Measuring the extent of linkage disequilibrium in commercial pig populations

To evaluate the extent of linkage disequilibrium in domestic pigs, we genotyped 33 and 44 unrelated individuals from two commercial populations for 29 and five microsatellite markers located on chromosomes 15 and 2 respectively. A high proportion of marker pairs up to 40 cM apart exhibited significant linkage disequilibrium in both populations. Pair-wise r(2) values averaged between 0.15 and 0.50 (depending on chromosome and population) for markers <1 cM apart and declined to values of 0.05 for more distant syntenic markers. Our results suggest that both populations underwent a bottleneck approximately 20 generations ago, which reduced the effective population size from thousands to <200 animals.     

Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation

Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.     

Estimating effective population size from linkage disequilibrium: severe bias in small samples

Effective population size (N _e) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, fixation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of N _e from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of N _e using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small (<‰100) and below the true N _e. This is probably due to the linkage disequilibrium generated by the sampling process itself and the inadequate correction for this phenomenon in the method. Results suggest that N _e estimates derived using this method should be regarded with caution in many cases. To improve the method’s reliability and usefulness we propose a way to determine whether a given sample size exceeds the population N _e and can therefore be used for the computation of an unbiased estimate.     

The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies

Several previous studies concluded that linkage disequilibrium (LD) in livestock populations from developed countries originated from the impact of strong selection. Here, we assessed the extent of LD in a cattle population from western Africa that was bred in an extensive farming system. The analyses were performed on 363 individuals in a Bos indicus x Bos taurus population using 42 microsatellite markers on BTA04, BTA07 and BTA13. A high level of expected heterozygosity (0.71), a high mean number of alleles per locus (9.7) and a mild shift in Hardy-Weinberg equilibrium were found. Linkage disequilibrium extended over shorter distances than what has been observed in cattle from developed countries. Effective population size was assessed using two methods; both methods produced large values: 1388 when considering heterozygosity (assuming a mutation rate of 10(-3)) and 2344 when considering LD on whole linkage groups (assuming a constant population size over generations). However, analysing the decay of LD as a function of marker spacing indicated a decreasing trend in effective population size over generations. This decrease could be explained by increasing selective pressure and/or by an admixture process. Finally, LD extended over small distances, which suggested that whole-genome scans will require a large number of markers. However, association studies using such populations will be effective.     

Migration and inbreeding: the importance of recipient population size for genetic management

Sewall Wright demonstrated 70 years ago thatthe number of migrants required to maintainspecified levels of gene flow (i.e. avoidexcessive inbreeding) is virtually independentof the size of the recipient population. According to conventional wisdom, this idea isvalid provided population size exceeds 20. Itis well known that this independence implicitlyassumes that a population's effective size(N _e) is equal to its census size(N). However, it is not obvious whetherindependence between the required number ofmigrants (to avoid excessive inbreeding) andpopulation size constitutes a reasonableassumption for real populations of conservationconcern. Relying on empirical data, wedemonstrate that for real populations, theassumption (i.e. N _e = N) isroutinely violated to a degree such that therequired number of migrants is stronglydependent on the size of the recipientpopulation. Because a population's effectivesize (N _e) is typically much smallerthan its census size (N), the number ofmigrants required to avoid inbreeding isactually dependent on N even when it isconsiderably greater than 20. For example,when N _e/N = 0.1, the number ofmigrants required to maintain the inbreedingcoefficient (F) at 0.2 doubles (from 4 to8) as N increases from 9 to 60. Similarly, when N _e/N = 0.05, thenumber of migrants required increases by 50%as N increases from 18 to 45, andincreases again by 50% as N increasesfrom 45 to 260. Thus, for populations muchlarger than 20, the required number of migrantsincreases asymptotically with N, anddramatically so when N _e/N1. Simple conventions regarding the requisitenumber of migrants may not apply to manypopulations of conservation concern. Geneticmanagement should routinely rely on models thatexplicitly account for this and other recentconsiderations. Failure to do so mayjeopardize the viability of populations thatare sensitive to altered levels of inbreeding.     

Genetic population structure of central Oregon Coast coho salmon (<Emphasis Type="Italic">Oncorhynchus kisutch</Emphasis>)

We surveyed microsatellite variation from 22 spawning populations of coho salmon (Oncorhynchus kisutch) from the Oregon Coast to help identify populations for conservation planning. All of our samples were temporally replicated, with most samples obtained in 2000 and 2001. We had three goals: (1) to confirm the status of populations identified on the basis of spawning location and life history; (2) to estimate effective population sizes and migration rates in order to determine demographic independence at different spatial scales; and (3) to determine if releases of Washington hatchery coho salmon in the 1980's into Oregon Coast streams resulted in measurable introgression into nearby wild Oregon Coast coho populations. For the last question, our study included a hatchery broodstock sample from 1985, after the Puget Sound introduction, and a 1975 sample taken from the same area prior to the introduction. Our results generally supported previously hypothesized population structure. Most importantly, we found unique lake-rearing groups identified on the basis of a common life-history type were genetically related. Estimates of immigrant fraction using several different methods also generally supported previously identified populations. Estimates of effective population size were highly correlated with estimates of spawning abundance. The 1985 hatchery sample was genetically similar to contemporary Washington samples, and the contemporary Oregon Coast samples were similar to the 1975 Oregon Coast sample, suggesting that introductions of Washington coho salmon did not result in large scale introgression into Oregon populations.     

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.     

Effective population size and the rate and pattern of nucleotide substitutions

Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size (N_e). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N_e is often substantial, however, and must be accounted for in analyses of molecular evolution.     

Effect of parasitic sex-ratio distorters on host gene frequencies in a mainland-island context

It was previously argued that infection by parasitic sex-ratio distorters can enhance both random genetic drift and genetic influx from outside the population. However, these two enhancement effects have been studied independently. Here, we study the equilibrium frequencies of alleles (neutral and selected) in a mainland-island scenario where both genetic drift and genetic influx are enhanced due to infection by a cytoplasmic feminizing element. Interestingly, our model reveals that at neutral loci, the two effects almost exactly cancel each other out, such that infection has only a very minor effect on the equilibrium frequency distributions of alleles. At selected loci, in contrast, the two effects are unbalanced and infection has conspicuous effects. Despite the cryptic effects of infection at neutral loci, we demonstrate that temporally spaced data can be used to evaluate the effect of infection on genetic drift and that on gene flow separately.