Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids

Bartoš, Oldřich; Bohlen, Jörg; Šlechtová, Vendula; Kočí, Ján; Röslein, Jan; Janko, Karel

doi:10.1111/1755-0998.13806

Cited by 2 publications

(3 citation statements)

References 75 publications

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“…As expected, the success of target‐capture (assessed from on‐target mapping rates) decreased with increasing genetic distance from the reference species C. finmarchicus (Choquet et al., 2019), with C. hyperboreus (presumably the most genetically divergent species) having the lowest number of sequences captured, behind C. helgolandicus . This trend is typical of target‐capture‐based methods (Bartoš et al., 2023) and was also reported in Choo et al. (2020) using a similar protocol, with capture probes designed for the pteropod Limacina bulimoides and applied to congeneric species.…”

Section: Discussionsupporting

confidence: 71%

“…As expected, the success of target-capture (assessed from on-target mapping rates) decreased with increasing genetic distance from the reference species C. finmarchicus (Choquet et al, 2019), with C. hyperboreus (presumably the most genetically divergent species) having the lowest number of sequences captured, behind C. helgolandicus. This trend is typical of target-capture-based methods (Bartoš et al, 2023) and was also reported in Choo et al (2020) using a similar protocol, with capture probes designed for the pteropod Limacina bulimoides and applied to congeneric species. We were able to yield 1535 high-quality SNPs across four Calanus species, and 6030 SNPs for the investigation focused TA B L E 4 Results from the investigation of the 10 microsatellite loci from which hybrids between Calanus finmarchicus and C. glacialis were detected.…”

Section: Scaling Up the Exploration Of Hybridization In Calanus Spp W...supporting

confidence: 64%

“…This study represents the first attempt to use a protocol of target‐capture to explore putative introgression in non‐model organisms (Bartoš et al., 2023). Beyond simulations, the power of our target‐capture SNPs was further demonstrated by our parallel analyses of an independent SNP dataset generated from RNA‐seq, which displayed the exact same patterns of clustering and differentiation among species, only with better resolution, which is expected from a higher number of markers.…”

Section: Discussionmentioning

confidence: 99%

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Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Choquet,

Lizano,

Le Moan

et al. 2023

Molecular Ecology

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Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high‐throughput sequencing easing the generation of genome‐wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target‐capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP‐based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re‐assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.

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Section: Discussionsupporting

confidence: 71%

Section: Scaling Up the Exploration Of Hybridization In Calanus Spp W...supporting

confidence: 64%

Section: Discussionmentioning

confidence: 99%

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Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Choquet,

Lizano,

Le Moan

et al. 2023

Molecular Ecology

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Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

Walden,

Kiefer,

Koch

2024

Preprint

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Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing paralog status of targeted loci and incorporating them into tree reconstruction methods. Using a target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of paralogous sequences into a diploid tree. We call this approach Paralog PhyloGenomics (PPG), and show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach will be a valuable addition to phylogenomic methods available for the study of polyploids.

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Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids

Cited by 2 publications

References 75 publications

Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

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