From: colby@bu-bio.bu.edu (Chris Colby)
Newsgroups: talk.origins
Subject: microevolution (the rest of the post)
Date: 12 Nov 92 20:26:31 GMT
Organization: animal -- coelomate -- deuterostome

My previous post was somehow truncated; here is the rest of the post.

EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
*************************************** 

The following sections deal with evolution within a population or lineage 
-- this is called anagenesis. Several mechanisms can bring about 
anagenetic change. I have grouped them into two classes -- those that 
decrease genetic variation and those that increase it. 

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

MECHANISMS OF EVOLUTION: NATURAL SELECTION 

Natural selection is the only mechanism of adaptive evolution; it is 
defined as differential reproductive success of pre-existing classes of 
genetic variants in the gene pool. In other words, some genotypes are (on 
average) better at contributing their alleles to the subsequent 
generations gene pool. 

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. 

Natural selection allows organisms to adapt to their current environment 
only; it does not have any foresight. Structures or behaviors do not evolve 
for future utility. The organism must be, to some degree, adapted to its 
environment at each stage of its evolution. As the environment changes, 
new traits (new combinations of alleles) may be selected for. 

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 its past utility. It can evolve for one purpose, and be used 
later for another. A trait evolved for its current utility is called an 
adaptation; one that evolved for another utility is an exaptation. An 
example of an exaptation is a penguin's wing. Penguins evolved from 
flying ancestors; now 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. Genes are not the unit of selection (because their 
success depends on the organism's other genes as well); neither 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 its reproductive 
success. For this reason organisms do not perform any behaviors 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 any altruistic act.

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 "reciprocal altruism", an 
oxymoron if there ever was one. 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 some 
blood into the others mouth. Biologists have found that these bats form 
bonds with partners and help each other out when the other is needy. If 
a bat is found to be a "cheater", (i.e. he accepts blood when starving, but 
does not donate when his partner is) his partner will abandon him. 
Helping closely related organisms can appear altruistic; but this is also a 
selfish behavior. An organisms reproductive success (or fitness) has two 
components; direct fitness and indirect fitness. An organisms direct 
fitness is a measure of how many alleles it contributes to the subsequent 
generation's gene pool by reproducing. An organisms indirect fitness is a 
measure of how many alleles that are identical it's own it helps enter the 
gene pool. An organism's direct fitness plus its indirect fitness is called 
its inclusive fitness. Natural selection favors behaviors increase an 
organism's inclusive fitness. Closely related organisms share many of the 
same alleles. For example, in diploid species, siblings share at least 50% 
of their alleles -- the percent is higher if the parents are related. So, 
helping close relatives to reproduce gets an organisms own alleles better 
represented in the gene pool. The benefit of helping relatives increases 
dramatically in highly inbred species. In some cases, organisms will 
completely forgo reproducing and only help their relatives reproduce. 
Ants, for example, have sterile castes that only serve the queen and 
allow her to reproduce. The sterile workers are reproducing by proxy. 

Keep in mind that the words "selfish" and "altruistic" have connotations in 
everyday use that biologists do not intend. "Selfish" simply means 
behaving in an attempt to maximize ones' own inclusive fitness; 
"altruistic" means behaving in an attempt to increase anothers fitness 
without regard to ones' own. This is not meant to imply that organisms 
consciously understand their motives. 

The opportunity for natural selection to operate does not induce genetic 
variation to occur -- selection only distinguishes between existing 
variants. Variation is not possible along every imaginable axis, so all 
possible adaptive solutions are not open to populations. 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 -- this is 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 optimal 
structures or behaviors. Selection targets 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 
would 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 yield 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. 

SEXUAL SELECTION -- A SUBSET OF NATURAL SELECTION

Darwin, and others, noticed that in many species males developed 
prominent secondary sexual characteristics. A few oft cited examples are 
the peacock's tail, coloring and patterns in male birds in general, voice 
calls in frogs and flashes in fireflies. Many/most of these traits are a 
liability from the standpoint of survival, mainly because any ostentatious 
trait or noisy, attention-getting behavior will alert predators as well as 
potential mates. How then could natural selection favor these traits? 

Natural selection can be broken down into many components, of which 
survival is only one. Sexual attractiveness is a very important component 
of selection, so much so that biologists use the term sexual selection 
when they talk about this subset of natural selection 

Sexual selection occurs when the sexual attractiveness of a trait 
outweighs the liability incurred for survival. A male who lives a short 
time, but produces many offspring is much more successful than a long 
lived one that produces few. His genes will eventually dominate the gene 
pool of his species. In many species, especially polygynous species where 
only a few males monopolize all the females, sexual selection has caused 
pronounced sexual dimorphism. In these species males compete against 
other males for mates. The competition can be either direct (i.e. the 
largest males guarding their harems and fending off other males 
physically) or mediated by female choice.

In species where females chose, males compete by displaying striking 
phenotypic characteristics and/or performing elaborate courtship 
behaviors or both. The females then mate with the males that most 
interest them, usually the ones with the most outlandish displays. There 
are many competing theories as to why females are attracted to these 
displays. One model, the "good genes" model, states that the display 
indicates some component of male fitness. A "good genes" advocate 
would say that bright coloring in male birds indicates a lack of parasites. 
The females are cueing on some signal that is correlated with some other 
component of fitness.

Another model, proposed by Fisher, is called the "runaway sexual 
selection" model. In his model he proposes that females develop a 
preference for some male trait (without regards to fitness) and then 
mate with these males. The offspring of these matings will therefore 
have the genes for both the trait _and_ the preference for the trait. Note, 
these genes would be expressed in the males and females respectively. 
As a result, the process snowballs out of control until natural selection 
brings it into check. Here is an example to clarify.

Suppose that, due to some quirk of brain chemistry, female birds of one 
species prefer males with longer than average tail feathers. Males with 
longer than average feather will therefore produce more offspring than 
the short feathered males. In the next generation, the average tail 
feather length will increase. 

As the generations progress, feather length will increase because females 
do not prefer a specific length tail, but a longer than average tail. 
Eventually tail feather length will increase to the point were the liability 
to survival is matched by the sexual attractiveness of the trait and an 
equilibrium will be established. Note that in many exotic birds male 
plumage is often very showy and many species do in fact have males 
with greatly elongated feathers. In some cases these feathers are shed 
after the breeding season. 

A third model, called "the handicap hypothesis" states that males with the 
most costly displays (in terms of detriment to survival) are advertising 
the fact that, despite their "handicap", they still had what it took to 
survive. 

None of the above models are mutually exclusive. There are millions of 
sexually dimorphic species on this planet and the forms of sexual 
selection probably varies amongst them.

Natural selection is the only non-random mechanism of evolution. It is 
the only mechanism that causes adaptive evolution. The phrase "survival 
of the fittest" is often used synonymously with natural selection. IMHO, 
the phrase is both incomplete and misleading. For one thing, survival is 
only one component of selection -- and perhaps one of the less important 
ones in many populations. For example, in polygynous species, a number 
of males survive to reproductive age, but only a few ever mate. Males 
may differ little in their ability to survive, but greatly in their ability to 
attract mates -- the difference in reproductive success stems mainly 
from the latter consideration. Also, the word "fit" is often confused with 
physically fit. Fitness, in an evolutionary sense, is the average 
reproductive output of a class of genetic variants in a gene pool. Fit does 
not mean biggest, fastest or strongest -- sexiest might be closer to the 
truth in most animal species. 

Of all the mechanisms of evolution, natural selection has the potential to 
change gene frequencies the fastest. It usually acts to keep gene 
frequencies 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.

Drift is a rather abstract concept to some; I will try to explain it via an 
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.

In small populations, the rate of change in the frequency of alleles is 
greater than in large populations. However, the overall rate of genetic 
drift is independent of population size. If the mutation rate is constant, 
large and small populations lose alleles to drift at the same rate. This is 
because large populations will have more alleles in the gene pool, but 
they will lose them more slowly. Smaller populations will have fewer 
alleles, but these will quickly cycle through. This assumes that selection 
is not operating on any of these alleles.

Sharp drops in population size can greatly affect the gene pool. When a 
population crashes, the alleles in the surviving sample may not be 
representative of the pre-crash gene pool. This change in the gene pool is 
called the founder effect, because small populations of organisms that 
invade a new territory (founders) are subject to this. Many biologist feel 
the genetic changes brought about by founder effects may contribute to 
isolated populations developing reproductive isolation from their parent 
populations. 

Both natural selection and genetic drift decrease genetic variation. If they 
were the only mechanisms of evolution, populations would eventually 
become genetically homogeneous 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 the 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 mosquito _Culex_ 
_pipiens_. In this organism, a gene that was involved with breaking down 
organophosphates - common insecticide ingredients - became duplicated. 
Progeny of the organism with this mutation quickly swept across the 
worldwide mosquito population. There are numerous examples of insects 
developing resistance to chemicals, especially DDT - which was once 
heavily used in this country. And, most importantly, even though "good" 
mutations happen much less frequently than "bad" ones, organisms with 
"good" mutations thrive while organisms with "bad" ones die out. 
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 occurring is independent of the potential 
effect it would have, with one exception. 

A new class of mutation has recently been documented in bacteria and 
yeast. It appears that unicellular organisms can undergo directed 
mutagenesis to repair "broken genes". The reversion mutation that 
restores a gene to normal functioning occurs several orders of magnitude 
more frequently when the gene is needed than when it isn't. The 
mechanism of directed mutagenesis is unknown at this time, but it has 
been shown that it is under genetic control - - i.e. directed mutations are 
not errors like normal mutations are, the are actively created (or 
selectively retained) by the organism in response to the environment. 

The importance of directed mutagenesis is not yet known. Biologists have 
not yet studied if directed mutations can produce novel solutions to 
environmental challenges. It is also unknown if it can occur in multi-
cellular organisms with separate germ and somatic cell lines. In any case 
it appears that in at least a few instances, the potential for selection to 
operate induces adaptive genetic variation to occur. 

MECHANISMS OF EVOLUTION: RECOMBINATION 

Recombination can be loosely thought of as gene shuffling. Most 
organisms have linear chromosomes and their genes lie at specific 
location (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 that divide and become 
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 
chromosome with the alleles A1, B1 and C1. From the mother the 
organism inherited A2,B2 and C2 alleles. In meiosis the two 
chromosomes would line up and the two A alleles would line up, as 
would the B and C alleles. If recombination occurred between locus A 
and locus B, the resulting chromosomes 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 together onto the same chromosome, even if the mutations 
originally occurred 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. 

Gene flow between more distantly related species occurs infrequently. 
One interesting case of this involves genetic elements called P elements. 
In the genus _Drosophila_, P elements were transfered from some 
species in the _willistoni_ group, to _D. melanogaster_. These two species 
of fruit flies are distantly related and hybrids do not form. Their ranges 
do, however, overlap. The P elements were vectored into _D. 
melanogaster_ via a parasitic mite that targets both these species. This 
mite punctures the exoskeleton of the flies and feeds on the "juices". 
Material, including DNA, from one fly can be transfered to another when 
the mite feeds. Since P elements actively move in the genome (they are 
themselves parasites of DNA), one incorporated itself into the genome of 
a _melanogaster_ fly and subsequently spread through the species. 
Laboratory stocks of _melanogaster_ caught prior to the 1940's are 
devoid of P elements. All natural populations today harbor them.

OVERVIEW OF EVOLUTION WITHIN A LINEAGE (ANAGENESIS)
--------------------------------------------------- 

Evolution is a change in the gene pool of a population over time; it can 
occur due to several factors. Three mechanisms add new alleles to the 
gene pool: mutation, recombination and gene flow. Two mechanisms 
remove alleles, genetic drift and natural selection. Drift removes alleles 
randomly from the gene pool. Selection removes deleterious alleles from 
the gene pool. Natural selection can also increase the frequency of an 
allele (or combination of alleles) in the gene pool. Selection that weeds 
out harmful alleles is called negative selection. Selection that increases 
the frequency of helpful alleles is called positive, or sometimes positive 
Darwinian, selection. 

A new allele can also drift to high frequency. But, since the change in 
frequency of an allele each generation is random, nobody speaks of 
positive or negative drift. 

Except in rare cases of high gene flow, all new alleles enter the gene pool 
as a single copy. Most new alleles added to the gene pool are lost almost 
immediately due to drift or selection; only a small percent ever reach a 
high frequency in the population. Even most moderately beneficial 
alleles are lost due to drift when they appear. 

The fate of any given new allele depends a great deal on the organism it 
first appears in. This allele will be linked to the other alleles near it for 
many generations. A mutant allele can increase in frequency in the gene 
pool simply because it is linked to a beneficial allele at a nearby locus. 
This can occur even if the mutant allele is deleterious, although it must 
not be so deleterious as to offset the benefit of the other allele. Likewise 
a potentially beneficial new allele can be eliminated from the gene pool 
because it was linked to deleterious alleles when it first arose.

An allele "riding on the coat tails" of a beneficial allele is called a 
hitchhiker. Eventually, recombination will bring the two loci to linkage 
equilibrium. But, the more closely linked two alleles are, the longer the 
hitchhiking will last. 

The effects of selection and drift are coupled. Drift is intensified as 
selection pressures increase. This is because increased selection (i.e. a 
greater difference in reproductive success among organisms in a 
population) reduces the effective population size, the number of 
individuals contributing to the next generation's gene pool. 

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"