Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Benestan, Laura; Moore, Jean‐Sébastien; Sutherland, Ben J. G.; Luyer, Jérémy Le; Maaroufi, Halim; Rougeux, Clément; Normandeau, Éric; Rycroft, Nathan; Atema, Jelle; Harris, Les N.; Tallman, Ross F.; Greenwood, Spencer J.; Clark, Kevin; Bernatchez, Louis

doi:10.1101/096065

Cited by 26 publications

(46 citation statements)

References 102 publications

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“…In addition, 94 putatively sex‐linked markers were removed (see Fig. & in supplementary materials and Benestan et al., ; for details) leaving a total of 6,136 SNPs used in all subsequent analyses (Table ). Replicate individuals ( n = 11) sequenced twice had identical genotypes at 92.0%–97.1% of the markers (mean 94.6%), which was comparable to error rates reported in Mastretta‐Yanes et al.…”

Section: Resultsmentioning

confidence: 99%

Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

et al. 2017

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Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of nonmodel organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise F = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in nonbreeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in nonmodel organisms in logistically challenging environments such as the Arctic.

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Section: Resultsmentioning

confidence: 99%

Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

et al. 2017

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“…Estimates of genetic structure ( F ST or k ) are necessary in many oa and eaa programs (e.g., Frichot et al., ; Günther & Coop, ; Whitlock & Lotterhos, ). Importantly, estimating genetic structure requires identifying neutral loci, and despite notions that few selective loci are inconsequential for estimating structure, even small numbers of loci under selection can exert strong effects on population genetic parameters (e.g., sex‐linked markers Benestan et al., ).…”

Section: Discussionmentioning

confidence: 99%

The search for loci under selection: trends, biases and progress

et al. 2018

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Detecting genetic variants under selection using F outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.

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“…Therefore, projects such as the ‘Functional Annotation of All Salmonid Genomes’ (Macqueen et al, ) should be encouraged and developed. It is also important not to underestimate or neglect the computing power and bioinformatics expertise required to produce high quality genome scaffolds and annotations, and also to recognise and account for biases in next generation sequencing data (Benestan et al, ).…”

Section: Molecular Toolsmentioning

confidence: 99%

Understanding and managing fish populations: keeping the toolbox fit for purpose

Paris

Sherman

Bell

et al. 2018

Journal of Fish Biology

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Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of The Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.

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Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Cited by 26 publications

References 102 publications

Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

The search for loci under selection: trends, biases and progress

Understanding and managing fish populations: keeping the toolbox fit for purpose

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