific tasks, different types of materials, more efficient use of materials) seems to follow (lead??) the evolution of increase cranial capacity. These both seem to increase noticeably about 2 mybp. One theme that involves each of the different sequences of evolution is that there was some feedback that lead to the increase in cranial capacity, e.g., becoming bipedal creates selection pressure for a more elaborate brain to control motor function and to process incoming sensory information. This in turn would allow for more successful bipedalism, etc. The same argument could be leveled about culture leading to an increase in brain size, and vice versa, so the sequence cannot be resolved just on the logic of feedback loops alone.
Origin of "modern humans": Two alternative scenarios for origins: 1) humans originated in more than one site ("Multiregional" model). Evidence supporting this are modern Homo sapiens samples found in Asia and Africa 2) a single origin ("Noah's Ark" model: one origin and dispersal out from site of origin). Homo sapiens are believed to have originated ~100,000 - 200,000 years ago.
Paleontological evidence suggests a single origin in Africa. Molecular data shows low genetic diversity worldwide with the highest diversity in Africa, aslo suggsting an African origin. Recent re-analyses shown that the cladograms of mtDNA cannot support an African origin on statistical grounds. Moreover, some recent fossil finds have put humans outside Africa about 2.4 MYBP, but these may be due to early migrations. However, three independent, recent articles in Nature (March 31, 1994; vol. 368, pgs. 449-457) all support an African origin for humans; two are based on fossil analyses and one is based on DNA analyses of microsatellites (next lecture).
The analysis of the evolution of culture and civilization in humans clearly must be based in materials other than human bones alone. The evolution of tools is one reliable correlate (they are recognizable as being rocks reworked as tools and, being rocks, they preserve well). The patterns of tool form show some suggestive trends regarding civilization: through time more types of tools become apparent and there is less variation among specimens in the shape/form of a given tool (see figure). This has been interpreted as evidence for communication or "training", since 'word may have spread' on just how to improve that stone ax so that it can be used more effectively for certain tasks.
The spread of Homo out of Africa is presumed to have taken place about 1.5 MYBP by Homo erectus. This species seems to be on a trajectory of brain size and body size that looks anagenetic, whereas one lineage that lead to Australopithecus robustus seems to be on another line. In a broad sweep of time, the notion of the chimp leading to the Australopithecine, to Homo, to the Neanderthal to the modern American family standing in their driveway is a myth. There were lineages that diverged in a branching cladogram, some of which did not make it to the present. Evidence for this is provided by more than one distinct morphological type of early humans present at the same time (see below). As time gets closer to modern humans, however (Homo erectus on up), a phyletic gradualist anagenesis is more easy to accept.
Once a big brain is achieved and this provides the intellect for an organism to anticipate its environment, the notion that an organism evolves in response to changes of the environment becomes too simplistic. Humans evolved the power to alter their environment so as to protect themselves from its abiotic pressures. This means that they are altering their own selective pressures and a dialectic emerges between the organism and the environment such that these cannot be separated. Other organisms do this (beaver dams, deciduous trees), but in humans this cycle is accelerating. The rest is history.

Extinction

EXTINCTION

Almost all professional football players are still alive. 4% of all human beings that have ever lived are still alive. What percent of all species that have ever lived are still alive? 0.1%; thus 99.9 % are extinct. Looking ahead, things look numerically bad for humans: chances are that we will go extinct.
What is extinction? => Termination of a lineage. What are the units of extinction? Genus Family ? Do we determine extinction of a genus by the last remaining species that makes up that genus? What happens if 99% of the genus goes extinct and one "hanger-on" last millions of more years? No solution to the problem, these are the sorts of biases that are inherent in tabulating higher-level phenomena.
What can we say about adaptation and extinction rates? is extinction due to: Bad luck or Bad genes? (book by David Raup, W.W. Norton, Co.).
As to the causes of extinction here are some questions to "ask" the fossil record:
intrinsic/extrinsic: was extinction due to a characteristic of the organism (intrinsic) or of the physical environment (extrinsic)? Was extinction due to competition (mutituberculates and rodents) or was it due to major events like sea level changes or asteroid impact? One "asks" the fossil record by looking at the data:
Taxonomic survivorship curves were tabulated by Van Valen, U. Chicago (see figure below). Horizontal axis in the number of years that a group has survived (could be 50 Myr. in the Cenozoic or 50 Myr. in the Paleozoic); vertical axis in the log of the number of taxa that survived for the stated number of years. The ~ straight lines indicate that a constant proportion of the taxa are becoming extinct at various stages of duration, which Van Valen interpreted to mean that the probability of extinction is independent of age of taxon. This further implies that taxa are not becoming better adapted (if one defines increased adaptedness as a decreasing probability of going extinct). Note that these survivorship curves are different than the ones presented for moluscs and carnivores. Note also that the graphs do not imply that there is a constant extinction rate per unit time. The approximately linear relationship indicates that the taxa with a long duration do not appear more resistant to extinction.
Van Valen proposed the Red Queen hypothesis to account for the pattern of approximately linear survivorship curves. Van Valen hypothesized that 1) the environment is continually deteriorating (~ changing so that current adapted state is no longer applicable), 2) organisms have to adapt continually, i.e., you have to "run to stay in place" like the Red Queen said to Alice in Through the Looking Glass (Alice in Wonderland).

Figure 22.3 from Evolution, 1st Ed. There are other ways of looking at extinctions that contradict this idea. Extinction rates in the Phanerozoic show a pattern of decrease in background extinction rate (see figure below; "background" means excluding the five big peaks). Does this mean that species are becoming more adapted because they are more resistant to extinction? The jury is still out (i.e., we don't know). Moreover, some data sets show rates of extinction that vary dramatically over absolute time, suggesting that extinction rates are not constant over time but vary widely. Compare figure 22.13, page 633. Once question is how much variation one tolerates before saying that extinction rates are not approximately linear.
One interesting observation about extinction patterns is that a periodicity has been documented in one data set. The cycle appears to be 26 million years. See figure 23.7, page 652. Explanations for periodicity have been varied: Companion death star (Planet X out beyond Pluto) cycling past earth every 26 million years which hurls asteroids at earth killing many taxa. Needless to say, some of these ideas made astronomers HOWL with LAUGHTER.
Mass extinctions are quite a different type of extinction than the background extinctions. In some regards mass extinctions rekindled ideas of Catastrophism (as opposed to Uniformitarionism; see lecture 2). The impact extinction theory that mass extinctions were indeed caused by asteroid (or other) impact is a good one because it falls into the mainstream of scientific inquiry: an hypothesis that can be tested, and falsified, with further sampling or experimentation (although conclusive proof that it did not happen may be difficult).
The Cretaceous-Tertiary (K/T ) Extinctions are some of the best studied. What went extinct? marine reptiles, ammonites, dinosaurs, etc. However, many groups were relatively unaffected. This presents an interesting problem: how could something that might be so devastating as to kill off many diverse taxa be, at the same time, so selective with respect to different taxa? See figure 23.5, pg. 648.
The Alvarez's from Berkeley proposed that the K/T extinctions were caused by impact of a large asteroid. Some compelling evidence supports the notion: Excess of iridium (iridium anomaly or iridium "spike") at the K/T boundary (see fig. 23.6, pg. 649). This element is rare in earth's crust, but not uncommon in meteorites. The presence of "shocked" quartz (likely to be formed at asteroid impact, less likely to be formed by normal Earthly geological processes) is also in excess at the K/T. Evidence for these diagnostic markers of impact have been sought at the other "big five" mass extinctions and only one has any blip of excess iridium (no where near the spike at the K/T).
There are some problems with the impact explanation: why was it so selective? and: where is the impact crater? Well, sure, you know, ah, it, ah, it landed in the ocean! Or maybe it landed near a subduction zone and the evidence has been conveniently tucked under some continental plate. Also, there is evidence from magnetic reversals in the stratigraphic record that the K/T transition is varies in time from place to place. Every couple of years someone publishes a paper indicating that they found the impact crater; the most recent focus is somewhere near the Yucatan peninsula or western Caribbean. Keep an eye on Nature and Science.
The issue of impact extinction puts all that we learned about population genetics and adaptation in a very different perspective. So what if one allele is more fit than another, or the rate of evolution depends on the amount of additive genetic variation in the population, if an asteroid is going to blow us away tomorrow, thenmicroevolution really is decoupled from macroevolution. But what about those lineages that sail through the K/T boundary unaffected? Maybe they were adapted, pre-adapted or just exapted for the impact and there is a coupling.

Tempo and Mode II

MACROEVOLUTION: TEMPO AND MODE. II

Niles Eldredge and Steven Gould stirred up the mud of Tempo and Mode in Evolution with their paper in 1972 on so-called "punctuated equilibrium". The traditional view of evolution was one of phyletic gradualism. This encompassed slow, gradual change in phenotype and speciation by gradual change from one species into another. The alternative - punctuated equilibrium was put forward as a means of accounting for the ever present "gaps" in the fossil record (see figs. 20.4-20.5, pp. 561-562). Eldredge and Gould argued that the gaps were not artifacts of incomplete representation, but that there were essentially no intermediate forms. The general notion is that long periods of stasis or morphological equilibria are punctuated by periods of rapid morphological change.
This issue was a bit of a blow to the traditional "Darwinian" approach to evolution which largely focused on slow gradual change. This affiliation with "non-Darwinian" evolution is misguided and mislabeled because the original and updated versions of punctuated equilibrium invoked speciation in small isolated populations which fits squarely with Mayr's peripatric model of speciation. Moreover, Darwin described in the Origin of Species a pattern that is entirely consistent with stasis; Darwin did believe that the evolution of complex adaptations was gradual (the eye was built adaptively from preexisting parts in ancestors and did not pop into being quickly in evolutionary time).
The stratigraphic phenomena would be observed from 1) morphological stasis in a large population 2) an unrecorded founder event to a peripherally isolated population 3) speciation, perhaps through a "genetic revolution", where a new equilibrium morphology would be assumed and 4) Range expansion of this new form back into the range of the original form (see diagram below). These events, entirely consistent with "Darwinian" or "Modern Synthesis" phenomena, would be observed as a punctuational pattern (see fig. below). Note that there are other sequences of events that might give rise to the punctuational pattern.
Several questions arise:
1) What is rapid? 10,000 - 100,000 years can be an instant in geological time (especially in the context of some deposition rates) but is ample time for evolutionary events in populations. Recall that the shift from the peppered to the dark form of Biston betularia occured within the span of 100 years by a completely "Darwinian" mechanism.
2) Is rapid morphological evolution associated with speciation events? Answer: not always (many species of insects [lacewings, fruit flies] are "good species" but are very difficult to tell apart). It can be: there are convincing examples of punctuated patterns in fossil record: Williamson's mollusks.
3) How do we explain stasis? stabilizing selection, developmental constraints, absence of selection? Eldredge and Gould claim that stasis is data, i.e., the absence of change is interesting. If stasis is due to stabilizing selection, then there is perfectly good evolution going on: selection against individuals at the tails of the distributions within populations. If stasis is due to developmental constraints then there is an interesting "battle" going on between the environment and the homeostasis of the organism. The issue of punctuated equilibrium has contributed a lot to the science of paleontology since it has focused new attention on 1) changes at speciation in the fossil record (see pp. 567-570), and 2) the notion that stasis is interesting and important and needs explanation.
The publication of the idea of punctuated equilibria set off a bit of a challenge among paleontologists to show that their "own" mode of evolution was the correct one. Thus gradualists came out with papers showing convincing evidence of gradual evolution (figure 20.7, pg. 565) and the Punc. Eq. types came out with papers showing rapid shifts in phenotype in the fossil record. The absurd example is a data set by Gingerich which he interprets as gradual and is reinterpreted by Gould and Eldredge as punctuational! (see below). Like any polarized debate, there are two kinds of intermediates where reality lies: 1) some data sets show one mode, others show the other and 2) documented cases of punctuated gradualism: periods of stasis punctuated by short periods of gradual change. What remains to be confirmed is whether different lineages tend to show one pattern and others the other: the relative frequency of the two alternative modes in the fossil record will ultimately settle the debate.
The punctuation debated focused a lot of interest on the notion of hierarchical phenomena (sensu units of selection). One important hierarchical issue is Species Selection: differential rates of increase or decrease in species diversity among different lineages due to differences in rates of speciation and/or extinction. The basic principles of species selection are 1) speciation is random with respect to phenotype, 2) most changes occur at speciation, 3) different extinction and speciation rates are due to some biological properties of the different taxa.
Some consequences: 1) species selection can introduce evolutionary trends and 2) differences in morphological or taxonomic rates of evolution among different lineages can be due to species selection. The important point is that it is the pattern of speciation that drives such trends, not the direction of morphological changes.
An excellent example of the dynamics of species selection (or how one might interpret data from the fossil record in light of differences in extinction and speciation rates) is provided by Hansen's studies of planktotrophic vs. non-planktotrophic gastropod (snails). Planktotrophic lineages last longer in the fossil record (lower extinction rate) See fig. 23.3, page 643. However, the proportion of planktotrophs decreases in the fossil record (see figure 23.4, page 645 and note typo in figure caption). How can one account for this apparent paradox? If one invokes a higher speciation rate among non-planktotrophs, then this might do it; i.e., species selection might account for the patterns of diversity changes. Read the text for this section (pp. 641-644).
A general question about species selection: is it a pattern or a process? Following the parsimony of G. C. Williams, can we explain species selection by differential survival of individuals within populations, and if so is species selection just a by-product of individual selection., or do higher level processes operate? (thus the hierarchical issue in species selection). If the latter is true, the big question remains: is macroevolution decoupled from microevolution?? (i.e., are population-level processes insufficient to account for evolution above the species level? If you talk to a population geneticist they would say NO! If you talk to a paleontologist somewould say OBVIOUSLY!

Tempo and Mode I

MACROEVOLUTION: TEMPO AND MODE. I

We now consider the tempo (i.e., rate, and any modulation thereof) and the mode (i.e., the particular form or manner) of evolution. The use of these two words to focus the study of evolution is attributed to George Gaylord Simpson who's book, Tempo and Mode in Evolution, brought a paleontological perspective into the Modern Synthesis and applied the thinking of population variation and genetics the patterns of the fossil record. Thus, Simpson attempted to show thatmacroevolution (evolution above the species level) could be accounted for by familiar mechanisms of microevolution (genetic changes within population). He begins with the question: "How fast, as a matter of fact, do animals evolve in nature?"
To answer this question we consider evolutionary rates. Simpson identified two general classes of evolutionary rates: Phylogenetic (or morphological) ratesmeasure the rates of evolution of characters (single or complexes) within phylogenetic lineages and are quantified as measured change in a character(s) per unit time;taxonomic rates measure the rates at which taxa replace one another in the fossil record and are quantified by two reciprocal methods: 1) number of taxa originating and going extinct during a span of time, or reciprocally 2) the average number of years a taxon remains extant (more below).
Potential problems when taxonomy is based on morphology: high rate of morphological evolution may lead to the division of organisms into many chronospecies. This can result in a high rate of taxonomic evolution: with pseudoextinction and pseudoorignination, taxonomic rates of evolution can be correlated with morphological rates of evolution (graph A). But, the reverse (morphological rates correlated with taxonomic rates) will not necessarily hold in cases where real extinction of taxa, and replacement by newly evolved taxa, occurs at a high rate. The latter does not assume there is continuous change specific morphologies, thus we could have high rates of turnover of taxa without extensive morphological change (graph B).

The relationship between morphological and taxonomic rates also depends on which characters are used to determine taxonomic status. One character may evolve rapidly in a lineage but the lineage may not be split into chrono "genera" because "important" characters have not changed, i.e., there can be mosaic evolution.
Haldane proposed a unit of measure: 1 darwin = change by a factor of e per million years (e = base of natural logs = 2.71828). See page 553 and figure 20.1, pg.554.
Horse teeth: 0.04 darwins = 4% per million years
Triceratops lineage of dinosaurs: 0.06 darwins
Rates appear to vary between different groups. There are apparent living fossils that have changed very little, or not at all, in millions of years: the coelacanth, thehorseshoe crab (Limulus, see fig. 20.11, pg. 575) and the tadpole shrimp (Triops) are good examples. Other species or groups have evolved relatively rapidly (Horses, see figure).
Rates of change also can vary during the evolution of a lineage. In lungfish a "score" was tabulated for each taxon as to whether it possessed ancestral or derivedtraits. This score was plotted against the age of the taxonomic group for which the score was tabulated. Resulting graphs (See fig. 20.10, pg. 575) show a rapid loss of "primitive" characters (=acquisition of "new" characters) through time and the slope of this curve shows a peak early in the lineage.
The point is that morphological rates of evolution can be very different in both tempo and mode in different lineages of organisms.
Some of the between-group differences are real and some are an artifact of temporal scale. Gingerich recorded rates of change in selection experiments, colonization events, post-Pleistocene changes and long-term changes (domains I, II, III, IV in table figure below) and plotted them against the measurement interval in years. The clear relationship indicates that changes measured over short time spans exaggerate the changes one might predict if carried out for a long time. There are reversals of morphological trends and periods of no change (="stasis"; next lecture) that reduce the rate of change when averaged over a long time period. See table and fig. pp. 556-558.
Taxonomic rates can be quantified as number of genera / time span = average genera per million years, or one can take the reciprocal of this and ask: How long does a genus last? and thus quantify the duration of a taxon. By tabulating the period of first appearance of a taxon (genus, lets say) and the period of its last appearance in the fossil record one can obtain such taxonomic rates (see table below for example of data). In Pelecypod mollusks (bivalves) 13 genera appeared in the Ordovician and disappeared in the Ordovician; 4 genera appeared in the Ordovician and disappeared in the Triassic. Compiled over the entire data set the "average" genus of Pelecypod lasts 78 million years. Similar calculations for Carnivores show that in this group a genus lasts about 8 million years. See data below and compare with fig. 20.13, pg. 578.
These data can be plotted on survivorship curves which tabulate the percent of taxa alive today that originated at the time indicated on the horizontal axis (broken line). For extinct taxa the graphs show the percent of taxa with a known duration > the value indicated on the horizontal axis. Thus 100% of the extinct genera have a duration greater than or equal to 0 years and 0% of the Pelecypod genera have a duration greater than or equal to 275 million years; other genera have intermediate durations. Note the shorter range of the horizontal axis in the two graphs and the different shapes of the extant vs. extinct survivorship curves in the two graphs.
The point is that the taxonomic rates of evolution can be very different in both tempo and mode in different lineages. While the data are sound the interpretation of the data as a general phenomenon holds to the extent that the unit of a genus is comparable in the two lineages. Since the duration of genera in the two groups differs by about a factor of 10, this large a difference suggests that there is a real difference. In other comparisons with more subtle differences between lineages, the unit of measure (genus, family?) could become an important consideration.

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).