Biology subjects

Ness, R.

Publications and source records attributed to Ness, R..

8 recordsLinked to original sources

bioRxiv2026

Experimental evolution of Chlamydomonas reinhardtii in fluctuating versus constant temperature stress

Natural environmental variations are normal occurrences, however human-driven climatic changes continue to exacerbate the magnitude of these variations. This pushes organisms to their physiological limits where they must adapt or face extinction. The potential for organisms to adapt is of concern; however, the presence of fluctuating regimes to incorporate natural environmental variation is occasionally considered. Here, we investigate the standing variation in thermal optima of ten Chlamydomonas reinhardtii strains along a latitudinal gradient and determine whether adaptation to its temperature extremes is possible via long-term evolution. Despite their broad geographic origins, C. reinhardtii strains exhibited a similar thermal optimum (31.2{degrees}C - 32.4{degrees}C). We then evolved one strain for [~]900 generations under cold, hot and fluctuating growth conditions. Those grown in constant environmental conditions became specialized to their environment of 20{degrees}C or 37{degrees}C, whereas those evolved in a fluctuating regime performed comparably to the specialists, suggesting no long-term cost of adaptation via a fluctuating regime. We also found no differences in the amount of variation between fluctuating and constant conditions, suggesting similar amounts of divergence between conditions. Overall, despite our predictions that a fluctuating regime would hinder adaptation, we found that these lineages were able to adapt to this variable environment.

evolutionary biology↗

bioRxiv2024

Signatures of selective sweeps in urban and rural white clover populations

Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and mul{-} tifarious in rural habitats, and whether selection differs in either strength or its targets between habitats is rarely considered. Despite numerous examples of phe{-} notypic differentiation between urban and rural populations, we still lack an un{-} derstanding of the genes enabling adaptation to these contrasting habitats. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada and used these data to identify urban and rural signatures of positive selection. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/ development in both urban and rural populations, and clinal change in allele frequencies at SNPs within these regions. Patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete and our strongest signals of selective sweeps overlap known large-effect structural variants. These results highlight how both urban and rural habitats are driving ongoing selection in Toronto white clover populations, and mo{-} tivate future work disentangling the genetic architecture of ecologically important phenotypes underlying adaptation to contemporary anthropogenic habitats.

evolutionary biology↗

bioRxiv2023

Comparing the predictors of mutability among healthy human tissues inferred from mutations in single cell genome data

Studying mutation in healthy somatic tissues is key for understanding the genesis of cancer and other genetic diseases. Mutation rate varies from site to site in the human genome by up to 100-fold and is influenced by numerous epigenetic and genetic factors including GC content, trinucleotide sequence context, and DNAse accessibility. These factors influence mutation at both local and regional scales and are often interrelated with one another, meaning that predicting mutability or uncovering its drivers requires modelling multiple factors and scales simultaneously. Historically, most investigations have focused either on analyzing the local sequence scale through triplet signatures or on examining the impact of epigenetic processes at larger scales, but not both concurrently. Additionally, sequencing technology limitations have restricted analyses of healthy mutations to coding regions (RNA-seq) or to those that have been influenced by selection (e.g. bulk samples from cancer tissue). Here we leverage single cell mutations and present a comprehensive analysis of epigenetic and genetic factors at multiple scales in the germline and three healthy somatic tissues. We create models that predict mutability with on average 2% error, and find up to 63-fold variation among sites within the same tissue. We observe varying degrees of similarity between tissues: the mutability of genomic positions was 93.4% similar between liver and germline tissues, but sites in germline and skin were only 85.9% similar. We observe both universal and tissue-specific mutagenic processes in healthy tissues, with implications for understanding the maintenance of germline versus soma and the mechanisms underlying early tumorigenesis. SummaryMutations in healthy tissues can reveal how genetic diseases originate. In this study, we explore how mutation rates vary across the human genome and what influences these variations. We leverage advanced single-cell analysis to analyze genetic and epigenetic factors in germline and three healthy tissues. We trained models that exhibit high accuracy and discover large variation within the same tissue. We also identified differences in mutability between tissues, suggesting both universal and tissue-specific mutation patterns with implications for understanding oncogenesis.

genetics↗

bioRxiv2023

Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repens L., Fabaceae)

BackgroundWhite clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world, and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. FindingsHere, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively. ConclusionsWe provide two white clover genome assemblies as part of this project: (1) a haplotype-resolved, chromosome-level assembly, and (2) a functionally annotated haploid mapping assembly. These assemblies place white clover among the best sequenced legumes to date, and one of the best assemblies for a plant of recent polyploid origins. This work promises to facilitate ongoing and future work in agricultural and evolutionary genetics in this agronomically and ecologically important species.

genomics↗

bioRxiv2022

The effects of de novo mutation on gene expression and the consequences for fitness in Chlamydomonas reinhardtii.

Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from two independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only one gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing direct evidence of the deleterious effects of perturbing gene expression.

genomics↗

bioRxiv2021

How sequence context-dependent mutability drives mutation rate variation in the genome

The rate of mutations varies >100-fold across the genome, altering the rate of evolution, and susceptibility to genetic diseases. The strongest predictor of mutation rate is the sequence itself, varying 75-fold between trinucleotides. The fact that DNA sequence drives its own mutation rate raises a simple but important prediction; highly mutable sequences will mutate more frequently and eliminate themselves in favour of sequences with lower mutability, leading to a lower equilibrium mutation rate. However, purifying selection constrains changes in mutable sequences, causing higher rates of mutation. We conduct a simulation using real human mutation data to test if (1) DNA evolves to a low equilibrium mutation rate and (2) purifying selection causes a higher equilibrium mutation rate in the genomes most important regions. We explore how this simple process affects sequence evolution in the genome, and discuss the implications for modelling evolution and susceptibility to DNA damage.

evolutionary biology↗

bioRxiv2019

The effects of losing sex on the molecular evolution of plant defense

It is hypothesized that the loss of sexual reproduction and reduced recombination rates decrease the ability for hosts to evolve in response to selection by parasites. Using transcriptomes from 32 species, we test whether repeated losses of sex in the plant genus Oenothera has resulted in changes to the evolution of defense genes against herbivores and pathogens. To achieve this, the function of 2,431 Oenothera orthologous genes was determined based on GO annotations from Arabidopsis thaliana. Phylogenetic Analysis by Maximum Likelihood (PAML) was then used to examine how the patterns of molecular evolution in 721 defense and 1,710 non-defense genes differ between sexual (16 spp.) and asexual (16 spp.) taxa. We test whether the relative rates of nonsynonymous to synonymous substitutions ({omega} = dN/dS) in proteins with defensive function were higher in lineages with sexual reproduction ({omega}sexual> {omega}a-sexual), and we asked if such patterns were exclusive for defense genes or not. We detected variability in the rate of amino acid replacements of proteins in >50% of genes and positive selection on 3% of the genes examined. Nevertheless, our results clearly show that on average, signatures of positive and purifying selection on defense and non-defense genes are similar and only a small number of specific genes related to plant immune function may be affected by a loss of sex.

evolutionary biology↗

bioRxiv2019

Direct inference of the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

Spontaneous mutations are the source of new genetic variation and are thus central to the evolutionary process. In molecular evolution and quantitative genetics, the nature of genetic variation depends critically on the distribution of fitness effects (DFE) of mutations. Spontaneous mutation accumulation (MA) experiments have been the principal approach for investigating the overall rate of occurrence and cumulative effect of mutations, but have not allowed the effects of individual mutations to be studied directly. Here, we crossed MA lines of the green alga Chlamydomonas reinhardtii with its unmutated ancestral strain to create haploid recombinant lines, each carrying an average of 50% of the accumulated mutations in a variety of combinations. With the aid of the genome sequences of the MA lines, we inferred the genotypes of the mutations, assayed their growth rate as a measure of fitness, and inferred the DFE using a novel Bayesian mixture model that allows the effects of individual mutations to be estimated. We infer that the DFE is highly leptokurtic (L-shaped), and that a high proportion of mutations increase fitness in the laboratory environment. The inferred distribution of effects for deleterious mutations is consistent with a strong role for nearly neutral evolution. Specifically, such a distribution predicts that nucleotide variation and genetic variation for quantitative traits will be insensitive to change in the effective population size.

evolutionary biology↗