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 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 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 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 Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals A NEW METHOD FOR ESTIMATING THE EFFECTIVE POPULATION SIZE FROM ALLELE FREQUENCY CHANGES

Genetics ◽  
1983 ◽  
Vol 104 (3) ◽  
pp. 531-548
Author(s):  
Edward Pollak
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
New Method ◽  
Standard Errors ◽  
Effective Population ◽  
Census Size ◽  
Population Sizes ◽  
Frequency Changes ◽  
Approximate Expressions

ABSTRACT A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.

scholarly journals Relationship Between Phyllosphere Population Sizes of Xanthomonas translucens pv. translucens and Bacterial Leaf Streak Severity on Wheat Seedlings

1999 ◽  
Vol 89 (2) ◽  
pp. 131-135 ◽  
Author(s):  
Kurt D. Stromberg ◽  
Linda L. Kinkel ◽  
Kurt J. Leonard
Keyword(s):  
Disease Control ◽  
Population Size ◽  
Logistic Model ◽  
Bacterial Leaf Streak ◽  
Pathogen Population ◽  
Wheat Seedlings ◽  
Xanthomonas Translucens ◽  
Population Sizes ◽  
The Relationship ◽  
Disease Severity Level

The relationship between leaf-associated population sizes of Xanthomonas translucens pv. translucens on asymptomatic leaves and subsequent bacterial leaf streak (BLS) severity was investigated. In three experiments, X. translucens pv. translucens was spray-inoculated onto 10-day-old wheat seedlings over a range of inoculum densities (104, 105, 106, 107, and 108 CFU/ml). Lesions developed most rapidly on plants inoculated with higher densities of X. translucens pv. translucens. Leaf-associated pathogen population sizes recovered 48 h after inoculation were highly predictive of BLS severity 7 days after inoculation (R2 = 0.970, P < 0.0001). The relationship between pathogen population size on leaves and subsequent BLS severity was best described by the logistic model. Leaf-associated X. translucens pv. translucens population size and BLS severity from a particular pathogen inoculum density often varied among experiments; however, the disease severity level caused by a particular leaf-associated X. translucens pv. translucens population size was not significantly different among experiments. Biological and disease control implications of the X. translucens pv. translucens population size-BLS severity relationship are discussed.

scholarly journals Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

2010 ◽  
Vol 365 (1543) ◽  
pp. 1127-1138 ◽  
Author(s):  
Paquita E. A. Hoeck ◽  
Jennifer L. Bollmer ◽  
Patricia G. Parker ◽  
Lukas F. Keller
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Genetic Drift ◽  
Bird Species ◽  
Effective Population ◽  
Island Size ◽  
Island Populations ◽  
Population Sizes ◽  
Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Empirical Studies ◽  
Small Population ◽  
Native Plant ◽  
Effective Population ◽  
Term Survival ◽  
Inbreeding Coefficients ◽  
Native Populations ◽  
Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

scholarly journals The effect of population size on effective population size: an empirical study in the red flour beetle Tribolium castaneum

1996 ◽  
Vol 68 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Leslie A. Pray ◽  
Charles J. Goodnight ◽  
Lori Stevens ◽  
James M. Schwartz ◽  
Guiyun Yan
Keyword(s):  
Population Size ◽  
Tribolium Castaneum ◽  
Evolutionary Biology ◽  
Negative Relationship ◽  
Red Flour Beetle ◽  
Published Data ◽  
Effective Population ◽  
Flour Beetle ◽  
Large Populations ◽  
Population Sizes

SummaryDespite the increasing number of studies on the magnitude of Ne/N ratios, much remains unknown about the effects of demographic and environmental variables on Ne/N. We determined Ne/N for seven population size treatments, ranging from N = 2 to N = 960, in the red flour beetle Tribolium castaneum. Ne/N decreased with increasing N, as evidenced by a significant negative relationship between log N and Ne/N. Our results are consistent with other published data on the relationship between Ne/N and N. Effective population sizes in large populations may be much smaller than previously recognized. These results have important implications for conservation and evolutionary biology.

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