Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert

Changes in species diversity along the ephemeral streams in eastern Mediterranean Mountainous Ecosystem, a case study for Ahir Mountain (Kahramanmaraş-Türkiye)

Ephemeral streams are important habitats that support biodiversity, especially in mountainous ecosystems in arid and semi-arid regions, and are among those that will be most affected by global climate change. This study aimed to examine the trends in plant species diversity of ephemeral stream beds and their relationship with environmental variables (aspect, elevation, soil) in the eastern Mediterranean region.For this purpose, 40 sample plots were applied in the valley cross sections of the ephemeral stream beds (valley bottom, side and ridge) on two main slopes (north and south) in 2019. The abundance values of plant species were determined and the number of individuals in each sample plot was counted. In addition, soil samples were taken at a depth of 0-30 cm and analyzed. With the data obtained, the importance value index of all species was calculated, and the diversity and species richness of the sample plots were determined.A total of 130 plant taxa were identified in the study area. The most dominant species were Astragalus kurdicus (IVI value: 25.97), Helichrysum plicatum (21.94), Taeniatherum caput-medusae subsp. crinitum (15.51), Hordeum bulbosum (15.33), Bromus erectus (15.32), and Minuartia juniperina (14.14). Both plant richness and endemism rate showed a significant relationship with increasing elevation. Plant diversity values of south-facing slopes were higher (2.23) than those of north-facing slopes (2.21). In addition, we found that phosphorus is an important factor in the distribution of plant species along the ephemeral stream beds, and as the amount of phosphorus increases, species richness and diversity also increase.

Tree biodiversity of warm drylands is likely to decline in a drier world

Warm drylands represent 19% of land surfaces worldwide and host ca. 1100 tree species. The risk of decline due to climate aridification of this neglected biodiversity has been overlooked despite its ecological and societal importance. To fill this gap, we assessed the risk of decline due to climate aridification of tree species in warm drylands based on spatialized occurrence data and climate models. We considered both species vulnerability and exposure, compared the risk of tree species decline across five bioregions and searched for phylogenetic correlates. Depending on the future climate model, from 44% to 88% of warm drylands' tree species will undergo climate aridification with a high risk of decline even under the most optimistic conditions. On a regional scale, the rate of species that will undergo climate aridification in the future varies from 21% in the Old World North, to 90% in Australia, with a risk of decline confirming the high level of risk predicted at the global scale. Using generalized linear mixed models, we found that, species more exposed to climate aridification will be more at risk, but also that species vulnerability is a key driver of their risk of decline. Indeed, the warm drylands specialist species will be less at risk due to climate aridification than species being marginal in warm drylands. We also found that the risk of decline is widespread across the main clades of the phylogeny and involves several evolutionary distinct species. Estimating a high risk of decline for numerous tree species in all warm drylands, including emblematic dryland endemics, our work warns that future increase in aridity could result in an extensive erosion of tree biodiversity in these ecosystems.

Environmental regionalization and endemic plant distribution in the Maghreb

Clustering methods based on environmental variables are useful in the planning of conservation strategies for species and ecosystems. However, there is a lack of work on the regionalization of the vast space of North Africa and the distribution of plant species. The current lists of endemic plants are focused mostly on an occurrence at the country level and not on regions with different conditions. The aim of this work was to lay out an environmental scheme for northwest Africa and to collect data about the occurrence of endemic plants in this area. Clustering with 12 of 33 tested environmental rasters was performed to divide the Maghreb into environmental clusters. Then, a list of 1618 endemic plant taxa (1243 species and 375 subspecies) was prepared and their distribution in estimated environmental clusters was examined. Eleven clusters with different conditions were estimated. The main drivers of regionalization were temperature amplitude, precipitation seasonality, and precipitation of the warmest quarter. According to the occurrence of endemic plants, northwest Africa may be divided into three zones: Atlas, Mediterranean (two environmental clusters), and southern zone (eight environmental clusters). The presented results provide a good basis for understanding the spatial patterns of the Maghreb, including its environment and species diversity. A designed list of endemic plant species together with environmental data may facilitate the planning of future research in north Africa and arranging methods of biodiversity protection.

Contrasting Genetic Footprints among Saharan Olive Populations: Potential Causes and Conservation Implications

The Laperrine's olive is endemic to the Saharan Mountains. Adapted to arid environments, it may constitute a valuable genetic resource to improve water-stress tolerance in the cultivated olive. However, limited natural regeneration coupled with human pressures make it locally endangered in Central Sahara. Understanding past population dynamics is thus crucial to define management strategies. Nucleotide sequence diversity was first investigated on five nuclear genes and compared to the Mediterranean and African olives. These data confirm that the Laperrine's olive has a strong affinity with the Mediterranean olive, but it shows lower nucleotide diversity than other continental taxa. To investigate gene flows mediated by seeds and pollen, polymorphisms from nuclear and plastid microsatellites from 383 individuals from four Saharan massifs were analyzed. A higher genetic diversity in Ahaggar (Hoggar, Algeria) suggests that this population has maintained over the long term a larger number of individuals than other massifs. High-to-moderate genetic differentiation between massifs confirms the role of desert barriers in limiting gene flow. Yet contrasting patterns of isolation by distance were observed within massifs, and also between plastid and nuclear markers, stressing the role of local factors (e.g., habitat fragmentation, historical range shift) in seed and pollen dispersal. Implications of these results in the management of the Laperrine's olive genetic resources are discussed.

Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan

Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles.

A kingdom in decline: Holocene range contraction of the lion (Panthera leo) modelled with global environmental stratification

Aim

We use ecological niche models and environmental stratification of palaeoclimate to reconstruct the changing range of the lion (Panthera leo) during the late Pleistocene and Holocene.

Location

The modern (early 21st century) range of the lion extends from southern Africa to the western Indian Subcontinent, yet through the 20th century this range has been drastically reduced in extent and become increasingly fragmented as a result of human impacts.

Methods

We use Global Environmental Stratification with MaxEnt ecological niche models to map environmental suitability of the lion under current and palaeoclimatic scenarios. By examining modelled lion range in terms of categorical environmental strata, we characterise suitable bioclimatic conditions for the lion in a descriptive manner.

Results

We find that lion habitat suitability has reduced throughout the Holocene, controlled by pluvial/interpluvial cycles. The aridification of the Sahara  6ka dramatically reduced lion range throughout North Africa. The association of Saharan aridification with the development of pastoralism and the growth of sedentary communities, who practised animal husbandry, would have placed additional and lasting anthropogenic pressures on the lion.

Main Conclusions

This research highlights the need to integrate the full effects of the fluctuating vegetation and desiccation of the Sahara into palaeoclimatic models, and provides a starting point for further continental-scale analyses of shifting faunal ranges through North Africa and the Near East during the Holocene. This scale of ecological niche modelling does not explain the current pattern of genetic variation in the lion, and we conclude that narrow but substantial physical barriers, such as rivers, have likely played a major role in population vicariance throughout the Late Pleistocene.

The Role of Climate and Topography in Shaping the Diversity of Plant Communities in Cabo Verde Islands

The flora and vegetation of the archipelago of Cabo Verde is dominated by Macaronesian, Mediterranean, and particularly by African tropical elements, resulting from its southernmost location, when compared to the other islands of the Macaronesia (i.e., Azores, Madeira, Selvagens, and Canary Islands). Very likely, such a geographical position entailed higher susceptibility to extreme climatic fluctuations, namely those associated with the West African Monsoon oscillations. These fluctuations led to a continuous aridification, which is a clear trend shown by most recent studies based on continental shelf cores. Promoting important environmental shifts, such climatic fluctuations are accepted as determinant to explain the current spatial distribution patterns of taxa, as well as the composition of the plant communities. In this paper, we present a comprehensive characterization of the main plant communities in Cabo Verde, and we discuss the role of the climatic and topoclimatic diversity in shaping the vegetation composition and distribution of this archipelago. Our study reveals a strong variation in the diversity of plant communities across elevation gradients and distinct patterns of richness among plant communities. Moreover, we present an overview of the biogeographical relationships of the Cabo Verde flora and vegetation with the other Macaronesian Islands and northwestern Africa. We discuss how the distribution of plant communities and genetic patterns found among most of the endemic lineages can be related to Africa’s ongoing aridification, exploring the impacts of a process that marks northern Africa from the Late Miocene until the present.

The endangered Saharan cypress (Cupressus dupreziana): do not let it get into Charon's boat

The current state-of-the-art creates a sound basis for the preservation of unique species Cupressus dupreziana provided that targeted effort and care is devoted to the accomplishment of multiplication protocols. This review is to summarize known data on Cupressus dupreziana-specific characteristics, including abiotic stress resistance, and natural reproduction, and estimates the possibilities of ex situ conservation with an emphasis on the cultivation in vitro of this endangered species. As there is only limited information about the cultivation of C. dupreziana in vitro, we have included relevant data on the related species Cupressus sempervirens, where micropropagation techniques are well established, along with other information on species with similar fates and life strategies-Saharan olive Olea europaea subsp. laperrinei and myrtle Myrthus nivellei. The aim of this work is to enhance general understanding and to promote an interest in this relict plant species to contribute to more wide-ranging studies and to increase its chance of preservation. Besides others, reducing the number of species threatened with extinction is an essential and immediate task as high genetic variability of ecosystems is crucial for their stability under changing climatic conditions.

Mapping physiology: biophysical mechanisms define scales of climate change impacts

The rocky intertidal zone is a highly dynamic and thermally variable ecosystem, where the combined influences of solar radiation, air temperature and topography can lead to differences greater than 15°C over the scale of centimetres during aerial exposure at low tide. For most intertidal organisms this small-scale heterogeneity in microclimates can have enormous influences on survival and physiological performance. However, the potential ecological importance of environmental heterogeneity in determining ecological responses to climate change remains poorly understood. We present a novel framework for generating spatially explicit models of microclimate heterogeneity and patterns of thermal physiology among interacting organisms. We used drone photogrammetry to create a topographic map (digital elevation model) at a resolution of 2 × 2 cm from an intertidal site in Massachusetts, which was then fed into to a model of incident solar radiation based on sky view factor and solar position. These data were in turn used to drive a heat budget model that estimated hourly surface temperatures over the course of a year (2017). Body temperature layers were then converted to thermal performance layers for organisms, using thermal performance curves, creating 'physiological landscapes' that display spatially and temporally explicit patterns of 'microrefugia'. Our framework shows how non-linear interactions between these layers lead to predictions about organismal performance and survivorship that are distinct from those made using any individual layer (e.g. topography, temperature) alone. We propose a new metric for quantifying the 'thermal roughness' of a site (RqT, the root mean square of spatial deviations in temperature), which can be used to quantify spatial and temporal variability in temperature and performance at the site level. These methods facilitate an exploration of the role of micro-topographic variability in driving organismal vulnerability to environmental change using both spatially explicit and frequency-based approaches.

Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long-distance dispersal in North American palms

Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genomewide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognized species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genomewide divergence mediated by multiple effectors.

Environmental gradients shape the genetic structure of two medicinal Salvia species in Jordan

Environmental gradients, and particularly climatic variables, exert a strong influence on plant distribution and, potentially, population genetic diversity and differentiation. Differences in water availability can cause among-population variation in ecological processes and can thus interrupt populations' connectivity and isolate them environmentally. The present study examines the effect of environmental heterogeneity on plant populations due to environmental isolation unrelated to geographic distance. Using AFLP markers, we analyzed genetic diversity and differentiation among 12 Salvia spinosa populations and 13 Salvia syriaca populations from three phytogeographical regions (Mediterranean, Irano-Turanian and Saharo-Arabian) representing the extent of the species' geographic range in Jordan. Differences in geographic location and climate were considered in the analyses. For both species, flowering phenology varied among populations and regions. Irano-Turanian and Saharo-Arabian populations had higher genetic diversity than Mediterranean populations, and genetic diversity increased significantly with increasing temperature. Genetic diversity in Salvia syriaca was affected by population size, while genetic diversity responded to drought in S. spinosa. For both species, high levels of genetic differentiation were found as well as two well-supported phytogeographical groups of populations, with Mediterranean populations clustering in one group and the Irano-Turanian and Saharo-Arabian populations in another. Genetic distance was significantly correlated to environmental distance, but not to geographic distance. Our data indicate that populations from moist vs. arid environments are environmentally isolated, where environmental gradients affect their flowering phenology, limit gene flow and shape their genetic structure. We conclude that environmental heterogeneity may act as driver for the observed variation in genetic diversity.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo)

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

Climate relicts and their associated communities as natural ecology and evolution laboratories

Climate relicts, marginal populations that have become isolated via climate-driven range shifts, preserve ecological and evolutionary histories that can span millennia. Studies point to climate relicts as 'natural laboratories' for investigating how long-term environmental change impacts species and populations. However, we propose that such research should be expanded to reveal how climate change affects 'interacting' species in ways that reshape community composition and evolution. Biotic interactions and their community and ecosystem effects are often genetically based and driven by associations with foundation species. We discuss evolution in climate relicts within the context of the emerging fields of community and ecosystem genetics, exploring the idea that foundation relicts are also natural community and ecosystem laboratories and windows to future landscapes.