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

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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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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A checklist of the reptiles and amphibians found in protected areas along the South African Wild Coast, with notes on conservation implications

Koedoe ◽

10.4102/koedoe.v57i1.1247 ◽

2015 ◽

Vol 57 (1) ◽

Cited By ~ 3

Author(s):

Jan A. Venter ◽

Werner Conradie

Keyword(s):

Protected Areas ◽

South African ◽

Conservation Management ◽

Novel Species ◽

Survey Methods ◽

Grid Cell ◽

Eastern Cape ◽

Conservation Implications ◽

Species Of Conservation Concern ◽

Conservation Concern

We surveyed six protected areas along the Wild Coast of the Eastern Cape, South Africa, to determine general herpetofaunal diversity as well as the representation of species of special conservation concern. Visual encounter survey methods and standard Y-shape trap arrays were used to conduct surveys from 2011 to 2013. A total of 59 species (22 amphibians and 37 reptiles) were recorded. A number of previously unknown populations of threatened species and one potential novel species were discovered in these protected areas, and the known ranges of several other species were extended. A total of 243 quarter-degree grid-cell unit records were documented, of which 90 (23% amphibians and 50% reptiles) represented the first records for the area. Amphibian and reptile diversity increased along the coast and a number of species of conservation concern were well represented in current protected areas. Our study provides a comprehensive amphibian and reptile checklist for an under-sampled region and highlights the importance of baseline data for improving conservation management.Conservation implications: Small protected areas play an important role in conserving a number of threatened herpetofaunal species along the Wild Coast. The region is currently under significant and increasing pressure from anthropogenic-induced environmental degradation, which affects biodiversity and subsequently the local inhabitants. The information presented here represents an important baseline for future conservation management.

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Using miniaturized GPS archival tags to assess home range features of a small plunge-diving bird: the European Kingfisher (Alcedo atthis)

Avian Research ◽

10.1186/s40657-021-00267-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Raphaël Musseau ◽

Melina Bastianelli ◽

Clementine Bely ◽

Céline Rousselle ◽

Olivier Dehorter

Keyword(s):

Home Range ◽

Population Decline ◽

Gps Tracking ◽

Home Ranges ◽

Conservation Implications ◽

Small Wetlands ◽

Species Of Conservation Concern ◽

Archival Tags ◽

Conservation Concern ◽

Diving Bird

Abstract Background The European Kingfisher (Alcedo atthis) is a small plunge-diving bird, today considered a species of conservation concern in Europe given its rapid population decline observed across the continent. We implemented a pilot study aimed at providing first data allowing to: (1) assess home range features of the European Kingfisher for populations with unevenly distributed feeding habitats; (2) define conservation implications for habitats exploited by such populations; and (3) evaluate possibilities for developing GPS tracking schemes dedicated to home range studies for this species that could be possibly applied to other small plunge-diving birds. Methods In 2018 and 2019, we equipped 16 breeding European Kingfishers sampled within the marshes of the Gironde Estuary (France), with miniaturized and waterproof GPS archival tags deployed with leg-loop harnesses (total equipment mass = 1.4 g; average bird mass = 40.18 ± 1.12 g). Results On average, we collected 35.31 ± 6.66 locations usable for analyses, without a significant effect on bird body condition (n = 13 tags retrieved). Data analyses highlighted rather limited home ranges exploited by birds (average = 2.50 ± 0.55 ha), composed on average by 2.78 ± 0.40 location nuclei. Our results also underscore: (1) a rather important home range fragmentation index (0.36 ± 0.08); and (2) the use by birds of different types of small wetlands (wet ditches, small ponds or small waterholes), often exploited in addition to habitats encompassing nest locations. Conclusions Our study reveals interesting GPS tracking possibilities for small plunge-diving birds such as the European Kingfisher. For this species, today classified as vulnerable in Europe, our results underline the importance of developing conservation and ecological restoration policies for wetland networks that would integrate small wetlands particularly sensitive to global change.

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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

Molecular Ecology ◽

10.1111/mec.16096 ◽

2021 ◽

Author(s):

Soraia Barbosa ◽

Kimberly R. Andrews ◽

Amanda R. Goldberg ◽

Digpal S. Gour ◽

Paul A. Hohenlohe ◽

...

Keyword(s):

Ground Squirrel ◽

Genomic Variation ◽

Species Of Conservation Concern ◽

Conservation Concern

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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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Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽

10.1186/s12864-021-07546-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cooper J. Park ◽

Nicole A. Caimi ◽

Debbie C. Buecher ◽

Ernest W. Valdez ◽

Diana E. Northup ◽

...

Keyword(s):

New Mexico ◽

Genetic Manipulation ◽

Distinct Species ◽

Biosynthetic Gene Cluster ◽

Genomic Variation ◽

Species Variation ◽

Nucleotide Polymorphisms ◽

Peptide Synthetases ◽

Genome Wide ◽

Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

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