Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak

Understanding the factors determining genetic diversity and structure in peripheral populations is a long‐standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter‐population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak.     

Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander

Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.     

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range‐wide genetic diversity based on nuclear microsatellite data and detected four well‐differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra‐ and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.     

Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high‐latitude B. huntii habitats exhibit low ENS when compared to low‐latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low‐latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.     

Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species

The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long‐lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions.     

Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account

The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.     

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling

Background and Aims A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia.Methods Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM).Key Results A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction.Conclusions Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change.     

Landscape genetics of a specialized grasshopper inhabiting highly fragmented habitats: a role for spatial scale

Aim The study of geographical discontinuities in the distribution of genetic variability in natural populations is a central topic in both evolutionary and conservation research. In this study, we aimed to analyse (1) the factors associated with genetic diversity at the landscape spatial scale in the highly specialized grasshopper Mioscirtus wagneri and (2) to identify the relative contribution of alternative factors to the observed patterns of genetic structure in this species. Location La Mancha region, Central Spain. Methods We sampled 28 populations of the grasshopper M. wagneri and genotyped 648 individuals at seven microsatellite loci. We employed a causal modelling approach to identify the most influential variables associated with genetic differentiation within a multiple hypothesis‐testing framework. Results We found that genetic diversity differs among populations located in different river basins and decreases with population isolation. Causal modelling analyses showed variability in the relative influence of the studied landscape features across different spatial scales. When a highly isolated population is considered, the analyses suggested that geographical distance is the only factor explaining the genetic differentiation between populations. When that population is excluded, the causal modelling analysis revealed that elevation and river basins are also relevant factors contributing to explaining genetic differentiation between the studied populations. Main conclusions These results indicate that the spatial scale considered and the inclusion of outlier populations may have important consequences on the inferred contribution of alternative landscape factors on the patterns of genetic differentiation even when all populations are expected to similarly respond to landscape structure. Thus, a multiscale perspective should also be incorporated into the landscape genetics framework to avoid biased conclusions derived from the spatial scale analysed and/or the geographical distribution of the studied populations.     

Combining ecological niche modelling and morphology to assess the range‐wide population genetic structure of bobcats (Lynx rufus)

Despite a broad distribution, general habitat requirements, and a large dispersal potential, bobcats (Lynx rufus) exhibit a genetic division that longitudinally transects central North America. We investigated (1) whether the climate of the Last Glacial Maximum (LGM; 21 kya) isolated bobcats into refugia and also whether the current climate influences gene flow between the segregate populations and (2) whether the geographical patterns in cranial morphology reflect population identity. We created ecological niche models (ENMs) to evaluate climatic suitability and to estimate distributions of the disparate populations under both historical (LGM) and contemporary conditions. We used two‐dimensional geometric morphometric methods to evaluate variations in the cranium and mandible. These variations were then regressed across geographical variables to assess morphological differences throughout the range of the bobcat. ENMs projected onto LGM climate provided evidence of refugia during the LGM via increased suitability in the north‐west and south‐east portions of this species' range. Contemporarily, our models suggest that the Great Plains may be restricting bobcat migration and gene flow, effectively maintaining disparate populations. Morphological analyses identified a significant linear trend in shape variation across latitudinal and longitudinal gradients rather than distinct morphological divergence between lineages. Similar shape variations, however, did converge in approximate locations of assumed refugia. The findings of the present study provide a robust assessment of the biogeographical considerations for the population genetic structure of bobcats.     

Palaeodistribution modelling and genetic evidence highlight differential post‐glacial range shifts of a rain forest conifer distributed across a latitudinal gradient

Aim We examine the range expansion/contraction dynamics during the last glacial cycle of the late‐successional tropical rain forest conifer Podocarpus elatus using a combination of modelling and molecular marker analyses. Specifically, we test whether distributional changes predicted by environmental niche modelling are in agreement with (1) the glacial maximum contractions inferred from the southern fossil record, and (2) population genetic‐based estimates of range disjunctions and demographic dynamics. In addition, we test whether northern and southern ranges are likely to have experienced similar expansion/contraction dynamics. Location Eastern Australian tropical and subtropical rain forests. Methods Environmental niche modelling was completed for three time periods during the last glacial cycle and was interpreted in light of the known palynology. We collected 109 samples from 32 populations across the entire range of P. elatus. Six microsatellite loci and Bayesian coalescence analysis were used to infer population expansion/contraction dynamics, and five sequenced loci (one plastid and four nuclear) were used to quantify genetic structure/diversity. Results Environmental niche modelling suggested that the northern and southern ranges of P. elatus experienced different expansion/contraction dynamics. In the northern range, the habitat suitable for P. elatus persisted in a small refugial area during the Last Glacial Maximum (LGM, 21 ka) and then expanded during the post‐glacial period. Conversely, in the south suitable habitat was widespread during the LGM but subsequently contracted. These differential dynamics were supported by Bayesian analyses of the population genetic data (northern dispersal) and are consistent with the greater genetic diversity in the south compared with the north. A contact zone between the two genetically divergent groups (corresponding to the Macleay Overlap Zone) was supported by environmental niche modelling and molecular analyses. Main conclusions The climatic fluctuations of the Quaternary have differentially impacted the northern and southern ranges of a broadly distributed rain forest tree in Australia. Recurrent contraction/expansion cycles contributed to the genetic distinction between northern and southern distributions of P. elatus. By combining molecular and environmental niche modelling evidence, this unique study undermines the general assumption that broadly distributed species respond in a uniform way to climate change.     

Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora)

Understanding the impact of past climatic events on species may facilitate predictions of how species will respond to future climate change. To this end, we sampled populations of the common pond snail Radix balthica over the entire species range (northwestern Europe). Using a recently developed analytical framework that employs ecological niche modelling to obtain hypotheses that are subsequently tested with statistical phylogeography, we inferred the range dynamics of R. balthica over time. A Maxent modelling for present-day conditions was performed to infer the climate envelope for the species, and the modelled niche was used to hindcast climatically suitable range at the last glacial maximum (LGM) c . 21 000 years ago. Ecological niche modelling predicted two suitable areas at the LGM within the present species range. Phylogeographic model selection on a COI mitochondrial DNA data set confirmed that R. balthica most likely spread from these two disjunct refuges after the LGM. The match observed between the potential range of the species at the LGM given its present climatic requirements and the phylogeographically inferred refugial areas was a clear argument in favour of niche conservatism in R. balthica , thus allowing to predict the future range. The subsequent projection of the potential range under a global change scenario predicts a moderate pole-ward shift of the northern range limits, but a dramatic loss of areas currently occupied in France, western Great Britain and southern Germany.     

Phylogeographic insights into <Emphasis Type="Italic">Artemisia crithmifolia</Emphasis> (Asteraceae) reveal several areas of the Iberian Atlantic coast as refugia for genetic diversity

The study of fragmentation processes should be tackled using different approaches, in order to obtain solid and robust evidence that could help in identifying potential barriers and threats for species. In this study, we have evaluated the spatial fragmentation patterns in Artemisia crithmifolia (Asteraceae) along its current distribution along the Atlantic coastlines of Europe, from Portugal to the Netherlands and the UK. Niche modelling analyses considering current and past climatic conditions, combined with plastid markers, have been used to evaluate the disconnected distribution pattern of the species, genetic flow between populations and habitat suitability for present and past populations. Plastid markers showed very low variability, while suggesting that the westernmost populations from the Atlantic coast of the Iberian Peninsula are partially genetically isolated, due to the existence of a potential barrier for gene flow on the northern Spanish coast. However, niche models identify this area as a potential habitat for the species, even during the last glacial maximum (20,000 years ago). The combination of both techniques allows identification of potential refugia for the species, highlighting the most likely recolonisation routes and distribution patterns which resulted in the overall low levels of genetic diversity. Anthropogenic activities (urban sprawl, beach expansions, etc.) are most likely behind local extinctions, thus preventing the establishment and expansion of new populations.     

Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius

Aim Understanding how heterogeneous landscapes shape genetic structure not only sheds light on processes involved in population divergence and speciation, but can also guide management strategies to promote and maintain genetic connectivity of populations of endangered species. This study aimed to (1) identify barriers and corridors for gene flow among populations of the endangered frog, Atelopus varius and (2) assess the relative contributions of alternative landscape factors to patterns of genetic variation among these populations in a hypothesis testing framework. Location This study took place in western Panama and included all nine of the remaining known populations of A. varius at the time of study. Methods The influence of landscape variables on gene flow among populations was examined by testing for correlations between alternative landscape‐resistance scenarios and genetic distance. Fifteen alternative hypotheses about the influence of (1) riparian habitat corridors, (2) steep slopes, and (3) climatic suitability on patterns of genetic structure were tested in a causal modelling framework, using Mantel and partial‐Mantel tests, along with an analysis of molecular variation. Results Only the hypothesis attributing resistance to dispersal across steep slopes (genetic isolation by slope distance) was fully supported by the causal modelling approach. However, the analysis of molecular variance and the paths of least‐slope among populations suggest that riparian habitat connectivity may influence genetic structure as well. Main conclusions These results suggest that patterns of genetic variation among A. varius populations are affected by the slope of the landscape such that areas with steep slopes act as barriers to gene flow. In contrast, areas of low slope, such as streams and mountain ridges, appear to be important corridors for gene flow, especially among high elevation populations. These results engender important considerations for the management of this critically endangered species.     

Centaurea subsect. Phalolepis in Southern Italy: ongoing speciation or species overestimation? Genetic evidence based on SSRs analyses

In this paper, we investigated a set of narrow endemics of Centaurea subsect. Phalolepis from the mountains of South Italy (mainly Calabria and Salento), segregated from the widespread species Centaurea deusta, using microsatellite (SSR) markers. The goal was to analyse the genetic makeup (levels and structure) of C. deusta and the segregated species and verify whether genetic clusters were in agreement with current classification of the species. With C. deusta, we also carried out an ecological niche modelling (ENM) analysis to check its potential distribution under present climatic conditions and to project it to the Last Glacial Maximum (LGM). As also found in former studies with subsect. Phalolepis in Greece and Turkey using the same set of SSRs, genetic diversity for the segregated Italian species was higher than expected for narrow endemics with small populations. Genetic clusters, however, were not correlated with the described species and did not support the segregation of the purported narrow endemics from a widely defined C. deusta. The results of the ENM indicate that the Adriatic Sea was a migration corridor for C. deusta at the LGM.     

Distance,elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site‐associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius, across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, with B. vosnesenskii exhibiting relatively consistent levels of genetic diversity across its range, while B. bifarius has reduced genetic diversity at low latitudes, where it is restricted to high‐elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.     

Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory

We aimed to reveal the effects of range expansion and subsequent lineage admixture from separated glacial refugia on genetic diversity of Kalopanax septemlobus in Japan, by combining nuclear microsatellite data and ecological niche modelling. Allelic richness and gene diversity were compared at the population and regional level. We also statistically examined these indices as a function of population accessibility to the last glacial maximum (LGM) palaeodistribution reconstructed by ecological niche modelling to test a simple range expansion scenario from glacial refugia. Genetic diversity was highest in the populations of southern Japan and gradually decreased towards the north. However, an additional centre of genetic diversity, when measured as gene diversity, was found in northern Honshu Island, where distinct lineages were shown to be in contact. Positive effects of population accessibility to the LGM range were detected in both diversity indices at different spatial scales. The combined data support independent postglacial range expansions towards the north from the edge populations on the exposed coastal shelf of Pacific and Sea of Japan in northern Honshu during the LGM, which subsequently resulted in markedly low genetic diversity in the northernmost extant range, Hokkaido. The regional increase in gene diversity in northern Honshu is likely to be the result of postglacial lineage admixture. Relative difference in the spatial scales best relating population genetic diversity with the LGM distribution can be explained by a higher rate of allelic richness diversity loss during range expansions and stronger effects of lineage admixture on gene diversity.     

Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic

Intraspecific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial–interglacial cycles. We use ecological niche modelling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid‐Holocene (6,000 YBP), and the present. Changes in the genetic diversity within ancient refugia were projected for the future (year 2100) under two contrasting climate change scenarios (RCP2.6 and RCP8.5). Models predicted distributions that matched empirical distributions in cross‐validation, and identified distinct refugia at the low latitude ranges, which largely coincide among species with similar ecological niches. Transferred models into the future projected polewards expansions and substantial range losses in lower latitudes, where richer gene pools are expected (in Nova Scotia and Iberia for cold affinity species and Gibraltar, Alboran, and Morocco for warm‐temperate species). These effects were projected for both scenarios but were intensified under the extreme RCP8.5 scenario, with the complete borealization (circum‐Arctic colonization) of kelp forests, the redistribution of the biogeographical transitional zones of the North Atlantic, and the erosion of global gene pools across all species. As the geographic distribution of genetic variability is unknown for most marine species, our results represent a baseline for identification of locations potentially rich in unique phylogeographic lineages that are also climatic relics in threat of disappearing.     

Range and niche shifts in response to past climate change in the desert horned lizard Phrynosoma platyrhinos

During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last Glacial Maximum (LGM) in the desert horned lizard Phrynosoma platyrhinos, a species occupying the western deserts of North America. We used a phylogeographic approach with mitochondrial DNA sequences to approximate the species range during the LGM by identifying populations that exhibit a genetic signal of population stability versus those that exhibit a signal of a recent (likely post‐LGM) geographic expansion. We then compared the climatic niche that the species occupies today with the niche it occupied during the LGM using two models of simulated LGM climate. The genetic analyses indicated that P. platyrhinos persisted within the southern Mojave and Sonoran deserts throughout the latest glacial period and expanded from these deserts northwards, into the western and eastern Great Basin, after the LGM. The climatic niche comparisons revealed that P. platyrhinos expanded its climatic niche after the LGM towards novel, warmer and drier climates that allowed it to persist within the southern deserts. Simultaneously, the species shifted its climatic niche towards greater temperature and precipitation fluctuations after the LGM. We concluded that climatic changes at the end of the LGM promoted both range and niche shifts in this lizard. The mechanism that allowed the species to shift its niche remains unknown, but phenotypic plasticity likely contributes to the species ability to adjust to climate change.     

Conservatism of ecological niche characteristics in North American plant species over the Pleistocene-to-Recent transition

Aim  To provide a test of the conservatism of a species' niche over the last 20,000 years by tracking the distribution of eight pollen taxa relative to climate type as they migrated across eastern North America following the Last Glacial Maximum (LGM).
Location  North America.
Methods  We drew taxon occurrence data from the North American pollen records in the Global Pollen Database, representing eight pollen types – all taxa for which ≥5 distinct geographic occurrences were available in both the present day and at the LGM (21,000 years ago ± 3000 years). These data were incorporated into ecological niche models based on present-day and LGM climatological summaries available from the Palaeoclimate Modelling Intercomparison Project to produce predicted potential geographic distributions for each species at present and at the LGM. The output for each time period was projected onto the 'other' time period, and tested using independent known occurrence information from that period.
Results  The result of our analyses was that all species tested showed general conservatism in ecological characteristics over the climate changes associated with the Pleistocene-to-Recent transition.
Main conclusions  This analysis constitutes a further demonstration of general and pervasive conservatism in ecological niche characteristics over moderate periods of time despite profound changes in climate and environmental conditions. As such, our results reinforce the application of ecological niche modelling techniques to the reconstruction of Pleistocene biodiversity distribution patterns, and to project the future potential distribution range of species in the face of global-scale climatic changes.     

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate‐based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large‐scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.