Evolution – Biology 4250
Dr. Adams
Review Sheet 4 -Test 4
Chapter 16: Mechanisms of Speciation – Divergence
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
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 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
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)
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
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 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 3.7 and 4.0 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.
KNOW 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:
Land formations
Pangaea – from 335 mya (Carboniferous) to 175 mya (Jurassic); it finished breaking apart into
Laurasia (northern) and Gondwanaland (southern) – existed separate as long ago as the
immediate Precambrian (550 mya), fused to form Pangaea, and re-separated as
mentioned above
Mountains – time periods indicated are the beginning of formation of the indicated range
Applachians – Ordovician
Rockies – Cretaceous
Andes – Paleocene
Himalayas – Eocene
Alps – Oligocene
Animals
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
Plants
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,
chordates.
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).
Gradualism
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. 15.3). 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.