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 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. I have worked extensively with the AFLP technique in the past, and am currently using next-generation sequencing methods for the development of molecular markers. I am also using ancient DNA (DNA extracted from archaeological and ethnographic material) to look at changes in genetic diversity through time.

To date, my research has been focussed in Oceania — a region that includes some of the first and last locations to be settled by modern humans, as well as some of the oldest and youngest domesticated plant species. I am especially interested in pre-European contact between Polynesia and South America, and have carried out research on sweet potato and bottle gourd. These species are a proxy for human movement, and were probably introduced from South America into Oceania by Polynesian voyagers.

Most recently, I have been conducting research as part of the Genographic Project. For this, we collected DNA from indigenous Pacific peoples and have sequenced complete mitochondrial genomes using 454 technology. The aim of this work is to investigate some of the less well understood aspects of the human settlement of Oceania.

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

I am currently a Research Fellow in the Allaby Research Group in the School of Life Sciences at the University of Warwick.

 

 

Some Places I’ll be in 2012:

University of Otago — 6 January–13 February 2012, Dunedin, New Zealand
Massey University — 28 February–March 2012, Palmerston North, New Zealand
University of Warwick — April 2012—, Coventry, United Kingdom

Origins of Banana, Yam and Taro in Australia

I will be undertaking this research at the University of Warwick. More details to be added soon.

 

People

Robin AllabyUniversity of Warwick, Coventry, United Kingdom

Origins of Oceanic Peoples — The Genographic Project

The Genographic Project is a multi-national scientific project to reconstruct past migrations of human populations around the world. It is funded by the National Geographic Society in partnership with IBM and the Waitt Family Foundation.

The Genographic Project has two parts: the public participation project (where members of the public purchase a testing kit to determine their own ancestry), and field research of indigenous populations worldwide. The field research is being carried out by 12 Regional Centers.

The Oceania Regional Center, headed by Prof. Lisa Matisoo-Smith and based at the University of Otago, is responsible for collecting and analysing DNA samples from Oceanic regions including Island Melanesia and Polynesia. This research is done in consultation with local communities. Together with collaborators, we have collected DNA samples from people in Emirau (off the coast of Papua New Guinea), Tokelau and French Polynesia.

Lisa Matisoo-Smith explaining the consent and sampling protocols on Emirau Island (April 2009).

The Genographic Project is using mitochondrial (maternally inherited) and Y chromosome (paternally inherited) DNA markers. To obtain high resolution data, we have sequenced complete mitochondrial genomes using 454 next-generation sequencing technology.

The data we have collected are allowing us to address a number of important questions in Pacific prehistory, including:

  • The origins of the Lapita peoples — who are associated with the expansion of human populations into Remote Oceania about 3,100 yr BP — and their relationships with people currently living in Island Melanesia and Polynesia.
  • The genetic relationships between Micronesian and Polynesian populations.
  • The extent of sex-specific dispersal.
  • The amount of genetic variation in isolated populations.

We have also been working closely with the Australasian Regional Center, headed by John Mitchell and based at La Trobe University in Melbourne, Australia. The Australasian Regional Center is responsible for collecting and analysing samples from Aboriginal Australian and Māori populations. For Māori, some of the questions being asked are: How many migrations were there? From how many different locations did migrants come? What have been the movements within New Zealand? Integration of the genetic data with Māori oral history will be an important part of the research.

 

People

Lisa Matisoo-SmithUniversity of Otago, Dunedin, New Zealand
Jo-Ann StantonUniversity of Otago, Dunedin, New Zealand
Stefan Prost University of Otago, Dunedin, New Zealand
John MitchellLa Trobe University, Melbourne, Australia
The Genographic Consortium

Origins of the Polynesian Sweet Potato (Kūmara)

The sweet potato (Ipomoea batatas) was important in many agricultural systems in pre-European Polynesia, and its origins in this part of the world have been of long-standing interest.
 
  ‘Owairaka Red’, the most popular sweet potato cultivar in New Zealand, is probably derived from a mid-19th century introduction by whalers.

Linguistic evidence suggests a human-mediated, pre-European introduction of the sweet potato from South America into the Pacific (the word kumara is used by both Quechua speakers in South America, and by Polynesians). Archaeological and biological evidence is also consistent with this scenario. The introduction of sweet potato to the Pacific was most likely effected by Polynesian voyagers who sailed to the west coast of South America, collected the sweet potato and brought it back to Eastern Polynesia. From there it was carried east, north (to Hawai‘i) and south-west (to New Zealand).

Part of the pot-maintained Yen Sweet Potato Collection in Tsukuba, Japan (June 2004).

DNA fingerprinting techniques have been used to analyse several hundred sweet potato accessions. These data are now being applied to test specific hypotheses about: where on the South American coast Polynesians made contact, the number of lineages introduced into Polynesia, the origin of the sweet potato in western Oceania and the influence of European-era introductions on the modern diversity. The movement of sweet potato in the Pacific is a good proxy for patterns of human migration and mobility in Oceania, and we expect our findings to have implications in these areas.

 

People

David PennyMassey University, Palmerston North, New Zealand
Barbara HollandUniversity of Tasmania, Hobart, Australia
Roger Green — University of Auckland, Auckland, New Zealand
Makoto Nakatani — National Institute of Crop Science, Tsukuba, Japan
Steve Lewthwaite — Plant & Food Research, Pukekohe, New Zealand
Richard ScaglionUniversity of Pittsburgh, Pittsburgh, PA, United States
María Auxiliadora Cordero — University of Pittsburgh, Pittsburgh, PA, United States
Peter MatthewsNational Museum of Ethnology, Osaka, Japan

Molecular Markers in Plant Systematics — The Species Level

I am interested in the development and characterisation of molecular markers for plants, especially at the species level (species radiations, and population genetics), including:
   
1. Scoring of AFLP data.
I am interested in improving methods for the automated scoring of AFLP data. This includes adjusting scoring parameters to maximise the size and quality of the binary matrix. I am also working on software for easily re-formatting AFLP data.
Optimising AFLP scoring parameters can significantly increase phylogenetic resolution. This consensus network of 30 taxa shows how optimisation of scoring increased the number of internal edges with > 50% bootstrap from 14 to 25, out of a possible maximum of 27 (new edges shown as dashed red lines). See Holland et al. (2008) for more information.
   
2. Development of markers using next-generation sequencing technologies.
Future research will focus on using next-generation sequencing technologies for marker development at the species level.

 

People

Jing Wang — Massey University, Palmerston North, New Zealand
Barbara HollandUniversity of Tasmania, Hobart, Australia
Heidi MeudtMuseum of New Zealand Te Papa Tongarewa, Wellington, New Zealand

Other Projects

These are some other projects on which I am (or have been recently) collaborating:

 

Ecosourcing research on New Zealand native plants is being carried out in collaboration with Chrissen Gemmill at the University of Waikato.

We are determining levels of genetic diversity in populations of plants at Waiwhakareke Natural Heritage Park near Hamilton (an artificially revegetated site) and at a number of natural (wild) populations around the Waikato. Using ecosourced (locally sourced) plants for restoration projects is generally encouraged because the plants possess local alleles and are locally adapted. But using plants with too little genetic diversity can lead to a reduction in heterozygousity and inbreeding depression. To determine the extent to which an ecosourced population captures levels of genetic diversity observed in the wild we are using three species: kahikatea (Dacrycarpus dacrydioides), māhoe (Melicytus ramiflorus) and mānuka (Leptospermum scoparium).

 

People

Chrissen GemmillUniversity of Waikato, Hamilton, New Zealand
Mark StevensSouth Australian Museum, Adelaide, Australia

 


 

 
  A Japanese variety of taro growing at Albany, New Zealand.
Photo credit: Robin Atherton
Research on taro (Colocasia esculenta) is being carried out in collaboration with Mike Hendy at Massey University.

There are two aspects to this research: first, using DNA data to reconstruct the origins and dispersal of taro in South East Asia and Oceania; second, to test hypotheses of microevolution by examining DNA sequence repeat motifs.

 

People

Mike Hendy — University of Otago, Dunedin, New Zealand
Ibrar Ahmed — Massey University, Palmerston North, New Zealand
Atheer Matroud — Massey University, Palmerston North, New Zealand
Peter MatthewsNational Museum of Ethnology, Osaka, Japan

Read about previous research projects here.

 

Current Collaborators’ Websites

Robin Allaby Assoc. Prof. Robin Allaby, School of Life Sciences, University of Warwick, Coventry, United Kingdom   Peter Matthews Assoc. Prof. Peter Matthews, National Museum of Ethnology, Osaka, Japan
Chrissen Gemmill Dr Chrissen Gemmill, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand   Heidi Meudt Dr Heidi Meudt, Museum of New Zealand Te Papa Tongarewa, and Victoria University of Wellington, Wellington, New Zealand
Barbara Holland Dr Barbara Holland, School of Mathematics and Physics, University of Tasmania, Hobart, TAS, Australia   David Penny Prof. David Penny, Massey University, Palmerston North, New Zealand
Lisa Matisoo-Smith Prof. Lisa Matisoo-Smith, Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand