Lab

Conservation Systematics and Evolutionary Research Team (ConSERT)

About the lab

Kia ora! We are the Conservation, Systematics, and Evolution Research Team (ConSERT), based out of the School of Biological Sciences at the University of Canterbury in Christchurch, New Zealand. Our team is a collective of researchers collaborating in the labs of A/Prof Pieter Pelser and A/Prof Tammy Steeves. Check out our website for updates on current research projects from the ConSERT! You can also follow us on Twitter by using the hashtag #ConSERTeam.

Featured research (10)

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics ‐ the pedigree ‐ has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing (HTS) to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and local communities.
Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) datasets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and eco-evolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world’s most threatened species.
Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic diversity in threatened species via single nucleotide polymorphism (SNP) datasets, SVs remain understudied despite their potential influence on complex traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We identify three critical resources to characterize SVs de novo: 1) High-quality, contiguous, annotated reference genome(s); 2) Whole genome resequence data from representative individuals of the target species/populations; and 3) Well-curated metadata including pedigrees. We also leverage the existing literature–predominantly in human health, agriculture and eco-evol biology–to identify pangenomic approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we intensively manage some of the world’s most threatened species.
1. To achieve the vision outlined in the national strategy for biodiversity, Te Mana o te Taiao, we will need to unite diverse disciplines, including conservation genetics/genomics. 2. As conservation genetic/genomic data generated for—and associated with—taonga (treasured) species is also taonga, we highlight the need for collaborative research partnerships that centre the needs, aspirations and expertise of mana whenua. 3. As a team of predominantly early-career conservation genetics and genomics researchers working across institutions as Te Tiriti o Waitangi partners, each speaking to our own expertise, we review available and emerging tools in the conservation genetics/genomics toolbox. 4. To support practitioners in identifying appropriate and affordable tools from the toolbox, we present a table that encompasses resource requirements (including finances, time, and skill) to assist conservation practitioners in assessing the associated costs and benefits of these tools for informing conservation management. 5. To support researchers and practitioners in establishing long-lasting partnerships with mana whenua, we highlight key aspects of data management and data sovereignty for consideration. 6. Intended as a platform to initiate discussion within and among conservation practitioners and researchers, mana whenua, and local communities, the development of government policies is beyond the scope of this contribution. 7. To meet the vision of Te Mana o te Taiao, we conclude by calling for a transdisciplinary approach that includes conservation genetics/genomics.
Many species recovery programmes use pedigrees to understand the genetic ancestry of individuals to inform conservation management. However, incorrect parentage assignment may limit the accuracy of these pedigrees and subsequent management decisions. This is especially relevant for pedigrees that include wild individuals, where misassignment may not only be attributed to human error, but also promiscuity (i.e. extra-pair parentage) or egg-dumping (i.e. brood parasitism). Here, we evaluate pedigree accuracy in the socially monogamous and critically endangered kakī (black stilt, Himantopus novaezelandiae) using microsatellite allele-exclusion analyses for 56 wild family groups across three breeding seasons (2014–2016, n = 340). We identified 16 offspring where parentage was incorrectly assigned, representing 5.9% of all offspring. Of the 16 misassigned offspring, three can be attributed to non-kakī brood parasitism, one can be assigned to human error, but others cannot be readily distinguished between non-monogamous mating behaviours and human error. In the short term, we advise the continued use of microsatellites to identify misassigned offspring in the kakī pedigree, and to verify non-kakī brood parasitism. We also recommend the Department of Conservation’s Kakī Recovery Programme further evaluate the implications of pedigree error to the management of this critically endangered taonga species.

Lab head

Tammy Steeves
Department
  • School of Biological Sciences
About Tammy Steeves
  • I co-lead the Conservation, Systematics and Evolution Research Team (ConSERT) at Te Whare Wānanga o Waitaha/University of Canterbury. In partnership with relevant Māori (Indigenous peoples of Aotearoa New Zealand) tribes (iwi or hapū) and in collaboration with conservation practitioners and local communities, we use genomic and non-genomic data to co-develop conservation genetic management strategies for some of Aotearoa New Zealand’s rarest taonga (treasured) species.

Members (10)

Stephanie J. Galla
  • Boise State University
Natalie Forsdick
  • Manaaki Whenua - Landcare Research
Roger Moraga Martinez
  • Tea Break Bioinformatics Limited, New Zealand
Jana Wold
  • University of Canterbury
Ilina Cubrinovska
  • University of Canterbury
Jasper John A. Obico
  • University of the Philippines Manila
Molly Magid
  • University of Canterbury
Aisling Rayne
  • Cawthron Institute