Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review

Molecular Ecology Resources, Год журнала: 2023, Номер 24(1)

Опубликована: Окт. 24, 2023

Abstract The method to estimate contemporary effective population size ( N e ) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied natural and managed populations. underlying model makes many simplifying assumptions, most which have evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed summarized, with a focus information that facilitates practical application real populations nature. Potential sources bias discussed include calculation r 2 (a measure LD), adjustments for sampling error, physical linkage, age structure, migration spatial mutation selection, mating systems, changes abundance, rare alleles, missing data, genotyping errors, data filtering choices methods combining multiple estimates. Factors affect precision reviewed, including pseudoreplication limits gained from large genomics datasets, constraints imposed by small samples individuals, challenges obtaining robust estimates Topics merit further research potential weight values allele frequency, lump use genotypic likelihoods rather than called genotypes, prune LD apply species practising partial monogamy.

Язык: Английский

Variation in Flatwoods Salamander Survival Is Unrelated to Temperature and Rainfall

Ichthyology & Herpetology, Год журнала: 2024, Номер 112(1)

Опубликована: Фев. 13, 2024

Survival rates are known to vary over the course of an individual's lifetime and among individuals within a population. Quantifying natural variability in survival is crucial when scaling up infer dynamics populations. Using ten years mark–recapture data from two adjacent wetlands on Florida Panhandle, we investigated individual temporal Reticulated Flatwoods Salamanders (Ambystoma bishopi). Our objectives were 1) provide first estimates for species, 2) evaluate relationship between body size mortality risk, 3) quantify degree across study period, 4) discern whether or detection correlates with environmental conditions. To address these objectives, constructed modified Cormack-Jolly-Seber model that includes year as covariates. Mean annual was estimated be 0.72 strongly correlated size; smallest 0.5 those largest 0.85. also varied considerably years, but it did not correlate temperature extremes rainfall. Therefore, key priority future research should identify ecological risk A. bishopi. results can integrated into demographic projections will help managers population viability, alternative management strategies (e.g., habitat restoration), buffer impacts climate change. More broadly, our work highlights need more long-term studies garner accurate vital aid ongoing recovery efforts endangered at-risk species.

Язык: Английский

Predicting the population viability of an endangered amphibian under environmental and demographic uncertainty

Population Ecology, Год журнала: 2023, Номер 66(3), С. 184 - 195

Опубликована: Дек. 13, 2023

Abstract Population viability analyses (PVAs) represent a key component of many recovery plans for threatened and endangered species. Demography links the processes that affect individuals to population‐level patterns, hence projections constructed from demographic data are most common tools PVAs. We size‐structured integral projection model (IPM) United States federally Reticulated Flatwoods Salamander, Ambystoma bishopi , evaluate influences on population growth predict efficacy future management actions. salamanders breed in ephemeral wetlands Southeastern States. The nature breeding sites can result complete recruitment failure drought years when fail fill, or dry before metamorphosis occurs. As result, this species exhibits marked temporal variability vital rates must be accounted models. stochastic IPM using 13 mark‐recapture (2010–2023) two wetlands. Variable survival exhibited by flatwoods salamanders, coupled with high probability failure, low predicted persistence. Sensitivity revealed age at maturity frequency exerted greatest influence growth, thus managers should prioritize conservation efforts target these processes. Additional consider strategies dampen larval survival, something could achieved through emergency salvage operations, captive rearing efforts, manipulation wetland hydroperiods.

Язык: Английский