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

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

10.22541/au.162259496.69056230/v1 ◽

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

Molecular Ecology ◽

10.1111/mec.16141 ◽

2021 ◽

Author(s):

Jana Wold ◽

Klaus‐Peter Koepfli ◽

Stephanie J. Galla ◽

David Eccles ◽

Carolyn J. Hogg ◽

...

Keyword(s):

Structural Variants ◽

Conservation Genomics ◽

Species Of Conservation Concern ◽

Genomic Studies ◽

Conservation Concern

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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 functional studies for species of conservation concern

10.22541/au.161162800.09671016/v2 ◽

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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The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

10.22541/au.161555671.18655788/v1 ◽

2021 ◽

Author(s):

Soraia Barbosa ◽

Kimberly Andrews ◽

Amanda Goldberg ◽

Digpal Gour ◽

Paul Hohenlohe ◽

...

Keyword(s):

Ground Squirrels ◽

Genomic Variation ◽

Nucleotide Polymorphisms ◽

Environmental Pressures ◽

Specific Level ◽

Conservation Implications ◽

Species Of Conservation Concern ◽

Adaptive Processes ◽

Conservation Concern ◽

Adaptive Differentiation

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intra-specific level, and identified putatively adaptive SNPs using population structure outlier and genotype-environment association (GEA) analyses. At the interspecific level, we found a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation relating to differences in hibernation. At the intraspecific level, we identified 3 Evolutionarily Significant Units for NIDGS and 2 for SIDGS plus multiple Management and Adaptive Units. Elevation appears to be the main driver of adaptive differentiation in NIDGS, while neutral variation patterns match and extend that identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected the effect of natural geographic barriers, while adaptive variation reflected differences in land cover and temperature. These results clearly highlight the roles of neutral and adaptive processes for understanding species and population differentiation, which can have important conservation implications in threatened species.

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Effects of hunting camps on breeding grey-necked picathartes Picathartes oreas in south-east Nigeria

Oryx ◽

10.1017/s0030605313000719 ◽

2014 ◽

Vol 48 (3) ◽

pp. 460-464 ◽

Cited By ~ 4

Author(s):

Fidelis Akunke Atuo ◽

Samuel T. Ivande ◽

Zingfa Wala ◽

Timothy J. O'Connell

Keyword(s):

Threatened Species ◽

Wildlife Conservation ◽

Sub Saharan Africa ◽

Conservation Education ◽

Breeding Sites ◽

Cross River ◽

Species Of Conservation Concern ◽

Strict Enforcement ◽

Sub Saharan ◽

Conservation Concern

AbstractThe dependence of forest communities on bushmeat as a source of protein and income is a challenge to wildlife conservation in Sub-Saharan Africa. We investigated the use of caves and overhanging rocks as hunting camps and the consequences for breeding grey-necked picathartes Picathartes oreas in the forests of Cross River in south-east Nigeria. We recorded 84 nesting colonies during guided and random searches. We found 14 (16.7%) breeding sites that had been used as hunting camps, with evidence including fire stands, sleeping spots, cooking utensils and drying racks. Fire stands were the most frequently recorded evidence of camping and were found in 11 of the camps. At the 14 breeding sites only two nesting attempts were made by P. oreas during the survey. Thirty-seven nests (c. 95%) recorded in hunting camps were empty and showed no evidence of ongoing or potential breeding activities, suggesting that the nests may have been abandoned. We attributed the low nesting attempt rate to disturbance caused by hunters, who also affected breeding success through direct removal of eggs and fledglings from nests. We encourage conservation education for the protection of P. oreas and other threatened species in the region and recommend strict enforcement of wildlife laws and disciplinary sanctions. Given the role of the forests of Cross River as a critical habitat for several endemic and threatened species, management efforts targeted at improving the integrity of the forest will benefit grey-necked picathartes and other avian species of conservation concern.

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