A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X

Owens, Gregory L.; Todesco, Marco; Drummond, Emily B. M.; Yeaman, Sam

doi:10.1101/142356

Cited by 8 publications

(9 citation statements)

References 14 publications

(4 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Counts of the mismatch alleles were uniformly low (mean <0.5% of reads per site). Our results therefore concur with recent studies (Owens, Todesco, Drummond, Yeaman, & Rieseberg, ; van der Valk, Vezzi, Ormestad, Dalén, & Guschanski, ) that the rate of index swapping is low on the new Illumina platforms, and provide confidence that leakage between indexes did not greatly influence the inferred genotype likelihoods or the inferred genetic relationship among individuals.…”

Section: Methodssupporting

confidence: 92%

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

et al. 2019

View full text Add to dashboard Cite

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.

show abstract

Section: Methodssupporting

confidence: 92%

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

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Next, we combined the simulated libraries in four different pools (Supporting Information Table S5), one pool containing all 18 samples at 0.1× coverage and 1% endogenous content, one pool containing all samples at 1× coverage and 10% endogenous content, one pool containing all samples at 10× coverage and 100% endogenous content, and one pool containing an equal mixture of samples at 0.1× ( n = 6), 1× ( n = 6) and 10× ( n = 6) coverage, hereafter referred to as the mixed pool. Index hopping within each of the four pools was then simulated by giving each read a probability of randomly hopping into another sample, using the rates reported in the literature: 0.0% (Owens et al, ), ~0.5% (this study), ~2% (Griffiths et al, ), and the extreme case of ~10% (Sinha et al, ).…”

Section: Methodsmentioning

confidence: 99%

“…The reported rate of read misassignment on Illumina platforms that rely on the traditional bridge amplification for cluster generation is low (<1%) (Kircher et al, ; Nelson et al, ; Wright & Vetsigian, ) and therefore this source of error has been readily ignored. However, on the Illumina patterned flow cell platforms with ExAmp chemistry, the reported rate of read misassignment ranges from 0% to 10% (Costello et al, ; Griffiths, Richard, Bach, Lun, & Marioni, ; Owens, Todesco, Drummond, Yeaman, & Rieseberg, ; Sinha et al, ; Vodák et al, ; Yao et al, ).…”

Section: Introductionmentioning

confidence: 99%

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

Valk

Vezzi

Ormestad

et al. 2019

Molecular Ecology Resources

103

View full text Add to dashboard Cite

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.

show abstract

“…We trimmed a region of variable length at the 3′ end of each file, according to the average Phred score (minimum quality score of 28) of each MiSeq run. The Python script (MMIS; Vizcaíno et al, ) was then used to automatize sequence concatenation, OTU picking and to eliminate mistagging events (i.e., a recently described sequencing artefact that results in 1% to 10% of reads misassigned to the wrong sample; Esling, Lejzerowicz, & Pawlowski, ; Sinha, Stanley, & Gulati, ; Owens, Todesco, Drummond, Yeaman, & Rieseberg, ). Moreover, only OTUs with more than 100 identical reads were kept.…”

Section: Methodsmentioning

confidence: 99%

Unexpected bird–feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

et al. 2019

View full text Add to dashboard Cite

The high relevance of host‐switching for the diversification of highly host‐specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host‐switching dynamics at an ecological scale. Here, we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird–feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird–mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host‐specific symbionts. Thus, host‐switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario.

show abstract

A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X

Cited by 8 publications

References 14 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

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

Unexpected bird–feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

Contact Info

Product

Resources

About