Measuring genetic differentiation from Pool-seq data

Hivert, Valentin; Leblois, Raphaël; Petit, Éric; Gautier, Mathieu; Vitalis, Renaud

doi:10.1101/282400

Cited by 10 publications

(11 citation statements)

References 69 publications

(129 reference statements)

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“…Indeed, the drawback of these approaches, despite dedicated software (PoPoolation2, Kofler et al 2011) is that they can give strongly biaised estimates, or ones that do not consider evolutionary sampling (Hivert et al 2018). Therefore, they require further validation methods which usually value previously developed high-quality and lower-scale data (e.g.…”

Section: Cc-by-nc-ndmentioning

confidence: 99%

“…Given the increasing availability of markers in non-model species (usually SNPs), it has been shown by simulation (Willing et al 2012, Hivert et al 2018 and empirical data (Nazareno et al 2017) that sample sizes as small as 4 to 6 individuals can be sufficient to infer differentiation when a large number of bi-allelic loci (> 1000) are being used. A broadscale geographic sampling is however required if the aim is to better infer genetic structure and complex demographic scenarios involving recolonization and range shifts due to past glacial cycles, such as those assumed for many European species (Lascoux and Petit 2010, Keller et al 2010, Jeffries et al 2016, Sousa et al 2014.…”

Section: In Prunus Persica)mentioning

confidence: 99%

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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Anselmi¹,

Hub

2018

Preprint

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In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. We completed the analyses of Sanger sequences produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks in a range-wide sampling of 25 individuals (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes.Using a high-quality dedicated pipeline, we provide a detailed characterization of over 14500 polymorphisms, including ~12500 SNPs -218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di-and tri-nucleotide SSR loci. This catalog also includes various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity and differentiation across genic regions are also described for the first time in those species (mean  close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and mean F ST ~0.13 across SNPs). Robust patterns were observed which emphasize a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. These patterns are discussed in the context of both species documented introgression history despite strong reproductive barriers. The quality, representativity in terms of species genomic diversity, and usefulness of the resources provided are discussed for possible applications in medium scale landscape ecology projects, and as a reference resource for validation purposes in larger-scale re-sequencing projects. These are preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and low levels of linkage disequilibrium revealed.

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Section: Cc-by-nc-ndmentioning

confidence: 99%

Section: In Prunus Persica)mentioning

confidence: 99%

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Anselmi¹,

Hub

2018

Preprint

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“…Indeed, similarly to other species (e.g., 16 ), heterozygous individuals resulting from the cross of distinct homozygous H. axyridis forms produce black pigmentation in any part of the elytra that is black in either parental form 12 . Our results help to understand this phenomenon known as mosaic dominance at the molecular level.…”

mentioning

confidence: 99%

“…In addition to allelic variation, colour pattern diversity in H. axyridis is shaped by the dominance relationships among colour form alleles 12 . Indeed, similarly to other species (e.g., 16 ), heterozygous individuals resulting from the cross of distinct homozygous H. axyridis forms produce black pigmentation in any part of the elytra that is black in either parental form 12 .…”

mentioning

confidence: 99%

“…http://dx.doi.org/10.1101/345942 doi: bioRxiv preprint first posted online Jun. 13, 2018; 3 wild has been attributed to a combination of allelic diversity, interactions between allelic forms, and plastic response to environmental factors 12,13 . Genetic crosses have demonstrated that the majority of H. axyridis melanic forms result from variation of multiple alleles segregating at a single, uncharacterised, autosomal locus 9,10 , hereafter referred to as the colour pattern locus.…”

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confidence: 99%

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The genomic basis of colour pattern polymorphism in the harlequin ladybird

Gautier

Yamaguchi

Foucaud

et al. 2018

Preprint

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2Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research [1][2][3][4][5][6] . The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns 7,8 (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/345942 doi: bioRxiv preprint first posted online Jun. 13, 2018; 3 wild has been attributed to a combination of allelic diversity, interactions between allelic forms, and plastic response to environmental factors 12,13 . Genetic crosses have demonstrated that the majority of H. axyridis melanic forms result from variation of multiple alleles segregating at a single, uncharacterised, autosomal locus 9,10 , hereafter referred to as the colour pattern locus.To identify this colour pattern locus, and the mechanisms underlying discrete colour pattern variation, we used a population genomics approach, taking advantage of the cooccurrence of multiple colour pattern forms in natural populations. To that end, we first performed a de novo genome assembly of the H. axyridis Red-nSpots form (HaxR) using long reads produced by a MinION sequencer (Oxford Nanopore) (see Extended Data Table 1).Then, to fine map the colour pattern locus on this assembly, DNA from 14 pools of individuals (from n=40 to n=100 individuals per pool) representative of the world-wide genetic diversity and the four main colour pattern forms of H. axyridis was sequenced on a HiSeq 2500 (Illumina, Inc.) (Extended Data Table 2). Our aim was to characterize genetic variation associated with phenotypic differences across pool samples, using the proportion of individuals of a given colour form in each pool as a covariate. To do so, we called 18,425,210autosomal SNPs, and we performed a population-based genome-wide association study accounting for the covariance of allele frequencies across pools 14 . Given the dominance hierarchy of colour morph alleles with Black-2Spots > Black-4Spots > Black-nSpots > RednSpots 9,12,13 , we first performed the association study using the proportion of Red-nSpots individuals, carrying two copies of the most recessive allele, in each DNA pool as a covariate.We found 710 SNPs strongly associated with the proportion of the Red-nSpots form (Bayes factor > 30 db), the vast majority (86%) of which are located within a s...

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Contingency and chance erase necessity in the experimental evolution of ancestral proteins

Xie

Metzger

et al. 2020

Preprint

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The extent to which evolutionary outcomes reflect the unpredictable influences of chance and contingency is a central but unanswered question in evolutionary biology 1–4. A precise characterization requires evolutionary trajectories to be repeated multiple times under identical environmental conditions from multiple starting points across history, a scenario that rarely, if ever, occurs in nature. Here we combine continuous experimental evolution 5 with ancestral protein reconstruction 6 and manipulative genetic experiments to identify the causes and consequences of chance and contingency in the genetic outcomes of molecular evolution. By repeatedly evolving ancestral proteins in the B-cell lymphoma-2 (BCL-2) family of apoptosis regulators 7 to acquire the same protein-protein interaction specificities that evolved during history, we found that contingency and chance interact to make sequence evolution increasingly unpredictable over phylogenetic timescales. Although replicates from the same starting genotype sometimes share mutations – indicating partial predictability – there are multiple alternative sets of changes that can alter specificity, and chance decides which of these paths is taken. Contingency has a stronger effect: when trajectories are initiated from different starting points, outcomes are even more divergent, because substitutions that occurred during phylogenetic history repeatedly changed the potential of other mutations to confer new binding specificities. The impact of contingency increased steadily with phylogenetic distance and magnified the effects of chance, resulting in a >3-fold increase in genetic variance among evolutionary trajectories initiated from different starting points across the timescale of metazoan evolution. Our findings show how a particular cascade of chance evolutionary steps throughout history makes the outcomes of molecular evolution increasingly idiosyncratic and unpredictable, even under strong selection.

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Measuring genetic differentiation from Pool-seq data

Cited by 10 publications

References 69 publications

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

The genomic basis of colour pattern polymorphism in the harlequin ladybird

Contingency and chance erase necessity in the experimental evolution of ancestral proteins

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