@prefix dcat: . @prefix dct: . @prefix foaf: . @prefix xsd: . a dcat:Dataset ; dct:description """#Tranche 1: Project 1.4#\r \r ##Researchers are collecting DNA information from some of Aotearoa New Zealand’s most threatened species in an effort to make them more resilient to future environmental change.##\r \r Scientists leading this BioHeritage Challenge project took critical first steps towards building resilience in threatened taonga (treasured) species, partnering with Ngāi Tūāhuriri to embed mahinga kai values and mātauranga Māori (indigenous knowledge) into the project.\r \r The data gathered was used to comprehensively assess the genetic diversity of five diverse species, with a special focus on kōwaro (Canterbury mudfish) and kēkēwai (freshwater crayfish). The aim was to determine their capacity to evolve in response to environmental change – otherwise known as their adaptive potential.\r \r **Project Leader**\r \r - Tammy Steeves, University of Canterbury""" ; dct:identifier "0b5f5c68-8e7b-4f32-9925-bdd13bb387db" ; dct:issued "2024-07-03T21:09:55.366092"^^xsd:dateTime ; dct:modified "2024-07-31T04:36:11.186796"^^xsd:dateTime ; dct:publisher ; dct:title "Adaptive Evolution of Native Biota" ; dcat:distribution , , , , , , , , , , . a dcat:Distribution ; dct:description """###Centring Indigenous knowledge systems to re-imagine conservation translocations###\r \r **August 2020**\r \r **Rayne A, Byrnes G, Collier-Robinson L, Hollows J, McIntosh A, Ramsden M, Rupene M, Tamati-Elliffe P, Thoms C, Steeves TE 2020. [Centring Indigenous knowledge systems to re-imagine conservation translocations](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pan3.10126). People and Nature 2(3): 512-526.**\r \r **ABSTRACT**\r \r Now more than ever, creative solutions that bring together diverse ways of Knowing and seeing the world are needed to restore and enhance biocultural diversity (interwoven biological, cultural and linguistic systems). Mi’kmaq Elder Dr Albert Marshall describes the Mi’kmaq principle of Etuaptmumk or Two-Eyed Seeing as ‘learning to see from one eye with the strengths of Indigenous knowledges and ways of knowing, and from the other eye with the strengths of Western knowledges and ways of knowing ... and learning to use both these\r eyes together, for the benefit of all’.\r \r Moving plants and animals to establish new populations or strengthen existing ones (‘conservation translocations’) can 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 outcomes.\r \r In this Perspective, as Indigenous and non-Indigenous researchers and practitioners working in partnership under Te Tiriti o Waitangi (The Treaty of Waitangi, 1840), we demonstrate how Two-Eyed Seeing can better inform conservation translocation decisions — such as whether, or how, different populations should be mixed.\r \r **KEYWORDS**\r \r biocultural; conservation genomics; ecosystem resilience; freshwater biodiversity; Indigenous knowledge; mātauranga Māori; species recovery; Two-Eyed Seeing\r """ ; dct:issued "2024-07-03T22:06:58.199388"^^xsd:dateTime ; dct:modified "2024-07-03T22:06:58.199388"^^xsd:dateTime ; dct:title "PAPER: Centring Indigenous knowledge systems" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Embedding indigenous principles in genomic research of culturally significant species: a conservation genomics case study###\r \r **December 2019**\r \r **Collier-Robinson L, Rayne A, Rupene M, Thoms C, Steeves T 2019. [Embedding indigenous principles in genomic research of culturally significant species: a conservation genomics case study](https://newzealandecology.org/nzje/3389.pdf). New Zealand Journal of Ecology 43(3).**\r \r **ABSTRACT**\r \r 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 defined as genealogy, whakapapa layers the contemporary, historical and mythological aspects of bioheritage – thus genomic data obtained from taonga species are taonga in their own right and are best studied using Māori principles. We contend it is the responsibility of researchers working with genomic data from taonga species to move beyond one-off Māori consultation toward building meaningful relationships with relevant Māori communities. Here, we reflect on our experience embedding Māori principles in genomics research as leaders of a BioHeritage National Science Challenge project entitled ‘Characterising adaptive variation in Aotearoa NewZealand’s terrestrial and freshwater biota’. We are co-developing a culturally-responsive evidence-based position statement regarding the benefits and risks of prioritising adaptive potential to build resilience in threatened taonga species, including species destined for customary or commercial harvest. To achieve this, we co-developed a research programme with the local subtribe, Ngāi Tūāhuriri, that integrates Māori knowledge with emerging genomic technologies and extensive ecological data for two taonga species, kōwaro (Canterbury mudfish; *Neochanna burrowsius*) and kēkēwai (freshwater crayfish; *Paranephrops zealandicus*). The foundation of our research programme is an iterative decision-making framework that includes tissue sampling as well as data generation, storage and access. Beyond upholding the promises made in The Treaty\r \r \r **KEYWORDS**\r \r kaitiakitanga; kaupapa Māori; mahinga kai; Mātauranga Māori; rangatiratanga; taonga species""" ; dct:issued "2024-07-03T21:52:49.878187"^^xsd:dateTime ; dct:modified "2024-07-03T21:52:49.878187"^^xsd:dateTime ; dct:title "PAPER: Embedding indigenous principles in genomic research" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Evolution of the "world's only alpine parrot": Genomic adaptation or phenotypic plasticity, behaviour and ecology?##\r \r **May 2021**\r \r **Martini D, Dussex N, Robertson BC, Gemmell NJ, Knapp M. 2021. [Evolution of the "world's only alpine parrot": Genomic adaptation or phenotypic plasticity, behaviour and ecology?](https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.15978) Mol Ecol 30(23): 6370-6386.**\r \r **ABSTRACT**\r \r Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (*Nestor notabilis*) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes? We use whole genome data of the kea and its close, forest adapted sister species, the kākā (*Nestor meridionalis*) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both *Nestor *species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.\r \r **KEYWORDS**\r \r adaptation; alpine species; climate change; evolution; genomic comparison;""" ; dct:issued "2024-07-03T23:46:50.701920"^^xsd:dateTime ; dct:modified "2024-07-03T23:46:50.701920"^^xsd:dateTime ; dct:title "PAPER: Evolution of the alpine parrot" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Weaving place-based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future###\r \r **May 2022**\r \r **Rayne A, Blair S, Dale M, Flack B, Hollows J, Moraga R, Parata RN, Rupene M, Tamati-Elliffe P, Wehi PM and others 2022. [Weaving place-based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future](https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13367). Evol Appl 15(5): 751-772.**\r \r **ABSTRACT**\r \r 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 of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping-by-sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables-including temperature, precipitation, and water flow regimes-in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place-based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.\r \r **KEYWORDS**\r \r conservation, Indigenous knowledge, Indigenous peoples and local communities, landscape genomics, local adaptation, local knowledge, mātauranga Māori, translocation""" ; dct:issued "2024-07-04T00:04:22.650834"^^xsd:dateTime ; dct:modified "2024-07-04T00:04:22.650834"^^xsd:dateTime ; dct:title "PAPER: Weaving place-based knowledge into genomics" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Can threatened species adapt in a restored habitat? No expected evolutionary response in lay date for the New Zealand hihi###\r \r **December 2018**\r \r **de Villemereuil P, Rutschmann A, Ewen JG, Santure AW, Brekke P 2019. [Can threatened species adapt in a restored habitat? No expected evolutionary response in lay date for the New Zealand hihi](https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.12727). Evol Appl 12(3): 482-497.**\r \r \r **ABSTRACT**\r \r Many bird species have been observed shifting their laying date to earlier in the year in response to climate change. However, the vast majority of these studies were performed on non-threatened species, less impacted by reduced genetic diversity (which is expected to limit evolutionary response) as a consequence of genetic bottlenecks, drift and population isolation. Here, we study the relationship between lay date and fitness, as well as its genetic basis, to understand the evolutionary constraints on phenology faced by threatened species using a recently reintroduced population of the endangered New Zealand passerine, the hihi (*Notiomystis cincta*).\r \r \r **KEYWORDS**\r \r conservation biology; laying date; *Notiomystis cincta*; phenology; quantitative genetics\r """ ; dct:issued "2024-07-03T21:24:03.481711"^^xsd:dateTime ; dct:modified "2024-07-03T21:24:03.481711"^^xsd:dateTime ; dct:title "PAPER: Threatened species adaptability in restored habitats?" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Consequences of space sharing on individual phenotypes in the New Zealand hihi###\r \r **July 2020**\r \r **Rutschmann A, de Villemereuil P, Brekke P, Ewen JG, Anderson N, Santure AW 2020. [Consequences of space sharing on individual phenotypes in the New Zealand hihi](https://link.springer.com/content/pdf/10.1007/s10682-020-10063-z.pdf). Evolutionary Ecology 34(5): 821-839.**\r \r **ABSTRACT**\r \r In heterogeneous habitats, individuals sharing a larger part of their home-range are also likely to live in a very similar environment. This ‘common environment’ effect can generate phenotypic similarities between neighbours and lead to the structuring of phenotypes through the habitat. In this study, we used an intensely monitored population of hihi (or stitchbird, *Notiomystis cincta*) from New Zealand, to assess whether home-range overlap and genetic relatedness between birds could generate phenotypic resemblance for a wide panel of morphological and life-history traits.\r \r \r **KEYWORDS**\r \r Stitchbird;\r Animal model;\r Spatial matrix;\r Heritability;\r Common environment;\r Phenotypic variation""" ; dct:issued "2024-07-03T22:23:54.251261"^^xsd:dateTime ; dct:modified "2024-07-03T22:23:54.251261"^^xsd:dateTime ; dct:title "PAPER: Space sharing affects on hihi phenotypes" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Contribution of Indigenous Peoples' understandings and relational frameworks to invasive alien species management###\r \r **July 2023**\r \r **Wehi PM, Kamelamela KL, Whyte K, Watene K, Reo N 2023. [Contribution of Indigenous Peoples' understandings and relational frameworks to invasive alien species management](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pan3.10508). People and Nature 5(5): 1403-1414.**\r \r **ABSTRACT**\r \r Introduced species that spread and become invasive are recognised as a major threat to global biological diversity, ecosystem resilience and economic stability. Eradication is often a default conservation management strategy even when it may not be feasible for a variety of reasons. Assessment of the substantive socioeconomic and ecological impacts of invasive alien species (IAS), both negative and positive, is increasingly viewed as an important step in management.\r \r We argue that one solution to IAS management is to align models of alien species management with Indigenous management frameworks that are relational and biocultural. We make the theoretical case that centring Indigenous management frameworks promises to strengthen overall management responses and outcomes because they attend directly to human and environmental justice concerns.\r \r We unpack the origins of the ‘introduced species paradigm’ to understand how binary framing of so-called ‘aliens’ and ‘natives’ recalls harmful histories and alienates Indigenous stewardship. Such a paradigm thereby may limit application of Indigenous frameworks and management, and impede long-term biodiversity protection solutions.\r \r We highlight how biocultural practices applied by Indigenous Peoples to IAS centre protecting relationships, fulfilling responsibilities and realising justice.\r \r Finally, we argue for a pluralistic vision that acknowledges multiple alternative Indigenous relationships and responses to introduced and IAS which can contribute to vibrant futures where all elements of society, including kin in the natural world, are able to flourish.\r \r **KEYWORDS**\r \r alien species; biocultural diversity; Indigenous management; invasive species; novel ecosystems; socioecological systems""" ; dct:issued "2024-07-24T02:12:14.857376"^^xsd:dateTime ; dct:modified "2024-07-24T02:12:14.857376"^^xsd:dateTime ; dct:title "PAPER: Indigenous knowledge contribution to invasive species management." ; dcat:accessURL . a dcat:Distribution ; dct:description """###Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand's bioheritage###\r \r **June 2020**\r \r **Inwood SN, McLaughlin GM, Buckley TR, Cox MP, Handley KM, Steeves TE, Strabala TJ, McDougal R, Dearden PK 2020. [Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand's bioheritage](https://newzealandecology.org/nzje/3413.pdf). New Zealand Journal of Ecology 44(2).**\r \r **ABSTRACT**\r \r 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 threatened species, engineering proxies of extinct species and genetically controlling pests. While these technologies are often complex, they provide new opportunities that may help support New Zealand’s beleaguered flora and fauna, and thus warrant scientific examination. Here we discuss these genetic technologies, focussing on scientific benefits and risks of each. We also acknowledge the social, cultural, ethical and regulatory constraints on their use, with emphasis on the importance of partnership with tangata whenua to determine when, whether or how these technologies should be used in enhancing New Zealand’s bioheritage. We hope this will provide source material to support future decision making around the use of new genetic technologies in bioheritage.\r \r **KEYWORDS**\r \r conservation, de-extinction, gene editing, genetics, genomics, metagenomics, pest management""" ; dct:issued "2024-07-03T22:38:59.865304"^^xsd:dateTime ; dct:modified "2024-07-03T22:38:59.865304"^^xsd:dateTime ; dct:title "PAPER: Opportunities for modern genetic technologies" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Conservation translocations of fauna in Aotearoa New Zealand: a review###\r \r **December 2023**\r \r **Parker KA, Ewen JG, Innes J, Weiser EL, Rayne A, Steeves T, Seddon PJ, Adams L, Maitland M, Makan T, Martini D, Parlato E, Richardson K, Stone Z, Armstrong DP. 2023. [Conservation translocations in Aotearoa New Zealand in the Predator-Free era.](https://newzealandecology.org/nzje/3562.pdf) New Zealand Journal of Ecology 47(1).**\r \r **ABSTRACT**\r \r There have been numerous 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, including the use of conservation translocations to reduce extinction risk and restore depauperate ecosystems. Here we review conservation translocations in Aotearoa New Zealand. Our review assembles knowledge from Aotearoa New Zealand’s rich history of faunal translocations and describes six key considerations for successfully establishing translocated populations: (1) What values will be met by a translocation? (2) What is the natural and conservation history of the translocation candidate? (3) Does the release site habitat match that of the proposed source population, and if not, why is the release site considered appropriate and can management ameliorate differences? (4) Will dispersal be a problem? (5) Will genetic management be required and how realistic is it that this management will be implemented? (6) What do future developments mean for the management of translocated populations? We discourage a focus on any single element of translocation planning but rather encourage all people involved in translocations, particularly decision makers, to explicitly recognise that successful translocations typically have multiple, values-based objectives. We also support recommendations that the principles of good translocation decision-making are embedded in government policy.\r \r **KEYWORDS**\r \r conservation translocation, decision making, reintroduction, restoration\r """ ; dct:issued "2024-07-31T04:35:58.055243"^^xsd:dateTime ; dct:modified "2024-07-31T04:35:58.055243"^^xsd:dateTime ; dct:title "PAPER: Conservation translocations of fauna in NZ" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Little Adaptive Potential in a Threatened Passerine Bird###\r \r **February 2019**\r \r **de Villemereuil P, Rutschmann A, Lee KD, Ewen JG, Brekke P, Santure AW 2019. [Little Adaptive Potential in a Threatened Passerine Bird](https://www.sciencedirect.com/science/article/pii/S0960982219301319/pdfft?md5=be8bc25a3a841a6dcb746c35c368f25a&pid=1-s2.0-S0960982219301319-main.pdf). Curr Biol 29(5): 889-894 e3.**\r \r **ABSTRACT**\r \r Threatened species face numerous threats, including future challenges triggered by global change. A possible way to cope with these challenges is through adaptive evolution, which requires adaptive potential. Adaptive potential is defined as the genetic variance needed to respond to selection and can be assessed either on adaptive traits or fitness. However, a lack of high-quality data has made it difficult to rigorously test adaptive potential in threatened species, leading to controversy over its magnitude. In this paper we assess the adaptive potential of a threatened New Zealand passerine (the hihi, *Notiomystis cincta*).\r \r **KEYWORDS**\r \r adaptation; *Notiomystis cincta*; heritability; quantitative genetics; conservation genetics; conservation biology; nucleotide diversity; genetic variance of fitness""" ; dct:issued "2024-07-03T21:40:20.207434"^^xsd:dateTime ; dct:modified "2024-07-03T21:40:20.207434"^^xsd:dateTime ; dct:title "PAPER: Adaptive Potential in Threatened Passerine Bird" ; dcat:accessURL . a dcat:Distribution ; dct:description """### Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi###\r \r **July 2021**\r \r **Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW 2021. [Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi](https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.16068). Mol Ecol 30(23): 6006-6020.**\r \r **ABSTRACT**\r \r Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (*Notiomystis cincta*), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.\r \r **KEYWORDS**\r \r conservation genomics; genomic inbreeding; *Notiomystis cincta*; runs of homozygosity; SNP array; whole-genome resequencing""" ; dct:issued "2024-07-03T23:54:42.007364"^^xsd:dateTime ; dct:modified "2024-07-03T23:54:42.007364"^^xsd:dateTime ; dct:title "PAPER: Genomic data reveals hihi inbreeding" ; dcat:accessURL . a foaf:Organization ; foaf:name "Challenge Inventory" .