scholarly journals Natural selection constrains neutral diversity across a wide range of species.

2014 ◽  
Author(s):  
Russell B. Corbett-Detig ◽  
Daniel L. Hartl ◽  
Timothy B. Sackton
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Population Size ◽  
Neutral Theory ◽  
Genetic Maps ◽  
Modeling Framework ◽  
Neutral Genetic Diversity ◽  
Wide Range ◽  
Census Population Size ◽  
The Impact

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole-genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc, and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

scholarly journals Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

2020 ◽  
Vol 12 (2) ◽  
pp. 3803-3817 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Neutral Theory ◽  
Effective Population ◽  
Low Genetic Diversity

Abstract Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals The determinants of genetic diversity in butterflies – Lewontin’s paradox revisited

2019 ◽  
Author(s):  
Alexander Mackintosh ◽  
Dominik R. Laetsch ◽  
Alexander Hayward ◽  
Martin Waterfall ◽  
Roger Vila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Neutral Theory ◽  
Effective Population ◽  
Propagule Size ◽  
Animal Phyla ◽  
Order Of Magnitude ◽  
Population Sizes ◽  
Census Population Size ◽  
Host Plant Use

AbstractUnder the neutral theory genetic diversity is expected to be a simple function of population size. However, comparative studies have consistently failed to find any strong correlation between measures of census population size and genetic diversity. Instead, a recent comparative study across several animal phyla identified propagule size as the strongest predictor of genetic diversity, suggesting that r-strategists that produce many offspring but invest little in each, have greater long-term effective population sizes. We present a comparison of genome-wide levels of genetic diversity across 38 species of European butterflies (Papilionoidea). We show that across butterflies, genetic diversity varies over an order of magnitude and that this variation cannot be explained by differences in abundance, fecundity, host plant use or geographic range. Instead, we find that genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that variation in genetic diversity is determined both by fluctuation in Ne and the effect of selection on linked neutral sites.

scholarly journals Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Julien Hurbain ◽  
Darka Labavić ◽  
Quentin Thommen ◽  
Benjamin Pfeuty
Keyword(s):  
Cell Fate ◽  
Stochastic Dynamics ◽  
Biochemical Networks ◽  
Stochastic Bifurcation ◽  
Modeling Framework ◽  
Life And Death ◽  
Cell Fate Decisions ◽  
Wide Range ◽  
Adaptation Response ◽  
The Impact

Abstract Fractional killing illustrates the cell propensity to display a heterogeneous fate response over a wide range of stimuli. The interplay between the nonlinear and stochastic dynamics of biochemical networks plays a fundamental role in shaping this probabilistic response and in reconciling requirements for heterogeneity and controllability of cell-fate decisions. The stress-induced fate choice between life and death depends on an early adaptation response which may contribute to fractional killing by amplifying small differences between cells. To test this hypothesis, we consider a stochastic modeling framework suited for comprehensive sensitivity analysis of dose response curve through the computation of a fractionality index. Combining bifurcation analysis and Langevin simulation, we show that adaptation dynamics enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario. The generality of this result is further assessed by a computational analysis of a detailed regulatory network model of apoptosis initiation and by a theoretical analysis of stochastic bifurcation mechanisms. Overall, the present study identifies a cooperative interplay between stochastic, adaptation and decision intracellular processes that could promote cell-fate heterogeneity in many contexts.

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.

scholarly journals Conceptual Characterization of Threshold Concepts in Student Explanations of Evolution by Natural Selection and Effects of Item Context

2020 ◽  
Vol 19 (1) ◽  
pp. ar1 ◽  
Author(s):  
Andreas Göransson ◽  
Daniel Orraryd ◽  
Daniela Fiedler ◽  
Lena A. E. Tibell
Keyword(s):  
Natural Selection ◽  
Spatial Scale ◽  
Biology Education ◽  
Threshold Concepts ◽  
Differential Survival ◽  
Evolutionary Mechanisms ◽  
Biological Phenomena ◽  
Wide Range ◽  
Evolution By Natural Selection ◽  
The Impact

Evolutionary theory explains a wide range of biological phenomena. Proper understanding of evolutionary mechanisms such as natural selection is therefore an essential goal for biology education. Unfortunately, natural selection has time and again proven difficult to teach and learn, and students’ resulting understanding is often characterized by misconceptions. Previous research has often focused on the importance of certain key concepts such as variation, differential survival, and change in population. However, so-called threshold concepts (randomness, probability, spatial scale, and temporal scales) have also been suggested to be important for understanding of natural selection, but there is currently limited knowledge about how students use these concepts. We sought to address this lack of knowledge by collecting responses to three different natural selection items from 247 university students from Sweden and Germany. Content analysis (deductive and inductive coding) and subsequent statistical analysis of their responses showed that they overall use some spatial scale indicators, such as individuals and populations, but less often randomness or probability in their explanations. However, frequencies of use of threshold concepts were affected by the item context (e.g., the biological taxa and trait gain or loss). The results suggest that the impact of threshold concepts, especially randomness and probability, on natural selection understanding should be further explored.

scholarly journals SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Galeano ◽  
Jean Bousquet ◽  
Barb R. Thomas
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
White Spruce ◽  
Seed Orchard ◽  
Pedigree Reconstruction ◽  
Effective Population ◽  
Pollen Contamination ◽  
Contamination Levels ◽  
The Impact

AbstractAccurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

scholarly journals The Rate of Molecular Evolution When Mutation May Not Be Weak

2018 ◽  
Author(s):  
A.P. Jason de Koning ◽  
Bianca D. De Sanctis
Keyword(s):  
Natural Selection ◽  
Molecular Evolution ◽  
Population Size ◽  
Mutation Rate ◽  
Molecular Clock ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Systematic Bias ◽  
Effective Population ◽  
Sequence Comparisons

AbstractOne of the most fundamental rules of molecular evolution is that the rate of neutral evolution equals the mutation rate and is independent of effective population size. This result lies at the heart of the Neutral Theory, and is the basis for numerous analytic approaches that are widely applied to infer the action of natural selection across the genome and through time, and for dating divergence events using the molecular clock. However, this result was derived under the assumption that evolution is strongly mutation-limited, and it has not been known whether it generalizes across the range of mutation pressures or the spectrum of mutation types observed in natural populations. Validated by both simulations and exact computational analyses, we present a direct and transparent theoretical analysis of the Wright-Fisher model of population genetics, which shows that some of the most important rules of molecular evolution are fundamentally changed by considering recurrent mutation’s full effect. Surprisingly, the rate of the neutral molecular clock is found to have population-size dependence and to not equal the mutation rate in general. This is because, for increasing values of the population mutation rate parameter (θ), the time spent waiting for mutations quickly becomes smaller than the cumulative time mutants spend segregating before a substitution, resulting in a net deceleration compared to classical theory that depends on the population mutation rate. Furthermore, selection exacerbates this effect such that more adaptive alleles experience a greater deceleration than less adaptive alleles, introducing systematic bias in a wide variety of methods for inferring the strength and direction of natural selection from across-species sequence comparisons. Critically, the classical weak mutation approximation performs well only when θ< 0.1, a threshold that many biological populations seem to exceed.

scholarly journals Low genetic variation is associated with low mutation rate in the giant duckweed

2018 ◽  
Author(s):  
Shuqing Xu ◽  
Jessica Stapley ◽  
Saskia Gablenz ◽  
Justin Boyer ◽  
Klaus J. Appenroth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Effective Population ◽  
Spontaneous Mutation Rate ◽  
Low Genetic Diversity ◽  
Genome Wide ◽  
Census Population Size

AbstractMutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. We investigate genetic diversity, spontaneous mutation rate andNein the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals revealed extremely low within-species genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereasNeis large. These results demonstrate that low genetic diversity can be associated with large-Nespecies, where selection can reduce mutation rates to very low levels, and accurate estimates of mutation rate can help to explain seemingly counterintuitive patterns of genome-wide variation.One Sentence SummaryThe low-down on a tiny plant: extremely low genetic diversity in an aquatic plant is associated with its exceptionally low mutation rate.

scholarly journals Low Neutral Genetic Diversity in an Isolated Greater Sage Grouse (Centrocercus Urophasianus) Population in Northwest Wyoming

2012 ◽  
Vol 35 ◽  
pp. 119-133
Author(s):  
Sarah Schulwitz ◽  
Jeff Johnson ◽  
Bryan Bedrosian
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Centrocercus Urophasianus ◽  
Small Population ◽  
Suitable Habitat ◽  
Sage Grouse ◽  
Asymmetric Dispersal ◽  
Anthropogenic Habitat ◽  
Neutral Genetic Diversity

Habitat loss is well recognized as an immediate threat to biodiversity. Depending on the dispersal capabilities of the species, increased habitat fragmentation often results in reduced functional connectivity and gene flow followed by population decline and a higher likelihood of eventual extinction. Knowledge of the degree of connectivity between populations is therefore crucial for better management of small populations in a changing landscape. A small population of greater sage-grouse (Centrocercus urophasianus) exists in northwest Wyoming within the Jackson Hole valley, including Grand Teton National Park and the National Elk Refuge. To what degree the Jackson population is isolated is not known as natural dispersal barriers in the form of mountains and anthropogenic habitat fragmentation may limit the population’s connectivity to adjacent populations. Using 16 microsatellite loci and 300 greater sage-grouse samples collected throughout Wyoming and southeast Montana, significant population differentiation was found to exist among populations. Results indicated that the Jackson population was isolated relative to the other sampled populations, including Pinedale, its closest neighboring large population to the south. The one exception was a small population immediately to the east of Jackson, in which asymmetric dispersal from Jackson into Gros Ventre was detected. Both Jackson and Gros Ventre populations exhibited significantly reduced levels of neutral genetic diversity relative to other sampled populations. More work is warranted to determine the timing at which Jackson and Gros Ventre populations had become isolated and whether it was primarily due to recent habitat fragmentation or more historic processes. Due to its small population size, continual monitoring of the population is recommended with the goal of at least maintaining current population size and, if possible, increasing suitable habitat and population size to levels recorded in the past.

scholarly journals Impact of fertility variation on genetic diversity and phenotypic traits in second generation seed production areas and clonal seed orchards of Eucalyptus camaldulensis

2019 ◽  
Vol 68 (1) ◽  
pp. 29-40
Author(s):  
P.G. Suraj ◽  
K. Nagabhushana ◽  
R. Kamalakannan ◽  
M. Varghese
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Second Generation ◽  
Gene Diversity ◽  
Eucalyptus Camaldulensis ◽  
Phenotypic Traits ◽  
Effective Population ◽  
Fertility Variation ◽  
The Impact

Abstract Fertility and gene diversity were estimated in three second generation (F2) seed stands (SPA 1-3) and two clone trials (CSO 1&2) of Eucalyptus camaldulensis to assess the impact on seed crop. F2 seedlots were evaluated in comparison to native provenances, ten commercial clones and interspecific hybrids at diverse sites. SPA 1&2 were genetic gain trials of five first generation (F1) orchard seedlots, SPA 3 a plantation of one F1 orchard seedlot, and CSOs were clone trials of 21 commercial clones established at two contrasting sites. Fertility variation, as indicated by sibling coefficient, was high (Ψ, 9-14) in the SPAs as only about 26 % trees were fertile compared to 81 % trees in CSOs. Effective population size was higher in SPA 1 and 2 (Ns, 95 and 74, respectively) than SPA 3 (Ns = 39). Fertility was highly skewed in CSO 2 resulting in low effective population size (Ns = 2) compared to CSO 1 (Ns = 11). Constant seed collection enabled 3-fold increase in relative population size and 22 % higher predicted gene diversity in CSO 2. Genetic diversity (He) estimated using SSR markers was higher in SPA 1&2 and native provenances (NAT), compared to SPA 3 and CSO 1, whereas CSO 2 and clones had lower values. There was a high positive correlation between estimated He and predicted gene diversity values of SPAs and CSOs. He was positively correlated to mean field survival and negatively correlated to kraft pulp yield (KPY), evaluated at three years in progeny trials across three locations. Number of alleles per locus was higher in SPAs and native provenances compared to CSOs and clones. Discriminant principal component analysis clustered CSO, NAT and SPA seedlots in different groups while commercial E. camaldulensis clones clustered close to NAT. Multilocus outcrossing rate was generally high (tm, 91-100 %), though selfing was observed in two families of SPA 3 and CSO 2. Selected interspecific hybrid families of commercial E. camaldulensis clones (with E. urophylla and E. pellita) evaluated at two of the sites had higher He and KPY than clones at three years.

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