The Power of Natural Variation for Model Organism Biology

Telomere length, sibling competition and development of antioxidant defense in wild house mice

Antioxidants and telomere length are potential biomarkers for individuals' exposure and ability to cope with environmental stressors. However, intraspecific variations in antioxidant alterations due to natural, life cycle related stress, have been rarely estimated. We investigated those changes in wild-derived house mice in a longitudinal study with natural sibling competition as a stressor. Blood was used for telomere length measurements at 8-weeks age and for several selected antioxidants at 8-weeks and 6-months age. Our results show that most of the antioxidants increase during that time, indicating that antioxidant-system continues to develop after early development and sexual maturation. In addition females had higher antioxidant-levels than males. Mice with longer telomeres had also higher superoxide dismutase-activity and more glutathione than mice with shorter telomeres, meaning that long telomeres are associated with better antioxidant defense at maturation and during later life. Sibling competition at early age affected superoxide dismutase-levels at 6-months, but only in females. Females, which were lighter than the average of the litter had low superoxide dismutase -activity in later adulthood, indicating delayed negative effect of sibling competition on antioxidant defense. Our results highlight that sex and developmental stage are crucial in intraspecific comparisons of the antioxidant status and its alterations.

Why do Individuals Differ in Viral Susceptibility? A Story Told by Model Organisms

Viral susceptibility and disease progression is determined by host genetic variation that underlies individual differences. Genetic polymorphisms that affect the phenotype upon infection have been well-studied for only a few viruses, such as HIV-1 and Hepatitis C virus. However, even for well-studied viruses the genetic basis of individual susceptibility differences remains elusive. Investigating the effect of causal polymorphisms in humans is complicated, because genetic methods to detect rare or small-effect polymorphisms are limited and genetic manipulation is not possible in human populations. Model organisms have proven a powerful experimental platform to identify and characterize polymorphisms that underlie natural variations in viral susceptibility using quantitative genetic tools. We summarize and compare the genetic tools available in three main model organisms, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, and illustrate how these tools can be applied to detect polymorphisms that determine the viral susceptibility. Finally, we analyse how candidate polymorphisms from model organisms can be used to shed light on the underlying mechanism of individual variation. Insights in causal polymorphisms and mechanisms underlying individual differences in viral susceptibility in model organisms likely provide a better understanding in humans.

The background puzzle: how identical mutations in the same gene lead to different disease symptoms

Identical disease-causing mutations can lead to different symptoms in different people. The reason for this has been a puzzling problem for geneticists. Differential penetrance and expressivity of mutations has been observed within individuals with different and similar genetic backgrounds. Attempts have been made to uncover the underlying mechanisms that determine differential phenotypic effects of identical mutations through studies of model organisms. From these studies evidence is accumulating that to understand disease mechanism or predict disease prevalence, an understanding of the influence of genetic background is as important as the putative disease-causing mutations of relatively large effect. This review highlights current insights into phenotypic variation due to gene interactions, epigenetics and stochasticity in model organisms, and discusses their importance for understanding the mutational effect on disease symptoms.

Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis

Most of the biological understanding of mechanisms underlying coronary artery disease (CAD) derives from studies of mouse models. The identification of multiple CAD loci and strong candidate genes in large human genome-wide association studies (GWASs) presented an opportunity to examine the relevance of mouse models for the human disease. We comprehensively reviewed the mouse literature, including 827 literature-derived genes, and compared it to human data. First, we observed striking concordance of risk factors for atherosclerosis in mice and humans. Second, there was highly significant overlap of mouse genes with human genes identified by GWASs. In particular, of the 46 genes with strong association signals in CAD GWASs that were studied in mouse models, all but one exhibited consistent effects on atherosclerosis-related phenotypes. Third, we compared 178 CAD-associated pathways derived from human GWASs with 263 from mouse studies and observed that the majority were consistent between the species.

Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation

The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.

Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant

Studying the molecular consequences of rare genetic variants has the potential to identify novel and hitherto uncharacterized pathways causally contributing to phenotypic variation. Here, we characterize the functional consequences of a rare coding variant of TAO3, previously reported to contribute significantly to sporulation efficiency variation in Saccharomyces cerevisiae. During mitosis, the common TAO3 allele interacts with CBK1—a conserved NDR kinase. Both TAO3 and CBK1 are components of the RAM signaling network that regulates cell separation and polarization during mitosis. We demonstrate that the role of the rare allele TAO3(4477C) in meiosis is distinct from its role in mitosis by being independent of ACE2—a RAM network target gene. By quantitatively measuring cell morphological dynamics, and expressing the TAO3(4477C) allele conditionally during sporulation, we show that TAO3 has an early role in meiosis. This early role of TAO3 coincides with entry of cells into meiotic division. Time-resolved transcriptome analyses during early sporulation identified regulators of carbon and lipid metabolic pathways as candidate mediators. We show experimentally that, during sporulation, the TAO3(4477C) allele interacts genetically with ERT1 and PIP2, regulators of the tricarboxylic acid cycle and gluconeogenesis metabolic pathways, respectively. We thus uncover a meiotic functional role for TAO3, and identify ERT1 and PIP2 as novel regulators of sporulation efficiency. Our results demonstrate that studying the causal effects of genetic variation on the underlying molecular network has the potential to provide a more extensive understanding of the pathways driving a complex trait.

Cryptic Genetic Variation in Evolutionary Developmental Genetics

Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution

In our prior work by Hose et al., we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of S. cerevisiae. We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10–30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose et al., we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres et al. refutes our prior work. Here, we provide a response to Torres et al., along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of S. cerevisiae that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures.

DOI:http://dx.doi.org/10.7554/eLife.14409.001

Cells package their DNA into structures called chromosomes. Sometimes when a cell divides, it fails to allocate the right number of chromosomes to each new cell and so they end up with too many or too few chromosomes. The extra copies of the genes on an additional chromosome can be harmful to the cells, because the levels of the proteins encoded by those genes may rise abnormally.

Some organisms counteract the harmful effect of having additional chromosomes through a process called dosage compensation. Proteins are produced using genetic information via two steps: first a gene’s DNA sequence is copied into a molecule of RNA, which is then translated into a protein. Dosage compensation can inactivate single genes or whole chromosomes via various means to ensure that the levels of RNA expressed remain normal, even in the presence of extra genes.

In 2015, researchers from the University of Wisconsin-Madison reported that dosage compensation occurs in wild strains of budding yeast and effectively protects against the harmful effects of having extra chromosomes. However, these findings conflicted with earlier studies of laboratory strains of this yeast, and earlier in 2016, other researchers re-analysed the previous study’s data and challenged its findings.

Now, Gasch et al. – who conducted the work reported in 2015 – provide additional controls and computational experiments that support their original analysis. The latest analysis confirmed that the genes identified in the first study are indeed commonly duplicated in wild yeast populations, yet the expression of these genes remains controlled. This is consistent with a model of dosage compensation, for at least some of duplicated genes.

Gasch et al. believe that part of the difference in interpretation of the data relates to perspective. The challenging researchers tested to see if there was a mechanism of dosage compensation that acted across entire chromosomes, which is known to occur in the case of sex chromosomes in mammals. Gasch et al. on the other hand took a different approach and looked to identify effects at the level of individual genes.

Together, the analyses show that, while there is no evidence for a widespread mechanism, the expression of a select set of genes in wild yeast is consistent with gene-specific dosage compensation. Future work will now undoubtedly test the mechanisms behind the gene-specific effects, and explore why wild yeast strains are more tolerant to extra chromosomes than laboratory strains.

DOI:http://dx.doi.org/10.7554/eLife.14409.002