ORCID Profile
0000-0002-0274-4359
Current Organisation
University of Calgary
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Publisher: Springer Science and Business Media LLC
Date: 04-04-2016
Publisher: Cold Spring Harbor Laboratory
Date: 28-11-2018
Abstract: Mutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10 −6 per gene per generation), the presence of nickel and copper increased these rates fourfold. The realized mutation rate under selection was reduced to 0.4× that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of multicellular organisms.
Publisher: Wiley
Date: 24-05-2021
DOI: 10.1111/MEC.15946
Abstract: A fundamental aspect of evolutionary biology is natural selection on trait variation. Classically, selection has been estimated primarily on external morphological traits such as beak size and coloration, or on easily assayable physiological traits such as heat‐tolerance. As technologies and methods improved, evolutionary biologists began examining selection on molecular traits such as protein sequences and cellular processes. In a From the Cover paper in this issue of Molecular Ecology , Ahmad et al . continue this trend by estimating parasite‐driven selection on the molecular trait of transcript abundance in a wild population of brown trout ( Salmo trutta ) by uniquely combining a mark–recapture experimental design with noninvasive RNA s ling. Using transcript abundance to estimate selection allows for many different traits (each unique gene's transcript counts) to be tested in a single experiment, providing the opportunity to examine trends in selection. Ahmad et al . find directional selection strength on transcript counts is generally low and normally distributed. Surprisingly, transcripts under nonlinear selection showed a disruptive selection bias, contradicting previous comparative studies and theoretical work. This highlights the importance of within‐generation selection studies, where mechanisms may differ from longer time frames. Their paper also highlights the benefits of a cost‐effective 3′ RNA sequencing technique to measure gene expression.
Publisher: Oxford University Press (OUP)
Date: 2019
Abstract: In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.
Publisher: Wiley
Date: 03-2016
DOI: 10.1111/MEC.13547
Abstract: Genetic ersity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more erse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite ersity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic ersity and effective population size (N(e) < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.
Publisher: Public Library of Science (PLoS)
Date: 17-12-2013
Publisher: Public Library of Science (PLoS)
Date: 24-11-2009
Publisher: Copernicus GmbH
Date: 23-10-2012
Abstract: Abstract. Dissolved inorganic carbon (DIC), gaseous CO2 and alkalinity fluxes from intertidal sediments were investigated during periods of exposure and inundation, using laboratory core incubations, previously published field data and reactive transport model simulations. In the incubations and previous field data, it was found that during periods of alkalinity production (attributed to the accumulation of reduced sulfur species within the sediment), the flux of DIC out of the sediment was greater during inundation than the gaseous CO2 flux during exposure by a factor of up to 1.8. This finding was supported by computational simulations which indicated that large amounts of sulfate reduction and reduced sulfur burial (FeS) induce an alkalinity flux from the sediment during high tide conditions. Model simulations also found that the amount of reactive Fe in the sediment was a major driver of net alkalinity production. Our finding that CO2 fluxes can be significantly lower than total metabolism during exposure has implications for how total metabolism is quantified on tidal flats.
Publisher: Wiley
Date: 30-07-2018
Abstract: Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability validation was carried out with 100 additional Eurasian lynx s les not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of in iduals and in population genetic structure inference (including the assignment of in iduals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
Publisher: Oxford University Press (OUP)
Date: 23-01-2014
DOI: 10.1111/BIJ.12224
Publisher: Public Library of Science (PLoS)
Date: 09-12-2015
Publisher: The Royal Society
Date: 07-12-2022
Abstract: Billions of salmonids are produced annually by artificial reproduction for harvest and conservation. Morphologically, behaviourally and physiologically these fish differ from wild-born fish, including in ways consistent with domestication. Unlike most studied domesticates, which erged from wild ancestors millennia ago, salmonids offer a tractable model for early-stage domestication. Here, we review a fundamental mechanism for domestication-driven differences in early-stage domestication, differentially expressed genes (DEGs), in salmonids. We found 34 publications examining DEGs under domestication driven by environment and genotype, covering six species, over a range of life-history stages and tissues. Three trends emerged. First, domesticated genotypes have increased expression of growth hormone and related metabolic genes, with differences magnified under artificial environments with increased food. Regulatory consequences of these DEGs potentially drive overall DEG patterns. Second, immune genes are often DEGs under domestication and not simply owing to release from growth-immune trade-offs under increased food. Third, domesticated genotypes exhibit reduced gene expression plasticity, with plasticity further reduced in low-complexity environments typical of production systems. Recommendations for experimental design improvements, coupled with tissue-specific expression and emerging analytical approaches for DEGs present tractable avenues to understand the evolution of domestication in salmonids and other species.
Location: No location found
No related grants have been discovered for James Bull.