Biodiversity genomics research can inform conservation, management, and policy, including implementation and monitoring linked to the Kunming-Montreal Global Biodiversity Framework (KMGBF). Still, its societal relevance depends on how research is designed and interpreted with the people who live in, work with, and care for the species and places being studied. Local Communities often hold Local Ecological Knowledge that can improve sampling design, contextualise genomic patterns, and support the translation of findings into practice. Yet, community participation in biodiversity genomics remains limited, partly because researchers may lack practical guidance, training, incentives, or time for engagement. Here, we propose a five-step framework for engaging European Local Communities in biodiversity genomics projects. The framework covers early relationship building, respect for local context and knowledge, co-creation of research roles, transparent benefit sharing, and long-term knowledge transfer. We also outline biodiversity genomics-specific points that require early discussion, including biological sampling, genomic sequence data, genetic variant data, analytical outputs, associated ecological and locality information, Digital Sequence Information, repository deposition, interpretation, and reuse. The framework is intended as a practical starting point for research teams, funders, and community collaborators seeking to make biodiversity genomics research more transparent, locally informed, and useful for conservation decision-making.

There is growing interest in translocating freshwater fish and invertebrates for conservation and customary purposes. However, freshwater translocations in Aotearoa | New Zealand are complicated by limited access to scientific and technical guidance, fragmentary governance, and ongoing marginalisation of Indigenous rights and knowledge. In this paper, we review the past and present state of freshwater translocations in Aotearoa | New Zealand to identify key challenges for policy and practice. We reflect on two case studies: translocations of toitoi (common bully Gobiomorphus cotidianus) and k & amacr;kahi (freshwater mussel Echyridella spp.) at Zealandia Te M & amacr;ra a T & amacr;ne in the Wellington region, and an initiative led by Hokonui R & umacr;nanga to captive breed and translocate kanakana (pouched lamprey Geotria australis) in Murihiku | Southland. Drawing from these experiences, we outline how policy, practice, and research could support more participatory and evidence-informed freshwater translocations.

Human or 'social' dimensions are increasingly prominent in the conservation translocation literature yet in practice they tend to be infrequently or narrowly applied. To assist biophysical scientists and practitioners to act upon social dimensions, we distinguish four ways of thinking about the social dynamics of translocations: identified stakeholders, processes of decision-making, visions of nature, and values in science. We use three case studies to show how working through these four social dimensions together can help to illuminate the multiple meanings and effects of translocations. We discuss how biophysical scientists and practitioners can take responsibility for each social dimension and thus make better choices for people and nature.

Species recovery through captive breeding can be hindered by low reproductive success. However, we know little about the drivers of early reproductive failure in captive populations, due to difficulties distinguishing fertilisation failure from early embryo mortality in most animals. Here, we apply advanced fertility diagnostics on unhatched eggs from 30 avian captive-breeding programs, to assess true rates of fertilisation failure. We find that fertilisation failure is rare across all species, and the main driver of early reproductive failure is early embryo mortality. We also find that macroscopic examination of undeveloped eggs inflates estimates of fertilisation failure rates in breeding programmes. Finally, we find no evidence that fertilisation failure rates are higher in threatened than non-threatened captive birds, providing hope that with careful management, hatching outcomes may be improved in threatened captive populations. Our results show that accurate fertility diagnosis in managed oviparous species provides crucial information on individual reproductive potential, helping the design of more appropriate management interventions to improve recovery.

Mitochondrial genomes (mitogenomes) represent a relatively cost-effective tool for comparing diversity between contemporary and historical populations to assess impacts of past population processes, or the outcomes of conservation management. The Aotearoa New Zealand endemic kakī| black stilt (Himantopus novaezelandiae) is a critically endangered wading bird. Anthropogenic impacts contributed to kakī declining to 23 individuals in 1981 and promoted interspecific hybridisation with their more common congener, the poaka| pied stilt (H. leucocephalus). Conservation management of kakī has resulted in the population increasing to 169 wild adults at the end of the 2023–2024 breeding season. Here we use mitogenomes to enable comparisons of diversity between contemporary and historical (pre-1960s) stilts, and to understand the impacts of past interspecific hybridisation. We assemble a mitogenome for kakī and use this as a reference to facilitate downstream comparisons of mitochondrial diversity among kakī and poaka across a period of population decline and subsequent conservation management for kakī. Mitogenome haplotype data provides no evidence of introgression from poaka into kakī despite past hybridisation. This contributes to the behavioural, ecological, morphological and genetic evidence that conservation action has maintained the species integrity of this Critically Endangered bird. Furthermore, these results indicate that mitochondrial diversity has been maintained in kakī across a period of species decline and subsequent conservation management.

The need for effective conservation strategies to combat the ongoing biodiversity crisis is well recognised. Conservation translocations are an important and frequently used form of conservation management for species recovery. Despite this, the uncertainty prevalent throughout the translocation cycle often makes it challenging to determine whether translocations should be included in the suite of actions to achieve desired conservation outcomes. Further, the fundamental question of whether translocations should occur is seldom assessed as a formal decision. We applied a formal decision analysis for the conservation management of a highly threatened bird (karure / kakaruia / Chatham Island black robin / Petroica traversi) to evaluate whether translocation and/or other actions should be implemented for species recovery. The species' precarious status (<330 adults), combined with uncertainty about translocation outcomes, meant that for years, decision-makers were reluctant to act given the potentially severe consequences of translocation failure. We used structured decision-making in conjunction with population modelling to estimate the consequences of translocations and other actions across a range of objectives identified by Moriori and Ngati Mutunga o Wharekauri (Indigenous Peoples of Rekohu / Wharekauri / the Chatham Islands), the local community and government agencies. Structured decision-making facilitated an inclusive approach that ensured all participants were actively engaged in the decision-making process including the identification of the best management alternative while balancing multiple objectives. This process overcame the long-standing conservation impasse, resulting in rapid implementation of actions, including translocation, that would have otherwise been difficult to achieve. The preferred alternative across objectives involved multiple translocations, illustrating the vital role translocations have in the desired future management for the species. The methods used in our study can be readily applied in other species recovery programmes to help decision-makers navigate the complexities and uncertainties inherent in conservation decisions.

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

The current science system is unjust — from the systems that determine its membership to its outputs and outcomes. We advocate for contextually responsive, collective action to build a more just science system that demonstrates a relational duty of care to all its participants. To achieve this, we urge the science community to harness the powerful processes of complexity with deliberate intent.

The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.

Background Animal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations, can cause long-term demographic and behavioural problems. It is used in the recovery of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to New Zealand, to improve the slow population growth that is due to infrequent breeding, low fertility and low hatching success. Methods We applied Bayesian mixed models to examine whether hand-rearing and other factors were associated with clutch fertility in kākāpō. We used projection predictive variable selection to compare the relative contributions to fertility from the parents’ rearing environment, their age and previous copulation experience, the parental kinship, and the number of mates and copulations for each clutch. We also explored how the incidence of repeated copulations and multiple mates varied with kākāpō density. Results The rearing status of the clutch father and the number of mates and copulations of the clutch mother were the dominant factors in predicting fertility. Clutches were less likely to be fertile if the father was hand-reared compared to wild-reared, but there was no similar effect for mothers. Clutches produced by females copulating with different males were more likely to be fertile than those from repeated copulations with one male, which in turn had a higher probability of fertility than those from a single copulation. The likelihood of multiple copulations and mates increased with female:male adult sex ratio, perhaps as a result of mate guarding by females. Parental kinship, copulation experience and age all had negligible associations with clutch fertility. Conclusions These results provide a rare assessment of factors affecting fertility in a wild threatened bird species, with implications for conservation management. The increased fertility due to multiple mates and copulations, combined with the evidence for mate guarding and previous results of kākāpō sperm morphology, suggests that an evolutionary mechanism exists to optimise fertility through sperm competition in kākāpō. The high frequency of clutches produced from single copulations in the contemporary population may therefore represent an unnatural state, perhaps due to too few females. This suggests that opportunity for sperm competition should be maximised by increasing population densities, optimising sex ratios, and using artificial insemination. The lower fertility of hand-reared males may result from behavioural defects due to lack of exposure to conspecifics at critical development stages, as seen in other taxa. This potential negative impact of hand-rearing must be balanced against the short-term benefits it provides.

The 'research system' in Aotearoa New Zealand is rife with obstacles for entry and retention of diversity. The research system's complexity and longevity gives the impression of stability and fixity, but we argue it is characterised by a lack of imagination around leadership that generates change. In this article, we examine the embodied experiences of research leadership, as encountered by participants at Aotearoa New Zealand's universities and a nationally funded Centre of Research Excellence. It is within such institutions and organisations, built on colonial and patriarchal values, that experiences of marginalisation, oppression and harassment have been documented. We destabilise the apparently static nature of this 'research system monolith' by taking up MacLeavy, Fannin and Larner's (2021) provocation of a feminist approach to boldly do leadership differently. Drawing from interviews with researchers, we provoke that resistance to, and reworking of, the research system is hidden in feminist modes of practice: in the everyday, mundane practices of care-full research leadership, that does leadership differently.

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 recommendations that the principles of good translocation decision-making are embedded in government policy.

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

The use of conservation translocations as a transdisciplinary conservation tool to prevent extinction, recover populations, and restore ecological function is on the rise. The growing impact of reintroductions, reinforcements, assisted colonisations, and ecological replacements can be attributed to a number of factors including an escalation of benefits for species, ecosystems, and human communities driven by bold innovations and courageous ambitions of the global conservation translocation community. The inclusion of diverse philosophical perspectives combined with increased need, interest, scope, and policy alignment has driven a broadening of novel approaches, innovations, and tools, but associated aspects can be contentious. To advance conservation impact of conservation translocations, we group eleven of these contentious issues into three broad categories – genes, species, and ecosystems – and then reframe them as growth opportunities. Contentious issues can create conflict, but we suggest that identifying common ground on agreed conservation values, negotiating with respectful kindness, and advancing progress through collaboration will enable powerful advancements for effective conservation translocations in the future.

Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximize the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognize the growing need for guidance on comprehensive data management practices that minimize the risks of data loss, maximize efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting differing user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximize research impact and outcomes.

There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a biodiversity genomics perspective, the characterization of genome-wide SVs provides an exciting opportunity to complement single nucleotide polymorphisms (SNPs). However, little is known about the impacts of SV discovery and genotyping strategies on the characterization of genome-wide SV diversity within and among populations. Here, we explore a near whole-species resequence data set, and long-read sequence data for a subset of highly represented individuals in the critically endangered kākāpō (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterized genome-wide. Further, we found that the mean number of SVs in each of two kākāpō lineages differed both within and across generations. These combined results suggest that genome-wide characterization of SVs remains challenging at the population-scale. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches including multireference approaches like genome graphs will alleviate at least some of the challenges associated with resolving SV characteristics below the species level. In the meantime, we address caveats, highlight considerations, and provide recommendations for the characterization of genome-wide SVs in biodiversity genomic research.

There is growing interest in the role of structural variants (SVs) as drivers of local adaptation and speciation. From a conservation genomics perspective, the characterisation of SVs in threatened species provides an exciting opportunity to complement existing approaches that use single nucleotide polymorphisms (SNPs) to detect adaptive variation, identify conservation units, guide pairing decisions and inform conservation translocations. However, little is known about whole-genome SV frequency and size distributions, especially for small populations. To explore the impacts that SV discovery and genotyping strategies may have on characterisation of SV diversity in non-model organisms, we explore a near whole-species resequence dataset, and long-read sequence data for a subset of highly represented individuals in the critically endangered kākāpō (Strigops habroptilus). We demonstrate that even when using a highly contiguous reference genome, different discovery and genotyping strategies can significantly impact the type, size and location of SVs characterised, which indicates researchers should exercise caution when drawing conclusions at the individual-scale. Further, we find that genotyping SVs discovered with long-read data at the population-scale with short-read data remains challenging. Despite this, we found that all six strategies used to characterise SVs in kākāpō reflected similar trends at the population-scale including the identification of population structure. We are optimistic that increased accessibility to long-read sequencing and advancements in bioinformatic approaches (e.g., multi-reference approaches like genome graphs) will alleviate challenges associated with resolving SV characteristics below the species level and facilitate the characterisation of population- and individual-level SVs in threatened species around the globe.

Abstract 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.

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. Toll-like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species-specific primers and PCR. Here, we leverage an existing short-read reference genome, whole-genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat'/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat'/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.