Biology subjects

Hemker, J. A.

Publications and source records attributed to Hemker, J. A..

4 recordsLinked to original sources

bioRxiv2025

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin

The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the effect of the length of long-reads on automated variant callers is not well understood, especially for non-human species. Here we show that only ultra-long long-reads, with read N50s greater than 50kb, are capable of accurately calling structural variants of any size in Drosophila melanogaster euchromatin. We used Oxford Nanopore Technologies to long-read sequence eight, inbred D. melanogaster strains to extremely high coverage (mean 238x), and we then downsampled the reads to create read pools of different length distributions. We assembled genomes from these different read-length pools and used both read-based and assembly-based structural variant callers to call variants in each strain before merging the calls into population-level datasets. We manually validated over 2,300 putative structural variants to assess the accuracy of the variant calls across the different read-length distributions and to determine the cause and rates of false positive errors. We found that more than half of all structural-variant-calling errors stem from misaligned reads that contain mobile elements or are located in repetitive and complex regions. Overall, our results show that long reads need to be at least three times longer than the repetitive and mobile elements found in the genome in order to accurately call structural variants at the population level.

genomics↗

bioRxiv2024

Pervasive fitness trade-offs revealed by rapid adaption in large experimental populations of Drosophila melanogaster

Trade-offs are an inherent feature of organismal biology that are expected play a fundamental role in the evolution of natural populations. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of Drosophila melanogaster to directly measure the manifestation of trade-offs in response to fluctuating selection on ecological timescales. Specifically, we first conducted a lab-based selection experiment to quantify a genome-wide signal of antagonistic pleiotropy elicited in response to shifting population densities and associated with reproduction and stress tolerance selection. In doing so, we identified a putative role of two cosmopolitan inversions in these trade-offs. We then conducted an independent experiment to show that a simple manipulation of increasing population density under controlled lab-based conditions identified loci that are relevant to selection during population expansion and collapse in a complex, semi-natural setting. In concert, our results reveal how adaptation in complex, natural environments can be coarse-grained in such a manner to drive repeatable and predictable patterns of genomic variation, and further add credence to models positing a role of generic fitness trade-offs in the maintenance of variation in natural populations.

evolutionary biology↗

bioRxiv2024

Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming

Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in acute heat tolerance, which phenotypically trades off with tolerance to prolonged heat exposure. A simple evolutionary model based on our data shows that the estimated maximum rate of evolutionary adaptation in mosquito heat tolerance typically exceeds that of projected climate warming under idealized conditions. Our findings indicate that natural mosquito populations may have the potential to track projected warming via genetic adaptation. Prior climate-based projections may thus underestimate the range of mosquito and mosquito-borne disease distributions under future climate conditions. Significance StatementGlobal change may have profound impacts on the distribution of mosquito-borne diseases, which collectively cause nearly one million deaths each year. Accurately predicting these impacts is critical for disease control preparedness, and will depend, in part, on whether mosquitoes can adapt to warming--a key open question. Using experimental and genomic data from a relative of major vector species that already experiences a wide thermal gradient, we find that natural mosquito populations have high levels of genetically-based variation in heat tolerance that could enable adaptation on pace with warming. Incorporating the potential for adaptive responses may therefore be necessary for accurate predictions of mosquito-borne disease distributions under warming, which is critical for preparing mosquito control interventions.

evolutionary biology↗

bioRxiv2023

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

evolutionary biology↗