Past and future demographic dynamics of alpine species: limited genetic consequences despite dramatic range contraction in a plant from the Spanish Sierra Nevada

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS)

BACKGROUND

Anemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants.

RESULTS

In our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance.

CONCLUSIONS

Here, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species.

Genetic and demographic consequences of range contraction patterns during biological annihilation

Species range contractions both contribute to, and result from, biological annihilation, yet do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are usually characterized only by reduction in extent of range. For effective conservation, it is critical to recognize that not all range contractions are the same. We propose three distinct patterns of range contraction: shrinkage, amputation, and fragmentation. We tested the impact of these patterns on populations of a generalist species using forward-time simulations. All three patterns caused 86-88% reduction in population abundance and significantly increased average relatedness, with differing patterns in declines of nucleotide diversity relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for Earth's biodiversity would provide useful and necessary information to combat biological annihilation.

Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae)

Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures.

Biogeographic history and environmental niche evolution in the palearctic genus Helianthemum (Cistaceae)

The biogeographic history and the degree of environmental niche conservatism provide essential clues to decipher the underlying macroevolutionary processes of species diversification and to understand contemporary patterns of biodiversity. The genus Helianthemum constitutes an excellent case study to investigate the impact of the geo-climatic changes and the environmental niche shifts on the origins of plant species diversity in the Mediterranean hotspot. It is a palearctic species-rich lineage with c. 140 species and subspecies mostly belonging to three distinct evolutionary radiations, almost confined to the Mediterranean region and occurring across varied environmental conditions. In this work, we studied the ample and rapid diversification of the genus Helianthemum across its whole distribution range by performing phylogenetic reconstructions of ancestral ranges and environmental niche evolution. We observed a striking synchrony of biogeographic movements with niche shifts between the three major clades of the genus Helianthemum, likely related to the geo-climatic events occurred in the Mediterranean Basin since the Upper Miocene. In particular, Late Miocene and Early Pliocene were dominated by episodes of range expansions, the Late Pliocene by range contraction and vicariance events, and Pleistocene by most intense environmental niche shifts and in-situ diversification. Our study also provides evidence for four main environmental niches in Helianthemum (i.e., Mediterranean, subdesert, humid-montane and subtropical-insular) and a tendency toward environmental niche conservatism within different subclades, with few niche shifts mostly occurring from Mediterranean ancestors. The relative longer time spent in Mediterranean areas by the ancestors of Helianthemum suggests that the larger species diversity observed in the Mediterranean (i.e. Northern Africa and Southern Europe) may have been generated by a time-for-speciation effect reinforced by environmental niche conservatism. Overall, our work highlights the role of the Mediterranean Basin as a 'cradle of diversity' and an 'evolutionary hub', facilitating the environmental transitions and determining the building up of a global plant biodiversity hotspot.

Long-term ecological changes in Mediterranean mountain lakes linked to recent climate change and Saharan dust deposition revealed by diatom analyses

Anthropogenic climate change and the recent increase of Saharan dust deposition has had substantial effects on Mediterranean alpine regions. We examined changes in diatom assemblage composition over the past ~180 years from high-resolution, dated sediment cores retrieved from six remote lakes in the Sierra Nevada Mountains of Southern Spain. In all lakes, changes in diatom composition began over a century ago, but were more pronounced after ~1970 CE, concurrent with trends in rising regional air temperature, declining precipitation, and increased Saharan dust deposition. Temperature was identified as the main predictor of diatom assemblage changes, whereas both Saharan dust deposition drivers, the Sahel precipitation index and the winter North Atlantic Oscillation, were secondary explanatory variables. Diatom compositional shifts are indicative of lake alkalinization (linked to heightened evapoconcentration and an increase in calcium-rich Saharan dust input) and reduced lake water turbulence (linked to lower water levels and reduced inflows to the lakes). Moreover, decreases in epiphytic diatom species were indicative of increasing aridity and the drying of catchment meadows. Our results support the conclusions of previous chlorophyll-a and cladoceran-based paleolimnological analyses of these same dated sedimentary records which show a regional-scale response to climate change and Saharan dust deposition in Sierra Nevada lakes and their catchments during the 20th century. However, diatom assemblages seem to respond to different atmospheric and climate-related effects than cladoceran assemblages and chlorophyll-a concentrations. The recent impact of climate change and atmospheric Saharan deposition on lake biota assemblages and water chemistry, as well as catchment water availability, will have important implications for the valuable ecosystem services that the Sierra Nevada provides.

Spatial genetic structure and diversity of natural populations of Aesculus hippocastanum L. in Greece

Horse-chestnut (Aesculus hippocastanum L.) is an endemic and relict species from the Mediterranean biodiversity hotspot and a popular ornamental tree. Knowledge about the evolutionary history of this species remains scarce. Here, we ask what historical and ecological factors shaped the pattern of genetic diversity and differentiation of this species. We genotyped 717 individuals from nine natural populations using microsatellite markers. The influence of distance, topography and habitat variables on spatial genetic structure was tested within the approaches of isolation-by-distance and isolation-by-ecology. Species niche modeling was used to project the species theoretical range through time and space. The species showed high genetic diversity and moderate differentiation for which topography, progressive range contraction through the species’ history and long-term persistence in stable climatic refugia are likely responsible. A strong geographic component was revealed among five genetic clusters that are connected with very limited gene flow. The environmental variables were a significant factor in the spatial genetic structure. Modeling results indicated that future reduction of the species range may affect its survival. The possible impact of climate changes and high need of in situ conservation are discussed.

Fernández de Castro A, Seguí J, Traveset A, Sosa PA. Alpine species in dynamic insular ecosystems through time: conservation genetics and niche shift estimates of the endemic and vulnerable Viola cheiranthifolia

BACKGROUND AND AIMS

Alpine oceanic ecosystems are considered amongst the most ephemeral and restricted habitats, with a biota highly vulnerable to climate changes and disturbances. As an example of an alpine insular endemic, the past and future population genetic structure and diversity, and the future distribution of Viola cheiranthifolia (Violaceae), endemic to Tenerife (Canary Islands), were estimated. The main goals were to predict distribution changes of this alpine oceanic plant under climate change, and to assist in actions for its conservation.

METHODS

To perform population genetic analysis, 14 specific microsatellite markers and algorithms which considered the polyploid condition of V. cheiranthifolia were employed. The niche modelling approach incorporated temperature gradients, topography and snow cover maps. Models were projected into climate change scenarios to assess the extent of the altitudinal shifts of environmental suitability. Finally, simulations were performed to predict whether the environmental suitability loss will affect the genetic diversity of populations.

KEY RESULTS

Viola cheiranthifolia presents short dispersal capacity, moderate levels of genetic diversity and a clear population genetic structure divided into two main groups (Teide and Las Cañadas Wall), showing signs of recolonization dynamics after volcanic eruptions. Future estimates of the distribution of the study populations also showed that, despite being extremely vulnerable to climate change, the species will not lose all its potential area in the next decades. The simulations to estimate genetic diversity loss show that it is correlated to suitability loss, especially in Las Cañadas Wall.

CONCLUSIONS

The low dispersal capacity of V. cheiranthifolia, coupled with herbivory pressure, mainly from rabbits, will make its adaptation to future climate conditions in this fragile alpine ecosystem difficult. Conservation actions should be focused on herbivore control, population reinforcement and surveillance of niche shifts, especially in Guajara, which represents the oldest isolated population and a genetic reservoir for the species.

Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper

Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub‐legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west‐to‐east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories.

Terrestrial mountain islands and Pleistocene climate fluctuations as motors for speciation: A case study on the genus Pseudovelia (Hemiptera: Veliidae)

This study investigated the influences of geographic isolation and climate fluctuation on the genetic diversity, speciation, and biogeography of the genus Pseudovelia (Hemiptera: Veliidae) in subtropical China and tropic Indo-China Peninsula. Species nucleotide and haplotype diversities decreased with reduction in species distribution limits. The gene tree was congruent with the taxonomy of monophyly, except for four species, P. contorta, P. extensa, P. tibialis tibialis, and P. vittiformis. The conflicts between the genes and species tree could be due to long-term isolation and incomplete lineage sorting. Diversification analysis showed that the diversification rate (0.08 sp/My shifted to 0.5 sp/My) changed at 2.1 Ma, which occurred in the early Pleistocene period. Ancestral area reconstruction suggested that subtropical species possibly evolved from the tropics region (i.e., Indo-China Peninsula). Results implied that narrow endemics harbored relatively low genetic diversity because of small effective population and genetic drift. Radiation of subtropical Pseudovelia species was rapidly promoted by Pleistocene climate fluctuations and geographic isolation. The acute rising of the Hengduan Mountain with the entire uplift of the Qinghai-Tibet Plateau induced the initial differentiation of Pseudovelia species. These results highlighted the importance of geographical isolation and climate changes in promoting speciation in mountain habitat islands.

Genetic structure of the endangered Greater Short-horned Lizard (Phrynosoma hernandesi) in Canada: evidence from mitochondrial and nuclear genes

The northern edge of the range of the Greater Short-horned Lizard (Phrynosoma hernandesi Girard, 1858) occurs in western Canada, where the species has “endangered” status and exhibits a patchy distribution. Phylogenetic inference and genetic analyses were employed to investigate the genetic structure of P. hernandesi throughout its Canadian range. One nuclear and two mitochondrial DNA genes were sequenced from 94 lizard tail tips. Overall, sequences from lizards from both Alberta and Saskatchewan displayed very little variability, and the consistent clustering of all the P. hernandesi mitochondrial and nuclear DNA sequences from Canada in both phylogenetic and population genetic analyses is consistent with the lizards from all sampled localities having originated from a single glacial refugium, and with being, until recently (or currently) interconnected genetically. The genetic data obtained so far furnish no information useful for interpreting the species’ present-day patchy distribution patterns or for formulating conservation strategies.

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)

BACKGROUND AND AIMS

The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ~30 species and subspecies with highly specialized corollas.

METHODS

A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species.

KEY RESULTS

A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects.

CONCLUSIONS

The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes.

Autecological traits determined two evolutionary strategies in Mediterranean plants during the Quaternary: low differentiation and range expansion versus geographical speciation in Linaria

The evolutionary patterns of the Mediterranean flora during the Quaternary have been relatively well documented based on phylogenetic and biogeographic analyses, but few studies have addressed the evolutionary traits that determined diversification and range expansion success during this period. We analysed previously published and newly generated sequences of three plastid noncoding regions (rpl32-trnL(UAG) , trnS-trnG and trnL-trnF), the nuclear ribosomal internal transcribed spacer (ITS) and a low-copy nuclear gene intron (AGT1) of Linaria sect. Supinae, a group of angiosperms that diversified in the Quaternary. The origin and recent colonization dynamics of closely related lineages were inferred by biogeographic reconstruction and phylogeographic analyses, while breeding system experiments coupled with ecological and morphological data were used to test association with range expansion and diversification. A combination of traits, including selfing, short lifespan and the ability to tolerate a wide variety of substrates, were key factors underlying range expansion after long-distance dispersal throughout the Mediterranean basin. By contrast, self-incompatibility may have promoted higher diversification rates in narrow ranges of the Iberian Peninsula. We argue that a few traits contributed to the adoption of two contrasting strategies that may have been predominant in the evolution of Mediterranean angiosperms.