Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers

Extent of intraspecific trait variability in ecologically central and marginal populations of a dominant alpine plant across European mountains

BACKGROUND AND AIMS

Studying trait variability and restricted gene flow between populations of species can reveal species dynamics. Peripheral populations commonly exhibit lower genetic diversity and trait variability due to isolation and ecological marginality, unlike central populations experiencing gene flow and optimal conditions. This study focused on Carex curvula, the dominant species in alpine acidic meadows of European mountain regions. The species is sparser in dry areas such as the Pyrenees and Balkans, compared to the Central-Eastern Alps and Carpathians. We hypothesized that distinct population groups could be identified based on their mean functional trait values and their correlation with the environment; we predicted that ecologically marginal populations would have stronger trait correlations, lower within-population trait variability (intraspecific trait variability, ITV) and lower genetic diversity than populations of optimal habitats.

METHODS

Sampling was conducted in 34 populations that spanned the entire distribution range of C. curvula. We used hierarchical clustering to identify emergent functional groups of populations, defined by combinations of multiple traits associated with nutrient economy and drought tolerance (e.g. specific leaf area, anatomy). We contrasted the geographical distribution of these groups in relation to environment and genetic structure. We compared pairwise trait relationships, within-population trait variation (ITV) and neutral genetic diversity between groups.

KEY RESULTS

Our study identified emergent functional groups of populations. Those in the southernmost ranges, specifically the Pyrenees and Balkan region, showed drought-tolerant trait syndromes and correlated with indicators of limited water availability. While we noted a decline in population genetic diversity, we did not observe any significant changes in ITV in ecologically marginal (peripheral) populations.

CONCLUSIONS

Our research exemplifies the relationship between ecological marginality and geographical peripherality, which in this case study is linked to genetic depauperation but not to reduced ITV. Understanding these relationships is crucial for understanding the biogeographical factors shaping trait variation.

The molecular population structure of Swertia perennis (Gentianaceae) in Central Europe

Phylogeographic analysis of Swertia perennis, a typical European subalpine springtime species, revealed the existence of at least five major phylogenetic lineages. A large phylogeographic separation exists among these geographical regions, which confirms the existence of glacial refugia in the Pyrenees, but also in the Eastern and Central Alps. The results obtained from the analyzes indicate the existence of three major differences between the populations of the Alps and the Pyrenees, but also between the populations of the Alps and those of other geographical regions (Carpathians, southern Czech Republic, Sudetes and northern Poland). The studied populations from the Black Forest and from north-eastern and southern Poland are a relic of the former wider distribution of these (periglacial) genetic groups within Swertia perennis. Our results also confirm the existence of biogeographical links between the Carpathians and the Hercynian Range and the Alps. Certainly, there was an exchange of genes between populations located in the eastern Alps, the Carpathians and the Hercynian ranges (Czech Republic, Jeseníky, Sudetes, Ore Mountains). This confirms previous results of comparative studies on the genetic diversity of populations of other vascular plant species.

Development of SSR markers for Carex curvula (Cyperaceae) and their importance in investigating the species genetic structure

BACKGROUND

Microsatellite primers were developed and tested to genotype several populations of Carex curvula s. l. (Cyperaceae), in order to infer the phylogeographic relationships of the populations within species and the boundaries between the two described subspecies: C. curvula subsp. curvula and C. curvula subsp. rosae.

METHODS AND RESULTS

Candidate microsatellite loci were isolated based on next-generation sequencing. We tested 18 markers for polymorphism and replicability in seven C. curvula s. l. populations and identified 13 polymorphic loci with dinucleotide repeats. Genotyping results showed the total number of alleles per locus varied from four to 23 (including both infrataxa), and the observed and expected heterozygosity ranged between 0.1 to 0.82 and 0.219 to 0.711, respectively. Furthermore, the NJ tree showed a clear separation between C. curvula subsp. curvula and C. curvula subsp. rosae.

CONCLUSION

The development of these highly polymorphic markers proved to be very efficient not only in delineating between the two subspecies, but also in genetic discriminating at population level within each infrataxon. They are promising tools for evolutionary studies in Cariceae section, as well as in providing knowledge on patterns of the species phylogeography.

Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient

BACKGROUND

Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. The SGDC can be either positive or negative, depending on whether the species diversity and the genetic diversity of the measured species respond in the same or opposite way to drivers. Using a traditional species diversity approach together with ultra-conserved elements and high throughput sequencing, we evaluated the SGDCs in benthic macrofauna communities in the Baltic Sea, a geologically young brackish water sea characterised by its steep salinity gradient and low species richness. Assessing SGDCs from six focal marine invertebrate species from different taxonomic groups and with differing life histories and ecological functions on both a spatial and temporal scale gives a more comprehensive insight into the community dynamics of this young ecosystem and the extrinsic factors that might drive the SGDCs.

RESULTS

No significant correlations between species diversity and genetic diversity were found for any of the focal species. However, both negative and positive trends of SGDCs for the individual focal species were observed. When examining the environmental drivers, no common trends between the species were found, even when restricting the analysis to specific taxonomic classes. Additionally, there were no common environmental factors driving the diversity relationships for species sharing the same SGDC trend (positive or negative). Local population dynamics, together with the invasion history of the individual species and their unique adaptation to the distinctive environment of the Baltic Sea, are expected to be of major influence on the outcome of the SGDCs.

CONCLUSIONS

The present results highlight the importance of assessing SGDCs using multiple species, not just a single indicator species. This emphasises a need to pay attention to the ecology and life history of the focal species. This study also provides insight into the large differences in both patterns and drivers of genetic diversity, which is important when including genetic biodiversity in conservation plans. We conclude that the effects of environmental and biological factors and processes that affects diversity patterns at both the community and genetic levels are likely species dependent, even in an environment such as the Baltic Sea with strong environmental gradients.

Tempo and drivers of plant diversification in the European mountain system

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.

Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

Stability in the South, Turbulence Toward the North: Evolutionary History of Aurinia saxatilis (Brassicaceae) Revealed by Phylogenomic and Climatic Modelling Data

The Balkan Peninsula played an important role in the evolution of many Mediterranean plants and served as a major source for post-Pleistocene colonisation of central and northern Europe. Its complex geo-climatic history and environmental heterogeneity significantly influenced spatiotemporal diversification and resulted in intricate phylogeographic patterns. To explore the evolutionary dynamics and phylogeographic patterns within the widespread eastern Mediterranean and central European species Aurinia saxatilis, we used a combination of phylogenomic (restriction-site associated DNA sequencing, RADseq) and phylogenetic (sequences of the plastid marker ndhF) data as well as species distribution models generated for the present and the Last Glacial Maximum (LGM). The inferred phylogenies retrieved three main geographically distinct lineages. The southern lineage is restricted to the eastern Mediterranean, where it is distributed throughout the Aegean area, the southern Balkan Peninsula, and the southern Apennine Peninsula, and corresponds to the species main distribution area during the LGM. The eastern lineage extends from the eastern Balkan Peninsula over the Carpathians to central Europe, while the central lineage occupies the central Balkan Peninsula. Molecular dating places the divergence among all the three lineages to the early to middle Pleistocene, indicating their long-term independent evolutionary trajectories. Our data revealed an early divergence and stable in situ persistence of the southernmost, eastern Mediterranean lineage, whereas the mainland, south-east European lineages experienced more complex and turbulent evolutionary dynamics triggered by Pleistocene climatic oscillations. Our data also support the existence of multiple glacial refugia in southeast Europe and highlight the central Balkan Peninsula not only as a cradle of lineage diversifications but also as a source of lineage dispersal. Finally, the extant genetic variation within A. saxatilis is congruent with the taxonomic separation of peripatric A. saxatilis subsp. saxatilis and A. saxatilis subsp. orientalis, whereas the taxonomic status of A. saxatilis subsp. megalocarpa remains doubtful.

Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling

Phylogeographic studies of alpine plants have evolved considerably in the last two decades from ad hoc interpretations of genetic data to statistical model-based approaches. In this review we outline the developments in alpine plant phylogeography focusing on the recent approach of integrative distributional, demographic and coalescent (iDDC) modeling. By integrating distributional data with spatially explicit demographic modeling and subsequent coalescent simulations, the history of alpine species can be inferred and long-standing hypotheses, such as species-specific responses to climate change or survival on nunataks during the last glacial maximum, can be efficiently tested as exemplified by available case studies. We also discuss future prospects and improvements of iDDC.

Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps)

BACKGROUND

The Carpathians and the Alps are the largest mountain ranges of the European Alpine System and important centres of endemism. Among the distinctive endemic species of this area is Saxifraga wahlenbergii, a Western Carpathians member of the speciose genus Saxifraga. It was frequently considered a taxonomically isolated Tertiary palaeopolyploid and palaeoendemic, for which the closest relatives could not yet be traced. A recently described narrow endemic of the Eastern Alps, S. styriaca, was hypothesized to be closely related to S. wahlenbergii based on shared presence of peculiar glandular hairs. To elucidate the origin and phylogenetic relationships of both species we studied nuclear and plastid DNA markers based on multiple accessions and analysed the data in a wide taxonomic context. We applied Sanger sequencing, followed by targeted next-generation sequencing (NGS) for a refined analysis of nrITS variants to detect signatures of ancient hybridization. The ITS data were used to estimate divergence times of different lineages using a relaxed molecular clock.

RESULTS

We demonstrate divergent evolutionary histories for the two mountain endemics. For S. wahlenbergii we revealed a complicated hybrid origin. Its maternal parent belongs to a Western Eurasian lineage of high mountain taxa grouped in subsect. Androsaceae and is most likely the widespread S. androsacea. The putative second parent was most likely S. adscendens, which belongs to the distantly related subsect. Tridactylites. While Sanger sequencing of nrITS only showed S. adscendens-related variants in S. wahlenbergii, our NGS screening revealed presence of sequences from both lineages with clear predominance of the paternal over the maternal lineage.

CONCLUSIONS

Saxifraga styriaca was unambiguously assigned to subsect. Androsaceae and is not the sister taxon of S. wahlenbergii. Accordingly, the similarity of the glandular hairs observed in both taxa rests on parallelism and both species do not constitute an example of a close evolutionary link between the floras of the Western Carpathians and Eastern Alps. With the origin of its paternal, S. adscendens-like ITS DNA estimated to ca. 4.7 Ma, S. wahlenbergii is not a relict of the mid-Tertiary climate optimum. Its hybrid origin is much younger and most likely took place in the Pleistocene.

Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.

Geographical distribution of genetic diversity in Secale landrace and wild accessions

BACKGROUND

Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives.

RESULTS

A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev, S. ancestrale Zhuk., S. dighoricum (Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity.

CONCLUSIONS

With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported.

One or three species in Megadenia (Brassicaceae): insight from molecular studies

Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.

The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes

The Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis distribution range was analyzed using four chloroplast loci (trnH-psbA, matK, rpoB and rpoC1) and the nuclear ribosomal marker ITS2. The siliceous species display only two chloroplast haplotypes each and are both characterized by patterns of range expansions all over the Alps. Conversely, the calcareous species are on average more diverse (two to 13 haplotypes per species) with strong patterns of local structuring. We suggest that the occurrence of many calcareous refugia at the periphery of the Alps must have led to local adaptation and morphological diversification, and helped preserving intraspecific diversities during the last glaciations for the associated taxa. ITS2 was more efficient in delineating species boundaries than the chloroplast markers for which several haplotypes are shared among species. This might be either due to chloroplast capture among species and/or to recent divergence. Species adapted to the same substrate are generally only distantly related when they co-occur in the same place. For both types of markers, G. clusii is found genetically distant from all other species.

Working toward integrated models of alpine plant distribution

Species distribution models (SDMs) have been frequently employed to forecast the response of alpine plants to global changes. Efforts to model alpine plant distribution have thus far been primarily based on a correlative approach, in which ecological processes are implicitly addressed through a statistical relationship between observed species occurrences and environmental predictors. Recent evidence, however, highlights the shortcomings of correlative SDMs, especially in alpine landscapes where plant species tend to be decoupled from atmospheric conditions in micro-topographic habitats and are particularly exposed to geomorphic disturbances. While alpine plants respond to the same limiting factors as plants found at lower elevations, alpine environments impose a particular set of scale-dependent and hierarchical drivers that shape the realized niche of species and that require explicit consideration in a modelling context. Several recent studies in the European Alps have successfully integrated both correlative and process-based elements into distribution models of alpine plants, but for the time being a single integrative modelling framework that includes all key drivers remains elusive. As a first step in working toward a comprehensive integrated model applicable to alpine plant communities, we propose a conceptual framework that structures the primary mechanisms affecting alpine plant distributions. We group processes into four categories, including multi-scalar abiotic drivers, gradient dependent species interactions, dispersal and spatial-temporal plant responses to disturbance. Finally, we propose a methodological framework aimed at developing an integrated model to better predict alpine plant distribution.

The extreme disjunction between Beringia and Europe in Ranunculus glacialis s. l. (Ranunculaceae) does not coincide with the deepest genetic split - a story of the importance of temperate mountain ranges in arctic-alpine phylogeography

The arctic-alpine Ranunculus glacialis s. l. is distributed in high-mountain ranges of temperate Europe and in the North, where it displays an extreme disjunction between the North Atlantic Arctic and Beringia. Based on comprehensive sampling and employing plastid and nuclear marker systems, we (i) test whether the European/Beringian disjunction correlates with the main evolutionary diversification, (ii) reconstruct the phylogeographic history in the Arctic and in temperate mountains and (iii) assess the susceptibility of arctic and mountain populations to climate change. Both data sets revealed several well-defined lineages, mostly with a coherent geographic distribution. The deepest evolutionary split did not coincide with the European/Beringian disjunction but occurred within the Alps. The Beringian lineage and North Atlantic Arctic populations, which reached their current distribution via rapid postglacial colonization, show connections to two divergent pools of Central European populations. Thus, immigration into the Arctic probably occurred at least twice. The presence of a rare cpDNA lineage related to Beringia in the Carpathians supports the role of these mountains as a stepping stone between temperate Europe and the non-European Arctic, and as an important area of high-mountain biodiversity. The temperate and arctic ranges presented contrasting phylogeographic histories: a largely static distribution in the former and rapid latitudinal spread in the latter. The persistence of ancient lineages with a strictly regional distribution suggests that the ability of R. glacialis to survive repeated climatic changes within southern mountain ranges is greater than what recently was predicted for alpine plants from climatic envelope modelling.

Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance, Arabidopsis halleri (Brassicaceae)

Arabidopsis halleri is a pseudometallophyte involved in numerous molecular studies of the adaptation to anthropogenic metal stress. In order to test the representativeness of genetic accessions commonly used in these studies, we investigated the A. halleri population genetic structure in Europe. Microsatellite and nucleotide polymorphisms from the nuclear and chloroplast genomes, respectively, were used to genotype 65 populations scattered over Europe. The large-scale population structure was characterized by a significant phylogeographic signal between two major genetic units. The localization of the phylogeographic break was assumed to result from vicariance between large populations isolated in southern and central Europe, on either side of ice sheets covering the Alps during the Quaternary ice ages. Genetic isolation was shown to be maintained in western Europe by the high summits of the Alps, whereas admixture was detected in the Carpathians. Considering the phylogeographic literature, our results suggest a distinct phylogeographic pattern for European species occurring in both mountain and lowland habitats. Considering the evolution of metal adaptation in A. halleri, it appears that recent adaptations to anthropogenic metal stress that have occurred within either phylogeographic unit should be regarded as independent events that potentially have involved the evolution of a variety of genetic mechanisms.

In silico fingerprinting (ISIF): a user-friendly in silico AFLP program

The Amplified fragment Length Polymorphism (AFLP) is one of the cost-effective and useful fingerprinting techniques to study non-model species. One crucial AFLP step in the AFLP procedure is the choice of restriction enzymes and selective bases providing good-quality AFLP profiles. Here, we present a user-friendly program (ISIF) that allows carrying out in silico AFLPs on species for which whole genome sequences are available. Carrying out in silico analyses as preliminary tests can help to optimize the experimental work by allowing a rapid screening of candidate restriction enzymes and the combinations of selective bases to be used. Furthermore, using in silico AFLPs is of great interest to limit homoplasy and amplification of repetitive elements to target genomic regions of interest or to optimize complex and costly high-throughput genomic experiments.

AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species

We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were <200 years old. The oldest genets of D. octopetala, S. herbacea and V. uliginosum were found to be at least 500, 450 and 1400 years old, respectively. These results indicate that individuals in the studied populations have survived pronounced climatic oscillations, including the Little Ice Age and the postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change.

Phylogeography of the Japanese common sedge, Carex conica complex (Cyperaceae), based on chloroplast DNA sequence data and chromosomal variation

PREMISE OF THE STUDY

Genetic and chromosomal variations in plants are often reflected in the geographical distribution patterns. Therefore, identifying such phylogeographical patterns on population is important for understanding the process of plant diversification and speciation, and analyzing both molecular and cytological aspects is necessary. •

METHODS

We investigated the phylogeographic pattern and genetic diversity of the widespread Japanese sedge, Carex conica complex, based on chloroplast DNA haplotypes and chromosomal variations. •

KEY RESULTS

Sixteen distinct haplotypes were detected from 258 individuals in the C. conica complex inferred from the cpDNA sequences of intergenic spacer (IGS) between atpB and rbcL, IGS between trnT and trnL, trnL intron, and IGS between trnL and trnF. Most haplotypes showed distinct geographical structures. Phylogenetic analyses revealed two major clades, clades I and II, among 16 haplotypes of the complex. The haplotypes of clade I were mainly found in eastern Japan, while most haplotypes of clade II were found in western Japan. Four intraspecific aneuploids of 2n = 32, 34, 36, and 38, with forming normal bivalents in meiotic divisions, were also found in the complex. The geographical distribution of these intraspecific aneuploids corresponded well with those of the haplotypes. •

CONCLUSIONS

Our results suggest that the genetic diversity and chromosomal variations in the C. conica complex may have originated from contractions and expansions of geographical ranges affected by Quaternary climatic oscillations.

Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes

Background

Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species.

Results

Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples.

Conclusions

Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.

Biogeographical and evolutionary importance of the European high mountain systems

Europe is characterised by several high mountain systems dominating major parts of its area, and these structures have strongly influenced the evolution of taxa. For species now restricted to these high mountain systems, characteristic biogeographical patterns of differentiation exist. (i) Many local endemics are found in most of the European high mountain systems especially in the Alps and the more geographically peripheral regions of Europe. Populations isolated in these peripheral mountain ranges often have strongly differentiated endemic genetic lineages, which survived and evolved in the vicinity of these mountain areas over long time periods. (ii) Populations of taxa with wide distributions in the Alps often have two or more genetic lineages, which in some cases even have the status of cryptic species. In many cases, these lineages are the results of several centres of glacial survival in the perialpine areas. Similar patterns also apply to the other geographically extended European high mountain systems, especially the Pyrenees and Carpathians. (iii) Populations from adjoining high mountain systems often show similar genetic lineages, a phenomenon best explained by postglacial retreat to these mountains from one single differentiation centre between them. (iv) The populations of a number of species show gradients of genetic diversity from a genetically richer East to a poorer West. This might indicate better glacial survival conditions for this biogeographical group of species in the more eastern parts of Europe.

An AFLP clock for the absolute dating of shallow-time evolutionary history based on the intraspecific divergence of southwestern European alpine plant species

The dating of recent events in the history of organisms needs divergence rates based on molecular fingerprint markers. Here, we used amplified fragment length polymorphisms (AFLPs) of three distantly related alpine plant species co-occurring in the Spanish Sierra Nevada, the Pyrenees and the southwestern Alps/Massif Central to establish divergence rates. Within each of these species (Gentiana alpina, Kernera saxatilis and Silene rupestris), we found that the degree of AFLP divergence (D(N72)) between mountain phylogroups was significantly correlated with their time of divergence (as inferred from palaeoclimatic/palynological data), indicating constant AFLP divergence rates. As these rates did not differ significantly among species, a regression analysis based on the pooled data was utilized to generate a general AFLP rate. The application of this latter rate to AFLP data from other herbaceous plant species (Minuartia biflora: Schönswetter et al. 2006; Nigella degenii: Comes et al. 2008) resulted in a plausible timing of the recolonization of the Svalbard Islands and the separation of populations from the Alps and Scandinavia (Minuartia), and of island population separation in the Aegean Archipelago (Nigella). Furthermore, the AFLP mutation rate obtained in our study is of the same magnitude as AFLP mutation rates published previously. The temporal limits of our AFLP rate, which is based on intraspecific vicariance events at shallow (i.e. late glacial/Early Holocene) time scales, remains to be tested.