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This article highlights how the loose definition of the term 'refugia' has led to discrepancies in methods used to assess the vulnerability of species to the current trend of rising global temperatures. The term 'refugia' is commonly used without distinguishing between macrorefugia and microrefugia, ex situ refugia and in situ refugia, glacial and interglacial refugia or refugia based on habitat stability and refugia based on climatic stability. It is not always clear which definition is being used, and this makes it difficult to assess the appropriateness of the methods employed. For example, it is crucial to develop accurate fine-scale climate grids when identifying microrefugia, but coarse-scale macroclimate might be adequate for determining macrorefugia. Similarly, identifying in situ refugia might be more appropriate for species with poor dispersal ability but this may overestimate the extinction risk for good dispersers. More care needs to be taken to properly define the context when referring to refugia from climate change so that the validity of methods and the conservation significance of refugia can be assessed.

Aim The aim of this study was to conduct comprehensive phylogeographic and demographic analyses to examine the degree to which topographic and climatic conditions have affected the patterns of diversification and migration in a strictly montane inhabitant, the montane long‐tailed mole (Scaptonyx fusicaudus). Location The mountains of south‐western China and adjacent mountains including Mts. Bashan, Dalou and Qinling also known as the sky islands in south‐western China. Taxon The long‐tailed mole (S. fusicaudus), a semi‐fossorial mammal distributed in the sky islands of south‐western China, is a relict species and the sole representative of the tribe Scaptonychini. Methods We sequenced one mitochondrial and six nuclear genes from 113 samples across the species’ range. We estimated phylogenetic relationships and divergence times, conducted genetic structuring and species delimitation using multiple approaches and used Approximate Bayesian Computation to test potential gene flow. We conducted ecological niche modelling to predict the species’ potential distribution in the present, the last glacial maximum and the last interglacial (LIG). Results The species comprises a minimum of 17 operational taxonomic units which are isolated in different mountain ranges. The lowlands and large rivers act as barriers to dispersal, and have isolated evolutionary lineages for up to 11 million years. Long‐distance dispersal is evident among a few discrete montane archipelagos. Suitable climatic conditions during the LIG are limited to only a few sites, thus geographically restricting climatic stable areas across geological periods (from the LIG to the present). Main conclusions For low‐vagility species, the complex topography of the sky islands has promoted exceptional diversification through a combination of eco‐environmental stability as well as geographic fragmentation. The mountains have acted as a buffer against climate change, and have provided continuously suitable habitats for S. fusicaudus since the early Late Miocene, supporting the hypothesis that the sky islands constitute “museums” of ancient lineages. Lowlands and river valleys have acted as barriers preventing gene flow, while the montane archipelagos could have provided stepping stones to facilitate dispersal.

Pleistocene microrefugia (or cryptic refugia) may be distinguished from macrorefugia (or conventional refugia) on the basis of two characteristics. First, microrefugia were smaller than macrorefugia and consequently supported smaller refugial populations. Second, microrefugia harboured less diverse biotic communities than macrorefugia. We propose that these characteristics have important implications for the ecology and evolution of species and populations that have a history of isolation in microrefugia. We propose four hypotheses regarding the evolution of microrefugial populations: (1) small effective population sizes associated with survival in microrefugia lead to reduced genetic diversity and influence the evolution of mating systems; (2) differences in environmental conditions between macro‐ and microrefugia lead to local adaptation; (3) reduced diversity increases ecological opportunity and promotes ecological divergence in microrefugia; and (4) reduced species diversity in microrefugia allows more specific species interactions and promotes coevolution among species. We urge biogeographers to study the evolutionary implications of isolation in microrefugia.

Aim: We studied which factors shape contemporary patterns of genetic structure, diversity and admixture in the canyon live oak (Quereus chrysolepis). Specifically, we tested two alternative hypotheses: (1) that areas with high habitat suitability and stability since the Last Glacial Maximum (LGM) sustain higher effective population sizes, resulting in increased levels of genetic diversity; and (2) that populations from areas with lower habitat stability show higher levels of genetic admixture due to their recurrent colonization by individuals originating from genetically differentiated populations. Furthermore, we analysed the relative importance of past and current habitat suitability and their additive effects on contemporary patterns of genetic structure. Location: California, USA. Methods: We sampled 160 individuals from 33 localities across the distribution range of the canyon live oak in California and then combined information from 13 nuclear microsatellite DNA markers and climate niche modelling to study patterns of genetic variation in this species. We used Bayesian clustering analyses to analyse geographical patterns of genetic structure and admixture, and circuit theory to generate isolation-by-resistance (IBR) distance matrices. Results: We found that the degree of genetic admixture was higher in localities with lower inferred population stability, but that genetic diversity was not associated with habitat suitability or stability. Landscape genetic analyses identified habitat stability as the primary driver of population genetic differentiation. Main conclusions: This study shows that habitat stability can be a major factor shaping genetic variation in wind-pollinated trees and supports the idea that stable regions contribute to genetic connectivity across different climatic periods. To our knowledge, this study is the first to report an association between patterns of genetic admixture and stability of local habitat.

Background The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago. Results We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus). Conclusions These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.

Glacial relict plants are often endangered because extant populations can be small, geographically isolated and persist in suboptimal environments, leading to increased clonality and reduced genetic diversity putting their survival at further risk. This study examines how restriction to interglacial refugia has impacted the genetic diversity and structure of the threatened Tasmanian palaeoendemic, Pherosphaera hookeriana W. Archer bis. This species is a poorly dispersed, dioecious conifer that, having once been a major component of Last Glacial vegetation, is now limited to 30 known populations. Genetic diversity and structure were assessed using fifteen nuclear and nine chloroplast SSRs in 23 populations representing the species’ entire range. Changes in distribution and abundance from the Last Glacial to present were investigated by examining the fossil record, approximate Bayesian computation (ABC) and species distribution modelling. Despite fossil and ABC based evidence for a postglacial bottleneck, species-level genetic diversity (He = 0.56 and Ne = 2.86) exceeded that of some conifers with far wider distributions. Significant genetic structure (Fst = 0.127, Jost’s D = 0.203) was present, with most populations dominated by distinct nuclear SSR genetic clusters and having unique chloroplast haplotypes. Unexpectedly, clonality plays only a small role in population level regeneration. Genetic diversity has likely been maintained due to dioecy, persistence in multiple parts of its range and extant populations being directly descended from proximate glacial populations. Protecting populations from the mounting threat of fire will remain crucial for the in situ conservation of P. hookeriana.

The high genetic diversity of rear‐edge refugia populations is predicted to have resulted from species repeatedly migrating to low latitudes during glacial periods over the course of Quaternary climate change. However, several recent empirical studies of cold‐tolerant plants revealed the opposite pattern. We investigated whether current habitats of the cold‐adapted and range‐restricted Bupleurum euphorbioides in the Baekdudaegan, South Korea, and North Korea could be interglacial refugia, and documented how their rear‐edge populations differ genetically from those of typical temperate species. Phylogeographic analysis and ecological niche modeling (ENM) were used. The genetic structure was analyzed using microsatellite markers and chloroplast DNA sequences. The congener B. longiradiatum was included as a typical temperate plant species. Despite having almost identical life history traits, these congeneric species exhibited contrasting patterns of genetic diversity. ENM revealed an apparent maximum range contraction during the last interglacial. In contrast, its range expanded northward to the Russian Far East (Primorsky) during the Last Glacial Maximum. Thus, we hypothesize that B. euphorbioides retreated to its current refugia during interglacial periods. Unlike populations in the central region, the rear‐edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. The rear‐edge B. euphorbioides survived at least one past interglacial, contributing to the species’ genetic diversity. We believe that such genetic variation in the cold‐adapted B. euphorbioides gives the species the necessary adaptations to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change. The study shows a pattern that contrasts with the changes in the distribution range that typical temperate plants experienced in the course of Quaternary climate change. ENM revealed an apparent maximum range contraction during the last interglacial. In contrast, its range expanded northward to Russian Far East (Primorsky) during the Last Glacial Maximum. The rear‐edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. We believe that such genetic variation in the cold‐adapted Bupleurum euphorbioides gives it the necessary adaptations that will enable it to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change.

The glacial‐interglacial cycles of the upper Pleistocene have had a major impact on the recent evolutionary history of Arctic species. To assess the effects of these large‐scale climatic fluctuations to a large, migratory Arctic mammal, we assessed the phylogeography of reindeer (Rangifer tarandus) as inferred from mitochondrial DNA (mtDNA) sequence variation in the control region. Phylogenetic relationships among haplotypes seem to reflect historical patterns of fragmentation and colonization rather than clear‐cut relationships among extant populations and subspecies. Three major haplogroups were detected, presumably representing three separate populations during the last glacial. The most influential one has contributed to the gene pool of all extant subspecies and seems to represent a large and continuous glacial population extending from Beringia and far into Eurasia. A smaller, more localized refugium was most likely isolated in connection with ice expansion in western Eurasia. A third glacial refugium was presumably located south of the ice sheet in North America, possibly comprising several separate refugial populations. Significant demographic population expansion was detected for the two haplogroups representing the western Eurasian and Beringian glacial populations. The former apparently expanded when the ice cap retreated by the end of the last glacial. The large continuous one, in contrast, seems to have expanded by the end of the last interglacial, indicating that the warm interglacial climate accompanied by marine transgression and forest expansion significantly confined population size on the continental mainland. Our data demonstrate that the current subspecies designation does not reflect the mtDNA phylogeography of the species, which in turn may indicate that morphological differences among subspecies have evolved as adaptive responses to postglacial environmental change.

Mountain ice holes are microrefugia at low altitudes characterized by colder temperatures compared to the surrounding areas. Ice holes harbor extra-zonal plant communities composed of plant species that generally grow at higher altitudes in subalpine habitats. Understanding how subalpine species adjust their functional traits to extra-zonal environmental conditions in ice holes can improve our knowledge of plants’ ability to cope with environmental changes. We compared the intraspecific trait variability of four species growing in ice holes and in subalpine areas in the south-eastern Alps of Italy. Plant functional traits presented different patterns of variation between the two habitats. Leaf area, leaf nitrogen and phosphorus content and stomatal traits (stomatal density and stomatal length) differed consistently between habitats in all species. Conversely, specific leaf area and leaf dry matter content varied differently between habitats depending on species. The four species developed differing strategies for adapting leaf functional traits to the peculiar environment of ice holes. Two species, Vaccinium myrtillus and Rhododendron ferrugineum, took advantage of extra-zonal location by developing a more competitive ecological strategy. Conversely, Vaccinium vitis-idaea and Homogyne alpina adopted a more conservative strategy by optimizing adaptation of leaf traits to cold temperature. Our study represents a first attempt to understand the role of marginal populations within the total functional variation of a species. We highlighted the importance of protecting ice holes as important reservoirs of functional diversity for subalpine plant species.

The effects of Quaternary climatic oscillations on the distributions of organisms in different parts of the world are not equally well understood, limiting the ability to understand the determinants of biodiversity. Compared with the mountain regions in southern Europe and southwestern North America, such effects on high‐elevation species in the East Asian subtropical mountain systems located in southern and southeastern China have seldom been addressed. In this study, using Leptobrachium liui (Megophryidae), we made one of the earliest attempts to examine the interglacial high‐elevation refugia scenario in these Asian mountains. Based on our current understanding of the study system, we formulated a hypothesis that these frogs of western origin were distributed more widely and continuously during glacial phases, allowing eastward dispersal, and that they are currently isolated in interglacial refugia at higher elevations. Microsatellite data and mitochondrial and nuclear sequence data were obtained with extensive sampling followed by the synthesis of phylogeographic and population genetic analyses and modeling of the species distribution. The analyses revealed a sequential eastward divergence of microsatellite clusters and gene lineages accompanied by a decline in genetic diversity. Molecular dating estimates revealed divergence events in the Pleistocene, and a reduction in local populations was inferred to have occurred at a time comparable to the end of the last glacial. Strong genetic isolation by distance reflecting a more continuous historical distribution was detected. Furthermore, environmental niche models inferred a wide planar distribution during the last glacial maximum, providing further support for the hypothesis. The effects of Quaternary climatic oscillations on the distributions of high‐elevation species in the East Asian subtropical mountain systems have seldom been addressed. We tested a hypothesis that Pope's spiny toad of western origin was distributed more widely and continuously during glacial phases, allowing eastward dispersal, and that it is currently isolated in interglacial refugia at higher elevations on these mountains. Microsatellite data and mitochondrial and nuclear sequence data were obtained with extensive sampling followed by the synthesis of phylogeographic and population genetic analyses and modeling of the species distribution, and the results agree with the predictions of the hypothesis.