Newsgroups: cmu.cs.discussion
From: cbs+@GLOBE.EDRC.CMU.EDU (Clauss Strauch)
Subject: evolution & speciation (from talk.origins)
Date: Fri, 26 Mar 1993 19:38:40 -0500


The following is a section of a post I pulled off the net a long while back.
It gives some facts about evolution and speciation relevant to the discussion
here.  It's a little long.  People who just want an answer to the "why haven't
we seen new species being created?" question may want to skip to the end.
(The short answer:  "We have.")
							-- Clauss

-------
(from)
Chris Colby
email: colby@bu-bio.bu.edu

INTRODUCTION

	Evolution is one of the most powerful theories science has
ever known. For a variety of reasons, however, it is also one of
the most misunderstood. One common misunderstanding is that
the phrase "survival of the fittest" summarizes evolutionary theory.
In fact, it does not. The phrase is both incomplete and misleading. 
The notions that; evolution represents progress and, that organisms 
can be arranged on an evolutionary ladder from bacteria to man, are 
two other common misunderstandings.
 	
	This post is an outline of the basics of evolutionary 
theory. It is intended to be a brief overview of the concepts and
mechanisms of evolution. Creationist arguments are not addressed
directly here; nor is a "laundry list" of reasons to believe in 
evolution provided. Many interesting topics in evolutionary biology
are not covered here (symbiosis and endosymbiosis, origins of life,
punctuated equilibrium, sexual selection, human evolution and much
more) because I can't include everything and keep this down to a
readable length. Also, what I know the most about is the process of
evolution as it occurs within a lineage (anagenesis), so that is
the focus of this post.


WHAT IS EVOLUTION?

	Evolution is a change in the gene pool of a population over 
time. The gene pool is the set of all genes of a species or population. 
The English moth, _Biston__Bistularia_, is a frequently cited example
of observed evolution. In this moth, rare black variants spread through
the population as a result of their habitat becoming darkened by soot 
from factories. Birds could see the lighter colored moths more readily 
and ate more of them.

	Thus, the moth population changed from mostly light colored
moths to mostly dark colored moths. Since their color was determined 
by a single gene, the change in moth color represented a change in the 
gene pool. This change, by definition, was evolution.

 	Many creationists, when confronted with this example,
say "You started with moths and ended with moths... where's the
evolution?" The kind of evolution documented above is termed by
some "microevolution", while larger changes (taking more time)
are termed "macroevolution". Some biologists feel the mechanisms
of macroevolution are different from those of microevolutionary
change. Others, including myself, feel the distiction between the
two is arbitrary. Macroevolution is cummulative microevolution.

	In any case, evolution is defined as a change in the
gene pool. Later in this post I will discuss macroevolution as
well as microevolution. For the sake of brevity I will use the
terms as if it is useful to draw a distiction between them. 

	I have defined "evolution", here, as a process and that is
how I will use the term in this essay. Keep in mind, however, that in
everyday use "evolution" often refers to a variety of things. The
fact that all organisms are linked via descent to a common ancestor
is often called evolution. The theory that life arose solely via
natural processes is often called evolution (instead of abiogenesis).
Often, people use the word "evolution" when they really mean natural
selection -- one of the many mechanisms of evolution. 


WHAT ISN'T EVOLUTION?

	For many people evolution is equated with morphological
change, i.e. organisms changing shape or size over time. An example
would be a dinosaur species slowly turning into a bird species. 
It is important to note that evolution is often accompanied by 
morphological change, but this need not be the case. Evolution can
occur without morphological change; and morphological change can 
occur without evolution. For instance, humans are larger now than 
in the past few hundred years, but this is not an evolutionary
change. Better diet and medicine brought about this change,
so it is not an example of evolution. The gene pool did not
change -- only it's manifestation did.
 
	An organism's morphology is determined by both its genes and 
its environment. Morphological changes induced solely by changes in 
environment do not count as evolution, because this change is not 
heritable. In other words the change is not passed on to the organisms 
offspring. Most changes due to environment are fairly subtle (e.g. size 
differences). Large scale morphological changes (such as dinosaur to bird) 
are obviously due to genetic changes, and therefore are evolution.


WHAT EVOLUTION ISN'T

	Evolution is not progress. Organisms simply adapt to their
current surroundings and do not neccessarily become better over
time. A trait or strategy that is successful for an organism at one
time may be deleterious at another. Studies in yeast have shown that
"more evolved" strains of yeast can sometimes be competitively inferior
to "less evolved" strains. An organisms success or failure depends to
a great deal on the behavior of it's contemporaries; for most traits
or behaviors there is likely no optimal design or strategy, only
contingent designs/strategies.


HOW DOES EVOLUTION WORK?

	If evolution is a change in the gene pool; what causes the
gene pool to change? Several mechanisms can bring about a change in 
the gene pool, among them: natural selection, genetic drift, gene flow, 
mutation and recombination. I will discuss these in more detail later. 
It is important to understand the difference between evolution (change 
in the gene pool) and the mechanisms that bring about this change.

	Bringing about a change in the gene pool assumes that
there is genetic variation in the population to begin with, or a
way to generate it. Genetic variation is "grist for the evolutionary 
mill". For example, if there were no dark moths, the population could 
not have evolved from mostly light to mostly dark. In order for continuing
evolution there must be mechanisms to both increase genetic variation, 
or create it, (e.g. mutation) and decrease variation (e.g. natural 
selection, genetic drift).


HOW IS GENETIC VARIATION DESCRIBED?

	Genetic variation has two components: allelic diversity
and non-random associations of alleles. Alleles are different 
versions of the same gene at a given locus. For example,
at one eye color locus (locus means location) humans can have
the blue allele or the brown allele (there are other alleles also).
Most organisms, including humans, are diploid. This means they contain 
two alleles for every gene at every locus. If the two alleles are
the same type (for instance two blue eye alleles) the individual
would be termed "homozygous" for that locus. An individual with two
different alleles at a locus is called "heterozygous". 
	
	Allelic diversity is simply the number of alleles at 
each locus scaled by their frequency in the gene pool. At any 
given locus there can be many different alleles in the gene pool. 
It is important to realize that there can be more alleles in the 
gene pool (at a given locus) than any single organism can possess. 

	Linkage disequilibrium is a measure of association of
alleles in the gene pool. If each gene assorted entirely
independently, the gene pool would be at linkage equilibrium. 
However, if some alleles were often found togethor in organisms 
(ie. did not assort randomly) these alleles would be in linkage 
disequilibrium. Linkage disequilibrium can be the result of physical 
proximity of the genes or maintained by natural selection if some 
combinations of alleles work better as a team.


HOW MUCH GENETIC VARIATION IS THERE?

	Considerable variation has been detected in natural
populations. At about 70% of gene loci, there is more than
one allele present in the gene pool. Any given individual is
likely to be heterozygous at 30% of it's loci. Most loci
have been found to be assorting independently (i.e. they are 
at linkage equilibrium). In most populations, there are 
enough loci and enough different alleles that every individual 
(barring monozygotic twins) has a unique combination of alleles. 


MECHANISMS THAT DECREASE GENETIC VARIATION
------------------------------------------

MECHANISMS OF EVOLUTION: NATURAL SELECTION

		Natural selection is held to be the only
mechanism as far as _adaptive_ evolution is concerned; it
is defined as differential reproductive success. Selection is
not a force in the sense that gravity or magnetism is. However,
biologists often, for the sake of brevity, refer to it that way.
Selection is not a guided or cognizant entity; it is simply an effect. 
Some organisms have genes that enable them to reproduce more efficiently
than others of their species. Organisms with these genes, therefore
eventually replace the others of their species without these genes.

 	If environmental conditions change, new traits (new
combinations of alleles) will be selected for. Natural selection is a
mechanism that allows organisms to adapt to their current environment 
only; it does not have any foresight. Traits or structures do
not evolve for future utility. The organism must be, to some
degree, adapted to it's environment at each stage of it's evolution.

	Of course, this raises the question; how do complex traits
evolve? If half a wing is no good for flying, how did wings evolve?
Half a wing may be no good for flying, but it may be useful in other
ways. Feathers are thought to have evolved as insulation (ever
worn a down jacket?) and/or as a way to trap insects. Later, 
proto-birds may have learned to glide when leaping from tree to tree.
Eventually, the feathers that originally served as insulation
now became co-opted for use in flight. 

	This illustrates the point that a trait's current utility is 
not always indicative of it's past utility. It can evolve for one 
purpose, and be used later for another. A trait evolved for it's 
current utility is called an adaptation; a trait evolved for another 
utility than it's current use is termed an exaptation. An example of 
an exaptation would be a penguins wing. Penguins evolved from flying 
ancestors. Now, however, they are flightless and use their wings for 
swimming.

	Natural selection works at the level of the individual. 
The example I gave earlier was an example of evolution via natural
selection. Dark colored moths had higher reproductive success
because light colored moths suffered a higher predation rate.
The decline of light colored moths was caused by light colored
individuals being removed from the gene pool (selected against).
It is the individual organism that either reproduces or fails
to reproduce. Individual genes are not the unit of selection
(because their success depends on the organisms other genes as
well); niether are groups of organisms a unit of selection.
There are some exceptions to this "rule".

	The individual organism is what reproduces or fails to 
reproduce. It competes primarily with others of it own species for 
it's reproductive success. For this reason, organisms do not perform
any behaviours that are for the good of their species. Natural
selection favors selfish behavior because any truly altruistic
act increases the recipient's reproductive success while lowering
the donors. Altruists would quickly disappear from a population
as the non-altruists would reap the benefits, but not pay the cost, 
of being an altruist. 
	
	Of course, many observable behaviors appear, at first
glance, to be altruistic in nature. Biologists, however,
can demonstrate (in the cases they have studied) that these
behaviors are only apparently altruistic. Cooperating with or
helping other organisms is often the most selfish strategy for
an animal. Often, this is called by the oxymoronic name "reciprocal
altruism". A good example of this is blood sharing in vampire bats.
In these bats, those lucky enough to find a meal will often share part
of it with an unsuccessful bat by regurgitating the blood into the
others mouth. Biologists have found that these bats form bonds with
other bats and help each other out when the other is needy. If a bat
is found to be a "cheater", (ie. he accepts blood when starving, but 
does not donate when his partner is) the partner will abandon the
cheater.

	Keep in mind that the words "selfish" and "altruistic"
have connotations in everyday usage that biologists do not intend.
"Selfish" simply means behaving so that one's own best interest comes
first; "altruistic" means behaving so that anothers best interest
comes first.

	Natural selection does not induce genetic variation to
occur, it only distinquishes between existing variation. Variation
along all possible axis is not possible, so not every possible
adaptive solution is open to an organism. For example, a steel
shelled turtle would probably be an improvement. Turtles are
killed quite a bit by cars these days because, when confronted
with danger, they retreat into their shells -- not a great
strategy against a two ton automobile. However, there is no
variation in metal content of shells, so it would not be possible
to select for a steel shelled turtle.

	Natural selection does not necessarily produce individually
optimized structures or behaviors. Selection works on the organism
as a whole, not individual traits. So, specific traits are not
optimized, but rather combinations of traits. In addition, natural
selection may not necessarily even select for the the most optimal
set of traits. In any population, there may be a certain combination
of possible alleles that would produce the most optimal set of traits
(the global optima); but are probably several other sets of alleles
that would yeild a population almost as adapted (local optima). 
Transition from a local optima to the global optima may be hindered
or forbidden because the population would have to pass through less
adaptive states to make the transition. So, natural selection only
works to bring populations to the nearest optimal point.
 
	Of all the mechanisms of evolution, natural selection
has the potential to change gene frequencies the fastest. It usually
acts to keep gene frequncies constant, however. This led a
famous evolutionist, George Williams, to say "Evolution proceeds
in spite of natural selection".


MECHANISMS OF EVOLUTION: GENETIC DRIFT

	Another important mechanism of evolution is genetic drift.
Drift is a binomial sampling error of the gene pool. What this
means is, the alleles that form the next generation are a sample
of the alleles in the current generation. 

	Organisms produce more gametes than are needed. Females 
produce many more eggs than are ever fertilized and males produce 
billions of sperm that never fertilize an egg. The alleles in this 
sample of gametes are likely to be slightly different than the alleles 
in the parental gene pool due solely to chance. Drift is a rather 
abstract concept to some; I will try to explain it via a somewhat 
simple analogy.

	Imagine you had a swimming pool full of one million marbles
(this will represent the parental gene pool), half are red and
half are blue. If you repeatedly picked ten marbles out, do you think 
you would get five red and five blue every time (assume you replaced
your sample to the pool each time)? If you picked one hundred 
marbles out, do you think you would get fifty red and fifty blue out
every time? In both cases the answer is no, some times the
frequency of red marbles in the sample would deviate from 0.50.
In the case of the 100 marble sample, the frequency of red
marbles would deviate much less, however.

	If, after picking out ten or one hundred marbles, you refilled
the pool with marbles at the frequency of that sample and repeated
the process over and over; what do you think would happen? What
would happen is that the frequency of red to blue would fluctuate
over time. Eventually, there would be only one color marble left
in the pool. This is roughly analogous to how genetic drift works.

	Both natural selection and genetic drift decrease genetic
variation. If they were the only mechanisms of evolution, populations
would eventually become genetically homogenous and further evolution 
would be impossible. There are, however, mechanisms that replace
variation depleted by selection and drift. These are discussed below.


MECHANISMS THAT INCREASE GENETIC VARIATION
------------------------------------------

MECHANISMS OF EVOLUTION: MUTATION

	A mutation is a change in a gene. There are many kinds of 
mutations. A point mutation is a mutation in which one "letter" of 
the genetic code is changed to another. Lengths of DNA can also be deleted
or inserted in a gene; these are also mutations. Finally, genes or parts 
of genes can become inverted or duplicated. 
	
	Mutation is a mechanism of evolution because it changes
allele frequencies very slightly. If an allele "A" mutates to
another allele "a", the frequency of "a" has increased from zero
to some small number (1/2N in a diploid population where N is the
effective population size). The allele "A" will also decrease
slightly in frequency. Evolution via mutation alone is very slow;
for the most part, mutation just supplies the raw material for
evolution -- genetic variation.

	Most, but not all, mutations are slightly deleterious or
neutral. The genome of most organisms (certainly all eukaryotes)
contains enormous amounts of junk sequences. In addition, even in
coding regions, many sites can undergo mutation and still maintain
there original meaning. In other words, the genetic code is
redundant. So, most mutations are neutral or nearly so; but, the
overwhelming majority of mutations that produce any detectable
phenotypic effect are deleterious. "Good" mutations, however, do
occur.

	One example of a beneficial mutation comes from the
mosquitoe _Culex_ _pipiens_. In this organism, a gene that was
involved with breaking down organophophates - common insecticide
ingrediants - became duplicated. Progeny of the organism with
this mutation quickly swept across the worldwide mosquitoe population.
There are numerous examples of insects developing resistance to
chemicals, especially DDT - which was once heavily used in this
country.
	
	Mutations occur at random with respect to their adaptive significance.
Organisms cannot "decide" that they need a mutation and have it occur.
The frequency of a mutation occuring is independent of the potential
effect it would have.
	
	 Recently, certain exceptions have been found to the above
"rule" in some bacteria (E. Coli). It appears that these organisms can
undergoe directed mutagenesis to repair "broken genes". The reversion
mutation, that restores the gene to normal functioning, occurs at a
several orders of magnitude more frequently when the gene is needed 
than when it isn't. It is unlikely, however, that this could occur in
multi-cellular organisms.
	
	 
MECHANISMS OF EVOLUTION: RECOMBINATION

	Recombination can be loosely thought of as gene shuffling.
Most organisms have linear chromosomes and their genes lie at specific
locations  (loci) along them (bacteria have circular chromosomes).
In most sexually reproducing organisms, there are two of each chromosome
type in every cell. For instance in humans, there are two chromosomes
number one (through 22 and two sex chromosomes), one inherited from
the mother, the other inherited from the father. When an organism
produces gametes, the gametes end up with only of each chromosome
per cell. Haploid gametes are produced from diploid cells by a
process called meiosis.

	In meiosis, homologous chromosomes line up. The DNA of the
chromosome is broken on both chromosomes in several places and rejoined
with the other strand. Later in meiosis, the two homologous chromosomes
are split in to two separate cells (gametes). But, because of
recombination, both of the chromosomes are a mix of alleles from the
mother and father.
 
	For example, lets say an organism has a chromosome with
three genes, (A,B and C -- in that order). Assume that at each of
these three loci there are at least two alleles. From the father,
the organism inherited a chrosome with the alleles A1, B1 and C1.
From the mother the organism inherited A2,B2 and C2 alleles. In
meiosis the two chrosomes would line up and the two A alleles
would line up, as would the B and C alleles. If recombination occured
between locus A and locus B, the resulting chrosomes in the two
gametes would be; one chromosome carrying A1, B2 and C2 alleles and
one chromosome carrying A2, B1 and C1 alleles.
	
	Real chromosomes carry many more than three genes and 
recombination occurs at many locations along the chromosome. The end
result is that the two homologous chromosomes have "shuffled" alleles.

	Recombination can occur not only between genes, but within 
genes as well. Recombination within a gene can form a new allele.
Recombination is a mechanism of evolution because it adds new alleles
and combinations of alleles to the gene pool. 

	A beneficial aspect of recombination is that beneficial
new alleles can be brought togethor onto the same chromosome, even
if the mutations originally occured in separate organisms.


MECHANISMS OF EVOLUTION: GENE FLOW

	Gene flow simply means new genes added to a population by
migration from another population. In some closely related species,
fertile hybrids can result from interspecific matings. These hybrids
can vector genes from species to species. 


SPECIATION

	Speciation is the process of a single species becoming
two or more distinct species. Many biologists feel speciation is 
key to understanding evolution. These biologists believe 
certain evolutionary phenomena apply only at speciation
and macroevolutionary change cannot occur without speciation.

	Other biologists think major evolutionary change can occur
without speciation. Changes between lineages are only an extension
of the changes within each lineage. In general, paleontologists
fall into the former category and geneticists in the latter. 


MODES OF SPECIATION

	Biologists recognise two types of speciation: allopatric and 
sympatric speciation. The two differ in geological distribution of
the populations in question.
	
	Allopatric speciation is thought to be the most common form
of speciation. It occurs when a population is split into two (or
more) subdivisions that organisms cannot bridge. The two populations
are geographically isolated; organisms from subdivision A can
only breed with organisms from subdivision A and B organisms can
only breed with B organisms. Eventually, the two populations gene
pools change (both independently) until they could not interbreed even
if they were brought back togethor. In other words they have speciated.

	Sympatric speciation occurs when two subpopulations become
reproductively isolated without first becoming geographically
isolated. Monophytophagous insects (insects that live on a
single host plant) provide a model for sympatric speciation.
If a group of insects switched host plants they would not breed
with other members of their species still living on their former
host plant. The two subpopulations could diverge and speciate.
Some biologists call sympatric speciation microallopatric speciation
to emphasize that the subpopulations are still physically separate
not at a geographic level, but on an ecological level.

	 Biologists know little about the genetic mechanisms of
speciation. Some think series of small changes in each subdivision
gradually lead to speciation; others think there may be a few key
genes that could change and confer reproductive isolation. One
famous biologist thinks most speciation events are caused by
changes in internal symbionts. Most doubt this, however.

	Populations of organisms are very complicated. It is
likely that there are many ways speciation can occur. Thus, all of
the above ideas may be correct, each in different circumstances.


OBSERVED SPECIATIONS

	It comes as a surprize to some to hear that speciation has
been observed. One of the commonly cited examples involves three
new species in the plant genus _Tragopogon_. 
		

ARE WE STILL EVOLVING?

	Yes, evolution is still occurring; all organisms continue
to adapt to their surroundings and "invent" new ways of better
competing with members of their own species. In addition, allele
frequencies are being changed by drift, mutation and gene flow
constantly. 


MACROEVOLUTION VS. MICROEVOLUTION

	Evolution is not linear progress. The popular notion that
evolution can be represented as progress from simple cells through
complex life forms to humans (the pinnacle of evolution), can be
traced to Linneaus' Scale of Nature. This view is incorrect.

	Evolution is better viewed as a branching tree or bush,
with the tips of each branch representing currently living species.
Populations or species of organisms split and become two or more
species as time goes on. No living organisms today are our ancestors.
Every species we see today is as fully modern as we are; each has it's
own unique evolutionary history. No extant species are "lower life
forms", atavistic stepping stones paving the road to humanity. 

	If you view evolution as a branching tree, it's best to view
it as one that has been severely pruned a few times in it's life.
The history of life on this earth includes many episodes of mass
extinction in which many taxa (groups of organisms) were wiped off
the face of the planet. Mass extinctions are followed by periods of
radiation where new species evolve to fill the empty niches left 
behind. It is probable that surviving a mass extinction is largely
a function of luck.

 	The most famous extinction occured at the boundry between
the Cretaceous and Tertiary Periods (the K/T Boundry). This extinction
eradicated the dinosaurs. Following this extinction the mammalian
radiation occured. 


SOME GOOD EVOLUTION TEXTS (IMHO)

	A good introductory text in evolutionary biology is:
Evolutionary Biology, by Douglas Futuyma, 1986, Sinauer, Sunderland,
Mass

	The text assumes some previous knowledge of biology, but
reviews most critical background material. It contains numerous
references to the primary literature.

	A good introductory text into population genetics, the
field that mathematically describes changes in the gene pool is:
Principles of Population Genetics, by Hartl and Clark , 1989,
Sinauer, Sunderland, Mass

	None of the math is very daunting (it's just an intro
text after all) but it's really critical (IMHO) to really
understanding what evolution is all about. And again, lots of
refs.

	A text that deals with the interface of molecular biology
and evolution is:
Fundamentals of Molecular Evolution, Li and Graur, 1991, Sinauer,
Sunderland, Mass

	A very concise introduction to this field.


Chris Colby 	---	 email: colby@bu-bio.bu.edu	---
"'My boy,' he said, 'you are descended from a long line of determined,
resourceful, microscopic tadpoles--champions every one.'"
 	--Kurt Vonnegut from "Galapagos"

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



speciation has been observed

In article <13040@milton.u.washington.edu> jespah@milton.u.washington.edu (Kathleen Hunt) writes:
>
>6)  "Though evolution has been studied for years, scientists have never
>observed a single species evolving".  So what?  Evolution has been studied
>for just over a hundred years.  Speciation takes *LONGER* than just over
>a hundred years.  If you just study evolution for about a hundred years, 
>all you would expect to see is microevolution within species, and perhaps
>the splitting off of subspecies who might be on the road to speciation.
>Scientists *have* observed both of these events.

	Creationists seem to want to define species evolving solely
in terms of speciation. Microevolutionary change doesn't seem to
fit their bill as evolution. In fact I just responded via email
today to some guy who didn't understand how the English moths
had anything to do with evolution. (To be fair, I'm not sure if
he was a creationist or just didn't get my point.) As Kathleen
pointed out, evolution has been observed (microevolutionary
changes and the beginnings of speciation). Most creationists (as
well as many evolutionists, perhaps) would be surprised to know that
speciation _has_ been observed!

	In the genus _Tragopogon_ (a plant genus consisting mostly
of diploids), two new species (_T._ _mirus_ and _T._ _miscellus_)
have evolved. This occured within the past 50-60 years. The new
species are allopolyploid descendents of two separate diploid
parent species. 

	Here's how it happened. The new species were formed when
one diploid species fertilized a different diploid species and
produced a tetraploid offspring. This tetraploid offspring could
not fertilize or be fertilized by either of it's two parent
species types. It is reproductively isolated, the definition of
a species (well, the most common definition, at least.) The
paper I have corresponding to this are great. One new species,
_T._ _mirus_ has arizen at least three separate times. 

	So, speciation _has_ been observed in case they bring up
that again. In fact, it happened instantly in this case. Plants
are amazingly plastic in regards to genetics, so it really isn't
all that surprizing that the first (as far as I know) observed
speciation event would be something like this in plants.

>Kathleen Hunt

Chris Colby
email: colby@bu-bio.bu.edu

REFERENCES:

Soltis and Soltis, 1989, [the title is mangled on my photocopy],
Amer. J. Bot. 76(8): 1119 - 1124

Roose and Gottlieb, 1976, Genetic and Biochemical Consequences
of Polyploidy in _Tragopogon_, Evolution 30: 818 - 830

(The Soltis paper looks at chlorplast DNA, the Roose paper
examines allozyme data. Both are, IMHO, fairly decent papers.)
------------------------------------------------------------


