Tammy Steeves

Tammy Steeves
University of Canterbury | UC · School of Biological Sciences

PhD, MSc, BSc

About

78
Publications
21,755
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Introduction
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.

Publications

Publications (78)
Article
Full-text available
Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities...
Article
Full-text available
1. Conservation translocations—particularly those that weave diverse ways of knowing and seeing the world—promise to enhance species recovery and build ecosystem resilience. Yet, few studies to date have been led or co-led by Indigenous peoples; or consider how centring Indigenous knowledge systems can lead to better conservation translocation outc...
Article
Full-text available
Indigenous peoples around the world are leading discusions regarding genomic research of humans, and more recently, species of cultural significance, to ensure the ethical and equitable use of DNA. Within a Māori (indigenous people of Aotearoa New Zealand) worldview, genomic data obtained from taonga (treasured) species has whakapapa-generally defi...
Article
Full-text available
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 se...
Article
Full-text available
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 populati...
Article
Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly u...
Article
Full-text available
Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. To...
Preprint
There have been extensive declines and extinctions of native fauna in Aotearoa New Zealand since human settlement. Against this background of loss there have been remarkable advances in conservation management, particularly in the large-scale eradication and control of exotic mammalian pests. Pest control creates opportunities to return animals to...
Preprint
Researchers have long debated which genomic estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the method used to generate genomic markers (e.g., reduced-representation sequencing, whole genome resequencing), marker qual...
Preprint
Full-text available
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 the...
Article
Full-text available
Genetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small number...
Preprint
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 p...
Article
Full-text available
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 no...
Article
Full-text available
Cook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cyto...
Article
Full-text available
Imperfect detection of individuals in threatened wild populations is common and can obscure real population trends when it is unaccounted for in population monitoring, and therefore impede conservation decision making. For many threatened insects, there is a lack of biological information or available long-term data to inform how best to practice d...
Preprint
Full-text available
Genetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small number...
Article
Full-text available
Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice metho...
Article
Full-text available
In the past few years genetic technologies springing from advances in DNA sequencing (so-called high-throughput sequencing), and/or from CRISPR/Cas9 gene editing, have been proposed as being useful in bioheritage research. The potential scope for the use of these genetic technologies in bioheritage is vast, including enabling the recovery of threat...
Article
Full-text available
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...
Preprint
The future of Aotearoa New Zealand’s biodiversity is intimately linked to the health of Māori environmental knowledge, the ability to work within different philosophical traditions, and a willingness to work at the intersections of philosophy, cultural practice and science. Māori environmental philosophies and knowledge systems (mātauranga) are int...
Poster
Full-text available
Reduced reproductive fitness due to maladaptive traits, like reduced fertility, hampers recovery efforts for critically endangered species. To identify putative structural variants on the Z-chromosome, we are developing a workflow to generate high resolution long-read sequence data for kākāpō (Strigops habroptilus) with known reproductive success...
Preprint
Indigenous peoples around the world are leading discussion regarding genomic research of humans, and more recently, species of cultural significance, to ensure the ethical and equitable use of DNA. Within a Māori (indigenous people of Aotearoa New Zealand) worldview, genomic data obtained from taonga (culturally significant) species has whakapapa –...
Article
Full-text available
The Masked Booby is a highly vagile, pantropical seabird of which up to six subspecies have been recognised: S. d. dactylatra, S. d. californica, S. d. personata, S. d. melanops, S. d. bedouti and S. d. tasmani. The genetic distinction of several S. dactylatra colonies has been previously investigated, but this has not yet been conducted for the Be...
Preprint
Full-text available
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...
Article
Full-text available
Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-qual...
Article
Full-text available
We evaluate evidence that reducing mammalian predators benefits threatened and declining grasshoppers in the Mackenzie Basin, New Zealand. Long-term population trends of Sigaus minutus are investigated under three control regimes: high intensity, indirect control through prey reduction and no control. We then test whether predator control benefits...
Data
Source data for boxplot (Figure 2a). This Excel file contains the Average Path Velocity (VAP) data collected for males in stage 1 of the experiment.
Data
Source data for correlation analysis. This Excel file contains the Average Path Velocity (VAP) and Curvilinear Velocity (VCL) data for all sperm samples collected in this study.
Data
Source data for Figure 7. This Excel file contains the calculated difference in the proportion of eggs sired by a focal male in each male x male x female combination across seminal fluid treatments (either unmanipulated milt or recombined ejaculates). It also contains the calculated difference in relative sperm velocity between competing males in e...
Data
Source data for GLMM models predicting the fertilisation success of male chinook salmon in sperm competition trials. This Excel file contains data on the diffence in the number of eggs sired between males in each sperm competition trial and the relative sperm velocity of those males. The data is presented in two tabs, the first for the unmanipulate...
Data
Source data for boxplot (Figure 2b). This Excel file contains the Average Path Velocity (VAP) data collected for males in stage 2 of the experiment.
Data
Source data for boxplot (Figure 3a). This Excel file contains the sperm concentration data collected for males in stage 1 of the experiment.
Data
Source data for Figure 5. This Excel file contains the sperm velocity data recorded for each males sperm after incubation in either their own seminal fluid or the seminal fluid of their rival. Differences in sperm velocity are calculated for sperm from different males incubated in their own seminal fluid and also for sperm from the same male incuba...
Data
Source data for GLMM models predicting the fertilisation success of male chinook salmon in sperm competition trials. This Excel file contains data on the proportion of eggs sired by each male and the social status of those males. The data is presented in two tabs, the first for the unmanipulated milt and the second for the recombined ejaculate semi...
Data
Source data for boxplot (Figure 3b). This Excel file contains the sperm concentration data collected for males in stage 2 of the experiment.
Data
Source data for Figure 4a. This Excel file contains the Average Path Velocity (VAP) data collected for males at both stages 1 and 2 of the experiment.
Data
Source data for Figure 4b. This Excel file contains the sperm concentration data collected for males at both stages 1 and 2 of the experiment.
Article
Full-text available
In many species, males can make rapid adjustments to ejaculate performance in response to sperm competition risk; however, the mechanisms behind these changes are not understood. Here, we manipulate male social status in an externally fertilising fish, chinook salmon (Oncorhynchus tshawytscha), and find that in less than 48 hr, males can upregulate...
Poster
Full-text available
Hybridisation is of conservation concern when it involves a threatened native species hybridising with a more common non-native species. Genetic admixture (introgression) resulting from hybridisation can result in species extinction. Hybrids may have lower fitness, and hybridisation can waste resource, limiting population recovery of threatened spe...
Article
Full-text available
There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing a...
Article
Full-text available
De-extinction sensu stricto is the resurrection of phenotypic traits once possessed by extinct species to create extant functional proxies. To realise the ecological benefit of de-extinction, self-sustaining (genetically viable) populations of functional proxies are required. It is often implied, yet rarely stated, that the genetic challenges assoc...
Poster
Full-text available
Many researchers have used genotyping-by-sequencing to generate marker data since the method was published in PLoS ONE in 2011. Others have made modifications to the method resulting in different, but related, types of GBS data generated. Additional analysis pipelines have been developed, many of which are licensed under Free/Libre and Open Source...
Article
Full-text available
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing tech- nologies to inform conservation policy and the manage- ment of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective a...
Article
Full-text available
Two captive-reared birds of wild origin presumed to be Kakī/Black Stilt (Himantopus novaezelandiae) were found to display plumage atypical of Kakī. We have combined genetic and non-genetic data to test the hypothesis that these birds are a product of brood parasitism by “non-kakī” [i.e. Poaka/Pied Stilt (Himantopus himantopus leucocephalus) or Kakī...
Article
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Contents 79 The Chicken Leads the Way in Avian Genomics. Prepared by J. Smith. 80 The Chicken Genome: Current Status of Genome Assembly and Annotations. Prepared by D.W. Burt, L. Eöry, A.L. Archibald, B.L. Aken, P. Flicek, K. Howe, W. Chow, M. Dunn, J.M.D. Wood, R. Nag, and W.C. Warren. 83 The Avian RNAseq Consortium: A Community Effort to Annot...
Article
Full-text available
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-S...
Article
Full-text available
The remnant wild populations of the critically endangered orange-fronted kākāriki (Cyanoramphus malherbi) are restricted to 3 North Canterbury valleys where they co-occur with the yellow-crowned kākāriki (C. auriceps). Mixed pairs of Cyanoramphus kākāriki species have been documented throughout the genus, but the extent to which orange-fronted and...
Article
Full-text available
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...
Article
Full-text available
One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is "how many individuals do I need to sample from each population?" This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefact...
Data
Allele frequencies at each locus for each dataset. Ants (Formica lugubris, n = 547); squirrels (Sciurus vulgaris, n = 107), albatross (Thalassarche melanophris, n = 616), and kakī (Himantopus novaezelandiae, n = 98). Both the albatross and kakī dataset contained missing data for some loci, number of individuals genotyped at each locus is indicated...
Data
Supplementary Table 1 List of full genomes BFDV sequences used in maximum-likelihood phylogenetic analysis
Article
Full-text available
Beak and feather disease virus (BFDV) infections are often fatal to both captive and wild parrot populations. Its recent discovery in a wild population of native red-fronted parakeets has raised concerns for the conservation of native parrots, all of which are threatened or endangered. The question of a recent introduction versus a native genotype...
Article
Full-text available
Cyanoramphus malherbi is a critically endangered endemic parakeet, or kākāriki, restricted to three mainland valleys in North Canterbury and four translocated populations on predator-free offshore islands of New Zealand. Using genomic next generation sequencing to identify microsatellites, 16,497 sequenced fragments were obtained. Primers were desi...
Article
Full-text available
Pelagic seabirds are highly mobile, reducing the likelihood of allopatric speciation where disruption of gene flow between populations is caused by physically insurmountable, extrinsic barriers. Spatial segregation during the non-breeding season appears to provide an intrinsic barrier to gene flow among seabird populations that otherwise occupy nea...
Article
Full-text available
For threatened species with small captive populations, it is advisable to incorporate conservation management strategies that minimize inbreeding in an effort to avoid inbreeding depression. Using multilocus microsatellite genotype data, we found a significant negative relationship between genetic relatedness (inbreeding) and reproductive success (...
Article
Full-text available
Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk as...
Article
Full-text available
To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative...
Article
Full-text available
Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeonto...