Arrive, survive and thrive: essential stages in the re-colonization and recovery of zooplankton in urban lakes in Sudbury, Canada

Yan, Norman D.; Bailey, John D.; McGeer, James C.; Manca, Marina; Keller, Wendel; Celis-Salgado, Martha Patricia; Gunn, John M.

doi:10.4081/jlimnol.2016.1226

Cited by 10 publications

(11 citation statements)

References 51 publications

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“…A subset of MA lines in our experiment was exposed to metals (copper and nickel) that are prominent environmental stressors in aquatic habitats (Yan et al 2016). Variation in the mutation rate can arise if cellular stressors due to metals perturb DNA replication, increase DNA damage, or alter DNA repair (Baer et al 2007).…”

Section: Metal Stress Can Increase Large-scale Mutation Ratesmentioning

confidence: 99%

Accelerated rates of large-scale mutations in the presence of copper and nickel

et al. 2018

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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.

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Section: Metal Stress Can Increase Large-scale Mutation Ratesmentioning

confidence: 99%

Accelerated rates of large-scale mutations in the presence of copper and nickel

et al. 2018

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“…A subset of MA lines in our experiment was exposed to metals (copper and 159 nickel) that are prominent environmental stressors in aquatic habitats (Yan et al 2016). 160…”

Section: Metal Stress Can Increase Large-scale Mutation Rates 158mentioning

confidence: 99%

Highly accelerated rates of heritable large-scale mutations under prolonged exposure to a metal mixture of copper and nickel

et al. 2018

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30Mutation rate variation has been under intense investigation for decades. Despite 31 these efforts, little is known about the extent to which environmental stressors 32 accelerate mutation rates and influence the genetic load of populations. Moreover, most 33 studies have focused on point mutations rather than large-scale deletions and 34 duplications (copy number variations or "CNVs"). We estimated mutation rates in 35 Daphnia pulex exposed to low levels of environmental stressors as well as the effect of 36 selection on de novo mutations. We conducted a mutation accumulation (MA) 37 experiment in which selection was minimized, coupled with an experiment in which a 38 population was propagated under competitive conditions in a benign environment. After 39 an average of 103 generations of MA propagation, we sequenced 60 genomes and 40 found significantly accelerated rates of deletions and duplications in MA lines exposed 41 to ecologically relevant concentrations of metals. Whereas control lines had gene 42 deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10 -6 43 per gene per generation), a mixture of nickel and copper increased rates fourfold. The 44 realized mutation rate under selection was reduced to 0.4x that of control MA lines, 45 providing evidence that CNVs contribute to mutational load. Our CNV breakpoint 46 analysis revealed that nonhomologous recombination associated with regions of DNA 47 fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand 48 breaks with higher CNV rates. Our findings suggest that environmental stress, in 49 particular multiple stressors, can have profound effects on large-scale mutation rates 50 and mutational load of populations. 51 52 Introduction 53Germ-line mutations provide the raw material for evolutionary change, but also 54 the genetic variation associated with heritable diseases. Because spontaneous 55 mutations are more often harmful or neutral than beneficial, the accumulation of 56 mutations in the genome has important fitness consequences (Baer et al. 2007; Lynch 57 2010). The frequency at which mutations are generated, as well as the environmental 58 triggers and selective forces influencing mutation rates are therefore fundamental to 59 biology. Accurately measuring the mutation rate, however, poses a considerable 60 challenge due to the infrequent nature of mutations and the action of natural selection, 61 which eliminates many deleterious mutations to bias the sample of observed mutations. 62Mutation accumulation (MA) experiments have been particularly effective for directly 63 measuring mutation rates because repeated bottlenecks reduce the effect of selection, 64 allowing all but the most deleterious mutations to accrue over multiple generations 65 (Halligan and Keightley 2009). The comparison of MA experiments with a population 66 experiencing selection can then be used to infer the fitness consequences of new 67 mutations and their contribution to mutational load, ideally by using large popu...

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“…Following Yan et al (2016), we used the annual persistence of zooplankton species as one parameter to estimate the mechanism underpinning zooplankton recovery. Contrary to Middle and Clearwater lakes in Sudbury , the only other lakes where this metric has been used, annual persistence has changed over time in Lake Orta, suggesting that different processes regulate recovery of richness in these case studies.…”

Section: Discussionmentioning

confidence: 99%

“…Here we used the approach suggested by Yan et al (2016) to calculate rates that colonists arrived, survived and thrived each year from the encountering of species new to our records in the lake, and from annual species persistence metrics. While Yan et al (2016) compared lakes, here we mainly compared different blocks of times and differing groups of zooplankton (i.e., rotifers vs groups of Crustacea).…”

Section: Methodsmentioning

confidence: 99%

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Mechanisms underlying recovery of zooplankton in Lake Orta after liming

2016

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The goal of this study was to improve the understanding of the large-scale mechanisms underlying the recovery of the zooplankton of Lake Orta from historical contamination, following reduced input of ammonia and metals and the subsequent 1989/90 liming intervention. The industrial pollution had been severe and long-lasting (1929-1990 2001 and 2007 (0.55 and 0.72 for rotifers, 0.85 and 0.86 for crustacean, respectively), much higher than in limed lakes in Sudbury, Canada, and in adjacent Lake Maggiore. We hypothesize this could be related to the lack of Cladoceran predators and zooplanktivorous fish in the pelagic waters of Lake Orta.

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Arrive, survive and thrive: essential stages in the re-colonization and recovery of zooplankton in urban lakes in Sudbury, Canada

Abstract: The

Cited by 10 publications

References 51 publications

Accelerated rates of large-scale mutations in the presence of copper and nickel

Accelerated rates of large-scale mutations in the presence of copper and nickel

Highly accelerated rates of heritable large-scale mutations under prolonged exposure to a metal mixture of copper and nickel

Mechanisms underlying recovery of zooplankton in Lake Orta after liming

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