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 ilium and 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 the Sauropods.
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).

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 some would
say OBVIOUSLY!