scholarly journals The distribution of bacterial doubling times in the wild

2018 ◽  
Vol 285 (1880) ◽  
pp. 20180789 ◽  
Author(s):  
Beth Gibson ◽  
Daniel J. Wilson ◽  
Edward Feil ◽  
Adam Eyre-Walker
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
Generation Time ◽  
Doubling Time ◽  
Mutation Rates ◽  
Substantial Fraction ◽  
Rate Estimate ◽  
In The Wild ◽  
Doubling Times ◽  
Mutation Rate Estimate

Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.

scholarly journals The Distribution of Bacterial Doubling Times in the Wild

2017 ◽  
Author(s):  
Beth Gibson ◽  
Daniel Wilson ◽  
Edward Feil ◽  
Adam Eyre-Walker
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
Generation Time ◽  
Doubling Time ◽  
Mutation Rates ◽  
Substantial Fraction ◽  
Rate Estimate ◽  
In The Wild ◽  
Doubling Times ◽  
Mutation Rate Estimate

AbstractGeneration time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT), has been estimated for many bacteria in the lab, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the lab. If we assume the mutation rate per generation is the same in the wild and in the lab, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for four species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the lab, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.

scholarly journals Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate

2018 ◽  
Author(s):  
Søren Besenbacher ◽  
Christina Hvilsom ◽  
Tomas Marques-Bonet ◽  
Thomas Mailund ◽  
Mikkel Heide Schierup
Keyword(s):  
Linear Relationship ◽  
Mutation Rate ◽  
Fossil Record ◽  
Great Apes ◽  
Mutation Rates ◽  
Rate Estimate ◽  
The Past ◽  
Divergence Estimates ◽  
Human Mutation ◽  
Mutation Rate Estimate

AbstractThe human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother. The yearly trio-based mutation rate estimate of ~0.43×10−9 is markedly lower than prior indirect estimates of ~1×10−9 per year from phylogenetic comparisons of the great apes. This suggests either a slowdown over the past 10 million years or an inaccurate interpretation of the fossil record. Here we use sequencing of chimpanzee, gorilla and orangutan trios and find that each species has higher estimated mutation rates per year by factors of 1.67+/− 0.22, 1.54+/− 0.2 and 1.84+/− 0.19, respectively. These estimates suggest a very recent and appreciable slowdown in human mutation rate, and, if extrapolated over the great apes phylogeny, yields divergence estimates much more in line with the fossil record and the biogeography.

scholarly journals A review of the life cycles and life-history adaptations of pelagic tunicates to environmental conditions

2011 ◽  
Vol 69 (3) ◽  
pp. 358-369 ◽  
Author(s):  
Don Deibel ◽  
Ben Lowen
Keyword(s):  
Life History ◽  
Environmental Conditions ◽  
Generation Time ◽  
Egg Production ◽  
Food Concentration ◽  
Life Cycles ◽  
Population Doubling ◽  
Event Scale ◽  
Generation Times ◽  
Doubling Times

Abstract Deibel, D., and Lowen, B. 2012. A review of the life cycles and life-history adaptations of pelagic tunicates to environmental conditions. – ICES Journal of Marine Science, 69: 358–369. Phylogeny, life cycles, and life-history adaptations of pelagic tunicates to temperature and food concentration are reviewed. Using literature data on lifetime egg production and generation time of appendicularians, salps, and doliolids, rmax, the maximum rate of lifetime reproductive fitness, is calculated as a common metric of adaptation to environmental conditions. The rmax values are high for all three groups, ranging from ∼0.1 to 1.9 d−1, so population doubling times range from ∼8 h to 1 week. These high values of rmax are attributable primarily to short generation times, ranging from 2 to 50 d. Clearly, pelagic tunicates are adapted to event-scale (i.e. days to weeks) rather than seasonal-scale changes in environmental conditions. Although they are not closely related phylogenetically, all three groups have a unique life-history adaptation promoting high lifetime fitness. Appendicularians have late oocyte selection, salps are viviparous, and doliolids possess a polymorphic asexual phase. There has been little research on hermaphroditic appendicularians, on large oceanic salps, and on doliolids generally. Research is needed on factors regulating generation time, on the heritability of life-history traits, and on age- and size-specific rates of mortality.

scholarly journals Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171721 ◽  
Author(s):  
David Berger ◽  
Josefine Stångberg ◽  
Karl Grieshop ◽  
Ivain Martinossi-Allibert ◽  
Göran Arnqvist
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
Climate Warming ◽  
Cost Of Reproduction ◽  
Mutation Rates ◽  
Induced Mutations ◽  
Evolutionary Processes ◽  
Trade Offs ◽  
Simulated Climate ◽  
Multicellular Organisms

Mutation has a fundamental influence over evolutionary processes, but how evolutionary processes shape mutation rate remains less clear. In asexual unicellular organism, increased mutation rates have been observed in stressful environments and the reigning paradigm ascribes this increase to selection for evolvability. However, this explanation does not apply in sexually reproducing species, where little is known about how the environment affects mutation rate. Here we challenged experimental lines of seed beetle, evolved at ancestral temperature or under simulated climate warming, to repair induced mutations at ancestral and stressful temperature. Results show that temperature stress causes individuals to pass on a greater mutation load to their grand-offspring. This suggests that stress-induced mutation rates, in unicellular and multicellular organisms alike, can result from compromised germline DNA repair in low condition individuals. Moreover, lines adapted to simulated climate warming had evolved increased longevity at the cost of reproduction, and this allocation decision improved germline repair. These results suggest that mutation rates can be modulated by resource allocation trade-offs encompassing life-history traits and the germline and have important implications for rates of adaptation and extinction as well as our understanding of genetic diversity in multicellular organisms.

scholarly journals Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed

2013 ◽  
Vol 280 (1750) ◽  
pp. 20122047 ◽  
Author(s):  
Roland R. Regoes ◽  
Steven Hamblin ◽  
Mark M. Tanaka
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
High Rate ◽  
Mutation Rates ◽  
Viral Dynamics ◽  
Trade Off ◽  
Trade Offs ◽  
Very High ◽  
Host Death

Many viruses, particularly RNA viruses, mutate at a very high rate per genome per replication. One possible explanation is that high mutation rates are selected to meet the challenge of fluctuating environments, including the host immune response. Alternatively, recent studies argue that viruses evolve under a trade-off between replication speed and fidelity such that fast replication is selected, and, along with it, high mutation rates. Here, in addition to these factors, we consider the role of viral life-history properties: namely, the within-host dynamics of viruses resulting from their interaction with the host. We develop mathematical models incorporating factors occurring within and between hosts, including deleterious and advantageous mutations, host death owing to virulence and clearance of viruses by the host. Beneficial mutations confer both a within-host and a transmission advantage. First, we find that advantageous mutations have only a weak effect on the optimal genomic mutation rate. Second, viral life-history properties have a large effect on the mutation rate. Third, when the speed–fidelity trade-off is included, there can be two locally optimal mutation rates. Our analysis provides a way to consider how life-history properties combine with biochemical trade-offs to shape mutation rates.

Prey tell: what quillback rockfish early life history traits reveal about their survival in encounters with juvenile coho salmon

2020 ◽  
Vol 650 ◽  
pp. 7-18 ◽  
Author(s):  
HW Fennie ◽  
S Sponaugle ◽  
EA Daly ◽  
RD Brodeur
Keyword(s):  
Life History ◽  
Early Life ◽  
Life History Traits ◽  
Direct Evidence ◽  
Coho Salmon ◽  
Larval Fish ◽  
Early Life History ◽  
In The Wild ◽  
Otolith Microstructure Analysis ◽  
Pelagic Juvenile

Predation is a major source of mortality in the early life stages of fishes and a driving force in shaping fish populations. Theoretical, modeling, and laboratory studies have generated hypotheses that larval fish size, age, growth rate, and development rate affect their susceptibility to predation. Empirical data on predator selection in the wild are challenging to obtain, and most selective mortality studies must repeatedly sample populations of survivors to indirectly examine survivorship. While valuable on a population scale, these approaches can obscure selection by particular predators. In May 2018, along the coast of Washington, USA, we simultaneously collected juvenile quillback rockfish Sebastes maliger from both the environment and the stomachs of juvenile coho salmon Oncorhynchus kisutch. We used otolith microstructure analysis to examine whether juvenile coho salmon were age-, size-, and/or growth-selective predators of juvenile quillback rockfish. Our results indicate that juvenile rockfish consumed by salmon were significantly smaller, slower growing at capture, and younger than surviving (unconsumed) juvenile rockfish, providing direct evidence that juvenile coho salmon are selective predators on juvenile quillback rockfish. These differences in early life history traits between consumed and surviving rockfish are related to timing of parturition and the environmental conditions larval rockfish experienced, suggesting that maternal effects may substantially influence survival at this stage. Our results demonstrate that variability in timing of parturition and sea surface temperature leads to tradeoffs in early life history traits between growth in the larval stage and survival when encountering predators in the pelagic juvenile stage.

scholarly journals Assessing Early Heterogeneity in Doubling Times of the COVID-19 Epidemic across Prefectures in Mainland China, January–February, 2020

Epidemiologia ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 95-113 ◽  
Author(s):  
Isaac Chun-Hai Fung ◽  
Xiaolu Zhou ◽  
Chi-Ngai Cheung ◽  
Sylvia K. Ofori ◽  
Kamalich Muniz-Rodriguez ◽  
...  
Keyword(s):  
Regression Models ◽  
Doubling Time ◽  
Metropolitan Areas ◽  
Mainland China ◽  
Linear Regression Models ◽  
Case Count ◽  
Daily Time Series ◽  
The Mean ◽  
Doubling Times ◽  
Daily Time

To describe the geographical heterogeneity of COVID-19 across prefectures in mainland China, we estimated doubling times from daily time series of the cumulative case count between 24 January and 24 February 2020. We analyzed the prefecture-level COVID-19 case burden using linear regression models and used the local Moran’s I to test for spatial autocorrelation and clustering. Four hundred prefectures (~98% population) had at least one COVID-19 case and 39 prefectures had zero cases by 24 February 2020. Excluding Wuhan and those prefectures where there was only one case or none, 76 (17.3% of 439) prefectures had an arithmetic mean of the epidemic doubling time <2 d. Low-population prefectures had a higher per capita cumulative incidence than high-population prefectures during the study period. An increase in population size was associated with a very small reduction in the mean doubling time (−0.012, 95% CI, −0.017, −0.006) where the cumulative case count doubled ≥3 times. Spatial analysis revealed high case count clusters in Hubei and Heilongjiang and fast epidemic growth in several metropolitan areas by mid-February 2020. Prefectures in Hubei and neighboring provinces and several metropolitan areas in coastal and northeastern China experienced rapid growth with cumulative case count doubling multiple times with a small mean doubling time.

scholarly journals Phenotypic plasticity of labile traits in the wild

2013 ◽  
Vol 59 (4) ◽  
pp. 485-505 ◽  
Author(s):  
Jon E. Brommer
Keyword(s):  
Life History ◽  
Phenotypic Plasticity ◽  
Statistical Approach ◽  
Scale Up ◽  
Population Level ◽  
Wild Populations ◽  
Quantitative Genetic ◽  
In The Wild ◽  
The Individual ◽  
Quantitative Genetic Parameters

Abstract Individual-based studies allow quantification of phenotypic plasticity in behavioural, life-history and other labile traits. The study of phenotypic plasticity in the wild can shed new light on the ultimate objectives (1) whether plasticity itself can evolve or is constrained by its genetic architecture, and (2) whether plasticity is associated to other traits, including fitness (selection). I describe the main statistical approach for how repeated records of individuals and a description of the environment (E) allow quantification of variation in plasticity across individuals (IxE) and genotypes (GxE) in wild populations. Based on a literature review of life-history and behavioural studies on plasticity in the wild, I discuss the present state of the two objectives listed above. Few studies have quantified GxE of labile traits in wild populations, and it is likely that power to detect statistically significant GxE is lacking. Apart from the issue of whether it is heritable, plasticity tends to correlate with average trait expression (not fully supported by the few genetic estimates available) and may thus be evolutionary constrained in this way. Individual-specific estimates of plasticity tend to be related to other traits of the individual (including fitness), but these analyses may be anti-conservative because they predominantly concern stats-on-stats. Despite the increased interest in plasticity in wild populations, the putative lack of power to detect GxE in such populations hinders achieving general insights. I discuss possible steps to invigorate the field by moving away from simply testing for presence of GxE to analyses that ‘scale up’ to population level processes and by the development of new behavioural theory to identify quantitative genetic parameters which can be estimated.

scholarly journals The application of life history information to the conservation management of Chrysoritis butterflies (Lepidoptera: Lycaenidae) in South Africa

Koedoe ◽  
2004 ◽  
Vol 47 (1) ◽  
Author(s):  
R.F. Terblanche ◽  
H. Van Hamburg
Keyword(s):  
South Africa ◽  
Life History ◽  
Life Histories ◽  
Host Plants ◽  
Conservation Management ◽  
Aesthetic Value ◽  
Wing Patterns ◽  
In The Wild ◽  
History Of ◽  
Voucher Specimens

Due to their intricate life histories and the unique wing patterns and colouring the butterflies of the genus Chrysoritis are of significant conservation and aesthetic value. Thisoverview probes into practical examples of butterfly life history research applicable to environmental management of this relatively well-known invertebrate group in South Africa. Despite the pioneer work on life histories of Chrysoritis in the past, more should be done to understand the life history of the butterflies in the wild, especially their natural host plants and the behaviour of adults and larvae. A system of voucher specimens of host plants should be introduced in South Africa. Although various host plant species in nature are used by the members of Chrysoritis, including the Chrysoritis chrysaor group, the choice of these in nature by each species is significant for conservation management and in the case of Chrysoritis aureus perhaps even as a specific characteristic.A revision of the ant genus Crematogaster will benefit the conservation management of Chrysoritis species since some of these ant species may consist of a number of specieswith much more restricted distributions than previously thought. Rigorous quantified tudies of population dynamics of Chrysoritis butterflies are absent and the introductionof such studies will benefit conservation management of these localised butterflies extensively.

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