Biology subjects

Schaack, S.

Publications and source records attributed to Schaack, S..

8 recordsLinked to original sources

bioRxiv2026

The effects of estrogen exposure on survival, growth, and fecundity of Daphnia magna

High concentrations of steroidal hormone compounds are a growing source of concern for environmental pollution in aquatic ecosystems. In this study, we examine the effects of two estrogenic compounds (estriol and 17-ethinylestradiol) on fitness traits in the aquatic microcrustacean, Daphnia magna, a key bioindicator species for toxicology studies. The impacts were compared of two forms representing a natural and synthetic estrogenic compound. Growth and reproduction traits were assayed by exposing Daphnia to each estrogen type at four concentrations reflecting potential environmental exposure conditions up to acute toxicity levels (ranging from 0.1 - 50 {micro}g/L). Assaying the effects at a variety of concentrations is important given that it is known that hormone exposures can often result in non-monotonic responses. Both forms of estrogen impact a subset of the traits assessed, in some cases leading to beneficial changes and others causing harm. Estriol, the naturally-occurring estrogen, and EE2, the synthetic version, at high doses shift fitness traits in opposite directions such as adult growth rate as do at low doses for fecundity. In conclusion, our results support the need to assay a wide array of traits using multiple forms of steroidal hormones at a range of doses in order to assess non-monotonic patterns and their impact on an organismal fitness. In particular, assays that extend beyond the conventional measurements of lethality during acute exposure windows will be essential for understanding the impact of increased levels of hormone pollution on aquatic organisms and ecosystem health.

pharmacology and toxicology↗

bioRxiv2022

Estimating somatic mutation rates by Duplex Sequencing in non-model organisms: Daphnia magna as a case study

Somatic mutations are evolutionarily important as determinants of individual organismal fitness, as well as being a focus of clinical research on age-related disease, such as cancer. Identifying somatic mutations and quantifying mutation rates, however, is extremely challenging and genome-wide somatic mutation rates have only been reported for a few model organisms. Here, we describe the application of Duplex Sequencing on bottlenecked WGS libraries to quantify genome-wide somatic base substitution rates in Daphnia magna. Daphnia, historically an ecological model system, has more recently been the focus of mutation studies, in part because of its high germline mutation rates. Using our protocol and pipeline, we estimate a somatic mutation rate of 2.14 x 10-7 substitutions per site (in a genotype where the germline rate is 3.60 x 10-9 substitutions per site per generation). To obtain this estimate, we tested multiple dilution levels to maximize sequencing efficiency, and developed bioinformatic filters needed to minimize false positives when a high quality reference genome is not available. In addition to laying the groundwork for estimating genotypic variation in rates of somatic mutations within D. magna, we provide a framework for quantifying somatic mutations in other non-model systems, and also highlight recent innovations to single molecule sequencing that will help to further refine such estimates.

bioinformatics↗

bioRxiv2021

Heat shock protein gene expression is higher and more variable with thermal stress and mutation accumulation in Daphnia

Understanding the genetic architecture of the stress response and its ability to evolve in response to different stressors requires an integrative approach. Here we quantify gene expression changes in response to two stressors associated with global climate change and habitat loss--heat shock and mutation accumulation. We measure expression levels for two Heat Shock Proteins (HSP90 and HSP60)--members of an important family of conserved molecular chaperones that have been shown to play numerous roles in the cell. While HSP90 assists with protein folding, stabilization, and degradation throughout the cell, HSP60 primarily localizes to the mitochondria and mediates de novo folding and stress-induced refolding of proteins. We perform these assays in Daphnia magna originally collected from multiple genotypes and populations along a latitudinal gradient, which differ in their annual mean, maximum, and range of temperatures. We find significant differences in overall expression between loci (10-fold), in response to thermal stress (~6x increase) and with mutation accumulation (~4x increase). Importantly, stressors interact synergistically to increase gene expression levels when more than one is applied (increasing, on average, >20x). While there is no evidence for differences among the three populations assayed, individual genotypes vary considerably in HSP90 expression. Overall, our results support previous proposals that HSP90 may act as an important buffer against not only heat, but also mutation, and expands this hypothesis to include another member of the gene family acting in a different domain of the cell.

genetics↗

bioRxiv2020

Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

Transposable elements (TEs) represent a large and dynamic portion of most eukaryotic genomes, yet little is known about their mutation rates or the correspondence between rates and long-term patterns of accrual. We compare TE activity over long and short time periods by quantifying TE profiles and mutation rates (with and without minimizing selection) among 9 genotypes from three populations of Daphnia magna sampled along a latitudinal gradient. The patterns of genome-wide variation observed in nature mirror direct estimates of rates and spectra observed in a multi-year laboratory mutation accumulation experiment, where net rates range from -11.98 to 12.79 x 10-5 per copy per generation across genotypes. Overall, gains outnumber losses and both types of events are highly deleterious based on comparing lines with and without selection minimized. The rate and spectrum of TE mutations vary widely among genotypes and across TE families/types, even within the same population. We compare TE mutation rates to previously published rates of base substitution, microsatellite mutation, and gene conversion for the same genotypes, and show a correlation only with the latter. Our study provides strong evidence for the notion that TEs represent a highly mutagenic force in the genome. Furthermore, the variation we observe underscores the need to expand the repertoire of mutations studied to include a wider array of mutation types with different underlying mechanisms in order to better understand the evolution of the mutation rate and the ways in which genetic variation is generated genome wide.

genomics↗

bioRxiv2020

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary lifecycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. These high-quality genomic resources capture natural genetic and phenotypic variation across bumblebees, offering new opportunities to advance our understanding of their remarkable ecological success and to identify and manage current and future threats.

genomics↗

bioRxiv2019

Genome-wide identification of accessible chromatin regions in bumblebee (Bombus terrestris) by ATAC-seq

Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To date, while the protein-coding sequences of bumblebees have been extensively annotated, regulatory elements, such as promoters and enhancers, have been poorly annotated in the bumblebee genome. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) for B. terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and the accessible chromatin regions of bumblebee were identified and characterized by using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology. The ATAC-seq data generated in this study has been deposited in NCBI GEO (accession#: GSE131063).

genomics↗

bioRxiv2019

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and are often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species and have rarely been compared across genotypes and populations and intraspecific differences in overall microsatellite content have rarely been explored. To investigate the accumulation of microsatellite DNA over long-and short-time periods, we quantified the abundance and genome-wide mutation rates in whole-genome sequences of 47 mutation accumulation (MA) lines and 12 non-MA lines derived from six different genotypes of the crustacean Daphnia magna collected from three populations (Finland, Germany, and Israel). Each genotype possessed a distinctive microsatellite profile and clustered according to their population of origin. During the period of mutation accumulation, we observed very high microsatellite mutation rates (a net change of -0.19 to 0.33 per copy per generation), which surpass rates reported from a closely-related congener, D. pulex, by an order of magnitude. Rates vary between microsatellite motifs and among genotypes, with those starting with high microsatellite content exhibiting greater losses and those with low microsatellite content exhibiting greater gains. Our results show that microsatellite mutation rates depend both on characteristics of the microsatellites and the genomic background. These context-dependent mutation dynamics may, in conjunction with other evolutionary forces that may differ among populations, explain the differential accumulation of repeat content in the genome over long time periods.

genomics↗

bioRxiv2017

Tandem repeats contribute to coding sequence variation in bumblebees (Hymenoptera: Apidae)

Tandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potential adaptation of bumblebees to diverse habitats are largely unknown. In the present study, we investigate how TRs contribute to genetic variation in bumblebees, thus potentially facilitating adaptation. We identified 26,595 TRs in the buff-tailed bumblebee (Bombus terrestris) genome, 66.7% of which reside in genic regions. We also compared TRs found in B. terrestris with those present in the whole genome sequence of a congener, B. impatiens. We found that a total of 1,137 TRs were variable in length between the two sequenced bumblebee species, and further analysis reveals that 101 of them are located within coding regions. The 101 TRs were responsible for coding sequence variation and corresponded to protein sequence length variation between the two bumblebee species. The variability of identified TRs in coding regions between bumblebees was confirmed by PCR amplification of a subset of loci. Functional classification of bumblebee genes where coding sequences include variable-length TRs suggests that a majority of these genes are related to transcriptional regulation. Our results show that TRs contribute to coding sequence variation in bumblebees and TRs may facilitate the adaptation of bumblebees through diversifying proteins involved in controlling gene expression.

genomics↗