Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

Schlötterer, Christian; Tobler, Raymond; Kofler, Robert; Nolte, Viola

doi:10.1038/nrg3803

Cited by 687 publications

(808 citation statements)

References 155 publications

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“…Here, we show that the P-element has recently invaded natural D. simulans populations. We sequenced D. simulans collected from South Africa (in 2012) and from Florida (in 2010) as pools (Pool-seq) (23) and analyzed TE insertions in these samples using the method of Kofler et al (24). We found P-element insertions at 624 sites in the South African sample, and at nine sites in the population from Florida (Fig.…”

Section: Resultsmentioning

confidence: 99%

The recent invasion of natural Drosophila simulans populations by the P-element

Kofler¹,

Hill²,

Nolte³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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113

154

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The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades but was thought to be absent from close relatives, including Drosophila simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germ line of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides a unique opportunity to understand the dynamics of transposable element spread and the associated piwi-interacting RNAs defense mechanisms.T he P-element, one of the best understood eukaryotic transposable elements (TEs), was originally discovered as the causal factor for a syndrome of abnormal phenotypes in Drosophila melanogaster. Crosses in which males derived from newly collected strains were mated with females from long established laboratory stocks produced offspring with spontaneous male recombination, high rates of sterility, and malformed gonadsthat is, "hybrid dysgenesis" (1-4). Eventually it was discovered that hybrid dysgenesis was due to the presence of a TE, the P-element (5, 6), which rapidly became the workhorse of Drosophila transgenesis (5, 7-9). Surveys of strains collected over 70 y show that the P-element spread rapidly in natural D. melanogaster populations, between 1950 and 1990 (10-12), and surveys of other Drosophila species revealed that the P-element had been horizontally transferred (HT) from a distantly related species, Drosophila willistoni (13). As there could be a considerable lag time between the initial transmission of a TE and its invasion of worldwide populations, it is unclear exactly when the P-element first entered D. melanogaster. However, the initial HT event likely occurred somewhere between the spread of D. melanogaster populations into the habitat of D. willistoni, around 1800 (14), and the onset of the worldwide invasion of D. melanogaster populations, around 1950 (10). In any case, the P-element had not been found in close relatives of D. melanogaster, including Drosophila simulans (13-18). The failure of the P-element to invade D. simulans is surprising, as both species are cosmopolitan, are mostly sympatric, and share insertions from many TE families via horizontal transfer (19,20). Furthermore, when artificially injected, the P-element can transpose in D. simulans, albeit at a reduced rate (21, 22). Results and DiscussionThe Recent Invasion of D. simulans Populations. Here, we show that the P-element has recently invaded natural D. simulans populations. We sequenced D. simulans collected from South Africa (in 2012) and from Florida (in 2010) as pools (Pool-seq) (23) and analyzed TE insertions in these ...

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Section: Resultsmentioning

confidence: 99%

The recent invasion of natural Drosophila simulans populations by the P-element

Kofler¹,

Hill²,

Nolte³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

113

154

View full text Add to dashboard Cite

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“…A sexually reproducing population of N diploid individuals is evolved in discrete, non-overlapping generations. Pooled DNA sequencing [37,38] is performed T times at generations t 1 < t 2 < Á Á Á < t T . At each segregating site in the resulting data set, we assume that there are two alleles, denoted A 0 and A 1 .…”

Section: A Brief Overview Of the Methodsmentioning

confidence: 99%

Multi-locus analysis of genomic time series data from experimental evolution

Terhorst

Song

2014

Preprint

122

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Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures. Author SummaryA growing number of experimental biologists are generating "evolve-and-resequence" (E&R) data in which the genomes of an experimental population are repeatedly sequenced over time. The resulting time series data provide important new insights into the dynamics of evolution. This type of analysis has only recently been made possible by next-generation PLOS Genetics |

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“…The genomewide scans used for the detection of genetic differentiation among herring populations were based on the comparison of allele frequencies estimated from pooled DNA-sequencing data. Such data can be prone to biases caused by various factors, such as sequencing and mapping errors or differences in library or sequencing protocols, that could lead to uneven read depth distribution among loci and populations which could affect allele frequency estimates (28). Hence, to validate the results from pooled DNA sequencing, we genotyped a subset of highly differentiated SNPs between spring-and autumn-spawning populations in 377 individual fish (about 30 individuals from each of 13 populations).…”

Section: Evidence Of Parallel Evolution At Tshr a Major Locus Associmentioning

confidence: 99%

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Lamichhaney

Fuentes‐Pardo

Rafati

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

110

142

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Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroidstimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5′ end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.genetic adaptation | Atlantic herring | parallel evolution | reproductive strategies | whole-genome resequencing

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Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

Cited by 687 publications

References 155 publications

The recent invasion of natural Drosophila simulans populations by the P-element

The recent invasion of natural Drosophila simulans populations by the P-element

Multi-locus analysis of genomic time series data from experimental evolution

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

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