scholarly journals Why do species get a thin slice of π? Revisiting Lewontin’s Paradox of Variation

2021 ◽  
Author(s):  
Vince Buffalo
Keyword(s):  
Phylogenetic Signal ◽  
Neutral Theory ◽  
Evolutionary Genetics ◽  
Genomic Diversity ◽  
Background Selection ◽  
Census Size ◽  
Size Relationship ◽  
Population Sizes ◽  
The Impact ◽  
Linked Selection

AbstractUnder neutral theory, the level of polymorphism in an equilibrium population is expected to increase with population size. However, observed levels of diversity across metazoans vary only two orders of magnitude, while census population sizes (Nc) are expected to vary over several. This unexpectedly narrow range of diversity is a longstanding enigma in evolutionary genetics known as Lewontin’s Paradox of Variation (1974). Since Lewontin’s observation, it has been argued that selection constrains diversity across species, yet tests of this hypothesis seem to fall short of explaining the orders-of-magnitude reduction in diversity observed in nature. In this work, I revisit Lewontin’s Paradox and assess whether current models of linked selection are likely to constrain diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine genetic data from 172 metazoan taxa with estimates of census sizes from geographic occurrence data and population densities estimated from body mass. Next, I fit the relationship between previously-published estimates of genomic diversity and these approximate census sizes to quantify Lewontin’s Paradox. While previous across-taxa population genetic studies have avoided accounting for phylogenetic non-independence, I use phylogenetic comparative methods to investigate the diversity census size relationship, estimate phylogenetic signal, and explore how diversity changes along the phylogeny. I consider whether the reduction in diversity predicted by models of recurrent hitch-hiking and background selection could explain the observed pattern of diversity across species. Since the impact of linked selection is mediated by recombination map length, I also investigate how map lengths vary with census sizes. I find species with large census sizes have shorter map lengths, leading these species to experience greater reductions in diversity due to linked selection. Even after using high estimates of the strength of sweeps and background selection, I find linked selection likely cannot explain the shortfall between predicted and observed diversity levels across metazoan species. Furthermore, the predicted diversity under linked selection does not fit the observed diversity–census-size relationship, implying that processes other than background selection and recurrent hitchhiking must be limiting diversity.

scholarly journals Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin's paradox

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Vince Buffalo
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Phylogenetic Signal ◽  
Neutral Theory ◽  
Negative Relationship ◽  
Abundant Species ◽  
Census Size ◽  
Population Sizes ◽  
The Relationship ◽  
Linked Selection

Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontin’s Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontin’s Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with newly derived estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even assuming strong and abundant selection, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.

Characterizing the impact of recovering sea otters on commercially important crabs in California estuaries

2020 ◽  
Vol 655 ◽  
pp. 123-137
Author(s):  
TM Grimes ◽  
MT Tinker ◽  
BB Hughes ◽  
KE Boyer ◽  
L Needles ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Sea Otter ◽  
Dungeness Crab ◽  
Sea Otters ◽  
Elkhorn Slough ◽  
Enhydra Lutris Nereis ◽  
Crab Abundance ◽  
Population Sizes ◽  
Commercially Important ◽  
The Impact

Protective legislation and management have led to an increase in California’s sea otter Enhydra lutris nereis population. While sea otter recovery has been linked to ecosystem benefits, sea otter predation may negatively affect commercially valuable species. Understanding the potential influence of sea otters is of particular importance as their range expands into estuaries that function as nurseries for commercially valuable species like Dungeness crab Metacarcinus magister. We consider how sea otter predation has affected the abundance and size of juvenile Dungeness crab in Elkhorn Slough, California, USA, and analyzed cancrid crab abundance and size across 4 California estuaries with and without sea otters to understand how biotic and abiotic factors contribute to observed variation in crab size and abundance. We compared trends in southern sea otters relative to Dungeness crab landings in California to assess whether increasing sea otter abundance have negatively impacted landings. In Elkhorn Slough, juvenile Dungeness crab abundance and size have declined since 2012, coinciding with sea otter population growth. However, the impact of sea otters on juvenile Dungeness crab size was habitat-specific and only significant in unvegetated habitat. Across estuaries, we found that cancrid crab abundance and size were negatively associated with sea otter presence. While abiotic factors varied among estuaries, these factors explained little of the observed variation in crab abundance or size. Although we found evidence that sea otters can have localized effects on cancrid crab populations within estuaries, we found no evidence that southern sea otters, at recent population sizes, have negatively impacted Dungeness crab landings in California from 2000-2014.

scholarly journals The Impact of Health Policies and Sociodemographic Factors on Doubling Time of the COVID-19 Pandemic in Mexico

2021 ◽  
Vol 18 (5) ◽  
pp. 2354
Author(s):  
Lina Díaz-Castro ◽  
Héctor Cabello-Rangel ◽  
Kurt Hoffman
Keyword(s):  
Population Density ◽  
Doubling Time ◽  
Sociodemographic Factors ◽  
Health Policies ◽  
Government Response ◽  
University Of Oxford ◽  
Negative Effect ◽  
Population Sizes ◽  
The University ◽  
The Impact

Background. The doubling time is the best indicator of the course of the current COVID-19 pandemic. The aim of the present investigation was to determine the impact of policies and several sociodemographic factors on the COVID-19 doubling time in Mexico. Methods. A retrospective longitudinal study was carried out across March–August, 2020. Policies issued by each of the 32 Mexican states during each week of this period were classified according to the University of Oxford Coronavirus Government Response Tracker (OxCGRT), and the doubling time of COVID-19 cases was calculated. Additionally, variables such as population size and density, poverty and mobility were included. A panel data model was applied to measure the effect of these variables on doubling time. Results. States with larger population sizes issued a larger number of policies. Delay in the issuance of policies was associated with accelerated propagation. The policy index (coefficient 0.60, p < 0.01) and the income per capita (coefficient 3.36, p < 0.01) had a positive effect on doubling time; by contrast, the population density (coefficient −0.012, p < 0.05), the mobility in parks (coefficient −1.10, p < 0.01) and the residential mobility (coefficient −4.14, p < 0.01) had a negative effect. Conclusions. Health policies had an effect on slowing the pandemic’s propagation, but population density and mobility played a fundamental role. Therefore, it is necessary to implement policies that consider these variables.

scholarly journals Genomic and phenotypic characterisation of invasive neonatal and colonising group B Streptococcus isolates from Slovenia, 2001–2018

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Tina Perme ◽  
Daniel Golparian ◽  
Maja Bombek Ihan ◽  
Andrej Rojnik ◽  
Miha Lučovnik ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Virulence Factors ◽  
Late Onset ◽  
Group B Streptococcus ◽  
Genomic Diversity ◽  
Neonatal Disease ◽  
Phenotypic Characterisation ◽  
High Prevalence ◽  
Group B ◽  
The Impact

Abstract Background Group B Streptococcus (GBS) is the leading cause of invasive neonatal disease in the industrialized world. We aimed to genomically and phenotypically characterise invasive GBS isolates in Slovenia from 2001 to 2018 and contemporary colonising GBS isolates from screening cultures in 2018. Methods GBS isolates from 101 patients (invasive isolates) and 70 pregnant women (colonising isolates) were analysed. Basic clinical characteristics of the patients were collected from medical records. Antimicrobial susceptibility and phenotypic capsular serotype were determined. Whole-genome sequencing was performed to assign multilocus sequence types (STs), clonal complexes (CCs), pathogenicity/virulence factors, including capsular genotypes, and genome-based phylogeny. Results Among invasive neonatal disease patients, 42.6% (n = 43) were females, 41.5% (n = 39/94) were from preterm deliveries (< 37 weeks gestation), and 41.6% (n = 42) had early-onset disease (EOD). All isolates were susceptible to benzylpenicillin with low minimum inhibitory concentrations (MICs; ≤0.125 mg/L). Overall, 7 serotypes were identified (Ia, Ib, II-V and VIII); serotype III being the most prevalent (59.6%). Twenty-eight MLST STs were detected that clustered into 6 CCs. CC-17 was the most common CC overall (53.2%), as well as among invasive (67.3%) and non-invasive (32.9%) isolates (p < 0.001). CC-17 was more common among patients with late-onset disease (LOD) (81.4%) compared to EOD (47.6%) (p < 0.001). The prevalence of other CCs was 12.9% (CC-23), 11.1% (CC-12), 10.5% (CC-1), 8.2% (CC-19), and 1.8% (CC-498). Of all isolates, 2.3% were singletons. Conclusions A high prevalence of hypervirulent CC-17 isolates, with low genomic diversity and characteristic profile of pathogenicity/virulence factors, was detected among invasive neonatal and colonising GBS isolates from pregnant women in Slovenia. This is the first genomic characterisation of GBS isolates in Slovenia and provides valuable microbiological and genomic baseline data regarding the invasive and colonising GBS population nationally. Continuous genomic surveillance of GBS infections is crucial to analyse the impact of IND prevention strategies on the population structure of GBS locally, nationally, and internationally.

scholarly journals The impact of large terrestrial carnivores on Pleistocene ecosystems

2015 ◽  
Vol 113 (4) ◽  
pp. 862-867 ◽  
Author(s):  
Blaire Van Valkenburgh ◽  
Matthew W. Hayward ◽  
William J. Ripple ◽  
Carlo Meloro ◽  
V. Louise Roth
Keyword(s):  
Prey Size ◽  
Habitat Degradation ◽  
Terrestrial Ecosystems ◽  
Growth Data ◽  
Predator Prey ◽  
Body Sizes ◽  
Population Sizes ◽  
Potential Impact ◽  
The Impact ◽  
Ground Sloths

Large mammalian terrestrial herbivores, such as elephants, have dramatic effects on the ecosystems they inhabit and at high population densities their environmental impacts can be devastating. Pleistocene terrestrial ecosystems included a much greater diversity of megaherbivores (e.g., mammoths, mastodons, giant ground sloths) and thus a greater potential for widespread habitat degradation if population sizes were not limited. Nevertheless, based on modern observations, it is generally believed that populations of megaherbivores (>800 kg) are largely immune to the effects of predation and this perception has been extended into the Pleistocene. However, as shown here, the species richness of big carnivores was greater in the Pleistocene and many of them were significantly larger than their modern counterparts. Fossil evidence suggests that interspecific competition among carnivores was relatively intense and reveals that some individuals specialized in consuming megaherbivores. To estimate the potential impact of Pleistocene large carnivores, we use both historic and modern data on predator–prey body mass relationships to predict size ranges of their typical and maximum prey when hunting as individuals and in groups. These prey size ranges are then compared with estimates of juvenile and subadult proboscidean body sizes derived from extant elephant growth data. Young proboscideans at their most vulnerable age fall within the predicted prey size ranges of many of the Pleistocene carnivores. Predation on juveniles can have a greater impact on megaherbivores because of their long interbirth intervals, and consequently, we argue that Pleistocene carnivores had the capacity to, and likely did, limit megaherbivore population sizes.

scholarly journals COVID-19 Cases and Deaths: A Comparison among Bangladesh, India and Pakistan

2021 ◽  
Vol 3 (5) ◽  
pp. 01-06
Author(s):  
B. M. Kibria
Keyword(s):  
Population Sizes ◽  
The Impact

This paper compares the number of infected cases and deaths of an ongoing pandemic of COVID-19 outbreak for Bangladesh, India and Pakistan for the period of March 8, 2020 to September 21, 2020. Comparisons among countries using absolute numbers are not comparable due to different factors, such as population sizes, rates of per 100,000 and also because not all countries are affected equally and at the same time. Following Middelburg and Rosendaal (2020), we graphically compare the number of cases and deaths expressed as a percentage of the cases and deaths on the reference day 25 after the first reported death. To see the impact of reference days, several later reference days are also considered in this study. From these comparisons, clear differences were observed among countries. Among these three countries, it is observed that Bangladesh had the most extreme flattening of the curve, followed by Pakistan and then India. We observed that the epidemic developed in India much more rapidly as compare to Bangladesh and Pakistan.

scholarly journals On mechanisms of trophic cascade caused by anti-predation response in food chain systems

2020 ◽  
Vol 1 (2) ◽  
pp. 1-27
Author(s):  
Yang Wang ◽  
Xingfu Zou
Keyword(s):  
Food Chain ◽  
Trophic Cascade ◽  
Predation Rate ◽  
Model Systems ◽  
Large Carnivores ◽  
Response Level ◽  
Population Sizes ◽  
The Cost ◽  
The Impact ◽  
D Model

Motivated by a recent field study [Nat. Commun. 7(2016), 10698] on the impact of fear of large carnivores on the populations in a cascading ecosystem of food chain type with the large carnivores as the top predator, in this paper we propose two model systems in the form of ordinary differential equations to mechanistically explore the cascade of such a fear effect. The models are of the Lotka-Volterra type, one is three imensional and the other four dimensional. The 3-D model only considers the cost of the anti-predation response reflected in the decrease of the production, while the 4-D model considers also the benefit of the response in reducing the predation rate, in addition to the cost by reducing the production. We perform a thorough analysis on the dynamics of the two models. The results reveal that the 3-D model and 4-model demonstrate opposite patterns for trophic cascade in terms of the dependence of population sizes for each species at the co-existence equilibrium on the anti-predation response level parameter, and such a difference is attributed to whether or not there is a benefit for the anti-predation response by the meso-carnivore species.

scholarly journals The ecology of ponds in the context of human activity and geography – environmental DNA and beyond

2021 ◽  
Vol 4 ◽  
Author(s):  
Karolina Bacela-Spychalska ◽  
Annette Taugbøl ◽  
Wiesław Babik ◽  
Maciej Pabijan ◽  
David Strand ◽  
...  
Keyword(s):  
Alien Species ◽  
Invasive Alien Species ◽  
Environmental Dna ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Parasitic Fungus ◽  
Detailed Knowledge ◽  
Geographic Regions ◽  
The Impact ◽  
Pond Ecosystems

Pond ecosystems are hotspots of freshwater biodiversity, often containing many rare and protected species that are not commonly found elsewhere (Harper et al. 2018;Harper et al. 2019). However, even if they constitute c.a. 30% of freshwaters by area, still not enough effort has been put into pond monitoring and management and pond ecosystems are hence relatively poorly understood. Results of ECOPOND project will lead to add valuable knowledge upon pond diversity in geographic gradient taking for consideration human impact by comparing rural and urban areas. The sample design in ECOPOND includes six geographic regions, spanning from the south of Poland to the middle of Norway, where we will sample five replicates of urban and rural ponds in close geographic proximity, making it possible to test the impact of urbanization on biodiversity and biotic homogenization across latitude. We will sample all ponds at spring and late summer, making it possible to assess also seasonality in biodiversity. ECOPOND will utilize environmental DNA and RNA to perform biodiversity screening. The extracted eDNA and eRNA fragments will be amplified with the use of several selected markers for vertebrates, invertebrates, fungi and bacteria. Comparisons between eDNA and eRNA metabarcoding are hypothesized to allow inference between present and past diversity, as eRNA is thought to be only available from live organisms in the community. Moreover, ECOPOND aims at testing the effects of selected invasives species that can have on whole ecosystems. By sampling a range of biotic and abiotic parameters describing studied ponds, we will incorporate the available data for the ponds and employ occupancy modelling methods to assess the habitat preferences of selected invasive alien species. Then we will develop a method that can contribute towards an earlywarning system of evaluating threats to ecosystem status. One of the focus species will be the parasitic fungus Batrachochytrium dendrobatidis (Bd), an infectious fungal pathogen that has caused a number of amphibian declines and extinctions. The European amphibians seem less affected by the parasite at present. However, the fungi could be a direct driver of reduced genetic variation due to selection, or directly reduce the infected amphibian’s overall fitness by reducing the microbiotic diversity on their skin, which in many cases acts as a second immune system. ECOPOND will therefore provide data on genomic variation (using RADseq) for two amphibian species: the smooth newt (Lissotriton vulgaris) and the common toad (Bufo bufo). We will investigate populations of these species inhabiting ponds that are infected and not infected by Bd as well as collect data on their skin microbes (identified using metabarcoding). We will also contrast the genomic diversity between the replicated urban/rural setup and look for repeatable genomic changes. This setup will also be compared for the genomic variation for a potential native prey, the blue-tailed dragonfly, as will ponds with and without fish and/or amphibians (possibly also comparing between native and IAS top-predators) in order to look for predatory selective sweeps in the genome and transcriptome (experimental setup). All ponds will also be analyzed for over 20 water quality parameters and include data on a range of site characteristics that will be used as explanatory variables in all models. ECOPOND will compare large datasets across large geographic regions and will provide detailed knowledge of biodiversity patterns in vertebrates, invertebrates, fungal and microbial species, as well as genomic composition and skin biodiversity for animals inhabiting the same ponds set in an urban context. As a total, ECOPOND will obtain data on the location and status of biodiversity interests, gather data that can help in preventing the establishment of invasive alien species, and eradicating or controlling species that have already become established. And finally, ECOPOND will work closely with stakeholders and develop statistical techniques that can be used for monitoring, detection and protection of biodiversity.

scholarly journals Incorporating genetic selection into individual-based models (IBMs) of malaria and other infectious diseases

2019 ◽  
Author(s):  
Ian M. Hastings ◽  
Raman Sharma
Keyword(s):  
Control Strategies ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Wait Time ◽  
Antimicrobial Drug Resistance ◽  
Infinite Population ◽  
Individual Based Models ◽  
Population Sizes ◽  
Human Infections ◽  
The Impact

AbstractOptimal control strategies for human infections are often investigated by computational approaches using individual-based models (IBMs). These typically track humans and evaluate the impact of control interventions in terms of human deaths, clinical cases averted, interruption of transmission etc. Genetic selection can be incorporated into these IBMs and used to track the spread of mutations whose origin and spread are often driven by the intervention, and which subsequently undermine the control strategy; for example, mutations which encode antimicrobial drug resistance or diagnosis- or vaccine-escape phenotypes. Basic population genetic descriptions of selection are based on infinite population sizes (so that chance fluctuations in allele frequency are absent) but IBMs track finite population sizes. We describe how the finite sizes of IBMs affect simulating the dynamics of genetic selection and how best to incorporate genetic selection into these models. We use the OpenMalaria IBM of malaria as an example, but the same principles apply to IBMs of other diseases. We identify four strategies to incorporate selection into IBMs and make the following four recommendations. Firstly, calculate and report the selection coefficients, s, of the advantageous allele as the key genetic parameter. Secondly, use these values of ‘s’ to calculate the wait-time until a mutation successful establishes itself in the population. The wait time for the mutation can be added to speed of selection, s, to calculate when the mutation will reach significant, operationally important levels. Thirdly, quantify the ability of the IBM to robustly estimate small selection coefficients. Fourthly, optimise computational efficacy: when ‘s’ is small it is plausible that fewer replicates of larger IBMs will be more efficient than a larger number of replicates of smaller size.

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