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Climate change in the past has led to significant changes in species' distributions. However, how individual species respond to climate change depends largely on their adaptations and environmental tolerances. In the Quaternary, temperate-adapted taxa are in general confined to refugia during glacials while cold-adapted taxa are in refugia during interglacials. In the Northern Hemisphere, evidence appears to be mounting that in addition to traditional southern refugia for temperate species, cryptic refugia existed in the North during glacials. Equivalent cryptic southern refugia, to the south of the more conventional high-latitude polar refugia, exist in montane areas during periods of warm climate, such as the current interglacial. There is also a continental/oceanic longitudinal gradient, which should be included in a more complete consideration of the interaction between species ranges and climates. Overall, it seems clear that there is large variation in both the size of refugia and the duration during which species are confined to them. This has implications for the role of refugia in the evolution of species and their genetic diversity.

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.

1. The Pleistocene is an important period for assessing the impact of climate change on biodiversity. During the Last Glacial Maximum (LGM; 21 000 years ago), large glaciers and permafrost reached far south in Europe. Trees are traditionally thought to have survived only in scattered Mediterranean refugia (southern refugia hypothesis), but a recent proposal suggests that trees may have been much more widely and northerly distributed (northern refugia hypothesis). 2. In this study, the southern vs. northern refugia hypotheses were investigated by estimating the potential LGM distributions of 7 boreal and 15 nemoral widespread European tree species using species distribution modelling. The models were calibrated using data for modern species distributions and climate and projected onto two LGM climate simulations for Europe. Five modelling variants were implemented. 3. Models with moderate to good predictive ability for current species range limits and species richness patterns were developed. 4. Broadly consistent results were obtained irrespective of the climate simulation and modelling variant used. Our results indicate that LGM climatic conditions suitable for boreal species existed across Central and Eastern Europe and into the Russian Plain. In contrast, suitable climatic conditions for nemoral tree species were largely restricted to the Mediterranean and Black Sea regions. Large proportions of these northern and southern regions would have been suitable for a number of boreal or boreal plus nemoral tree species, respectively. 5. These findings are consistent with recent palaeoecological and phylogeographic data regarding LGM distributions of trees and other boreal and nemoral taxa. 6. Synthesis. It is clear that the view of the LGM landscape in Europe as largely treeless, especially north of the Alps, needs to be revised. Trees were probably much more widespread during the LGM than hitherto thought, although patchily distributed at low densities due to low atmospheric CO₂ concentrations and high wind-speeds. The findings presented here help explain the occurrence of mammal assemblages with mixtures of forest, tundra and steppe species at many localities in southern Central and Eastern Europe during the LGM, as well as the phylogeographic evidence for the extra-Mediterranean persistence of many boreal species.

Despite their critical importance for understanding the local effects of global climate change on biodiversity, glacial microrefugia are not well studied because they are difficult to detect by using classical palaeoecological or population genetics approaches. We used soil macrofossil charcoal analysis to uncover the presence of cryptic glacial refugia for European beech (Fagus sylvatica) and other tree species in the Landes de Gascogne (southwestern France). Using botanical identification and direct radiocarbon dating (140 (14) C-dates) of macrofossil charcoal extracted from mineral soils, we reconstructed the glacial and postglacial history of all extant beech stands in the region (n = 11). Soil charcoal macrofossils were found in all sites, allowing the identification of up to at least 14 distinct fire events per site. There was direct evidence of the presence of beech during the last glacial period at three sites. Beech was detected during Heinrich stadial-1, one of the coldest and driest intervals of the last glacial period in Western Europe. Together with previous results on the genetic structure of the species in the region, these findings suggest that beech persisted in situ in several microrefugia through full glacial and interglacial periods up to the present day.

Aim To assess the origin and genetic relationship of the northernmost population of Rhododendron ferrugineum in the Karkonosze Mts. (the Sudetes), located 350 km north of the previously acknowledged species limit, in the context of the whole species range; to discuss, based on this case study, the glacial history of the Central European mountain flora and importance of rare, relict populations for biogeographical inference and diversity conservation. Location European mountains: Sudetes, Alps, Pyrenees. Methods We sampled 90 individuals from 26 R. ferrugineum populations spanning the whole species’ range. To infer genetic structure, diversity and relationships among populations and isolated parts of the geographical range, we applied genome‐wide amplified fragment length polymorphism (AFLP) genotyping and sequencing of four cpDNA fragments and nrDNA ITS region. Results Our AFLP analysis revealed four distinct genetic groups in R. ferrugineum, one formed by the northernmost population from (a) the Karkonosze Mts. (the Sudetes) and the other three comprising populations from the (b) Western Alps and Pyrenees, (c) South‐Westernmost Alps and (d) Eastern Alps. Genetic isolation of the Karkonosze population was further corroborated by a repetitive pattern differentiation in plastid DNA sequences, otherwise almost monomorphic across the range. Population from the Karkonosze was most closely related to those from the Western Alps and not from the geographically closest Eastern Alps. Main conclusions We show that the population of R. ferrugineum in the Karkonosze Mts. is a glacial relict and not a recently established or introduced population. Its distinctiveness and high genetic diversity show that it represents a northern, previously undetected, genetic lineage of the species in Europe, which persisted through climatic changes in a small but stable microrefugium. Our case study highlights the importance of an adequate coverage of a species’ range in phylogeographical studies and the significance of peripheral parts of the range to reveal biogeographical history of lineages. It also supports the Karkonosze Mountains as an important refugium for the Central European mountain flora.

Aim: The Bering Land Bridge (BLB) connected Asia and North America during glacial periods, supported a diverse ecosystem of now-vanished megafauna, and is a proposed glacial refugium. This study tests whether southern coastal Beringia was a refugium for woody taxa during the Last Glacial Maximum (LGM) and hypotheses about habitats available on the BLB before and after megafaunal extinction. Location: St. Paul Island, Alaska. Methods: We analysed sediment cores from the Lake Hill, with a new age model anchored by 18 radiocarbon dates and multiple palaeoecological indicators (sedimentary ancient DNA [sedaDNA], macrobotanical fossils, and pollen) for the presence/absence of four woody genera: Picea, Betula, Alnus and Salix. We reconstructed vegetation history and compare St. Paul tundra composition to mainland counterparts. Results: St. Paul has been continuously occupied by graminoid-forb tundra with prostrate shrubs (Salix y Ericaceae) since 18,000 years before present (yr BP). Fossil pollen of Picea, Pinus, Betula and Alnus is present in the Lake Hill sediments at low relative abundances and accumulation rates, consistent with long-distance transport. Macrobotanical fossils and sedaDNA analyses do not support Picea, Betula and Alnus presence. The St. Paul modern and fossil pollen assemblages are compositionally unlike mainland counterparts, but most closely resemble Arctic herbaceous tundra. Stratigraphically constrained cluster analysis indicates no major change in the vegetation after woolly mammoth extinction at 5600 yr BP, although Poaceae, Cyperaceae, Equisetum and forb abundances increase. Main conclusions: This study strongly indicates that St. Paul and, by implication, southern coastal Beringia were not refugia for woody taxa during the LGM. The persistence of prostrate shrub-graminoid tundra supports interpretations that herbaceous tundra prevailed on southern Beringia during the LGM, whilst not ruling out the possibility of mesic shrub tundra in the interior. This herbaceous tundra supported an island refugium for woolly mammoth for 8000 years, showing no major vegetation composition changes after extinction.

Background and AimsDistribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM).MethodsGenetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis.Key ResultsSTRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia.ConclusionsThe combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis.

Species‐level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species‐wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid‐Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations. We explore whether phylogeographic lineages of the bank vole originating from different glacial refugia show environmental niche differentiation. We found that niches were significantly different between all pairs of lineages in geographic and environmental space and these differences cannot be explained by habitat availability within their respective ranges, suggesting that ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole.

Aim Beringia, far north-eastern Siberia and north-western North America, was largely unglaciated during the Pleistocene. Although this region has long been considered an ice-age refugium for arctic herbs and shrubs, little is known about its role as a refugium for boreal trees and shrubs during the last glacial maximum (LGM, c. 28,000-15,000 calibrated years before present). We examine mapped patterns of pollen percentages to infer whether six boreal tree and shrub taxa (Populus, Larix, Picea, Pinus, Betula, Alnus/Duschekia) survived the harsh glacial conditions within Beringia. Methods Extensive networks of pollen records have the potential to reveal distinctive temporal-spatial patterns that discriminate between local- and long-distance sources of pollen. We assembled pollen records for 149 lake, peat and alluvial sites from the Palaeoenvironmental Arctic Sciences database, plotting pollen percentages at 1000-year time intervals from 21,000 to 6000 calibrated years before present. Pollen percentages are interpreted with an understanding of modern pollen representation and potential sources of long-distance pollen during the glacial maximum. Inferences from pollen data are supplemented by published radiocarbon dates of identified macrofossils, where available. Results Pollen maps for individual taxa show unique temporal-spatial patterns, but the data for each taxon argue more strongly for survival within Beringia than for immigration from outside regions. The first increase of Populus pollen percentages in the western Brooks Ranges is evidence that Populus trees survived the LGM in central Beringia. Both pollen and macrofossil evidence support Larix survival in western Beringia (WB), but data for Larix in eastern Beringia (EB) are unclear. Given the similar distances of WB and EB to glacial-age boreal forests in temperate latitudes of Asia and North America, the widespread presence of Picea pollen in EB and Pinus pollen in WB indicates that Picea and Pinus survived within these respective regions. Betula pollen is broadly distributed but highly variable in glacial-maximum samples, suggesting that Betula trees or shrubs survived in restricted populations throughout Beringia. Alnus/Duschekia percentages show complex patterns, but generally support a glacial refugium in WB. Main conclusions Our interpretations have several implications, including: (1) the rapid post-glacial migration rate reported for Picea in western Canada may be over estimated, (2) the expansion of trees and shrubs within Beringia should have been nearly contemporaneous with climatic change, (3) boreal trees and shrubs are capable of surviving long periods in relatively small populations (at the lower limit of detection in pollen data) and (4) long-distance migration may not have been the predominant mode of vegetation response to climatic change in Beringia.