Quantifying quaternary climate variability in the Southern Caucasus using land snail shell isotope transfer functions and climatic niche modeling

Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of naturally established individuals because this improves the accuracy of predictions about their distribution ranges.

Predicting the geographic range of species and their response to climatic variation and change are entwined goals in conservation and evolutionary ecology. Species distribution models (SDMs) are foundational in this effort and used to visualize the geographic range of species as the spatial representation of its realized niche. SDMs are also used to forecast range shifts under climate change, but often in the absence of empirical evidence that climate limits population growth. We explored the influence of climate on demography, seasonal migration, and the extent of the geographic range in song sparrows (Melospiza melodia), a species thought to display marked local adaptation to regional climate. To do so, we developed SDMs to predict the demographic and climate niches of migratory and resident song sparrows across our study area in western North America from California to Alaska, using 48years of demographic data from a focal population in British Columbia and 1.2million continental-scale citizen science observations. Spatial agreement of our demographic and climate niche models in the region of our focal population was strong (76%), supporting the hypothesis that demographic performance and the occurrence of seasonal migration varied predictably with climatic conditions. In contrast, agreement at the northern (58%) and southern (40%) extents of our study area was lower, as expected if the factors limiting population growth vary regionally. Our results support the hypothesis that local climate drives spatial variation in the occurrence of seasonal migration in song sparrows by limiting the fitness of year-round residents, and suggest that climate warming has favored range expansions and facilitated an upward shift in elevational range song sparrows that forgo seasonal migration. Our work highlights the potential role of seasonal migration in climate adaptation and limits on the reliability of climate niche models not validated with demographic data.

Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau.

For the first time we present a multi-proxy data set for the Russian Altai, consisting of Siberian larch tree-ring width (TRW), latewood density (MXD), δ13C and δ18O in cellulose chronologies obtained for the period 1779–2007 and cell wall thickness (CWT) for 1900–2008. All of these parameters agree well between each other in the high-frequency variability, while the low-frequency climate information shows systematic differences. The correlation analysis with temperature and precipitation data from the closest weather station and gridded data revealed that annual TRW, MXD, CWT, and δ13C data contain a strong summer temperature signal, while δ18O in cellulose represents a mixed summer and winter temperature and precipitation signal. The temperature and precipitation reconstructions from the Belukha ice core and Teletskoe lake sediments were used to investigate the correspondence of different independent proxies. Low frequency patterns in TRW and δ13C chronologies are consistent with temperature reconstructions from nearby Belukha ice core and Teletskoe lake sediments showing a pronounced warming trend in the last century. Their combination could be used for the regional temperature reconstruction. The long-term δ18O trend agrees with the precipitation reconstruction from the Teletskoe lake sediment indicating more humid conditions during the twentieth century. Therefore, these two proxies could be combined for the precipitation reconstruction.

Puccinia psidii sensu lato (s.l.) is an invasive rust fungus threatening a wide range of plant species in the family Myrtaceae. Originating from Central and South America, it has invaded mainland USA and Hawai'i, parts of Asia and Australia. We used CLIMEX to develop a semi-mechanistic global climatic niche model based on new data on the distribution and biology of P. psidii s.l. The model was validated using independent distribution data from recently invaded areas in Australia, China and Japan. We combined this model with distribution data of its potential Myrtaceae host plant species present in Australia to identify areas and ecosystems most at risk. Myrtaceaeous species richness, threatened Myrtaceae and eucalypt plantations within the climatically suitable envelope for P. psidii s.l in Australia were mapped. Globally the model identifies climatically suitable areas for P. psidii s.l. throughout the wet tropics and sub-tropics where moist conditions with moderate temperatures prevail, and also into some cool regions with a mild Mediterranean climate. In Australia, the map of species richness of Myrtaceae within the P. psidii s.l. climatic envelope shows areas where epidemics are hypothetically more likely to be frequent and severe. These hotspots for epidemics are along the eastern coast of New South Wales, including the Sydney Basin, in the Brisbane and Cairns areas in Queensland, and in the coastal region from the south of Bunbury to Esperance in Western Australia. This new climatic niche model for P. psidii s.l. indicates a higher degree of cold tolerance; and hence a potential range that extends into higher altitudes and latitudes than has been indicated previously. The methods demonstrated here provide some insight into the impacts an invasive species might have within its climatically suited range, and can help inform biosecurity policies regarding the management of its spread and protection of valued threatened assets.

Using climatic suitability thresholds to identify past, present and future population viability

In Mexico, buffelgrass (Cenchrus ciliaris) was introduced in the middle of the 20th century. Currently, buffelgrass has become an invasive species and has colonized various ecosystems in the country. In addition to its invasive capacity, climate change is a factor that has to be taken into account when considering how to effectively manage and control this species. The climatic niche models (CNM) and their projections for climate change scenarios allow for estimating the extent of biological invasions. Our study aimed to calibrate a CNM for buffelgrass in Mexico under the current climatic conditions and to project the extent of its biological invasion under climate change scenarios. For that, we used MaxEnt to generate the current CNM and to detect if climate change could cause future changes, we then evaluated the distribution patterns over the periods of 2041–2060, 2061–2080, and 2081–2100 for all the shared socioeconomic pathways (SSPs). Linear regressions were used to compare the outputs between current and future scenarios. Under the current climate, the CNM estimated that 42.2% of the continental surface of Mexico is highly suitable for buffelgrass. The regression analyses indicated no effects from climate change on the distribution of buffelgrass. Moreover, when the projected period is further in the future, and when the SSPs intensify, the surface of suitable areas for the species increases. These analyses clearly suggest Mexico is facing a biological invasion from buffelgrass, which may represent a threat to native biodiversity.

Quantitative reconstructions of past precipitation and temperature variations at the seasonal scale are essential for understanding East Asian Monsoon (EAM) dynamics. However, archives capable of capturing seasonal climate signals on land are limited. Here, we present high-resolution stable oxygen isotope (δ18Oshell) and carbonate clumped isotope (Δ47) data from modern and fossil land snail shells collected from the eastern (Lingbao, LB) and western (Yuanbao, YB) edge of the Chinese Loess Plateau (CLP).The δ18Oshell of modern snails similarly reflect the seasonal variation in precipitation oxygen isotopic signals at both locations. The Δ47-derived temperatures for the same snails indicate that the seasonal temperature difference (summer vs. winter) is larger at YB than LB, aligning with modern observations from the western edge of the CLP, where a higher elevation results in a larger seasonality. The averaged whole shell Δ47-derived temperatures (T47) from modern Cathaica pulveritrix shells at LB and their related Cathaica richthofeni snails at YB resemble growing season temperatures. Interestingly, the T47 of shells of three smaller snail species, Pupilla muscorum, Kaliella lamprocystis, and Vallonia sp. are substantially (up to 10 ºC) lower than those of C. richthofeni from the same site. The temperature difference between snail species and among specimens suggests that optimal living conditions and micro-environments likely play a key role in the temperature signal recorded in the snail shells.Fossil snails from LB show a larger variability in δ18Oshell  during the Last Glacial Maximum (LGM, 19–18 ka), with wet season values approximately 3‰ more depleted than modern shells. In contrast, the seasonal temperature difference in fossil snails is smaller than in their modern counterparts, and growing season temperatures are ~10 °C lower than the present at LB. Fossil shells from YB also have a more negative δ18Oshell during the last deglaciation (14‒13 ka) than their modern counterparts. Similar to LB snails, the whole shell T47 of fossil snail shells at YB indicates that growing season temperatures were ~10 °C lower than recorded by their modern counterparts, and the temperature variability on a seasonal scale is smaller than in modern snails. The relatively large variability, negative δ18Oshell values and low T47 values in fossil shells suggests weaker evaporation or longer water vapor transportation under glacial conditions. While snail shells can capture high-resolution climate signals, variations in living conditions and micro-environments among snail species and specimens should be considered in future Δ47-based temperature studies and their applications.

QuestionDark diversity refers to the set of species that are not observed in an area but could potentially occur based on suitable local environmental conditions. In this paper, we applied both niche‐based and co‐occurrence‐based methods to estimate the dark diversity of vascular plant species in the subarctic mountains. We then aimed to unravel the drivers explaining (a) why some locations were missing relatively more suitable species than others, and (b) why certain plant species were more often absent from suitable locations than others.LocationThe Scandinavian mountains around Abisko, northern Sweden.MethodsWe calculated the dark diversity in 107 plots spread out across four mountain trails using four different methods: two co‐occurrence‐based (Beals’ index and the hypergeometric method) and two niche‐based (the climatic niche model and climatic niche model followed by species‐specific threshold). We then applied multiple Generalized Linear Mixed‐Effects Models and General Linear Models to determine which habitat characteristics and species traits contributed the most to dark diversity.ResultsThe study showed a notable divergence in the predicted drivers of dark diversity depending on the method used. Nevertheless, we can conclude that plot‐level dark diversity was generally 17% higher in areas at low elevations and 31% higher in areas with a low species richness.ConclusionOur findings call for caution when interpreting statistical findings of dark‐diversity estimates. Even so, all analyses point toward an important role for natural processes such as competitive dominance as the main driver of the spatial patterns found in dark diversity in the northern Scandes.

The Lonicera clade Caprifolium contains approximately 25 species distributed around the Northern Hemisphere, including in the Mediterranean climates of California and Europe. We sequenced the second intron of LFY to help resolve relationships within the clade where the internal transcribed spacer and chloroplast markers had previously failed to do so. Divergence time estimation and biogeographic analyses over the posterior distribution of dated trees suggest that a widespread ancestor was distributed across the Northern Hemisphere some 7-17 million years ago. Asian species form a sister group to a clade in which the European species are sister to the North American species. We use climatic niche modeling and divergence time estimates to explore the evolution of climate variables in the group. Principal component analyses help to identify instances of convergence, especially between distantly related species in the Mediterranean basin and in the chaparral of California. We document several cases of significant divergence between sister species in eastern North America and western North America. Climatic models were projected from one continent into the others (e.g., North American species projected into Asia and Europe) to examine whether species living in these areas occupy similar climates. This study demonstrates the utility of combining niche modeling with historical biogeographic analyses and documents significant climatic niche evolution within a group of species distributed throughout the Northern Hemisphere. These results suggest a possible model for the origin of the Madrean-Tethyan disjunction pattern.

Aim Our aim was to understand the processes that have shaped the present‐day distribution of the freshwater limpet Ancylus fluviatilis sensu stricto in order to predict the consequences of global climate change for the geographical range of this species.Location North‐western Europe.Methods We sampled populations of A. fluviatilis sensu stricto over the entire range of the species (north‐western Europe) and sequenced 16S ribosomal RNA (16S) and cytochrome oxidase subunit I (COI) mitochondrial fragments to perform phylogenetic and phylogeographical analyses. Climatic niche modelling allowed us to infer the climatic preferences of the species. A principal components analysis identified the most important climatic factors explaining the actual range of A. fluviatilis. We also identified which climatic factor was the most limiting at range margins, and predicted the species’ geographical range under a climate change scenario [Community Climate Model 3 (CCM3)].Results By means of the phylogeographical analysis, we infer that A. fluviatilis sensu stricto occupied northern refuges during the Last Glacial Maximum. We show that the climatic preferences of Baltic populations are significantly different from those of Central European populations. The projection of the occupied area under the CCM3 climate model predicts a moderate poleward shift of the northern range limits, but a dramatic loss of areas currently occupied, for instance in northern Germany and in southern Great Britain.Main conclusions The post‐glacial range dynamics of A. fluviatilis are not governed by niche conservatism. Therefore, we must be cautious about bioclimatic model predictions: the expected impact of climate change could be tempered by the adaptive potential this species has already shown in its evolutionary history. Thus, modelling approaches should rather be seen as conservative forecasts of altered species ranges as long as the adaptive potential of the organisms in question cannot be predicted.

Boundaries between vegetation types, known as ecotones, can be dynamic in response to climatic changes. The North American Great Plains includes a forest‐grassland ecotone in the southcentral United States that has expanded and contracted in recent decades in response to historical periods of drought and pluvial conditions. This dynamic region also marks a western distributional limit for many passerine birds that typically breed in forests of the eastern United States. To better understand the influence that variability can exert on broad‐scale biodiversity, we explored historical longitudinal shifts in the western extent of breeding ranges of eastern forest songbirds in response to the variable climate of the southern Great Plains. We used climatic niche modeling to estimate current distributional limits of nine species of forest‐breeding passerines from 30‐year average climate conditions from 1980 to 2010. During this time, the southern Great Plains experienced an unprecedented wet period without periodic multi‐year droughts that characterized the region's long‐term climate from the early 1900s. Species’ climatic niche models were then projected onto two historical drought periods: 1952–1958 and 1966–1972. Threshold models for each of the three time periods revealed dramatic breeding range contraction and expansion along the forest‐grassland ecotone. Precipitation was the most important climate variable defining breeding ranges of these nine eastern forest songbirds. Range limits extended farther west into southern Great Plains during the more recent pluvial conditions of 1980–2010 and contracted during historical drought periods. An independent dataset from BBS was used to validate 1966–1972 range limit projections. Periods of lower precipitation in the forest‐grassland ecotone are likely responsible for limiting the western extent of eastern forest songbird breeding distributions. Projected increases in temperature and drought conditions in the southern Great Plains associated with climate change may reverse range expansions observed in the past 30 years.

Based on the niche conservatism hypothesis, i.e. the idea that niches remain unchanged over space and time, climatic niche modelling (CNM) is a useful tool for predicting the spread of introduced taxa. Recent advances have extended such predictions deeper in time for plant species dispersed by humans before the modern era. The latest CNMs successfully evaluate niche differentiation and estimate potential source areas for intriguing taxa such as archaeophytes (i.e., species introduced before 1492 AD). Here, we performed CNMs for Acacia caven, a common Fabaceae tree in South America, considered an archaeophyte west of the Andes, in Central Chile. Accounting for the infraspecific delimitation of the species, our results showed that even when climates are different, climatic spaces used by the species overlap largely between the eastern and western ranges. Despite slight variation, results were consistent when considering one, two, or even three-environmental dimensions, and in accordance with the niche conservatism hypothesis. Specific distribution models calibrated for each region (east vs west) and projected to the past, indicate a common area of occupancy available in southern Bolivia—northwest Argentina since the late Pleistocene, which could have acted as a source-area, and this signal becomes stronger through the Holocene. Then, in accordance with a taxon introduced in the past, and comparing regional vs continental distribution models calibrated at the infraspecific or species level, the western populations showed their spread status to be mostly in equilibrium with the environment. Our study thus indicates how niche and species distribution models are useful to improve our knowledge related to taxa introduced before the modern era.

Pest Risk Assessments (PRAs) routinely employ climatic niche models to identify endangered areas. Typically, these models consider only climatic factors, ignoring the ‘Swiss Cheese’ nature of species ranges due to the interplay of climatic and habitat factors. As part of a PRA conducted for the European and Mediterranean Plant Protection Organization, we developed a climatic niche model for Parthenium hysterophorus, explicitly including the effects of irrigation where it was known to be practiced. We then downscaled the climatic risk model using two different methods to identify the suitable habitat types: expert opinion (following the EPPO PRA guidelines) and inferred from the global spatial distribution. The PRA revealed a substantial risk to the EPPO region and Central and Western Africa, highlighting the desirability of avoiding an invasion by P. hysterophorus. We also consider the effects of climate change on the modelled risks. The climate change scenario indicated the risk of substantial further spread of P. hysterophorus in temperate northern hemisphere regions (North America, Europe and the northern Middle East), and also high elevation equatorial regions (Western Brazil, Central Africa, and South East Asia) if minimum temperatures increase substantially. Downscaling the climate model using habitat factors resulted in substantial (approximately 22–53%) reductions in the areas estimated to be endangered. Applying expert assessments as to suitable habitat classes resulted in the greatest reduction in the estimated endangered area, whereas inferring suitable habitats factors from distribution data identified more land use classes and a larger endangered area. Despite some scaling issues with using a globally conformal Land Use Systems dataset, the inferential downscaling method shows promise as a routine addition to the PRA toolkit, as either a direct model component, or simply as a means of better informing an expert assessment of the suitable habitat types.

<p>The main objective of this study is to develop and test a method of bias correction for paleoclimate model simulations using the “Cumulative Distribution Functions – transform” (CDF-t) method. The CDF-t is a quantile-mapping based method, extended to account for climate change signal. Here we apply the CDF-t to climate model outputs for the Mid-Holocene and the Last Glacial Maximum, simulated by the climate model of intermediate complexity iLOVECLIM at 5.625° resolution. Additionally, we test the proposed methodology on iLOVECLIM model outputs dynamically downscaled on a  0.25° resolution.</p><p>The results are validated through inverse and forward modelling approaches. The inverse approach implies comparing the obtained results with proxy-based reconstructed climatic variables. Here we use temperature and precipitation reconstructions, obtained with inverse modelling methods from pollen data. In this study, both gridded and point-based multi-proxy reconstruction datasets were used for the analysis.</p><p>The forward approach includes a further step of vegetation modelling, using the climatologies derived from bias-corrected outputs of the iLOVECLIM model in CARAIB (CARbon Assimilation In the Biosphere) global dynamic vegetation model. The modelled biomes are evaluated in comparison with pollen-based biome reconstructions BIOME6000.</p><p>The findings of this study indicate that the use of the proposed methodology results in significant improvements in climate and vegetation modelling and suggest that the CDF-t method is an valuable approach to reduce biases in paleoclimate modelling.</p>