Transcript lecture 14, history of life, condensed - Cal State LA

Characteristics of Life
Living organisms have two principle characteristics:
(1) the ability to store and transmit information (genotype)
- reproduction: ability to pass information to offspring
(2) the ability to express that information (phenotype)
- growth, morphology, etc.
Both contribute to evolution:
(1) the ability to store information in a changeable way
(mutation, heritability) is handled by the genotype
(2) good vs. bad changes in phenotype are sorted out by
selection (sees your appearance, not your genes)
Origin of Life on Earth: First genetic material
DNA is amazingly stable; the double helix leads to reliable
storage and replication (copying) of genetic information
However, DNA can’t express information: it doesn’t do anything
What were the 1st molecules that had a genotype & phenotype?
- that is, both stored information and performed jobs?
Evidence suggests that RNA may have been the original source
material for life, in the earliest primitive cells
An RNA world?
RNA is found in all cells
- integral part of ribosomes
- ribonuceoside triphosphates (ATP, GTP) are basic units
for energy transfer in cells
Unlike DNA, RNA can fold into a 3-D shape by base pairing
this shape can have an active site that performs a
chemical reaction, just like a protein enzyme
RNA can catalyze chemical reactions
thus, some RNAs have a phenotype which means they
could evolve by natural selection on their function
RNA catalysis
RNA catalysis was discovered in protozoans with selfsplicing RNA
- introns in ribosomal RNA sequences can cut themselves
out of the rRNA transcript
The RNA component of ribosomes actually performs the critical
reaction of joining 2 amino acids together in peptide synthesis
RNAs have been made that catalyze diverse reactions, all
relevant to early life:
- carbon-carbon bond formation
- phosphorylation
- cleavage of DNA
Can a catalytic RNA sequence evolve?
RNA has the 3 necessary features for evolution: heritability,
variation through mutations, selection based on its phenotype
Experiments show RNA sequences can evolve in the laboratory,
“adapting” to perform a reaction more efficiently
After 10 generations of selection, RNAs were 30 times better at
catalyzing a DNA cleavage reaction
- mutations at 4 particular sites  improved function
Specific RNAs therefore had higher fitness after selection,
showing that they can evolve like living things
Snag: no RNAs are yet known that can copy themselves,
the essential requirement for a true “RNA world”
A common ancestor for all life on earth
All lineages of life are believed to be descendents of one
common ancestor, due to universal shared characteristics:
- all use DNA; RNA-based ribosomes; proteins
- same basic genetic code with few modifications
- same 20 amino acids
Critical development: membranes around earliest cell
- concentration gradients could be established
- this kept phenotypes localized to the genotype that made
them
Microfossils and the earliest life…?
Earth formed about 4.5 billion years ago
- heavily bombarded by meteors until 4 billion years ago
Earliest terrestrial rocks dated at 3.85 billion years old
- do these rocks contain fossil evidence of the earliest life?
Actual earliest fossils of life
Earliest probable fossil cells are 3.46 billion years old
- believed to be chains of filamentous bacteria
These are complex cells that
were already pretty evolved
- cannot represent the
earliest bacteria
Cells thus appeared on
earth very soon after
earth was cool enough
to support life at all
Archaea + Eubacteria ruled the earth
earth is
habitable
earth
forms
1st fossil
bacteria
4.5
billion
3.5
billion
1st fossil
eukaryotes
1st fossil
animals
1.5
billion
575
million
YEARS BEFORE PRESENT
Phylogeny of all living things
A universal phylogeny can be used to try to figure out what
the earliest common ancestor of all living things was like
Compare a gene that is so important, it is widely conserved in all
living organisms
- that way, creatures as different as a person and a bacteria
have sequences similar enough to compare
Nuclear small ribosomal RNA gene is strongly conserved
by stabilizing selection; this permits comparisons of its DNA
sequence across all living things
Phylogeny of all living things
“extremeophiles”
Universal phylogeny and the Tree of Life
Genetic analyses do not support classical 5 kingdom system:
- animals, plants, fungi, “protists”, “bacteria”
“bacteria” actually comprise two distinct branches:
(1) Eubacteria include most common bacteria
- photosynthetic cyanobacteria (made our atmosphere)
(2) Archaea are poorly known, often “extremophiles”
- thermophiles from hot springs, halophiles from high salt
- more closely related to eukaryotes than to Eubacteria
- widespread (but unculturable) in ocean plankton
 may actually contain 2 divergent kingdoms
Endosymbiosis & the Eukaryotes
Key events in the success of complex cells:
eukaryotes acquired endosymbionts (their mitochondria &
chloroplasts)
burst of morphological diversification
Based on genome analysis:
mitochondria are descended from a-proteobacteria
- mitochondria evolved from an intracellular bacterium that
gave its host cell a much more efficient metabolism
chloroplasts are descended from cyanobacteria, a group of
photosynthetic bacteria
less than 10%
of sequence
diversity of life
Eukaryotes
Many groups were traditionally lumped together as “protists”
but protists are not a monophyletic group
- ameobas, ciliates, slime mold, seaweeds...
- most of these groups are very divergent from each other
Animals, plants and fungi all lump together on the tip of the
eukaryote branch of the tree
- each group is descended from a protist ancestor
- contain less than 10% of the gene sequence diversity of life
- however, these 3 multi-cellular groups represent the
pinnacle of body plan diversity and complexity
Cambrian
explosion
start finish
earth is
habitable
1st fossil
eukaryotes
earth
forms
1st fossil
bacteria
4.5
billion
3.45
billion
1st fossil
animals
1.5
billion
YEARS BEFORE PRESENT
565 523
MYA
The Cambrian explosion
1st multicellular animal fossils date to 575 million years ago (Ma)
Over a 20-million yr period (532-512 MYA), all modern animal
phyla and several extinct groups appeared
animals having no tissues (sponges),
or only 2 embryonic tissues (cnidarians: corals, anemones)
animals with 3 early tissue types and bilateral symmetry,
the Bilateria: - all higher invertebrates
- vertebrates (early fish)
basically, everything with a head and crawling direction
All major body plans, tons of morphological diversity appeared
“overnight” in geological terms
The Cambrian explosion: fossil records
Early multicellular animals are well preserved in 2 fossil faunas
(1) Ediacaran fauna (late Pre-Cambrian; before the Explosion)
- soft-bodied impressions of sponges, jellyfish
- trace fossils (tracks) of bilaterally symmetric animals?
jellyfish impression fossils
trace
fossil –
worm
tracks?
The Cambrian explosion: fossil records
Early multicellular animals are well preserved in 2 fossil faunas
(1) Ediacaran fauna (late Pre-Cambrian; before the Explosion)
- soft-bodied impressions of sponges, jellyfish
- trace fossils (tracks) of bilaterally symmetric animals?
(2) Burgess Shale (520 Mil yr ago; after the Cambrian began)
- most existing Bilaterian animals
- extraordinary details of diverse arthropods, worms, molluscs
- primitive vertebrates (like hagfish) already present
- some forms so wild, cannot be classified
Some Bilaterians existed in late Pre-Cambrian, but did not
diversify until the early Cambrian
Burgess Shale recorded the Cambrian fauna
worms
arthropods
What led to the Cambrian explosion?
Explosive innovation in body plans stemmed from 2 factors:
(1) morphologies of major groups diversified via changes in
genetic regulatory networks that organize development
(2) environmental changes triggered ecological interactions,
and led to adaptive radiations in new ecosystems
- higher oxygen levels (abiotic environmental change)
- arms races among predators and prey
- mass extinction that opened new niches?
Cambrian explosion 1: Developmental regulation
Bilaterian body plan diversity may have arisen via changes in
gene networks or interactions, rather than changes in the
actual genes themselves
Certain master regulatory genes are called homeotic genes
- conserved across all animals
- contain DNA-binding domain, the homeobox
- transcription factors that turn on other, functional genes
- specify positional information early in development
Some are found in a cluster of related Hox genes
same cluster of genes, in same order, found in all animals!
- mutations in Hox genes cause huge changes to body
Homeobox genes and body plans
Flies with mutations in Antennapedia Hox gene grew legs on
their heads, instead of antennae
- without this gene saying “you are on the head,” cells grew
into legs by default
normal
mutant
Homeobox genes and body plans
Hox dictate
head-to-tail position
in all animals
Are arranged in the same
order on the chromosome
in which they act to
specify body position!
Cambrian explosion 2a: Oxygen
Primitive animals depended on inefficient diffusion to get O2
distributed to their cells
Oxygen levels in the atmosphere were low until early Cambrian
- produced by photosynthetic cyanobacteria
Higher O2 could have made larger animal bodies possible at
the beginning of the Cambrian era
perhaps allowed natural selection to overcome a
functional constraint that limited prior evolution
(can’t be big if you can’t get enough O2 to your cells)
Cambrian explosion 2b: Arms races
Environmental change  adaptive radiation  predation
Diversification of new predatory animals resulted in appearance
of morphological features like tubes, armor, skeletons
- animals became a major part of the selective landscape
- ecology played a prominent role in the explosive origin of
diverse new body plans and structures
Both environmental and ecological changes produced new
opportunities for bilaterian groups that were “biding their time”
- the Cambrian explosion resulted from the interplay between
genetic possibility and environmental opportunity
Cambrian explosion 2c: Mass extinction
Geological evidence indicates a major disruption in the global
carbon cycle between the Ediacaran and Cambrian faunas
- comparable disruptions are known for other points that
coincide with mass extinctions
Removed dominant diploblastic competitors, allowing Bilaterian
animals to flourish
- removal of dominant species allowed existing Bilaterian
clades to undergo adaptive radiation & morphological evolution
Mass extinctions
Cambrian explosion was a rapid appearance of new lineages
At 5 points in history, 50-90% of extant species disappeared
over a period of just one million years: mass extinctions
- end Permian, 250 million years ago (Ma)
- most severe of all; 90% of marine species vanished
- Triassic-Jurassic boundary, 215 Ma
- Cretaceous-Tertiary (K-T event), 65 Ma
- killed the dinosaurs
Big 5 mass extinctions
5 events eliminated 20-60% of all families of plants and animals
- not species, not genera -- whole families got wiped out
end Permian extinction: 90% of all marine
species gone
end Cretaceous extinction,
65 million years ago:
bye-bye dinosaurs
Mass extinctions vs. background extinctions
Despite their immediate impact, the Big 5 mass extinctions only
account for 4% of total extinctions over the last 500 million yrs
- 96% of species suffer background extinctions
- they just die out, or differentiate into new species
Episodic mass extinctions are important because they clear the
way for new adaptive radiations
(1) what causes them?
(2) why do some species survive them?
Causes of mass extinction: Deep Impact
Many forms of evidence support asteroid impact theory of K-T
mass extinction, possibly others as well
(1) iridium layer in rocks at the K-T boundary
- rare on earth, common in meteors
(2) microtektites also found in rocks at K-T boundary
- little glass particles formed when minerals melt at impact
- cool while flying through the air
(3) huge crater found off Mexican coast, 180 Km diameter,
dating to K-T boundary
(4) extraterrestrial origin suggested for noble gases trapped in
“buckey balls”, carbon spheres found at extinction boundaries
Causes of mass extinction: Deep Impact
K-T Impact likely had numerous environmental consequences
(1) injected SO2 and water into atmosphere, producing acid rain
(2) global cooling as dust blocked sunlight
(3) huge wildfires
(4) massive earthquake and tidal wave, supported by geological
evidence
(5) massive die-off in ocean phytoplankton
(photosynthetic plankton) disrupted marine food chains
Survivor’s guide to mass extinction
Studies on marine snails (good fossil record) indicate that the
lineages which survived mass extinctions had member species
scattered in many different biomes, or environmentally
different regions of the world
In other words, more biogeographically diverse lineages had less
chance of being wiped out
- good to have some species in the deep sea, some tropical,
some at the poles, etc
- hedges against the total wipeout of any one niche or region
following a deep impact
# of families
Plant Evolution following Mass Extinctions
Gymnosperms
Seedless
dominate
plants
Angiosperms dominate
First
First
gymnosperms angiosperms
Lineages are often around, but not very successful, until a mass
extinction event wipes out the dominant competitors
 clears the way for adaptive radiation
Mackenzie 2003
Humans & the current mass extinction
North America used to have lions, camels, elephants, and other
giant land-animals
- all disappeared roughly 10,000 years ago, same time that
humans first crossed the land bridge from Asia
Australian used to have many species of giant marsupials
- all disappeared after humans first arrived
Same pattern all over the world: on every continent or island,
all large land animals disappeared within 1,000 years of the
arrival of humans
Humans & the current mass extinction
The only place large mammals survived: Africa & southern Asia
- there, animals had co-evolved with humans for hundreds of
thousands of years
Did elephants, lions etc learned to avoid the intelligent monkeys
who were taking over the place?
- on other continents, we likely wiped them out before they had
a chance to learn to stay away from us
Humans & the current mass extinction
Following human colonization of Pacific Islands, 2000 species
of birds have gone extinct in the last 2000 years
- as only 9000 species of birds exist, humans have recently
erased 20% of all bird species
Extinctions now occur at 10 to 1000 times background rate
- primarily a result of habitat loss due to human incursion
- also a byproduct of invasive species wiping out endemics
- if sustained for another few centuries, will produce the 6th
mass extinction event (the Human Meteor)
Extinction
Why don’t organisms simply adapt to human predation, or to
invasive species, or to climate change?
Adaptation takes time..
- for mutations to occur, supplying new alleles in the 1st place
- for beneficial alleles to be fixed by selection
The major challenge facing organisms today is rate of change
in their environment
- conditions change too fast for adaptation to occur
- extinction follows
Body Plan evolution
Body plan is the product of development: genetic information
is converted into tissues + organs, relative positions, numbers
and shape of limbs...
“Why should there be so much variety and so little real novelty?”
- Darwin, 1872
 why are there only a handful of different body plans,
but so many variations on each plan?
Holland (1998) proposed 6 major developmental transitions
during the evolution of animals
 big changes in master genes controlling development,
leading to major alterations to body plans
origins of
four limbs,
jaw arches
6
5 double genome
4 axis flip
duplication
3 bilateral symmetry, mesoderm
2 radial symmetry
1 multi-cellularity
Last common ancestor of all animals
Step #1 – evolution of multi-cellularity
- no tissues yet, no gut
Last common ancestor of Metazoans
Step #2 – tissues, including nerves
- radial symmetry
- incomplete gut
Last common ancestor of Bilaterians
Step #3 – Bilateral symmetry + head
- 3rd tissue layer in embryos
- complete digestive system
Body Plan evolution
Step 4 - inversion of dorsal-ventral axis of deuterostomes
- front-to-back axis flipped in the ancestor of deuterostomes
(starfish and vertebrates)
dorsal (back)
ventral (belly)
worm
you
gut
gut
nerve
chord
nerve chord
(backbone)
origins of
four limbs,
jaw arches
6
5 double genome
4 axis flip
duplication
3 bilateral symmetry, mesoderm
2 radial symmetry
1 multi-cellularity
By step 2: one ancestral Hox gene had duplicated into a
cluster of related genes controlling body pattern
Step 5 involved duplication of whole gene clusters
- double-duplication of Hox cluster produced new master
regulatory genes that could diversify & adopt new roles
- produced changes in body plan complexity
double-duplication of Hox gene cluster in vertebrate ancestor
Hox
genes
Bilaterians
duplication
ancestral
vertebrate
duplication
mouse
vertebrates got 4 sets of genes controlling body patterning
 huge increase in complexity, especially of nervous system
Why you can think
The diversification of gene function, made possible by big
duplications, may have made possible the development of
complex nervous systems in the vertebrates