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Anth 151.2 Evolutionary dynamics and genetics

Week 2 lecture for 'Human evolution & diversity'
by Greg Downey on 9 August 2013

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Transcript of Anth 151.2 Evolutionary dynamics and genetics

Population selection
In 1860s, began to report research on inheritance of traits.
Traits didn’t blend (dominant & recessive traits).
Acquired traits not transmitted.
Work rediscovered in the 20th century.
Gregor Mendel and Genetics
Thus, from the war of nature, from famine and death, the most exalted object of which we are capable of conceiving, namely, the production of the higher animals, directly follows.
Changed the shape and tenor of biology.
Wallace-Darwin public presentation
Before the Beagle
Born 1809.
Established, well-to-do family (father a doctor).
Could all species change arise from random DNA transcription errors?
* Julian Huxley
‘The Modern Synthesis’*
Neo-Darwinism

Worked on inheritance of traits.
Realised that offspring received traits from both parents, but that only the dominant traits were expressed.
Helped natural selection regain acceptance after 1900.
Gregor Mendel’s 29,000 pea plants
(1856-63)
Darwin tended to focus on gradual change, and long periods of similar fossils supported this vision.
But moments in fossil record where pace accelerates.
No inherent reason pace of evolution needs to be consistent if environment was not (& environment includes animals).
‘Punctuated equilibrium’
Selection disposes.
Nature proposes.
Darwin died renowned for ‘evolution’ — he was uncomfortable with the term, preferred ‘transmutation’.
Darwin’s intellectual legacy
Staggering breadth: finches, pigeons, cave fish, gooseberries, honeybees, wingless beetles...

Piling up of evidence is overwhelming (Darwin was to title it An abstract for an essay...).

Suddenly, instead of description, we have also explanation.
What was so special about Origin?
Marella splendens in the Burgess Shale, Canada
The context of his ideas.
The voyage on the Beagle.
On the Origin of Species...
His intellectual legacy.
Charles Darwin
Darwin on natural selection
Updating Darwin
Neo-Darwinism
The Genetics Revolution & Evolving Complexity
Topics for today
hang on tight, we’re going to move fast.
warning!
graphic http://en.wikipedia.org/wiki/File:DNA_Overview2.png
1868: Friedrich Miescher isolates what he calls ‘nuclein’ in cells (now nucleic acid).
1953: James Watson & Francis Crick, drawing on the work of others including Rosalind Franklin, first described the double helix structure of DNA in chromosomes.
Discovery of DNA
How fast is evolution?
How did variation arise?
Extensions to Darwin
Adaptation
Species have significant inheritable variation.
More individuals are born than can survive to reproduce.
Variation affects reproductive success.
Over time, species adapt to ecological niches.
90’ long, the Beagle carried 74 people.
The Beagle
Contemporaries considering species change.
Sense of time depth growing due to geology.
Most theorists, however, believed in degeneration (‘post-Lapsarian’), aspirational change, or catastrophism.
Many proposals of evolution, but none were compelling until Darwin’s.
Darwin’s context
Anth 151: Human evolution & diversity
Week Two

Evolutionary dynamics & genetics
graphic from: upload.wikimedia.org/wikipedia/commons/7/79/Types-of-mutation.png
During DNA replication, part of a DNA sequence can be:
deleted
duplicated
inverted, or
inserted in the wrong place.
Mutations
Barnacles (2 volumes)
Coral reefs
Earthworms
Carnivorous plants
Orchid reproduction
Domestication of animals
Climbing plants
Emotions across species
Volcanic islands
South American geology
Travel account of Beagle
Autobiography
Descent of humans
Darwin’s books
“The tree of life should perhaps be called the coral of life, base of branches dead; so that passages cannot be seen – this again offers contradiction to the constant succession of germs in progress.”
5 year voyage.
Voyage of the Beagle
“I do not remember, since leaving England, having passed a more dull and uninteresting time.”
(Voyage)
Toxodon platensis skeleton with drawing by George Scharf from Darwin’s specimen.
1 July 1858, at the Linnean Society in London – Wallace’s very clear statement of principles of evolution read out with part of Darwin’s unpublished 1844 manuscript and an 1857 letter.
Rocked the scientific world to its foundations?
Key dimensions of Darwin’s thought
Species change. Found bones of related, but distinct, earlier forms.
Population ever increasing (Malthus), so survival not guaranteed. Evidence of extinct animals.
Species varied from place to place. Islands with isolated species.
Variation emerged; species had deep relations & shared origins.
graphic http://en.wikipedia.org/wiki/File:Punnett_square_mendel_flowers.svg
If purple is dominant, two phenotypes, but three genotypes.
Phenotype
= expressed trait.
Genotype
= underlying genetic type.
Genes & expression
Directional
Diversifying
Stabilising
Artificial
Patterns of selection
Important: ‘Selection’ always occurring.
Periods of stability due to ‘stabilizing selection.’
Tutorial
Darwin’s first diagram of an evolutionary ‘tree’ or 'coral' from his First Notebook on Transmutation of Species (1837).
(Museum of Natural History in Manhattan)
Darwin returned with Beagle in 1836.
William Wells had described natural selection in 1818; Patrick Matthew in 1831.
Theorizing about Natural Selection
The Beagle in Sydney Harbour
Darwin in Australia
“On the whole I do not like New South Wales. It is no doubt an admirable place to accumulate pounds and shillings; but heaven forbid that I should live where every man is sure be somewhere between a petty rogue and a bloodthirsty villain.” (Darwin to Henslow)
Darwin stopped three times in Australia (Jan-Mar, 1836) at Sydney, Hobart & Albany.
Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck—species change for environment.
Will to change; inheritance; & law of use and disuse.
Focused on adaptation.
Lamarck
Buffon
George-Louis Leclerc, Comte du Buffon—against idea of stable, perfect creation.
Imperfections in organisms.
Linnaeus
Carl von Linne (Linnaeus)— Swedish classifier of species.
Highlighted their similarities.
Species have
inherent genetic variation
including unexpressed traits.
Selection acts on phenotype, but is affecting the
underlying pool of genetic variation
.
We need to realise that variation is always present & constantly generated in all populations.
introduction of antibiotics
For Staphylococcus, antibiotics become a selective pressure.
Individuals with resistance become dominant (selected trait).
‘Natural’ selection; e.g., Staphylococcus
Charles Lyell
Darwin’s predecessors
James Hutton
James Hutton & Charles Lyell—geological uniformitarianism.
Suggested earth was very old (‘deep time’).
Erasmus Darwin
Erasmus Darwin—Divine creation, but process of speciation.
Inheritance + Variation + Selection (Time) = Adaptation
*
*remember: genetic pool also already contains variation.
graphic: en.wikipedia.org/wiki/Image:Mutation_and_selection_diagram.svg
Errors in DNA transcription might produce unusual variants.
Variants have differential possibility of survival.
Over time, mutated alleles might be eliminated, or might become dominant genotype.
E.g., mutated coloration in peppered moths, light coloration in humans...
DNA variation + mutation + natural selection = evolution
Voyage of the Beagle
Failed as doctor, indifferent student of clergy.
Loved hunting, collecting, beetles.
Replaced a last minute absence.
Father opposed voyage.
On board to keep captain company.
More interested in geology than biology.
In 1844, Darwin wrote book but held it in secret (to be published if he died). His ideas emerged early in notebooks.
In 1858, after 20 years writing about biology, Darwin received package from Alfred Russel Wallace.
Evolutionary ‘coral’:
1859 — On the Origin of Species by Means of Natural Selection; or, The Preservation of Favoured Races in the Struggle for Life.

Best-seller that went through six editions in his life.
http://upload.wikimedia.org/wikipedia/commons/b/b2/Alfred_Russel_Wallace_1862_-_Project_Gutenberg_eText_15997.png
Barely caused a stir.
‘The year which has passed has not, indeed, been marked by any of those striking discoveries which at once revolutionise, so to speak, the department of science on which they bear.’ (President of Linnaean Society of London, year-end report 1858)
Alfred Russel Wallace in 1862
Natural selection not widely accepted, even by Darwin’s ‘supporters.’ By 1875, largely neglected by biologists.
A reluctant revolutionary— natural selection ‘like confessing a murder.’
Worried about religion, social respectability, even about hurting his wife, Emma, who worried for his soul.
Placed human among other animal species for study.
Suggested that species did not have ‘essence’; instead dynamic populations with inherent, constant variation, liable to speciation or change over time.
‘Evolution’ was not a result of design, striving, or effort.
The dawning recognition that we are linked to all life, an unbroken tree from speciation.
Natural selection
Variation
Inheritance
Selection
Time
+
+
+
=
There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
Examples of rapid change:
Queensland frog-eating snakes (since 1935 cane toad).
Croatian lizards changing stomachs.
California field mustard (7 years to early flowering!)
Antibiotic resistant bacteria (and from your reading).
Sweeping revolution in biology, but even Darwin knew it was incomplete.
Understanding ‘punctuated equilibrium’
The stability or ‘equilibrium’ can be ‘punctuated’ by sudden change, often due to shift in environment, new niche, new competitor, or new trait that spreads quickly.
In fossil record, change can look like ‘gap’ or ‘missing link’ due to rarity of remains & consistency during equilibrium.
If offspring are ‘blending of inheritance,’ all variation should disappear through sexual reproduction.
What was the mechanism of inheritance?
DNA is like the ‘patterns book’ for creating proteins at genes; other parts of DNA regulate the production of these proteins (regulatory DNA, mRNA).
What is DNA?
Most mutations result in some form of damage, or neutral outcomes if the DNA is sufficiently buttressed.
Problems
http://cdn.cloudfiles.mosso.com/c114612/video/2009/rd-natgeo.jpg
Richard Dawkins
'Genes are replicators; organisms and groups of organisms are best not regarded as replicators; they are vehicles in which replicators travel about. Replicator selection is the process by which some replicators survive at the expense of other replicators. Vehicle selection is the process by which some vehicles are more successful than other vehicles in ensuring the survival of their replicators.'
Evolution is a
‘change in allele frequency over time.’

Ironically, this caused many evolutionary theorists to focus on the DNA, not organism: ‘Life is just DNA trying to replicate.’
inherent or mutation
genotype (phenotype not inherited)
change in population's genetic pool
If selection only works on inherent variation, variation should steadily decrease.
Is nuclear DNA the only thing animals inherit?
Are 'genes' the only thing that DNA carries?
Are all changes in species only due to natural selection?
Can selection work equally on all traits?
the 'selfish gene'
Genes are competing directly with their alleles for survival, since their alleles in the gene pool are rivals for their slot on the chromosomes of future generations. Any gene that behaves in such a way as to increase its own survival chances in the gene pool at the expense of its alleles will, by definition, tautologously, tend to survive. The gene is the basic unit of selfishness.
Adaptation
Variation
Inheritance
Selection
Time
+
+
+
=
natural
gradual (after 1972, punctuated)
When we no longer look at an organic being as a savage looks at a ship, as at something wholly beyond his comprehension;

when we regard every production of nature as one which has had a history;

when we contemplate every complex structure and instinct as the summing up of many contrivances, each useful to the possessor . . .

how far more interesting, I speak from experience, will the study of natural history become!
Charles Darwin, On the Origin of Species
Other forms of species change: it’s not all just mutation & ‘natural selection’...
Change without selection?
endangered Florida panther, numerous fixed deleterious mutations
‘Bottleneck event’
Example: Northern Elephant Seal in 1896 c. 20 individuals.

Now virtually no genetic variation in 30,000 seals.
Example: Atlantic population of lionfish (Pterois volitans).
Founding group was perhaps 10 individuals.
‘Founder effect’
Genetic drift
Non-selective forces
Greg Downey
Associate Professor
Department of Anthropology
http://blogs.plos.org/neuroanthropology
greg.downey@mq.edu.au

evolution
beaver dam in Yellowstone National Park USA
A broader inheritance
inheritance & variation
DNA once considered ‘blueprint’ for organism.
Only about
1.5% of DNA
codes for proteins.
DNA & inheritance
DNA in other parts of the cell (e.g., mitochondria).
RNA in sperm cells.
In utero transmission - epigenetics.
Long-term, inter-generational effects on gene expression of some parental experience.
Effect of maternal immune system through nursing.
Transfer of gut flora.
Anthill Northern Teritory
Many animals shape the environment to favour their own survival.

Others use the environment as a non-genetic form of heredity (e.g., diet).
Phytoplankton creates an oxygenated atmosphere 500 million years ago.
But wait, only 24,000 protein-coding genes (about the same as mouse)...
Only 1.5% of the genome actually has genes.... (at first, the rest was called ‘junk DNA’ -- no longer)
Most of the genes were the same as other animals (homologous genes)...
Human genome sequenced! (2000)
genetics
niche creation
phytoplankton bloom, seen from space
organism
environment
'new synthesis' tended to focus only on how environment influenced organism.
niche creation
Some
non-coding DNA is ‘regulatory'
affecting
gene expression
.
Other molecules
act on DNA
information; DNA INERT by itself.
Punchline: DNA does not act alone.
Other channels of inheritance as well.
examples:
graphic http://learn.genetics.utah.edu/content/begin/cells/organelles/images/endosymbiosis.jpg
Digestion depends on gut fauna. There are more cells in your body that do NOT have your nuclear DNA than those that do!
Diagram from Jern, Sperber & Blomberg 2005.
Human genome littered with ancient endogenous retrovirus (ERV) DNA.
8% of all the human genome.
Retroviral insertions
Can evolution select ‘traits’?
http://www.biology.lsu.edu/heydrjay/1202/Chapter24/TheOriginsofForm.html
‘Evo-Devo’
Instead of thinking that there would be a gene ‘for’ a trait, many evolutionary changes may involve alterations to regulatory or signaling genes.
graphic from http://www.nytimes.com/2008/11/11/science/11gene.html
Most sections of DNA are expressed in a variety of tissues. Estimated 90+% of DNA is
pleiotropic
(multi-purpose).
How does selection act on individual traits?
Pax-6, the gene responsible for forming eyes, appears in flies, humans, mice, squid...
Biological toolbox is versatile & limited.
Few protein-coding ‘genes’ that are 'conserved' across species.
Great similarity among even diverse species (highly
conserved
).
‘Homeobox’ genes
Fruit fly with antennapedia and probicipedia
labial palps become 1st thorax legs
Fruit fly with antennapedia
antenna become 2nd thorax legs
Normal fruit fly
Drosophila
photos from: http://www.sdbonline.org/fly/aimain/images.htm
Ed Lewis in 1978 studied startling mutations in insects (‘antennapedia’).

Lewis suggested that problem was a mutation in a ‘control gene’ that directed formation of different segments of insect’s body.

Eight basic body segment types; geneticists searched for eight genes.
Mouse embryo with hox gene Hlx knocked out to study nervous system formation.
Photo: http://www.biomedcentral.com/bmcdevbiol/imageofthemonth/archive/2006/08
‘Homeobox’ or ‘Hox’ genes
Homeosis – developmental transformation of body segment.

Create proteins in developing embryo that turn on genes and start developmental cascades.
Evolving new body types
Given a structure, slight variations to the signaling genes could produce new types of segments, and thus new body architectures.
(example of stem cells)
The same gene produces different outcomes
Hoxc-6 (purple) in chick & garter snake embryos
Humans have 39 hox genes shaping body structure.

Mutation in human Hoxd13 can lead to polydactyly (1 in 500).
Hox genes & human structure
Integrating evolutionary & developmental biology
symbiosis
Eukaryotic cells (complex cells) produced by endosymbiosis (mitochondria, chloroplasts). Simple bacteria take on oxygen-breathing and sunlight metabolising symbiots.
http://blogs.discovermagazine.com/loom/files/2012/02/davincifetus.png
Placenta dependent on ERVs.
Chimpanzee resistance to AIDS.
bottom line: more mechanisms both for variation & for inheritance than just genes & mutations.
Hoxc-6 highlighted in developing chick and garter snake
Preliminary mouse genome showed that most genes (99%) have homologues across all mammals. Ironically, ‘developmental-genetic toolkit’ may be quite small.
Diagram shows methylation levels at different points on chromosome 22 in different tissues (skin, placenta, heart, liver, white blood cells...)
Variation occurs through
expression
of the same genes.
Here’s what it gets interesting: the same genes showed up in almost all bilateral animals.
Organism shape depends upon concentration, location, timing & target gene of hox protein.
Tails, atavisms and homologous organs show how gene regulation (not entirely new genes or structures) can produce profound variation.
Back to our tails...
9.5 day-old mouse embryo
Change the regulatory, signaling or developmental processes, and homologous genes & structures can produce quite rapid change.
Photo: http://www.biomedcentral.com/browse/browse.asp?abbrev=bmcdevbiol&imageofthemonth=y&imageoftheyear=y=y&year=2006
Adaptation
Variation
Inheritance
Selection
Time
+
+
+
=
inherent or mutation, developmental, phenotype actually crucial
genotype, niche, epigenetic, other (learning...)
change in gene pool or phenotype
natural, symbiosis
gradual, punctuated, even quite quick
a broader synthesis
The basic picture holds—heredity, variation, selection, time—it’s just more interesting (as Darwin predicted). Organisms like little interacting systems.
What to make of it?

The more we understand biology, the more we realise that the same tools (genes, developmental sequences) get used to produce a wide variety of organisms.
Evolution affects developmental processes & configuration but generally doesn't create things without precedent.
Our distinct features likely not completely novel genes (some are!) but novel ways of using old ones.
Week Three
Humans among primates
Lamarck
sexual selection?
back to this in Week Six!
deserves its own lecture.
particulate inheritance
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