LSCI1012 Introduction to Life Forms in the Biosphere

Understanding the biosphere: basic principles of ecology and evolution

Prof. Jerome Hui ([email protected]; MMW603A)

• E-mail: [email protected]
– promised to reply students in LSCI1012 usually within 24 hours or at most by 72 hours
– otherwise, it must be a missed e-mail, please either send again, or…

• Office: Room 603A, Mong Man Wai Building

• Research interests:
– Animal evolution
– Non-coding RNAs (such as microRNAs)
– Transcription factors (such as homeobox genes)
– Genomics and transcriptomics
– Developmental biology
– Endocrinology
– Marine Biology (and some environmental studies)
 Course overview
• Prof. Jerome Hui ([email protected])(MMW603A)(Course Convenor)
• Prof. Apple Chui ([email protected])(SC412A)
• Dr. Michelle Law ([email protected])(MMW525)

• Venue: YIA LT7

• Time: 10:30am-1:15pm on Tuesday
 Assessment
A. Exams
1. Mid-term exam (23%) (Jerome) 18 February 2025
2. Final exam (46%)(Apple and Michelle) To be scheduled

B. MCQ design / Exercise (3 assignments)(10+10+10+1%=31%)

- Assignment 1 (11 February 2025)
- Assignment 2 (25 March 2025)
- Assignment 3 (22 April 2025)

C. Tutorial (Optional)
- Online

Recommended Readings:
- Mader SS. Essentials of Biology. McGraw Hill, New York.
- Reece JB et al. Campbell Biology Plus Mastering Biology Student Access Kit: Global Edition.
Pearson Higher Education. (QH308.2 .C338 2011)
 What is this course about?
- Bio = Life

- All living organisms

 Life diversity
Fish Chimpanzee Human Jellyfish Peanut worm

Amphioxus Sea squirt Sea urchin Fly Coral

Lobster Polychaete Placozoan Nematode Limpet

- Where did Earth’s organisms come from?

- Why are there so many different kinds and forms?

- How did they come to be so “suitable”/“well-designed” to live

where they live and do what they do?
Lecture Outline

I . Darwin and Evolution (Chapter 22)

II . Basic Genetics and Evolution of Populations (Chapter 14, 16, 23)

III. Origin of Species (Chapter 24)

IV. History of Life (Chapters 25, 26, 34)

V. Diversity of Life (Chapters 32, 33)

VI. Population Ecology (Chapter 53)

VII. Community Ecology (Chapter 54)

VIII. Ecosystems (Chapter 55)

I . Darwin and Evolution
I . Darwin and Evolution

A) Darwinian Evolution

Ideas about change over time

Lamarck’s hypothesis of evolution

B) Descent with modification by natural selection explains the adaptations

of organisms and the unity and diversity of life

Darwin’s research and Voyage of the Beagle

Adaptation
Descent with modifications
Artificial selection, natural selection, and adaptation

C) Evolution is supported by an overwhelming amount of scientific evidence

Homology
Anatomical and molecular homologies
Fossil record
Convergent evolution
Endemic
A) Darwinian Evolution
Nothing in biology makes sense except in the light of evolution

(Dobzhansky 1973)
Evolution – common descent of living organisms, with modifications

- viewed as both a pattern and a process

- a unifying theme in biological science because it can explain different

observations in living organisms
Charles Darwin (1809-1882)

• Provided much evidence that supports evolution

• Proposed the theory of natural selection as the mechanism of evolutionary changes

Charles Darwin published The Origin of Species (物種起源) in 1859

Mechanism of evolution
Lamarck’s proposal Darwin’s proposal

Originally, giraffes had Originally, giraffe neck

short necks. length varied.

Inheritance of Natural selection

acquired proposed by
characters Darwin
proposed by
Lamarck Giraffes stretched their
necks in order to reach
Struggle to exist causes
long-necked giraffes to
food. have the most offspring.

NOT supported by
modern genetics

With continual stretching, Due to natural selection,

most giraffes now have most giraffes now have
long necks. long necks.
 Ideas About Change over Time

• The study of fossils helped to lay the groundwork for Darwin’s ideas

• Fossils are remains or traces of organisms from the past, usually found in sedimentary
rock, which appears in layers or strata

Rivers carry sediment into aquatic habitats such as seas and swamps.
Over time, sedimentary rock layers (strata) form under water.
Some strata contain fossils.

Sedimentary rock
layers (strata)

As water levels change and the bottom surface is pushed upward,

the strata and their fossils are exposed.

Younger stratum
with more recent
fossils

Older stratum
with older fossils
B) Descent with modification by natural selection explains the adaptations
of organisms and the unity and diversity of life
• As a boy and into adulthood, Charles Darwin had a consuming interest in nature

• Darwin first studied medicine (unsuccessfully), and then theology at Cambridge

University

• After graduating, he took an unpaid position as naturalist and companion to Captain

Robert FitzRoy for a 5-year around the world voyage on the Beagle
 Voyage of HMS Beagle (1831-1836) –
observation leads Darwin to conclude that biological evolution occurs

• He observed that fossils resembled living species from the same region, and living species
resembled other species from nearby regions

• His interest in geographic distribution of species was kindled by a stop at the Galápagos
Islands west of South America

• He hypothesized that species from South America had colonized the Galápagos and
speciated on the islands

• Galápagos Islands – off coast of South America

– Too far from mainland for most terrestrial plants and animals to colonize

– Species there slightly different from mainland forms

– Where did they come from? Why are they different?

Darwin’s finches
Each species adapted to eating a different type of food
Could have descended from a mainland finch

A cactus-eater, an insect-eater, and a seed-eater

- long sharp beak - narrow, pointed beak - large beak

- help to tear and eat - help to grasp insects - crack seeds

cactus flowers and pulp
• Darwin explained three broad observations:

– The unity of life

– The diversity of life

– The match between organisms and their environment

• In reassessing his observations, Darwin perceived adaptation to the

environment and the origin of new species as closely related
processes

• Descent with Modification

The common misconception

???
What we have learnt from Taxonomy – useful to tell relationships between organisms?

Kingdom: Animalia Animalia Animalia Animalia Animalia Animalia

Phylum/: Echinodermata Chordata Arthropoda Urochordata Cephalochordata Chordata

Subphylum

Order: Echioidea Primates Insecta Enterogona - Primates

Family: Strongylocentrotidae Hominidae Drosophilidae Cionidae Brachiostomidae Hominidae

Genus: Strongylocentrotus Pan Drosophila Ciona Brachiostoma Homo

Species: S. purpuratus P. troglodytes D. melanogaster C. intestinalis B. floridae H. sapiens

- which one is a closer relative to human after the chimp?

 Chordata Chordata Chordata Cnidaria Sipuncula

Cephalochordata Urochordata Echinodermata Insecta Porifera

Crustacea Annelida Placozoa Nematoda Mollusca

- NO, but they are essential and useful to study different characteristics
Descent with modification.
Hyracoidea
(Hyraxes)
Sirenia
(Manatees
and relatives)
†Moeritherium

†Barytherium

†Deinotherium

†Mammut

†Platybelodon

†Stegodon

†Mammuthus

Elephas maximus
(Asia)
Loxodonta africana
(Africa)

Loxodonta cyclotis
(Africa)
60 34 24 5.5 2 104 0

Millions of years ago Years ago

We share a common ancestor with the chimp, rather than evolving from a chimp!

Time Chimpanzee-Human Last Common Ancestor (CHLCA)

extinct 5-7 million years ago
Darwin noted that humans have modified other species by selecting and
breeding individuals with desired traits, a process called artificial selection
Members of a population often vary in their inherited traits

Variations are the raw materials of evolutionary changes

The theory of natural selection

• Mechanism for evolution

• Process that results in the evolution of organisms well adapted to their

environment

▪ Members of a population have heritable

variations

▪ The population produce more offspring

than the environment can support

▪ Individuals with favorable traits survive

and reproduce more than those lacking
the traits

▪ Across generations, a larger proportion of

the population possesses the favorable
traits and become adapted to the
environment Puffball fungus
 Don’t get confused!

• Note that individuals do not evolve; populations evolve over time

• Natural selection can only increase or decrease heritable traits

that vary in a population

• The local environment determines which traits will be selected for

or selected against in any specific population, therefore,
adaptations vary with different environments
C) Evolution is supported by an overwhelming amount of scientific evidence
 Anatomical homologies
Homology is similarity resulting from common ancestry

Anatomical homologies - similar structures explainable by inheritance from a common

ancestor

All vertebrate forelimbs contain the same set of bones organized in similar ways
despite dissimilar functions – an example of homologous structures
Comparative embryology reveals anatomical homologies not visible in adult organisms
Vestigial structures

• Anatomical features that are fully developed in one group of organisms

but reduced and nonfunctional in other similar groups

• Examples: Human tailbone and hairs

• Presence explained by common descent hypothesis

Skeleton of a right whale (A) and sperm whale (B). The loss of pelvic girdle and
hind limbs but the presence of vestigial hip and leg bones indicate affinity of
whales with land mammals
 Fossil Record

Archaeopteryx – intermediate between reptiles and birds

wing
feathers

teeth tail with

vertebrae
claws

• The fossil record provides evidence of the extinction of species,

the origin of new groups, and changes within groups over time
Evolution of whales - The transition to life in the sea.
 Be careful!
Convergent evolution and analogous structures –
structures that share the same function but not common ancestry
Molecular homologies

– All living organisms use the same biochemical molecules, including

DNA, ATP, and many nearly identical enzymes.

– Life’s vast diversity has come about from only slight differences in
the same genes.

– Cytochrome c is a molecule used in the electron transport chain of

all organisms.
 Significance of molecular differences
Types of Organisms

human monkey pig duck turtle fish moth yeast (Candida)

0

Number of Amino Acid Differences Compared to Human Cytochrome c

10

20

30

Branch points tell the number of amino acids that differ

between human cytochrome c and the organisms depicted
40

50
 Endemic species

• Endemic species are species that are not found anywhere else in the world

• Islands have many endemic species that are often closely related to
species on the nearest mainland or island

• Darwin explained that species on islands gave rise to new species as they
adapted to new environments
I . Darwin and Evolution

A) Darwinian Evolution

Ideas about change over time

Lamarck’s hypothesis of evolution

B) Descent with modification by natural selection explains the adaptations

of organisms and the unity and diversity of life

Darwin’s research and Voyage of the Beagle

Adaptation
Descent with modifications
Artificial selection, natural selection, and adaptation

C) Evolution is supported by an overwhelming amount of scientific evidence

Homology
Anatomical and molecular homologies
Fossil record
Convergent evolution
Endemic
II . Basic Genetics and Evolution of population
II. Basic Genetics and Evolution of population

A) Genetic variation makes evolution possible

B) Hardy-Weinberg equation to test whether a population is evolving

C) Mechanisms of microevolution

D) Preservation of genetic variation

E) Why natural selection cannot fashion perfect organisms

A) Genetic variation makes evolution possible
DNA is the genetic material
Asexual vs Sexual Reproduction
Chromosomes
Meiosis reduces chromosome number
Sexual life cycles
 Evolution of Populations – Microevolution

• Individuals do not evolve.

• As evolution occurs, genetic and phenotypic changes occur within a

population.

• Population is all the members of a single species occupying a

particular area at the same time and reproducing with one another.

• Microevolution – small measurable evolutionary changes within a

population from generation to generation (change in allele frequencies
in a population over generations)
 Genetic variation makes evolution possible

• Variation in heritable traits is a prerequisite for evolution

• Genetic variation among individuals is caused by differences in genes

or other DNA segments

• Phenotype is the product of inherited genotype and environmental

influences

• Natural selection can only act on variation with a genetic component

Industrial melanism as an example of microevolution

▪ Increase in the frequency of a dark phenotype

due to pollution

▪ Before soot darkened tree trunks, light moths

escaped detection of birds and were more
a.
common.

▪ After the advent of industry, dark-colored

moths became more common as light moths
were detected and eaten.

▪ Natural selection can occur within a short time

frame.
b.
Evolution in a genetic context

– Gene pool – all copies of alleles at every locus in all members of a population

• Described in terms of genotype and allele frequency

– Peppered moth color example

• D= dark color d= light color

• From the genotype frequencies, you can calculate the allele frequencies of
a population.

F1 generation

Genotypes: DD Dd dd
Genotype frequencies: 0.04 0.32 0.64
Allele and gamete frequencies: D = 0.20 d = 0.80
– Assuming random mating, can use allele frequencies (gamete
frequencies) to calculate the ratio of genotypes in the next generation
(see next slides)

– Allele frequencies remain the same – sexual reproduction alone does

not bring about a change in allele frequencies.

– Dominance does not cause an allele to become a common allele.

Hardy-Weinberg equilibrium
eggs

0.20 D 0.80 d

0.20
D

sperm
0.04 DD 0.16 Dd
F2 generation

0.80
d

0.16 Dd 0.64 dd
Offspring

Genotype frequencies: 0.04 DD + 0.32 Dd + 0.64 dd = 1

p2 + 2pq + q2 = 1

p2 = frequency of DD genotype (dark-colored) = (0.20)2 = 0.04

2pq = frequency of Dd genotype (dark-colored) = 2(0.20)(0.80) = 0.32

q2 = frequency of dd genotype (light-colored) = (0.80)2 = 0.64

1.00
B) Hardy-Weinberg equation to test whether a population is evolving
G.H. Hardy and W. Weinberg used the binomial equation to
calculate the genotypic and allele frequencies of a population.

▪p = frequency of dominant allele

▪q = frequency of recessive allele
▪p2 + 2pq + q2 = 1

For 3 alleles in a locus,

▪p2+q2+r2+2pq+2qr+2pr = 1
• For example, consider a population of wildflowers:
– 320 red flowers (CRCR)
– 160 red flowers (CRCW)
– 20 white flowers (CWCW)

• Calculate the number of copies of each allele:

– CR = (320  2) + 160 = 800
– CW = (20  2) + 160 = 200

• To calculate the frequency of each allele:

– p = freq CR = 800 / (800 + 200) = 0.8
– q = freq CW = 200 / (800 + 200) = 0.2

• The sum of alleles is always 1

– 0.8 + 0.2 = 1
 Selecting alleles at random from a gene pool.

Alleles in the population

Frequencies of alleles Gametes produced
p = frequency of Each egg: Each sperm:
CR allele = 0.8

q = frequency of 80% 20% 80% 20%

CW allele = 0.2 chance chance chance chance
• Hardy-Weinberg equilibrium describes the constant frequency of alleles
in such a gene pool

• Consider, for example, the same population of 500 wildflowers and 100
alleles where
– p = freq CR = 0.8
– q = freq CW = 0.2

• The frequency of genotypes can be calculated

– CRCR = p2 = (0.8)2 = 0.64
– CRCW = 2pq = 2(0.8)(0.2) = 0.32
– CWCW = q2 = (0.2)2 = 0.04

• The frequency of genotypes can be confirmed using a Punnett square

 Figure 23.8
80% CR (p = 0.8) 20% CW (q = 0.2)

Sperm
CR (80%) CW (20%)

CR
(80%)
64% (p2) 16% (pq)
Eggs CRCR CRCW

CW 16% (qp) 4% (q2)

(20%) CRCW CWCW

64% CRCR, 32% CRCW, and 4% CWCW

Gametes of this generation:

64% CR R
+ 16% C R W = 80% CR = 0.8 = p
(from CRCR plants) (from C C plants)
4% CW W
+ 16% C R W = 20% CW = 0.2 = q
(from CWCW plants) (from C C plants)
Genotypes in the next generation:

64% CRCR, 32% CRCW, and 4% CWCW plants

Hardy-Weinberg principle states that an equilibrium of allele
frequencies in a gene pool will remain in equilibrium as long as 5
conditions are met.

1. No mutations

2. Random mating

3. No gene flow (migration)

4. Extremely large population size (No genetic drift)

5. No natural selection

In the example of industrial melanism, natural selection occurs.

• These conditions are rarely if ever met.

• Allele frequencies do change from one generation to the next.

• Therefore microevolution occurs.

• Hardy-Weinberg equation is significant because it tells us what

factors cause evolution.

• Evolution can be detected and measured by noting the amount of

deviation from a Hardy-Weinberg equilibrium of allele frequencies in
the gene pool of a population.
C) Mechanisms of microevolution
Mechanisms of microevolution

– Any condition that deviates from the list of conditions for allelic
equilibrium causes evolutionary change.

1. Mutation

2. Gene flow

3. Nonrandom mating

4. Genetic drift

5. Natural selection
1. Mutations

– Ultimate source for allele

differences

– Without mutation there would be

no new variations among
members of a population for
natural selection to act on.

– Adaptive value of mutation

depends on current environmental
conditions.

Freckles are caused by a dominant allele

Sickle cell anemia – due to a point mutation in the hemoglobin gene
2. Gene Flow

– Gene flow – transfer of alleles among populations

– Can increase variation within a population by introducing

novel alleles from another population

– Continued gene flow reduces differences among

populations – can prevent speciation
Gene flow between 2 populations of caribou in North America
3. Nonrandom mating

– Selection of mate according to genotype or phenotype (not chance)

– Assortative mating – tend to mate with individuals with the same phenotype
• Homozygotes increase in frequency

– Sexual selection – favors characteristics that increase the likelihood of

obtaining mates
4. Genetic drift

– Random changes in the allele frequencies of a gene pool due to

chance

– Allele frequencies “drift” over time depending on which members

reproduce.

– Significant in small populations

– Can lead of a loss in genetic variation (more likely the loss of rare
alleles)

– Can cause harmful alleles to become fixed

– 2 types – founder and bottleneck effects

Founder effect

- Rare alleles occur at a higher

frequency in a population isolated
from the general population.

- Alleles carried by founders are

dictated by chance alone.

- Amish in Pennsylvania, USA from

Germany – 1 in 14 carries
recessive allele for unusual form of
dwarfism linked with polydactylism
compared to 1 in 1000 in most
populations.
Bottleneck effect

- a sudden reduction in population size due to a change in

the environment

- The resulting gene pool may no longer be reflective of the

original population’s gene pool

- If the population remains small, it may be further affected

by genetic drift

- Therefore, species suffers a near extinction and only a few

survivors go on to produce the next generation.
Bottleneck effect

bottleneck:
catastrophic
reduction
in population

original chance new population

population survivors
5. Natural Selection

▪ Darwin’s mechanism for evolution

▪ The only mechanism that consistently causes adaptive evolution

▪ Members of a population different in fitness

– Fitness – reproductive success of an individual relative to other

members of the population

• Determined by comparing the number of surviving fertile offspring

produced by each member of a population

– Most-fit individuals reproduce more than others because they are

better adapted

– What determines fitness varies for different populations.

▪ The most fit individuals become more prevalent in a population, leading to

change in allele frequency over time
Modes of selection
Directional selection - the evolution of horses
initial distribution

Number of Individuals
Hyracotherium

Key:
Small body size
Intermediate body size
Large body size

Body Size

Merychippus

after time
Number of Individuals

Body Size

Equus

after more time

Number of Individuals

Body Size
 Disruptive selection - a land snail in Britain

initial distribution
Birds feed on this in the field;
Individuals
Number of

Higher fitness in the forest

Banding Pattern

after time
Individuals
Number of

no banding

Banding Pattern

after more time

Individuals
Number of

Key:
No banding
Some banding
Banding

Banding Pattern
a. b. banding

Birds feed on this in the forest;

Higher fitness in the field
Stabilizing selection – Clutch size of Swiss starlings
initial distribution

Survival of
Young
Clutch Size

after time
Survival of
Young

Clutch Size

after more time

Survival of

Key:
Young

Less than 4 eggs

4 to 5 eggs
More than 5 eggs

Clutch Size
D) Preservation of genetic variation
Preservation of genetic variations

– A population always shows some genotypic variations.

– Population with limited variation may not be able to adapt to

changing environmental conditions.

– Forces promoting variation constantly at work

• Mutations, recombination, independent assortment, and

fertilization create new combinations.

• Gene flow

• Natural selection favors certain phenotypes but other remain.

Diploidy

– Only alleles that are expressed are subject to natural selection.

• Expressed = cause phenotypic differences

– Heterozygotes can protect recessive alleles.

– Recessive allele might have greater fitness in a changing

environment

Balancing Selection

– when natural selection maintains 2 or more forms in a population

– Sickle cell anemia

Sickle cell anemia

– Individuals with sickle cell anemia HbSHbS

• Red blood cells sickle under low oxygen conditions, clumped together and
block capillaries concentrations

• Patients tend to die early

– Heterozygotes carry the trait HbSHbA

• Some red blood cells become sickled, but no enough to cause the disease

– Ordinarily the normal genotype HbAHbA is most fit

– Recessive allele HbS has a higher frequency in regions in Africa where malaria is
present.

– Malaria is caused by parasite that invades and destroys normal red blood cells.
Malaria and sickle cell alleles
– Parasite unable to infect the sickled red blood cells

– Each of the homozygotes is selected against but is maintained

because the heterozygote is favored in those parts of Africa –
heterozygous advantage
E) Why natural selection cannot fashion perfect organisms
Why natural selection cannot produce perfect organisms

1. Selection can act only on existing variations

2. Evolution is limited by historical constraints

3. Adaptations are often compromises

4. Chance, natural selection, and the environment interact

Imperfections are common, e.g., Panda’s thumb
II. Basic Genetics and Evolution of population

A) Genetic variation makes evolution possible

B) Hardy-Weinberg equation to test whether a population is evolving

C) Mechanisms of microevolution

D) Preservation of genetic variation

E) Why natural selection cannot fashion perfect organisms