Evolution week3

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Causes
Fossils & Fossilization
DNA & learning from DNA.

A. Proximate vs Ultimate?
B. Fossilization & learning from Fossils

Why is X? Why does ?
Two types of answer:
Proximate explanations: mechanisms responsible for the trait.
(generally within ...

Some examples
•Why do waxwings migrate South in winter?
•Proximate: a mechanism in their brains senses days are getting
sh...

Fossils & Fossilization
1. How fossilization works. Some examples of fossils.
2. Dating fossils.
3. What we can learn from...

Geological context
Three broad classes of rock:
•Sedimentary rocks: formed by particles (mineral
or organic) gradually set...

Fossils: only in sedimentary rocks (deposited on oceanic
shorelines, lake beds, ﬂood plains...)
Weathering or erosion can ...

Fossilization
•Two main types:
•Permineralization
• “Natural cast” process
•Fossilization is rare & only in sediment...
•A...

Fossil formation at
Sterkfontein
Limestone deposits were laid
down 2.5 billion years ago when
the area was a shallow sea.
...

Fossil preservation
•Hard part like shells, bones and teeth are usually all that remain
•Soft tissues fossils are rare

Why are fossils rare?
•Fossils don’t form often:
•Predators, scavengers, insects consume corpses
•Bacteria and fungi decom...

Recent continental
movements...
TETHYS
SEA
LAURASIA
GONDWANA
EquatorTriassic 200
Mya
Pangaea - single
supercontinent

Why are fossils rare?
•Fossils don’t form often:
•Predators, scavengers, insects consume corpses
•Bacteria and fungi decom...

A few examples...

Aquatic reptile; not a dinosaur. But same time (Mesozoic Era). 
A typical fossil skeleton.
Plesiosaur fossil

Parts of head, and anvil/brush
of Akmonistion zangerli, shark
from Carboniferous of
Scotland
More typical…

Belemnites
•very abundant during Mezosoic

Ammonites
http://www.bbc.co.uk/
nature/life/
Ammonite#p00bkt26

Ammonites
Ammonite
Nautilus

Feathers, like soft tissue, are rarely preserved.
But here imprinted in the rock.
Archaeopteryx - late Jurassic (150Mya)

“Fuzzy Raptor” (a dromaeosaur)

The earliest Eutherian Mammal? 
Lower Cretaceous of China, 125 Mya
Eomaia scansoria
Ji et al., (2002) Nature
416, 816-822
...

Leptictidium tobieni
Paleogene (Messel Shales, Germany)
Soft tissues + gut contents are
preserved
Bipedal (extinct) mammal.

Dinosaur footprint
•At the time, this footprint of a dinosaur pressed into soft mud and
became preserved in the now harden...

INSECT IN AMBER
• This mosquito was imbedded in tree sap that subsequently
hardened into amber, preserving the insect with...

Neanderthal skull from
Iraq
(≈50,000 years old)
Very rarely, DNA can
be extracted and
sequenced from such
sub-fossils

Some animals get trapped in ice

Fossils & Fossilization
1. How fossilization happens & some examples.
2. Dating fossils
3. What we can learn from fossils?

Dating methods
• Absolute - the item itself is dated
• Relative - strata above (younger) and below (older)
are dated and t...

Principles of
radiometric dating

Dating methods

Stratigraphy
As sediment collects, deeper layers are compacted by the ones
above until they harden and become rock.
Deeper...

Index (Zone) Fossils
•Here, Locality 3 has no layer B (wasn’t formed or eroded).
•Index fossils: diagnostic fossil species...

Photo taken by (Luca Galuzzi) * http://www.galuzzi.it

Fossils & Fossilization
1. How fossilization happens & some examples.
2. Dating fossils
3. What we can learn from fossils?

What can we learn?
Fossils can sometimes directly or indirectly tell us a great
deal about the behavior of an organism, or...

Fossilized tracks at
Laetoli (Tanzania)
Footprints preserved in
volcanic ash from: 3 hominids
(Australopithecus afarensis)...

Fossil Ichthyosaur giving birth
•Such special preservations can inform us about the reproductive
pattern in this species (...

Fossil Eggs
Information on development and social/reproductive behavior

Interpreting fossils
•Careful interpretation: helps make sense of fossilized remains
•Analysis of hard parts can tell some...

Hallucigenia sparsa (Cambrian Period)
From the Burgess Shale (Canada). Example of a soft bodied
animal fossil, also very o...

Now re-interpreted as an
Onychophoran ("velvet worm")
© BBC - Life in the Undergrowth

…or do they? (discovered fossilised melanosomes)
Colors don’t fossilize...

Fossils - Summary
• Fossils form in sedimentary rock
• Fossilization is a rare process
• Usually, only the hard parts like...

DNA & learning from DNA.

DNA in evolution
•Species relationships previously based on:
•bone structures
•morphologies
•development
•behavior
•ecolog...

1. DNA sequences change
DNA mutations occur all the time.
Reasons:
•mistakes in DNA replication or recombination
•mutagens...

Types of mutations
•Small: replacement, insertion, deletion. E.g.:  
 
 
 
 
•Big: inversions, duplications, deletions
ori...

What happens to a mutation?
•Most point mutations are neutral: no effect.
•Some are very deleterious;
See population genet...

2. DNA clariﬁes evolutionary
relationships between species

Linnaeus 1735 classiﬁcation of animals

Molecular clock
•Basic hypothesis: more differences - more time has passed
•Allows relative timing
•Allows “absolute timin...

Human: GATTACA
Pigeon: GATTGCA
Amoeba: GGCTCCA
Human
Pigeon
Amoeba

Carl Woese in 1977

An issue with sequence
phylogenies
•Can be ambiguous if not enough information.

Ambiguities in mutations
ancestral
sequence
species 1. species 2. What happened

•Can be ambiguous if not enough information.
An issue with sequence
phylogenies
•Whole genome sequencing is now dirt cheap...

This changes
everything.454
Illumina
Solid...
Any lab can
sequence
anything!

With enough data...

Artiodactyla
Cetartiodactyla
Cetacea
Cows are more
closely related to
whales than to
horses

Bat echolocation
Teeling 2002
Echolocation
Evolved twice!
Flight

Ancient DNA

Ancient DNA
Hair sequencing

Ancient DNA: below 2km of icecriterion
many p
abundan
as is typ
efficientl
low-leve
due to D
Appr
the John
signed to
tion ...

Their presence indicates a northern boreal for-
est ecosystem rather than today’s Arctic environ-
ment. The other groups i...

Consensus with fossil record?

Molecular evolution analysis:
•Earliest placental mammals (ie. eutherians)
•body mass >1kg; lifespan >25years
Genomic Evid...

3. DNA sequence clariﬁes current
relationships

Three-spined stickleback
Gasterosteus aculeatus
Bill Cresko et al; David Kingsley et al
Example 1.

Independent
colonization events 
less than 10,000
years ago
in Saltwater:
in Freshwater:
The freshwater populations, despi...

RAD = Restriction-site Associated DNA sequencing
each locus sequenced
5–10 times per ﬁsh.
Bill Cresko et al;
The freshwate...

Differentiation between populations (FST)
Saltwater vs.
Saltwater
Population Genomics
Freshwater
vs.
Freshwater
Figure 6. ...

Nine identiﬁed regions
• Identiﬁed regions include:
• 31 that likely to affect morphology or osmoregulation
• some previou...

Example 2: Little ﬁre ant Wasmannia
DNA identiﬁes family relationships
Fournier et al 2005
Normally,
* males (haploid) car...

reproduction (that is, by ameiotic parthenogenesis). In 33 of the 34
nests, all queens (n ¼ 135) and gynes (n ¼ 9) cohabit...

reproduction (that is, by ameiotic parthenogenesis). In 33 of th
nests, all queens (n ¼ 135) and gynes (n ¼ 9) cohabiting ...

Example 3: Species-interactions via
DNA sequencing
Screening mammal
biodiversity using
DNA from leeches
Ida Bærholm Schnel...

Example 4.
Fire ant social structure

Solenopsis invicta ﬁre ant:
two social forms
•1 large queen
•Independent founding
•Highly territorial
•Many sizes of worke...

Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues

>500 genome sequences
(+ behavioral assays etc)
Wang et al (2013) Nature

brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303
brc_m013_0304
brc_m013_0305..brc_m013_0307
brc_m01...

Sex chromosomes
X Y
Gp-9 B
Gp-9 b
SB Sb
“Social chromosomes”
= supergene
multiple rearrangements
Wang et al (2013) Nature

Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues

bbbbBB BB Bb bb
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form co...

bbBB BB Bb
x
Gp-9 bb females rare
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen f...

BB BB Bb
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completel...

BB BB Bb
x
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form complet...

BB BB Bb
x x
Ken Ross and colleagues
Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
Single ...

BB BB Bb
x x x
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
(>15% )(< 5% )
...

DNA analysis is powerful

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