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 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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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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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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Climatic Variables Differentially Influence Neotropical Plant Species of Conservation Concern

Journal of Sustainable Forestry ◽

10.1080/10549811.2021.1944878 ◽

2021 ◽

pp. 1-16

Author(s):

Pablo Antúnez ◽

Christian Wehenkel ◽

Collins Byobona Kukunda ◽

José Ciro Hernández-Díaz

Keyword(s):

Plant Species ◽

Climatic Variables ◽

Species Of Conservation Concern ◽

Conservation Concern

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Using impact assessment study designs for addressing impacts to species of conservation concern

Wildlife Society Bulletin ◽

10.1002/wsb.179 ◽

2012 ◽

Vol 36 (3) ◽

pp. 450-456 ◽

Cited By ~ 2

Author(s):

Mike E. Marshall ◽

Ashley M. Long ◽

Shannon L. Farrell ◽

Heather A. Mathewson ◽

Michael L. Morrison ◽

...

Keyword(s):

Impact Assessment ◽

Impact Assessment Study ◽

Assessment Study ◽

Species Of Conservation Concern ◽

Conservation Concern ◽

Study Designs

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White-nose syndrome-related changes to Mid-Atlantic bat communities across an urban-to-rural gradient

BMC Zoology ◽

10.1186/s40850-021-00079-5 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Sabrina Deeley ◽

Joshua B. Johnson ◽

W. Mark Ford ◽

J. Edward Gates

Keyword(s):

The United States ◽

Myotis Lucifugus ◽

National Capital Region ◽

Conservation Areas ◽

White Nose Syndrome ◽

Species Of Conservation Concern ◽

National Capital ◽

Park Service ◽

Bat Conservation ◽

Conservation Concern

Abstract Background White-nose Syndrome (WNS) has reduced the abundance of many bat species within the United States’ Mid-Atlantic region. To determine changes within the National Park Service National Capital Region (NCR) bat communities, we surveyed the area with mist netting and active acoustic sampling (2016–2018) and compared findings to pre-WNS (2003–2004) data. Results The results indicated the continued presence of the threatened Myotis septentrionalis (Northern Long-eared bat) and species of conservation concern, including Perimyotis subflavus (Tri-colored bat), Myotis leibii (Eastern Small-footed bat) and Myotis lucifugus (Little Brown bat). However, we documented a significant reduction in the abundance and distribution of M. lucifugus and P. subflavus, a decrease in the distribution of M. septentrionalis, and an increase in the abundance of Eptesicus fuscus (Big Brown bat). Conclusions Documented post-WNS M. septentrionalis recruitment suggests that portions of the NCR may be important bat conservation areas. Decreases in distribution and abundance of P. subflavus and M. lucifugus indicate probable extirpation from many previously occupied portions of the region.

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Deep genetic structure at a small spatial scale in the endangered land snail Xerocrassa montserratensis

Scientific Reports ◽

10.1038/s41598-021-87741-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Cristina Català ◽

Vicenç Bros ◽

Xavier Castelltort ◽

Xavier Santos ◽

Marta Pascual

Keyword(s):

Genetic Structure ◽

Land Snail ◽

Snail Species ◽

Small Spatial Scale ◽

Geographic Ranges ◽

Genetic Groups ◽

Species Of Conservation Concern ◽

Conservation Actions ◽

Conservation Concern ◽

Single Locality

AbstractSpecies with small geographic ranges do not tend to have a high genetic structure, but some land snail species seem to be an exception. Xerocrassa montserratensis, an endangered land snail endemic to Catalonia (northeastern Iberian Peninsula), is an excellent model to study the processes affecting the phylogeography of specialized species of conservation concern. This species is restricted to xerophilous stony slopes and occurs within a small and fragmented area of ca. 500 km2. We sequenced the COI barcode region of 152 individuals from eight sites covering the entire range of the species. We found four genetic groups mostly coincident with their geographic distribution: a central ancestral group containing shared haplotypes among five localities and three groups restricted to a single locality each. Two of these derived groups were geographically and genetically isolated, while the third and most differentiated group was not geographically isolated. Geomorphologic and paleoclimatic processes during the Pleistocene can explain the divergence found between populations of this low dispersal species with historical fragmentation and secondary contacts. Nonetheless, recent passive large dispersal through streams was also detected in the central group. Overall, our study uncovered four evolutionary units, partially matching morphologically described subspecies, which should be considered in future conservation actions.

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Integrating citizen science and remotely sensed data to help inform time-sensitive policy decisions for species of conservation concern

Biological Conservation ◽

10.1016/j.biocon.2019.07.025 ◽

2019 ◽

Vol 237 ◽

pp. 463-469 ◽

Cited By ~ 1

Author(s):

Ashley M. Long ◽

Brian L. Pierce ◽

Amanda D. Anderson ◽

Kevin L. Skow ◽

Addie Smith ◽

...

Keyword(s):

Citizen Science ◽

Remotely Sensed ◽

Policy Decisions ◽

Remotely Sensed Data ◽

Species Of Conservation Concern ◽

Conservation Concern

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Using a capture-recapture approach for modelling the detectability and distribution of Houbara Bustard in southern Tunisia

Bird Conservation International ◽

10.1017/s0959270911000487 ◽

2011 ◽

Vol 22 (3) ◽

pp. 288-298 ◽

Cited By ~ 5

Author(s):

M. CHAMMEM ◽

S. SELMI ◽

T. KHORCHANI ◽

S. NOUIRA

Keyword(s):

Regression Analyses ◽

Species Occurrence ◽

Imperfect Detection ◽

Southern Tunisia ◽

Species Of Conservation Concern ◽

Habitat Factors ◽

Houbara Bustard ◽

Capture Recapture ◽

Conservation Concern ◽

Free Ranging

SummaryModelling the distribution of species of conservation concern is an important issue in population ecology. Classically, logistic regression analyses are conducted to estimate species’ distributions from detection/non-detection data in a sample of sites and to test for the significance of several environmental variables in predicting the probability of occurrence. These modelling approaches assume that species detection probability is constant and equals one in all sampled sites, which is critical, notably in the case of rare, shy and cryptic species. The capture-recapture-like approach developed by Mackenzie et al. (2002, 2003) provides a reliable tool that accounts for imperfect detection when estimating species occurrence, as well as for assessing the relevance of site features as predictors of species occurrence probability. The aim of this study was to explore the possibility of using this approach in the context of Houbara Bustard Chlamydotis undulata in southern Tunisia. Our results show once more the low detectability of this emblematic species and stress the need to take this factor into account when estimating Houbara spatial distribution. The distribution of Houbara in southern Tunisia is more likely to be shaped by human-related than by habitat factors. In particular, Houbara occurrence was positively associated with site remoteness and camel numbers. Houbara seemed to avoid areas with high human presence and shared the most remote and agriculture-free zones with free-ranging camels.

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Intrinsic Prey Preference and Selection of the Giant Gartersnake: A Threatened Predator in a Nonnative Prey-Dominated Community

Journal of Fish and Wildlife Management ◽

10.3996/062019-jfwm-051 ◽

2020 ◽

Vol 11 (1) ◽

pp. 164-173

Author(s):

Julia S.M. Ersan ◽

Brian J. Halstead ◽

Erica L. Wildy ◽

Michael L. Casazza ◽

Glenn D. Wylie

Keyword(s):

Exotic Species ◽

Native Species ◽

Prey Selection ◽

Central Valley ◽

Prey Preference ◽

Live Prey ◽

Species Of Conservation Concern ◽

Conservation Concern ◽

Behavioral Trials ◽

Selection Of

Abstract The introduction of exotic species into an environment can introduce great change in the trophic dynamics of native species. This is of even greater concern if the native species is of conservation concern. The giant gartersnake, Thamnophis gigas, an endemic predator of the Central Valley of California and a species of conservation concern at the state and federal levels, has declined as a result of conversion of its once vast wetland habitat to agriculture. Another anthropogenic factor contributing to this snake's changing ecology is the introduction of nonnative prey into the species' habitats. These introductions have resulted in a prey community that is almost completely composed of exotic species and have potential for considerable effects. In order to assess prey preference and selection we performed three sets of behavioral trials on naïve neonates. We examined 1) neonate prey preference in response to olfactory cues of prepared prey extracts, 2) neonate consumption of different live prey items presented simultaneously; and 3) terrestrial feeding behavior and/or latency to successful attack. Results from the olfactory study suggest that native Sierran treefrogs, Pseudacris sierra, are preferred by neonates. Results from consumption trials suggest that neonates are more likely to select frog species than fish species. This is the first study that we are aware of that examines prey selection of this threatened species and serves to inform its conservation and management.

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