Biodiversity and Human Impacts

Each activity is made up of a number of projects. Some of these projects are described here and the project leader/s is listed.

Activity: Biodiversity knowledge and strategy for New Zealand


Title:  Genetic Variation and Conservation of Tuatara
Project leaders:  Professor Charles Daugherty and Dr Nicola Nelson

Genetic variation is considered essential to population survival, but demonstrating this is wild species and then using the information to support conservation have proven difficult.  We use molecular genetic information to approach this subject from multiple directions in the iconic New Zealand species tuatara (Sphenodon).  Analyses of MHC (immune) variation allow insights into both reproductive issues (mate choice) and health (resistance to parasitic ticks).  Additionally, continued exploration of the genetics of the unique sex-determining system of tuatara provides improved understanding of survival probabilities of individual tuatara populations in the face of global warming.  Collectively, this information supports improved management of tuatara in support of the New Zealand Biodiversity Strategy.  It also informs ongoing collaborations with Māori and outreach to the New Zealand public.

Questions: 

  • How much variation exists at MHC genes in tuatara, and how does this variation relate to health and mate choice?
  • How does the temperature-dependent sex determining system of tuatara affect their probability of survival on individual islands?


Title:  Iconic Species
Project leader:  Professor Charles Daugherty

Molecular tools for analyses of genetic variation continue to develop rapidly, allowing detailed insights into the genome of all species.  As a Centre, we wish to use these new technologies to support improved management of New Zealand’s rare and iconic species.  Because iconic species are of special interest to Māori and the Department of Conservation, the first step is consultation to explore topics of greatest importance for initial investigations and establish a collegial approach to the work.  In parallel with stakeholder consultation, feasibility studies of new technologies will be undertaken to identify new levels of genetic variation.  By the end of 2009, pilot studies will be well advanced in such iconic species as tuatara, little spotted kiwi, hoki, stick insects, and Pachycladon.  In turn, these studies will be the foundation for comprehensive genomic programmes that will ultimately provide a strong and dynamic scientific basis for management of biological resources in New Zealand.


Title: Plant adaptation and evolutionary prediction
Project leader: Professor Peter Lockhart

Predicting the evolutionary response of biota to environmental change is one of the outstanding challenges of our time. It requires understanding constraints of evolution operating at the levels of species-environment interactions, genetic plasticity and adaptation. Next-generation genetics and the study of natural variation have the potential to provide us with an understanding of these constraints. We are using evolutionary genomics and studies of natural populations to study the adaptive potential of plant species and the evolutionary significance of hybridisation in facilitating rapid adaptation to environmental change. Our studies involve using automated gene ontology analyses to identify candidate genes potentially important for understanding adaptation and monitoring the response of alpine plants to environmental change.

Questions

  • What is the adaptive potential of alpine plants to climate change?
  • What is the evolutionary significance of hybridisation? 


Title: DNA barcoding the birds of New Zealand and the Antarctic
Project leader: Dr Craig Millar

Our ability to accurately identify organism is fundamental to modern biology. DNA barcoding is based on the proposition that all species can be identified using short ‘signature’ regions of their mitochondrial genome.  There is currently intense worldwide interest around this idea and the suggestion that DNA barcoding could radically change the way we conduct taxonomy and species identifications in the future. A series of recent DNA barcoding studies have identified the necessary ‘signature’ regions for a range of vertebrate groups including birds. The aim of this research project is to DNA barcode the birds of New Zealand and Antarctica (~340 species). The birds represent one of the best studied, and most important components of the New Zealand and Antarctic ecosystem. The DNA barcoding of the birds of New Zealand and the Antarctic has broad theoretical and practical implications. It will allow the better management of our avian biodiversity as well as assisting in the conservation of endangered species and importantly in the trade in endangered species and biosecurity.  In addition the proposed project will secure our involvement in the international effort to DNA barcode the bird of the world.  More over this research will also contribute to a better understanding of the evolution of the New Zealand and Antarctica avian fauna.  We have collected may of the specimens necessary for this project and have now started to sequence and construct the DNA reference database that will be used in the identification process.

Questions:

  • Does DNA barcoding based on the signature region developed for North Hemisphere birds allow the identification, to the species level, of all the birds of New Zealand and the Antarctic?
  • Does DNA bardcoding identify any new species of New Zealand or Antarctic birds?
  • Using DNA barcoding what species of New Zealand birds where historically used in the construction of Moari feathers cloaks and what species are involved today in bird-strike at New Zealand’s airports?


Title:  Dispersal and Colonization in the Southern Hemisphere
Project leaders:  Professor Hamish Spencer and Dr Jon Waters

The role of long-distance dispersal in determining the distribution of organisms and the generation of biodiversity has been controversial ever since panbiogeographers and vicariance biogeographers noted that many explanations invoking dispersal were little better than just-so stories.  Today’s molecular tools and phylogenetic analyses, however, mean that dispersalist hypotheses can be rigorously tested.  Moreover, the biota of New Zealand and, indeed, the Southern Hemisphere in general is ideally suited to such investigations.  Geological history and a far-flung geography mean the long-distance dispersal events have almost certainly played an important role in generating current patterns of biodiversity.  Although such events may be rare, they may lead to fundamentally important evolutionary changes (e.g., initiating cladogenesis).  This project will examine various putative examples of long-distance dispersal, searching for patterns and reasons for the biodiversity observed.  Collaborations with other parts of the AWC will be important in many aspects, from field work to the development of improved analytical tools.

Questions

    • What is the role of long-distance dispersal in generating biodiversity?
    • Are there new exemplars of long-distance dispersal?
    • Can these exemplars aid in the development of new phylogenetic tools?

 

Activity: Tracing the origins and histories of the peoples and biota of New Zealand and the Pacific


Title:  Interpreting Nested Tandem Repeats as markers for the spread of agriculture across the Pacific
Project leader:  Professor Mike Hendy

Nested tandem repeats (NTR) are complexes of two interspersed repeating segments of DNA. One example is known in the IGS region of Colocasia esculenta (taro), a major staple crop throughout the Pacific, thought to have been domesticated in South Asia 6-8000 years bp, and clonally cultivated. A preliminary analysis of several cultivars providenced from different sources across the Pacific reveals there is sufficient variation in the NTRs to infer a dated history of their common origins on a 1000 year time scale, with the numbers of the single nucleotide substitutions, deletions and duplications well correlated. As the rate of duplication is approximately twice the substitution rate, the frequencies of repeat unit variants obey an exponential distribution, so we expect ancestral states to be conserved. A comparison of the phylogenies of the NTRs of different varieties should exhibit the extent of their common ancestry. Further samples are being accessed from other sites in the Pacific, Australia and South Asia and will be sequenced. We are developing new assembly software for repeated regions to exploit the high accuracy of Solexa technology.

Questions:

  • What can we learn of the process of concerted evolution by which mutations are spread to the all (most) IGS copies?
  • Can we determine whether there was a single or multiple domestications and introductions into the Pacific?
  • Do the dates of the spread across the Pacific consistent with current settlement hypotheses?
  • Are NTRs ubiquitous in other genomes?


Title:  Linking the Past and the Present - Ancient DNA and Pacific Origins and Interactions
Project leader: Professor Lisa Matisoo-Smith

In the past ancient DNA studies of human remains were limited to analyses of mtDNA and were hindered by issues of contamination and the poor quality of DNA recovered from ancient remains. The new generation sequencing technology gets around both of these issues. We can now potentially obtain data on complete mtDNA genomes, Y chromosome and other nuclear markers of population origin. Once we have developed the massively parallel DNA sequencing methods we can also apply these to the analysis of ancient human remains to look for particular genetic markers associated with health problems affecting Pacific peoples today and in the past (e.g. gout, diabetes etc).Working in conjunction with iwi, Pacific communities and national museums, we have been given access to human skeletal remains from several key populations that will allow us to address important questions in Pacific prehistory.

Questions:

  • Considering Wairau Bar, Marlborough NZ material: what is the Origin of the first New Zealanders
  •  Using material from Teouma, Vanuatu and Watom, PNG Lapita sites: Who were the First Lapita people and how do they relate to Pacific populations today?;
  • Considering material gathered at Mocha Island, Chile: what was the extent of Polynesian contact with South America?

 

Activity: Genetic studies in Health, Agriculture and Environmental Change


Title:  The molecular basis of speciation in New Zealand endemic leafroller moths
Project leader: Associate Professor Richard Newcomb

How new species are formed is still a major question in evolutionary and conservation biology.  The speciation process has produced the rich diversity of biota around us.  We wish to examine the molecular processes that have contributed to the production of new species through studying a recently evolved complex of 14 endemic NZ leafroller moths (genera Ctenopseustis and Planotortrix).  We are especially fortunate in that much is known of their mating system, including the sex pheromones they utilise to recognise mates and even many of the genes that encode important elements of this communication system. Already we have identified a multigene family of desaturase genes involved in pheromone biosynthesis and established that members of this family are differentially regulated among members of the species complex.  Using this model system we will ask what molecular changes are responsible for the evolution of new species and what is driving this process through focusing on the genetic basis of change in pheromone biosynthesis (desaturases) and pheromone recognition (pheromone binding proteins and pheromone receptors).  We have developed methods (e.g. RNAi) that allow us to manipulate gene expression levels in leafroller moths, thus giving us the ability to theoretically transform one species into another.

Questions

  • What is the molecular basis of species formation in leafroller moths.
  • What processes drive speciation in New Zealand’s biota?


Title: Tackling New Zealand’s increasing Staphylococcus aureus problem
Project leader:  Professor Paul Rainey

Infectious disease – of people, animals, and plants – is a fact of life.  Despite impressive developments in medicine and disease control, infectious disease remains a significant cause of death. New Zealand, like all nations, has a history of established infections, but epidemics (and non-epidemics) of new and old infectious diseases continue to arise (the late 1990s epidemic of a NZ-specific lineage of meningococcal disease in the provides a particularly poignant example).  The causes of disease persistence and outbreaks are not clear, but there is increasing recognition that much infectious disease emerges from non-pathogenic strains (commensals) influenced by complex ecological and evolutionary relationships between microbe, host and the environment (particularly environmental impacts wrought by humans). As an island nation NZ needs to understand how disease emerges and is maintained over a regional scale.

While a range of diseases threatens New Zealand, the most significant is due to the opportunistic pathogen Staphylococcus aureus (SA).  SA infections affect many parts of the body – from skin (boils) through serious blood stream infections (bacteremia). In NZ one in four people harbour SA; in 2007 47,000 people were screened for SA (cost ~ $1 million); in 2005 there were 252 cases of bacteremia in Auckland and Middlemore Hospitals with a 19% mortality rate (the mortality rate for Maori and South Pacific Islanders is four times greater).  By way of comparison, in 2005 there were 229 cases of meningococcal disease nation wide with a mortality rate of 4%.  Much of NZ’s SA infections stem from the so-named WSPP strain which is thought to have originated in Western Samoa and which was first isolated in NZ in 1982.  In recent times there has been a significant increase in the emergence of methicillin resistant SA (MRSA).

Tackling NZ’s SA problem is no easy task, however, essential for progress is an understanding of the evolutionary processes determining patterns of SA diversity in both community and hospital environments at both local and regional levels of scale.  In addition, evolution of the WSPP lineage of SA will be unravelled by sequencing a series of WSPP genomes (from 1982 to present).  Collaborations with physicians, ESR, the Maurice Wilkins Centre and investigators within the AWC are central to the success of this project.

Questions

  • What is the connection between Staphylococcus aureus (SA) in the community, the evolution of virulence and invasive disease? 
  • How do the genetic structures of SA from NZ and the South Pacific compare?
  • Where did the WSPP lineage of SA originate and how is it evolving in the NZ context.


Title:  The evolution of individuality during the transition to multicellularity.
Project leader: Professor Paul Rainey

The evolution of multicellular life from unicellular organisms is one of the most significant evolutionary events in the history of life.  Multicellularity brought with it the division of labour, development and a wealth of plant and animal forms.  In metazoans, such as humans, lower level entities (cells) have given up their ability to reproduce as independent units and instead replicate exclusively as part of the larger whole.  Explaining how this happened is a challenge of major proportion.  This project will focus on a central and largely unrecognized paradox, that is, how the first groups evolve by natural selection, given that the first groups are seemingly unable to participate in the process of evolution by natural selection, because they are unable to leave offspring. A solution to this catch-22 has been devised and a series of experiments planned to test the central thesis.

Questions.

  • What are the selective causes for the transition from single cells to groups of cells?
  • Can selection imposed at multiple levels enhance the fitness of groups?
  • Does the germline originate from cheating genotypes?