Download Figure 2. A pedigree for a half

1
INTRODUCTION
What is a population from a genetic perspective? (The quote is from Introduction to
Quantitative Genetics by D. S. Falconer, 1960, Ronald Press.)
"A population in the genetic sense, is not just a group of individuals, but a breeding group;
and the genetics of a population is concerned not only with the genetic constitution of the
individuals but also with the transmission of the genes from one generation to the next. In
the transmission the genotypes of the parents are broken down and a new set of genotypes
is constituted in the progeny, from the genes transmitted in the gametes. The genes carried
by the population thus have continuity from generation to generation, but the genotypes in
which they appear do not. The genetic constitution of a population, referring to the genes it
carries, is described by the array of gene frequencies, that is by specification of the alleles
present at every locus and the numbers or proportions of the different alleles at each
locus."
Goals of Population Genetics
1. To describe how the frequency of an allele which controls a trait changes over time
2. To analyze the factors that lead to changes in gene (allele) frequencies
3. To determine how changes in gene (allele) frequencies affect evolution and speciation
Why Study Populations and Gene Frequencies



Genetic variability necessary for evolutionary success
Measuring genetic variability at many loci can characterize a population
Variability of phenotypic and molecular traits are analyzed
Variability and Gene (or Allelic) Frequencies




Genetic data for a population can be expressed as gene or allelic frequencies
All genes have at least two alleles
Summation of all the allelic frequencies for a population can be considered a description of
the population
Frequencies can vary widely among the alleles in a population
Two populations of the same species do not have to have the same allelic
frequencies
2
HARD-WEINBERG PRINCIPLE



The unifying concept of population genetics
Named after the two scientists who simultaneously discovered the law . G.H. Hardy (the
English mathematician) and W. Weinberg (the German physician) independently worked out
the mathematical basis of population genetics in 1908 They were concerned with questions
like "what happens to the frequencies of alleles in a population over time?" and "would you
expect to see alleles disappear or become more frequent over time?"
The law predicts how gene frequencies will be transmitted from generation to generation
given a specific set of assumptions. Specifically,
If an infinitely large, random mating population is free from outside evolutionary forces (i.e.
mutation, migration and natural selection),
then the gene frequencies will not change over time, and the frequencies in the next generation
will be:
p2 for the AA genotype
2pq for the Aa genotype, and
q2 for the aa genotype
If the frequencies of allele A and a (of a biallelic locus) are p and q, then (p + q) = 1. This means (p
+ q)2 = 1 too. It is also correct that (p + q)2 = p2 + 2pq +q2 = 1. In this formula, p2 corresponds to the
frequency of homozygous genotype AA, q2 to aa, and 2pq to Aa. Since 'AA, Aa, aa' are the three
possible genotypes for a biallelic locus, the sum of their frequencies should be 1. In summary,
Hardy-Weinberg formula shows that:
p2 + 2pq + q2 = 1
AA ... Aa .. aa
Mathematical Derivation of the Hardy-Weinberg Law
If p equals the frequency of allele A in a population and q is the frequency of allele a in the same
population, union of gametes would occur with the following genotypic frequencies:
Female Gametes*
p
(A)
Male
Gametes q
(a)
*The
p
(A)
q
(a)
p2
(AA)
pq
(Aa)
pq
(Aa)
q2
(aa)
gamete and offspring genotypes are in parentheses.
If the observed frequencies do not show a significant difference from these expected frequencies,
the population is said to be in Hardy-Weinberg equilibrium (HWE). If not, there is a violation of the
following assumptions of the formula, and the population is not in HWE.
The assumptions of HWE
1. Population size is effectively infinite,
3
2. Mating is random in the population (the most common deviation results from inbreeding),
3. Males and females have similar allele frequencies,
4. There are no mutations and migrations affecting the allele frequencies in the population,
5. The genotypes have equal fitness, i.e., there is no selection.
The Hardy-Weinberg law suggests that as long as the assumptions are valid, allele and genotype
frequencies will not change in a population in successive generations. Thus, any deviation from
HWE may indicate:
1. Small population size results in random sampling errors and unpredictable genotype frequencies
(a real population's size is always finite and the frequency of an allele may fluctuate from
generation to generation due to chance events),
2. Assortative mating which may be positive (increases homozygosity; self-fertilization is an
extreme example) or negative (increases heterozygosity), or inbreeding which increases
homozygosity in the whole genome without changing the allele frequencies. Rare-male mating
advantage also tends to increase the frequency of the rare allele and heterozygosity for it (in
reality, random mating does not occur all the time),
3. A very high mutation rate in the population (typical mutation rates are < 10-5 per generation) or
massive migration from a genotypically different population interfering with the allele frequencies,
4. Selection of one or a combination of genotypes (selection may be negative or positive). Another
reason would be unequal transmission ratio of alternative alleles from parents to offspring (as in
mouse t-haplotypes).
The implications of the HWE
1. The allele frequencies remain constant from generation to generation. This means that
hereditary mechanism itself does not change allele frequencies. It is possible for one or more
assumptions of the equilibrium to be violated and still not produce deviations from the expected
frequencies that are large enough to be detected by the goodness of fit test,
2. When an allele is rare, there are many more heterozygotes than homozygotes for it. Thus, rare
alleles will be impossible to eliminate even if there is selection against homozygosity for them,
3. For populations in HWE, the proportion of heterozygotes is maximal when allele frequencies are
equal (p = q = 0.50),
4. An application of HWE is that when the frequency of an autosomal recessive disease (e.g.,
sickle cell disease, hereditary hemochromatosis, congenital adrenal hyperplasia) is known in a
population and unless there is reason to believe HWE does not hold in that population, the gene
frequency of the disease gene can be calculated (for an example visit the Cancer Genetics website
and choose Topics).
It has to be remembered that when HWE is tested, mathematical thinking is necessary. When the
population is found in equilibrium, it does not necessarily mean that all assumptions are valid since
there may be counterbalancing forces. Similarly, a significant deviance may be due to sampling
errors (including Wahlund effect, see below and Glossary), misclassification of genotypes,
measuring two or more systems as a single system, failure to detect rare alleles and the inclusion
of non-existent alleles. The Hardy-Weinberg laws rarely holds true in nature (otherwise evolution
would not occur). Organisms are subject to mutations, selective forces and they move about, or the
allele frequencies may be different in males and females. The gene frequencies are constantly
changing in a population, but the effects of these processes can be assessed by using the HardyWeinberg law as the starting point.
4
The direction of departure of observed from expected frequency cannot be used to infer the type
of selection acting on the locus even if it is known that selection is acting. If selection is operating,
the frequency of each genotype in the next generation will be determined by its relative fitness (W).
Relative fitness is a measure of the relative contribution that a genotype makes to the next
generation. It can be measured in terms of the intensity of selection (s), where W = 1 1]. The frequencies of each genotype after selection will be p 2 W AA, 2pq W Aa, and q2 W aa. The
highest fitness is always 1 and the others are estimated proportional to this. For example, in the
case of heterozygote advantage (or overdominance), the fitness of the heterozygous genotype
(Aa) is 1, and the fitnesses of the homozygous genotypes negatively selected are W AA = 1 - sAA
and W aa = 1 - saa. It can be shown mathematically that only in this case a stable polymorphism is
possible. Other selection forms, underdominance and directional selection, result in unstable
polymorphisms. The weighted average of the fitnesses of all genotypes is the mean witness. It is
important that genetic fitness is determined by both fertility and viability. This means that diseases
that are fatal to the bearer but do not reduce the number of progeny are not genetic lethals and do
not have reduced fitness (like the adult onset genetic diseases: Huntington's chorea, hereditary
hemochromatosis). The detection of selection is not easy because the impact on changes in allele
frequency occur very slowly and selective forces are not static (may even vary in one generation as
in antagonistic pleiotropy).
All discussions presented so far concerns a simple biallelic locus. In real life, however, there are
many loci which are multiallelic, and interacting with each other as well as with the environmental
factors. The Hardy-Weinberg principle is equally applicable to multiallelic loci but the mathematics
is slightly more complicated. For multigenic and multifactorial traits, which are mathematically
continuous as opposed to discrete, more complex techniques of quantitative genetics are required.
In a final note on the practical use of HWE, it has to be emphasized that its violation in daily life is
most frequently due to genotyping errors. Allelic misassignments, as frequently happens when
PCR-SSP method is used, sometimes due to allelic dropout are the most frequent causes of the
Hardy-Weinberg disequilibrium. When this is observed, the genotyping protocol should be
reviewed. In a case-control association study, it is of paramount importance that the control group
is in HWE to rule out any technical errors. The violation of HWE in the case group, however, may
be due to a real association.
Some concepts relevant to HWE
Wahlund effect: Reduction in observed heterozygosity (increased homozygosity) because of
considering pooled discrete subpopulations that do not interbreed as a single randomly mating unit.
When all subpopulations have the same gene frequencies, no variance among subpopulations
exists, and no Wahlund effect occurs (FST=0). Isolate breaking is the phenomenon that the average
homozygosity temporarily increases when subpopulations make contact and interbreed (this is due
to decrease in homozygotes). It is the opposite of Wahlund effect.
Let's examine the assumptions and conclusions in more detail starting first with the
assumptions.
1. Infinitely large population


No such population actually exists.
The effect that is of concern is genetic drift a problem in small populations.
Genetic drift - is a change in gene frequency that is the result of chance deviation from expected
genotypic frequencies.
2. Random mating
5
Random mating - matings in a population that occur in proportion to their allelic frequencies
For example, if the allelic frequencies in a population are:
f(M) = 0.91
f(N) = 0.09
then the probability of MM individuals occurring is 0.91 x 0.91 =0.828.
If a significant deviation occurred, then random mating did not happen in this population.
Point to remember about random mating: Within a population, random mating can be occurring
at some loci but not at others.
Examples of random mating loci - blood type, RFLP patterns
Examples of non-random mating loci - intelligence , physical stature
3. No evolutionary forces affecting the population
The principal forces are:



Mutation
Migration
Selection
Some loci in a population may be affected by these forces, and others may not; those loci not
affected by the forces can by analyzed as a Hardy-Weinberg population
From the table, it is clear that the prediction regarding genotypic frequencies after one generation
of random mating is correct. That is:
AA = p2; Aa = 2pq; and aa = q2
Deviations from Hardy-Weinberg
Deviations from expected values may be due to a variety of causes. If an excess of heterozygotes
is observed this may indicate the presence of overdominant selection or the occurance of
outbreeding. Alternatively, if an excess of homozygotes is detected it may be due to four factors.
First, the locus is under selection. Second, 'null alleles' may be present which are leading to a false
observation of excess homozygotes. Third, inbreeding may be common in the population. Fourth,
the presence of population substructure may lead to Wahlunds' effect. The likelihood of each of
these explanations must be assessed from additional data, such as demographic information, i.e.
population distribution.
The analysis of known pedigrees will aid in this regard. Examination of the inheritance of alleles will
allow for the identification of null alleles (Callen et al. 1993; Paetkau and Strobeck 1995;
Pemberton et al. 1995). Null alleles are usually caused by a mutation in the primer binding site
leading to an allele that will not amplify (Callen et al. 1993; Paetkau and Strobeck 1995).
Traditional linkage analysis can be performed to ensure that independent assortment of alleles at
different loci is occurring.
The analysis of a large number of loci will increase the power of detecting population substructure
because each locus will contain an independent history of the population depending on the
amounts of random drift, mutation, and migration that have occurred. If this information is not
independent (i.e. the loci are genetically linked) then the results may be biased towards the events
of a single linkage group since this information will be over represented in the combined data set. If
a substantial amount of pedigree information is not available, linkage analysis may not be useful. In
this situation an analysis of gamete phase equilibrium (Chakraborty 1984) can be performed to test
for the random association of alleles at different loci (e.g. Edwards et al. 1992).
6
Processes Causing Deviations from the Hardy-Weinberg Equilibrium
Deviations from expected values may be due to a variety of causes
1.
Mutation
.A very high mutation rate in the population (typical mutation rates are < 10 -5 per generation).
2. Genetic Drift
1. Small population size results in random sampling errors and unpredictable genotype frequencies
(a real population's size is always finite and the frequency of an allele may fluctuate from
generation to generation due to chance events),
3. Migration
3 or massive migration from a genotypically different population interfering with the allele
frequencies,
4. Nonrandom Mating
Assortative mating which may be positive (increases homozygosity; self-fertilization is an extreme
example) or negative (increases heterozygosity), or inbreeding which increases homozygosity in
the whole genome without changing the allele frequencies. Outbreeding causes an excess of
heterozygotes in the population. If inbreeding occurs there will be an excess of homozygotes. .
Rare-male mating advantage also tends to increase the frequency of the rare allele and
heterozygosity for it (in reality, random mating does not occur all the time). Another reason would
be unequal transmission ratio of alternative alleles from parents to offspring (as in mouse thaplotypes).
5. Selection
Selection of one or a combination of genotypes (selection may be negative or positive). If an
excess of heterozygotes is observed this may indicate the presence of overdominant selection
(heterozygote are selected for). Selection might also cause an excess of homozygotes if it is
against heterozygotes.
6. Wauhland Effect
The presence of population substructure may lead to Wahlunds' effect. Reduction in observed
heterozygosity (increased homozygosity) because of considering pooled discrete subpopulations
that do not interbreed as a single randomly mating unit. When all subpopulations have the same
gene frequencies, no variance among subpopulations exists, and no Wahlund effect occurs
(FST=0). Isolate breaking is the phenomenon that the average homozygosity temporarily increases
when subpopulations make contact and interbreed (this is due to decrease in homozygotes). It is
the opposite of Wahlund effect.
7. Null Alleles
'Null alleles' may be present which are leading to a false observation of excess homozygotes
7
CALCULATION OF GENOTYPIC AND ALLELE FREQUENCES
Deriving Genotypic Frequencies
Allele frequencies:
allele frequency: the proportion of a certain allele within a population.
Fact: allele frequency = gene frequency = gametic frequency
gene pool: the set of all alleles at all loci in a population.
Genotypic frequencies - describes the distribution of genotypes in a population
Example: blood type locus; two alleles , M or N, and three MM, MN, NN genotypes are possible
(the following data was collected from a single human population)
Genotye # of Individuals Genotypic Frequencies
MM
1787
MM=1787/6129=0.289
MN
3039
MN=3039/6129=0.50
NN
1303
NN=1303/6129=0.21
Total
6129
Deriving Gene (or Allelic) Frequencies
To determine the allelic frequencies we simply count the number of M or N alleles and divide by the
total number of alleles.
f(M) = [(2 x 1787) + 3039]/12,258 = 0.5395
f(N) = [(2 x 1303) + 3039]/12,258 = 0.4605
By convention one of the alleles is given the designation p and the other q. Also p + q = 1.
p=0.5395 and q=0.4605
Furthermore, a population is considered by population geneticists to be polymorphic if two alleles
are segregating and the frequency of the most frequent allele is less than or equal to 0.95
Deriving allelic frequencies from genotypic frequencies
The following example will illustrate how to calculate allelic frequencies from genotypic frequencies.
It will also demonstrate that two different populations from the same species do not have to have
the same allelic frequencies.
Percent
Allelic Frequencies
Location MM MN
NN
p
q
Greenland 83.5 15.6
0.90
0.913
0.087
31.2 51.5 17.30
0.569
0.431
Iceland
Let p=f(M) and q=f(N)
Thus, p=f(MM) + ½ f(MN) and q=f(NN) + ½ f(MN).
So the results of the above data are:
Greenland: p=0.835 + ½ (0.156)=0.913 and q=0.009 + ½ (0.156)=0.087
Iceland: p=0.312 + ½ (0.515)=0.569 and q=0.173 + ½ (0.515)=0.431.
Clearly the allelic frequencies vary between these populations.
Prediction regarding stability of gene frequencies
The following is a mathematical proof of the second prediction. To determine the allelic frequency,
they can be derived from the genotypic frequencies as shown above.
p = f(AA) + ½f(Aa) (substitute from the table on previous page)
8
p = p2 + ½(2pq)
(factor out p and divide)
p = p(p + q)
(p + q =1; therefore q =1 - p; make this substitution)
p = p [p + (1 - p)]
(subtract and multiply)
p=p
Examples:
Deriving Genotypic Frequencies
Genotypic frequencies - describes the distribution of genotypes in a population
Example: blood type locus; two alleles , M or N, and three MM, MN, NN genotypes are possible
(the following data was collected from a single human population)
Genotye # of Individuals Genotypic Frequencies
MM
1787
MM=1787/6129=0.289
MN
3039
MN=3039/6129=0.50
NN
1303
NN=1303/6129=0.21
Total
6129
Deriving Gene (or Allelic) Frequencies
To determine the allelic frequencies we simply count the number of M or N alleles and divide by the
total number of alleles.
f(M) = [(2 x 1787) + 3039]/12,258 = 0.5395
f(N) = [(2 x 1303) + 3039]/12,258 = 0.4605
By convention one of the alleles is given the designation p and the other q. Also p + q = 1.
p=0.5395 and q=0.4605
Furthermore, a population is considered by population geneticists to be polymorphic if two alleles
are segregating and the frequency of the most frequent allele is less than 0.99.
Deriving allelic frequencies from genotypic frequencies
The following example will illustrate how to calculate allelic frequencies from genotypic frequencies.
It will also demonstrate that two different populations from the same species do not have to have
the same allelic frequencies.
Percent
Location
MM MN
NN
p
q
0.90
0.913
0.087
31.2 51.5 17.30
0.569
0.431
Greenland 83.5 15.6
Iceland
Allelic Frequencies
Let p=f(M) and q=f(N)
Thus, p=f(MM) + ½ f(MN) and q=f(NN) + ½ f(MN).
So the results of the above data are:
Greenland: p=0.835 + ½ (0.156)=0.913 and q=0.009 + ½ (0.156)=0.087
Iceland: p=0.312 + ½ (0.515)=0.569 and q=0.173 + ½ (0.515)=0.431.
Clearly the allelic frequencies vary between these populations.
9
EXTENTIONS OF THE HARDY-WEINBERG PRINCIPLE
 One of the implicit assumptions of the HWP is that the parents of both sexes have the same
allelic frequencies
 In natural populations, female & male parents may have different genotypic/allelic
frequencies because of:
 Differential selection
 Gene flow or
 Sampling
Autosomal genes
These are genes located on non-sex chromosomes
Let pf and pm represent the frequencies of A1 in females and males, respectively, and qf and qm the
analogous frequencies of A2.
The frequencies of each type of zygote formed from a random union of gametes are
P = pfpm
H = pfqm + pmqf
Q = qfqm
10
A2 (qm)
Male gamets
(frequency)
A1(pm
)
Female gametes (frequency)
A1 (pf)
A2(qf)
A1A1(pfpm)
A1A2 (pmqf)
A1A2 (pfqm)
A2A2 (qfqm)
 When the allelic frequencies differ between the sexes there will be an excess of
heterozygotes over the H-W proportions
 The allelic frequency of A1 in progeny (p’) of both sexes is:
P’ = P + ½ H
= pmpf + ½(pmpf + pfqm)
= ½(pf + pm)
 In the next generation:
p’ = p’m = p’f
X-linked Genes or Genes in Haplo-diploid Organisms
 Genes on the X-chromosome in mammals and other organisms have the same pattern of
inheritance as all genes in haplo-diploid organisms, e.g hymenoptera
 If there is an initial difference in allelic frequencies in the two sexes, then equal frequencies
in the two sexes is achieved only over several generations
 In mammals, females are the homogametic (XX) sex and males the heterogametic (XY)
(situation is reversed for such organisms as birds & Lepidoptera)
 For the mammals and hymenoptera, which have haploid males and diploid females the
following analysis holds for all loci:
 For a gene polymorphic with two alleles, there are six mating types and five types of
progeny as shown in the table below:
11
Table 1.The genotypic frequencies after one generation of random mating for an X-linked
locus or haplo-diploid organism
Mating type
F
M
A1A1xA1
A1A1xA2
A1A2xA1
A1A2xA2
A2A2xA1
A2A2xA2
Total
Frequency
PfPm
PfQm
HfPm
HfQm
QfPm
QfQm
1
Female offspring
A1A1
A1A2
PfPm
__
-PfQm
A2A2
__
--
Male offspring
A1
A2
PfPm
-PfQm
--
½HfPm
--
½HfPm
½HfQm
QfPm
-½HfQm
½HfPm
½HfQm
pfqm
Pfqm + pmqf
QfQm
qfqm
pf
½HfPm
½HfQm
QfPm
QfQm
qf
 The male receive all their gamets from the their mothers, and females receive half their
gametes from their mother and half from their fathers
Pf, Hf and Qf refer to the frequencies of the diploid genotypes A1A1, A2A1, & A2A2 in females
and Pm and Qm refer to the frequencies of the haploid genotypes A1 and A2 in the males
 Frequencies of the A2 in the two sexes are:
qf = Qf + ½Hf
qm = Qm
 Because two-thirds of the alleles that are contributed to the next generation are in the
females and one third in the males, the mean allelic frequency is
q- = 2/3qf + 1/3qm
 The genotypic frequencies in the female progeny are calculated in the same manner as for
an autosomal locus.
 The allelic frequency of A2 in the female progeny is
q’ = ½ (qf + qm)
 The allelic frequency in males is equal to that of their female parents, because they obtain
all their genes from their mothers. Therefore, allelic frequency in males is simply:
q’m = qf
12
Systems
Two alleles
Codominance
Dominance
Three alleles
Codominance
Dominant series
ABO, null allele
N alleles
codominance
Dominant series
Number of
Phenotypic
classes
Number of parameters
Degrees of
freedom
3
2
1
1
1
0
6
3
4
2
2
2
3
0
1
n(n+1)/2
n
n-1
n-1
n(n-1)/2
0
13
Determining Gene Frequencies When Three Alleles Are Involved
 In the preceding examples the genes involved existed as two alleles.
 In many situations three or more alleles exist in a population.
 Consider the ABO blood groups with the three alleles IA,IB and IO and let p = IA frequency of
, q = frequency of IB, and r = frequency of IO. Then p+q+r = 1.
 The frequencies of the different blood groups are tabulated in Table below for a
randomly mating population with the gene frequencies p, q and r.
Phenotype
Genotype
A
IAIA,IAIO
B
IBIB,IBIO
AB
IA IB
O
IOIO
A
B
*Note that both I and I are dominant to IO
Frequency
p2 + 2pr
q2 + 2qr
2pq
r2
 The table above can be summarised as follows:
the population should consist of p2 (IAIA) + 2pr (IAIO) + q2 (IBIB) + 2qr (IBIO) + 2qp (IAIB) + r2
(IOIO)
 Estimation of Gene Frequencies:
 Calculation of the frequency of IO (r):
r2 = frequency of the O phenotype
r = square root of the frequency of the O phenotype
 Calculation of the frequency of IA (p):
2
p + 2pr + r2 = (p+r)2 = freq of A phenotype + freq of O phenotype
p+r = freq of A phenotype + freq of O phenotype
p
= p2 + 2pr + r2 – r
 Calculation of the frequency of IB (q):
This may be obtained most conveniently by subtraction, since p and r have already
been determined.
q = 1 – (p+r)
Example
A population of students taking a basic genetics class had their blood types classified in the ABO
blood group system. The following numbers were recorded:
Phenotype
Number
A
724
B
110
AB
20
O
763
Total
1617
(a) Calculate the genotypic frequencies.
(b) Estimate the allelic frequencies.
(c) Are the data in H-W proportions?
14
MATING SYSTEMS
 Refer the relative frequencies of the various genetic types of matings that occur in the
population in so far as these bear on transmission of particular genes
 There are three major categories of mating systems-random, assortative & inbreeding.
Random mating:
 Occurs when the probability of mating between individuals is independent of their genetic
constitution
 Matings between genotypes occur according to proportions in which the genotypes exist (to
obtain the probability of a given type of mating, we simply multiply the frequencies of the two
genotypes involved; the frequencies of all types of matings must add up to 1)
 Random mating may occur with respect to a given locus or trait, even though matings are
not random w.r.t some other loci or traits
Assortative mating:
 Occurs when choices of mates are affected by phenotypes rather than genotypes
 Individuals tend to choose mates because of their degree of resemblance to each other at
some locus
 Bias torward mating of like is called positive assortative mating whereas mating of with
unlike partners is negative assortative mating
 Does not, by itself, change allelic frequencies, but genotypic frequencies
 Assortative mating affects the genotypic frequencies of only those loci involved in
determining the phenotypes for mate selection (but inbreeding affect all loci the genome)
Positive assortative mating:
Occurs when mated pairs in a population are composed of individuals with similar
phenotypes more often than is expected by chance
Some assortative matings do not change allelic frequencies do affect genotypic frequencies
There appears to be positive-assortative mating in humans for many traits such as height,
skin colour & intelligence
Negative assortative mating:
Occurs when mated pairs in a population are composed of individuals with unlike
phenotypes more often than is expected by chance
Does not change allelic frequencies but does affect genotypic frequencies
Inbreeding:
 Matings between relatives more frequent than is expected from randomness
 Because relatives are genetically more similar than unrelated individuals, inbreeding
increases the frequency of homozygotes and decreases the frequency of
heterozygotes relative to the expectations of random mating (but does not change
allele frequencies)
 Most extreme type of inbreeding is selfing
 Genetic changes due to inbreeding occur at all loci
15
INBREEDING
 The genetic consequences of inbreeding are measure by the coefficient of inbreeding (F)
 F=the probability that the two homologous alleles in an individual are identical by descent
(they are both copies of one particular allele possessed by a common ancestor)
 F measure the increase in the frequency of homozygous individuals at a locus, it also
measures the increase in the proportion of homozygous loci per individual
 General formulae of the proportion of the three genotypes with inbreeding level f are:
P = p2 + Fpq
H = 2pq – 2Fpq
Q = q2 + Fpq
Where the first term is the H-W proportion and the second is the deviation
from that value
 The size and sign of the coefficient of inbreeding reflect the deviation from H-W proportions
of the genotypes such that when f is zero, the zygotes are in H-W proportions, and when F
is positive, there is deficiency in heterozygotes
 The most extreme type of inbreeding generally found, is self-fertilisation
 With only selfing in the population, there are just three mating types & they occur in the
relative proportions of the genotypes in the population
 Allowing for segregation in the heterozygotes, the proportions of the genotypes in the
progeny are:
P1 = Po + ¼Ho
H1 = ½Ho
Q1 = Qo + ¼Ho
16
Generally:
Pt = Po + ½[1 – (½)t]Ho
Ht = (½)tHo
Qt = Qo + ½[1 – (½)t]Ho
where Pt, Ht & Qt are genotypic frequencies of A1A1, A2A1 &
A2A2 after t generations of selfing, Po, Ho & Qo are initial
frequencies of the genotype
¼ A 1A 1
½ A 1A 2
¼ A 2A 2
all
¼
½
3/8 A1A1
all
¼ A 1A 2
¼
7/16A1A1
All
¼
A1A1
¼
½
all
3/8 A2A2
¼
all
2/16A1A2
½
¼
7/16A2A2
all
A1A2
A2A2
Figure 1. Results of selfing in a population that started with ¼ A1A1
½ A 1A 2 , & ¼ A 2A 2
Estimating inbreeding coefficient: chain counting technique:
 A straight forward approach used to calculate f
 A chain for a given common ancestor starts with one parent of the
inbred individual, goes up to the common ancestor, and comes back
down to the other parent
CA
½
17
½
W
V
½
½
X
Y
½
½
Z
Figure 2. A pedigree for a half-cousin mating
In Figure 2, the chain would be X-V-CA-W-Y for offspring Z
The number of individuals in the chain, N, can be used in the following
formula to calculate the expected inbreeding coefficient due to the
presence of this common ancestor, so that:
F = (½)N
where N = number of individuals in the chain
**if you include the offspring in the chain, you subtract 1 to get N
if there is more than one common ancestor, then the inbreeding coefficient is the sum of the f
values for the different chains:
F = ∑m (½ )Ni
Where m = number of common ancestors & Ni =
number
individuals in chain i
Effect
of of
Inbreeding:
 Breeders try to achieve homogeneity in breeds by inbreeding
individuals with favourable traits
18
 Inbreeding usually leads to a reduction in fitness, owing to
deterioration in important attributes-e.g fertility, vigour & resistance to
disease-a phenomenon called inbreeding depression
 Inbreeding depression results from homozygosis for deleterious
recessive alleles
 The effects of inbreeding depression can be counteracted by
crossing independent inbred lines (the hybrids usually show a
marked increase in fitness called hybrid vigour or heterosis)
Independent inbred lines are likely to become homozygous for different deleterious
recessive alleles. Intercrossing two inbred lines may retain homogeneity for the
artificially selected traits while making the deleterious alleles heterozygous
19
SPECIATION
The Species Concept & Speciation
The Species Concept
I. What are species concepts for?
Individual organisms can usually be recognized, but the larger units we use to describe the diversity
of life, such as populations, subspecies, or species are not so easily identifiable. Taxonomists further
group species into genera, families, orders, and kingdoms etc., while ecologists group species into
higher structures such as communities and ecosystems. The justification for these group terms is
utility, rather than intrinsic naturalness, but as far as possible we attempt to delimit groups of
organisms along natural fault lines, so that approximately the same groupings can be recovered by
independent observers. However there will be a virtually infinite number of different, albeit nested,
ways of classifying the same organisms, given that life has evolved hierarchically.
Darwin (1859) felt that species were similar in kind to groupings at lower and higher taxonomic levels;
in contrast, most recent authors suggest that species are more objectively identifiable, and thus more
"real" than, say, populations or genera. Much of ecology and biodiversity today appears to depend on
the idea that the species is the fundamental taxon, and these fields could be undermined if, say,
genera, or subspecies had the same logical status.
Species concepts originate in taxonomy, where the species is "the basic rank of classification"
according to the International Commission of Zoological Nomenclature. The main use of species in
taxonomy and derivative sciences is to order and retrieve information on individual specimens in
collections or data banks. In evolution, we would like to delimit a particular kind of evolution,
speciation, which produces a result qualitatively different from within-population evolution, although it
may of course involve the same processes. In ecology, the species is a group of individuals within which
variation can often be ignored for the purposes of studying local populations or communities, so that
species can compete, for example, while subspecies or genera are not usually considered in this light.
In biodiversity and conservation studies, and in environmental legislation, species are important as
units, which we would like to be able to count both regionally or globally.
It would be enormously helpful if a single definition of species could satisfy all these uses, but a
generally accepted definition has yet to be found, and indeed is believed by some to be an
impossibility. A unitary definition should be possible, however, if species are "real", objectively
definable and fundamental biological units. Conversely, even if species have no greater objectivity
than other taxa, unitary nominalistic guidelines for defining species might still be found, perhaps
after much diplomacy, via international agreement among biologists; after all, if we can adopt metres
and kilograms, we should be able to agree on units of biodiversity in a similar way. In either case,
knowledge of the full gamut of today's competing solutions to the species concept problem will
probably be necessary for a universal species definition to be found. This article reviews the
proposals currently on the table, and their usefulness in ecology, evolution, and conservation.




Recall that Darwin argued that "species" are not "real" entities in nature
Since Darwin, there has been considerable debate about the definition of species
There are three general views:
Species are real and the unit that evolves [realism]
20











Species are not real and it is breeding populations (demes) that evolve (hence, no
definition is really required) [nominalism]
Species are not real but they are the theoretical unit of evolution (hence, a definition
is required) [nominalism]
Numerous definitions have been suggested
Some (such as one offered by numerical taxonomists (pheneticists)) use a trait
comparison technique
Five are currently defended and employed:
Phenetic (morphospecies) concept
Biological species concept
Recognition species concept
Ecological species concept
Cladistic (phylogenetic) species concept
Each has its strengths and weaknesses
The Phenetic Species Concept
Strengths:



Is in fact the way we recognize species differences
Works well for sexual and asexual organisms
Applies well to past species
Weaknesses:

Does not connect with genetics
Biological Species Concept
For a long time, ornithologists almost universally used the biological species concept (BSC). This
definition of "species" is based on species being reproductively isolated from each other. Under this
definition, distinctive geographical forms of the same "kind" of bird are usually lumped as one species.
This is because the geographic forms interbreed (or probably would, if they had the chance) where
they intersect on the map. The problem with this definition is slightly different, geographicallyisolated, forms rarely present us with "tests" of their willingness to interbreed. According to to
adherents of the BSC, if the forms are only slightly different, they would probably interbreed if
given the chance. Thus, they should be considered the same species. However, proponents of the BSC
also say that because two things rarely interbreed (and produce viable hybrids) doesn't mean they
belong to the same species. For example, wolves and coyotes (there's no educated disagreement that
these are different species) can mate and have fertile and healthy pups.
Strengths:



Fits within population genetics
Gives an unambiguous empirical criteria
It provides an important conceptual framework for speciation
21
Weaknesses:


"ring" species
Only really applicable to the present (paleobiological work on evolution cannot use this
concept)


No evolutionary dimension
Recognition Species Concept
Strengths:



Fits within population genetics (it is based on reproduction)
Complements the biological species concept
Mate recognition can be more easily determined than ability to breed (especially in
non-living species)
Weaknesses:


Isolating mechanisms which lead to speciation are more difficult to conceptualize
No evolutionary dimension
Ecological Species Concept
Strengths:

It corresponds to the findings of a considerable body of ecological research which
suggests that species occupy "adaptive zones" which are determined and reinforced by
the resources exploited and the habitats occupied
Weaknesses:



Is only loosely connected to genetics
Is rigidly tied to ecological niches determining species (consider that even in different
life stages an organism will occupy different niches). Perhaps the best that can be said
is that ecological processes influence phenetic and genetic aspects of species
Has no evolutionary dimension
The Cladistic (Phylogenetic) Species Concept
The phylogenetic species concept (PSC) says that diagnosable geographic forms of the same basic
"kind" of bird should be treated as distinct species. This is because these forms have evolved
separately, and have unique evolutionary histories. The PSC is gaining favor because there is no worry
about whether slightly-different geeographic forms might interbreed. If they don't, for whatever
reason (for example, migration to different breeding areas), they are full species. Obviously, the PSC
22
is less restrictive than the the BSC. There would be many more species of birds under the PSC than
under the BSC.
The debate over how species should be defined will continue as long as people are allowed to think
freely. Perhaps the argument is rhetorical, because every kind of organism presents a unique situation.
It is possiblew that neither definition can be applied consistently in nature.
Strengths:



A clear evolutionary dimension
Establishing phylogenies and, hence, branching points uses micro (e.g., DNA) and macro
characteristics.
Is richest concept in palaeontological study
Weaknesses:


Only a very small number of lineages have been uncovered given the detail required for
this approach
Disconnected from population genetics
Pluralists approach: combining concepts





A word about definitions (necessary and sufficient condition definition)
Usually unattainable
In practice, species identification is usually phenetic
The most common operational definition is the biological species concept
The recognition species concept is the next most useful
Species and Speciation
Species are distinctly different kinds of organisms. Birds of one species are, under most
circumstances, incapable of interbreeding with individuals of other species. Indeed, the "biological
species concept" centers on this inability to successfully hybridize, and is what most biologists mean
by "distinctly different." That concept works very well when two different kinds of birds live in the
same area. For example, Townsend's and Yellow-rumped Warblers are clearly distinct kinds because
their breeding ranges overlap, but they do not mate with one another. If they did, they might produce
hybrid young, which in turn could "backcross" to the parental types, and (eventually) this process
could cause the two kinds of warblers to lose their distinctness.
On the other hand, when relatively similar populations occur in different areas, it is much more
difficult to decide whether to classify them as different species. For example, the western
populations of the Yellow-rumped Warbler (which have yellow throats) were previously considered a
species, Audubon's Warbler, distinct from the eastern Myrtle Warblers (which have white throats),
largely because of differences in appearance. Then it was discovered that the breeding ranges of
Audubon's and Myrtle Warblers overlap broadly in a band from southeastern Alaska through central
British Columbia to southern Alberta, and that the two "species" hybridize freely within this area.
The forms intergrade, and taxonomists now consider them to be subspecies of a single species, the
23
Yellow-rumped Warbler. Subspecies are simply populations or sets of populations within a species
that are sufficiently distinct that taxonomists have found it convenient to formally name them, but
not distinct enough to prevent hybridization where two populations come into contact.
Judgments about whether two populations should be considered different species or just different
subspecies may be very difficult to make. For instance, in some areas where populations of Redbreasted and Yellow-bellied Sapsuckers meet, they hybridize, whereas in other areas of overlap they
do not. As a result, ornithologists do not agree upon whether to consider the two forms as separate
species or as subspecies of the same species. In situations where differentiated, but clearly closely
related forms replace one another geographically, taxonomists often consider them to be separate
species within a superspecies.
These complications are a natural result of applying a hierarchical taxonomic system, developed a
century before Darwin, to the results of a continuous evolutionary process. Geographic variation -birds showing different characteristics in different areas -- is inevitable among the populations of all
species with extensive breeding distributions. It is largely the result of populations responding to
different pressures of natural selection in different habitats. If populations of a single bird species
become geographically isolated, those different selection pressures may, given enough time, cause the
populations to differentiate sufficiently to prevent interbreeding if contact is reestablished. In
nature, degrees of differentiation and of abilities to hybridize fall along a continuum, so one finds
what is expected in an evolving avifauna -- some populations intermediate between subspecies and
species, populations (members of superspecies) that have differentiated to the point where they will
not hybridize but have not yet regained full contact, and populations so distinct that they can be
recognized as full species whether or not they occur together. As an example of the latter, the
Three-toed Woodpecker and the Red-cockaded Woodpecker have separate distributions, but clearly
are separate species.
Biologists differ on the details of both the definition of species and the mechanisms of speciation,
and our treatment is necessarily simplified. Changing views of the specific status of North American
birds can be an annoyance, since they may result in new names for familiar birds. But changes reflect
increasing knowledge of the biology of the birds involved, and by careful observations of hybrids,
mating pairs, and species distributions, you should be able to add to that knowledge.

Natural Selection
The characteristics of birds result from evolutionary processes, the most important process being
natural selection. It was Charles Darwin who first pointed out that just as stockmen shaped their
herds by selecting which animals would be allowed to breed, so too nature shaped all organisms by
"selecting" the progenitors of the next generation. Darwin's thinking had been influenced by the
great economist Thomas Malthus, who emphasized the capacity of people and other organisms to
multiply their numbers much more rapidly than their means of subsistence. Darwin realized,
therefore, that most individuals born of any species could not have survived long enough to reproduce.
He concluded that those that had been able to survive and reproduce had not been a random sample
of those born, but rather variants especially suited to their environments.
Darwin knew nothing about genetics; the work of Gregor Mendel remained undiscovered until early in
this century -- almost 50 years after the publication of Origin of Species. We now know that variation
among individuals is due to both environmental and hereditary factors. The latter result from the
joint action of mutation (changes in the genes themselves) and, in birds and all other sexually
24
reproducing organisms, recombination. Basically, recombination is the reshuffling of genes that
occurs during the process of sperm and egg production. Because of mutation and recombination, each
individual bird is genetically unique -- that is, each has a unique "genotype." Geneticists typically
examine only a small portion of the genetic endowment of an individual, such as the two pairs of genes
(out of many thousands) that cause a cock's comb to be single and large or pea-shaped and small. Thus
one might speak of the "single-comb" and "pea-comb" genotypes.
In modem evolutionary genetics, natural selection is defined as the differential reproduction of
genotypes (individuals of some genotypes have more offspring than those of others). Natural selection
would be occurring if, in a population of jungle fowl (the wild progenitors of chickens), single-comb
genotypes were more reproductively successful than pea-comb genotypes. Note that the emphasis is
not on survival (as it was in Herbert Spencer's famous phrase "survival of the fittest") but on
reproduction. Thus while selection can occur because some individuals do not survive long enough to
reproduce, sterile individuals also lack "fitness" in an evolutionary sense, as do individuals unable to
find mates. We emphasize that fitness here refers only to the reproductive success of a kind of
individual -- if big, handsome, male grouse madly displaying on a lek turn out to have fewer offspring
than smaller, drab males that skulk in the bushes and waylay females, it is the wimpy males that are
more fit.
Natural selection provides a context in which to view the physical and behavioral characteristics of
birds. Whether it is the large size of a female Harris' Hawk in comparison with the male, the
territorial behavior of a sandpiper, the bill shape of a Clark's Nutcracker, or the coloniality of a
Common Murre, a key question to ask is "how did natural selection manage that?
25
What is a "species"?
This question is important. The scientific system of naming "kinds" of plants and animals
revolves around the species level. A scientific name, such as Turdus migratorius (American
robin), is always written in italics, and contains first the genus and then the species names. A
name like Pinicola enucleator californica (California pine grosbeak) also contains a subspecies
name (= californica). For many species (ones that vary in size and/or color over geography),
subspecies names are used for distinctive geographic forms.
For a long time, ornithologists almost universally used the biological species concept (BSC). This
definition of "species" is based on species being reproductively isolated from each other. Under this
definition, distinctive geographical forms of the same "kind" of bird are usually lumped as one species.
This is because the geographic forms interbreed (or probably would, if they had the chance) where
they intersect on the map. The problem with this definition is slightly different, geographicallyisolated, forms rarely present us with "tests" of their willingness to interbreed. According to to
adherents of the BSC, if the forms are only slightly different, they would probably interbreed if
given the chance. Thus, they should be considered the same species. However, proponents of the BSC
also say that because two things rarely interbreed (and produce viable hybrids) doesn't mean they
belong to the same species. For example, wolves and coyotes (there's no educated disagreement that
these are different species) can mate and have fertile and healthy pups.
The phylogenetic species concept (PSC) says that diagnosable geographic forms of the same basic
"kind" of bird should be treated as distinct species. This is because these forms have evolved
separately, and have unique evolutionary histories. The PSC is gaining favor because there is no worry
about whether slightly-different geeographic forms might interbreed. If they don't, for whatever
reason (for example, migration to different breeding areas), they are full species. Obviously, the PSC
is less restrictive than the the BSC. There would be many more species of birds under the PSC than
under the BSC.
The debate over how species should be defined will continue as long as people are allowed to think
freely. Perhaps the argument is rhetorical, because every kind of organism presents a unique situation.
It is possiblew that neither definition can be applied consistently in nature.
Are "types" of red crossbill different species?
The different types of red crossbill, Loxia curvirostra, are separate biological species. This
is the more restrictive concept, so I'm not dividing crossbills simply upon changing to the
more liberal PSC. Crossbill species demonstrate their reproductively isolated status in the
many areas in which different forms overlap. Individuals only mate with their own kind, even
though they have plenty of chances to interact socially with other kinds. The different forms
cannot be called subspecies, because their geographic ranges overlap.
The different kinds of crossbills are also phylogenetic species. They are geneological/evolutionary
units. They should not be lumped into one species becuase they have diagnostic vocal and
morphological differences.
SPECIES ARE CRUCIAL IN MANY BIODIVERSITY ISSUES: much of conservation, biodiversity
studies, ecology, and legislation concerns this taxonomic level. It may therefore seem rather
surprising that biologists have failed to agree on a single species concept. The disagreement means
26
that species counts could easily differ by an order of magnitude or more when the same data is
examined by different taxonomies. This article explores the controversy on species concepts and its
implications for evolution and conservation.
I. What are species concepts for?
Individual organisms can usually be recognized, but the larger units we use to describe the diversity
of life, such as populations, subspecies, or species are not so easily identifiable. Taxonomists further
group species into genera, families, orders, and kingdoms etc., while ecologists group species into
higher structures such as communities and ecosystems. The justification for these group terms is
utility, rather than intrinsic naturalness, but as far as possible we attempt to delimit groups of
organisms along natural fault lines, so that approximately the same groupings can be recovered by
independent observers. However there will be a virtually infinite number of different, albeit nested,
ways of classifying the same organisms, given that life has evolved hierarchically.
Darwin (1859) felt that species were similar in kind to groupings at lower and higher taxonomic levels;
in contrast, most recent authors suggest that species are more objectively identifiable, and thus more
"real" than, say, populations or genera. Much of ecology and biodiversity today appears to depend on
the idea that the species is the fundamental taxon, and these fields could be undermined if, say,
genera, or subspecies had the same logical status.
Species concepts originate in taxonomy, where the species is "the basic rank of classification"
according to the International Commission of Zoological Nomenclature. The main use of species in
taxonomy and derivative sciences is to order and retrieve information on individual specimens in
collections or data banks. In evolution, we would like to delimit a particular kind of evolution,
speciation, which produces a result qualitatively different from within-population evolution, although it
may of course involve the same processes. In ecology, the species is a group of individuals within which
variation can often be ignored for the purposes of studying local populations or communities, so that
species can compete, for example, while subspecies or genera are not usually considered in this light.
In biodiversity and conservation studies, and in environmental legislation, species are important as
units which we would like to be able to count both regionally or globally.
It would be enormously helpful if a single definition of species could satisfy all these uses, but a
generally accepted definition has yet to be found, and indeed is believed by some to be an
impossibility. A unitary definition should be possible, however, if species are "real", objectively
definable and fundamental biological units. Conversely, even if species have no greater objectivity
than other taxa, unitary nominalistic guidelines for definining species might still be found, perhaps
after much diplomacy, via international agreement among biologists; after all, if we can adopt metres
and kilograms, we should be able to agree on units of biodiversity in a similar way. In either case,
knowledge of the full gamut of today's competing solutions to the species concept problem will
probably be necessary for a universal species definition to be found. This article reviews the
proposals currently on the table, and their usefulness in ecology, evolution, and conservation.
II. Statement of bias
I am of the opinion that the "reality" of species in evolution, and in ecological and biodiversity studies
over large areas has been overestimated. In contrast, it is clear to any naturalist that species are
usually somewhat objectively definable in local communities. It is my belief that confusion over
species concepts has been caused by scientists not only attempting to extend this local objectivity of
species over space and evolutionary time, but also arguing fruitlessly among themselves as to the
nature of the important reality that underlies this illusory spatiotemporal objectivity. To me,
agreement on a unified species-level taxonomy is possible, but will be forthcoming only if we accept
that species lack
27
Reproductive Isolation and Speciation


Cladogenesis occurs because reproductive-isolating mechanisms prevents two subpopulations from interbreeding.
Different types of barriers are responsible for different types of speciation
Allopatric speciation - the isolation of one portion of the population by some physical barrier that
renders the new population incapable of reproducing offspring with the original population
Example: Tomato species
Parapatric speciation - a sub-population becoming established in a new ecological niche not
previously occupied by the species; this has occurred for some annual plants
Sympatric speciation - a subpopulation that occupies the same niche as the remainder of the
species develops a unique mutation that prevents it from mating with the original population; the
new mutation provides the new species an ecological advantage which permits its establishment
as the primary species in the same niche.
Example: Spartina townsendii
28
Allopatric speciation
From Wikipedia, the free encyclopedia
Jump to: navigation, search
Allopatric speciation, also known as geographic speciation, occurs when populations physically isolated
by an extrinsic barrier evolve intrinsic (genetic) reproductive isolation such that if the barrier between the
populations breaks down, individuals of the two populations can no longer interbreed. Although there is
some debate about the frequency of other types of speciation (such as sympatric speciation and parapatric
speciation), all evolutionary biologists agree that allopatry is a common way that new species arise.
The evolution of reproductive isolation is generally thought to be an incidental by-product of genetic
divergence of other traits, particularly adaptive changes that evolve through natural selection in response to
different environmental conditions in separate geographic areas. Ernst Mayr, an evolutionary biologist and
famous proponent of allopatric speciation, hypothesized that adaptive genetic changes that accumulate
between allopatric populations cause negative epistasis in hybrids, resulting in sterility or inviability.
Allopatric speciation may occur when a species is subdivided into two large populations (vicariant or
dichopatric speciation) or when a small number of individuals colonize a novel habitat on the periphery of a
species' geographic range (peripatric speciation). Because natural selection is a powerful evolutionary force
in large populations, adaptive evolution likely causes the genetic changes that results in reproductive
isolation in vicariant speciation. In peripatric specation, however, the genetic changes that are thought to
occur within the peripheral isolate are more controversial. Proponents of peripatric speciation contend that
small population size in the peripheral isolate allows genetic drift, which can be a more powerful force than
natural selection in small populations, to deconstruct complex genotypes, allowing the creation of novel
gene combinations.
Perhaps the most famous example of allopatric speciation is Darwin's Galápagos Finches.
29
Parapatric speciation
From Wikipedia, the free encyclopedia
Jump to: navigation, search
Parapatric speciation is a form of speciation in which the evolution of reproductive isolating mechanisms
occurs when a population enters a new niche or habitat within the range of the parent species. Generally,
this occurs when there has been a drastic change to the environment within the original species' habitat. An
example of this is the grass Anthoxanthum, which has been known to undergo parapatric speciation in
such cases as mine contamination of an area. Selection for resistance/tolerance to certain metals occurs.
Flowering time generally changes (in an attempt at character displacement-- strong selection against
interbreeding-- as the hybrids are generally ill-suited to the environment) and often plants will become selfpollinating.
In parapatric speciation there is no specific extrinsic barrier to gene flow. The population is continuous, but
nonetheless, the population does not mate randomly. Individuals are more likely to mate with their
geographic neighbors than with individuals in a different part of the population’s range. In this mode,
divergence may happen because of reduced gene flow within the population and varying selection
pressures across the population’s range.
Sympatric speciation
From Wikipedia, the free encyclopedia
Jump to: navigation, search
Sympatry is one of three theoretical models for the phenomenon of speciation. In complete contrast to
allopatry, species undergoing sympatric speciation are not geographically isolated by, for example, a
mountain or a river. The speciating populations share the same territory.
A debate almost since the beginning of popular evolutionary thought, sympatric speciation is still a highly
contentious issue. By 1980 the theory was largely unfavourable given the devoid of empirical evidence
available and more critically the required conditions which must be met. One of the foremost thinkers on
evolution Ernst Mayr completely rejected it outright creating a climate of hostility towards the theory. Since
the 1980’s a more progressive ideology has been adopted, well documented empirical evidence, while still
debatable exists and the development of sophisticated theories incorporating multilocus genetics have been
produced.
A number of models have been proposed to account for this mode of speciation. The most popular,
disruptive speciation, was first put forward by John Maynard Smith in 1962. Smith suggested that
homozygous individuals may, under particular environmental conditions, have a greater fitness than those
with alleles heterozygous for a certain trait. Under the mechanism of natural selection, therefore,
homozygosity would be favoured over heterozygosity, eventually leading to speciation.
Rhagoletis pomonella (Apple maggot) may be currently undergoing sympatric speciation. The apple feeding
race of this species appears to have spontaneously emerged from the hawthorn feeding race in the 1800 1850 AD time frame after apples were introduced into North America. The apple feeding race does not now
normally feed on hawthorns and the hawthorn feeding race does not now normally feed on apples. This may
be an early step towards the emergence of a new species. [1]
Sympatric speciation events are most common in plants when they double or triple the number of
chromosomes, resulting in a condition called polyploidy. See also: adaptive radiation
Polyploidy
From Wikipedia, the free encyclopedia
Jump to: navigation, search
Polyploidy is the condition of cells or organisms that contain more than two copies of each of
their chromosomes. Where an organism is normally diploid, some spontaneous aberrations may
occur which are usually caused by a hampered cell division. Polyploid types are termed
30
corresponding to the number of chromosome sets in the nucleus: triploid (three sets; 3n),
tetraploid (four sets; 4n), pentaploid (five sets; 5n), hexaploid (six sets; 6n) and so on. A haploid
(n) only has one set of chromosomes. Haploidy may also occur as a normal stage in an
organism's life cycle as in ferns and fungi. In some instances not all the chromosomes are
duplicated and the condition is called
Examples
Polyploidy occurs in some animals, such as goldfish, but is especially common among ferns and flowering
plants, including both wild and cultivated species. Wheat, for example, after millennia of hybridization and
modification by humans, has strains that are diploid (two sets of chromosomes), tetraploid (four sets of
chromosomes) with the common name of durum or macaroni wheat, and hexaploid (six sets of
chromosomes) with the common name of bread wheat. Many agriculturally important plants of the genus
Brassica are also tetraploids; their relationship is described by the Triangle of U.
Examples in animals are more common in the ‘lower’ forms such as flatworms, leeches, and brine shrimp.
Reproduction is often by parthenogenesis since polyploid animals are often sterile. Polyploid salamanders
and lizards are also quite common and parthenogenetic. Rare instances of polyploid mammals are known,
but most often result in prenatal death.
Polyploidy can be induced in cell culture by some chemicals: the best known is colchicine, which can result
in chromosome doubling, though its use may have other less obvious consequences as well.
In plant breeding, the induction of polyploids is a common technique to overcome the sterility of a hybrid
species. Triticale is the hybrid of wheat (Triticum turgidum) and rye (Secale cereale). It combines soughtafter characteristics of the parents, but the initial hybrids are sterile. After polyploidization, the hybrid
becomes fertile and can thus be further propagated to become triticale.
Salsify is another example of polyploidy resulting in new species.
As a result of the above forces operating on populations, genetic and phenotypic differences
emerge and accumulate over time. This process, called differentiation, leads ultimately to the
emergence of new forms, races and species.
31
QUANTITATIVE TRAITS
 All of the traits that we have studied to date fall into a few distinct
classes -these types of phenotypes are called discontinuous traits.
 Other traits do not fall into discrete classes. Rather, when a
segregating population is analyzed, a continuous distribution of
phenotypes is found-the distribution resembles the bell-shaped curve
for a normal distribution.
 These types of traits are called continuous - because continuous
traits are often measured and given a quantitative value, they are
often referred to as quantitative traits,
 These traits are controlled by:
 multiple genes- each segregating according to Mendel's laws.
 the environment to varying degrees.
 The following are examples of quantitative traits that we are
concerned with in our daily life.
 Crop Yield
 Some Plant Disease Resistances
 Weight Gain in Animals
 Fat Content of Meat
 IQ
 Learning Ability
 Blood Pressure
Genetic and Environmental Effects on Quantitative Traits

As more and more genes control a trait, a greater
number of
genotypes are possible.

The formula that predicts the number of genotypes
from
the number of genes is 3 to the power n:
No. of genotypes = 3n
where n is the number of genes

The following is the number of genotypes for a selected
number (n) of genes which control an arbitrary trait.
# of Genes # of Genotypes
1
3
2
9
32
5
243
10
59,049

Let's look at an example with two genes, A and B

We will assign metric values to each of the alleles.

The A allele will give 4 units while the a allele will
provide 2
units.

At the other locus, the B allele will contribute 2 units
while the
b allele will provide 1 units.

With two genes controlling a trait, nine different
genotypes are
possible. Below are the genotypes and their associated metric
values:
Genotype Ratio in F2 Metric value
AABB
1
12
AABb
2
11
AAbb
1
10
AaBB
2
10
AaBb
4
9
Aabb
2
8
aaBB
1
8
aaBb
2
7
aabb
1
6
These results can be presented in a graphical format.
33
The above graph shows the distribution of the data in the above table.

the
This graph has the bell-shaped curve that is indicative of
normal distribution.

This example demonstrates additive gene action (this
means
that each allele has a specific value that it contributes to the final
phenotype)

Therefore, each genotypes has a slightly different metric
or
quantitative value that results in a distribution (or curve) of
metric values that is similar approach a continuous curve.

Other genetic interactions such as dominance or
epistasis also
affect the phenotype.
 For example, if dominant gene action controls a trait, then the
homozygous dominant and heterozygote will have the same
phenotypic value.
 Therefore, the number of phenotypes is less than for additive gene
action.
 Furthermore, the number of phenotypes that result from a specific
genotype will be reduced further if epistatic interactions between
several loci affects the phenotype
Variance Components of a Quantitative Trait
As we discussed earlier, the metric value (or phenotypic value) for a
specific individual, is the result of genetic factors, environmental factors,
and the environmental factors that interact with the genetic factors.
The sum of these factors in a population of individuals segregating for a
quantitative trait contributes to the variance of that population. Thus the
total variance can be partitioned in the following manner.
VP = VG + VE + VGE
where
 VP = total phenotypic variation of the segregating population
 VG = genetic variation that contributes to the total phenotypic
variation
34
 VE = environmental contribution to the total phenotypic
variation
 VGE = variation associated with the genetic and environmental
factor interactions

The genetic variation can be further subdivided into three
components.
 The first component is called the additive genetic variation.
Some alleles may contribute a fixed value to the metric value of
quantitative value. For example, if genes A and B control corn
yield (it is actually controlled by many genes), and each allele c
ontributes differently to yield in the following manner:
A = 4 bu/aca = 2 bu/acB = 6 bu/acb = 3 bu/ac
Then the AABB genotype will have a yield of 20 (4+4+6+6)
bu/ac and the AaBb genotype will yield 15 (4+2+6+3) bu/ac.
Genes that act in this manner are additive, and they contribute
to the additive genetic variance (VA).
 In addition to genes which have an additive effect on the
quantitative trait, other genes may exhibit a dominant gene
action which will mask the contribution of the recessive alleles
at the locus. For example, if the two genes just mentioned
exhibited dominance the metric value of the AaBb heterozygote
would be 20 bu/ac. This value equals the homozygous
dominant genotype in the example where the alleles were
acting additively. This source of variability is attributed to the
dominance genetic variance (VD).
 The final type of genetic variance is associated with the
interactions between genes. The genetic basis of this variance
is epistasis, and it is called the interaction genetic variance
(VI).

The total genetic variance can be partitioned into the three
forms of variance
VG = V A + V D + V I
and the total phenotypic variance can be rewritten as
VP = VA + VD + VI + VE + VGE
 By performing specific experiments quantitative geneticists can
estimate the proportion of the total variance that is attributable to the
total genetic variance and the environmental genetic variance.
35
 If geneticists are trying to improve a specific quantitative trait (such
as crop yield or weight gain of an animal), estimates of the proportion
of these variances to the total variance provide direction to their
research.
 If a large portion of the variance is genetic, then gains can be made
from selecting individuals with the metric value you wish to obtain.
 On the other hand if the genetic variance is low, which implies that
the environmental variance is high, more success would be obtained
if the environmental conditions under which the individual will be
grown are optimized.
Heritability
 Finally, if you are interested in predicting the phenotype of an
offspring from a cross of two parents, the portion of additive variance
is important because you will know the relative contributions that the
parents will make to the F1 population.
 Again, using our example above, if the genotype of one parent is
AABB and the other parent is aabb we will know that the F1 genotype
is AaBb. And if a larger portion of the genetic variance is additive
then we can predict that the metric value of the F1 will be 15 bu/ac
(4+2+6+3).
 The general term that describes the proportion of the genetic
variance to the total variance is heritability.
 Two specific types of heritability can be estimated.
 The broad-sense heritability is the ratio of total genetic variance to
total phenotypic variance.
H2 = VG/VP
 The narrow-sense heritability is the ratio of additive genetic
variance to the total phenotypic variance.
h2 = VA/VP
36
 The heritability of a trait is the proportion of the total (i.e.
phenotypic) variation (VP) that is explained by the genetic
variation. This is the total genetic variation (VG) in broad sense
heritabilities (H2), while only the additive genetic variation (VA)
is used for narrow sense heritabilities (h2), often simply called
heritability. The latter gives an indication how a trait will
respond to natural or artificial selection.
 The "narrow-sense" heritability (h2), is a technical statistical
parameter. Instead of including all genetic variation, it only
includes additive genetic variation (note upper case H2 for
broad sense, lower case h2 for narrow sense). When one is
interested, e.g., in trying to improve livestock via artificial
selection, knowing the narrow-sense heritability of the trait of
interest will allow one to predict by how much the mean of the
trait will increase in the next generation as a function of how
much the mean of the selected parents differs from the mean
of the population from which the selected parents were
chosen. Calculating the actual progress from selection can
give an estimate of the realized heritability, which is an
estimate of the narrow-sense heritability.
 By now, of course, you are wondering what all this is good for,
and why algebra has any relevance to animal behavior.
Heritability is useful in two ways:
o It can be used to predict how animals will respond to
artificial or natural selection. If a trait has a high
heritability, selection or controlled breeding can change
that trait. Narrow sense heritability is particularly useful in
making this type of prediction.
o Broad sense heritability is used as a measure of the
magnitude of genetic influences on a trait.
37
Important points about heritability
 The heritability estimate is specific to the population and
environment you are analyzing.
 The estimate is a population, not an individual parameter.
 Heritability does not indicate the degree to which a trait is genetic,
it measures the proportion of the phenotypic variance that is the
result of genetic factors.
Estimating the Offspring Phenotype

If we have determined the narrow sense heritability of a trait
and know several population values we can estimate the phenotypic
value for an offspring.

The following formula can be used for the prediction
To = T + h2(T*-T) where
To = predicted offspring phenotype
T = population mean
2
h = narrow sense heritability
T* = midparent value [(Tf + Tm)/2]



Let's use the following information to estimate the
offspring phenotype
T = 80 seeds/plant
Tf = 90 seeds/plant
Tm = 120 seeds/plant
T* = (90 +120)/2 = 105
h2 = 0.5
Then:
To = 80 + 0.5 (105-80)
To = 80 + 12.5
To = 92.5 seeds/plant
The conclusion that we can draw is not that each plant in the
next generation will have 92.5 seeds/plant, but rather that on
average the population derived from mating these two parents will
have 92.5 seeds/plant. Remember that quantitative traits are affected
by the environment, and the environment will be responsible for the
deviations that we would see from the estimated phenotype.
38

will



Predicting Response to Selection
Another use of heritability is to determine how a population
respond to selection.
Typically parents with the phenotypic value of interest are
selected from a base population.
These parents are crossed, and a new population is
developed. The following distributions illustrate this point.
The selection differential (s) is the difference of the base
population mean and the mean of the selected parents.
39

when



The selection response (R)is how much gain you make
mating the selected parents.
Remember, the narrow sense heritability is a measure of the
genetic component that is contributed by the additive genetic
variance.
The response to selection can thus be dervied by multiply the
heriability by the selection differntial.
The following example illustrates how we can predict the
response to selection.
The base sunflower population has a mean of 100 days to
flowering. Two parents were selected that had a mean of
90 days to flowering. The quantitative trait days to
flowering has a heritability of 0.2. What would be the mean
of a population derived from crossing these two parents.
R = h2S
R = 0.2(90 - 100) days to flowering
R = -2 days
The new population mean would therefore be 98 days to
flowering (100 days - 2 days).
Estimation of the number of Genes affecting a Quantitative
Character
 The number of genes that contribute to quantitative traits is
not always large
 When the number of genes is relatively small, the number
can often be estimated from t5he means and variances
observed in different strains and their hybrids and
backcrosses
n = D2/8σg2
where n = effective no . of genes
D = difference between means of P1 & P2
40
σg2 = genotypic variance (F2Vp – F1Vp)
*F1 populations are genetically uniform- so the only source of variation is
the environment
*In F2 generation variation in phenotype results in part from genetic variation & in part from
environment