The genomics of phenotypically differentiated <i>Asellus</i><i>aquaticus</i> cave, surface stream and lake ecotypes

Baković, Vid; Cerezo, Maria Luisa Martin; Höglund, Andrey; Fogelholm, Jesper; Henriksen, Rie; Hargeby, Anders; Wright, I. A.

doi:10.1111/mec.15987

Cited by 14 publications

(16 citation statements)

References 111 publications

(192 reference statements)

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“…Finally, from a methodological point of view, individuals of A. aquaticus can be collected readily from the wild, and populations easily established and maintained over multiple generations in the laboratory at low-cost (e.g., Bloor, 2010Bloor, , 2011. Asellus aquaticus is also well-suited for large scale phenotypic and genetic studies, with several phenotyping and genotyping tools already available, including a high throughput phenotyping pipeline (Lürig, 2021), a genome-wide linkage map and hundreds of genetic markers (Protas et al, 2011;Bakovic et al, 2021). This combination makes A. aquaticus highly amenable to controlled laboratory and mesocosm experiments (Rossi and Fano, 1979;Maltby, 1995;Lürig et al, 2019), as well as to in-depth genetic and phenotypic studies (e.g., Protas et al, 2011;Lürig et al, 2019, Bakovic et al, 2021.…”

Section: Asellus Aquaticus As a Model System For Integrative Studiesmentioning

confidence: 99%

“…The latter has led to subterranean phenotypic adaptation and to the formation of troglomorphic subspecies (e.g., Kosswig and Kosswig, 1940;Turk-Prevorčnik and Blejec, 1998). On a regional scale, A. aquaticus has undergone repeated ecotype differentiation within lakes (Eroukhmanoff et al, 2009a,b), with divergence having been associated to both genetic (e.g., Bakovic et al, 2021) and plastic effects (Karlsson et al, 2010). Locally, A. aquaticus shows evidence of assortative mating (e.g., Ridley and Thompson, 1979;Adams et al, 1985), which has the potential to contribute to sexual selection and reproductive isolation (Jiang et al, 2013).…”

Section: Phenotypic Divergencementioning

confidence: 99%

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Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

et al. 2021

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Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.

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Section: Asellus Aquaticus As a Model System For Integrative Studiesmentioning

confidence: 99%

Section: Phenotypic Divergencementioning

confidence: 99%

Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

et al. 2021

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“…The genus Anococcus includes multiple radiation-resistant bacterial species, which have been shown to have degradative effects on nuclear and other toxic substances ( Li et al, 2017 ). Thermophila included many thermotolerant genera, among which thermotolerant DNA polymerase (Taq enzyme) isolated from Thermous aquaticus was widely used in polymerase chain reactions ( Bakovic et al, 2021 ). In many extreme environments, such as deserts, hot springs, and high-salt environments, Cyanobacteria was a locally dominant producer.…”

Section: Analysis and Discussionmentioning

confidence: 99%

Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau

Zhang

Feng

Zhang³

et al. 2023

Front. Microbiol.

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Introduction:In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.Methods:In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.Results:Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.Discussion:In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.

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“…Few other studies have addressed the issue of ecotype formation using model-based inference methods. When such methods are used, they are commonly focused on testing whether divergence occurred with or without gene flow (Klütsch, Manseau, Trim, Polfus, & Wilson, 2016), whether there is ongoing gene flow (Bakovic et al, 2021), as well as on finding the most likely population tree for a given set of sampled populations (Louis et al, 2014) or estimating relevant demographic parameters (Andrew, Kane, Baute, Grassa, & Rieseberg, 2013). Thus, model-based inference methods were rarely used to explicitly contrast different demographic scenarios of ecotype formation, but some examples exist using coalescent-based approaches (Hume, Recknagel, Bean, Adams, & Mable, 2018) coupled with maximum composite-likelihoods (Le Moan, Gagnaire, & Bonhomme, 2016) or ABC (Butlin et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Integrating Pool-seq uncertainties into demographic inference

Carvalho

Morales

Faria

et al. 2022

Preprint

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Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a method to simulate Pool-seq data, implemented in an Approximate Bayesian Computation (ABC) framework to infer demographic history under models with two and four populations. By jointly modeling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Rather than simulating genome-wide data, we perform ABC on subsets of loci, using relative summary statistics and parameter estimates. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin), and to infer relevant demographic parameters (e.g., effective sizes, split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod \textit{Littorina saxatilis}, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (wave and crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e., single origin) and are maintained despite gene flow. These results indicate that demographic modeling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.

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The genomics of phenotypically differentiated Asellusaquaticus cave, surface stream and lake ecotypes

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 14 publications

References 111 publications

Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System

Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau

Integrating Pool-seq uncertainties into demographic inference

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