Outline:

1. Sex

2. Mitochondrial Eve

3. Adam?

4. Clothing and lice!

5. Homo sapiens v. Neanderthals!

Readings: Shriver, M.D. & Kittles, R.A. (2004). Genetic ancestry and the search for personalized genetic histories. Nature Genetics, 5, 611-618.Stix, G. (2008). Traces of a distant past. Scientific American, July, pp 57-63.

Lecture 12: Evolutionary genetics

Message from David Turk:

my lab are conducting fMRI experiments in December and we are looking for volunteers to get their brain scanned.  They will get a picture of their brain and course credits.  It will be a great opportunity for them to get first hand experience of brain imaging research and might be useful in their understanding of this work.  They can go to my website for the screening forms and contact information.

http://www.abdn.ac.uk/~psy434/dept/SelfLab/Volunteer_for_a_Brain_Imaging_Study.html

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Compared amino acid sequences in hemoglobin and serum albumen of Homo sapiens to chimps, monkeys and other species

Used estimates of horse—Human divergence of 75 million years to calibrate the clock:

Conclude humans and chimps diverged about 5 m.y.a

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oldest modern Homo sapiens

~195,000 years ago, in Ethiopia

Where did we come from?

“Out-of-Africa" hypothesis: modern Homo sapiens evolved in Africa (200,000 y.a.?) and migrated from there recently (~40-50,000 y.a.), driving H. erectus and H. neaderthalensis into extinction.

“Multiregional" hypothesis: H. erectus populations evolved into modern humans in many places-- these groups later bred with each other and with groups that emigrated from Africa later.

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From Tattersall, I. (1997). Out of Africa again…and again? Scientific American, 13, 38-45.

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http://www.chg.duke.edu/education/online.html

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http://openlearn.open.ac.uk/mod/resource/view.php?id=181168

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http://ghr.nlm.nih.gov/handbook/illustrations/chromosomes.jpg

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The production of gametes (haploid cells—sperm and egg)

Note the gametes have some maternal and some paternal genetic material—and none of them are the same, even with the same parent cell!

The great shuffler of sexual reproduction!

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From Stix (2009)

polymorphism: a DNA sequence variation found in a subsample of a population

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http://www.nbii.gov/portal/server.pt?open=512&objID=402&&PageID=571&mode=2&in_hi_userid=2&cached=true

DNA sequencing :

lets investigators determine the order of the bases along a strip of DNA in an individual

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“Mitochondrial Eve”

We inherit mitochondrial DNA only through the female line. Therefore it doesn’t recombine--you never have two genetic mums do you? easier to trace lineages

(Cann & Wilson, 2003)

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genome.wellcome.ac.uk/assets/GEN10000726.jpg

Haplotype: a particular pattern of genes from a specific chunk of DNA

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Cann, R.L. et al. (1987). Mitochondrial DNA and human evolution. Nature, 325, 31-36

147 people’s mDNA mapped. Everyone’s mDNA can be traced back to a woman who lived ~200,000 y.a.

(revised to 120,000 y.a. by 2003)

Cited 1581 times!

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“Mitochondrial Eve”

It also mutates faster than normal “nuclear” DNA

Its pretty much the same in about 1016 molecules of it in you

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Mitochondrial Eve – last living female from whom all existing mDNA is derived

She was not the first Homo sapien woman

We have plenty of DNA in our genes from other women

Her lineage survives—every time a woman has no children, or only males, that line ends (with respect to existing mDNA!)

From Cann, R.L. & Wilson, A.C. (1997). The recent African genesis of humans. Scientific American, 13, 54-61.

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From the fig caption: “The numbers refer to mDNA haplotypes, no 1 being from the aboriginal South Africian (Kung!) cell line…”

134 haplotypes identified, and they clump in regions that represent the spread of Homo sapiens

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2003 version: 182 mDNA haplotypes. Red circles=the probable minimum number of unrelated females who colonised the area !!

Cann & Wilson (2003)

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From Shriver, M.D. & Kittles, R.A. (2004). Genetic ancestry and the search for personalized genetic histories. Nature Genetics, 5, 611-618.

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Mitochondrial Eve – last female from whom all existing mDNA is derived

2323PLoS One article is at: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0000829

Tamm et al. (2007). Beringian standstill and spread of native American founders. PLoS ONE 2(9): e829. doi:10.1371/journal.pone.0000829

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Underhill, P.A. & Kivisild, T. (2007). Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations. Annual Review of Genetics, 41, 539–64.

“The human mtDNA tree (Figure 2) splits at its core layers into branches that carry exclusively African sequences and just one, more peripheral haplogroup L3, that the Africans share with the rest of the world”.

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You can do the same thing with patrilinear lineages using the Y chromosome (after all you only have one genetic dad!)

Millions of base pairs rather than the 16,000 or so in mitochondrial DNA

18 main haplogroups (so far)

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18 main haplogroups (so far)

A Y chromosome “Adam”? 30-80,000 years ago?

https://genographic.nationalgeographic.com/genographic/lan/en/atlas.html

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Single nucleotide polymorphism: A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Almost all common SNPs have only two alleles.

Microsatellites, or Simple Sequence Repeats (SSRs), are polymorphic loci present in nuclear and organellar DNA that consist of repeating units of 1-6 base pairs in length. They are typically neutral, co-dominant and are used as molecular markers which have wide-ranging applications in the field of genetics, including kinship and population studies

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Use a least error method of estimating ancestors of all individuals from 650,000 single nucleotide polymorphisms

Come up with an out of Africa model pretty similar (but in more detail) than the mDNA and Y methods

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http://news.nationalgeographic.com/news/2003/03/photogalleries/neanderthal/

The Neanderthals (Homo neanderthalensis)

Fossils found in the Neander valley in Germany in 1856

Widely dispersed from about 138,000 until 30-20,000 years ago?

Bigger brains?

Did Homo sapiens wipe them out, interbreed with them, or both?

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“One bone (Vi-80) from Vindija Cave, Croatia, stood out in that 99% of the 63-base-pair mtDNA segments and 94% of the 119-base pair segments are of Neanderthal origin. Assuming that the ratio of Neanderthal to contaminating modern human DNA is the same for mtDNA as it is for nuclear DNA, the Vi-80 bone therefore yields DNA fragments that are predominantly of Neanderthal.”

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“By split time, we mean the time, in the past, after which there was no more interbreeding between two groups. By divergence, we mean the time, in the past, at which two genetic regions separated and began to accumulate substitutions independently. Effective population size is the number of individuals needed under ideal conditions to produce the amount of observed genetic diversity within a population.”

Estimate divergence of Neanderthal and Homo sapiens at ~ 500,000 years ago

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Some debate about fossils in eastern Eurasia actually being Homo erectus or Neanderthal

Retrieved mDNA from the left femur of Teshik Tash (Uzbekistan) and the three fragmentary long bones from Okladnikov (southern Siberia)

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Green, R.E. et al. (2008). A complete…..Cell, 134, 416–426, August 8, 2008

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HVRI=highly variable region 1 of mDNA; HVRII=…region 2…

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“To allow divergences of mtDNA sequences to be transformed to calendar years, we assumed—based on the fossil record—that humans and chimpanzees diverged between six (Galik et al., 2004) and eight million years ago (Brunet et al., 2002; Lebatard et al., 2008). This results is an estimate of the mean divergence time between Neandertal and extant human mtDNAs of 660,000, with a 95% credibility interval of 520,000–800,000 years ago (Figure 3B).”

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Lecture 12 conclusions:

1. This stuff is useful for understanding divergence of various primate species from one another using “the molecular clock”

2. There seem to be technical reasons why you can’t sequence DNA more than 100,000 years old. But when they solve that……THE TIME MACHINE!!

3. Lots of very interesting stuff that we haven’t covered but you might read more about: PREHISTORY.

Course conclusions:

1. The days of a linear straight to Homo sapiens model of evolution are long gone.

2. Big brains were a consequence of what sorts of evolutionary selection pressures and bottlenecks?

3. What is the relevance of walking on two feet?

4. Social brain, the cognitive brain or the linguistic brain?

5. Will genetics surpass archeology/physical anthropology as the domain for understanding human origins?