Josephine Paris

Josephine Paris
University of L'Aquila

PhD

About

22
Publications
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469
Citations

Publications

Publications (22)
Article
Full-text available
Restriction site Associated DNA sequencing (RAD-seq) has become a widely adopted method for genotyping populations of model and non-model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program Stacks. 2.Using three empirical RAD-seq datasets, we demonstrate a met...
Article
Full-text available
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water wash-out continues to negatively impact water quality across the regi...
Article
Full-text available
Male colour patterns of the Trinidadian guppy ( Poecilia reticulata ) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘s...
Article
The repeatability of evolution at the genetic level has been demonstrated to vary along a continuum from complete parallelism to divergence. In order to better understand why this continuum exists within and among systems, hypotheses must be tested using high‐confidence candidate loci for repeatability. However, few methods have been developed to s...
Article
Full-text available
Although rapid phenotypic evolution has been documented often, the genomic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that...
Article
Full-text available
The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently a...
Article
Full-text available
The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted ge...
Preprint
Full-text available
1) The repeatability of evolution at the genetic level has been demonstrated to vary along a continuum from complete parallelism to divergence. In order to better understand why this continuum exists within and among systems, hypotheses must be tested using high-confidence sets of candidate loci for repeatability. Despite this, few methods have bee...
Article
Full-text available
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demogr...
Preprint
Full-text available
Colour polymorphism provides a tractable trait that can be harnessed to explore the evolution of sexual selection and sexual conflict. Male colour patterns of the Trinidadian guppy ( Poecilia reticulata ) are governed by both natural and sexual selection, and are typified by extreme pattern colour variation as a result of negative frequency depende...
Preprint
Full-text available
The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to tes...
Preprint
Full-text available
It is now accepted that phenotypic evolution can occur quickly but the genetic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations t...
Article
Exposure of male fish to estrogenic substances from wastewater treatment works (WwTWs) results in feminization and reduced reproductive fitness. Nevertheless, self-sustaining populations of roach (Rutilus rutilus) inhabit river stretches polluted with estrogenic WwTW effluents. In this study, we examine whether such roach populations have evolved a...
Preprint
Full-text available
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demogr...
Article
Full-text available
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome asse...
Preprint
Full-text available
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome asse...
Article
Full-text available
Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to co...
Article
Full-text available
Nassau grouper (Epinephelus striatus, Bloch 1792) are globally critically endangered and an important fishery species in The Commonwealth of The Bahamas (hereafter The Bahamas) and parts of the Caribbean, with an urgent need for better management and conservation. Here, we adopted a combined approach, integrating restriction-site-associated DNA seq...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
Metal pollution has made a significant impact on the earth’s ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England ar...
Article
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations...

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Projects (3)
Project
This project uses state-of-the-art genomic sequencing to explore the evolutionary adaptations of trout populations in SW England, central Wales and SE Ireland (all regions with trout populations affected by continuing metal pollution), to disentangle the relative importance of the three factors most likely to affect the ability of trout to adapt: evolutionary history (post-glacial colonisation lineage), local adaptation (natural geochemistry, river location) and human-driven pollution (mining and persistent heavy metal contamination).
Project
Ecological genomics of adaptive polymorphism in guppies