Transcript Life Origins, Classification, Evolution

Life Origins, Evolution, Classification
Edited by L. Bridge
Nov. 2015
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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1.1 Biology: The Study of Life
(A review)
• Biology: The study of living & once living (“paleobiology”) things
• Scientists find it difficult to come up with one single definition for
life, so we use a list of criteria.
• Living things share the following characteristics in common (Is it
alive?):
–
–
–
–
–
–
–
–
Made of cells
Display organization
Require input of energy and materials
Reproduce
Respond to stimuli
Are homeostatic
Grow and develop
Adapt to their environment, evolve
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Evolution of Life
28-3
Origin of Life
• Age of Planet Earth - 4.6
billion years
• Oldest fossils - 3.5 billion
years
– Australian microfossils
– Marine
– Resemble Archaebacteria
4
Chemical Evolution of Life
– The common ancestor for all living things was
the first cell or cells.
– Under the conditions of the primitive Earth, it is
a possibility that a chemical reaction produced
the first organic compounds & then first cell(s).
• Most Probable Formation of the First Cells:
Step 1: Inorganic molecules reacted to form organic
molecules
Step 2: Organic molecules polymerized to become
macromolecules
Step 3: Plasma membrane formed
Step 4: “Protocells” formed
28-5
Oparin’s “Chemosynthesis” Hypothesis
1924- Theorized that small organic molecules
would have then given rise to larger organic
molecules and finally macromolecules (Proteins,
Carbohydrates, Fats, Nucleic Acids)
Alexander Oparin
What we know about the “young” planet earth:
• Early atmosphere: methane, ammonia, hydrogen, carbon
dioxide, & water vapor (no oxygen)
• volatile, volcanic activity, electrical storms, lots of UV (no
ozone)
• To Oparin, this sounded like the “recipe” for a chemical
reaction that would lead to formation of organic molecules
(like amino acids) that would be the components of early
cells!
6
Origin of the First Cell(s)
Can we test/prove
this? Yes, to a point
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Origin of Life
• Evolution of Small
Organic Molecules
– Early life may have
arose in the primitive
oceans, out of a
“primordial soup” of
organic molecules
– Miller and Urey
Experiment (1953)
• Hypothesized that
formation of small
organic molecules is
possible, from
inorganic raw
materials
8
The Result
• At the end of one week of continuous operation Miller
and Urey observed that as much as 10-15% of the
carbon within the system was now in the form of
organic compounds.
• Two percent of the carbon had formed amino acids
• Sugars, lipids, and some of the building blocks for
nucleic acids were also formed.
• Nucleic acids (DNA, RNA) themselves were not
formed.
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Origin of Life
• Evolution of Small
Organic Molecules
– Some scientists
hypothesize life
began in
hydrothermal vents
deep in the ocean
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“Panspermia”
• An alternate theory is
that the earliest
organic molecules
may have arrived on
our young planet in
meteorites
• These molecules
reacted and
condensed into the
earliest cells
Evidence of organic
compounds HAS been
found in recovered
meteorites. The
Murchison and Murray
meteorites are some of
the best-studied
examples.
http://science.nasa.gov/
headlines/y2001/ast20d
ec_1.htm
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More evidence on the origin of the
first cells (“protocells”):
– Under specific conditions of pH, ionic composition, and
temperature concentrated mixtures of macromolecules form
coacervates
– These are cell-like droplets formed from dissimilar substances; linked
a.a. and sugars
– Coacervate droplets absorb and incorporate many substances
– May form a semi permeable boundary around droplet
– In lipid environment, phospholipids are known to automatically
form liposomes-may be the way plasma membranes first formed
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Sidney Fox (1957) created
membrane-bound “microspheres” in
the laboratory
• Although roughly cellular in appearance,
microspheres in and of themselves are not
alive.
• Although they do reproduce asexually by
budding, they do not pass on any type of
genetic material.
• However they may have been important in
the development of life, providing a
membrane-enclosed volume which is
similar to that of a cell.
• Microspheres, like cells, can grow and
contain a double membrane which
undergoes diffusion of materials and
osmosis.
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Origin of Life
• The “True Cell”
– …Is a membrane-bounded structure that can produce
proteins (enzymes) that allow DNA replication
• DNA RNA  Protein
– “RNA-first” hypothesis suggests that RNA developed
before DNA, so first true cell would have had RNA genes
• Some viruses have RNA genes
• Reverse transcriptase produces DNA from RNA
• RNA can act as both a carrier of information and as an
enzyme (“ribozyme”)
• Thomas Cech
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27.1 Origin of Life
• The True Cell – other hypotheses:
– “Protein-first” hypothesis suggest proteins evolved first
• Complex enzymatic processes may have been necessary for
formation of DNA and RNA
• Enzymes may have been needed to produce nucleotides and nucleic
acids
– The Cairnes-Smith hypothesis suggests RNA and protein
evolved at the same time
• RNA genes could replicate because proteins were already present to
catalyze the reactions
• But this supposes that two unlikely spontaneous processes would
occur at once- formation of RNA and formation of protein
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Origin of Life
• The True Cell
– Once protocells had genes, they could selfreplicate, they became capable of
reproducing, and biological evolution began.
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Origin of Life
• The Heterotroph Hypothesis
– Nutrition was plentiful in the ocean: “primordial soup”
– Protocells were most likely heterotrophs
• Implies that heterotrophs preceded autotrophs
– Protocells probably used preformed ATP at first
• Natural selection favored those that could extract ATP from
carbohydrates
• Fermentative process because oxygen was not available
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The probable sequence of events:
1st Heterotrophic prokaryotes: unicellular, simple,
anaerobic, heterotrophic
2nd Chemotrophic autotrophs: “Chemosynthesis”:
carbon dioxide serves as carbon source for creating
organic molecules, like methane; energy derived from
chemical reactions
Archaebacteria similar to 1st autotrophs because
make glucose by chemosynthesis rather than by
photosynthesis
3rd Photosynthetic autotrophs: brought about changes on
earth...helped to add oxygen to the air...
Cyanobacteria
...atmosphere forming, cloud cover, ozone (protection)
4th Cells become aerobic
Important initial function of aerobic respiration may have been to bind oxygen &
prevent damage to early organisms
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• Prokaryotes arose about 3.5 billion
years ago
• Eukaryotes came about 2.1 billion years
ago
• Multicellularity came much later at 700
million years ago
– First Eukaryotes: unicellular; membrane bound
nucleus & organelles
Most evolutionary events occurred in less
than 20% of the history of life!
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How cells are organized
What are the two major types of cells in
all living organisms?
- Prokaryotic cells
Thought to be the first cells to evolve
Lack a nucleus
Represented by bacteria and archaea
- Eukaryotic cells
Have a nucleus that houses DNA
Many membrane-bound organelles
All plant and animal cells are eukaryotic
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The “Endosymbiont Hypothesis”
Endosymbiosis:
• Eukaryotic cells may have evolved
from large prokaryotic cells invaded
by small prokaryotic cells
• Smaller, embedded cells may be
ancestors of organelles;
mitochondria/chloroplasts
• Supporting evidence
– Both mitochondria & chloroplasts
contain own genes, different
from rest of cell
– Replicate independently from
replication cycle of cell
– Found in circular piece of DNA;
prokaryotic arrangement
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The Concept of Evolution
• In biology evolution is simply defined as biological
changes that have occurred in living organisms since the
beginning of life.
• Evolution is “descent with modification”, which is possible
because of the changeability/malleability of the DNA code.
– “Modifications” = random mutations can constantly change
genotypes/phenotypes from generation to generation = novel
variations of traits in the population
• Evolution assumes a certain relatedness (“common
ancestry”) between organisms.
Evolution “for dummies 9:58
http://www.youtube.com/watch?v=SeTssvexa9s
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Evolution is the Unifying Principle of Biology
Evolution accounts for life’s unity and diversity
• The history of life
– Is a saga of a changing Earth billions of years old
• The evolutionary view of life
– Came into sharp focus in 1859 when Charles
Darwin published On the Origin of Species by
Natural Selection
Figure 1.18
Darwin based his
idea on the
understanding of
human-influenced
selective breeding of
domestic animals
Darwin’s basic suppositions in “On the Origin of Species…”
• Variation (due to?)
• Competition (for?)
• Natural selection (the environment
decides…)
– “the cruelty of nature”
– “the struggle for existence”
– differential reproduction
– “survival of the fittest” (Herbert
Spencer)
Figure 1.19
Natural Selection
• Darwin proposed natural selection as the
mechanism for evolutionary adaptation of
populations to their environments
Population
of organisms
Hereditary
variations
Define
“adaptation”?
Figure 1.20
Overproduction
and struggle for
existence
Differences in
reproductive success
Evolution of adaptations
in the population
• Natural selection is the evolutionary process that
occurs when a population’s heritable variations are
exposed to environmental factors that favor the
reproductive success of some individuals over others
1
Populations with varied inherited traits
2 Elimination of individuals with certain traits.
3 Reproduction of survivors.
Figure 1.21
4 Increasing frequency of traits that enhance
survival and reproductive success.
• Each species is one “twig”
of a branching tree of life
(phylogeny)
– Extending back in time
through ancestral species
more and more remote
• All of life
– Is connected through its
long evolutionary history
A Case Study in Natural Selection: Mimicry
• In mimicry
– A harmless species resembles a harmful
species
Flower fly
(non-stinging)
Honeybee (stinging)
Figure 1.26
Evolutionary Divergence
http://whyevolutionistrue.wordpress.com/2012/07/24/a-new-study-ofpolar-bears-underlines-the-dangers-of-reconstructing-evolution-frommitochondrial-dna/
• Darwin proposed that natural selection
– Could enable an ancestral species to “split” into two or
more descendant species, resulting in a “tree of life”
Large
ground finch
Large cactus
ground finch
Small
ground
finch
Large
tree finch
Camarhynchus
Green
Geospiza
Gray
Geospiza
magnirostris
psitacula
warbler
warbler
Sharp-beaked
fuliginosa
Woodpecker Medium
Geospiza Medium
finch
finch
tree
finch
ground finch
finch
conirostris ground
finch
Certhidea Certhidea
GeospizaCactus
Cactospiza Camarhynchus olivacea fusca
difficilis ground finch
pauper
pallida
Geospiza Mangrove
Small tree finch
finch
fortis
Geospiza
Camarhynchus
Cactospiza
scandens
parvulus
heliobates
Vegetarian
Cactus flower
Seed eater
Seed eater
finch
eater
Platyspiza
crassirostris
Insect eaters
Ground finches
Tree finches
Bud eater
Warbler finches
Ex: Allopatric speciation
Figure 1.23
Common ancestor from
South American mainland
Unity in the Diversity of Life
• As diverse as life is
– There is also evidence of remarkable unity
15 µm
1.0 µm
Cilia of Paramecium.
The cilia of Paramecium
propel the cell through
pond water.
5 µm
Figure 1.16
Cross section of cilium, as viewed
with an electron microscope
Cilia of windpipe cells. The cells that line the human windpipe
are equipped with cilia that help keep the lungs clean by moving
a film of debris-trapping mucus upward.
Drawing evolutionary trees
The phenetic approach is popular with molecular
evolutionists because it relies heavily on character data
- such as sequences - and requires relatively few
assumptions.
In this approach, a tree is constructed by considering
the phenotypic similarities of the species without trying
to understand the evolutionary history that brought the
species to their current phenotypes.
Evolutionary trees (Berkeley)
Cladistics bases classification of a
group of species solely on their most
recent common ancestor. Cladistics
uses shared derived characters.
Animation “How to build a cladogram”
YouTube lesson on how to make a cladogram
(10 min)
Practice worksheet
• Concept 1.3: Biologists explore life across
its great diversity of species
• Diversity is a hallmark of life
Figure 1.13
Classification of Living Things
• Over a million species
named (so far)
• More identified every day
• 2-20 Million left to find?
• Why? Need to organize
information
• Taxonomy = science of
identifying and classifying
organisms
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Classifying life
• Taxonomy
–
Is the branch of
biology that names
and classifies
species according
to a system of
broader and
broader groups
Species Genus Family
Order
Class
Phylum
Ursus
americanus
(American
black bear)
Ursus
Ursidae
Carnivora
Mammalia
Chordata
Animalia
Figure 1.14
Eukarya
Kingdom
Domain
The Three Domains of Life
–
Distinguished based on biochemical
evidence (differences in rRNA, genes)
–
Domains Archaea and Bacteria are
unicellular organisms lacking
membrane-bound organelles like
nuclei (Prokaryotes)
–
Domain Eukarya is organisms whose
cells have nuclei (Plants, Animals,
Fungi and Protists)
Classification of Living Things
• 3 Domains
• Kingdom
• Phylum (Division for
plants)
• Class
• Order
• Family
• Genus
•
Species
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Domain Archae
• Prokaryotes
– Single celled
– Complex metabolic ability
• Kingdom Archaebacteria
– Found in extreme
environments
– Environments similar to
those of early earth
– First organisms similar to
Archaea?
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Domain Bacteria
• Kingdom Eubacteria
– Found almost everywhere
– More of them than any other
living thing
– Some are parasites, causing
diseases
– Most are harmless and many are
vital to human well being
• Decompose our wastes
• Make vitamins in our guts
• Producing certain products
that we use (yogurt, cheese)
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Domain Eukarya
– Protista- one celled
organisms- producers or
consumers (or both)
– Fungi- molds, mushrooms;
mostly decomposers
– Plantae- multicellular
plants; mostly producers
– Animalia - multicellular
animals from sponges to
humans; consumers
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Classification of Living Things
• Within Kingdoms, organisms are sorted into Phylum,
Class etc.
• At species level organisms so closely related they can
interbreed
• Scientific name = Genus and species names (binomial
nomenclature
ex. Felis catus, Drosophila melanogaster, Homo sapiens
• Genus includes other similar species
ex. F. leo and F. tigris or Quercus rubra, Quercus alba
• Genus ALWAYS starts with cap, species lower case
• Genus and species names are always either underlined or
italicized
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Example: How are humans related to other
animals?
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Human
Eukarya
Animalia
Chordata
Mammalia
Primates
Hominidae
Homo
sapiens
House cat
Eukarya
Animalia
Chordata
Mammalia
Carnivora
Felidae
Felis
catus
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Evidence for Evolution
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Phylogeny: the study of the evolutionary
history of groups of organisms
Plant evolution
(cladogram)
Like a “family tree”
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Primates
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Fossils as Evidence of Evolution
– Hard body parts are preserved
in most cases
trilobite
– Often embedded in sedimentary
rock
– Deposited in layers called strata
• Each stratum is older than the one
above and younger than the one
below
– “Transitional fossils”
• Especially significant finds;
represent evolutionary links
between groups
However fossilization is a relatively
uncommon occurrence, usually
requiring hard body parts and death
near a site where sediments are
being deposited, the fossil record
only provides sparse and intermittent
information about the evolution of
life.
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Transitional Fossils
example: Archaeopteryx
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Vertebrate groups
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New Fossils Of Extremely Primitive 4-Legged Creatures Close The
Gap Between Fish And Land Animals
ScienceDaily (June 27, 2008)
— New exquisitely
preserved fossils from
Latvia cast light on a key
event in our own
evolutionary history, when
our ancestors left the
water and ventured onto
land. Swedish researcher
Per Ahlberg from Uppsala
University and colleagues
have reconstructed parts
of the animal and explain
the transformation in the
new issue of Nature.
Tiktaalik
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Geological Evidence of Evolution
• Geological Timescale
– History of Earth is divided into eras, then periods, and then
epochs
– Based on dating of fossil evidence
– Relative dating method – determines the relative
order of fossils because the fossil-containing
sedimentary rocks occur in layers. Top layers are
younger and thus the fossils in them are younger.
Thus it is a matter of “What came first, second, third”
– Absolute dating method - radioactive carbon dating
(radiometric dating): Makes use of radioactive
elements that decay into other more stable elements
according to a strict timetable.
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Radioisotope Dating
• Ex: Radioactive 14C (In Organic Matter) changes into 14N
(1/2 of 14C will change into 14N in 5,730 yrs)
• Assuming that organic matter always begins with the same
amount of 14C.
• Goal is to compare the 14C radioactivity of the fossil to that
of a modern sample of organic matter. The amount of
radiation left in the fossil can be converted to the age of the
fossil.
• Other similar methods are used to date rocks that are
thought to be billions of years old.
ex: Starting with 8g of 14C, down to 1g; how much time has elapsed?
ans: 8  4  2  1 = 5730 + 5730 + 5730 = 17,190 yrs
27-54
Commonly used radioisotopes for dating:
Parent
Daughter
Change in…
Carbon-14
Nitrogen-14
5730 years
Uranium-235
Lead-206
4,470 million yrs
Potassium-40
Argon-40
1,208 million yrs
Thorium-232
Lead-208
14,010 million yrs
Rubidium-87
Strontium-87
48,800 million yrs
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Geological/Fossil Evidence of Evolution
• Background extinctions
• “Mass Extinctions”
– Large numbers of species become extinct in a short period of time
• Remaining species may spread out and fill habitats left vacant
– Five Major Extinctions have occurred
– It is proposed that many mass extinctions have resulted from
extra-terrestrial events, volcanism, atmospheric fluctuations, global
warming, cooling (ice ages), sea levels, etc.
• However, a current SIXTH one is in progress due to human
encroachment
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The last major mass extinction
• The K-T Event
– 65 million yrs ago
– Killed off the dinosaurs, among others
– Marked the end of the Cretaceous period,
beginning of Tertiary
• Clay from that period is high in iridium, an
element in meteorites
• Proposed that meteorites hit Earth and dust
filled the atmosphere
– Blocked sunlight, plants died
– One reason why we don’t see some of the
evolutionary ancestors today is because of
mass extinctions.
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Biogeographical Evidence of Evolution
Biogeography is the study of the geographic
distribution of species throughout the world
– The Earth has six biogeographical regions
• Each has its own distinctive mix of species
– Barriers prevented evolving species from migrating to other
regions
– Continental Drift• The positions of continents and oceans has shifted
through time
• The distribution of fossils and existing species allows us
to determine approximate timeline
• Example: oldest camel fossils 45-40 mya in N. America!
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Continental Drift
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Distribution of Large
Cats
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Evidence of Evolution: Anatomical Evidence
• Common descent offers
explanation for anatomical
similarities
• Homologous
Structures
– Same underlying structure,
adapted for different
functions, same embryologic
origin
– Likely inherited from a
common ancestor
• Ex: human arm and whale
forelimb
63
Analogous Structures
Same basic function but
different hereditary
origins.
Underlying anatomy is
different, thus unlikely
to have evolved from
common ancestor
ex: wing of bird and wing
of an insect
Not a good indicator of relatedness. More
likely due to convergence.
64
Anatomical Evidence: Vestigial Structures
Anatomical structures fully functional in one group and reduced,
nonfunctional in another
Ex: Modern whales have a pelvic girdle and hind leg bones
65
Probable origin of appendix
Gastric caecum in herbivores
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Evidence of evolution
: Embryological Development
67
Biochemical Evidence
of Evolution
– All organisms use same basic biochemical
molecules
• DNA coding: A,T,C,G
• Amino acid sequence of proteins
– Many developmental genes are shared
(homeotic)
– Degree of similarity between DNA base
sequences (and amino acid sequences of
similar protein) indicates the degree of
relatedness
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Compare a homologous (shared) gene sequence.
This can be used to quantify similarities/differences.
•
•
•
•
•
Canis lupus familiaris
Canis lupus lupus
Canis lupus dingo
Vulpes vulpes
Canis rufus
Provides verifiable data.
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70
…Or can use a shared protein sequence for
comparison
Muscle myosin
sequence
71
The Molecular Clock
• Based on the molecular clock
hypothesis (MCH), this relates the
amount of time since two species
diverged to the number of molecular
differences measured between the
species' DNA or protein sequences or
proteins.
• It is sometimes called a “gene clock” or
“evolutionary clock”.
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The Molecular Clock
73
Significance of Biochemical Differences
74