PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Kofler, Robert; Pandey, Ram Vinay; Schlötterer, Christian

doi:10.1093/bioinformatics/btr589

Cited by 724 publications

(807 citation statements)

References 23 publications

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“…Per-locus F ST was inferred from read counts of pooled samples using PoPoolation2 (Kofler et al, 2011), setting the 'pool size' parameter to the number of chromosomes appropriate for each comparison by analyzing Z-linked and autosomal loci separately. Expected heterozygosity and the proportion of pairwise differences (π) were computed with Arlequin v. 3.5.1.2 (Excoffier and Lischer, 2010) based on inferred genotypes, representing diploid loci as unphased pseudo-haplotypes and allowing up to 50% missing genotypes.…”

Section: Resultsmentioning

confidence: 99%

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

et al. 2015

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Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher F ST for Z-linked loci than for autosomes, as expected. The π Z /π A ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N eZ /N eA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.

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Section: Resultsmentioning

confidence: 99%

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

et al. 2015

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“…Differentiation between Australian and Canadian mitochondrial (mt) genomes were assessed using two measures of genetic differentiation, the fixation index (F ST ) and Fisher's exact test for allele frequency differences (as implemented in Popoolation2 [41]). We combined mitochondrial sequence data from the two lines containing Australian mt genomes (AA and AC) and from the two containing Canadian mt genomes (CC and CA) into single Australian and Canadian pools, respectively.…”

Section: Cytoplasms Differ In Mitochondrial Genomes and Wolbachia Prementioning

confidence: 99%

“…Repeat sequences, identified by RepeatMasker v4.0.6 (http://www.repeatmasker.org), together with 5-bp windows around indels were masked in the subsequent analysis. Differences in allele frequencies per SNP were assessed by F ST and Fisher's exact test as implemented in Popoolation2 v1.201 [41], controlled for false discovery rate (FDR) [66].…”

Section: Sequence Analysismentioning

confidence: 99%

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

et al. 2018

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Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.

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“…To estimate F ST we used the PoPoolation2 package (Kofler et al 2011b), which corrects for possible allele sampling biases associated with pool sequencing as well as sequencing errors. We corrected for unequal sampling of alleles among positions using an unbiased estimator of F ST (Karlsson et al 2007) as implemented in the PoPoolation2 package.…”

Section: Mapping Of the Dwarf Mutationmentioning

confidence: 99%

“…F ST was calculated between breeds in windows of 500 kb with 250 kb steps using the PoPoolation2 package (Kofler et al 2011b). We applied the same filtering requirements as before for the dw/dw and Dw/dw pools F ST contrast.…”

Section: Scan For Selective Sweepsmentioning

confidence: 99%

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

Carneiro

Archer

et al. 2017

Genetics

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The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a 12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4-29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

Cited by 724 publications

References 23 publications

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

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