Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes)

Marques, Adam; Hanson, Jeffrey O.; Camacho‐Sanchez, Miguel; Martínez‐Solano, Íñigo; Moritz, Craig; Tarroso, Pedro; Velo‐Antón, Guillermo; Veríssimo, Ana; Carvalho, Sílvia B.

doi:10.1007/s10592-021-01425-3

Cited by 3 publications

(4 citation statements)

References 88 publications

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“…First, as others have done (Bryc et al, 2010; Decker et al, 2014; Marques et al, 2022), principal components analysis (PCA) and Gaussian finite mixture modelling methods were used as an independent means of exploring the broad phylogenomic relationship between individuals, independent of models of sequence evolution. For the PCA, but not other analyses, the filtered variant calling file was first pruned using plink v1.9 (Purcell et al, 2007), then linkage‐pruned sites were used to generate eigenvalues and vectors.…”

Section: Methodsmentioning

confidence: 99%

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Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Gonzalez

Saenko

Davison

2022

J of Evolutionary Biology

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Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post‐glacial history of Cepaea nemoralis, with a long‐term aim to understand the roles that selection and drift have in determining both European‐wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present‐day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long‐distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.

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Section: Methodsmentioning

confidence: 99%

Section: Analyses Of Genomic Variationmentioning

confidence: 99%

Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Gonzalez

Saenko

Davison

2022

J of Evolutionary Biology

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“…Recent studies have detailed approaches for multiple testing correction (Austin et al, 2022;Flores-Manzanero et al, 2022;Marques et al, 2022). Correction procedures are straightforward to apply, and are often included with statistical analysis packages such as p.adjust command in R (https:// www.…”

Section: Correcting For Multiple Testingmentioning

confidence: 99%

“…Recent studies have detailed approaches for multiple testing correction (Austin et al., 2022; Flores‐Manzanero et al., 2022; Marques et al., 2022). Correction procedures are straightforward to apply, and are often included with statistical analysis packages such as p.adjust command in R (https://www.r-project.org/), FDRestimation package in R (Murray & Blume, 2020) and multipletests function in the Python statsmodels module (Seabold & Perktold, 2010).…”

Section: Introductionmentioning

confidence: 99%

Genomics and conservation: Guidance from training to analyses and applications

Schiebelhut,

Guillaume,

Kuhn

et al. 2023

Molecular Ecology Resources

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Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

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Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation

SANTOS,

MARQUES,

CERÍACO

2024

An. Acad. Bras. Ciênc.

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Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.

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Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes)

Cited by 3 publications

References 88 publications

Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Genomics and conservation: Guidance from training to analyses and applications

Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation

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