Geography 140
Introduction to Physical Geography

Lecture: Basics of Evolution

I. Evolutionary theory is the core of biogeography, and the ultimate source
of the theories tested in it. Though it is the reigning paradigm in
biogeography, ecology, and other biosciences, it is not widely accepted
among the general public (e.g., the recent Kansas debacle) and, as such,
is not well-treated in the K-12 curriculum.
A. Contrary to popular opinion, neither the term nor the idea of
biological evolution began with Charles Darwin and his foremost work,
On the Origin of Species by Means of Natural Selection (1859).
B. Many scholars from the ancient Greek philosophers on had inferred that
similar species were descended from a common ancestor, most famously
Jean-Baptiste Lamarck (1744-1829).
C. In 1799 an engineer named William Smith reported that, in undisrupted
layers of rock, fossils occurred in a definite sequential order, with
more modern-appearing ones closer to the top.
1. Because bottom layers of rock logically were laid down earlier and
thus are older than top layers, the sequence of fossils also could
be given a chronology from oldest to youngest.
2. His findings were confirmed and extended in the 1830s by the
paleontologist, William Lonsdale, who recognized that fossil
remains of organisms from lower strata were more primitive or
general looking than the ones above. Today, many thousands of
ancient rock deposits have been identified that show corresponding
successions of fossil organisms.
D. Thus, the general sequence of fossils had already been recognized
before Darwin conceived of descent with modification. The
paleontologists and geologists before Darwin used the sequence of
fossils in rocks not as proof of biological evolution, but as a basis
for working out the original sequence of rock strata that had been
structurally disturbed by earthquakes and other forces.
E. Darwin's great contribution, then, was NOT the idea of evolution, for
that had long been established as fact; rather, it was a coherent and
testable mechanism for evolution, or what he called "descent
with modification."
1. Darwin proposed that evolution could be explained by the
differential survival of organisms following their naturally
occurring variation--a process he termed "natural selection."
2. According to this view, the offspring of organisms differ from one
another and from their parents.
3. Some of these differences are heritable--that is, organisms can
pass on the differences genetically to their own offspring.
4. Furthermore, organisms in nature typically produce more offspring
than can survive and reproduce given the constraints of food,
space, and other environmental resources. This is an idea he got
from Robert Malthus (An Essay on the Principle of Population,
1798), who had said that food supply can only grow arithmetically
(for humans, who engage in farming, and not really at all for other
species), but population can grow exponentially (producing more and
more offspring at faster and faster). See the graph below for the
growing contrast in population levels produced by arithmetic and
exponential growth functions:

5. If a particular offspring has traits that give it even a slight
advantage in a particular environment, that organism will be
more likely to survive and pass on those traits in that particular
environment.
6. As differences accumulate over generations, populations of
organisms diverge more and more widely from their ancestors. Over
millions of years, this can produce tremendous numbers of wildly
different species.
F. Darwin's original hypothesis has undergone extensive modification and
expansion, but the central concepts stand firm.
1. For example, he had no clear idea how heritable traits were
inherited: He thought it had to do with some kind of blending of
substances from parents, which he understood made systematic
directional change difficult to explain (you'd lose the
distinctiveness of new traits as they were blended in with other
traits in the offspring). Darwin didn't live long enough to see
the solution to what was for him a big problem.
2. The mechanism awaited Gregor Mendel's experiments with peas.
a. Mendel was the Augustinian monk in Austria who followed seven
clearly different pairs of genetic traits through time (he
experimented on 28,000 plants!).
b. He was the first to approach a biological question with a
statistical and mathematical methodology.
c. He presented and then published his work in a local scientific
society's conference and journal series back in 1865, where no-
one seemed to know what he had accomplished. A few people did
cite his work now and again, but, again, didn't seem fully to
comprehend what he had achieved.
d. His work was independently rediscovered by Carl Correns in
Germany, Hugo de Vries in the Netherlands, and Erich von
Tschermak-Seysenegg in Austria, who all three separately
realized what a gold mine they'd found in Mendel's work and
began to promote it.
e. The mechanism is of discrete gene units, called alleles, of
which more than one type can be found at a gene locus.
i. The alleles are inherited wholly, one from each parent.
ii. The offspring can have two copies of the same allele at a
given gene locus, which makes them "homozygous" for that
gene, or they can have one copy of two different alleles,
which makes them "heterozygous" for that gene.
iii. This genetic inheritance is called the offspring's
genotype.
f. The alleles then enter into relationships with one another that
determine much of the offspring's phenotype, which is how the
genotype expresses itself. These relationships include:
i. Dominant-recessive interactions among homozygous individual
(e.g., in humans, the interaction between brown eyes and
light blue eyes, where two homozygous people, one with
brown eyes and the other with light blue eyes, can only
produce brown-eyed children, because brown is dominant and
light blue is recessive).
ii. Dominant-recessive interactions among heterozygous
individuals (e.g., two brown-eyed people who each had a
light blue-eyed parent getting together will typically
produce one blue-eyed homozygous child who resembles two of
the grandparents, two heterozygous brown-eyed children like
themselves, and one homozygous brown-eyed child like the
other two of the grandparents).
iii. Blending forms among heterozygous individuals (e.g.,
crossing a white or cream colored horse with pink skin with
a chestnut or solid red horse will produce palominos, gold-
colored horses with white or cream-colored manes and tails,
but, if you breed two palominos, you'll only get half of
the offspring being palomino, with one quarter being white,
and one quarter being chestnut).
3. The incorporation of Mendellian genetics into Darwin's idea is
termed the "Modern Synthesis."
G. The Modern Synthesis has received still further support through
studies in molecular biology -- a field unimaginable either to Darwin
or Mendel.
1. These have explained the occurrence of the hereditary variations
that are essential to natural selection.
2. Genetic variations result from changes, or mutations, in the
nucleotide sequence of DNA, the molecule that genes are made from.

3. Such changes in DNA now can be detected and described with great
precision, and, indeed, the complete genetic map for
humans was finished in 2003. You can learn more about the Human
Genome Project at http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml.
H. Genetic mutations arise by chance.
1. They may or may not equip the organism with better means for
surviving in its environment.
2. Indeed, the vast majority are harmful.
3. But if a gene variant does improve adaptation to the environment
(for example, by allowing an organism to make better use of an
available nutrient, or to escape predators more effectively -- such
as through stronger legs or disguising coloration), the organisms
carrying that gene are statistically more likely to survive and
reproduce than those without it.
4. Over time, their descendants will tend to increase, changing the
average range of characteristics of the population.
5. Although the genetic variation on which natural selection works is
based on random or chance elements at the molecular level, natural
selection itself produces "adaptive" change -- which is the very
opposite of chance.
a. To give you a sense of this distinction between random, chance
generation of change and the very non-random process of natural
selection, consider the famous million monkeys and Shakespeare
analogy for the probability of evolution.
b. One million monkeys, given typewriters and pecking away at them
randomly, would need 78,800 years to produce the single sentence,
"To be or not to be" from Hamlet.
c. But if you incorporate selection acting on the random chaos,
you get startlingly higher probabilities and shorter timeframes.
d. Richard Hardison up at Glendale College wrote a computer program
that mimics the million monkeys but every time one of the virtual
monkeys happens to type a letter in the right place, it is
allowed to keep it there: "natural" selection.
e. His program can produce "To be or not to be" in 366 iterations
in under 90 seconds!
f. In fact, his program can reproduce all of Hamlet in just
4.5 days!
g. The very non-random selection pressure acting on randomly given
variations can produce directional change very fast, which might
be why life seems to have arisen so soon after Earth solidified
(the planet goes back about 4.5 billion years and the first
traces of simple life forms about 3.5 billion years ago.

II. We have also gained an understanding of the processes by which new
species originate, and this is where geography comes in big time.
A. A new species is one in which the individuals cannot mate and produce
viable descendants with individuals of a pre-existing species.
B. Now, viability doesn't just mean the creation of living offspring,
because you can get mule hybrids between distinct species (e.g., when
you cross a female horse with a jackass, you get a mule, and such
hybrids have been produced between other species, such as between
street pigeons and ring-neck doves).
1. Most such mules cannot themselves reproduce: You want a baby mule,
you have to go back to a mare and a jackass.
2. Some hybrids can produce babies, but the resulting creature does
not have an ecological niche in which it competes equally with or
better than either parent species, so it's a waste of the parents'
reproductive labor to make such a mating, and this generates
pressure to make darned sure you're messing just with your own
species (reproductive isolation).
C. The split of one species into two often starts because a group of
individuals becomes geographically separated from the rest.
1. This is particularly apparent in distant remote islands, such as
the Galápagos and the Hawaiian archipelago, whose great
distance from the Americas and Asia means that arriving colonizers
will have little or no opportunity ever to mate with individuals
remaining on those continents.
2. Mountains, rivers, lakes, and other natural barriers also account
for geographic separation between populations that once belonged to
the same species.
3. There is some evidence accumulating that even something like an
interstate highway is creating reproductive isolation among
populations of small species, causing them to diverge in traits!
D. Once isolated, geographically separated groups of individuals become
genetically differentiated as a consequence of mutation and other
processes, such as the founder effect, gene drift, and natural
selection.
1. Founder effect means that a small, isolated population does not
have the full range of alleles in its gene pool, so natural
selection starts working with different material, which biases the
population's genetic evolution.
2. Gene drift means that small populations tend to lose even more
alleles, just due to random events wiping out the rare individuals
with uncommon alleles. If you have two alleles present in a small
population at one gene locus, and one is slightly less common than
the other and if the population commonly experiences random
episodes of high mortality (e.g., a hurricane coming through), the
less common one typically disappears entirely within a few
generations. The impact of such disasters is disproportionate on
the less common allele from generation to generation.
3. The environment in which the small population is isolated will
almost certain differ from the range of environments that the large
bulk of the species experiences. This means that natural
selection, working through different environmental conditions, will
also cause the isolated population to evolve in a different
direction than the big parent population.
E. The origin of a species is often a gradual process, so that at first
the reproductive isolation between separated groups of organisms is
only partial, but it eventually becomes complete. Biogeographers and
other life scientists pay special attention to these intermediate
situations, because they help to reconstruct the details of the
process and to identify particular genes or sets of genes that account
for the reproductive isolation between species. There's an
interesting case in Southern California:
1. Penstemon spectabilis is a five-petalled flower with a showy
blue-purple flower that is short and plump in profile, because it
is pollinated by bees
2. P. centranthifolia is another five-petalled flower, but it's
bright red with a long slender profile, being pollinated by
hummingbirds.
3. These two species have moved into one another's ranges.
4. Bees can't pollinate P. centranthifolia, but hummingbirds
can pollinate P. spectabilis.
5. The result is a beautiful, perfectly intermediate hybrid: It's a
bright violet color and intermediate in profile between its two
parents.
6. Unfortunately, the hybrid doesn't compete as well as either parent,
particularly for pollination, so it's a waste of reproductive
effort for P. spectabilis to let those pesky hummingbirds in
to mess things up.
7. Over the millenia, the pressure will be on P. spectabilis to
find some way to gross out hummingbirds.
8. Had the hybrid been able to compete with its parents, then the two
species would have merged, because that would have been the smart
way to invest their reproductive charms.
F. Evolution can be sped up by aggressive selection processes, such as
the pressures we humans have exerted on the other species with which
we interact:
1. We have sped up evolution in the last few thousand years in the
case of animal and plant domestications.
a. Dogs have been genetically determined to be wolves, all of
them, including chihuahuas and poodles (oh, how the mighty wolf
has fallen <G>!). All dogs are the same species, but we
have pushed the definition of a species when its end points
(say, trying to mate a chihuahua female with an Irish wolfhound
male) are not viable, though the end points can eventually share
genes through a long series of mutts.
b. We have also accidentally created new strains of bacteria,
through careless use of antibiotics, which create severe
selection pressure on pestilential species, which only
eventually creates "superbugs."
i. The worst abuses of antibiotics as superbug breeders
involves the meat industry, where it's cheaper to medicate
animals than to keep meat animals clean enough and in
uncrowded conditions to reduce the transmission of
bacteria.
ii. People help this process along in their everyday lives, too
-- demanding antibiotics of their doctors for every cold
they or their kids get -- antibiotics are utterly useless
in fighting colds and flus, since those diseases
are caused by viruses, which do not respond to antibiotics
G. We used to think that all speciation involved geographic (allopatric)
isolation, but we now have evidence that this can happen in a
sympatric (non-geographically separated) situation.
1. In plants, it can happen instantaneously through polyploidy. That
is, some organisms occasionally make a mistake in meiotic cell
division (the kind that is supposed to divide chromosome pairs into
single chromosomes in sex cells, so that fertilization of the
female sex cell will restore the normal number of pairs of
chromosomes, this time having one set of each pair from the mother
and the other set from the father). As a result, plants can create
daughter cells with twice the number of chromosomes normal to the
species. The offspring grows up, functioning normally, but cannot
reproduce with anyone of its parents' species, because half of its
chromosomes can't link up with its mate's chromosomes. In complex
animals, this kind of accident would be the end of the new species.
In many plants (and even a few species of animal, such as
earthworms), however, the offspring can fertilize itself. Thus
a new species can be born instantly.
2. In sexually reproducing species, mate selection by females can lead
to sympatric reproductive isolation, and it can take place quite
quickly. Probably the most famous case of this is the brightly
colored cichlid fishes of Lake Victoria in East Africa. For a map,
click here.
This lake is known to have dried up completely about 12,400 years
ago. The ancestor of the cichlids got in there after the lake
water level began to rise, and, though the fish environment shows
relatively little variation, there are now more than 300
reproductively isolated cichlid species in there! It turns out
that, while the females often resemble those of other species, the
males are wildly different, and the females of each species are
really, really picky about exactly which color and pattern they
will accept in a boyfriend. The result is the popular types of
guys got to breed and each generation picked mutant guys even more
extreme along the favored line of appearance and the process
snowballed into 300+ species that cannot swap genes because the
females are so darned fussy. There's a troublesome footnote to
this example: The lake is being polluted so bady that the
underwater visibility is declining, and that means the gals can't
see clearly enough to pick the pretty guys and there's some
evidence that some interbreeding is starting to happen, which will
eventually wipe out the unbelievable diversity of this unique bunch
of fish.
3. There's also evidence of sympatric evolution when a new, acceptable
food source shows up in a region. Some of the members of a species
will start exploiting that resource and will start to develop
quirks that help them exploit it better. This means that
interbreeding back with everyone still using the traditional
resource will disrupt their new adaptation, and so pretty soon they
get snotty towards the other members of their species still
concentrating on the traditional resource and that leads to
reproductive isolation. This happened very famously in the case of
the hawthorne/apple maggot fly, Rhagoletis pomonella, which
lives in the north central USA. Its traditional resource was
hawthorne fruit, in which it would lay its eggs. The maggots would
have a grand old time in the fruit, which would eventually fall on
the ground and the maggots would then burrow into the ground to
pupate and eventually emerge as flies. Well, apple trees were
introduced to the area and, sure enough, some of the flies
discovered it and accidentally lay eggs in the apples. The maggots
hatched to a surprising new environment and some of them managed to
thrive and that led to more of the indiscriminant flies dumping
eggs on apples. They began to adapt to this strange and yummy new
resource, and now there are two races of the fly: the hawthorne
maggot fly and the apple maggot fly. They are now reproductively
isolated by the different timings of the peak fruiting seasons of
their host species.

III. Evidence
A. In Darwin's time, paleontology was still a rudimentary science. Large
parts of the geological succession of stratified rocks were unknown or
inadequately studied. Darwin, therefore, worried about the rarity of
intermediate forms between some major groups of organisms. This is
the origin of that misleading term, "missing links."
B. Today, many of the gaps in the paleontological record have, in fact,
been filled by the research of paleontologists. Hundreds of thousands
of fossil organisms, found in well-dated rock sequences, represent
successions of forms through time and manifest many evolutionary
transitions.
1. Microbial life of the simplest type was already in existence 3.5
billion years ago.
2. The oldest evidence of more complex organisms (that is, eucaryotic
cells, which are more complex than bacteria) has been discovered in
fossils sealed in rocks approximately 2 billion years old.
3. Multicellular organisms, which are the familiar fungi, plants, and
animals, have been found only in younger geological strata.

Life Form Millions of Years Since
First Known Appearance
(Approximate)
-----------------------------------------------------------

Microbial (procaryotic cells) 3,500

Complex (eucaryotic cells) 2,000

First multicellular animals 670

Shell-bearing animals 540

Vertebrates (simple fishes) 490

Amphibians 350

Reptiles 310

Mammals 200

Nonhuman primates 60

Earliest apes 25

Australopithecine ancestors of humans 4

Modern humans 0.15 (150,000 years)

---------------------------------------------------------------------

4. So many intermediate forms have been discovered between fish and
amphibians, between amphibians and reptiles, between reptiles and
mammals, and along the primate lines of descent that it often is
difficult to identify categorically when the transition occurs from
one to another particular species. Actually, nearly all fossils can
be regarded as intermediates in some sense; they are life forms
that come between the forms that preceded them and those that
followed (we are the intermediates between our parents and our
children, so to speak).
5. The fossil record thus provides consistent evidence of systematic
change through time--of descent with modification. From this huge
body of evidence, it can be predicted that no reversals will be
found in future paleontological studies. That is, amphibians will
not appear before fishes, nor mammals before reptiles, and no
complex life will occur in the geological record before the oldest
eucaryotic cells. This prediction has been upheld by the evidence
that has accumulated until now: no reversals have been found.
C. Other evidence includes:
1. Common structures (homologies) most economically explained as
descent with modification of a common ancestral form.
a. Limb bones show direct homologies across wildly different
species.
i. For example, examination of a horse's hoof and leg bones
show that the hoof is homologous to our fingernails and
that horses run on their middle finger bones. Two of the
other "fingers" exist as "splints" or toothpick-sized bones
on either side of their lower legs, which become evident
only when they manage to break them! Their thumbs are
reduced to soft fingernail-like areas on their upper limbs,
called "chestnuts." Their "knees" are homologous to our
wrists! The development of the modern equine's limb bones
can be traced very clearly through the fossil record from
the early Hyracotherium or Eohippus ancestor
that had four hoofed toes in front and three in back,
through a number of other genera with gradually reduced
outer toes to the modern Equus.
ii. Other examples of homologies are the hand bones that
support whale fins and bird wings.
b. The mammalian ear and jaw are instances in which paleontology
and comparative anatomy combine to show common ancestry through
transitional stages. The lower jaws of mammals contain only one
bone, whereas those of reptiles have several. The other bones in
the reptile jaw are homologous with bones now found in the
mammalian ear. Paleontologists have discovered intermediate
forms of mammal-like reptiles (Therapsida) with a double jaw
joint--one composed of the bones that persist in mammalian jaws,
the other consisting of bones that eventually became the hammer
and anvil of the mammalian ear.
c. A good review of such homologies and transitions can be found here,
if you're curious about this subject.
2. Biogeography
a. Island groups closely related to distinct species on the
mainland, but which diversify like crazy in isolation: Hawai'is
diversity of species in certain groups -- adaptive radiation by
accidental colonizer species into virtually unoccupied niches
(kind of like those fruit maggot flies).
b. Extinctions caused by new exotic invaders:
i. One of the derivatives from the Modern Synthesis is called
the competitive exclusion principle: Two species cannot
indefinitely co-exist on the same resources in the same
area at the same time. One species will always
outreproduce the other in that circumstance, unless there
is enough time for the two to hit on some specialization
that will allow them to co-exist.
ii. Humans have often introduced species to other areas and
produced extinctions through this effect, such as the
extinction of indigenous island rodent species by the
introduction of ship rats.
3. Similarities during embryological development
a. Embryos of vertebrates look virtually identical early on
b. Barnacles are crustaceans, like lobsters and shrimps, that they
do not resemble, due to their sedentary adult lives, but their
larvae are free-swimming and strongly resemble other crustacean
larvae.
4. New evidence from molecular biology
a. The code used to translate nucleotide sequences into amino acid
sequences is essentially the same in all organisms. Moreover,
proteins in all organisms are invariably composed of the same
set of 20 amino acids. This unity of composition and function is
a powerful argument in favor of the common descent of the most
diverse organisms.
b. Family histories have been obtained from the three-dimensional
structures and amino acid sequences of all sorts of proteins.
The examination of molecular structure offers a new and
extremely powerful tool for studying evolutionary relationships.
i. These molecular clocks run rapidly for less constrained
proteins and slowly for more constrained proteins, but they
all time the same evolutionary events the same way.
ii. Pseudogenes are very interesting. They are remnants of
genes that no longer function but continue to be carried
along in DNA as excess baggage, usually kept out of action
by the folding of the DNA to keep it from generating
proteins that might be disruptive if produced. Like all
other genes, pseudogenes also mutate and change through
time.
a. This junk DNA offers an especially useful way of
reconstructing evolutionary relationships.
b. With functioning genes, one possible explanation for the
relative similarity between genes from different
organisms is that their ways of life are similar -- for
example, the genes from a horse and a zebra could be
more similar because of their similar habitats and
behaviors than the genes from a horse and a tiger.
c. But this possible explanation does not work for
pseudogenes, since they perform no function. Rather, the
degree of similarity between pseudogenes must simply
reflect nothing more than their evolutionary
relatedness.

Well, that's enough for now. Come away from this lecture knowing the basics
of Darwin's and Mendel's achievements. Understand the source of novelty in
genetic makeup (chance mutations) and how that random chaos is converted into
well-ordered life forms (natural selection for survival and reproductive
success in a particular environment in a particular timeframe). Know what
alleles are and how they relate to genes (which are segments of DNA grouped
along chromosomes). Be able to differentiate the two big forms of speciation:
allopatric (geographical) speciation and sympatric speciation. Know what the
founder effect and gene drift are and how they affect allopatric speciation.
Be able to describe two main mechanisms of sympatric speciation (sexual
selection and ecological selection). Be able to identify two forms of
accelerated evolutionary change associated with human activities
(domestication and the creation of resistant pest species). Know why the
term, "missing links," is so misleading now.

In the next lectures, I'll introduce systems of classifying the astounding
diversity of life on Earth: genetically, morphologically, and by vegetation
typologies.

Geography 140 Introduction to Physical Geography

Lecture: Basics of Evolution

Geography 140
Introduction to Physical Geography