Evolution – Biology 4250
                                                                                                         Dr. Adams
Review Sheet 4 -Test 4

Chapter 16: Mechanisms of SpeciationDivergence
    Speciation is fundamental to the concept of evolution; there have been many millions, perhaps
more, such events in the history of life on the planet.

        Species Concepts: All agree on one point – a "real" species has evolutionary independence,
which, in turn, means a boundary for spread/sharing of alleles.

Morphospecies concept: main criterion (though clearly shared with the PSC) is morphological
similarity.  This was the "original" species concept, and widely used by most people today.
        As with the PSC, the main problem is what constitutes significant enough difference
to call two things different; particularly difficult with extinct species, where color, soft tissues,
behaviors are completely untestable.  The application tends to be somewhat arbitrary, and what
are called cryptic species may easily be missed.

Phylogenetic Species concept: main criterion is monophyly; a shared history and now evolutionary
independence from all other species.
        The idea here is that populations are looked at and many characteristics are compared to
determine if two different populations are monophyletic, and more than that, monophyletic at a level
that indicates little if any differentiation between them. Comparisons of characteristics can, of course,
include molecular comparisons: DNA, protein structure, etc., If the two populations haven’t diverged
"significantly", then they may be considered the same species.
        The main problem(s) with applying this concept is (are) . . . ?  . . . that it requires phylogenies
for close relatives, criterion standardization, or necessary non-standardization [not all characteristics
are of equal importance]; so application becomes the main problem.

Biological Species concept: main criterion is INTRINSIC reproductive isolation. This is a useful
criterion, as lack of interbreeding confirms the lack of gene flow.
        The main problem(s) with applying this concept is (are) . . . ?
                . . . asexuality, allopatry, extinct species, hybridization [in plants]
        For allopatric populations, can bringing them into the lab and see if they mate be considered
an appropriate test?  Anyone?

        As indicated above, the application of molecular techniques has added both protein similarities
and DNA similarities to the list of characteristics that can be compared. Although you might think that
this should illuminate everything in terms of who is most closely related to whom, and who is
from whom, this has been far from reality, and the Molecular Species concept has not
gotten wide support (yet). [Boy, I’ve gotta’ get me a tricorder . . .]

The different concepts have different efficacy among different groups of organisms. The concepts may
be differently applied by different evolutionary workers. As we learn more, even our own opinions
about species evolves. The same organism may be considered independent by application of one species
concept and not by application of another. End result: there will never be a single classification that is

agreed upon by all. (Don’t lose sight of the fact that the ORGANISMS don’t care about what we call
them taxonomically, and that we are trying to apply static concepts [a snapshot in time] to dynamic
situations . . .).

Applying species concepts:  Examples
        Marine phytoplankton (diatoms)
        Common skates -- armed with phylogenetic information, morphological difs were discovered
        Leopard frogs
        African elephants -- studies such as this one clearly influence conservation issues

Mechanisms of Isolation – stopping gene flow between pops.; the first step in speciation
    Physical Isolation – the establishment of allopatry
Geographic (vicariance) events, Peripheral populations, Population establishment through
dispersal and colonization, dispersal on "islands" (island hopping with the founder events)
        Examples: MANY.
            Island Founder (radiation) events: Drosophiliids (Hawaii); Darwin’s Finches (Galapagos).
                Predictions: Closest relatives should be on closest islands, and younger species on younger
            Vicariance events – may include mountain building, land bridge formation, canyon formation
                        (river cutting), habitat fragmentation (drying, lava flow, etc.).
                Snapping Shrimp (Carribean & Pacific; Panama; see text); Tufted Squirrels (Kaibab and
                    Abert’s; Grand Canyon)
    Mutational changes: Polyploidy and other chromosomal changes –
        Examples: Polyploidy and hybridization (mostly in plants); autopolyploids/allopolyploids.
                Estimates of polyploidy in plants vary, though conservatively 300,000+ species surveyed,
                    2-4% at least showed direct evidence of polyploidy; clearly, this is a tremendously
                    important speciation mechanism in the history of plants. Animal examples much less
                    frequent, thought there are recorded instances in freshwater fish, frogs, whiptail lizards.
                Smaller changes – chromosome fragmentation/fusion. Must be careful here, however, in
                    claiming causative (versus after the fact) effects in speciation.  Dik-diks, horse/donkey,
                    various butterfly species, etc. Sympatric congeners more likely to differ in chromosome
                    number than allopatric congeners -- why?  See Agrodiaetus butterfly example, pg. 621.
    Other mechanisms of isolation -- temporal, behavioral, different pollinators (for flowers), different
        hostplant choices (for herbivores, especially insects), morphological (fit of parts; eg., snails)
            An example of sympatric temporal separation – the Callosamia giant silkmoth story.

Mechanisms of Divergence: Already discussed in great detail earlier in the course.
        Definitions: Allopatric, Parapatric, Sympatric speciation.
    Adaptation to different habitats -- Mimulus ecotypes and an inverted section of the DNA
         Another example: host plant differentiation; the Apple and Hawthorn maggot fly (Rhagoletis)
story. Apples introduced to U.S. from Europe approximately 300 years ago.  The flies on the two
hosts are incipient if not full species at this point (even though a bit of gene sharing is still going on). 
A Sympatric speciation event.  For species which are host specific (herbivores on plants, parasites
on animals), a host shift could be an important part of the speciation event.
        The above example is an example of Assortative Mating as well.   
    Assortative mating and Hawaiian Laupala crickets: male song and female preference, even though
         controlled by a complex set of genes at different loci, completely tied together.    

Hybridization and Gene flow between species
    Secondary Contact
        Possible outcomes: populations fuse (no significant divergence); populations treat each other as
completely separate species (species level divergence); hybridization followed by fusion; hybridization
with reinforcement; or even hybridization with resultant new populations/species (again, most frequent in
        Reinforcement – occurs in the hybrid zone; involves prezygotic (premating or postmating) or
isolating mechanisms. Will give example of pre- and postzygotic isolating mechanisms in
class which you will be responsible for!
            In the long run, which should be selected for, in all cases?
            As might be expected: prezygotic isolation evolves much faster in sympatric species pairs than
allopatric species pairs in the Drosophila.
        Hybridization – reinforcement should occur when hybrid offspring have reduced fitness. But what
should happen if hybrids survive and reproduce well?
        Hybrid species -- Audubon's Warbler, butterfly species
Hybrid Zones
        What determines how wide, how long-lasting, etc. hybrid zones are? Fitness of the parental and
hybrid individuals, which in turn also helps determines the eventual outcome (reinforcement with
complete divergence, fusion, etc.).  See Figure 16.18.

What drives diversification?  Ecological controls and adaptive radiation, range size and dispersal ability.

Chapter 17: Origin of Life and Precambrian Evolution
    The origins of life were somewhere between 3.7 – 4 bya.
        No direct evidence for origin of life – no physical record exists; as such, the beginning of life on
            Earth can only be studied using indirect evidence alone (where's a time machine when you
            need one??)
    So, important questions arise:
        1. What was the first living thing?
        2. Where did the first living thing come from?
        3. What was the environment like when life first appeared on the planet?
        4. What was the last common ancestor (cenancestor or LUCA) of all living things?

At Earth’s formation (4.5 – 4.6 bya), conditions too hot for life.  An early impact with another large body
added to the Earth's size, but kept Earth uninhabitable.  This early impact did form our moon, and, more
importantly, gave Earth its stable spin on its axis, which would later, of course, shape our day length and
the evolutionary effects of this on organisms.  As smaller planetismals finished colliding to form earth, and
collisions with other "rocks" slowed, earth’s crust cooled. Water vapor released from planet’s interior
condensed during cooling with LOTS of rain to form oceans. The timing of these events is not completely
worked out, but most evidence gathered suggests the above did happen during the first few hmy.

Chemical Evolution
    Discovery of "ribozymes" – Altman and Cech (won a Nobel Prize for this).  The original ribozymes
discovered could break/reform nucleotide bonds.  This discovery, indicated that RNA, which can
store information, could also do biological work – RNA, in essence, can possess both genotype AND
phenotype. It is possible, indeed likely, that RNA formation preceded formation of both proteins and

DNA in terms of its original formation (and with enough stability, since RNA can fold back on itself and
give it a characteristic shape and, of course, its functionality as a ribozyme; see Fig. 17.2).
        We now consider the ability to evolve an important characteristic of life – the ability to record and
make alterations (function of the genotype) and a way of distinguishing valuable changes from detrimental
ones (function of the phenotype). In this respect, RNA can be considered to "have" this characteristic of
life -- the ability to EVOLVE.
        Besides the existence of ribozymes (which can make more RNA), the ubiquitous ribosomes
(themselves made of RNA [and protein]) are an extremely highly conservative structure in cells. (What 
do ribosomes do again, and how do they do it? . . . ) RNA is intimately involved in the most basic func-
tion of protein synthesis. And, the main ENERGY currency of cells (that would be . . . .?) is based on 
an RNA nucleotide, not to mention other important molecules (like NAD and FAD). So there is plenty
of evidence that RNA may be truly ancient. And, don’t forget retroviruses, that inject RNA, complete
with a transcript to make reverse transcriptase in the host.
        Experimental evolution of RNA predated discovery of ribozymes by about 15 years – a bacterio-
phage (virus) had its RNA replicated in a test tube by replicase enzymes from the virus. Seeding fresh
test tubes with replicated RNA and continuing to treat with replicase resulted in independently different
RNA strands (due to miscopy by replicase), and with differing abilities to infect bacteria. The most
abundant versions of RNA ended up being those that were most quickly replicated by the enzyme –
natural selection of molecules. With the discovery of ribozymes, it was further demonstrated that RNA
molecules can have a particular "fitness" (how well they catalyze and in turn "make" more), and that the
fitness is a phenotypically expressed function – one ribozyme with poor DNA manipulative (cleavage
and attachment) capability, when amplified with enzymes (which in turn allowed for mutations) resulted
in a version with mutations at four loci that "manipulated" DNA >100 times faster. Indeed, ribozymes
with improved or entirely new functions have evolved many times in test tube environs. When we go
back to the "four assumptions" of Natural Selection, the first two are about the genotype, the fourth
about the phenotype, and the third (overproduction of offspring) is about being replicative. So, RNA
can fit 1,2 and 4; what about 3?

Self-Replication – can RNA do this?
        One problem with an "RNA First" world – in the above experiments, protein enzymes were use for
the replication of RNA strands. Ooops. So far experiments have failed to produce a truly self-replicating
RNA, though short sequences within RNA molecules appear selectively advantageous in certain experi-
ments. IF we can discover/select for an RNA that is truly self-replicating, then we could move on to the
OTHER remaining important questions about origin of CELLS:
        1. Can a self-replicating RNA evolve a sister (more stable) DNA molecule with replicative and
transcriptive capabilities.
        2. Could the DNA and RNA in turn work together to form proteins (what about them ribosomes?)?
        3. Could this machinery, in turn "make" or "take over" cellular structures and cells?
        Still a LOT of unanswered questions of HOW to get from one step to the next. That doesn’t mean 
it couldn’t have happened (though it can’t happen again in nature on the current Earth – Why?)

The Original Biomolecular Evolution – the Organic from Abiotic?
            If we assume organics came from the Earth’s abiotic environment, then:
        1. There must be some way of making these organics (without living organisms).
        2. There must be a source of energy to build these larger molecules.
        3. These larger organics must be able to polymerize.
        4. These larger organics must be stabilized – they’d have to persist in a harsh environment.

    Two major alternative hypotheses exist on the source of original simple organics:
        1. Earth was "seeded" with organics from space; cometary dust, meteorites (still leaves the
question of where and how these organics formed). For example, the 1969 Murchison, Australia
meteorite contained several amino acids (glycine, alanine, valine, proline, etc.; pg. 651).  Since life
produces almost exclusively L-stereoisomers of A. A.'s, and the meteorite contained approx. equal
amounts of L- and D-stereoisomers, then the source of the A. A.'s was unlikely biological.  One
problem is surviving the heat of atmospheric entry; space dust may account for much of what
makes it to the ground.
        2. Abiotic C, H, O & N components of early atmosphere combined – debate rages over the
contents of the atmosphere and water early in Earth’s history.  After all, conditions were extremely
harsh, and it is unclear what the pressure, temperature and early atmospheric components were like.
(Note info from first page of the chapter about the atmosphere of Saturn's moon Titan).
        Experiments: Miller (1953, 1992); Fox (1972) – ammonia, methane, and H. Provide sparks
(lightning)/UV radiation – tremendous number of organics (A.A.’s, sugars, nucleotides). However,
better understanding of the geochemical processes suggest early atmosphere contained lots of
CO2 and N2, and not a lot of other things, which is much less conducive to organics formation.
        Still, the Oparin-Haldane Model was formulated, and is at least a null hypothesis against
which to test new findings. The model basically approaches the three questions (and four state-
ments listed above): 1. – biotic from abiotic; 2. – polymers formed that can a) store information
and b) catalyze reactions; 3. – add membranes (and energy sources) to get a cell (Fig. 17.10).
        1. Biotic from abiotic: So far, experiments have not produced large amounts of one stereoiso-
mer only of nucleotides or amino acids. Nor have large amounts of ribose (as opposed to other
sugars) been made. Nucleotides can attach at several places to ribose (and do so). And without a
chemical energy source, no polymerization takes place. Getting to specific, self-replicating RNA
molecules (with appropriate chirality) seems difficult to say the least – perhaps other self-replicating
systems evolved first (3rd paragraph, pg. 660) that in turn promoted development of RNA chains.
Certainly, we don’t know much (yet).
        2. Polymerization: in water, although monomers can easily be polymerized (with an energy
source), they also hydrolyze rapidly. Need some stability – how?  Ferris, et al, have demonstrated
that the aluminum-silicate clay mineral Montmorillonite slows hydrolyzing decay, and short polynucle-
otides have been formed (and remained) on clay surfaces; with repeated application of more nucle-
otides, the clay catalyzes the reaction and the polynucleotides can be made longer, now up to 50
nucleotides long.  Ferris and others have similarly assembled polypeptides up to 55 A.A.’s long. So,
certainly more experimental support than for step one.  Interestingly, the oldest known exposed rocks
on Earth (3.7 byo) already contain evidence of life.  Older rocks with evidence for life may be very
difficult to find due to erosive/tectonic/volcanic disruptions, and the conditions were unlikely conducive
to life on the planet much earlier than that.
        3. Life becomes cellular -- the ancestor of all extant organisms: it seems pretty clear that,
regardless of how many times life may have "started" on the planet, that eventually one main
interbreeding lineage may have become THE one – the ancestor of all living things on the planet. We
all use the same coding mechanism, the same A.A.’s, etc., and this machinery is housed in a membrane
– a cell (see experiments of Fox, below).  As you already know, phospholipids thrown in water spon-
taneously organize into bilayers; these protein/phospholipid membranes can fuse. Still, even if "taken
up" by these "cells", how do DNA/RNA take control? Still unanswered by anything experimental.


Who is/are the Common Ancestor(s)
        Many experiments, particularly by Fox, et al, have generated protein containing "membranes", 
with, characteristics of cells (pick up other molecules, "division", etc.).
        Direct fossil evidence of life begins between 3.2 and 3.5 bya, and appears to be similar to extant
cyanobacteria (photosynthetic); this is already too advanced to give us a view of the early common
ancestor(s) (cenancestor), and early fossils are too uncommon. Fossils can’t help us here.
        Phylogenetic reconstruction, however, can help out – we look for the synapomorphies to assemble
the Tree of Life. However, morphological characteristics of the primitive prokaryotes lacked enough
diversity to assemble the tree. DNA/RNA/ Protein sequencing techniques give us much more character
diversity – similar (but not identical sequences – why?) for the same gene. The more the differences, the
longer the lineages have been apart (straightforward) – a sort of "molecular clock". Of course, if you
want to do this for all life, you need a gene that codes for the same, and an essential, functioning molecule
in ALL living things – the gene for small subunit ribosomal RNA is such a molecule.
        The phylogeny intimated by this rRNA, which is counter to the five kingdom classification of life, is
shown in Fig. 17.18, 17.21, and 17.24-25 (but see fig. 17.23). Prokaryotes have two VERY distinctive
separate evolutionary lines, one including virtually all the commonly known types, the other represented
by "extremists", living in various harsh conditions (Archaea). Interestingly, these Archaea (formerly
Archaebacteria) are apparently more closely related to Eukaryotes than the "typical" Bacteria. Eukarya
are relative newcomers, with less than 10% of the variation seen in the rRNA small subunit gene.  With
complete genomes now being sequenced with ever increasing speed, we have the unprecedented oppor-
tunity to accurately estimate evolutionary relationships, including testing further the universal phylogeny.
With this, we find, oddly, that different genes estimate different relationships between the domains (Fig.
17.23).  Some of this can be explained however, through another phenomenon -- lateral gene transfer.    
Some Archaea actually have what appear to be bacterial genes – why? Because they ARE bacterial,
picked up by the organism from another. This gene transfer can, and does, happen between these prokar-
yotic forms, and new studies suggest it is possible on a much broader scale. As for the common ancestor,
all evidence points to a rather sophisticated, evolved organism, or SET of organisms, not unlike modern
bacteria, sometime as early as 4 to perhaps as recently as 2 bya.  It may very well be that extant life's
history does NOT originate with a single life form, but an interconnected set of roots to the tree, a com-
munity of interacting species readily swapping genes (which, needless to say, makes for an interesting
base to the phylogeny-- see Fig. 17.27).  Read pages 675 – 677 for date of oldest known eukaryotes
[prob. 1.85-2.1 bya] and cyanobacteria [similar to extant forms, apparently barely changed for 2 by])

Hypotheses for the evolution of the "Tree of Life" -- the descent from the "common" ancestor
        1.  The Universal Gene-Exchange Pool -- three ancestors of todays domains emerged from the
            pool at different times, with later emergence of Archaea and Eucarya making them appear more
            more closely related.
        2.  The Ring of Life -- the first eukaryote arose by the fusion of an archaen and bacterium.  Less
            support for this hypothesis (though see discussion of mitochondria, below), as there are
            significant gaps in molecular development with this theory, and no cytoskeletal control in
            either makes it difficult to envision the necessary phagocytotic event
        3.  The Chronocyte -- an independent organism that developed a cytoskeleton and phagocytotic
            capabilities.  Eventually, a digestion-resistant archaen is eaten and becomes the "nucleus".
            Several holes in this theory as well, including lack of evidence for such a chronocyte.
        4.  The Three Viruses/Three Domains --  viruses, with RNA gene for reverse transcriptase, in
            turn generates host DNA from host RNA.  Host, with developed resistance, in turn has more
            stable DNA than RNA, and DNA becomes THE molecule.

Origin of Organelles

        Mitochondria, widespread but not universal in Eukarya, and chloroplasts, more restricted in their
distribution, are therefore not defining characteristics of the Eukarya. Where did they come from? Both
have their own DNA, and analysis puts chloroplasts rRNA small subunit gene with the cyanobacteria,
and that for mitochondria within the Bacteria as well. Lynn Margulis’ endosymbiosis theory is correct!!

Chapter 18:  Evolution and the Fossil Record

The Nature of the Fossil Record:  Understand how organic remains fossilize, and that occasionally
    flesh can be preserved under very restricted conditions.  Understand, also, that, like any data set,
    fossils present a biased look at the history of life, for several reasons.  Different organisms/organs
    fossilize or don't (presenting a DISTINCT taxonomic bias in the fossil record), different conditions 
    at time of fossilization and after fossil formation, different access to fossils, etc.  See * below.

the following:
Timeline – pages 695:
        Time (mya) for beginning and end of each period:
Proterozoic – Precambrian times
Phanerozoic eon:
   Paleozoic – with Cambrian, Ordovician, Silurian, Devonian, Carboniferous (M & P), Permian
   Mesozoic – with Triassic, Jurassic, Cretaceous
   Cenozoic – with Paleogene (Paleocene, Eocene, Oligocene), Neogene (Miocene, Pliocene),
            Quaternary (Pleistocene, Holocene)

Note that both the Paleozoic and Mesozoic end with a mass extinction event, which in turn leads to
    the next Era.  Note also there are three other smaller mass extinctions.  See below.

Know times for:
            First shelled organisms
            First vertebrates
                    First jawed fishes (cartilaginous), bony fish, tetrapods (amphibians), dinosaurs,
                        mammals, placental (eutherian) mammals, birds, primates, humans
            Arthropods already present prior to Cambrian, First insects, and first winged insects
            First land plants
            First vascular plants (ferns), first seed plants (end of Devonian), first flowering plants            

You should also understand connections, such as why land animals came after land plants, and
why insect diversification really took off after evolution of flowering plants

*Understand what we know comes largely from fossils, which have some inherent biases
(geographical [require some minimal sedimentation at least], taxonomic [organisms with hard
parts preserved better], and temporal [older fossils less numerous]).
        Some famous fossil deposits:
            Ediacaran Hills in south Australia
            Burgess Shales in British Columbia

Was Cambrian Explosion really Explosive?
        Molecular clocks suggest derivation of some lineages older than fossils suggest (NOT a
surprise). Older fossil finds starting to confirm these older dates.
        Even so, there DOES appear to be a very rapid evolution of morphological traits, not only
in complexity (meaning more complex developmental program) but size as well.  Increasing
oxygen levels, more ecological interactions, etc. may have driven this evolution, but still there
would have had to have been some significant genetic variability available to ALLOW for this
evolution. Indeed, the fossil beds above do show members of virtually all major animal lineages
appearing relatively suddenly and simultaneously in the fossil record in distant parts of the globe.

Macroevolutionary patterns -- know the following:
        Deuterostomes vs. protostomes (vs. neither) -- big nine animal phyla: Porifera (sponges),
            Cnidaria, Platyhelminthes (flatworms).  Protostomes: Aschleminthes (roundworms),
            annelids (segmented worms), arthropods, mollusks.  Deuterostomes: echinoderms,
        Important transitions: fish-tetrapod, dinosaur-bird, synapsid-mammal
        Global taxonomic diversity: Fig. 18.22, pg. 707. Notice general increase with "dips".
        Mass Extinctions: The "Big Five" – especially P-T Siberian Traps and the K-T asteroid
        Background Extinction
        Human driven Extinction (see middle paragraph page 718) -- the sixth mass extinction
        Punctuated Equilibrium (stasis [in morphology] followed by rapid diversification).
              Are both punctuated equilibrium and gradualism happening?

One last tidbit:
    Chapter 15, section 15.1:  Diversity among genomes
        C values (handout) -- total DNA per cell does NOT correlate with organisms
    perceived morphological complexity or phylogenetic position.
        Amount of DNA that is protein coding versus non-protein coding (Fig. 15.1)
        Non coding DNA, however, can be involved in regulating protein-coding regions, though a
            good percentage can be non-coding mobile genetic elements, that typically have no effect
            on the organism's phenotype.  See fig. 15.2.  
        Included in the non-coding DNA, however, are also introns.  Note contribution of these to
            total genome size as well (Fig. 5.3).  Positions of introns in the genome are quite conserved
            across distantly related organisms, which suggest they serve SOME purpose, though it is
            not at all clear what they do.