<scp>ldne</scp>: a program for estimating effective population size from data on linkage disequilibrium

Waples, Robin S.; Do, Chi

doi:10.1111/j.1755-0998.2007.02061.x

Cited by 1,157 publications

(1,178 citation statements)

References 14 publications

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“…Population pairwise F ST and associated p ‐values were also estimated using GENEPOP v4.2. The genetically effective size ( N e ) of each population was estimated using NeEstimator v2.01 (Do et al., 2014) under the random mating model using the linkage disequilibrium method (Waples & Do, 2008), with an MAF cutoff of 0.05 (R. Waples, NOAA, personal communication ).…”

Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction‐site‐associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation‐by‐distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low F ST marine species.

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Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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“…With genotypes coded in this way, r 2 is identical to Burrows' composite measure of linkage disequilibrium (r Δ ) (Weir, 1996;Zaykin, 2004). To mirror the approach implemented in the software LDNe (Waples and Do, 2008), where a sample-size adjustment factor of [S/(S − 1)] 2 was used (Weir, 1979), we multiplied each r 2 value by this term, subtracted the expected contribution from sampling error to obtain the adjusted r 2 ', and then calculatedN e as in Waples (2006).…”

Section: Simulation Proceduresmentioning

confidence: 99%

“…This naive approach mirrors the lack of genomic resources, such as a reference genome or linkage map, that is present in most non-model species and in nearly all species of conservation concern. N e estimates were generated with a custom version of the LDNe program (Waples and Do, 2008) available from the authors upon request. This estimation procedure closely matches the calculations made in the analysis of the simulated data, except a weighted mean r 2 was calculated based on the sample size of each locus due to some missing data.…”

Section: Empirical Examplementioning

confidence: 99%

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

2016

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Contemporary effective population size (N e ) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these N e estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause N e estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based N e estimates (N e ). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r 2 values, simply removing large r 2 values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias inN e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision ofN e is much lower than expected based on the assumption that each pair of loci provides completely independent information. Heredity (Wright, 1931), which determines the rate of evolutionary change due to genetic drift and informs the equilibrium level of genetic variation and the effectiveness of selection. N e is often much lower than census size (Frankham, 1995), demonstrating that simply counting individuals is insufficient to predict rates of evolutionary change. In addition to the number of mating individuals, N e is affected by sex ratio, variation in reproductive success, age structure, migration and other demographic factors. It is an extremely relevant metric in conservation biology, with low N e leading to inbreeding and reduced genetic diversity (Ellstrand and Elam, 1993). See Charlesworth (2009) for a primer on N e , and Wang (2005) for a review of estimation methods.Populations with smaller N e undergo more genetic drift than larger populations. This genetic drift randomly generates associations between alleles at different loci, known as linkage (or gametic) disequilibrium (LD) at a rate inversely proportional to N e . As a result, measures of LD between independently-segregating loci can be used to provide an estimate of N e (Sved, 1971;Hill, 1981;Waples, 1991). Over the past decades, many studies have leveraged data sets consisting of a few dozen loci for genetic estimates of N e (Luikart et al., 2010). While these studies continue to be useful, especially for long-running

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“…To infer the contemporary N e in each time period, we used the linkage disequilibrium method (LD) as implemented in the program LDN e , [58]. The LD method is based on the theoretical expectation that when N e decreases, linkage disequilibrium due to drift will increase [59,60].…”

Section: Methodsmentioning

confidence: 99%

Temporal patterns of genetic diversity in Kirtland’s warblers (Dendroica kirtlandii), the rarest songbird in North America

2012

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BackgroundKirtland’s warblers are the rarest songbird species in North America, rarity due in part to a reliance on early successional Jack Pine forests. Habitat loss due to fire suppression led to population declines to fewer than 200 males during the 1970s. Subsequent conservation management has allowed the species to recover to over 1700 males by 2010. In this study, we directly examine the impact that low population sizes have had on genetic variation in Kirtland’s warblers. We compare the molecular variation of samples collected in Oscoda County, Michigan across three time periods: 1903–1912, 1929–1955 and 2008–2009.ResultsIn a hierarchical rarified sample of 20 genes and one time period, allelic richness was highest in 1903–1912 sample (ar = 5.96), followed by the 1929–1955 sample (ar = 5.74), and was lowest in the 2008–2009 sample (ar = 5.54). Heterozygosity measures were not different between the 1929–1955 and 2008–2009 samples, but were lower in the 1903–1912 sample. Under some models, a genetic bottleneck signature was present in the 1929–1955 and 2008–2009 samples but not in the 1903–1912 sample.ConclusionsWe suggest that these temporal genetic patterns are the result of the declining Kirtland’s warbler population compressing into available habitat and a consequence of existing at low numbers for several decades.

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ldne: a program for estimating effective population size from data on linkage disequilibrium

Cited by 1,157 publications

References 14 publications

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

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

Temporal patterns of genetic diversity in Kirtland’s warblers (Dendroica kirtlandii), the rarest songbird in North America

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