Evolution – Biology 4250
                                                                                                         Dr. Adams
Review Sheet 4.1 – Test 4

Chapter 16: Mechanisms of SpeciationDivergence
        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.
        Again, as with the PSC, the problem of what constitutes significant enough difference still exists.
Application tends to be somewhat arbitrary, and what are called cryptic species may easily be
missed.

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])

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) . . . ?
                (requires phylogenies for close relatives, criterion standardization, or necessary non-
standardization [not all characteristics are of equal importance]; so application becomes the main
problem)

        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
DISTINCT
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 copepods
        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
                    islands.
            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)
    Chromosome Change
        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 (though see the discussion of fish genus Barbus on pg. 616)
                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.

Mechanisms of Divergence: Already discussed in great detail earlier in the course.
        Definitions: Allopatric, Parapatric, Sympatric speciation.
    Genetic Drift – only important in small populations; importance has probably been overstated in past.
Many small populations of many organisms established by humans have failed to show any significant
divergence.
    Natural Selection – one example to recall: 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 (see Table 16.1).       
        Another possible example of sympatric speciation involves temporal separation – the Callosamia
story (another Georgia example).
        Sexual selection – back to the Hawaiian Drosophila; males fight in locations where there are leks,
and novel traits (broader head) that help you "win" should be selected for (Fig. 16.10)

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
plants).
        Reinforcement – occurs in the hybrid zone; involves prezygotic (premating or postmating) or
postzygotic
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 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 Table 16.3.  

The Genetics of Speciation (Isolation and Differentiation)
        Genetic models (and real organisms) have shown that large-scale changes are unnecessary for
divergence and speciation to occur.
        Examples: Leopard Frogs, Three-spined Sticklebacks

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 function 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 bacteriophage
(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 mutation 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 experiments.
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?)