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M Ratio. Garza and Williamson () demonstrate how M, the ratio of the number of alleles to range in allele size, for a sample of microsatellite.


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How to find your computer's bottlenecks [a quick tutorial]

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Keywords: bottleneck test, extinction, heterozygosity, microsatellite, M-ratio, mutation Tests for reductions in M-ratios are conducted by comparing the mean​.


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CPU and GPU Bottleneck: A Detailed Guide to Diagnose and Fix Bottlenecks.

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We used two approaches to test for genetic bottlenecks at the microsatellite loci – for each population, we calculated M, a ratio based on the.


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Identifying Your Rig's Bottleneck

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convex body K is defined as M(K)=(VolK)(VolK∘). Mahler conjectured that this volume is minimized when K is a cube. We introduce the bottleneck conjecture.


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Conversely, a statistic testing for a bottleneck signature in the ratio of allele number to allele size range (M-ratio) was significant for both the Afognak and source.


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Is Your Gaming Rig Being Bottlenecked??

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Conversely, a statistic testing for a bottleneck signature in the ratio of allele number to allele size range (M-ratio) was significant for both the Afognak and source.


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How to Identify a CPU/GPU Bottleneck

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Three different methods to detect bottlenecks were tested. These where the heterozygosity excess, the mode-shift indicator (Piry et al. ), and the M ratio​.


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Conversely, a statistic testing for a bottleneck signature in the ratio of allele number to allele size range (M-ratio) was significant for both the Afognak and source.


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Direct and dual Information Bottleneck frameworks for Deep Learning - Tali Tishby

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Conversely, a statistic testing for a bottleneck signature in the ratio of allele number to allele size range (M-ratio) was significant for both the Afognak and source.


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M is defined as the ratio of the total number of alleles (k) to the overall range in allele size (r). With genetic drift in populations reduced in size, the.


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How to Overclock an AMD FX4100 w\\ an ASUS M5A78L-M LX MOBO+ How to reduce CPU Bottleneck

Unravelling the demographic histories of species is a fundamental goal of population biology and has tremendous implications for understanding the genetic variability observed today 1 , 2. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. Furthermore, up to five-fold variation in genetic diversity across species is explained by a combination of bottleneck history, global abundance and breeding habitat. A Nature Research Journal. By contrast, although the pre-bottleneck effective population size N e hist also had a prediction error below one in both models, visual inspection of the cross-validation results revealed high variation in the estimates and a systematic underestimation of larger N e hist values, so this parameter was not considered further. Consequently, to disentangle the forces shaping population bottlenecks, we need comparative studies incorporating genetic, ecological and life-history data from multiple closely related species within a consistent analytical framework. The fact that none of these species supported the non-bottleneck model with postglacial expansion indicates that the reduction in genetic diversity produced by a recent bottleneck can be clearly distinguished from the reduction in diversity due to a small population size at the end of the last ice age. First, we hypothesised that breeding habitat would be important as ice-breeding species are less accessible and more widely dispersed than their land-breeding counterparts. As another indicator of model quality, posterior predictive checks 21 , 46 showed that the preferred models across all species were largely able to reproduce the relevant observed summary statistics Supplementary Fig. We hypothesised that i extreme variation in the extent to which species were exploited by man should be reflected in their genetic bottleneck signatures; ii ecological and life-history traits could have an impact on the strength of bottleneck signatures across species; iii past bottlenecks should reduce contemporary genetic diversity; and iv heavily bottlenecked species with reduced genetic diversity will be more likely to be of conservation concern. Finally, we used Bayesian phylogenetic mixed models to investigate the potential causes and consequences of past bottlenecks while controlling for phylogenetic relatedness among species. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Another question that remains elusive due to a lack of comparative studies is to what extent recent bottlenecks have impacted the genetic diversity of wild populations. By contrast, the majority of ice-breeding seals exhibited heterozygosity-deficiency, consistent with historical population expansions. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. This is to be expected as many of our summary statistics such as the M-ratio are sensitive towards recent population size changes Conceivably both ecological and life-history variables could have impacted the extent to which commercial exploitation affected different pinniped species. Therefore, although studies of individual species are usually limited by uncertainty over the underlying mutation characteristics, our ABC analyses converged on similar estimates of mutation model and rate across species, allowing us to appropriately parameterise our bottleneck analyses. Prior distributions are not shown as N e bot was drawn from a uniform distribution with U[1, ]. Determinants of contemporary genetic diversity across pinnipeds.{/INSERTKEYS}{/PARAGRAPH} Second, we used ABC to select between a bottleneck and a non-bottleneck model as well as to estimate posterior distributions of relevant parameters. For 11 species, the bottleneck model was supported with a higher probability than the non-bottleneck model i. Of particular interest are sharp reductions in the effective population size N e known as population bottlenecks 3 , 4 , which may negatively impact the viability and adaptive evolutionary potential of species through a variety of stochastic demographic processes and the loss of genetic diversity 5 , 6 , 7 , 8. A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. Thus, breeding habitat and SSD explain variation in prop het-exc whereas only breeding habitat explains variation in p bot. We used two different coalescent-based approaches to infer the extent of recent population bottlenecks. Recent bottlenecks therefore generate a transient excess of heterozygosity relative to a population at equilibrium with an equivalent number of alleles Considerable heterogeneity was found across species, with northern and southern elephant seals, grey seals, Guadalupe fur seals and Antarctic fur seals showing the strongest bottlenecks signals. Here, we conducted a broad-scale comparative analysis of population bottlenecks using a combination of genetic, ecological and life-history data for 30 pinniped species. A small amount of overlap between the models and therefore misclassification is unavoidable because both models were specified using broad priors to optimally fit a variety of species with vastly different population sizes. For example, species occupying breeding habitats that are more accessible to humans would be expected to be at higher risk of declines, while species with highly skewed mating systems tend to have lower effective population sizes 30 and might also experience stronger demographic declines as only a fraction of individuals contribute towards the genetic makeup of subsequent generations. In addition, prop het-exc was positively associated with SSD Fig. We therefore know very little about the intensity of demographic declines and how these are influenced by anthropogenic impacts as well as by factors intrinsic to a given species. Ecological and life-history effects on bottleneck signatures. Using the largest genetic clusters did not appreciably affect our results, with repeatabilities for the genetic summary statistics and bottleneck signatures all being greater than 0. Here, we combined genetic data from over 11, individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. We inferred the strength of historical declines across species from the genetic data using two complimentary coalescent-based approaches, heterozygosity-excess and ABC. The phylogeny shows 30 species with branches colour coded according to breeding habitat and tip points coloured and sized according to their IUCN status and global abundance respectively. Third, the length of the breeding season may have impacted the vulnerability of a given species to exploitation and finally, generation time could potentially mediate population recovery. Breeding habitat showed the largest overall effect size in both models Fig. An outstanding opportunity to address these questions is provided by the pinnipeds, a clade of marine carnivores inhabiting nearly all marine environments ranging from the poles to the tropics and showing remarkable variation in their ecological and life-history adaptations Pinnipeds include some of the most extreme examples of commercial exploitation known to man, with several species including the northern elephant seal having been driven to the brink of extinction for their fur and blubber by 18th to early 20th century sealers By contrast, other pinniped species inhabiting pristine environments such as Antarctica have probably had very little contact with humans Hence, pinnipeds show large differences in their demographic histories within the highly constrained time window of commercial sealing and thereby represent a unique natural experiment for exploring the causes and consequences of recent bottlenecks. While the structure coefficient of generation time in the prop het-exc model did not have CIs overlapping zero, a negative relationship is contrary to expectations and probably reflects the longer generation times of ice-breeding seals Supplementary Fig. The pinniped art in this figure was created by Rebecca Carter www. Specifically, small bottlenecked populations have elevated levels of inbreeding and genetic drift, which decrease genetic variability and can lead to the fixation of mildly deleterious alleles and ultimately drive a vortex of extinction 6 , 8 , 9 , Hence, investigating the bottleneck histories of wild populations and their determinants and consequences is more critical than ever before, as we live in an era where global anthropogenic alteration and destruction of natural habitats are driving species declines on an unprecedented scale 11 , Unfortunately, detailed information about past population declines across species is sparse because historical population size estimates are often either non-existent or highly uncertain 13 , A versatile solution for inferring population bottlenecks from a single sample of individuals is to compare levels of observed and expected genetic diversity, the latter of which can be simulated under virtually any demographic scenario based on the coalescent 15 , 16 , A variety of approaches based on this principle have been developed, one of the most widely used being the heterozygosity-excess test, which compares the heterozygosity of a panel of neutral genetic markers to the expectation in a stable population under mutation-drift equilibrium Although theoretically well grounded, these methods are highly sensitive to the assumed mutation model, which is seldom known A more sophisticated framework for inferring demographic histories is coalescent-based approximate Bayesian computation ABC ABC has the compelling advantages of making it possible to i compare virtually any demographic scenario as long as it can be simulated, ii estimate key parameters of the model such as the bottleneck effective population size and iii incorporate uncertainty in the specification of models by defining priors. Therefore, both models incorporate longer-term declines or expansions within realistic bounds for all species but only the bottleneck model captures a recent and severe decrease in N e due to anthropogenic exploitation. We report striking variation in genetic bottleneck signatures across pinnipeds, with 11 species exhibiting strong genetic signatures of population declines and estimated bottleneck effective population sizes reflecting just a few tens of surviving individuals in the most extreme cases. We therefore investigated the effects of four different variables on bottleneck signatures. Finally, exploring the consequences of historical bottlenecks for conservation, we show that genetic bottleneck signatures are unrelated to IUCN status across all species, although three of the four most heavily bottlenecked species are currently endangered. While a number of influential studies of heavily bottlenecked species have indeed found very low levels of genetic variability 31 , 32 , 33 , 34 , others have reported unexpectedly high genetic variation after supposedly strong population declines 23 , 35 , 36 , 37 , Hence, it is not yet clear how population size changes contribute towards one of the most fundamental questions in evolutionary genetics—how and why genetic diversity varies across species 2 , 39 , 40 , To tackle this question, we need to compare closely related species because deeply divergent taxa vary so profoundly in their genetic diversity due to differences in their life-history strategies that any effects caused by variation in N e will be hard to detect and decipher 40 , Finally, the relative contributions of genetic diversity and demographic factors towards extinction risk remain unclear. Despite being caused by human exploitation, these genetic bottlenecks are mediated by both breeding habitat and mating system variation, implying that species ecology and life-history contribute towards responses to anthropogenic exploitation. However, we did not find the expected positive relationships with either breeding season length or generation time see below. By contrast, structure coefficients showed that breeding habitat and SSD were both strongly correlated to the fitted response in the prop het-exc model, while SSD indeed had a much weaker effect in the p bot model Fig. Second, we considered sexual size dimorphism SSD an important life-history variable as species with a high SSD aggregate in denser breeding colonies, making them more valuable to hunters, and polygyny reduces effective population size. To investigate the determinants of contemporary genetic diversity across pinnipeds, we constructed a phylogenetic mixed model of allelic richness A r with log transformed global abundance, breeding habitat and SSD fitted as predictor variables together with the two bottleneck measures prop het-exc and p bot Fig. To investigate this further, we constructed two Bayesian phylogenetic mixed models with prop het-exc and p bot as response variables respectively and breeding habitat, SSD, breeding season length and generation time fitted as predictors see Methods for details. You are using a browser version with limited support for CSS. For each species, parameter values for accepted simulations are presented as a sinaplot, which arranges the data points to reflect the estimated posterior distribution. Estimated bottleneck effective population sizes. {PARAGRAPH}{INSERTKEYS}Thank you for visiting nature. Patterns of genetic diversity and bottleneck signatures across the pinnipeds. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity. We found clear differences between ice-breeding and land-breeding seals in both prop het-exc and p bot , with land-breeders on average showing stronger bottleneck signatures Fig. Furthermore, we tested all loci from each dataset for deviations from Hardy-Weinberg equilibrium HWE, see the Methods for details. Due to this flexibility, ABC has become a state of the art approach for inferring population bottlenecks as well as demographic histories in general 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , Although the widespread availability of neutral molecular markers such as microsatellites has facilitated numerous genetic studies of bottlenecks in wild populations, the vast majority of studies focused exclusively on single species and were confined to testing for the presence or absence of bottlenecks. Subsequent parameter estimation was therefore based on the bottleneck model for eleven species and on the non-bottleneck model for the other 19 species. Nevertheless, due to a lack of studies measuring bottlenecks consistently across species, it remains an open question as to how the loss of genetic diversity caused by demographic declines ultimately translates into a species' extinction risk, which can be assessed by its International Union for Conservation of Nature IUCN status. This is reflected by the low unique R 2 values of the predictors relative to the marginal R 2 of the full model Fig. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Heterozygosity-excess was used as a measure of the relative strength of recent population declines, while a consistent ABC framework was used to evaluate the probability of each species having experienced a severe bottleneck during the known timeframe of commercial exploitation, as well as to estimate relevant model parameters. Species abbreviations are given in Fig. To investigate whether including these loci could have affected our results, we recalculated the genetic summary statistics and repeated our bottleneck analyses after excluding them. In particular, increased ice cover during the last glacial maximum LGM could have reduced habitat availability and consequently population sizes 48 , 49 , 50 , 51 , Specifically, we used ABC to simulate two additional demographic scenarios that were identical to the bottleneck and non-bottleneck models but which also incorporated a small population size during the LGM and subsequent expansion. All rights reserved. The results remained largely unaltered, with repeatabilities all being greater than 0. First, the amount of heterozygosity-excess at selectively neutral loci such as microsatellites is an indicator of recent bottlenecks because during a population decline the number of alleles decreases faster than heterozygosity 3. While historically there has been a debate about the immediate importance of genetic factors towards species viability 5 , 7 , there is now growing evidence that low genetic diversity increases extinction risk 8 , 42 and on a broader scale that threatened species tend to show reduced diversity 7. These rates are much lower than in our main analysis based on two models, indicating that ABC cannot reliably distinguish on the basis of our data between broadly equivalent models that do and do not include ice age effects. The parameter estimates were indicative of strong bottlenecks i. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Posterior distributions of N e bot are shown for 11 species for which the bottleneck model was supported in the ABC analysis, ranked according to the modes of their density distributions which reflect the estimated most likely N e bot. To optimally capture recent population size changes across species, we allowed N e to vary from pre-bottleneck to post-bottleneck in both models within realistic priors see Methods for details while the bottleneck model also included a severe decrease in N e to below during the time of peak sealing. We show that around one third of these species exhibit strong signatures of recent population declines. However, the structure coefficients Fig.