On microrefugia and cryptic refugia

The existence of microrefugia and/or cryptic refugia has been proposed to explain the colonization patterns of temperate continents after the Last Glacial Maximum, as well as to gain an understanding of the present genetic structure of species and their populations. The concepts ‘microrefugia’ and ‘cryptic refugia’ largely overlap but do not fully coincide, which may lead to terminological duplication and eventual semantic misconceptions. Here, after a terminological and conceptual analysis, it is proposed that most situations currently characterized as cryptic refugia can be accommodated within the definition of microrefugia, with one single exception, for which some alternative terms are suggested. Moreover, the concept and definition of cryptic refugia are considered to be more imprecise, perishable and subjective than those of microrefugia, which is the preferred term in the current context.     

Identifying refugia from climate change using coupled ecological and genetic data in a transitional Mediterranean‐temperate tree species

Populations occurring in areas of overlap between the current and future distribution of a species are particularly important because they can represent “refugia from climate change”. We coupled ecological and range‐wide genetic variation data to detect such areas and to evaluate the impacts of habitat suitability changes on the genetic diversity of the transitional Mediterranean‐temperate tree Fraxinus angustifolia. We sampled and genotyped 38 natural populations comprising 1006 individuals from across Europe. We found the highest genetic diversity in western and northern Mediterranean populations, as well as a significant west to east decline in genetic diversity. Areas of potential refugia that correspond to approximately 70% of the suitable habitat may support the persistence of more than 90% of the total number of alleles in the future. Moreover, based on correlations between Bayesian genetic assignment and climate, climate change may favour the westward spread of the Black Sea gene pool in the long term. Overall, our results suggest that the northerly core areas of the current distribution contain the most important part of the genetic variation for this species and may serve as in situ macrorefugia from ongoing climate change. However, rear‐edge populations of the southern Mediterranean may be exposed to a potential loss of unique genetic diversity owing to habitat suitability changes unless populations can persist in microrefugia that have facilitated such persistence in the past.     

Climate refugia for Pinus spp. in topographic and bioclimatic environments of the Madrean sky islands of México and the United States

Climate refugia, or places where habitats are expected to remain relatively buffered from regional climate extremes, provide an important focus for science and conservation planning. Within high-priority, multi-jurisdictional landscapes like the Madrean sky islands of the United States and México, efforts to identify and manage climate refugia are hindered by the lack of high-quality and consistent transboundary datasets. To fill these data gaps, we assembled a bi-national field dataset (n?=?1416) for five pine species (Pinus spp.) and used generalized boosted regression to model pine habitats in relation to topographic variability as a basis for identifying potential microrefugia at local scales in the context of current species’ distribution patterns. We developed additional models to quantify climatic refugial attributes using coarse scale bioclimatic variables and finer scale seasonal remote sensing indices. Terrain metrics including ruggedness, slope position, and aspect defined microrefugia for pines within elevation ranges preferred by each species. Response to bioclimatic variables indicated that small shifts in climate were important to some species (e.g., P. chihuahuana, P. strobiformis), but others exhibited a broader tolerance (e.g., P. arizonica). Response to seasonal climate was particularly important in modeling microrefugia for species with open canopy structure and where regular fires occur (e.g., P. engelmannii and P. chihuahuana). Hotspots of microrefugia differed among species and were either limited to northern islands or occurred across central or southern latitudes. Mapping and validation of refugia and their ecological functions are necessary steps in developing regional conservation strategies that cross jurisdictional boundaries. A salient application will be incorporation of climate refugia in management of fire to restore and maintain pine ecology. Una versión en español de este artículo está disponible como descarga.

     

Hydrologic refugia,plants, and climate change

Climate, physical landscapes, and biota interact to generate heterogeneous hydrologic conditions in space and over time, which are reflected in spatial patterns of species distributions. As these species distributions respond to rapid climate change, microrefugia may support local species persistence in the face of deteriorating climatic suitability. Recent focus on temperature as a determinant of microrefugia insufficiently accounts for the importance of hydrologic processes and changing water availability with changing climate. Where water scarcity is a major limitation now or under future climates, hydrologic microrefugia are likely to prove essential for species persistence, particularly for sessile species and plants. Zones of high relative water availability – mesic microenvironments – are generated by a wide array of hydrologic processes, and may be loosely coupled to climatic processes and therefore buffered from climate change. Here, we review the mechanisms that generate mesic microenvironments and their likely robustness in the face of climate change. We argue that mesic microenvironments will act as species‐specific refugia only if the nature and space/time variability in water availability are compatible with the ecological requirements of a target species. We illustrate this argument with case studies drawn from California oak woodland ecosystems. We posit that identification of hydrologic refugia could form a cornerstone of climate‐cognizant conservation strategies, but that this would require improved understanding of climate change effects on key hydrologic processes, including frequently cryptic processes such as groundwater flow.     

Potential warm-stage microrefugia for alpine plants: Feedback between geomorphological and biological processes

During interglacial stages, microrefugia are sites that support locally favorable climates within larger areas with unfavorable warmer climates. Despite recent theoretical representations of microrefugia, an appropriate ecological characterization is still lacking, mostly for warm periods. Across mountain/alpine areas, cold-adapted plant species could adopt different strategies to manage the effects of climate warming: (A) migration toward higher elevations and summits; (B) in situ resilience of communities and species populations within microrefugia; and C) adaptation and evolution by genetic differentiation. This review aims to distinguish and characterize from an ecological perspective glacial, nival, periglacial and composite landforms and deposits that may function as potential microrefugia during interglacial warm periods.We conducted a literature screening related to the geomorphological processes and landforms associated with vegetation and plant communities in alpine/mountain environments of Europe. They include glacial deposits rock glaciers, debris-covered glaciers, composite cones and channels. In Alpine regions, geomorphologic niches that constantly maintain cold-air pooling and temperature inversions are the main candidates for microrefugia. Within such microrefugia, microhabitat diversity modulates the responses of plants to disturbances caused by geomorphologic processes and supports their aptitude for surviving under extreme conditions on unstable surfaces in isolated patches. Currently, European marginal mountain chains may be considered as examples of macrorefugia where relict boreo-alpine species persist within peculiar geomorphological niches that act as microrefugia.This review contributes to identifying potential warm-stage microrefugia areas across alpine and mountain regions and determining certain landforms that play or may play such role under global-change scenarios. The occurrence of warm-stage microrefugia within these locations may be of great importance for the modeling of future distributions of species and assessing the risk of extinction for alpine species. Microrefugia may have important implications in micro-evolutionary processes that occur across alternating climatic phases.     

Refugia within refugia – patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula

In Europe, southern peninsulas served as major refugia during Pleistocene cold periods. However, growing evidence has revealed complex patterns of glacial survival within these southern regions, with multiple glacial refugia within each larger refugial area. We investigated the extent to which patterns of endemism and phylogeographic are concordant across animal species in the Iberian Peninsula, one of the most important unglaciated areas in Europe during the Pleistocene, can be explained in terms of climatic stability. We found that historical climatic stability (notably climate velocity measures integrating macroclimatic shifts with local spatial topoclimate gradients) was often among the most important predictors of endemic species richness for different taxonomic groups using models that also incorporated measures of modern climate. Furthermore, for some taxonomic groups, climatic stability was also correlated with patterns of spatial concordance in interpopulation genetic divergence across multiple taxa, and private haplotypes were more frequently found in relatively stable areas. Overall, our results suggest that both endemism patterns and cross‐taxa concordant phylogeographic patterns across the Iberian Peninsula to some extent are linked to spatial variation in Late Quaternary climate stability, in agreement with the proposed ‘refugia‐within‐refugia’ scenario. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 13–28.     

Topo‐climatic microrefugia explain the persistence of a rare endemic plant in the Alps during the last 21 millennia

Ongoing rapid climate change is predicted to cause local extinction of plant species in mountain regions. However, some plant species could have persisted during Quaternary climate oscillations without shifting their range, despite the limited evidence from fossils. Here, we tested two candidate mechanisms of persistence by comparing the macrorefugia and microrefugia (MR) hypotheses. We used the rare and endemic Saxifraga florulenta as a model taxon and combined ensembles of species distribution models (SDMs) with a high‐resolution paleoclimatic and topographic dataset to reconstruct its potential current and past distribution since the last glacial maximum. To test the macrorefugia hypothesis, we verified whether the species could have persisted in or shifted to geographic areas defined by its realized niche. We then identified potential MR based on climatic and topographic properties of the landscape and applied refined scenarios of MR dynamics and functions over time. Last, we quantified the number of known occurrences that could be explained by either the macrorefugia or MR model. A consensus of two or three SDM techniques predicted absence between 14–10, 3–4 and 1 ka bp , which did not support the macrorefugia model. In contrast, we showed that S. florulenta could have contracted into MR during periods of absence predicted by the SDMs and later re‐colonized suitable areas according to the macrorefugia model. Assuming a limited and realistic seed dispersal distance for our species, we explained a large number of the current occurrences (61–96%). Additionally, we showed that MR could have facilitated range expansions or shifts of S. florulenta. Finally, we found that the most recent and the most stable MR were the ones closest to current occurrences. Hence, we propose a novel paradigm to explain plant persistence by highlighting the importance of supporting functions of MR when forecasting the fate of plant species under climate change.     

Reef‐coral refugia in a rapidly changing ocean

This study sought to identify climate‐change thermal‐stress refugia for reef corals in the Indian and Pacific Oceans. A species distribution modeling approach was used to identify refugia for 12 coral species that differed considerably in their local response to thermal stress. We hypothesized that the local response of coral species to thermal stress might be similarly reflected as a regional response to climate change. We assessed the contemporary geographic range of each species and determined their temperature and irradiance preferences using a k‐fold algorithm to randomly select training and evaluation sites. That information was applied to downscaled outputs of global climate models to predict where each species is likely to exist by the year 2100. Our model was run with and without a 1 °C capacity to adapt to the rising ocean temperature. The results show a positive exponential relationship between the current area of habitat that coral species occupy and the predicted area of habitat that they will occupy by 2100. There was considerable decoupling between scales of response, however, and with further ocean warming some ‘winners’ at local scales will likely become ‘losers’ at regional scales. We predicted that nine of the 12 species examined will lose 24–50% of their current habitat. Most reductions are predicted to occur between the latitudes 5–15°, in both hemispheres. Yet when we modeled a 1 °C capacity to adapt, two ubiquitous species, Acropora hyacinthus and Acropora digitifera, were predicted to retain much of their current habitat. By contrast, the thermally tolerant Porites lobata is expected to increase its current distribution by 14%, particularly southward along the east and west coasts of Australia. Five areas were identified as Indian Ocean refugia, and seven areas were identified as Pacific Ocean refugia for reef corals under climate change. All 12 of these reef‐coral refugia deserve high‐conservation status.     

Genetic diversity in the two endangered endemic species Kirengeshoma koreana (Hydrangeaceae) and Parasenecio pseudotaimingasa (Asteraceae) from Korea: Insights into population history and implications for conservation

As mountains have been hypothesized as harboring important Quaternary refugia for plants, one would expect high within-population genetic variation and low or moderate among-population differentiation for those species occurring there. We selected Kirengeshoma koreana and Parasenecio pseudotaimingasa, endemic to mountains of Korea to test the scenario that the main mountain ranges of the Peninsula would also have acted as refugia. We undertook a population genetic analysis using 15 and 12 putative allozyme loci of K. koreana and P. pseudotaimingasa, respectively. We found contrasting levels of genetic diversity in the two species; extremely low within-population genetic variation and high among-population divergence in K. koreana and high within-population genetic variation and moderate among-population divergence in P. pseudotaimingasa. We can conclude that, whereas Korean mountains would have provided large refugial areas (i.e., ‘macrorefugia’) for P. pseudotaimingasa, K. koreana would have endured the Quaternary climate oscillations in small, isolated populations (i.e., ‘microrefugia’). Given the lack of genetic diversity and the extremely low number of populations and individuals of K. koreana, a comprehensive conservation program is urgently needed for this rare and critically endangered species.     

Report of the Alpine Section

Background: Under climate-change scenarios, rock outcrops, by providing microclimatically diverse habitats, different from those of surrounding zonal vegetation matrix, may serve as climatic refugia and thereby facilitate the persistence of specialist species.

Aim: We tested whether rock outcrops of southern temperate latitudes could act as local refugia for a cold-adapted flora in the face of global warming.

Methods: We related species composition of 50 outcrops and that of their surrounding vegetation to climatic data at local and regional scales to establish whether species distributions reflected differences that could indicate the existence of climatic refugia.

Results: While at a regional scale, species composition of the outcrops across the study area was related to mean annual precipitation and mean annual maximum temperature, locally, southern faces of outcrops had different species and lower maximum temperatures than insolated north faces and surrounding vegetation plots.

Conclusions: South faces of outcrops by providing cool microhabitats, and currently harbouring species not found in the surrounding zonal vegetation matrix, could serve as local refugia for heat-intolerant plants and other microthermic organism. The degree of ‘stability’ of these refugia will depend on the degree of future change in climate. Therefore, it is important to plan protected area networks that maximise local environmental heterogeneity, including the protection of rock outcrops both as refugia for cold-adapted species and as potential stepping stones that would allow dispersal of these species between supportive environments through unfavourable ones.     

The relative contributions of refugium types to the persistence of benthic invertebrates in a seasonal snowmelt flood

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Scale‐dependent complementarity of climatic velocity and environmental diversity for identifying priority areas for conservation under climate change

As most regions of the earth transition to altered climatic conditions, new methods are needed to identify refugia and other areas whose conservation would facilitate persistence of biodiversity under climate change. We compared several common approaches to conservation planning focused on climate resilience over a broad range of ecological settings across North America and evaluated how commonalities in the priority areas identified by different methods varied with regional context and spatial scale. Our results indicate that priority areas based on different environmental diversity metrics differed substantially from each other and from priorities based on spatiotemporal metrics such as climatic velocity. Refugia identified by diversity or velocity metrics were not strongly associated with the current protected area system, suggesting the need for additional conservation measures including protection of refugia. Despite the inherent uncertainties in predicting future climate, we found that variation among climatic velocities derived from different general circulation models and emissions pathways was less than the variation among the suite of environmental diversity metrics. To address uncertainty created by this variation, planners can combine priorities identified by alternative metrics at a single resolution and downweight areas of high variation between metrics. Alternately, coarse‐resolution velocity metrics can be combined with fine‐resolution diversity metrics in order to leverage the respective strengths of the two groups of metrics as tools for identification of potential macro‐ and microrefugia that in combination maximize both transient and long‐term resilience to climate change. Planners should compare and integrate approaches that span a range of model complexity and spatial scale to match the range of ecological and physical processes influencing persistence of biodiversity and identify a conservation network resilient to threats operating at multiple scales.     

Characteristics of climate change refugia for Australian biodiversity

Identifying refugia is a critical component of effective conservation of biodiversity under anthropogenic climate change. However, despite a surge in conceptual and practical interest, identifying refugia remains a significant challenge across diverse continental landscapes. We provide an overview of the key properties of refugia that promote species' persistence under climate change, including their capacity to (i) buffer species from climate change; (ii) sustain long‐term population viability and evolutionary processes; (iii) minimize the potential for deleterious species interactions, provided that the refugia are (iv) available and accessible to species under threat. Further, we classify refugia in terms of the environmental and biotic stressors that they provide protection from (i.e. thermal, hydric, cyclonic, pyric and biotic refugia), but ideally refugia should provide protection from a multitude of stressors. Our systematic characterization of refugia facilitates the identification of refugia in the Australian landscape. Challenges remain, however, specifically with respect to how to assess the quality of refugia at the level of individual species and whole species assemblages. It is essential that these challenges are overcome before refugia can live up to their acclaim as useful targets for conservation and management in the context of climate change.     

A novel approach to quantify and locate potential microrefugia using topoclimate,climate stability,and isolation from the matrix

Ecologists are increasingly recognizing the conservation significance of microrefugia, but it is inherently difficult to locate these small patches with unusual climates, and hence they are also referred to as cryptic refugia. Here we introduce a new methodology to quantify and locate potential microrefugia using fine‐scale topoclimatic grids that capture extreme conditions, stable climates, and distinct differences from the surrounding matrix. We collected hourly temperature data from 150 sites in a large (200 km by 300 km) and diverse region of New South Wales, Australia, for a total of 671 days over 2 years. Sites spanned a range of habitats including coastal dune shrublands, eucalypt forests, exposed woodland ridges, sheltered rainforest gullies, upland swamps, and lowland pastures. Climate grids were interpolated using a regional regression approach based on elevation, distance to coast, canopy cover, latitude, cold‐air drainage, and topographical exposure to winds and radiation. We identified extreme temperatures on two separate climatic gradients: the 5th percentile of minimum temperatures and the 95th percentile of maximum temperatures. For each gradient, climatic stability was assessed on three different time scales (intra‐seasonal, intra‐annual and inter‐annual). Differences from the matrix were assessed using a moving window with a 5 km radius. We averaged the Z‐scores for these extreme, stable and isolated climates to identify potential locations of microrefugia. We found that our method successfully predicted the location of communities that were considered to occupy refugia, such as rainforests that have progressively contracted in distribution over the last 2.5 million years, and alpine grasslands that have contracted over the last 15 thousand years. However, the method was inherently sensitive to the gradient selected and other aspects of the modelling process. These uncertainties could be dealt with in a conservation planning context by repeating the methodology with various parameterizations and identifying areas that were consistently identified as microrefugia.     

Phylogeography of the burnet moth Zygaena transalpina complex: molecular and morphometric differentiation suggests glacial refugia in Southern France,Western France and micro‐refugia within the Alps

Patterns of common recolonization routes from glacial refugia to Central Europe during the Pleistocene are generalized to paradigms of postglacial recolonization in Europe. Recent studies indicate, however, that the actual phylogeographic history of many species might be more complex and cannot be simplified to generalized patterns. Burnet moths of the Zygaena transalpina complex represent a group of closely related taxa, which are considered as a typical example for these generalized patterns. At present, three groups are recognized that are assumed to have spread from three classical refugia in Western Europe, Italy and the Balkans to Central Europe. Here, we re‐investigate their phylogeography using a combined molecular and morphometric approach. Phylogenetic and nested clade phylogeographic analyses of 476 samples from 55 localities taken from Southern and Central Europe reveal that the Zygaena transalpina complex consists of three distinct haplotype clusters, which geographically roughly correspond to possible refugia in Western Europe, Italy and the Balkans. A synthesis of the data with a geometric morphometry dataset of 425 specimens from 46 localities corroborates this molecular result but differs in several aspects. Important new aspects are multiple refugia of the western ‘hippocrepidis’ branch and micro‐habitats within the Alps of the central ‘transalpina’ branch. Further, our results display a more complex phylogeographic pattern for this species complex, which is not tractable with a rigid, generalized pattern.     

Modelling the spatial distribution of selected North American woodland mammals under future climate scenarios

1. North America has a diverse array of mammalian species. Model projections indicate significant variations in future climate conditions of North America, and the habitats of woodland mammals of this continent may be particularly sensitive to changes in climate.
2. We report on the potential spatial distributions of 13 wide-ranging, relatively common species of North American woodland mammals under future climate scenarios.
3. We examined the potential influence of the mean and seasonal climate variables on the distribution of species. Presence-only occurrence records of species, four predictor variables, two future climate scenarios (Representative Concentration Pathways 4.5 and 8.5), and two time steps (current and 2070) were used to build species’ distribution models using a maximum entropy algorithm (MaxEnt).
4. Our results suggested that overall, 11 of the 13 species are likely to gain climatically suitable space (regions where climate conditions will be similar to those of area currently occupied) at the continental scale, but American marten Martes americana and ‘woodland’ caribou Rangifer tarandus are likely to lose suitable climate range by 2070. Furthermore, climate space is likely to be expanding northwards under future climate scenarios for most of the mammals, and many jurisdictions in the border region between Canada and the USA are likely to lose iconic species, such as moose Alces alces. We identified regions as potential in situ and ex situ climate change refugia, which are increasingly considered to be important for biodiversity conservation.
5. The model results suggest significant implications for conservation planning for the 13 mammalian species under global climate change, especially at fine spatial scales. Numerous species that are presently common at their southern range edge will be functionally or completely extirpated in 50 years. The potential in situ and ex situ climate change refugia could provide an effective support for adaptive strategies aimed at species conservation planning.

     

Pelagic marine refugia and climatically sensitive areas in an eastern boundary current upwelling system

Refugia are areas relatively buffered from contemporary climate change that enable the persistence of valued physical, ecological, or sociocultural resources. Spatially identifying refugia is important for conservation and applied management. Yet the concept of refugia has not been broadly extended to marine ecosystems. Here, we analyze data from a unique and long‐term (1999–2015) standardized survey of pelagic marine and anadromous species off Oregon and Washington in the northern California Current to identify such refugia. We use quantitative approaches to assess locations with high species richness and community persistence relative to local and basin‐scale environmental fluctuations. We have identified a potential climate change refugial zone along the continental shelf of Washington State in the Northeastern Pacific Ocean, characterized by a species‐rich community with low interannual temporal community change. This region contrasts with adjacent areas to the south and offshore that have lower species richness, and higher temporal species community change. Also, using spatially variant generalized additive mixed models, we identify areas with species compositions that are more influenced by basin‐scale climatic fluctuations than others. We propose that upwelling regions with retentive topographic features, such as wide continental shelves, can function as marine refugia for pelagic fauna, whereas offshore locations are potentially more climatically sensitive and experience high temporal change in species composition. Further identification of these marine refugia using in situ data for pelagic biodiversity and climatically sensitive areas can help guide management in the face of inevitable climatically driven change.     

Unpacking the mechanisms captured by a correlative species distribution model to improve predictions of climate refugia

Climate refugia are regions that animals can retreat to, persist in and potentially then expand from under changing environmental conditions. Most forecasts of climate change refugia for species are based on correlative species distribution models (SDMs) using long‐term climate averages, projected to future climate scenarios. Limitations of such methods include the need to extrapolate into novel environments and uncertainty regarding the extent to which proximate variables included in the model capture processes driving distribution limits (and thus can be assumed to provide reliable predictions under new conditions). These limitations are well documented; however, their impact on the quality of climate refugia predictions is difficult to quantify. Here, we develop a detailed bioenergetics model for the koala. It indicates that range limits are driven by heat‐induced water stress, with the timing of rainfall and heat waves limiting the koala in the warmer parts of its range. We compare refugia predictions from the bioenergetics model with predictions from a suite of competing correlative SDMs under a range of future climate scenarios. SDMs were fitted using combinations of long‐term climate and weather extremes variables, to test how well each set of predictions captures the knowledge embedded in the bioenergetics model. Correlative models produced broadly similar predictions to the bioenergetics model across much of the species' current range – with SDMs that included weather extremes showing highest congruence. However, predictions in some regions diverged significantly when projecting to future climates due to the breakdown in correlation between climate variables. We provide unique insight into the mechanisms driving koala distribution and illustrate the importance of subtle relationships between the timing of weather events, particularly rain relative to hot‐spells, in driving species–climate relationships and distributions. By unpacking the mechanisms captured by correlative SDMs, we can increase our certainty in forecasts of climate change impacts on species.     

Northern richness and cryptic refugia: phylogeography of the Italian smooth newt Lissotriton vulgaris meridionalis

Recent phylogeographical studies have re‐evaluated the role of refugia in central and northern Europe for glacial persistence and postglacial assembly of temperate biota. Yet, on a regional scale within Mediterranean peninsulas, putative ‘northern’ refugia's contribution to the current structure of biodiversity still needs to be fully appreciated. To this end, we investigated the phylogeographical structure and the evolutionary history of the Italian smooth newt, Lissotriton vulgaris meridionalis, through phylogeographical, molecular dating and historical demographic analyses. We found ten differentiated mitochondrial lineages with a clear geographical association, mainly distributed in northern Italy. The most ancient divergence among these lineages was estimated at the Early Pleistocene and was followed by a series of splits throughout the Middle Pleistocene. No haplogroup turned out to be derived from another one, each one occupying terminal positions within the phylogenetic network topologies. These results suggest an unprecedented scenario involving long‐term survival of distinct evolutionary lineages in multiple northern Mediterranean refugia. This scenario mirrors on a smaller geographical scale what has been previously observed in the literature concerning northern European environments; it also sheds more light on how northern Italy has contributed to temperate species' long‐term survival and to the assembly of regional biota. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 590–603.