A demonstration of conservation genomics for threatened species management

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.

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Hi, Reddit! We’re scientists at the Smithsonian’s National Zoo and Conservation Biology Institute’s Center for Conservation Genomics. We use genomics to save threatened species – ask us anything!

The Winnower ◽

10.15200/winn.152457.74257 ◽

2018 ◽

Author(s):

National_Zoo ◽

r/Science

Keyword(s):

Conservation Biology ◽

Threatened Species ◽

Conservation Genomics ◽

National Zoo

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The relevance of pedigrees in the conservation genomics era.

10.22541/au.162577430.03067651/v2 ◽

2021 ◽

Author(s):

Stephanie Galla ◽

Liz Brown ◽

Yvette Couch-Lewis ◽

Ilina Cubrinovska ◽

Daryl Eason ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genomic Data ◽

Data Uncertainty ◽

Ex Situ ◽

Conservation Genomics ◽

Evolutionary Potential ◽

Genome Wide ◽

Species Management ◽

Quantitative Analyses

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. Keywords: conservation genomics, quantitative genetics, pedigree, kinship,ex situ , in situ

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Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

10.22541/au.161162800.09671016/v1 ◽

2021 ◽

Author(s):

Jana Wold ◽

Stephanie Galla ◽

David Eccles ◽

Carolyn J. Hogg ◽

Klaus-Peter Koepfli ◽

...

Keyword(s):

Functional Diversity ◽

Threatened Species ◽

Conservation Management ◽

Sequence Data ◽

Regulation Of Gene Expression ◽

Whole Genome Sequence ◽

Structural Variants ◽

Conservation Genomics ◽

Genomic Context ◽

Snp Data

Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species around the world. However, SNP data alone may not sufficiently capture all of the information necessary for the effective conservation management of critically endangered species that suffer from severe inbreeding depression. For threatened species that require significant intervention, it is critical that we as conservation genomicists expand our repertoire to include assessments of functional diversity. Structural variants are a likely source of functional diversity, as their frequency and genomic context affect the dosage and regulation of gene expression through mechanisms that alter genome organization and impact fitness. In this future-focused Opinion, we leverage the existing literature - predominantly focused on model and agricultural species - to identify pan-genomic and chromosomic approaches for readily characterizing structural variants and to consider how integrating these into the conservation genomics toolbox will transform the way we manage some of the world’s most threatened species.

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Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern

10.22541/au.162259496.69056230/v2 ◽

2021 ◽

Author(s):

Jana Wold ◽

Stephanie Galla ◽

Anna Santure ◽

David Eccles ◽

Carolyn J. Hogg ◽

...

Keyword(s):

Threatened Species ◽

Complex Traits ◽

De Novo ◽

Genomic Diversity ◽

Functional Genomic ◽

Structural Variants ◽

Conservation Genomics ◽

Species Of Conservation Concern ◽

Genomic Studies ◽

Large Rearrangements

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.

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Future direction for the conservation of New Zealand?s biodiversity

Pacific Conservation Biology ◽

10.1071/pc090153 ◽

2009 ◽

Vol 15 (3) ◽

pp. 153 ◽

Cited By ~ 2

Author(s):

Mark N. H. Seabrook-Davison ◽

Dianne H. Brunton ◽

Weihong Ji

Keyword(s):

New Zealand ◽

Threatened Species ◽

Management Practices ◽

Conservation Management ◽

Management Strategies ◽

Limited Resources ◽

Allocation Of Resources ◽

Species Management ◽

Future Direction ◽

Biodiversity Changes

Recent analyses (Clout, 2001; Cullen et al. 2005; Hartley, 1997; Joseph et al. 2008; Joseph et al. 2009) of the management of New Zealand?s biodiversity have highlighted the challenge of allocating limited resources, especially the funding of threatened species. Our essay includes frequent citation of Joseph et al. (2008, 2009) as the Project Prioritization Protocol (PPP) modal proposed in their papers is co-written by Department of Conservation (DOC) staff, and may be the metric used in future allocation of resources to New Zealand?s threatened species. Limited resourcing of threatened species management and recovery is a worldwide problem, extensively documented in the conservation literature (Spring et al. 2007; Sutherland, 2009). Reviews of conservation management practices (Craig and Stewart, 1994; Sutherland, 2009; Sutherland et al. 2004; Ussher, 1999) have called for the justification of conservation research by quantifying biodiversity changes and testing solutions. Therefore it is appropriate that novel strategies such as those presented by Joseph et al. (2008, 2009) are available for assessment. Any suggestions for improvement must engage a full debate on the current demands on natural resources (Sarukhan and Whyte, 2005) and the emerging threats to biodiversity, such as climate change (Kostyack and Rohlf, 2008). Development and Implementation of management strategies for threatened species need to be cognizant of not only the ecological (Clark et al. 1994; Tear et al. 1993) needs of threatened species, but also cultural (Charnley, 2006; Craig and Stewart, 1994; McBride et al. 2007) and economic (Craig, 1998; Cullen et al. 2005; Moran, 2003; Perhans et al. 2008; Sinden, 2004) factors.

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Conservation education in threatened species management in Africa

Bird Conservation International ◽

10.1017/s0959270900001179 ◽

1995 ◽

Vol 5 (4) ◽

pp. 455-462 ◽

Cited By ~ 3

Author(s):

Yaa Ntiamoa-Baidu

Keyword(s):

Threatened Species ◽

Monitoring And Evaluation ◽

Conservation Education ◽

Local People ◽

Clear Definition ◽

Target Groups ◽

Problem Identification ◽

Species Management ◽

Definition Of ◽

Reallocation Of Resources

SummaryThe issues that need to be addressed in conservation education programmes aimed at saving threatened species in Africa are discussed. Elements considered as crucial for the success of such programmes include a clear definition of the problem, identification of the target groups, definition of appropriate messages for each group, and development of suitable strategies for dissemination. The advantages of using local people to implement education programmes are outlined. A system for monitoring and evaluation is essential for the assessment of the success of programmes and provides opportunities for improvement, re-definition of priorities and reallocation of resources.

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To mix or not to mix gene pools for threatened species management? Few studies use genetic data to examine the risks of both actions, but failing to do so leads disproportionately to recommendations for separate management

Biological Conservation ◽

10.1016/j.biocon.2021.109072 ◽

2021 ◽

Vol 256 ◽

pp. 109072

Author(s):

Erin Liddell ◽

Paul Sunnucks ◽

Carly N. Cook

Keyword(s):

Threatened Species ◽

Genetic Data ◽

Gene Pools ◽

Species Management ◽

Do So

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The relevance of pedigrees in the conservation genomics era.

10.22541/au.162577430.03067651/v1 ◽

2021 ◽

Author(s):

Stephanie Galla ◽

Liz Brown ◽

Yvette Couch-Lewis ◽

Ilina Cubrinovska ◽

Daryl Eason ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genomic Data ◽

Data Uncertainty ◽

Sampling Strategies ◽

Conservation Genomics ◽

Evolutionary Potential ◽

The Past ◽

Genome Wide ◽

Species Management ◽

Quantitative Analyses

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.

Download Full-text