biol 1010 introduction to biology: the evolution and diversity of...

BIOL 1010 Introduction to Biology: The

Evolution and Diversity of Life. Spring 2011

Sections A & BSteve Thompson: [email protected]

http://www.bioinfo4u.net1

Tuesday, January 25, 2011

mailto:[email protected]

mailto:[email protected]

http://www.bioinfo4u.net

http://www.bioinfo4u.net

First, what about that Hippogryph!

2

eats

fres

h m

eat,

flies

(bad

choic

e),

runs

(bad

choic

e),

live b

irth,

hair,

feat

hers

,

beak

,

face

,

eyes

,

win

gs,

uppe

r for

elim

bs,

talon

s,

ears

,

man

e,

ches

t,

abdo

men

,

tail,

hind

legs

,

hoov

es

✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔ ✔

✔ ✔ ✔ ✔ ✔ ✔ ✔

✔ ✔ ✔ ✔ ✔ ✔ ✔

Ungu

late

Car

nivo

re

Bi

rd

10 counts

7 counts

7 counts

2 1 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1


We can look at this a couple of different ways.

If we take a phenetic, total evidence, sort of approach, then the hippogryph must be a bird because more characters argue for ‘birdness,’ even if we exclude possible convergences like running and flying (8 versus 6 versus 6).However, if we use the rules of parsimony and only consider shared derived characters then we can really only consider the light blue shaded columns. Counted that way the best explanation is that it is a carnivore (1 versus 3 versus 2).So, you see, there really is no ‘correct’ answer.

3Tuesday, January 25, 2011

On to . . .Origins and Deep Time

— hard to imagineThe earth is so old that is is hard to get a real feeling for the length of time, and yet, relatively speaking, life began in the blink of an eye.

4

http://en.wikipedia.org/wiki/Geologic_time_scale and http://www.palaeos.com/


http://en.wikipedia.org/wiki/Geologic_time_scale

http://en.wikipedia.org/wiki/Geologic_time_scale

http://www.palaeos.com/

http://www.palaeos.com/

4.6 Billion Years is a very long time!John McPhee in Basin and Range (1981): “Consider the earth's history as the old measure of the English yard, the distance from the King's nose to the tip of his outstretched hand. One stroke of a nail file on his middle finger erases [all of] human history.” This video does a great job: http://seedmagazine.com/content/article/the_evolution_of_life_in_60_seconds/, and see . . .http://bcn.boulder.co.us/basin/local/sustain2.htmhttp://www.rps.psu.edu/time/deep_time.htmlThe PBS Evolution series does a really nice job on the topic: http://www.pbs.org/wgbh/evolution/change/deeptime/index.html and see http://exploringtime.org/ 5


http://seedmagazine.com/content/article/the_evolution_of_life_in_60_seconds/






http://bcn.boulder.co.us/basin/local/sustain2.htm

http://bcn.boulder.co.us/basin/local/sustain2.htm

http://www.rps.psu.edu/time/deep_time.html

http://www.rps.psu.edu/time/deep_time.html

http://www.pbs.org/wgbh/evolution/change/deeptime/index.html




http://exploringtime.org/




It was a really nasty place for over 500 Million years!

Solid matter condensed to form the solar system, hence planets, about 4.6 BYA.The Earth cooled enough to have a crust (≈900-1800º F) about 4.2-4.1 BYA.Most theories say ≈400 Million years of heat high enough to keep rock molten!


And then, BANG . . . Life’s OriginsMost scientists accept that life arose from simple chemical substances on Earth at the time — the “primordial soup.”This is consistent with cell theory, because the conditions under which life originally formed no longer exist on earth. There was nothing bigger and badder to ‘eat’ what was forming!Fact (based on microfossils): Simple cells arose 4.2–3.85 BYA, only around a 100 Million years after the crust formed!http://science.nationalgeographic.com/science/prehistoric-world/prehistoric-time-line.html


http://science.nationalgeographic.com/science/prehistoric-world/prehistoric-time-line.html




The Hadean/Archean world4 BYA was very different!Today’s atmosphere is rich in CO2, N2, H2O, and O2. However, . . .Oparin (1938) thought the early atmosphere had CH4, NH3, H2O and H2. Little O2 would have been available.Without O2 the chemical reactions that form amino acids and nucleotides would have been possible. Perhaps . . .


Something really cool could happen. Based on that sort of reasoning, Miller’s (1953) experiment . . .

Glass enclosure with Oparin’s four gases;Electric discharge to simulate lightning ;Made glycine and other amino acids.First prebiotic simulation.


Subsequent refinements, e.g. including high concentrations of CO2, continue to produce

many organic compounds, including nucleotides.Hydrothermal vents may mimic early conditions.

More recent simulations duplicate deep sea vents, . . .Where hot water meets cold water, alongwith a . . .Rich brew of chemicals from the Earth’s interior.

And there’s a possible role of clays! Clays . . .Can form templates that molecules bind to.Some can release electrons to provide energy.First RNA molecules may have formed on clay.


Chains of nucleotides could have built up on clay surfaces.Minerals may have served as a catalyst, and . . .The sun may have provided energy.


Many think that RNA ‘ruled’ for a while.This is known as the “RNA World” hypothesis.It describes how self-replicating RNA may have been the first independent form of life on Earth.RNA is informational, can replicate, and can also be catalytic, “ribosymes.”“Once a genetic material can replicate, life would have taken off.” (Stanley Miller).The RNA could have begun encoding polypeptides. Those that made more sophisticated ones would outcompete RNAs that made less competitive polypeptides.Reverse transcriptase may have eventually evolved, which would have then made DNA from RNA.And DNA is much more stable than RNA.


Eventually membranes were needed to compartmentalize the biochemistry.Liposomes are phospholipid bilayer membrane bound ‘bubbles,’ that form spontaneously . . .Under the right conditions. Lipid membranes may have formed on surfaces and broken free, forming bubbles capturing biotic molecules.


With just the ‘right stuff’ inside, a primordial liposome could have

outcompeted others . . .Carl Woese called this the progenote!It’s a hypothetical ancient aggregate of RNA, perhaps DNA, proteins, and lipids.Also called protocell or protobiont.This was the precursor to all more complex cells. Life may have gone through a number of progenotes, but eventually one was very successful and went on to evolve into LUCA. 14


LUCA is the Last Universal Common Ancestor.

LUCA lived 3.5-3.8 BYA.Every living cell on the planet descended from LUCA.And it had to have metabolism!Here’s a possible scenario for how the progenote may have came to be . . .


And to get to LUCA metabolism

(ability to acquire and use energy to

maintain the organization

necessary for life) was needed.

How to evolve a LUCA from a progenote:

Over time, an enzyme-catalyzed

sequence of reactions could arise.

More pathways would evolve.

Intermediates spawn other pathways. 17


Here’s another hypothetical pathway from the RNA World to three domains.

18

This is from Computational Approaches in Comparative Genomics, Koonin & Galperin (2002)


Once LUCA hit, the race was on . . .Evidence of life seen in 3.85 BY old rocks from Greenland — organic carbon isotopes common to life forms found within them.The oldest definite fossils are stromatolites. They occur in 3.7 BY old rock and represent large mattes of cyanobacteria-like unicellular organisms.By 3 BYA unicellular life was everywhere.The first autotrophs were probably anaerobes that metabolized hydrogen sulfide and/or methanogens.


And then along came sunlight based

photosynthesis!And the world changed forever.The rise of photosynthesis radically altered the Earth:It decreased CO2, lowered global temperature, and added oxygen gas to the atmosphere, eventually reaching the present day 20% level.O2 ➔ Ozone in upper atmosphere, which began blocking harmful UV.Aerobic organisms beganto evolve . . . 20

!

e.g. http://earthobservatory.nasa.gov/IOTD/view.php?id=6956


http://earthobservatory.nasa.gov/IOTD/view.php?id=6956

http://earthobservatory.nasa.gov/IOTD/view.php?id=6956

21

With O2 all sorts of life forms

could originate.

. . . Including Eukaryotes and multicellularity.Tuesday, January 25, 2011

Eukaryotic complexity . . .

22

Eukaryotic cells arose during the Proterozoic eon (1.9-1.4 BYA)Eukaryotic cells are characterized by interior compartmentalization.They may have formed as the outer membrane folded in on itself.This fossil contains organics similar to Eukaryote membranes.


And . . . Endosymbiosis!Expounded by Lynn Margulis (1967) — a wonderful thing.Mitochondria and chloroplasts originated as free-living Bacteria that were engulfed by other, perhaps Archaeal, cells.Evidence:

Similarities in structure between these organelles and certain types of Bacteria;Mitochondria and chloroplasts both reproduce by splitting in two (binary fission), as do Bacteria;The photosynthetic pigments in chloroplasts are similar to those in Cyanobacteria;Mitochondria and chloroplasts both contain DNA, RNA, and ribosomes similar to those in Bacterial cells;There are many similarities in DNA sequences between mitochondria and chloroplasts to Bacteria, but much of original bacterial genome migrated to the nucleus over eons of evolution. 23


Here’s an illustration of a possible scenario.

And it all worked out pretty well for us Eukaryotes!24

LUCAAnd the nucleus

develops


Multicellularity evolves . . .It occurred about 1.2 BYA.The earliest fossils clearly multicellular are from Canada dated 1.25-0.95 BYA and look like a red algae.How it happened is open to conjecture.Perhaps many individual cells came together, joined, and took on specialized tasks, or . . .Alternatively, a single cell may have divided and the daughters remained stuck together. 25


And diversity ‘exploded’ in the last 0.5 BY!Especially starting with the Cambrian explosion.However, the late Precambrian probably had plenty of diversity too; just that most were soft-bodied organisms that did not fossilize very well.Nonetheless, the four billion years of the Precambrian were incredibly eventful:

Life originated, reproduced, and diversified;Photosynthesis evolved;Eukaryotes arose; and . . .Multicellular algae and animals appeared; e.g Spriggina:


But the Cambrian (543-490 MYA) was extra special.The Cambrian seas exploded with diversity — wild forms and body plans we would never see again, http://www.pbs.org/wgbh/evolution/library/03/4/l_034_02.html, and the topic of Gould’s book Wonderful Life.These included the earliest known organisms with hard (easily fossilized) parts.Many forms would die out, e.g. trilobites.Others gave rise to all modern animal phyla. 27 http://en.wikipedia.org/wiki/Cambrian_explosion


http://www.pbs.org/wgbh/evolution/library/03/4/l_034_02.html








http://en.wikipedia.org/wiki/Cambrian_explosion

http://en.wikipedia.org/wiki/Cambrian_explosion

Four big extinction events, with the last being the baddest, ended the Cambrian

and took a bunch of life with it.Next was the . . .Ordovician Period (490-443MYA).The seas continued to support huge communities of invertebrates and algae.

28

The first vertebrates to leave fossil evidence appear — the Ostracoderms (a jawless fish).Primitive spore-bearing plants ventured onto land.And then another huge mass extinction! The second biggest ever.


Next was the Silurian Period (443-417 MYA).

First simple vascular plants appear on land. And the . . .First terrestrial animals evolve — some resemble scorpions, millipedes, worms, . . .Fungi also colonize the land.Jawed, jawless, and freshwater fish are all widespread.


Then the Devonian Period (417-354 MYA).

Often known as the “Age of Fishes.”The seas continue to have more life than land.Still lots of invertebrates, but also cartilaginous and bony fishes; including . . .Lobe-finned fishes in both salt and fresh water, and the first . . .Amphibians appeared, e.g. Acanthostega.The plants are also diversifying – ferns, horsetails, and seed plants all appear.


The Carboniferous Period (354-290 MYA) followed.

31

This is also known as the “Age of Amphibians”Some types evolved hard shelled eggs. This allowed them to spend more time away from the water. And . . .Eventually some diverge into reptiles, birds, and mammals.Primitive reptiles first appear living totally on land about 300 MYA.As huge forests die and get buried, today’s coal beds form.Bony fish and sharks resemble modern forms.


And then the Permian Period (290-248 MYA).Gymnosperms (conifers) became prominent.Reptiles became more prevalent, and they had an amniote egg.This foreshadowed the dawn of the dinosaur age.But, the Permian extinction — the biggest, baddest of them all!The Paleozoic era and Permian period ends with the “mother of mass extinctions:” http://www.pbs.org/wgbh/evolution/library/03/2/l_032_02.html.>90% of species in shallow seas die and 70% of land organisms!Causes could include a drop in sea levels, ocean outgassing, volcanic eruptions, impact events, and later rises in sea levels.








Whatever the causes, lots of empty niches in the Triassic Period (248-206 MYA) . . .

Left plenty of room for the ancestors of the dinosaurs, the Archosaurs, to evolve!And the ancestors of the mammals, known as therapsids, in particular the Cynodonts, became abundant. 33

Thrinaxodon, aCynodont


And then the Jurassic (206-144 MYA) and Cretaceous Periods (144-65 MYA).

This was the “Age of Dinosaurs!”See, e.g. http://dsc.discovery.com/dinosaurs/dinosaur-videos/dinosaur-videos.htmlGiant reptiles were everywhere: Dinosaurs on land; Pterosaurs in the sky; Ichthyosaurs, Plesiosaurs and huge crocodilian critters in the water. Oh my!But the first birds, flowering plants, true frogs, and true mammals also appeared.It was a time of great biological change.Flowering plants appeared and diversified. And . . .Modern insects arose.


http://dsc.discovery.com/dinosaurs/dinosaur-videos/dinosaur-videos.html




And then another huge extinction, the K-T boundary.

This was that huge asteroid impact about 65 MYA that we discussed earlier. It prevented photosynthesis around the entire earth for at least several months, perhaps years, and . . .Nearly 75% of all species perished. In particular all of the giant reptiles, including all of the non-avian dinosaurs disappeared.One more time — this opened up habitats for the survivors and adaptive radiation ran amuck.In particular, the “Age of Mammals,” and Humans was to begin! And that’s where we’ll start next.


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