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

By Robin S. Waples, C. Do. Molecular Ecology Resources, 2008

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In Genetics

Citations in the corpus

Genetic variation and effective population size in isolated populations of coastal cutthroat trout (2010, methodology): “ONeSAMP provided smaller credible limits than those from LDNE (Table 2).”
Responsible genetic approach to stock restoration, sea ranching and stock enhancement of marine fishes and invertebrates (2017, background): “The genetic effective size of a wild population can be estimated before supplementation begins with a single sample of molecular data (Tallmon et al. 2008; Waples and Do 2008) or with generational samples (Wang et al.”
Strategies for the retention of high genetic variability in European flat oyster (Ostrea edulis) restoration programmes (2010, methodology): “The linkage disequilibrium method (Hill 1981) was 248 implemented in LDNE program (Waples and Do 2008).”
Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution (2009, methodology): “In de pe nd en t a lle lic c om pa ris on s (n ) 0 2000 4000 6000 8000 10 000 N = 50; S = 25 N = 100; S = 50 N = 5000; S = 200 0 2000 4000 6000 8000 10 000 N = 100; S = 50; L = 20 A = 10; L = 20 0.000.020.040.060.080.10 0 10 000 20 000 30 000”
Aquatic insects in a sea of desert: population genetic structure is shaped by limited dispersal in a naturally fragmented landscape (2013, methodology): “For comparison, we also estimated Ne using the linkage disequilibrium method in the program LDNe (Waples and Do 2008).”
Fragmentation and patch size shape genetic structure of brook trout populations (2013, background): “02, which has been shown to provide an adequate balance between precision and bias across sample sizes (Waples and Do 2008).”
SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data (2015, methodology): “To our knowledge the only software available that estimate N e through LD is NeEstimator (Do et al., 2014), an upgraded version of the former LDNE (Waples and Do, 2008) allowing the analysis of large dataset (as 50k SNPChip).”
Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes (2012, methodology): “The program LDNe Version 1.31 (Waples & Do 2008) was used to produce CNe estimates for Australia as a whole and for each region, since CNe estimates may be biased where population structure exists (Palstra & Ruzzante 2008).”
Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches (2010, methodology): “Assumptions of LD-Ne are similar to the temporal method (Tables 3, 4), and require that the source of LD is from small Ne. LD-Ne assumes random mating, although an estimator exists for monogamous mating (Waples and Do 2008).”
NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data (2014, methodology): “N E E STIMATOR software (v2) provides options for screening out rare alleles for all methods except molecular coances-try (for which allele frequency is not an issue), using the same protocols as LDNe (Waples & Do 2008).”