Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non-neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels.

Global climate change (GCC) significantly affects distributional patterns of organisms 1 , and considerable impacts on biodiversity are predicted for the next decades. Inferred effects include large-scale range shifts towards higher altitudes and latitudes 2 , facilitation of biological invasions 3 and species extinctions 1,3 . Alterations of biotic patterns caused by GCC have usually been predicted on the scale of taxonomically recognized morphospecies 1 . However, the effects of climate change at the most fundamental level of biodiversityintraspecific genetic diversity-remain elusive 4 . Here we show that the use of morphospecies-based assessments of GCC effects will result in underestimations of the true scale of biodiversity loss. Species distribution modelling and assessments of mitochondrial DNA variability in nine montane aquatic insect species in Europe indicate that future range contractions will be accompanied by severe losses of cryptic evolutionary lineages and genetic diversity within these lineages. These losses greatly exceed those at the scale of morphospecies. We also document that the extent of range reduction may be a useful proxy when predicting losses of genetic diversity. Our results demonstrate that intraspecific patterns of genetic diversity should be considered when estimating the effects of climate change on biodiversity.Numerous studies document the effects of GCC on biodiversity both at the ecosystem and species level, but not at the level of intraspecific genetic diversity. This is surprising, given that the use of molecular techniques in biodiversity research increasingly results in the recognition of high levels of cryptic biodiversity below the morphospecies level 5 . Efforts to delimit evolutionarily significant units (ESUs) for biodiversity-related fields acknowledge the fact that the morphospecies concept seems increasingly insufficient for holistic biodiversity estimates 6 . However, a concise framework for estimating the effects of GCC on cryptic biodiversity and spatial genetic differentiation is still lacking. Here we introduce a widely applicable approach based on the use of range-wide phylogeographic mitochondrial DNA data and species distribution modelling (SDM), which allows estimation of climate-related future changes of genetic and cryptic biodiversity. We reason that species with strong genetic population structure will experience massive losses of cryptic diversity and ESUs under GCC, and that examining GCC effects solely at the level of morphospecies will underestimate the extent of climate-driven biodiversity loss.To test our hypotheses, we used range-wide mitochondrial sequence data (mitochondrial cytochrome c oxidase subunit I)