Biology subjects

Shpak, M.

Publications and source records attributed to Shpak, M..

4 recordsLinked to original sources

bioRxiv2024

The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation

Population branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variable Ne), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation. Significance StatementPopulation branch statistics are widely used in genome-wide scans to identify loci associated with local adaptation. This study finds that branch statistics are more accurate than FST at identifying local selective sweeps under a wide range of demographic parameters and models of evolution. It also demonstrates that certain branch statistics have improved ability to distinguish local adaptation from other models of natural selection.

evolutionary biology↗

bioRxiv2023

Genomes From 25 Historical Drosophila melanogaster Specimens Illuminate Adaptive and Demographic Changes Across More Than 200 Years of Evolution

The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially profound in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern day genomes, we document evolution across thousands of generations, including time periods that encompass the species initial occupation of northern Europe and an era of rapidly increasing human activity. At the genome-wide level, we find that historical flies from the same time and place show much greater evidence for relatedness than flies from modern collections, and some show evidence of inbreeding as well, potentially reflecting either much smaller local population sizes in the past or else the specific circumstances of the collections. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to accelerated drift) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.

evolutionary biology↗

bioRxiv2017

The Moran coalescent in a discrete one-dimensional spatial model

Among many organisms, offspring are constrained to occur at sites adjacent to their parents. This applies to plants and animals with limited dispersal ability, to colonies of microbes in biofilms, and to other genetically heterogeneous aggregates of cells, such as cancerous tumors. The spatial structure of such populations leads to greater relatedness among proximate individuals while increasing the genetic divergence between distant individuals. In this study, we analyze a Moran coa-lescent in a one-dimensional spatial model where a randomly selected individual dies and is replaced by the progeny of an adjacent neighbor in every generation. We derive a recursive system of equations using the spatial distance among haplotypes as a state variable to compute coalescent probabilities and coalescent times. The coalescent probabilities near the branch termini are smaller than in the unstructured Moran model (except for t = 1, where they are equal), corresponding to longer branch lengths and greater expected pairwise coalescent times. The lower terminal coalescent probabilities result from a spatial separation of lineages, i.e. a coalescent event between a haplotype and its neighbor in one spatial direction at time t cannot co-occur with a coalescent event with a haplotype in the opposite direction at t + 1. The concomitant increased pairwise genetic distance among randomly sampled haplotypes in spatially constrained populations could lead to incorrect inferences of recent diversifying selection or of population bottlenecks when analyzed using an unconstrained coalescent model as a null hypothesis.

genetics↗

bioRxiv2017

Estimation of Pairwise Genetic Distances Under Independent Sampling of Segregating Sites vs. Haplotype Sampling

Genetic distance is a standard measure of variation in populations. When sequencing genomes individually, genetic distances are computed over all pairs of multilocus haplotypes in a sample. However, when next-generation sequencing methods obtain reads from heterogeneous assemblages of genomes (e.g. for microbial samples in a biofilm or cells from a tumor), individual reads are often drawn from different genomes. This means that pairwise genetic distances are calculated across independently sampled sites rather than across haplotype pairs. In this paper, we show that while the expected pairwise distance under whole haplotype sampling (WHS) is the same as with independent locus sampling (ILS), the sample variances of pairwise distance differ and depend on the direction and magnitude of linkage disequilibrium (LD) among polymorphic sites. We derive a weighted LD value that, when positive, predicts higher sample variance in estimated genetic distance for WHS. Weighted LD is positive when on average, the most common alleles at two loci are in positive LD. Using individual-based simulations of an infinite sites model under Fisher-Wright genetic drift, variances of estimated genetic distance are found to be almost always higher under WHS than under ILS, suggesting a reduction in estimation error when sites are sampled independently. We apply these results to haplotype frequencies from a lung cancer tumor to compute weighted LD and the variances in estimated genetic distance under ILS vs. WHS, and find that the the relative magnitudes of variances under WHS vs. ILS are sensitive to sampled allele frequencies.

genetics↗