Anth 3234: Lectures and Reading Assignments

In the list below, the numbers indicate lecture topics. Click on one, and you'll get the slides I showed in class. Under each lecture topic, the open circles indicate reading assignments. Many of these are clickable too and take you to the reading itself, in pdf format. If the reading is under copyright, you'll be asked for a username and password. If you didn't get this in class, then email me (sregorra@gmail.com).

Links labeled "optional" are for students who want to dip into the professional literature.

As the semester progresses, I will add new readings and may subtract old ones. These changes will mainly affect the list of optional readings. The lecture slides will change too. As the semester begins, the available lectures are from the last time I taught the course. I will replace these with current lectures as we proceed.

1. DNA; Molecular fossils  [24 August 2021 16:14:48.] 

   • Fairbanks 2007: intro and ch 1

2. Jumping genes  [26 August 2021 15:46:23.] 

   • Fairbanks. 2007. Ch 2.

3. Pseudogenes  [20 January 2016 17:23:41.] 

   • Fairbanks. 2007. Ch 3.

4. Molecular evolution  [31 August 2021 16:16:00.] 

   • Fairbanks 2007: Ch 5

   Optional

   • Rogers. 2014 The molecular clock.

5. Mitochondrial genetic evidence about population size  [02 September 2021 16:08:30.] 

   • Rogers and Jorde. 1995. pp. 1-8 only.

     The first few pages of this review paper explain why genetic differences contain information about the history of population size. The review itself is out of date, so I am only assigning these introductory pages.

   • Reich. 2018. Ch 1.

6. Nuclear genetic evidence about population size  [10 September 2021 18:58:27.] 

   • Reich. 2018. Ch 1.

   Optional

   • Li and Durbin. 2011. Inference of human population history from individual whole-genome sequences.

7. Genetic evidence about subdivision and gene flow  [09 September 2021 16:29:31.] 

   • Rogers 2021. Using genetic data to build intuition about population history

8. Genetic evidence about selection  [14 September 2021 16:19:47.] 

   • To be announced

   Optional

   • Rogers. 2014 Why linkage disequilibrium helps us find selective sweeps.

9. Archaic admixture  [23 September 2021 16:18:05.] 

   • Rogers. 2016. Admixture between archaic and modern humans.
   • Cochran and Harpending. 2009. Ch 2.
   • Callaway. 2015. Neaderthals had outsized effect on human biology.
   • Wong. 2015. Neandertal minds.
   • Sanchez-Quinto and Lalueza-Fox. 2015. Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction.
   • Kahn. 2015 Ancient DNA analyses are accurate.

   Optional

   • Meyer et al. 2014. A high-coverage genome sequence from an archaic Denisovan individual.
   • Prufer et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains.
   • Vernot and Akey. 2014. Resurrecting surviving Neandertal lineages from modern human genomes
   • Kahn. 2015. Admixture beyond the single pulse.
   • Gibbons. 2016 Neanderthal genes linked to modern diseases.

10. Superarchaic admixture  [28 September 2021 15:11:49.] 

    • Bower. 2020 The earliest known hominid interbreeding occurred 700,000 years ago.
    • [Gibbons. 2020] [gibbons20:superarchaic] Mysterious 'ghost' populations had multiple trysts with human ancestors

    Optional

    • Rogers et al. 2020. Neanderthal-Denisovan ancestors interbred with a distantly-related hominin.

11. Origin of modern humans  [19 October 2021 20:32:08.] 

    • Fairbanks. 2007. Ch 7.

    Optional

    • Xing et al. 2010. Genetic diversity in India and the inference of Eurasian population expansion.
    • Olalde et al 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
    • Lazaridis et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans.
    • Fu et al. 2014. Genome sequence of a 45,000-year-old modern human from western Siberia.
    • Seguin-Orlando et al. 2014. Genomic structure in Europeans dating back at least 36,200 years.
    • Raghvan et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans.
    • Posth et al. 2016. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe.

12. Early Modern Eurasians  [19 October 2021 20:57:02.] 

    • Manco:3
    • Reich:4
    • Callaway 2015. Neanderthals gain a human neighbor.
    • Dienekes 2015. Neanderthal in the immediate family tree.

    Optional

    • Olalde et al 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
    • Lazaridis et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans.
    • Fu et al. 2014. Genome sequence of a 45,000-year-old modern human from western Siberia.
    • Seguin-Orlando et al. 2014. Genomic structure in Europeans dating back at least 36,200 years.
    • Raghvan et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans.
    • Posth et al. 2016. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe.

13. How archaics shaped the modern immune system  [07 October 2021 16:33:46.] 

    • Yong. 2011. Did sex with Neanderthals and Denisovans shape our immune systems? The jury's still out.
    • Sample. 2015 Human-Neanderthal relationships may be at root of modern allergies
    • Paabo. 2015.

    Optional

    • Abi-Rached et al. 2014. The shaping of modern human immune systems by multiregional admixture with archaic humans.
    • Mendez et al. 2012a. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations.
    • Mendez et al. 2012b. A haplotype at STAT2 introgressed from Neanderthals and serves as a candidate of positive selection in Papua New Guinea.
    • Mendez et al. 2013. Neandertal origin of genetic variation at the cluster of OAS immunity genes.
    • Racimo et al. 2015. Evidence for archaic adaptive introgression in humans.

14. Mesolithic Scandanavia  [19 October 2021 19:08:01.] 

    • Manco:3-4
    • Kahn. 2015. When "Europeans" Almost Went Extinct.

    Optional

    • Gunther et al. 2018 The shaping

15. Adaptive contributions of European Mesolithic foragers  [23 April 2016 18:18:32.] 

    • Key et al. 2016. Human adaptation and population differentiation in the light of ancient genomes.

16. Genetics and the European Neolithic  [23 October 2021 23:35:23.] 

    • Reich:5

17. European Neolithic: movement of people or ideas?  [19 October 2021 20:15:10.] 

    • Manco:5

18. Health in the Neolithic  [19 October 2021 20:01:02.] 

    • Larsen 2006. The agricultural revolution as environmental catastrophe: implications for health and lifestyle in the Holocene.

    Optional

    • Larsen. 2003. Animal source foods and human health during evolution.
    • Wood at al. 1992

19. Hemochromatosis (John McCullough)  [27 October 2021 22:52:53.] 

    Optional

    • McCullough et al. 2015. Hemochromatosis: niche construction and the genetic domino effect in the European Neolithic.
    • Heath et al 2016 The evolutionary adaptation of the C282Y mutation to culture and climate during the European Neolithic.

20. Digesting starch  [26 October 2021 16:22:53.] 

    • Novembre et al. 2007. Adaptive drool in the gene pool.

21. Crohn's disease  [11 March 2018 15:36:21.] 

    • Kahn. 2011. Crohn's disease is about barely keeping you alive.

    Optional

    • Huff et al. 2011. Crohn's disease and genetic hitchhiking at IBD5

22. Language and history  [02 November 2021 15:54:37.] 

    • Manco:1-2,8.
    • Grant. 2015 What's old is new again.

    • Veeramah and Novembre. 2014. Demographic events and evolutionary forces shaping European genetic diversity.

      This is a rather long review, which you need not read all at once. It will be useful throughout the semester.

23. Indo-Europeans  [07 November 2021 20:24:47.] 

    • Cochran. 2009. Ch. 6.
    • Manco:7-8
    • Balter and Gibbons. 2015. Indo-European languages tied to herders.
    • Balter. 2015. Mysterious Indo-European homeland may have been in the steppes of Ukraine and Russia.

    Optional

    • Haak et al. 2015. Massive migration from the steppe is a source for Indo-European languages in Europe.

24. Bell Beaker culture  [09 November 2021 03:27:08.] 

    • Manco:10

    • Reich:5

    • Borkhataria and Allen. 2018

    Optional

    • Olalde et al. 2018. The Beaker phenomenon and the genomic transformation of northwest Europe.

25. Milk in Europe  [04 November 2021 21:37:08.] 

    • Manco:6

26. Ecology and biogeography of human infectious disease  [09 April 2018 17:41:38.] 

    • Ewald:1 (To be scanned)

27. Skin color  [11 November 2021 17:25:34.] 

    • Gibbons. 2015. How Europeans evolved white skin.
    • Dienekes. 2015. A story of 69 ancient Europeans.
    • Kahn. 2015. Selection in Europeans, but it still sweeps.

    Optional

    • Beleza et al. 2013. Genetic architecture of skin and eye color
    • Berg and Coop. 2014. A population genetic signal of polygenic adaptation
    • Mathieson et al. 2015. Eight thousand years of natural selection in Europe.
    • Wollstein and Stephan. 2015 Inferring positive selection in humans from genomic data

28. Males and females in stratified societies  [09 April 2015 21:02:08.] 

    • Wikipedia Descent from Genghis Khan.
    • Callaway. 2015. Genghis Khan's genetic legacy has competition.
    • Wade. 2006. If Irish claim nobility, science may approve.
    • Dienekes. 2015. Bottleneck in human Y-chromosomes in the last 10,000 years.
    • Cochran. 2015. Y-chromosome crash.

    Optional

    • Zerjal. 2003. The genetic legacy of the Mongols.
    • Karmin et al. 2015. A recent bottleneck in Y chromosome diversity coincides with a global change in culture.

29. Native Americans  [18 November 2021 18:45:59.] 

    • Reich:7

30. South Asia  [23 November 2021 17:30:00.] 

    • Reich:6

31. Denisovan Anatomy  [30 November 2021 03:53:30.] 

    • Callaway 2019 First portrait of mysterious Denisovans drawn from DNA

    • Learn 2021 How do you tell a Neanderthal from a Denisovan?

    Optional

    • Gokhman et al. 2019 Reconstructing Denisovan anatomy using DNA methylation maps.

32. Geographic population structure  [23 April 2015 18:58:26.] 

    • Callaway. 2013. Most Europeans share recent ancestors.
    • Dienekes. 2013. The Geography of Recent Genetic Ancestry across Europe (Ralph and Coop 2013).
    • Ralph and Coop. 2012. Our paper: the geography of recent genetic ancestry across Europe.
    • Knapton. 2015. Britons still live in Anglo-Saxon tribal kingdoms, Oxford University finds.
    • Kahn. 2015. Cuius Regio, Eius Religio, in Anglo-Saxon England.

    • Gross. 2015. Genetic traces of mankind's migrations.

      In this article, Michael Gross provides a good review of recent work on human gene flow. He also adds an unfortunate political spin. As Gross tells it, evidence of past migrations shows that migration is natural and good, so we ought to welcome immigrants into our own borders. Perhaps we should, but this conclusion doesn't follow from the fact that migrations happened often in the past. Immigration into an area is not always good for those who already live there. Ask the Native Americans.

    Optional

    • Ralph and Coop. 2013. The geography of recent genetic ancestry across Europe.
    • Leslie et al. 2015. The fine-scale genetic structure of the British population.
    • Gurdasani et al. 2015. The African Genome Variation Project shapes medical genetics in Africa.
    • Montinaro et al. 2014. Unravelling the hidden ancestry of African admixed populations.

33. Africa  [07 December 2021 17:26:43.] 

    • Reich:9

34. Milk in Africa and Arabia  [01 April 2016 16:23:13.] 

35. Wrapup  [09 December 2021 17:30:44.] 

[gibbons20:superarchaic] https://www.science.org/news/2020/02/mysterious-ghost-populations-had-multiple-trysts-human-ancestors