The standard temporal method for estimating effective population size (Ne) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\hat{N}}_{\mathrm{e}}\) \end{document}$ caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age-structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\hat{N}}_{\mathrm{e}}\) \end{document}$. The direction and magnitude of the bias are shown to depend on the sampling method and the species' life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde–Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.

Aim: As climate change presents a major threat to biodiversity in the next decades, it is critical to assess its impact on species habitat suitability to inform biodiversity conservation. Species distribution models (SDMs) are a widely used tool to assess climate change impacts on species’ geographical distributions. As the name of these models suggests, the species level is the most commonly used taxonomic unit in SDMs. However, recently it has been demonstrated that SDMs considering taxonomic resolution below (or above) the species level can make more reliable predictions of biodiversity change when different populations exhibit local adaptation. Here, we tested this idea using the Japanese crayfish (Cambaroides japonicus), a threatened species encompassing two geographically structured and phylogenetically distinct genetic lineages.Location: Northern Japan.Methods: We first estimated niche differentiation between the two lineages of C. japonicus using n‐dimensional hypervolumes and then made climate change predictions of habitat suitability using SDMs constructed at two phylogenetic levels: species and intraspecific lineage.Results: Our results showed only intermediate niche overlap, demonstrating measurable niche differences between the two lineages. The species‐level SDM made future predictions that predicted much broader and severe impacts of climate change. However, the lineage‐level SDMs led to reduced climate change impacts overall and also suggested that the eastern lineage may be more resilient to climate change than the western one.Main conclusions: The two lineages of C. japonicus occupy different niche spaces. Compared with lineage‐level models, species‐level models can overestimate climate change impacts. These results not only have important implications for designing future conservation strategies for this threatened species, but also highlight the need for incorporating genetic information into SDMs to obtain realistic predictions of biodiversity change.