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

This work presents the first assessment of the birds of the Entella river (Genoa, Liguria), a small wetland embedded in an urbanized matrix. Data were collected through standardized in situ censuses from April 2012 to June 2017 and integrated with historical and recent data from other verified sources. A total of 278 species are known from the site; 53 species (19.06%) breed in the area, whereas 62 (22.30%) species are vagrant and 81 species (29.14%) are included in the Annex I of the Birds Directive (79/409/CEE). We determined the following indices: NP/P ratio = 1.48, O.V.I. (Ornithological Value Index) = 20.53. In-depth data are provided for vagrant species and for species of conservation concern, to prioritize conservation efforts. The results underline the importance of the Entella river as a local biodiversity hotspot and suggest a possible role of the area as a stepping stone in the regional ecological network. The study highlights a dichotomy between urbanization and high bird diversity in the area and acts as a first step towards its conservation and implementation.

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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/v3 ◽

2021 ◽

Author(s):

Jana Wold ◽

Klaus-Peter Koepfli ◽

Stephanie Galla ◽

Carolyn J. Hogg ◽

David Eccles ◽

...

Keyword(s):

Threatened Species ◽

Evolutionary Biology ◽

Genomic Variation ◽

Functional Genomic ◽

Structural Variants ◽

Conservation Genomics ◽

Species Of Conservation Concern ◽

Genomic Studies ◽

Conservation Concern ◽

Large Rearrangements

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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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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A Problem Based Learning Exercise on Food Security: Understanding the Role of Genomic Variation and Plant Breeding

10.1534/gsaprep.2018.004 ◽

2018 ◽

Author(s):

Jolie WAX ◽

Zhu Zhuo ◽

Anna Bower ◽

Jessica Cooper ◽

Susan Gachara ◽

...

Keyword(s):

Food Security ◽

Plant Breeding ◽

Problem Based Learning ◽

Genomic Variation

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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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