Anna Santure is a Senior Lecturer in Genetics in the School of Biological Sciences, University of Auckland. Anna completed a BSc (Honours) in Genetics and Mathematics and a PhD in Genetics at the University of Otago, Dunedin, with Prof Hamish Spencer. In 2006 she moved to London to start a postdoctoral position with Dr Jinliang Wang at the Institute of Zoology, Zoological Society of London. She did a second postdoc in the Molecular Ecology Lab at the University of Sheffield with Prof Jon Slate.
Anna is interested in the genetic basis of quantitative traits, such as body size, which are usually influenced by many genes as well as environmental influences. Most of the traits linked to survival and reproduction, and hence the overall fitness of individuals in a population, are complex and quantitative. Gaining an understanding of the genetic basis of these important traits in wild populations allows us to explore and predict the adaptive potential of populations, which is particularly important for threatened species.
Annabel Whibley is a Research Fellow in the School of Biological Sciences and a Senior Technologist at Auckland Genomics. She is fascinated by how adaptive traits evolve in natural populations, and increasingly leverages powerful genomics technologies in combination with more classical genetics approaches to address these questions. Most recently Annabel has been searching for functional variants and genomic architectures that account for colour pattern differences in Antirrhinum (snapdragon) flowers and Heliconius butterfly wings but also has an interest in exploring any systems that offer the potential to provide insights into the mechanisms of evolutionary processes.
With our collaborators Rebecca Johnson and Richard Major at the Australian Museum Research Institute, Sydney, Annabel is currently working to improve the draft genome of the Indian myna (Acridotheres tristis) ahead of hopefully developing this as a model system to investigate whether transposable element activity plays a key role in facilitating adaptation in invasive species.
Annabel is also leading the assembly of the hihi (Notiomystis cincta) genome for the Genomics Aotearoa High Quality Genomes and Population Genomics project.
Caroline Lees is a PhD candidate at The University of Auckland, supervised by Prof Jacqueline Beggs and co-supervised by Anna Santure. Caroline is a Programme Officer for the IUCN Species Survival Comission Conservation Planning Specialist Group and her PhD investigates the impact of conservation planning in species recovery, with a particular focus on evaluating science-based, inclusive and participatory species conservation planning.
Laura Duntsch is a PhD candidate at the University of Auckland under the supervision of Dr Anna Santure and in collaboration with Dr Patricia Brekke and Dr John Ewen at the Institute of Zoology, Zoological Society of London.
She obtained her Bachelor’s degree in biology from the Technical University Braunschweig in Germany, where for her bachelor thesis she analysed the phylogenetic diversity and structure of cutaneous bacterial communities among different body parts and habitats of fire salamander larvae. After a volunteering internship at the Rotokare Scenic Reserve, New Zealand, Laura completed her Master’s degree in Animal Ecology at Lund University, Sweden. In her thesis project, she investigated chromosomal regions associated with bill morphology in the endemic Nesospiza bunting of the Tristan da Cunha archipelago. Last year, she conducted an Animal Breeding Genetics internship in a multi-species breeding company in the Netherlands.
During her PhD, Laura will be using hihi (Notiomystis cincta) SNP chip data to validate the Tiritiri Matangi island pedigree and measure individual inbreeding levels within the population. She will make use of additional data on morphological and life history traits and environmental variables to investigate the strength of inbreeding depression in the Tiritiri Matangi population and to better understand the underlying genetic mechanisms. The goal is to identify loci with large effects contributing to inbreeding depression and to be able to make predictions about the adaptive potential of the species.
Christina Flammensbeck is a PhD candidate at the University of Auckland under the supervision of Dr Maren Wellenreuther and co-supervision of Dr Anna Santure. Christina obtained her bachelor’s degree in biology and her masters’ degree from the Munich Graduate School for Evolution, Ecology and Systematics (EES), both from the Ludwig-Maximilians-Universität Munich (LMU) in Germany. For her bachelor thesis, Christina studied the microanatomy and ultrastructure of a vermiform nudibranch living in the mesopsammon (Pseudovermis paradoxus). Her Masters research estimated divergence times and phylogenetic relationships of deep-sea sharks (order: Squaliformes) using Bayesian inference.
For her PhD, Christina is based off-campus at the Plant and Food Research Institute in Nelson. Christina is going to study the genome and transcriptome of the Australasian snapper (Chrysophrys auratus) to understand molecular mechanisms underpinning temperature stress resilience. She is interested in the identification of key genes involved in adaptation to a changing climate, particularly in respect of increasing temperatures.
Kamolphat Atsawawaranunt – known as A – is a PhD candidate at the University of Auckland under the supervision of Dr Anna Santure and Dr Annabel Whibley. A completed his BSc degree in Natural Science at University College London and his MRes degree in Ecology, Evolution and Conservation at Imperial College London. He did two research projects during his Masters. The first project was about canopy temperature and air temperature, and the second project was about resolving the phylogeny of the Dendrobium orchids using plastid genes. After completing his Master’s degree, he worked as a research assistant at the University of Reading until mid-2020 where he created and managed palaeoclimate databases (e.g. SISAL database) and helped with analyses within the lab group.
For his PhD, A is studying the population and adaptation genomics of two invasive birds in New Zealand – the common myna (Acridotheres tristis) and the common starling (Sturnus vulgaris). He is interested in identifying the population structure of the invasive birds in New Zealand and whether there are underlying genetic reasons to the adaptability and the invasiveness of the common myna and the common starling despite their likely low founding genetic diversity.
Eirian Perkins is a PhD candidate in the School of Biological Sciences, supervised by Dr Anna Santure and Distinguished Professor Marti Anderson at Massey University. Eirian is co-supervised by Dr Nicholas Matzke and Prof Allen Rodrigo at the University of Auckland.
She obtained a triple Bachelor’s degree in biology, zoology, and computer science from Colorado State University in the United States, and a dual Master’s degree in engineering management and computer science from the University of Colorado Boulder. After working many years as a software engineer in industry, Eirian is delighted to return to the academic world and earn a doctorate.
For her PhD, Eirian aims to refine aspects of genetic diversity measurements. Genetic diversity is typically measured in terms of population-level average metrics, but adapting ecological measures of diversity can describe complementary aspects of genetic variation within a population. There is considerable promise to extend similarity and dissimilarity measures to higher-order groups, including families, populations, and species, to capture different aspects of genetic variation. Eirian plans to fill this important gap in the literature by adapting existing metrics and multivariate analytical methodologies from other fields, as well as introducing new models. Existing conservation efforts emphasise the maintenance of genetic diversity, where total genetic diversity is often used as a proxy for adaptive potential. Adaptive potential is the capacity of a population to respond to selection, and improving predictions of it will likely empower decision-makers to more effectively protect native and endangered wildlife.
Sarah Bailey is a Masters student at the University of Auckland supervised by Dr Annabel Whibley and co-supervised by Anna Santure. She obtained her Bachelor’s degree in biological sciences and statistics and PGDipSci in biological sciences at the University of Auckland.
For her Masters, Sarah is investigating the genome of the threatened hihi (Notiomystis cincta, stitchbird). She is producing and annotating a reference genome assembly for a female hihi, including a highly detailed W chromosome sequence. She will look at the gene and repeat content of the hihi genome to identify unique genetic features to hihi. Insights into these genetic features can improve our understanding of the genomic mechanisms shaping adaptive traits in hihi.
Annika Beesley – summer research student, 2020-21, and current short term research assistant, co-supervised by Anna Santure, Dr Annabel Whibley and Dr Heather Battles.
Annika is tracking the history of introductions of common myna (Acridotheres tristis) to New Zealand based on archival research.
Past group members
Former Postdoctoral Fellows
Alexis Rutschmann was a Research Fellow in the School of Biological Sciences from 2017-2018 and is interested in the transmission of extra-genetic elements from parents to their progeny. He is also very interested in studying different environmental characteristics that can shape the evolution of phenotypic plasticity.
He completed his BSc in Biology, Physiology and ecology in Strasbourg (Université de Strasbourg, France) and Montreal (Université de Montréal, Canada). During his Masters degree (Université de Montpellier, France) and under the supervision of Dr Isabelle Chuine and Dr Anne Duputié, he studied the adaptive potential of phenotypic plasticity under different climate change scenarios, using a process-based species distribution model. Then, he performed his PhD in the Station d’ Ecologie Théorique et Expérimentale (Moulis, France) under the supervision of Dr Jean Clobert, Dr Murielle Richard and Prof Don Miles. His work was mainly focused on the environmental determinants that shape plastic responses and life history trade-offs in the common lizard (Zootoca vivipara).
At the University of Auckland, Alexis was working on the influence of both genetic and spatial relationships between individuals on the heritability of life-history traits. He developed a pedigree for the Zealandia Karori Wildlife Sanctuary hihi (Notiomystis cincta) population and modified existing quantitative genetic models to determine the role of space sharing on phenotypic similarity between individuals.
Pierre de Villemereuil was a Research Fellow in the School of Biological Sciences from 2016-2017 and is interested in the study of adaptive phenomenons on a micro-evolutionary scale in wild populations. To do so, he combines approaches from evolutionary ecology, quantitative genetics and population genomics.
He completed his B.Sc. in Biology and Masters in Evolutionary Ecology at the École Normale Supérieure in Paris (France). In 2012, he started a Ph.D. in the University of Grenoble – Alpes (France) with Irène Till-Bottraud and Oscar Gaggiotti on the study of local adaptation in the Alpine plant Arabis alpina. During this Ph.D., he performed methodological developments as well as empirical studies (see more).
While in Auckland, Pierre was working on measuring the adaptive potential of the hihi, Notiomystis cincta, as well as the evolutionary constraints on this species, especially on the Tiritiri Matangi island population, by combining the pedigree and phenotypic data available over 20 years from the population.
Former Postgraduate Students
Priscila M Salloum, PhD student, completed 2020
Genetic and phenotypic variation of Onithochiton neglectus across a heterogeneous marine environment
Priscila M Salloum was a PhD candidate at The University of Auckland, supervised by Dr Shane Lavery and co-supervised by Anna Santure and Pierre de Villemereuil. Priscila completed a Bachelors and Teaching Degree in Biological Sciences and a Masters Degree in Genetics and Evolution at the State University of Campinas (Brazil). In her Masters Degree, she was supervised by Professor Vera Solferini and studied factors affecting the genetic variability and population structure of marine invertebrates, with a project focused on the Brazilian smallest seashore winkles (Echinolittorina lineolata) and the genetic patterns exhibited by them in two neighbouring locations. Priscila is also interested in education, having worked as a biology and science teacher in two Brazilian secondary schools.
For her PhD, Priscila assessed the connectivity and local adaptation of the chiton Onithochiton neglectus, a marine invertebrate that has reduced mobility and invests high amounts of energy in brooding their eggs. She discovered very high levels of structure between North, South and Central New Zealand, with connectivity in the South likely mediated by high levels of kelp rafting. She also demonstrated that differences in selection pressures across the New Zealand latitudinal gradient are likely to have lead to local adaptation in the species.
Priscila is now a research and teaching assistant in the School of Biological Sciences, University of Auckland.
Alex Knight, PhD student, completed 2020
The conservation genetics of the hihi (Notiomystis cincta) and epidemiology of coccidian infection
Alex was a PhD candidate at the University of Auckland supervised by Anna Santure, and co-supervised by Dr Patricia Brekke (Institute of Zoology, Zoological Society of London), Dr John Ewen (Institute of Zoology, Zoological Society of London) and Assoc Prof Craig Millar (School of Biological Sciences, University of Auckland).
He received a BSc and MSc first class with Honours from the University of Canterbury. His Masters research investigated the population genetics of West African chimpanzees in Eastern Nigeria under the supervision of Dr Hazel Chapman and Dr Marie Hale. This project examined gene flow and sex biased dispersal in communities of chimpanzees inhabiting the region and included a population viability analysis of a small and potentially isolated community in a forest fragment.
For his PhD Alex investigated the genetics and epidemiology of coccidia, an intestinal parasite, of the threatened hihi (Notiomystis cincta), with particular focus on the population on Tiritiri Matangi Island, near Auckland. The work revealed that hihi juveniles are more likely to be infected with coccidia, and revealed genetic variants at toll-like receptor immune loci are associated with coccidial infection in adult birds.
Alex is now a Restoration Advisor for the Pest Free Kaipātiki project.
Stephanie Galla – PhD student, completed 2019
Conservation genomic management of two critically endangered New Zealand birds
Stephanie Galla was a PhD candidate at the University of Canterbury under the supervision of Assoc Prof Tammy Steeves (senior supervisor) and Anna Santure (associate supervisor). Before arriving to New Zealand, Stephanie earned her BSc degree in Wildlife Biology at Murray State University and her MSc degree at the University of North Texas, where she studied the phylogenetics of North American prairie grouse (Genus: Tympanuchus). Stephanie’s broad research interests include the application of genetic and genomic data to inform the management of critically-endangered species.
At the University of Canterbury, Stephanie’s PhD evaluated relatedness estimates in the critically-endangered kakī/black stilt (Himantopus novaezelandiae) using pedigrees, microsatellites, and high-throughput sequencing techniques (i.e., genotyping-by-sequencing and low/high coverage genome sequencing). By evaluating these approaches, Stephanie hopes to better inform captive management efforts for kakī and other captive breeding programmes worldwide.
Stephanie is now a postdoc at Boise State University.
Kate D Lee – PhD student, completed 2019
Genomics in Reintroduction Biology: a case study with New Zealand hihi (Notiomystis cincta)
Supervised by Anna Santure, and co-supervised by Dr Patricia Brekke (Institute of Zoology, Zoological Society of London), Dr John Ewen (Institute of Zoology, Zoological Society of London) and Assoc Prof Craig Millar (School of Biological Sciences, University of Auckland).
For her PhD, Kate developed a genomic toolkit for the hihi (Notiomystis cincta) and used this to investigate the accumulation of inbreeding as a consequence of translocation events and ongoing population bottlenecks. Hihi is an endemic New Zealand forest-dwelling bird, which were last seen on the mainland in 1883. A hihi recovery program has been operating since the 1980’s, and the birds have been translocated to predator-free islands and fenced wildlife parks with increasing success. In particular the birds on Tiritiri Matangi island have been monitored through every breeding season since they were translocated there in 1995 and their pedigree has been established by a microsatellite genetics study.
Kate is now a Research Officer at Statistics New Zealand, Wellington.
Agustín L Santos – PhD student, completed 2018
Heterotaxy in Caenorhabditis elegans: Defects in embryo gut organogenesis underlie natural variation in hermaphrodite left/right organ arrangement
Supervised by Prof Joel Rothman (Department of Molecular, Cellular, and Developmental Biology at the University of California, Santa Barbara) and co-supervised by Anna Santure
During his PhD, Agustín examined the molecular and genetic basis of, and evolutionary variation in, handedness reversal, using the model system Caenorhabditis elegans. He described a novel phenotype of incomplete handedness reversal (i.e. partial or complete swap of gut and gonad arms to the opposite side than normal) in C. elegans hermaphrodites, including measuring the temperature sensitivity of reversal, the natural variation in rates of reversal between wild strains, variation in rates of reversal in a RIL (recombinant inbred lines) collection, and the impact of reversal on fertility and survival. He also established a correlation between a very early event, a defect in the twist of the intestinal primordium, and later handedness reversal in a collection of RILs, suggesting a mechanism for the establishment of handedness reversal. Finally, Agustin explored the genetic basis of variation in handedness reversal, using QTL mapping and GWAS on the RIL collection and on the wild strains.
Agustín is now an embryologist in Spain.
Phoebe Scherer – Honours student in Biology, 2017
A high-density genetic linkage map provides insights into the sex-specific recombination landscape of the hihi (Notiomystis cincta)
Phoebe is now working for a horticulture consultancy company in Tauranga.
Edwardo Reynolds – Honours student in Bioinformatics, 2016
Investigation of an imprinting effect in the bovine genome while accounting for high levels of population structure in linear and mixed models
Co-supervised by Dr Matt Littlejohn, Livestock Improvement Corporation
Edwardo is now a PhD student at Massey University
Sian Glazier – Honours student in Biology, 2015
Acoustic ecology for seabird conservation: Common Diving Petrel (Pelecanoides urinatrix) and Fluttering Shearwaters
Supervised by Dr Anne Gaskett and co-supervised by Anna Santure and Megan Friesen
Sian is now a PhD student at Murdoch University
Past Undergraduate / Visiting Students
Rhys McArthur-Tomes – summer research student, 2020-21, supervised by Annabel Whibley
Rhys conducted genome comparisons of different snapdragon (Antirrhinum majus) accession genome assemblies.
Bailee Baxter – third year science scholars student, 2019
Bailee completed morphological measurements of common myna (Acridotheres tristis) to describe adaptation across their New Zealand range.
Isabel Cantera – Internship student, 2015, during her Master’s degree in Ecology at Paul Sabatier University (Toulouse, France).
Isabel completed an assembly of genotyping-by-sequencing data of the hihi (Notiomystis cincta) in order to detect variation across the hihi genome