Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

Valk, Tom van der; Vezzi, Francesco; Ormestad, Mattias; Dalén, Love; Guschanski, Katerina

doi:10.1111/1755-0998.13009

Cited by 103 publications

(100 citation statements)

References 54 publications

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“…In summary, the global data set of genomes analysed here contributes further to the emerging consensus (Árnason, Lammers, Kumar, Nilsson, & Janke, 2018;Arnold, 2016;Gopalakrishnan et al, 2018;Malinsky et al, 2018;Sinding et al, 2018;Tusso et al, 2018) that the relationship among natural populations is rarely well represented as a bifurcating tree. The evolutionary history of natural populations can include episodic long-range dispersal, population replacement and admixture which greatly transform the distribution of global genetic variation.…”

Section: Discussionmentioning

confidence: 65%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

et al. 2019

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Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree‐like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non‐Antarctic lineages is further driven by ancestry segments with up to four‐fold older coalescence time than the genome‐wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome‐wide data to sample the variation in ancestry within individuals.

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Section: Discussionmentioning

confidence: 65%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

et al. 2019

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“…Nonetheless, we observed that many spurious taxa most likely originate from samples multiplexed with the de ned communities in one sequencing run, despite the implementation of multiple negative controls and an automated sample processing work ow. One cause for spurious sequences, termed index-hopping, was previously identi ed to account for 0.47% of reads, with samples with the fewest reads being affected the most [36]. As de ned in the present study by using de ned communities as references, spurious taxa do not necessarily represent true artifacts (i.e.…”

Section: Discussionmentioning

confidence: 64%

Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

Reitmeier

Hitch

Fikas

et al. 2020

Preprint

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Background: 16S rRNA gene amplicon sequencing is a very popular approach for studying microbiomes. However, varying standards exist for sample and data processing and some basic concepts such as the occurrence of spurious sequences have not been investigated in a comprehensive manner, which was done in the present study. Methods: Using defined communities of bacteria in vitro and in vivo , we searched for sequences not matching the expected species ( i.e. , spurious taxa) and determine a threshold of occurrence relevant for adequate data analysis. The origin of spurious taxa was then investigated via large-scale amplicon queries. We also assessed the impact of varying sequence filtering stringency on diversity readouts in human fecal and peat soil communities. Results: 16S rRNA gene amplicon data processing based on Operational Taxonomic Units (OTUs) clustering and singleton removal, a commonly used approach that discards any taxa represented by only one sequence across all samples, delivered approx. 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa on average. This spurious fraction of taxa was lower based on amplicon sequence variants (ASVs) analysis but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was identified as a threshold below which the analysis of spurious taxa can be prevented to a large extent. Most spurious taxa (approx. 70%) detected in simplified communities occurred in samples multiplexed in the same sequencing run and were present in only one of ten runs. Use of the 0.25% relative abundance threshold decreased the coefficient of variations calculated on richness in the same six human fecal samples across seven sequencing runs by 38% compared with singleton filtering. The output of beta -diversity analyses of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparing samples. Importantly, major findings were confirmed by using data generated in a second sequencing facility. Conclusions: Handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. A threshold of relative abundance of 0.25% is more appropriate than singleton removal, although study-specific analysis strategies are mandatory. We propose the concept of effective richness, which will help comparing results across studies.

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“…Specifically, for all loci at all AT samples, more than 90% of read pairs had the AT allele, and for all loci at all A. coluzzii samples, more than 90% of read pairs had the A. coluzzii allele. The small numbers of incorrect reads could be due to index hopping among these jointly-sequenced samples (van der Valk, Vezzi, Ormestad, Dalén, & Guschanski, 2019) or low-level contamination. Coverage at the negative control was lower but non-negligible (76 to 1460 read pairs per locus, mean = 411.6), presumably due to similar errors.…”

Section: Resultsmentioning

confidence: 99%

A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmittingAnopheles gambiaecomplex

Tennessen

Ingham

Toé

et al. 2020

Preprint

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16 17 The Anopheles gambiae complex consists of multiple morphologically indistinguishable 18 mosquito species including the most important vectors of the malaria parasite Plasmodium 19 falciparum in sub-Saharan Africa. Several lineages have only recently been described as 20 distinct, including the cryptic taxon GOUNDRY in central Burkina Faso. The ecological, 21 immunological, and reproductive differences among these taxa will critically impact 22 population responses to disease control strategies and environmental changes. Here we 23 2 examine whole-genome sequencing data from a longitudinal study of putative A. coluzzii in 24 western Burkina Faso. Surprisingly, many samples are genetically divergent from A. 25 coluzzii and all other Anopheles species and represent a new taxon, here designated 26 Anopheles TENGRELA (AT). Population genetic analysis suggests that GOUNDRY sensu 27 stricto represents an admixed population descended from both A. coluzzii and AT. AT 28 harbors low nucleotide diversity except for the 2La inversion polymorphism which is 29 maintained by overdominance. It shows numerous fixed differences with A. coluzzii 30 concentrated in several regions reflecting selective sweeps, but the two taxa are identical at 31 standard diagnostic loci used for taxon identification and thus AT may often go unnoticed. 32 We present an amplicon-based genotyping assay for identifying AT which could be usefully 33 applied to numerous existing samples. Misidentified cryptic taxa could seriously confound 34 ongoing studies of Anopheles ecology and evolution in western Africa, including phenotypic 35 and genotypic surveys of insecticide resistance. Reproductive barriers between cryptic 36 species may also complicate novel vector control efforts, for example gene drives, and 37 hinder predictions about evolutionary dynamics of Anopheles and Plasmodium. 38 39

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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

Cited by 103 publications

References 54 publications

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmittingAnopheles gambiaecomplex

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