Genetic structure of Saxifraga tridactylites (Saxifragaceae) from natural and man-made habitats

The impact of environment on genetic and epigenetic variation in Trifolium pratense populations from two contrasting semi-natural grasslands

Central European grasslands, such as calcareous grasslands and oat-grass meadows, are characterized by diverse environmental conditions and management regimes. Therefore, we aimed to determine potential differences in genetic and epigenetic variation patterns between the contrasting habitats and to identify the drivers of genetic and epigenetic variation. We investigated the genetic and epigenetic variation of the ecologically variable plant species Trifolium pratense L. applying amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses. We observed low levels of genetic and epigenetic differentiation among populations and between habitat types. Genetic and epigenetic variations were not interdependent. Thus, genetic variation was significantly isolated by habitat dissimilarity, whereas epigenetic variation was affected by environment. More specifically, we observed a significant correlation of epigenetic diversity with soil moisture and soil pH (the latter potentially resulting in phosphorus limitation). Genetic variation was, therefore, affected more strongly by habitat-specific environmental conditions induced by land use-related disturbance and gene flow patterns, while epigenetic variation was driven by challenging environmental conditions.

Restoration of species-rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation-Findings of a practical restoration project in southeastern Germany

Restoration of species-rich grasslands is a key issue of conservation. The transfer of seed-containing local plant material is a proven technique to restore species-rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species Knautia arvensis and Plantago lanceolata. For our study, we selected fifteen study sites in southeastern Germany. We analyzed species diversity and composition and used molecular markers to investigate genetic variation within and among populations of the study species from grasslands that served as source sites for restoration and grasslands, which were restored by transfer of green hay and threshed local plant material. The results revealed no significant differences in species diversity and composition between grasslands at source and restoration sites. Levels of genetic variation within populations of the study species Knautia arvensis and Plantago lanceolata were comparable at source and restoration sites and genetic variation among populations at source and their corresponding restoration sites were only marginal different. Our study suggests that the transfer of local plant material is a restoration approach highly suited to preserve the composition of species-rich grasslands and the natural genetic pattern of typical grassland plant species.

Impact of river dynamics on the genetic variation of Gypsophila repens (Caryophyllaceae): a comparison of heath forest and more dynamic gravel bank populations along an alpine river

Alpine rivers are, despite anthropogenic water flow regulation, still often highly dynamic ecosystems. Plant species occurring along these rivers are subject to ecological disturbance, mainly caused by seasonal flooding. Gypsophila repens typically grows at higher altitudes in the Alps, but also occurs at lower altitudes on gravel banks directly along the river and in heath forests at larger distances from the river. Populations on gravel banks are considered non-permanent and it is assumed that new individuals originate from seed periodically washed down from higher altitudes. Populations in heath forests are, in contrast, permanent and not regularly provided with seeds from higher altitudes through flooding. If the genetic structure of this plant species is strongly affected by gene flow via seed dispersal, then higher levels of genetic diversity in populations but less differentiation among populations on gravel banks than in heath forests can be expected. In this study, we analysed genetic diversity within and differentiation among 15 populations of G. repens from gravel banks and heath forests along the alpine River Isar using amplified fragment length polymorphisms (AFLP). Genetic diversity was, as assumed, slightly higher in gravel bank than in heath forest populations, but genetic differentiation was, in contrast to our expectations, comparable among populations in both habitat types. Our study provides evidence for increased genetic diversity under conditions of higher ecological disturbance and increased seed dispersal on gravel banks. Similar levels of genetic differentiation among populations in both habitat types can be attributed to the species' long lifetime, a permanent soil seed bank and gene flow by pollinators among different habitats/locations.

Genetic Variation of Typical Plant Species in Hay Meadows: The Effect of Land Use History, Landscape Structure, and Habitat Quality

Global changes in land use are threatening the diversity of many ecosystems on both the intra- and interspecific levels. Among these ecosystems are the species-rich hay meadows, which have drastically declined in quality and quantity, due to land use intensification or abandonment in recent decades. The remaining genetic resources of their plant species must therefore be protected. To determine the driving forces impacting genetic variation in common hay meadow species (Dactylis glomerata, Heracleum sphondylium, andTrifolium pratense), we used data on the land use history, historic and present landscape structure and habitat quality. Our results showed average genetic diversity within the study sites, with low differentiation levels and a high gene flow among grasslands. Land use history, landscape structure and habitat quality were found to be related to the distribution of genetic diversity in the studied species, highlighting the complex forces acting in these ecosystems and showing the specific impact of litter accumulation on genetic diversity. Both historic and current environmental variables influence genetic diversity, demonstrating the importance of the land use history of a habitat. The most important group of variables impacting genetic variation in all three species was the landscape structure (e.g., distance to the nearest-located urban area or grassland). Also important was the influence of litter cover on genetic diversity inD. glomerata, which provides an interesting starting point for further research.

Habitat matters - Strong genetic and epigenetic differentiation in Linum catharticum from dry and wet grasslands

Plant species differ in their ecological amplitude, with some species occurring in very different habitats under strongly differentiated environmental conditions. We were interested in to what extent the occurrence of Linum catharticum in dry calcareous grasslands (Bromion) and wet litter meadows (Molinion), two habitats on opposing ends concerning, for example, moisture level, is reflected on the genetic and epigenetic level. Using AFLP (amplified fragment length polymorphisms) and MSAP (methylation sensitive amplification polymorphisms) analyses, we studied the genetic and epigenetic variation of L. catharticum from calcareous grasslands and litter meadows. From each habitat, we included five study sites with 16 individuals per sampling location. We observed lower genetic than epigenetic diversity, but considerable differentiation among habitats, which was stronger on the genetic than the epigenetic level. Additionally, we observed a strong correlation of genetic and epigenetic distance, irrespective of geographic distance. The dataset included a large portion of fragments exclusively found in individuals from one or the other habitat. Some epigenetic fragments even occurred in different methylation states depending on the habitat. We conclude that environmental effects act on both the genetic and epigenetic level, producing the clear differentiation among plant individuals from calcareous grasslands and litter meadows. These results may also point into the direction of ecotype formation in this species.

Genetic variation of litter meadow species reflects gene flow by hay transfer and mowing with agricultural machines

Litter meadows, historically established for litter production, are species-rich and diverse ecosystems. These meadows drastically declined during the last decades along with decreasing litter use in modern livestock housing. The aim of our study was to identify the drivers of genetic variation in litter meadow species. Therefore, we tested whether genetic diversity and differentiation depend on habitat age, landscape structure, habitat quality, and/or population size. We analysed 892 individuals of Angelica sylvestris, Filipendula ulmaria, and Succisa pratensis from 20 litter meadows across the Allgäu in Baden-Württemberg (Germany) using AFLP analyses. All study species showed moderate levels of genetic diversity, while genetic differentiation among populations was low. Neither genetic diversity nor differentiation were clearly driven by habitat age. However, landscape structure, habitat quality as well as population size revealed different impacts on the genetic diversity of our study species. Past and present landscape structures shaped the genetic diversity patterns of A. sylvestris and F. ulmaria. The genetic diversity of F. ulmaria populations was, moreover, influenced by the local habitat quality. S. pratensis populations seemed to be affected only by population size. All explanatory variables represent past as well as present gene flow patterns by anthropogenic land use. Therefore, we assume that genetic diversity and differentiation were shaped by both historical creation of litter meadows via hay transfer and present mowing with agricultural machines. These land use practices caused and still cause gene flow among populations in the declining habitats.

Machine-learning-based detection of adaptive divergence of the stream mayfly Ephemera strigata populations

Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We applied a new machine-learning method (i.e., random forest) besides traditional distance-based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non-neutral loci. Spatial autocorrelation analysis based on neutral loci was employed to examine the dispersal ability of this species. We conclude the following: (a) E. strigata show altitudinal adaptive divergence among the populations in the Natori River Basin; (b) random forest showed higher resolution for detecting adaptive divergence than traditional statistical analysis; and (c) separating all markers into neutral and non-neutral loci could provide full insight into parameters such as genetic diversity, local adaptation, and dispersal ability.

Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients

In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.

Reintroduction of the endangered and endemic plant species Cochlearia bavarica-Implications from conservation genetics

Population reintroduction is a common practice in conservation, but often fails, also due to the effects of inbreeding or outbreeding depression. Cochlearia bavarica is a strongly endangered plant species endemic to Bavaria in Germany, constantly declining since the late 1980s. Therefore, population reintroduction is intended. In this study, we analyzed genetic diversity within and genetic differentiation between all 32 remnant populations of the species in Swabia and Upper Bavaria using amplified fragment length polymorphisms. Our aim was to increase reintroduction success by providing data to avoid negative effects of inbreeding and outbreeding and to preserve the natural genetic pattern of the species. Genetic diversity within populations was low but similar to other rare and endemic species and varied strongly between populations but did not depend on population size. Our analysis revealed a strong geographic pattern of genetic variation. Genetic differentiation was strongest between Swabia and Upper Bavaria and at the population level, whereas differentiation between subpopulations was comparatively low. Isolation by distance and genetic differentiation was stronger among populations from Upper Bavaria than from Swabia. From the results of our study, we derived recommendations for a successful reintroduction of the species. We suggest using rather genetically variable than large populations as reintroduction sources. Moreover, the exchange of plant material between Swabia and Upper Bavaria should be completely avoided. Within these regions, plant material from genetically similar populations should preferably be used for reintroduction, whereas the exchange among subpopulations seems to be possible without a negative impact on genetic variation due to natural gene flow.

Species distribution modeling and molecular markers suggest longitudinal range shifts and cryptic northern refugia of the typical calcareous grassland species Hippocrepis comosa (horseshoe vetch)

Calcareous grasslands belong to the most diverse, endangered habitats in Europe, but there is still insufficient information about the origin of the plant species related to these grasslands. In order to illuminate this question, we chose for our study the representative grassland species Hippocrepis comosa (Horseshoe vetch). Based on species distribution modeling and molecular markers, we identified the glacial refugia and the postglacial migration routes of the species to Central Europe. We clearly demonstrate that H. comosa followed a latitudinal and due to its oceanity also a longitudinal gradient during the last glacial maximum (LGM), restricting the species to southern refugia situated on the Peninsulas of Iberia, the Balkans, and Italy during the last glaciation. However, we also found evidence for cryptic northern refugia in the UK, the Alps, and Central Germany. Both species distribution modeling and molecular markers underline that refugia of temperate, oceanic species such as H. comosa must not be exclusively located in southern but also in western of parts of Europe. The analysis showed a distinct separation of the southern refugia into a western cluster embracing Iberia and an eastern group including the Balkans and Italy, which determined the postglacial recolonization of Central Europe. At the end of the LGM, H. comosa seems to have expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, and Germany.

Unidirectional hybridization and reproductive barriers between two heterostylous primrose species in north-west Yunnan, China

BACKGROUND AND AIMS

Heteromorphy in flowers has a profound effect on breeding patterns within a species, but little is known about how it affects reproductive barriers between species. The heterostylous genus Primula is very diverse in the Himalaya region, but hybrids there have been little researched. This study examines in detail a natural hybrid zone between P. beesiana and P. bulleyana.

METHODS

Chloroplast sequencing, AFLP (amplified fragment length polymorphism) markers and morphological comparisons were employed to characterize putative hybrids in the field, using synthetic F1s from hand pollination as controls. Pollinator visits to parent species and hybrids were observed in the field. Hand pollinations were conducted to compare pollen tube growth, seed production and seed viability for crosses involving different morphs, species and directions of crossing.

KEY RESULTS

Molecular data revealed all hybrid derivatives examined to be backcrosses of first or later generations towards P. bulleyana: all had the chloroplast DNA (cpDNA) of this species. Some individuals had morphological traits suggesting they were hybrids, but they were genetically similar to P. bulleyana; they might have been advanced generation backcrosses. Viable F1s could not be produced with P. bulleyana pollen on P. beesiana females, irrespective of the flower morphs used. Within-morph crosses for each species had very low (<10 %) seed viability, whereas crosses between pin P. bulleyana (female) and pin P. beesiana had a higher seed viability of 30 %. Thus genetic incompatibility mechanisms back up mechanical barriers to within-morph crosses in each species, but are not the same between the two species. The two species share their main pollinators, and pollinators were observed to fly between P. bulleyana and hybrids, suggesting that pollinator behaviour may not be an important isolating factor.

CONCLUSIONS

Hybridization is strongly asymmetric, with P. bulleyana the only possible mother and all detected hybrids being backcrosses in this direction. Partial ecological isolation and inhibition of heterospecific pollen, and possibly complete barriers to F1 formation on P. beesiana, may be enough to make F1 formation very rare in these species. Therefore, with no F1 detected, this hybrid zone may have a finite life span as successive generations become more similar to P. bulleyana.

Phylogeographic structure of Terminalia franchetii (combretaceae) in southwest China and its implications for drainage geological history

Following the rapid uplift of the Qinghai-Tibetan Plateau, the reorganization of the major river drainages in southwest China was primarily caused by river capture events. However, the impact of these past changes in drainage patterns on the current distribution and genetic structure of the endemic flora of this region remains largely unknown. Here we report a survey of amplified fragment length polymorphism (AFLP) in Terminalia franchetii, an endemic shrub or small tree of the deep and dry-hot river valleys of this region. We surveyed AFLP variation within and among 21 populations (251 individuals) of T. franchetii, distributed disjunctively between northern and southern drainage systems. Using STRUCTURE, principal coordinates analysis, and genetic distance methods, we identified two main population genetic groups (I and II) and four subgroups within the species, as follows: (I) the Upper Jinshajiang Valley (subgroup I((north))) and the Honghe drainage area (subgroup I((south))); (II) the Middle and Lower Jinshajiang and Yalongjiang Valleys (subgroup II((north))) and the Nanpanjiang drainage area (subgroup II((south))). Genetic diversity was lower in group I than in group II. According to the genetic diversity and genetic structure results, we suggest that the modern disjunctive distribution and associated patterns of genetic structure of T. franchetii result from vicariance caused by several historical drainage capture events, involving the separation of the Upper Jinshajiang, Yalongjiang and Daduhe from the Honghe or Nanpanjiang in southwest China.

Unusual patterns of hybridization involving a narrow endemic Rhododendron species (Ericaceae) in Yunnan, China

PREMISE OF THE STUDY

One potential threat to rare species is genetic swamping caused by hybridization, but few studies have quantified this threat. Rhododendron cyanocarpum is a narrow endemic species that occurs sympatrically with potentially interfertile congeners throughout its range within Yunnan, China. We searched the entire distribution of R. cyanocarpum for hybrids and examined the patterns of hybridization to assess potential threat from hybridization. •

METHODS

In a comprehensive field survey, we detected only one instance of hybridization involving R. cyanocarpum, with R. delavayi, at Huadianba near Dali. Material of both species and putative hybrids was examined using morphology, chloroplast DNA, nuclear ribosomal DNA, and Bayesian analysis of AFLP profiles. •

KEY RESULTS

Of 10 putative hybrids, two were F(1)(')s and at least seven were F(2)(')s. Four backcrosses to R. delavayi were detected among material with R. delavayi-like morphology within the hybrid zone. Backcrosses to R. cyanocarpum were not detected. Therefore F(2)(')s outnumbered all other classes within the hybrid zone, a situation not previously confirmed for plants and extremely rare generally. Hybridization was asymmetrical, with R. delavayi as the maternal parent in all but one of the hybrids detected. •

CONCLUSIONS

Although natural hybridization is common in Rhododendron, it is rare in R. cyanocarpum and is apparently not accompanied by backcrossing toward R. cyanocarpum. Hence, there is no immediate risk of genetic swamping, unless habitat disturbance increases and changes the patterns of hybridization. Our study is the first to report a plant hybrid zone dominated by F(2) hybrids. This pattern might contribute to species barrier maintenance.

Genetic variation of Mimetes hirtus and Mimetes fimbriifolius (Proteaceae) - a comparative analysis of two closely related fynbos species

We investigated the influence of differing life history traits on the genetic structure of the related species Mimetes fimbriifolius and Mimetes hirtus (Proteaceae), which occur in the South African fynbos. Both species are bird-pollinated and ant-dispersed, but differ in rarity, longevity, ecological strategy and the fragmentation of their distribution area. We used AFLPs to study genetic variation within and between 21 populations of these two species across their distribution range. AFLP analysis revealed significantly higher genetic variation within populations of M. fimbriifolius than within M. hirtus. While M. fimbriifolius clearly lacked any significant genetic differentiation between populations, a distinct geographic pattern was observed for M. hirtus. Differentiation was, however, stronger at the regional (Phi(PT) = 0.57) than at the local scale (Phi(PT) = 0.08). Our results clearly indicate that even closely related species that share the same mode of pollination and seed dispersal can differ in their genetic structure, depending on the magnitude of fragmentation, longevity of individuals and ecological strategy.

A conceptual framework for the colonisation of urban areas: the blackbird Turdus merula as a case study

Despite increasing interest in urban ecology the factors limiting the colonisation of towns and cities by species from rural areas are poorly understood. This is largely due to the lack of a detailed conceptual framework for this urbanisation process, and of sufficient case studies. Here, we develop such a framework. This draws upon a wide range of ecological and evolutionary theory and the increasing number of studies of how the markedly divergent conditions in urban and rural areas influence the traits of urban populations and the structure of urban assemblages. We illustrate the importance of this framework by compiling a detailed case study of spatial and temporal variation in the urbanisation of the blackbird Turdus merula. Our framework identifies three separate stages in the urbanisation process: (i) arrival, (ii) adjustment, and (iii) spread. The rate of progress through each stage is influenced by environmental factors, especially human attitudes and socio-economic factors that determine the history of urban development and the quality of urban habitats, and by species' ecological and life-history traits. Some traits can positively influence progression through one stage, but delay progression through another. Rigorous assessment of the factors influencing urbanisation should thus ideally pay attention to the different stages. Urbanisation has some similarities to invasion of exotic species, but the two clearly differ. Invasion concerns geographic range expansion that is external to the species' original geographic range, whilst urbanisation typically relates to filling gaps within a species' original range. This process is exemplified by the blackbird which is now one of the commonest urban bird species throughout its Western Palearctic range. This is in stark contrast to the situation 150 years ago when the species was principally confined to forest. Blackbird urbanisation was first recorded in Germany in 1820, yet some European cities still lack urban blackbirds. This is especially so in the east, where urbanisation has spread more slowly than in the west. The timing of blackbird urbanisation exhibits a marked spatial pattern, with latitude and longitude explaining 76% of the variation. This strong spatial pattern contrasts with the weaker spatial pattern in timing of urbanisation exhibited by the woodpigeon Columba palumbus (with location explaining 39% of the variation), and with the very weak spatial pattern in timing of black-billed magpie Pica pica urbanisation (in which location explains 12% of the variation). Strong spatial patterns in timing of urbanisation are more compatible with the leap-frog urbanisation model, in which urban adapted or imprinted birds colonise other towns and cities, than with the independent urbanisation model, in which urban colonisation events occur independently of each other. Spatial patterns in isolation do not, however, confirm one particular model. Factors relating to the arrival and adjustment stages appear particularly likely to have influenced the timing of blackbird urbanisation. Spatial variation in the occurrence of urban populations and the timing of their establishment creates opportunities to assess the factors regulating urbanisation rates, and how the composition of urban assemblages develops as a result. These are major issues for urban ecology.