Comparative phylogeography of two related plant species with overlapping ranges in Europe, and the potential effects of climate change on their intraspecific genetic diversity

Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum

Some plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (F_ST = 0.106 for nuclear microsatellites and F_ST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (R_r = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between F ST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.

Past, current, and potential future distributions of unique genetic diversity in a cold-adapted mountain butterfly

AIM

Climatic changes throughout the Pleistocene have strongly modified species distributions. We examine how these range shifts have affected the genetic diversity of a montane butterfly species and whether the genetic diversity in the extant populations is threatened by future climate change.

LOCATION

Europe.

TAXON

Erebia epiphron Lepidoptera: Nymphalidae.

METHODS

We analyzed mtDNA to map current genetic diversity and differentiation of E. epiphron across Europe to identify population refugia and postglacial range shifts. We used species distribution modeling (SDM) to hindcast distributions over the last 21,000 years to identify source locations of extant populations and to project distributions into the future (2070) to predict potential losses in genetic diversity.

RESULTS

We found substantial genetic diversity unique to specific regions within Europe (total number of haplotypes = 31, number of unique haplotypes = 27, H d = 0.9). Genetic data and SDM hindcasting suggest long-term separation and survival of discrete populations. Particularly, high rates of unique diversity in postglacially colonized sites in England (H d = 0.64) suggest this population was colonized from a now extinct cryptic refugium. Under future climate change, SDMs predict loss of climate suitability for E. epiphron, particularly at lower elevations (<1,000 meters above sea level) equating to 1 to 12 unique haplotypes being at risk under climate scenarios projecting 1°C and 2-3°C increases respectfully in global temperature by 2070.

MAIN CONCLUSIONS

Our results suggest that historical range expansion and retraction processes by a cold-adapted mountain species caused diversification between populations, resulting in unique genetic diversity which may be at risk if distributions of cold-adapted species shrink in future. Assisted colonizations of individuals from at-risk populations into climatically suitable unoccupied habitat might help conserve unique genetic diversity, and translocations into remaining populations might increase their genetic diversity and hence their ability to adapt to future climate change.

Phylogeography and niche modelling: reciprocal enlightenment

Phylogeography examines the spatial genetic structure of species. Environmental niche modelling (or ecological niche modelling; ENM) examines the environmental limits of a species’ ecological niche. These two fields have great potential to be used together. ENM can shed light on how phylogeographical patterns develop and help identify possible drivers of spatial structure that need to be further investigated. Specifically, ENM can be used to test for niche differentiation among clades, identify factors limiting individual clades and identify barriers and contact zones. It can also be used to test hypotheses regarding the effects of historical and future climate change on spatial genetic patterns by projecting niches using palaeoclimate or future climate data. Conversely, phylogeographical information can populate ENM with within-species genetic diversity. Where adaptive variation exists among clades within a species, modelling their niches separately can improve predictions of historical distribution patterns and future responses to climate change. Awareness of patterns of genetic diversity in niche modelling can also alert conservationists to the potential loss of genetically diverse areas in a species’ range. Here, we provide a simplistic overview of both fields, and focus on their potential for integration, encouraging researchers on both sides to take advantage of the opportunities available.

Cross-genera SSR transferability in cacti revealed by a case study using Cereus (Cereeae, Cactaceae)

The study of transferability of simple sequence repeats (SSR) among closely related species is a well-known strategy in population genetics, however transferability among distinct genera is less common. We tested cross-genera SSR amplification in the family Cactaceae using a total of 20 heterologous primers previously developed for the genera Ariocarpus, Echinocactus, Polaskia and Pilosocereus, in four taxa of the genus Cereus: C. fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, C. jamacaru and C. insularis. Nine microsatellite loci were amplified in Cereus resulting in 35.2% of success in transferability, which is higher than the average rate of 10% reported in the literature for cross-genera transferability in eudicots. The genetic variation in the transferred markers was sufficient to perform standard clustering analysis, indicating each population as a cohesive genetic cluster. Overall, the amount of genetic variation found indicates that the transferred SSR markers might be useful in large-scale population studies within the genus Cereus.

Phylogeography of Swertia perennis in Europe based on cpDNA markers

Background

Swertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species.

Methods

In this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations.

Results

A total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA.

Discussion

The lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and the origin and distribution of this species in Europe. Today, it seems to be restricted due to the occurrence of plants which clearly reflects the genetic variability from the ancient period.

Large- and small-scale environmental factors drive distributions of cool-adapted plants in karstic microrefugia

BACKGROUND AND AIMS

Dolines are small- to large-sized bowl-shaped depressions of karst surfaces. They may constitute important microrefugia, as thermal inversion often maintains cooler conditions within them. This study aimed to identify the effects of large- (macroclimate) and small-scale (slope aspect and vegetation type) environmental factors on cool-adapted plants in karst dolines of East-Central Europe. We also evaluated the potential of these dolines to be microrefugia that mitigate the effects of climate change on cool-adapted plants in both forest and grassland ecosystems.

METHODS

We compared surveys of plant species composition that were made between 2007 and 2015 in 21 dolines distributed across four mountain ranges (sites) in Hungary and Romania. We examined the effects of environmental factors on the distribution and number of cool-adapted plants on three scales: (1) regional (all sites); (2) within sites and; (3) within dolines. Generalized linear models and non-parametric tests were used for the analyses.

KEY RESULTS

Macroclimate, vegetation type and aspect were all significant predictors of the diversity of cool-adapted plants. More cool-adapted plants were recorded in the coolest site, with only few found in the warmest site. At the warmest site, the distribution of cool-adapted plants was restricted to the deepest parts of dolines. Within sites of intermediate temperature and humidity, the effect of vegetation type and aspect on the diversity of cool-adapted plants was often significant, with more taxa being found in grasslands (versus forests) and on north-facing slopes (versus south-facing slopes).

CONCLUSIONS

There is large variation in the number and spatial distribution of cool-adapted plants in karst dolines, which is related to large- and small-scale environmental factors. Both macro- and microrefugia are therefore likely to play important roles in facilitating the persistence of cool-adapted plants under global warming.

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.

Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history

A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.

Retreating or standing: responses of forest species and steppe species to climate change in arid Eastern Central Asia

Background

The temperature in arid Eastern Central Asia is projected to increase in the future, accompanied by increased variability of precipitation. To investigate the impacts of climate change on plant species in this area, we selected two widespread species as candidates, Clematis sibirica and C. songorica, from montane coniferous forest and arid steppe habitats respectively.

Methodology/Principal Findings

We employed a combined approach of molecular phylogeography and species distribution modelling (SDM) to predict the future responses of these two species to climate change, utilizing evidence of responses from the past. Genetic data for C. sibirica shows a significant phylogeographical signal (N_ST > F_ST, P<0.05) and demographic contraction during the glacial-interglacial cycles in the Pleistocene. This forest species would likely experience range reduction, though without genetic loss, in the face of future climate change. In contrast, SDMs predict that C. songorica, a steppe species, should maintain a consistently stable potential distribution under the Last Glacial Maximum (LGM) and the future climatic conditions referring to its existing potential distribution. Molecular results indicate that the presence of significant phylogeographical signal in this steppe species is rejected and this species contains a high level of genetic differentiation among populations in cpDNA, likely benefiting from stable habitats over a lengthy time period.

Conclusions/Significance

Evidence from the molecular phylogeography of these two species, the forest species is more sensitive to past climate changes than the steppe species. SDMs predict that the forest species will face the challenge of potential range contraction in the future more than the steppe species. This provides a perspective on ecological management in arid Eastern Central Asia, indicating that increased attention should be paid to montane forest species, due to their high sensitivity to disturbance.

Soil warming alters seed-bank responses across the geographic range of freshwater Taxodium distichum (Cupressaceae) swamps

PREMISE OF THE STUDY

Climate warming is predicted to have far-reaching effects on the distribution of species, but those effects may depend on the flexibility of regenerating species in responding to climate gradients. We conducted a study to determine whether the variation in the response of seed banks to temperature varied across the latitudinal range of Taxodium distichum swamps in North America.

METHODS

The soil was collected in a long-term research network and heated experimentally to three current-day spring normal soil temperatures (average maximum daily spring normal soil temperatures during May in Illinois, Arkansas, and Louisiana, USA, respectively: 22°, 25°, and 29°C). A "normal" is the mean temperature calculated over a 30-yr interval (1971-2000). Seed-bank density and biomass responses were examined in relation to latitude and difference in the soil temperature of the experiment and the spring normal.

KEY RESULTS

Using first- and second-order regression analysis, we determined that the variation in total germination density was lowest mid-range and in experimental soil temperatures similar to the spring normal. For some dominant species, the variance in germination density was higher in the northern (Cephalanthus occidentalis) or the southern part of the network (Saururus cernuus and Polygonum pensylvanicum). Overall, the variance of total biomass (root, shoot, whole plant) was higher if the experimental soil temperature was warmer than the spring normal.

CONCLUSIONS

Our results suggest that the regeneration of some populations of swamp species may have more flexibility to respond to climate warming than others.

Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae)

Aims

Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations.

Methods

Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation.

Important Findings

The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.

Unique genetic variation at a species' rear edge is under threat from global climate change

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming.

High clonal diversity in threatened peripheral populations of the yellow bird's nest (Hypopitys monotropa; syn. Monotropa hypopitys)

BACKGROUND AND AIMS

Peripheral populations of plant species are often characterized by low levels of genetic diversity as a result of genetic drift, restricted gene flow, inbreeding and asexual reproduction. These effects can be exacerbated where range-edge populations are fragmented. The main aim of the present study was to assess the levels of genetic diversity in remnant populations of Hypopitys monotropa (syn. Monotropa hypopitys; yellow bird's nest) at the edge of the species' European range in Northern Ireland, since these remnant populations are small and highly fragmented.

METHODS

Every plant found through surveys of 21 extant populations was genotyped for eight microsatellite loci to estimate levels and patterns of genetic diversity and clonality.

KEY RESULTS

Levels of genetic diversity were relatively high in the populations studied, and the incidence of clonal reproduction was generally low, with a mean of only 14·45 % of clonal individuals. Clones were small and highly spatially structured. Levels of inbreeding, however, were high.

CONCLUSIONS

The observed low levels of clonality suggest that the majority of genets in the populations of H. monotropa studied are fertile and that reproduction is predominantly sexual. As the species is highly self-compatible, it is likely that the high levels of inbreeding observed in the populations in the present study are the result of self-pollination, particularly given the small numbers of individuals in most of the patches. Given this extent of inbreeding, further genetic monitoring would be advisable to ensure that genetic diversity is maintained.