Sample genealogies and genetic variation in populations of variable size

We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies. Within the coalescent approximation we have obtained a general expression, Eq. (27), for the moments of these distributions for an arbitrary smooth dependence of the population size on time. We investigate how the frequency of population-size variations alters the distributions. This allows us to discuss their influence on the distribution of the number of mutations, and on the population homozygosity in populations with variable size.Comment: 19 pages, 8 figures, 1 tabl

The effect of multiple paternity on genetic diversity during and after colonisation

In metapopulations, genetic variation of local populations is influenced by the genetic content of the founders, and of migrants following establishment. We analyse the effect of multiple paternity on genetic diversity using a model in which the highly promiscuous marine snail Littorina saxatilis expands from a mainland to colonise initially empty islands of an archipelago. Migrant females carry a large number of eggs fertilised by 1 - 10 mates. We quantify the genetic diversity of the population in terms of its heterozygosity: initially during the transient colonisation process, and at long times when the population has reached an equilibrium state with migration. During colonisation, multiple paternity increases the heterozygosity by 10 - 300 % in comparison with the case of single paternity. The equilibrium state, by contrast, is less strongly affected: multiple paternity gives rise to 10 - 50 % higher heterozygosity compared with single paternity. Further we find that far from the mainland, new mutations spreading from the mainland cause bursts of high genetic diversity separated by long periods of low diversity. This effect is boosted by multiple paternity. We conclude that multiple paternity facilitates colonisation and maintenance of small populations, whether or not this is the main cause for the evolution of extreme promiscuity in Littorina saxatilis.Comment: 7 pages, 5 figures, electronic supplementary materia

Linkage disequilibrium under recurrent bottlenecks

Understanding patterns of selectively neutral genetic variation is essential in order to model deviations from neutrality, caused for example by different forms of selection. Best understood is neutral genetic variation at a single locus, but additional insights can be gained by investigating genetic variation at multiple loci. The corresponding patterns of variation reflect linkage disequilibrium and provide information about the underlying multi-locus gene genealogies. The statistical properties of two-locus genealogies have been intensively studied for populations of constant census size, as well as for simple demographic histories such as exponential population growth, and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright-Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci. We find, first, that an effective population-size approximation describes the numerically observed linkage disequilibrium provided that recombination occurs either much faster or much more slowly than the population size changes. Second, when recombination occurs frequently between bottlenecks but rarely within bottlenecks, we observe long-range linkage disequilibrium. Third, we show that in the latter case, a commonly used measure of linkage disequilibrium, sigma_d^2 (closely related to r^2), fails to capture long-range linkage disequilibrium because constituent terms, each reflecting long-range linkage disequilibrium, cancel. Fourth, we analyse a limiting case in which long-range linkage disequilibrium can be described in terms of a Xi-coalescent process allowing for simultaneous multiple mergers of ancestral lines.Comment: 34 pages, 7 figure

Agriculture in the Trans-Pacific Partnership

The Trans-Pacific Partnership is a trade and investment agreement under negotiation by 12 countries in the Pacific Rim. This report assesses this partnership's potential impacts on the region's agriculture in 2025

What explains rare and conspicuous colours in a snail? A test of time-series data against models of drift, migration or selection

It is intriguing that conspicuous colour morphs of a prey species may be maintained at low frequencies alongside cryptic morphs. Negative frequency-dependent selection by predators using search images ('apostatic selection') is often suggested without rejecting alternative explanations. Using a maximum likelihood approach we fitted predictions from models of genetic drift, migration, constant selection, heterozygote advantage or negative frequency-dependent selection to time-series data of colour frequencies in isolated populations of a marine snail (Littorina saxatilis), re-established with perturbed colour morph frequencies and followed for >20 generations. Snails of conspicuous colours (white, red, banded) are naturally rare in the study area (usually <10%) but frequencies were manipulated to levels of ~50% (one colour per population) in 8 populations at the start of the experiment in 1992. In 2013, frequencies had declined to ~15-45%. Drift alone could not explain these changes. Migration could not be rejected in any population, but required rates much higher than those recorded. Directional selection was rejected in three populations in favour of balancing selection. Heterozygote advantage and negative frequency-dependent selection could not be distinguished statistically, although overall the results favoured the latter. Populations varied idiosyncratically as mild or variable colour selection (3-11%) interacted with demographic stochasticity, and the overall conclusion was that multiple mechanisms may contribute to maintaining the polymorphisms.Heredity advance online publication, 21 September 2016; doi:10.1038/hdy.2016.77

The Total Branch Length of Sample Genealogies in Populations of Variable Size

We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we study the distribution of the total branch lengths of its sample genealogies. Within the coalescent approximation we have obtained a general expression—Equation 20—for the moments of this distribution with a given arbitrary dependence of the population size on time. We investigate how the frequency of population-size variations alters the total branch length

Demography-adjusted tests of neutrality based on genome-wide SNP data

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and the population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key ingredients are the first two moments of the site frequency spectrum. We show how these moments can be computed analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's D, Fay & Wu's H, and Zeng's E. Our results show that demography-adjusted test statistics facilitate the direct comparison between populations and that most of the differences among populations seen in the original unadjusted tests can be explained by their underlying demographies. Upon carrying out whole-genome screens for deviations from neutrality, we identify candidate regions of recent positive selection. We provide track files with values of the adjusted and unadjusted tests for upload to the UCSC genome browser. (C) 2014 Elsevier Inc. All rights reserved

Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina

When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment

Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients