Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Charbonnel, Emeline; Daguin‐Thiébaut, Claire; Caradec, Lucille; Moittié, Eléonore; Gilg, Olivier; Gavrilo, Maria; Strøm, Hallvard; Morrison, R. I. Guy; Gilchrist, H. Grant; Leblois, Raphaël; Roux, Camille; Yearsley, Jonathan M.; Yannic, Glenn; Broquet, Thomas

doi:10.1038/s41437-022-00515-3

Cited by 8 publications

(7 citation statements)

References 90 publications

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“…This is not necessarily surprising given that genomic library preparation requires DNA quantities that are largely obtainable by swabs, e.g., ideally 120 ng in the RAD-seq protocol followed here (Brelsford et al, 2016). Accordingly, the technique was successfully used for genotyping by sequencing analyses in other vertebrates such as birds (Charbonnel et al, 2022) and mammals (Curto et al, 2019). The ultimate validation would now come from quantifying genotyping error rates in downstream analyses, i.e., by comparing swabs against other types of samples taken from the same individuals.…”

Section: Resultsmentioning

confidence: 99%

Buccal swabs for amphibian genomics

Ambu

Dufresnes

2023

Amphib.-Reptilia

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Conservation genetics must find the balance between the technical challenges of DNA sampling while promoting animal welfare. In amphibians, buccal swabs offer a least intrusive source of DNA, but most herpetologists still refrain to use them, partly due to doubts regarding their effectiveness to provide enough material now that next-generation sequencing (NGS) analyses have become routine. In this article, we hope to change their minds through an empirical demonstration that buccal swabs offer DNA amounts and success rates for a widely used NGS approach (RAD-sequencing) that are equivalent to those of more intrusive yet commonly used samples in frogs and toads. We thus call for a shift of DNA sampling practices, and stress the fact that beyond their proven reliability, buccal swabs facilitate the issue of collection permits by increasingly restrictive ethical committees, especially when it comes to endangered species. With this purpose in mind, we share our long-term experience with amphibian buccal swabs through visual and textual pointers.

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Section: Resultsmentioning

confidence: 99%

Buccal swabs for amphibian genomics

Ambu

Dufresnes

2023

Amphib.-Reptilia

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“…However, the genomic signal of this very recent impact was not strong enough to be picked up by our analyses. Long‐lived species with overlapping generation times pose limitations to the recognition of recent genetic bottlenecks, and this detection may be delayed over many generations (Charbonnel et al 2022). It is therefore possible that future generations of Paraná pine trees may be severely impacted by even lower levels of genetic diversity and higher levels of inbreeding (Lauterjung et al 2019) – adding stress to the ongoing scenario of high levels of forest fragmentation and ongoing global warming, which are predicted to dramatically reduce areas of suitable climate for this tree (Bergamin et al 2019, Wilson et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Evaluating the impact of historical climate and early human groups in the Araucaria Forest of eastern South America

Vasconcellos,

Varela,

Reginato

et al. 2024

Ecography

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It has been hypothesized that the Araucaria Forest in southern Brazil underwent expansions in the past, driven either by human groups or by climate fluctuations of the Holocene and Pleistocene. Fossil pollen records of the Paraná pine Araucaria angustifolia, a dominant tree in that forest, provide some insights into when those may have occurred. Still, the timing of those expansions has never been estimated. To infer past range shifts and shed light on their main drivers, we employed next‐generation DNA sequencing (ddRADseq), machine learning, and a comprehensive database of fossil pollen records into a study of historical demographic inference and paleo‐distribution modeling of the Paraná pine. We found that A. angustifolia comprises two populations expanding at different times: one in the Mantiqueira mountain chain, the other in the southern Brazilian plateau. The southern population began to expand during the Last Glacial Period ~ 70 kya, long before human arrival in South America. Still, genetic analyses support that humans later impacted this population, resulting in lower genetic diversity, higher inbreeding, and high levels of gene flow over large distances with a weak pattern of isolation‐by‐distance. It is possible this resulted from human influence on seed dispersal and germination on the southern Brazilian plateau. The Mantiqueira population, in contrast, expanded only recently (~ 3 kya). This timing coincides with Holocene climatic changes and human settlements established further south, although, to date, there is little archeological evidence of human impact in the Mantiqueira. In addition, multitemporal species distribution models built from a combination of present‐day and pollen records infer a range expansion of the Araucaria Forest during glacial times until the cold humid HS1 event (~ 16 kya), when the forest was most widespread, with no evidence of glacial refugia. The combination of genomic and spatial analyses suggests that both human and climatic controls played a role in the dynamics of the Araucaria Forest.

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“…There are two interrelated factors that likely account for the high standing levels of genetic variation we observed. First, long and overlapping generations have been shown to reduce the sensitivity of populations to genetic loss following recent population decline in freshwater turtles [25,51,77] and other long-lived species [78]. Blanding's turtles can live more than 85 years and have generation times of 37 years, both of which are among the longest of any freshwater turtle [2].…”

Section: Analyses Within Localitiesmentioning

confidence: 99%

Conservation Genetic Analysis of Blanding’s Turtles across Ohio, Indiana, and Michigan

Guinto,

Cross,

Lipps

et al. 2023

Diversity

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The Blanding’s Turtle (Emydoidea blandingii) is a species in need of conservation across much of its geographic range. A key aspect to conserving a species is understanding the genetic diversity and population structure across the landscape. Several researchers have focused on E. blandingii genetic diversity in the northeastern United States, Canada, and parts of the Midwestern United States; however, little investigation has been carried out on localities within the Great Lakes region of Indiana, Michigan, and Ohio. Understanding genetic trends within this region will assist with conservation planning by documenting levels of genetic variation within and among localities and developing hypotheses that have led to the observed patterns. We used 14 microsatellite loci to characterize the genetic diversity of E. blandingii in 16 localities in Indiana, Ohio, and southeast Michigan (with one northwestern locality). Overall, genetic diversity within localities tended to be high and little differentiation was observed among sample localities. No consistent evidence of bottlenecks was detected, and effective population size (Ne) estimates were generally high, but likely biased by sample size. A minimum of two clusters, and as many as seven clusters in a hierarchical analysis, were identified using three methods for grouping individuals (STRUCTURE, TESS3r, and sPCA). A correlation between geographic distance and genetic differentiation (isolation by distance) was observed. The long lifespan and historic gene flow of E. blandingii is likely responsible for the observed genetic diversity and lack of differentiation between localities. This should not suggest that populations are secure in the Great Lakes Region. Modeling aimed at estimating future genetic variation in populations under realistic demographic scenarios indicates that many localities in the region are likely to be vulnerable to genetic loss in the next 200 years.

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Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

Cited by 8 publications

References 90 publications

Buccal swabs for amphibian genomics

Buccal swabs for amphibian genomics

Evaluating the impact of historical climate and early human groups in the Araucaria Forest of eastern South America

Conservation Genetic Analysis of Blanding’s Turtles across Ohio, Indiana, and Michigan

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