2303101 General Biology

Unit 5: Diversity of Life

Asst. Prof. Nontivich Tandavanitj, Ph.D.
Asst. Prof. Marut Fuangarworn, Ph.D.
Assoc. Prof. Chirasak Sutcharit, Ph.D.
Department of Biology, Faculty of Science, Chulalongkorn University

1
 Unit 5: Diversity of Life (5 hrs.)
5.1 Origin and History of Life
5.2 Biological Diversity (Biodiversity)
• Why there are a lot of biodiversity?
• The value of biodiversity
5.3 Taxonomy and Systematics
• Taxonomy: Classification, Identification,
Nomenclature
• Phylogenetic classification
5.4 Kingdoms of Life
2
 Origin of Life
• Age of the Earth = 4.6 BYA

• Creation of stable atmosphere by Earth’s

gravitation pull

(https://thumbs-prod.si-cdn.com/B3Zd_zJ6ixeSaQHEwXJJfnqecLc=/800x600/filters:no_upscale()/https://public-
media.smithsonianmag.com/filer/7e/59/7e593e43-c61b-4635-9fac-8a6cd1a36ed3/accretion-nature.jpg) 4
 Origin of Life
• Early atmosphere was composed of:
• Water vapor
• Nitrogen
• Carbon dioxide
• Traced gases, i.e., Hydrogen, methane,
ammonia, hydrogen sulfide, and carbon
monoxide
• Small amount of oxygen

• Cooling and condensation converted water

vapor into liquid

5
 extant organisms

Common ancestor

Stages of the Origin of Life

of all life on Earth or

Biological Evolution
LUCA (last universal
LUCA common ancestor)

extinct lineages Origin of Life:

1. Organic monomers - x first self-replicating cell

x x

amino acids, cell Stage 4

nucleotides
2. Organic polymers - Stage 4

Biological Evolution
proteins, DNA, RNA,
cell
DNA
RNA
origin of

fatty acid
genetic code

proto cell Stage 3

3. Protocells – organic
plasma
membrane

polymers enclosed in
polymers Stage 2

membrane =
polymerization

protobiont
Stage 1

Chemical Evolution
Small organic molecules

energy abiotic
capture synthesis

4. Living cells – self- Inorganic chemicals

replicating protobionts early Earth

6
Miller-Urey Experiment (1953)
electrode

electric
stopcock for spark
adding gases
CH4
NH3 gases
H2
H2O hot water out
stopcock for
withdrawing liquid
condenser cool water in

liquid droplets
boiler

heat small organic molecules

7
 Iron-Sulfur World Hypothesis
- Monomers came from
reactions at hydrothermal
vents.

- Dissolved gases (CO,

ammonia, hydrogen
sulfide)

- Iron and nickel sulfide

minerals acted as
catalyst.
8
 Extraterrestrial origin Hypothesis
- Comets and meteorites,
perhaps carrying
organic chemicals,
have pelted Earth
throughout history.

- Bacterium-like cells
could have been
carried to Earth on a
meteorite or comet.

9
(https://www.popsci.com/sites/popsci.com/files/styles/1000_1x_/public/import/2013/images/2013/02/meteor.jpg?itok=juem37Aw)
 Timeline of Life
thermophiles
Archaebacteria
3 halophiles
ARCHAEA methanogens
7
Animals
5
1
Fungi
heterotrophic
protists
4 6
EUKARYA Protists
first cells
mitochondria photosynthetic
protists 8
Plants
chloroplasts
2
BACTERIA
aerobic bacteria
Bacteria
photosynthetic bacteria (produce oxygen)

other photosynthetic bacteria (do not produce oxygen)

3.5 BYA 2.2 BYA 1.4 BYA 543 MYA

10
Early History of Life: Precambrian
• Little or no atmospheric oxygen in the early atmosphere
• Lack of ozone shield allowed UV radiation to bombard Earth

• The first cells came into existence in aquatic environments.

• Prokaryotes appeared about 3.5 BYA.
• Cyanobacteria fossils have been found in ancient stromatolites.
• Photosynthetic cyanobacteria added oxygen to the atmosphere.
• Aerobic bacteria proliferated in the oxygen-rich atmosphere.
• New metabolic pathways evolved.

11
• Eukaryotic Cells Arise
• About 2.1 BYA
• Most are aerobic
• Contain a nucleus and other membranous
organelles

• Endosymbiotic Theory
• Mitochondria were probably once free-living
aerobic prokaryotes.
• Chloroplasts were probably once free-living
photosynthetic prokaryotes.
• A nucleated cell probably engulfed these
prokaryotes that became various organelles.

12
• Support for the Endosymbiotic Theory
• Mitochondria and chloroplasts are similar in size to bacteria.

• Mitochondria and chloroplasts have their own DNA and

make some of their own proteins.

• Mitochondria and chloroplasts divide by binary fission.

• The outer membranes of mitochondria and chloroplasts

differ.

• The outer membrane resembles a eukaryotic membrane.

• The inner membrane resembles a prokaryotic

membrane.

13
13
 Timeline of Life
thermophiles
Archaebacteria
3 halophiles
ARCHAEA methanogens
7
Animals
5
1
Fungi
heterotrophic
protists
4 6
EUKARYA Protists
first cells
mitochondria photosynthetic
protists 8
Plants
chloroplasts
2
BACTERIA
aerobic bacteria
Bacteria
photosynthetic bacteria (produce oxygen)

other photosynthetic bacteria (do not produce oxygen)

3.5 BYA 2.2 BYA 1.4 BYA 543 MYA

14
• Multicellularity Arises
• Fossil of multicellular protists, about 1.4 BYA

• Early multicellular organisms lacked internal

organs and could have absorbed nutrients from
the sea.

• Separating germ cells from somatic cells may

have contributed to the diversity of organisms.

Ediacara 15
 History of Life
STATUS TODAY
mammals

mammals

birds

birds

dinosaurs dinosaurs extinct

insects

insects

ammonoids
brachiopods
poriferans
ammonoids extinct
brachiopods

poriferans

QUARTE
CAMBRIAN ORDOVICIAN SILURIAN DEVONIAN CARBONIFEROUS PERMIAN TRIASSIC JURASSIC CRETACEOUS TERTIARY PRESENT
-RNARY

Major
Extinctions 443.7 MYA 359.2 MYA 251 MYA 199.6 MYA 65.5 MYA

% Species
75% 70% 90% 60% 75%
Extinct

North North
Eurasia Eurasia
America America
Laurasia
India
Africa
Africa
South India South
America America Australia
Australia
Antarctica Antarctica

(251 million years ago) (135 million years ago) (65 million years ago) Present day
16
PALEOZOIC MESOZOIC CENOZOIC
2303101 General Biology:
Unit 5 - Diversity of Life
Asst. Prof. Nontivich Tandavanitj, Ph.D.
Asst. Prof. Marut Fuangarworn, Ph.D.
Assoc. Prof. Chirasak Sutcharit, Ph.D.
Department of Biology, Faculty of Science, Chulalongkorn University
Diversity of Life
Biodiversity Hotspots

(http://cnx.org/content/m47766/latest/Figure_47_01_03.jpg)
 Diversity of Life

•What is biodiversity?
• 3 components of biodiversity

•Biodiversity = Species
diversity + genetic diversity +
ecosystem diversity
Species Diversity

(https://figures.boundless.com/14555/full/undiscovered-species-chart.png)
Species Diversity
Species Diversity

(http://daphnedrouga.files.wordpress.com/2011/12/biodiversity-2.jpg)
 Evolution & Speciation
• Changes in biodiversity: extinction
of old forms vs. emergence of
new ones
• Evolutionary forces:
• Natural selection: genetic
modification, survival, and
fitness
• Isolation:
• Reproduction, separation
• Continental drift vs. formation
of islands
• Adaptive radiation: small
population in various niches
Sympatric vs. Allopatric
Fossil Records - Burgess Shale

Charles Walcott (1850-1927)

Past vs. Present
 Cambrian Explosion

•Could some Burgess Shale organisms

belong to extinct phyla?

•Is it possible that a phylum could be

represented by few or single species?

•If so, Cambrian Explosion produced

more phyla/classes than are present
today.
 Cambrian Explosion

J.S. Gould
“Wonderful Life”
 Cambrian Explosion
• Reasons
• Environmental: sudden
oxygen build-up that
allows big bodies and
skeletons, change in
ocean chemistry to
allow shells
• Biological: adaptive
radiation, breakthrough
in the genetic control of
development
 Genetic Diversity

•Genetic uniqueness
•Genetic variation is the
reflection of evolutionary
history and adaptation.

•Loss of genetic diversity =

loss of ability to adapt

(http://upload.wikimedia.org/wikipedia/commons/c/c4/Wilson's_Bird_of_Paradise_Best.jpg & http://cdn.lightgalleries.net/4bd5ec0079abc/images/MM7163_06091310638-2.jpg)

Ecosystem Diversity

(http://facultylounge.whfreeman.com)
 Ecosystem Diversity
•Ecosystem services: resources
and processes that are
supplied by the ecosystems

•Supporting service:
necessary for production of
other services i.e. nutrient
cycling, seed dispersal,
primary production

(http://en.wikipedia.org/wiki/Ecosystem_services & http://upload.wikimedia.org/wikipedia/commons/thumb/4/45/Taraxacum_sect._Ruderalia_MHNT.jpg/220px-Taraxacum_sect._Ruderalia_MHNT.jpg)

 Ecosystem Diversity

•Ecosystem services
(cont.)

•Provisional service:
products obtained
from the ecosystem
i.e. water, food,
pharmaceuticals, etc.

(http://en.wikipedia.org/wiki/Ecosystem_services & http://www.easierliving.com/blog/wp-content/uploads/2013/09/Natural-remedies-for-acne.jpgg)

 Ecosystem Diversity
• Ecosystem services (cont.)
• Regulating service: air purification, waste
decomposition, climate control etc.

(http://en.wikipedia.org/wiki/Ecosystem_services & http://www.earthlyissues.com/images/decomposition.jpg)

 Ecosystem Diversity

• Ecosystem services
(cont.)

• Cultural service:
nonmaterial benefits
i.e. recreational,
ecotourism, etc.

(http://en.wikipedia.org/wiki/Ecosystem_services)
 Biodiversity

•Biodiversity = Ecosystem
+ Species + Genetic
The 6th Mass Extinction

(http://fc03.deviantart.net/fs71/f/2012/265/6/5/sixth_mass_extinction___postcard_size_by_armonah-d5fjm5i.png)
The 6th Mass Extinction

• Habitat loss
• Population growth
• Hunting
• Introduced species
 Species Diversity

•Variety of plants and animals

•Different levels of organization
• Taxonomy and systematics
Taxonomy & Systematics

• Taxonomy is the study of organizing

organisms into groups.

• Systematics is an analytical approach to

understanding the diversity and
relationships of organisms, both present-
day and extinct (Taxonomy + Phylogeny).

• Phylogeny is the evolutionary history of a

species or group of related species.
Taxonomy & Systematics

•Classification: grouping of similar

organisms

•Identification: finding a group for an

unknown organism

•Nomenclature: naming a newly

described organism
 Taxonomy & Systematics
• Who was Carl Linnaeus? Greek: τάξις taxis = “arrangement”
• “Father of Taxonomy” νομία nomia = “method”
• Classification system for living
things

• Defined hierarchies and individual

names (binomial system)

• Named over 12,000 species of

plants and animals

• Systema naturae (published in

1748)
(http://www.linnean.org/Education+Resources/who_was_linnaeus)
 Classification
•Kingdom Animalia
•Phylum Chordata
•Class Mammalia
•Order Primates
•Family Hominidae
•Genus Homo
•Species Homo sapiens
Classification
Species

Genus Panthera
Panthera pardus

Family Felidae

Order Carnivora

Class Mammalia

Phylum Chordata

Kingdom Animalia

Domain Eukaryota
 Classification

Panthera Mephitis Lutra Canis Canis

pardus mephitis lutra familiaris lupus
Species

Panthera Mephitis Lutra Genus Canis

Felidae Mustelidae Family Canidae

Order Carnivora
 Identification

•Key to identification
•Dichotomous key to identification
•Dichotomous = divided into two
parts

•Determine the identities of living

things
(http://shs2.westport.k12.ct.us/mjvl/biology/animalia/dichotomous_key.GIF)
Identification

(http://biology-igcse.weebly.com/dichotomous-keys.html)
 Identification
•Morphological vs. molecular data
•Molecular data
•Use a particular length or sequence
of a particular gene

•8S RNA, 16S RNA, COXI, COXII

•Amplify the gene using PCR
•Compare length or sequence with
known database
 Nomenclature
•What is the binomial system?
•Species-naming system with two
names: genus and specific epithet

•Proposed by Carl Linnaeus

•ICZN: International Code of
Zoological Nomenclature

•ICBN: International Code of Botanical

Nomenclature
Nomenclature

เพรียง?
 Nomenclature
•What is the importance of the scientific
name?

•First letter of the genus is ALWAYS

capitalized.

•The first letter of the species is lowercase.

•The entire scientific name is italicized or
underlined, e.g. Panthera tigris or
Panthera tigris.
 Nomenclature

•Cryptozona siamensis (Pfeiffer, 1856)

(http://libutron.tumblr.com/post/83846705478/cryptozona-siamensis-krabi-province-m-c-claude)
 Nomenclature

• Pseudochelidon sirintarae Thonglongya, 1968

(http://th.wikipedia.org/wiki/นกเจ้าฟ้าหญิงสิรินธร#/media/File:White_eye.jpg)
 Nomenclature

• Cassiopea andromeda Forskål, 1775

(http://en.wikipedia.org/wiki/Cassiopea_andromeda#/media/File:Cassiopea_andromeda_-_Mangrovenqualle.jpg)
Nomenclature
2303101 General Biology:
Unit 5 - Diversity of Life
Asst. Prof. Nontivich Tandavanitj, Ph.D.
Asst. Prof. ar t an ar orn, Ph.D.
Assoc. Prof. Chirasak Sutcharit, Ph.D.
Department of Biology, Faculty of Science, Chulalongkorn University
Taxonomy & Systematics

•Taxonomy vs. systematics

•Taxonomy: the study of naming,
grouping and identification of
organisms.

•Systematics: the study of evolutionary

relationship between organisms.

•Systematics = Taxonomy + Phylogeny

 Phylogeny

• History of descent from a common

ancestor

• Common ancestries are inferred from

fossil, morphological, and molecular
evidence.

• Construction of cladogram and

phytogenetic tree
 Phylogeny

Panthera Mephitis Lutra Canis Canis

pardus mephitis lutra familiaris lupus

Species

Panthera Mephitis Lutra Genus Canis

Felidae Mustelidae Family Canidae

Order Carnivora
Cladogram vs. Phylogenetic Tree

• Cladogram:
reconstruction based on
shared derived characters
= synapomorphies

• Endpoints of the branches

represent the taxa or
group of organisms.

• Nodes represent the taxa

that diverged from
common ancestor.
Cladogram vs. Phylogenetic Tree
 Cladogram vs. Phylogenetic Tree

• Phylogenetic tree:
evolutionary
relationships among
various taxa based on
similarities and
differences in physical
and genetic
characteristics

• Branches represent
evolutionary time and
amount of change.

(https://www.scienceopen.com/document/vid/896686f3-d46d-456a-a986-ee0073de18ba;jsessionid=x-IBdZC5CU52XUSCSQp1iK0p.slave:so-app2-prd?0)
Terminologies
 Terminologies

• Monophyletic: ancestor species and all its

descendants
 Terminologies

• Paraphyletic: an ancestral species and

some, but not all, of the descendants
 Terminologies

• Polyphyletic group: various species that lack

a common ancestor.
Terminologies
Monophyletic Group
Monophyletic Group

• Taxa sharing a
common ancestor
more recent in time
are more closely
related than those
sharing common
ancestors more
distant in time.
 Phylogeny

•Phylogenetic analysis:
•Morphological data
•Physiological data
•Genetic data
•Geologic (fossil) data
 Phylogeny
• How are phylogenetic trees constructed?
• Synapomorphies, using the principle of
parsimony

• Other methods: maximum likelihood,

neighbor joining, Baysian

• Estimates of times of divergence of

lineages, as determined by a molecular
clock analysis
 Maximum Parsimony

•Character-based method that infers

a phylogenetic tree by minimizing the
total number of evolutionary steps
required to explain a given set of
data.

(http://www.icp.ucl.ac.be/~opperd/private/parsimony.html)
Maximum Parsimony
 Phylogenetic Tree

•The best hypotheses for phylogenetic

trees fit the most data:
morphological, molecular, and fossil.

•Sometimes the best hypothesis is not

the most parsimonious.
Phylogenetic Tree
 Molecular Clock

•The molecular clock is a yardstick for

measuring absolute time of
evolutionary change based on the
observation that some genes and
other regions of genomes seem to
evolve at constant rates.
Molecular Clock

(http://www.pnas.org/content/101/17/6536/F4.large.jpg)
Molecular Clock
Molecular Clock