scholarly journals High heritability of coral calcification rates and evolutionary potential under ocean acidification

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Christopher P. Jury ◽  
Mia N. Delano ◽  
Robert J. Toonen
Keyword(s):  
Large Population ◽  
Local Environment ◽  
Evolutionary Potential ◽  
Seawater Chemistry ◽  
Porites Compressa ◽  
Management Actions ◽  
Ph Tolerance ◽  
Population Sizes ◽  
Protected Polymorphism ◽  
High Heritability

AbstractEstimates of heritability inform evolutionary potential and the likely outcome of many management actions, but such estimates remain scarce for marine organisms. Here, we report high heritability of calcification rate among the eight most dominant Hawaiian coral species under reduced pH simulating future ocean conditions. Coral colonies were sampled from up to six locations across a natural mosaic in seawater chemistry throughout Hawaiʻi and fragmented into clonal replicates maintained under both ambient and high pCO2 conditions. Broad sense heritability of calcification rates was high among all eight species, ranging from a low of 0.32 in Porites evermanni to a high of 0.61 in Porites compressa. The overall results were inconsistent with short-term acclimatization to the local environment or adaptation to the mean or ideal conditions. Similarly, in ‘local vs. foreign’ and ‘home vs. away’ tests there was no clear signature of local adaptation. Instead, the data are most consistent with a protected polymorphism as the mechanism which maintains differential pH tolerance within the populations. Substantial individual variation, coupled with high heritability and large population sizes, imply considerable scope for natural selection and adaptive capacity, which has major implications for evolutionary potential and management of corals in response to climate change.

scholarly journals Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas

AoB Plants ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Amanda R Silva ◽  
Luciana C Resende-Moreira ◽  
Carolina S Carvalho ◽  
Eder C M Lanes ◽  
Mabel P Ortiz-Vera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Extinction Risk ◽  
Clustering Methods ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Management Actions ◽  
Temperature And Precipitation ◽  
Population Sizes ◽  
Genetic Clustering

Abstract Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species’ entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (FST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.

scholarly journals The rugged adaptive landscape of an emerging plant RNA virus

2014 ◽  
Author(s):  
Jasna Lalic ◽  
Santiago F. Elena
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Large Population ◽  
Emerging Infectious Diseases ◽  
Evolutionary Process ◽  
Adaptive Landscape ◽  
Evolutionary Potential ◽  
Recombination Rates ◽  
New Host ◽  
Population Sizes

RNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed the fitness landscape describing the adaptation of Tobacco etch potyvirus to its new host, Arabidopsis thaliana. Fitness was measured for most of the genotypes in the landscape, showing the existence of peaks and holes. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common at latter stages. Therefore, results suggest that the landscape was rugged and holey, with several local fitness peaks and a very limited number of potential neutral paths. The viral genotype fixed at the end of the evolutionary process was not on the global fitness optima but stuck into a suboptimal peak.

scholarly journals Determining asymptotically large population sizes in insect swarms

2014 ◽  
Vol 11 (99) ◽  
pp. 20140710 ◽  
Author(s):  
James G. Puckett ◽  
Nicholas T. Ouellette
Keyword(s):  
Group Dynamics ◽  
Large Population ◽  
Environmental Cues ◽  
Multi Agent Systems ◽  
Strong Constraint ◽  
Agent Systems ◽  
Self Organized ◽  
Large Numbers ◽  
Population Sizes ◽  
Multi Agent

Social animals commonly form aggregates that exhibit emergent collective behaviour, with group dynamics that are distinct from the behaviour of individuals. Simple models can qualitatively reproduce such behaviour, but only with large numbers of individuals. But how rapidly do the collective properties of animal aggregations in nature emerge with group size? Here, we study swarms of Chironomus riparius midges and measure how their statistical properties change as a function of the number of participating individuals. Once the swarms contain order 10 individuals, we find that all statistics saturate and the swarms enter an asymptotic regime. The influence of environmental cues on the swarm morphology decays on a similar scale. Our results provide a strong constraint on how rapidly swarm models must produce collective states. But our findings support the feasibility of using swarms as a design template for multi-agent systems, because self-organized states are possible even with few agents.

scholarly journals 2000 Fleming Lecture. The origin and evolution of hepatitis viruses in humans

2001 ◽  
Vol 82 (4) ◽  
pp. 693-712 ◽  
Author(s):  
Peter Simmonds
Keyword(s):  
Large Population ◽  
Human Populations ◽  
Hepatitis Viruses ◽  
Hepatitis G Virus ◽  
Origin And Evolution ◽  
Wide Range ◽  
Population Sizes ◽  
History Of ◽  
Virus C ◽  
Time Of Divergence

The spread and origins of hepatitis C virus (HCV) in human populations have been the subject of extensive investigations, not least because of the importance this information would provide in predicting clinical outcomes and controlling spread of HCV in the future. However, in the absence of historical and archaeological records of infection, the evolution of HCV and other human hepatitis viruses can only be inferred indirectly from their epidemiology and by genetic analysis of contemporary virus populations. Some information on the history of the latter may be obtained by dating the time of divergence of various genotypes of HCV, hepatitis B virus (HBV) and the non-pathogenic hepatitis G virus (HGV)/GB virus-C (GBV-C). However, the relatively recent times predicted for the origin of these viruses fit poorly with their epidemiological distributions and the recent evidence for species-associated variants of HBV and HGV/GBV-C in a wide range of non-human primates. The apparent conservatism of viruses over long periods implied by these latter observations may be the result of constraints on sequence change peculiar to viruses with single-stranded genomes, or with overlapping reading frames. Large population sizes and intense selection pressures that optimize fitness may be the factors that set virus evolution apart from that of their hosts.

scholarly journals Pairwise genetic interactions modulate lipid plasma levels and cellular uptake

2020 ◽  
Author(s):  
Magdalena Zimon ◽  
Yunfeng Huang ◽  
Anthi Trasta ◽  
Jimmy Z. Liu ◽  
Chia-Yen Chen ◽  
...  
Keyword(s):  
Complex Traits ◽  
Drug Target ◽  
Human Genetics ◽  
Large Population ◽  
Genetic Interactions ◽  
Model Systems ◽  
Lipid Lowering ◽  
Gene Pairs ◽  
Population Sizes ◽  
The Uk

SUMMARYGenetic interactions (GIs), the joint impact of different genes or variants on a phenotype, are foundational to the genetic architecture of complex traits. However, identifying GIs through human genetics is challenging since it necessitates very large population sizes, while findings from model systems not always translate to humans. Here, we combined exome-sequencing and genotyping in the UK Biobank with combinatorial RNA-interference (coRNAi) screening to systematically test for pairwise GIs between 30 lipid GWAS genes. Gene-based protein-truncating variant (PTV) burden analyses from 240,970 exomes revealed additive GIs for APOB with PCSK9 and LPL, respectively. Both, genetics and coRNAi identified additive GIs for 12 additional gene pairs. Overlapping non-additive GIs were detected only for TOMM40 at the APOE locus with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate both, plasma and cellular lipid levels via additive and non-additive effects and nominates drug target pairs for improved lipid-lowering combination therapies.

Looking forwards and backwards in a bisexual moran model

1989 ◽  
Vol 26 (04) ◽  
pp. 880-885 ◽  
Author(s):  
K. Kämmerle
Keyword(s):  
Diffusion Approximation ◽  
Large Population ◽  
Extinction Probability ◽  
Single Pair ◽  
Approximation Methods ◽  
Moran Model ◽  
Population Sizes ◽  
Limit Result

In this paper a bisexual Moran model is introduced. The population consists of N pairs of individuals. At times t = 1, 2, ·· ·two individuals are born, who ‘choose their parents randomly' and independently of each other. Then one of the pairs is removed and replaced by the two individuals born at that instant. The extinction probability of the descendants of a single pair and the number of ancestors of a whole generation are studied. A limit result for large population sizes has been derived by diffusion approximation methods.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 315
Author(s):  
Pria N. Ghosh ◽  
Lola M. Brookes ◽  
Hannah M. Edwards ◽  
Matthew C. Fisher ◽  
Phillip Jervis ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Fungal Infections ◽  
Large Population ◽  
Wildlife Health ◽  
Viral Pathogens ◽  
Population Sizes ◽  
Emerging Fungal Infections ◽  
Near Future ◽  
Supply Systems ◽  
Made In

Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.

scholarly journals Diagonal Acceleration for Covariance Matrix Adaptation Evolution Strategies

2020 ◽  
Vol 28 (3) ◽  
pp. 405-435 ◽  
Author(s):  
Y. Akimoto ◽  
N. Hansen
Keyword(s):  
Covariance Matrix ◽  
Large Population ◽  
Positive Definiteness ◽  
Diagonal Matrix ◽  
Evolution Strategies ◽  
Covariance Matrix Adaptation ◽  
Population Sizes ◽  
Matrix Formula ◽  
Adaptation Evolution ◽  
Landscape Feature

We introduce an acceleration for covariance matrix adaptation evolution strategies (CMA-ES) by means of adaptive diagonal decoding (dd-CMA). This diagonal acceleration endows the default CMA-ES with the advantages of separable CMA-ES without inheriting its drawbacks. Technically, we introduce a diagonal matrix [Formula: see text] that expresses coordinate-wise variances of the sampling distribution in DCD form. The diagonal matrix can learn a rescaling of the problem in the coordinates within a linear number of function evaluations. Diagonal decoding can also exploit separability of the problem, but, crucially, does not compromise the performance on nonseparable problems. The latter is accomplished by modulating the learning rate for the diagonal matrix based on the condition number of the underlying correlation matrix. dd-CMA-ES not only combines the advantages of default and separable CMA-ES, but may achieve overadditive speedup: it improves the performance, and even the scaling, of the better of default and separable CMA-ES on classes of nonseparable test functions that reflect, arguably, a landscape feature commonly observed in practice. The article makes two further secondary contributions: we introduce two different approaches to guarantee positive definiteness of the covariance matrix with active CMA, which is valuable in particular with large population size; we revise the default parameter setting in CMA-ES, proposing accelerated settings in particular for large dimension. All our contributions can be viewed as independent improvements of CMA-ES, yet they are also complementary and can be seamlessly combined. In numerical experiments with dd-CMA-ES up to dimension 5120, we observe remarkable improvements over the original covariance matrix adaptation on functions with coordinate-wise ill-conditioning. The improvement is observed also for large population sizes up to about dimension squared.

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