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 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 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 Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, 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 dataset to date from 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 non-synonymous to synonymous diversity, is also significantly negatively correlated to both range 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 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

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 Effective population size/adult population size ratios in wildlife: a review

1995 ◽  
Vol 66 (2) ◽  
pp. 95-107 ◽  
Author(s):  
Richard Frankham
Keyword(s):  
Sex Ratio ◽  
Population Size ◽  
Effective Population Size ◽  
Family Size ◽  
Adult Population ◽  
Effective Population ◽  
Total Size ◽  
Relevant Variables ◽  
Population Sizes ◽  
Census Population Size

SummaryThe effective population size is required to predict the rate of inbreeding and loss of genetic variation in wildlife. Since only census population size is normally available, it is critical to know the ratio of effective to actual population size (Ne/N). Published estimates ofNe/N(192 from 102 species) were analysed to identify major variables affecting the ratio, and to obtain a comprehensive estimate of the ratio with all relevant variables included. The five most important variables explaining variation among estimates, in order of importance, were fluctuation in population size, variance in family size, form ofNused (adults υ. breeders υ. total size), taxonomic group and unequal sex-ratio. There were no significant effects on the ratio of high υ. low fecundity, demographic υ. genetic methods of estimation, or of overlapping υ. non-overlapping generations when the same variables were included in estimates. Comprehensive estimates ofNe/N(that included the effects of fluctuation in population size, variance in family size and unequal sex-ratio) averaged only 0·10–0·11. Wildlife populations have much smaller effective population sizes than previously recognized.

scholarly journals Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

2021 ◽  
Author(s):  
Michaela Halsey ◽  
John Stuhler ◽  
Natalia J Bayona-Vasquez ◽  
Roy N Platt ◽  
Jim R Goetze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Population Fluctuations ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Demographic Dynamics ◽  
Population Sizes

Organisms with low effective population sizes are at greater risk of extinction because of reduced genetic diversity.   Dipodomys elator  is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread  D. ordii  is thought to exhibit relative geographic and demographic stability. Genetic variation between  D. elator  and  D. ordii  samples was assessed using 3RAD, a modified restriction site associated sequencing approach. It was hypothesized that  D. elator  would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to  D. ordii . Also of interest was identifying population structure within contemporary samples of  D. elator  and detecting genetic variation between temporal samples that could indicate demographic dynamics. Up to 61,000 single nucleotide polymorphisms were analyzed. It was determined that genetic variability and effective population size in contemporary  D. elator  populations were lower than that of  D. ordii, that there is only slight, if any, structure within contemporary  D. elator  populations, and there is little genetic differentiation between spatial or temporal historical samples suggesting little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of  D. elator  has remained stable despite claims of reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract any immediate decrease in fitness.

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