Linkage disequilibrium estimates of contemporary N_e using highly variable genetic markers: a largely untapped resource for applied conservation and evolution

Abstract

Genetic methods are routinely used to estimate contemporary effective population size (Ne) in natural populations, but the vast majority of applications have used only the temporal (two-sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single-sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low-frequency alleles upwardly bias , but a simple rule can reduce bias to <about 10% without sacrificing much precision. (2) With datasets routinely available today (10–20 loci with 10 alleles; 50 individuals), precise estimates can be obtained for relatively small populations (Ne < 200), and small populations are not likely to be mistaken for large ones. However, it is very difficult to obtain reliable estimates for large populations. (3) With ‘microsatellite’ data, the LD method has greater precision than the temporal method, unless the latter is based on samples taken many generations apart. Our results indicate the LD method has widespread applicability to conservation (which typically focuses on small populations) and the study of evolutionary processes in local populations. Considerable opportunity exists to extract more information about Ne in nature by wider use of single-sample estimators and by combining estimates from different methods.

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

“…This effect is larger with smaller sample sizes (S). This has been noted previously (for example, Waples and Do, 2010) and is likely due to a slight bias overcorrection in LDNe method relative to the original Hill method. Our results thus allow the user to simultaneously correct for bias due to linkage and the slight upward bias that occurs in LDNe.…”

“…Other methods have computed a weighted mean based on allele frequencies, number of alleles and/or missing data (for example, Peel et al, 2013;Sved et al, 2013), but here we simulate only bi-allelic loci without missing data and did not compute a weighted mean. Alleles observed in low numbers (⩽2) provide little information on LD and can upwardly bias estimates of r 2 (Waples and Do, 2010), so we excluded loci with an observed minor allele frequency of o0.05 in each replicate. Using the LD method, after correcting for sampling-induced LD, it is possible to produce estimates of infinite N e ; to incorporate these values into summary statistics we replaced infinite estimates with 10 000.…”

“…LD between neutral and independently-segregating loci should provide a nearly unbiased estimate of N e (Hill, 1981;Waples and Do, 2010). Bias in N e estimates was assessed by comparing estimates with census sizes (N) of Wright-Fisher ideal populations.…”

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

“…The rates of F and f only give estimates of N e based on limited time period, and taking into account the year of birth of individuals (that in local breeds as Cinisara and Modicana may be incorrect) may result in biased estimates. LD-based method uses more information, leads to an accurate estimate (Waples and Do, 2010;Waples and England, 2011;Saura et al, 2015), with the possibility of investigating the change of N e over time, as LD between loci at a specific recombination distance reflects the ancestral N e 1/2c generations ago (Hayes et al, 2003), if the population grows linearly over time. However, it should be Runs of homozygosity in three local cattle breeds underlined that some parameters, as density and frequency of SNP pairs and distribution of MAF, affect the estimations of LD (Ober et al, 2013) and then of N e .…”

Genome‐wide comparisons reveal a clinal species pattern within a holobenthic octopod—the Australian Southern blue‐ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae)

“…However, the Mandurah and Port Phillip Bay sites returned N eLD values of infinity. The N eLD estimates should be regarded with some caution, as the assumption of random sampling may not have been met at all sites (Do et al., 2014; Waples & Do, 2010). …”