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Dr Andrew Clarke

Dr Andrew Clarke

Leverhulme Early Career Fellow

Fellow, McDonald Institute for Archaeological Research

Research Associate, Corpus Christi College

Office: Glyn Daniel Laboratory for Archaeogenetics, Room 3.1, Courtyard Building

McDonald Institute for Archaeological Research
University of Cambridge
Downing Street

Cambridge CB2 3ER
Office Phone: +44 (0)1223 339330

Biography:

Academic Positions

  • 2012–2014 Research Fellow, School of Life Sciences, University of Warwick, Coventry, United Kingdom
  • 2009–2011 Postdoctoral Fellow, Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin, New Zealand
  • 2004 Summer Intern, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States
  • 2001–2002 Student Fellow, New Zealand Institute for Crop & Food Research, Lincoln, New Zealand

Education

  • 2009 PhD in Plant Biology, Massey University, New Zealand
  • 2002 BSc(Hons) with First Class Honours in Plant Biology, Massey University, New Zealand
  • 2001 BSc in Physiological & Molecular Plant Biology, and Ecology (Double Major), Massey University, New Zealand

Subject groups/Research projects

Glyn Daniel Laboratory:

Research Interests

My research interests span evolutionary biology, plant molecular systematics, (palaeo)ethnobotany, phylogeography and anthropology. I am particularly interested in using genetic data to understand the origins, domestication and dispersal of crop plants. This archaeogenetics research includes an emphasis on how the movement of humans has influenced, and been influenced by, the movement of their commensal plants.

This research requires a variety of genetic approaches, often including the development of molecular markers in non-model plant species and the use of ancient DNA (DNA extracted from archaeological and ethnographic plant material).

The research I do is inter-disciplinary, and I enjoy collaborating with researchers in archaeology, linguistics, ethnobotany, phylogenetics and plant molecular biology.

My main current project is on the phylogeography of bottle gourd (Lagenaria siceraria). The bottle gourd has been cultivated for at least 10,000 years, with its durable fruit shells being used worldwide for containers, apparel and musical instruments. Despite its importance and distribution across many cultures, very little is known about the origins and dispersal of bottle gourd. Using archaeological remains of bottle gourd, the evolutionary history of this crop is being reconstructed. This is expected to allow insights into the early domestication of plants, the spread of agriculture, and the mapping of prehistoric human migration.

I am also affiliated with the ERC-funded project Food Globalisation in Prehistory (FOGLIP) and am a member of the Editorial Board for Scientific Reports.

More information is available on my research website at www.clarkeresearch.org. I am on Twitter at @aclarkenz.


Research Supervision

Undergraduate Dissertation Students

  • Finnoula (Finny) Taylor (HSPS Tripos, 2015–2016)

Project title TBA

Interns

  • Emily Wilkes (University of Oxford, Sep–Dec 2015)

Project title TBA

Previous Students

  • Lisa Briggs (MPhil project, 2014–2015)

"Blooming into the light: single nucleotide polymorphisms in the EARLY FLOWERING 3 gene of Setaria italica and Setaria viridis (foxtail millet)"

  • Yang (Sunny) Lu (Visiting Student from Shanxi Agricultural University, China, 2014–2015; with Prof. Martin Jones)

"PCR amplification and sequence analysis of three genes related to flowering in Setaria italica"

Prospective Students

If you are interested in joining our group as a student (dissertation, MPhil, PhD), visiting student or intern, please contact me by e-mail.


Teaching

I am involved in the teaching of the following courses:

Part IIB

  • A38 Archaeological Science (Archaeogenetics section)

MPhil

  • G02 Core Archaeology (Human–environment interactions)
  • G10 Archaeological Science (Archaeogenetics section)

Other Professional Activities

Professional Responsibilities

  • Editorial Board Member, Scientific Reports (Nature Publishing Group)
  • Committee Member, New Zealand Plant Radiation Network (NZPRN)

Society Memberships

  • New Zealand Society of Plant Biologists
  • Royal Society of Biology, Member (MRSB)
  • Society for Economic Botany
  • Society of Systematic Biologists

Key Publications

Articles & Chapters

[1] Sandoval J.R., Lacerda D.R., Acosta O., Jota M.S., Robles-Ruiz P., Salazar-Granara A., Vieira P.P.R., Paz-y-Miño C., Fujita R., Santos F.R., Jin L., Li H., Li S., Swamikrishnan P., Javed A., Parida L., Royyuru A.K., Mitchell R.J., Zalloua P.A., Adhikarla S., Kumar A., Prasad G., Pitchappan R., Santhakumari A.V., Valampuri K., Wells R.S., Vilar M.G., Soodyall H., Balanovska E., Balanovsky O., Tyler-Smith C., Bertranpetit J., Comas D., Cooper A., Haak W., Kaplan M.E., Merchant N.C., Renfrew C., Clarke A.C., Matisoo-Smith E.A., Gaieski J.B. and Schurr T.G. (2016). The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations. Annals of Human Genetics, 80(2), 88-101. DOI: 10.1111/ahg.12145.
[2] Allaby R.G., Kistler L., Gutaker R.M., Ware R., Kitchen J.L., Smith O. and Clarke A.C. (2015). Archaeogenomic insights into the adaptation of plants to the human environment: Pushing plant-hominin co-evolution back to the Pliocene. Journal of Human Evolution, 79, 150-157. DOI: 10.1016/j.jhevol.2014.10.014.
[3] Kistler L., Newsom L.A., Ryan T.M., Clarke A.C., Smith B.D. and Perry G.H. (2015). Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication.. Proc Natl Acad Sci U S A, 112(49), 15107-15112. DOI: 10.1073/pnas.1516109112.
[4] Kushniarevich A., Utevska O., Chuhryaeva M., Agdzhoyan A., Dibirova K., Uktveryte I., Möls M., Mulahasanovic L., Pshenichnov A., Frolova S., Shanko A., Metspalu E., Reidla M., Tambets K., Tamm E., Koshel S., Zaporozhchenko V., Atramentova L., Kučinskas V., Davydenko O., Goncharova O., Evseeva I., Churnosov M., Pocheshchova E., Yunusbayev B., Khusnutdinova E., Marjanović D., Rudan P., Rootsi S., Yankovsky N., Endicott P., Kassian A., Dybo A., Tyler-Smith C., Balanovska E., Metspalu M., Kivisild T., Villems R., Balanovsky O., Jin L., Li H., Li S., Swamikrishnan P., Javed A., Parida L., Royyuru A.K., Mitchell R.J., Zalloua P.A., Adhikarla S., Kumar A., Prasad G., Pitchappan R., Santhakumari A.V., Wells R.S., Vilar M.G., Soodyall H., Lacerda D.R., Santos F.R., Bertranpetit J., Haber M., Melé M., Adler C.J., Cooper A., Der Sarkissian C.S.I., Haak W., Kaplan M.E., Merchant N.C., Renfrew C., Clarke A.C., Matisoo-Smith E.A., Gaieski J.B., Owings A.C. and Schurr T.G. (2015). Genetic heritage of the balto-slavic speaking populations: A synthesis of autosomal, mitochondrial and Y-chromosomal data. PLoS ONE DOI: 10.1371/journal.pone.0135820.
[5] Saslis-Lagoudakis C.H., Rønsted N., Clarke A.C. and Hawkins J.A. (2015). Evolutionary approaches to ethnobiology. Evolutionary Ethnobiology. 59-72. DOI: 10.1007/978-3-319-19917-7_5.
[6] Stevens M.I., Clarke A.C., Clarkson F.M., Goshorn M. and Gemmill C.E.C. (2015). Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus). New Zealand Journal of Ecology
[7] Allaby R.G., Gutaker R., Clarke A.C., Pearson N., Ware R., Palmer S.A., Kitchen J.L. and Smith O. (2014). Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130377. DOI: 10.1098/rstb.2013.0377.
[8] Clarke A.C., Prost S., Stanton J.A., White W.T., Kaplan M.E., Matisoo-Smith E.A. and Genographic Consortium (2014). From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.. BMC Genomics DOI: 10.1186/1471-2164-15-68.
[9] Der Sarkissian C., Brotherton P., Balanovsky O., Templeton J.E., Llamas B., Soubrier J., Moiseyev V., Khartanovich V., Cooper A., Haak W. and Genographic Consortium (2014). Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1.. PLoS One DOI: 10.1371/journal.pone.0087612.
[10] Elhaik E., Tatarinova T., Chebotarev D., Piras I.S., Maria Calò C., De Montis A., Atzori M., Marini M., Tofanelli S., Francalacci P., Pagani L., Tyler-Smith C., Xue Y., Cucca F., Schurr T.G., Gaieski J.B., Melendez C., Vilar M.G., Owings A.C., Gómez R., Fujita R., Santos F.R., Comas D., Balanovsky O., Balanovska E., Zalloua P., Soodyall H., Pitchappan R., Ganeshprasad A., Hammer M., Matisoo-Smith L., Wells R.S. and Genographic Consortium (2014). Geographic population structure analysis of worldwide human populations infers their biogeographical origins.. Nat Commun DOI: 10.1038/ncomms4513.
[11] Vilar M.G., Melendez C., Sanders A.B., Walia A., Gaieski J.B., Owings A.C., Schurr T.G., Adhikarla S., Adler C.J., Balanovska E., Balanovsky O., Bertranpetit J., Clarke A.C., Comas D., Cooper A., Der Sarkissian C.S.I., GaneshPrasad A., Haak W., Haber M., Hobbs A., Javed A., Jin L., Kaplan M.E., Li S., Martínez-Cruz B., Matisoo-Smith E.A., Melé M., Merchant N.C., Mitchell R.J., Parida L., Pitchappan R., Platt D.E., Quintana-Murci L., Renfrew C., Lacerda D.R., Royyuru A.K., Santos F.R., Soodyall H., Soria Hernanz D.F., Swamikrishnan P., Tyler-Smith C., Santhakumari A.V., Vieira P.P., Wells R.S., Zalloua P.A. and Ziegle J.S. (2014). Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. American Journal of Physical Anthropology, 155(3), 352-368. DOI: 10.1002/ajpa.22569.
[12] Boattini A., Martinez-Cruz B., Sarno S., Harmant C., Useli A., Sanz P., Yang-Yao D., Manry J., Ciani G., Luiselli D., Quintana-Murci L., Comas D., Pettener D. and Genographic Consortium (2013). Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.. PLoS One DOI: 10.1371/journal.pone.0065441.
[13] Brotherton P., Haak W., Templeton J., Brandt G., Soubrier J., Jane Adler C., Richards S.M., Sarkissian C.D., Ganslmeier R., Friederich S., Dresely V., van Oven M., Kenyon R., Van der Hoek M.B., Korlach J., Luong K., Ho S.Y., Quintana-Murci L., Behar D.M., Meller H., Alt K.W., Cooper A., Genographic Consortium, Adhikarla S., Ganesh Prasad A.K., Pitchappan R., Varatharajan Santhakumari A., Balanovska E., Balanovsky O., Bertranpetit J., Comas D., Martínez-Cruz B., Melé M., Clarke A.C., Matisoo-Smith E.A., Dulik M.C., Gaieski J.B., Owings A.C., Schurr T.G., Vilar M.G., Hobbs A., Soodyall H., Javed A., Parida L., Platt D.E., Royyuru A.K., Jin L., Li S., Kaplan M.E., Merchant N.C., John Mitchell R., Renfrew C., Lacerda D.R., Santos F.R., Soria Hernanz D.F., Spencer Wells R., Swamikrishnan P., Tyler-Smith C., Paulo Vieira P. and Ziegle J.S. (2013). Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.. Nat Commun DOI: 10.1038/ncomms2656.
[14] Saslis-Lagoudakis C.H. and Clarke A.C. (2013). Ethnobiology: the missing link in ecology and evolution. Trends in Ecology & Evolution, 28(2), 67-68. DOI: 10.1016/j.tree.2012.10.017.
[15] Storey A.A., Clarke A.C., Ladefoged T., Robins J. and Matisoo-Smith E. (2013). DNA and Pacific Commensal Models: Applications, Construction, Limitations, and Future Prospects. The Journal of Island and Coastal Archaeology, 8(1), 37-65. DOI: 10.1080/15564894.2012.761299.
[16] Knapp M., Clarke A.C., Horsburgh K.A. and Matisoo-Smith E.A. (2012). Setting the stage – Building and working in an ancient DNA laboratory. Annals of Anatomy - Anatomischer Anzeiger, 194(1), 3-6. DOI: 10.1016/j.aanat.2011.03.008.
[17] Jones T.L., Clarke A.C., Cordero M-A., Green R.C., Irwin G., Klar K.A., Matisoo-Smith E.A., Quiróz D., Ramírez-Aliaga J.M., Scaglion R., Storey A.A. and Weisler M.I. (2011). Summary and conclusions.. T.L. Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramírez-Aliaga (eds.), Polynesians in America: Pre-Columbian Contacts with the New World. Lanham, Maryland, United States: Rowman & Littlefield. 263-276.
[18] Storey A.A., Clarke A.C. and Matisoo-Smith E.A. (2011). Identifying contact with the Americas: a commensal-based approach.. T.L. Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramirez-Aliaga (eds.), Polynesians in America: Pre-Columbian Contacts with the New World. Lanham, Maryland, United States.: Rowman & Littlefield. 111-138.
[19] Stölting K.N., Clarke A.C., Meudt H.M., Blankenhorn W.U. and Wilson A.B. (2011). Cost-effective fluorescent amplified fragment length polymorphism (AFLP) analyses using a three primer system. Molecular Ecology Resources, 11(3), 494-502. DOI: 10.1111/j.1755-0998.2010.02957.x.
[20] Seelenfreund D., Clarke A.C., Oyanedel N., Piña R., Lobos S., Matisoo-Smith E.A. and Seelenfreund A. (2010). Paper mulberry (Broussonetia papyrifera) as a commensal model for human mobility in Oceania: Anthropological, botanical and genetic considerations. New Zealand Journal of Botany, 48(3-4), 231-247. DOI: 10.1080/0028825X.2010.520323.
[21] Holland B., Clarke A. and Meudt H. (2008). Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution. Systematic Biology, 57(3), 347-366. DOI: 10.1080/10635150802044037.
[22] McCallum J., Thomson S., Pither-Joyce M., Kenel F., Clarke A. and Havey M.J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818.
[23] Michel C., Hicks B.J., Stölting K.N., Clarke A.C., Stevens M.I., Tana R., Meyer A. and van den Heuvel M.R. (2008). Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation in island freshwater fish species. BMC Evolutionary Biology, 8(1), 49. DOI: 10.1186/1471-2148-8-49.
[24] Meudt H.M. and Clarke A.C. (2007). Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science, 12(3), 106-117. DOI: 10.1016/j.tplants.2007.02.001.
[25] van den Heuvel M.R., Michel C., Stevens M.I., Clarke A.C., Stölting K.N., Hicks B.J. and Tremblay L.A. (2007). Monitoring the Effects of Pulp and Paper Effluent Is Restricted in Genetically Distinct Populations of Common Bully ( Gobiomorphus cotidianus ). Environmental Science & Technology, 41(7), 2602-2608. DOI: 10.1021/es061922q.
[26] Clarke A.C., Burtenshaw M.K., McLenachan P.A., Erickson D.L. and Penny D. (2006). Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria). Molecular Biology and Evolution, 23(5), 893-900. DOI: 10.1093/molbev/msj092.
[27] McCallum J., Clarke A., Pither-Joyce M., Shaw M., Butler R., Brash D., Scheffer J., Sims I., van Heusden S., Shigyo M. and Havey M.J. (2006). Genetic mapping of a major gene affecting onion bulb fructan content. Theoretical and Applied Genetics, 112(5), 958-967. DOI: 10.1007/s00122-005-0199-5.
[28] Erickson D.L., Smith B.D., Clarke A.C., Sandweiss D.H. and Tuross N. (2005). An Asian origin for a 10,000-year-old domesticated plant in the Americas.. Proc Natl Acad Sci U S A, 102(51), 18315-18320. DOI: 10.1073/pnas.0509279102.
[29] McCallum J., Pither-Joyce M., Clarke A., Kik C., Van Heusden S., Jakse J. and Havey M.J. (2005). Towards a framework PCR-based map of onion (Allium cepa L.). Acta Horticulturae, 688, 173-178.