Presentation by:

Janine Kaysee Soriano, MSc.

Teaching Fellow, DFBS

Measuring Biodiversity:

Genetic Diversity
 BIODIVERSITY ?
The variability among living organisms from all
sources including, inter alia, terrestrial,
marine and other aquatic ecosystems and the
ecological complexes of which they are part;
this includes diversity within species, between
species and of ecosystems

United Nations Convention on Biodiversity

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Diversity at different
levels of biological
organization

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Diversity at different levels of biological organization

Diversity at the gene level

represents the finest scale of
diversity but the foundation of all
higher levels of diversity
EEA, Copenhagen, 1997

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 What is natural variation?
Gene  DNA  Chromosome
Hereditary unit

gene gene

gene gene

chromosome

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Let us review
Mendelian Inheritance.
Mt. Makiling Mt. Banahaw
1st Crossing Experiment

F1 Generation

Parents

F1 Generation
F2 Generation
2nd Crossing Experiment
Parents
F1 Generation (2)

F2 Generation (2)

F1 Generation (2)
Phenotypes (in terms of flower color)

red white pink

 Gene: Flower Color

Alleles:
P= red
p= white

Alleles are variants of a

gene controlling the
same trait and occupying
a specific region on a
chromosome (locus).
PP pp Genes are codes for
making other molecules
which make up the
phenotype
1st Crossing Experiment
F1 Generation

Parents

PP pp Pp Pp
P p p P

P p
P p
Pp
Pp
F1 Generation
F2 Generation
PP pp
Pp Pp

Pp
Pp
2nd Crossing Experiment F1 Generation (2)
Parents

PP pp
Pp Pp
P p p P
P p P p
Pp Pp

F2 Generation (2)
Pp Pp PP pp
F1 Generation (2)

Pp Pp
Character: Flower Color
Alleles: P=red, p=white

Phenotype

Genotype PP Pp Pp pp
 Mutation: Origin of Genetic Diversity

Random changes of
genetic information
- Errors in DNA replication
(primarily) point mutation
- Chromosomal aberrations

Chromosomes aberrations

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Mutation: Origin of Genetic Diversity
 Prerequisite for any genetic variation;
 It is the ultimate source of variation;
 It increases diversity but because spontaneous mutations are
rare, the rate of change in gene frequency is very low;
 Often lethal/detrimental
 Sometimes increases biological fitness of a population

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 GENETIC DIVERSITY
is the backbone of evolution.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Measuring Genetic Diversity
Diversity at varying spatial scales
Genetic structure of populations refers to the distribution of relative
frequencies of certain genetic types at a locus.
a) Genotypic structure
b) Gene (allelic) structure

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Genetic structure: Genotypic
Proportion of a particular genotype in the population
• Kinds and Frequencies of the genotypes present

For a character, there are three possible

genotypes in a population:

AA, Aa, aa

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Determination of genotypic frequency
(No Dominance of Alleles)

GENOTYPE NO. OF INDIVIDUALS

AA 100
Aa 600
aa 300
Total No. of Individuals 1,000

Given the preceding population of trees, the frequency of

the genotype AA, Aa, aa is A. 10% D. 40%
B. 20% E. 50%
C. 30% F. None of the above

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Genetic structure: Gene (allelic)
 Proportion of a particular gene/allele in the
population
 An estimate of percentage of A or a in a given
population
 Genes are the ones transmitted from generation to
generation.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Determination of gene/allele frequency
(No Dominance of Alleles)
1. By counting the number of alleles in the population

Number of No. of Alleles

Genotype
Individuals A a
AA 100 200
Aa 600 600 600
aa 300 600
Total 1,000 800 1200

What are the frequencies of alleles A and a?

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity
 Determination of gene/allele frequency
(No Dominance of Alleles)
2. By using the genotypic frequencies calculated
GENOTYPE FREQUENCIES
AA 0.10
Aa 0.60
aa 0.30
Frequency of a = Frequency of aa + ½ Frequency of Aa
= 0.30 + ½(0.60)
= 0.60
Frequency of A = Frequency of AA + ½ Frequency of Aa
= 0.10 + ½ (0.60)
= 0.40

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Nature of Genetic Diversity

A Genotype is the genetic make-up of a particular gene; we

cannot see it!
A genotype can be:
1. Homozygous Dominant – presence of 2 dominant alleles (PP)
2. Homozygous Recessive –presence of 2 recessive alleles (pp)
3. Heterozygous – 1 dominant and 1 recessive allele (Pp)

A Phenotype is the physical expression of the gene;

the physical appearance we see!

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Nature of Genetic Diversity

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

Genetic markers - any gene or allele the phenotypic expression of
which is generally easy to identify.

Markers

(CHESNOKOV et al., 2020)

 Isozymes Restriction Fragment Length Polymorphism
Methods of measuring
genetic diversity
Sequences
Genetic markers Microsatellites
• Morphological
• Biochemical
• Molecular (marker loci)

Molecular markers allow precise

estimates of genetic diversity
FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity
 Quantifying genetic diversity of populations

Population - group of individuals of

the same species living in same
geographical area

• Within an individual:
% heterozygosity (Are alleles the same or different in a given set of genes?)
• Among individuals in a population: allele frequencies for given genes
• Between populations: % heterozygosity, allele frequencies, unique (private)
molecular markers (alleles)

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Why is it important to assess genetic diversity?
Two important aspects of genetic diversity for conservation and
management of forest genetic resources

1) Levels of genetic diversity

It reflect the availability of genetic resources necessary for short-term ecological
adaptation and for long-term evolutionary change.
Low levels of genetic diversity within population can threaten their long-term
persistence by reducing their ability to adapt to the changing environment
conditions.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Why is it important to assess genetic diversity?
2) Spatial genetic structure - distribution of genotypes over the two-
dimensional space of a stand

If genetic diversity is EVENLY distributed over a population, the loss of individuals has negligible effect.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 However, if genetic diversity is SPATIALLY distributed over a population
the loss of individuals has large effect

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 The “bottleneck effect”: an analogy
A severe, temporary reduction in the population size, where the genetic variability
of all subsequent generations is contained in the few individuals that survive.

Small populations
that suffers loss of
genetic diversity
may experience
fitness reductions
and increased
extinction risk!

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Distribution of Genetic Variation
Knowledge on the distribution of genetic diversity within and among
populations is critical in the formulation of management strategies:

For species with high pop. differentiation values, more populations are
needed to be conserved to ensure that allelic and genotypic
diversity can be retained.

Species and population level genetic diversity is essential for

monitoring the effects of in situ or ex situ conservation on the
maintenance of genetic diversity.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Objectives

At the end of this exercise, you should be able to:

1. Compute the genetic diversity in a species
2. Evaluate the importance of assessing the genetic diversity in
species

Learn to quantify genetic diversity based on DNA/ molecular

markers, using hypothetical genotypic profile of two populations.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Activity Instruction
• Genotype scoring will be done using the profiles.
• Each student should have a laptop with pre-downloaded
GENALEX 6.5 (GenAlEx: Genetic Analysis in Excel) or higher
version

visit this site

https://biology-assets.anu.edu.au/GenAlEx/Download.html
And download GenAlEx 6.503

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 The nature of variability based on molecular marker
Below are variability pattern in populations as assessed by
microsatellites -- short repeats of DNA sequences motifs

Peak patterns

nucleotide base (microsatellite)

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Locus 1

1 2 3 4 5 6 7

Locus 1 Locus 1

1 400 300

2 350 300

3 450 400

4 350 350

5 500 550

6 350 250

7 400 350
 ACTIVITY – DATA INPUT

FBS 101 || Exercise

FBS 101 Exercise 1. 1.Measuring
Measuring Biodiversity:
Biodiversity: GeneticGenetic
Diversity Diversity
 ACTIVITY – DATA INPUT
Total no. of loci 04

Total no. of
samples
10

Total No. of
02
populations

No. of individuals 05
in Pop1 and Pop2

No. of region 01

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 ACTIVITY – DATA INPUT
A1 – Total no. of loci
A1 B1 C1 D1 E1 F1 G1 H1 J1 K1
B1 – Total no. of samples
A2 B2 C2 D2 E2
C1 – Total no. of populations
A3 B3 C3
D1, E1 – No. of individuals per pop
A4 B4 C4
F1 – No. of region
A5 B5 C5
G1 – Total no. of samples
A6 B6 C6
A2 – Title*
A7 B7 C7
D2, E2 – Code for Pop1 & Pop2
A8 B8 C8
A3– Sample*
A9 B9 C9
B3– Pop*
A10 C10 C10
C3…J3– Name of locus
A11 B11 C11
A4…A13– Sample number
A12 B12 C12
B4…B13– Population number
A13 B13 C13
C4..J13 – Data

FBS 101 || Exercise

FBS 101 Exercise 1. 1.Measuring
Measuring Biodiversity:
Biodiversity: GeneticGenetic
Diversity Diversity
 ACTIVITY – DATA INPUT

Datasheet format

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 When you see one peak,
the size of DNA fragment
for that peak should be e.g.
241, 241

Variant 1= 241
and
Variant 2 = 241

Two peaks = heterozygous

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Two peaks = heterozygous

When you see one peak, the

size of DNA fragment for that
peak should be eg. 241, 241

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 If successful, GenAlex will appear on Add-ins

Input/ copy raw data (Population in CARAGA & ISABELA) on empty

worksheet

Place the cursor in the A1 cell, then click GenAlEx, click the
Frequency
FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity
 Input/ copy raw data on empty worksheet
place the cursor in the A1 cell, then click GenAlEx, click the Frequency

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 A new window appears. Click OK!

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 A new window appears.
Check the following
boxes:
 Frequency by Pop
 Freq by Locus
 Het, Fstat & Poly by Pop
 Het, Fstat & Poly by Locus
 Allelic Patterns
 Graph patterns

Click OK again!

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 The results will appear.
The software automatically generates the
results in each worksheet.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 From the sample dataset in MS Excel

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 The worksheet HFP
contains the
estimates of genetic
diversity in each
population and in the
total species.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Quantifying genetic diversity in a species can be done at
different scales:
i. Within an individual: % heterozygosity (Are alleles same or
different in a given set of genes?)
ii. Among individuals in a population: allele frequencies for
given genes
iii. Between populations: % heterozygosity, allele frequencies,
unique alleles

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 For Exercise 1, complete the table using information of
the given 2 populations.

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Answer the following:
1. What do you mean by a single locus genotype 84, 84 or 241,
241, or 148, 148? What do you mean by a single locus
genotype 84, 86, or 241, 243, or 148, 150? (4)
2. Based on the output “Allele Frequencies by Population with
Graph over Loci for Codominant Data”, which particular locus
is most variable? Least variable? (4)

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Answer the following:
3. Use the table below to summarize your results. Append the
portion of the specific estimates as highlighted in yellow in
the previous page. (16)

4. Which of the population had the highest genetic diversity

(allelic diversity and heterozygosity)? (4)

FBS 101 | Exercise 1. Measuring Biodiversity: Genetic Diversity

 Population 1: LUZON

Malabayabas 1

90 92 260 262 150 156

257

Malabayabas 2

90 92 292 294 148 150

257

Malabayabas 3

90 94 257 292 150 152

301

Malabayabas 4

261 262 264 150

90 96

Malabayabas 5

260 296
90 257 261 146 152