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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 Characteristics of Life

Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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Page 1: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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)

Characteristics of Life

Page 2: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Origin of Life on Earth: First genetic material

Page 3: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 4: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

RNA catalysis was discovered in protozoans with self- splicing 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

RNA catalysis

Page 5: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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”

Can a catalytic RNA sequence evolve?

Page 6: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

A common ancestor for all life on earth

Page 7: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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?

Page 8: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 9: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

earthforms

4.5 3.5 1.5 billion billion billion

1st fossilbacteria

earth ishabitable

1st fossilanimals

575million

1st fossileukaryotes

Archaea + Eubacteria ruled the earth

YEARS BEFORE PRESENT

Page 10: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 11: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Phylogeny of all living things

“extreme-ophiles”

Page 12: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 13: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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 -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

Page 14: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

less than 10%of sequencediversity of life

Page 15: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 16: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

earthforms

4.5 3.45 1.5 billion billion billion

1st fossilbacteria

earth ishabitable

1st fossilanimals

Cambrianexplosion

start finish

565 523MYA

1st fossileukaryotes

YEARS BEFORE PRESENT

Page 17: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

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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?

Page 19: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 20: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Burgess Shale recorded the Cambrian fauna

worms

arthropods

Page 21: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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?

Page 22: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 23: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Homeobox genes and body plansFlies 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

Page 24: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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!

Page 25: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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)

Page 26: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 27: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 28: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 29: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Big 5 mass extinctions5 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

Page 30: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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?

Page 31: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 32: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 33: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 34: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Mackenzie 2003

Seedlessplants

Gymnospermsdominate

Angiosperms dominate

First gymnosperms

Plant Evolution following Mass Extinctions

# of

fam

ilies

First 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

Page 35: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 36: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 37: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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)

Page 38: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 39: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Body Plan evolution

Page 40: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

1 multi-cellularity

2 radial symmetry

3 bilateral symmetry, mesoderm

4 axis flip 6

5 double genome duplication

origins of four limbs, jaw arches

Page 41: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Sponges

Last common ancestor of all animals

Step #1 – evolution of multi-cellularity

- no tissues yet, no gut

Page 42: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Sponges

Cnidarians

Last common ancestor of Metazoans

Step #2 – tissues, including nerves

- radial symmetry

- incomplete gut

Page 43: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

Sponges

Cnidarians

Acoel’s

Last common ancestor of Bilaterians

Step #3 – Bilateral symmetry + head

- 3rd tissue layer in embryos

- complete digestive system

Page 44: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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)

worm

gut

nervechord

you

gut

nerve chord (backbone)

dorsal (back)

ventral (belly)

Page 45: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

1 multi-cellularity

2 radial symmetry

3 bilateral symmetry, mesoderm

4 axis flip 6

5 double genome duplication

origins of four limbs, jaw arches

Page 46: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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

Page 47: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

double-duplication of Hox gene cluster in vertebrate ancestor

Hoxgenes Bilaterians

ancestralvertebrate

mouse

vertebrates got 4 sets of genes controlling body patterning

huge increase in complexity, especially of nervous system

duplication

duplication

Page 48: Living organisms have two principle characteristics: (1) the ability to store and transmit information (genotype) - reproduction: ability to pass information

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