Balancing Openness with Indigenous Data Sovereignty — An Opportunity to Leave No One behind in the Journey to Sequence All of Life

McCartney, Ann; Anderson, Jane; Liggins, Libby; Hudson, Māui; Anderson, Matthew; TeAika, Ben; Geary, Janis; Cook-Deegan, Bob; Patel, Hardip R.; Phillippy, Adam M.

doi:10.2139/ssrn.3922996

Cited by 14 publications

(15 citation statements)

References 40 publications

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“…We present genomic data for Kakī and Kākāriki Karaka consistent with both FAIR and CARE data principles (Carroll et al, 2020, 2021; McCartney et al, 2022). Our research findings have been used to inform the conservation breeding programs herein and are broadly applicable to management of threatened species around the globe.…”

Section: Benefit Sharing Statementsupporting

confidence: 61%

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Galla

et al. 2021

Preprint

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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 quality, and levels of diversity in sampled individuals.Here, we compare six commonly used relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), KING-robust, RAB, allele-sharing co-ancestry) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data.Relatedness estimates varied widely across estimators, sequencing method, and species, yet the most consistent results with known pedigree data were found using KING-robust and to a lesser extent KGD. The allele-sharing estimator was sensitive to missing data and inbreeding, attributes that make this estimator ill-suited for use in captive breeding programs. Our combined results indicate there is not a single genomic based estimator that is ideal across different species and data types.To enable researchers to evaluate the most appropriate relatedness estimator for each new data set, we provide a structured workflow that is broadly applicable to conservation breeding programs, particularly where genomic estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in wild pedigrees, our results and workflow are also applicable to in situ wildlife management.

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Section: Benefit Sharing Statementsupporting

confidence: 61%

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Galla

et al. 2021

Preprint

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“…Going forward, we recommend that local communities and indigenous knowledge associated with the global reservoir of plant diversity 46,47 form the backbone of plant genome collaborations. Currently there are over a dozen plant genomics projects with African institutions as partners 23 , a growing number of projects integrating indigenous knowledge 46,48 , large-scale consortia with multinational participants are being established (for example, the Africa BioGenome Project) and some journals have implemented policies to minimize parachute science and encourage international collaboration (for example, PLOS's policy on inclusion in global research). These efforts all stand to broaden participation in plant genomics.…”

Section: Discussionmentioning

confidence: 99%

Representation and participation across 20 years of plant genome sequencing

et al. 2021

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The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism—both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.

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“…Our approach to engineering and building a bridge for the current genomic research–implementation gap is threefold: 1) use genome sequencing technologies that meet the needs of the conservation end-users while maximizing the limited conservation resources available (both funding and sample access), so genomic data can be developed for as many threatened species as possible; 2) develop an on-line interface where TSI project teams can obtain protocols and use a set of established bioinformatic tools and workflows to provide genetic outputs in a standardized reporting format for conservation practitioners; and 3) open-data access, where genomic data will be open access but other related metadata may be restricted due to threatened species and indigenous sensitivities ( 36 ). To ensure seamless delivery of the larger project, a pilot phase was commenced in August 2020, to test and bed down workflows and pipelines to ensure outputs were fit-for-purpose for conservation management and decision-making.…”

Section: Threatened Species Initiativementioning

confidence: 99%

Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.

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Balancing Openness with Indigenous Data Sovereignty — An Opportunity to Leave No One behind in the Journey to Sequence All of Life

Cited by 14 publications

References 40 publications

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Representation and participation across 20 years of plant genome sequencing

Threatened Species Initiative: Empowering conservation action using genomic resources

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