Contrasting ectomycorrhizal fungal communities on the roots of co-occurring oaks (Quercus spp.) in a California woodland

Plant host species is considered an important factor influencing ectomycorrhizal (EM) communities. To gain insights into the role of host species in structuring EM communities, EM communities on sympatric oak (Quercus) species were compared in the Sierra Nevada foothills of California. Using molecular methods (polymerase chain reaction, cloning, restriction fragment length polymorphism and DNA sequencing), EM fungi on roots of deciduous Quercus douglasii and evergreen Quercus wislizeni trees were identified from 64 soil cores. The total EM species richness was 140, of which 40 taxa were detected on both oak hosts. Greater diversity and frequency of EM fungi with epigeous fruiting habit were found on Q. wislizeni, while taxa in the Ascomycota were more frequent and diverse on Q. douglasii. Using ordination, it was determined that both soil extractable phosphorus and oak host species explained a significant proportion of the variation in EM species distribution. These results indicate that plant host species can be an important factor influencing EM fungal community composition, even within congeneric trees.     

Contrasting phylogeographic patterns in Sphagnum fimbriatum and Sphagnum squarrosum (Bryophyta, Sphagnopsida) in Europe

The chloroplast phylogeography of two peat mosses (Sphagnum fimbriatum and Sphagnum squarrosum) with similar distributions but different life history characteristics was investigated in Europe. Our main aim was to test whether similar distributions reflect similar phylogeographic and phylodemographic processes. Accessions covering the European distributions of the species were collected and approx. 2000 bp of the chloroplast genome of each species was sequenced. Maximum parsimony, statistical parsimony and phylodemographic analyses were used to address the question of whether these species with similar distributions show evidence of similar phylogeographic and phylodemographic processes. The chloroplast haplotypes of the currently spreading species S. fimbriatum showed strong geographic structure, whereas those of S. squarrosum, which has stable historical population sizes, showed only very weak geographic affinity and were widely distributed. We hypothesize that S. fimbriatum survived the last glaciations along the Atlantic coast of Europe, whereas S. squarrosum had numerous, scattered refugia in Europe. The dominance of one haplotype of S. fimbriatum across almost all of Europe suggests rapid colonization after the last glacial maximum. We hypothesize that high colonizing ability is an inherent characteristic of the species and its recent expansion in Europe is a response to climate change.     

Comparative phylogeography and postglacial colonization routes in Europe

The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals ( Ursus arctos , Sorex spp., Crocidura suaveolens , Arvicola spp.), amphibians ( Triturus spp.), arthropods ( Chorthippus parallelus ), and plants ( Abies alba , Picea abies , Fagus sylvatica , Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.     

Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe

We used chloroplast polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad-leaved wind-pollinated and wind-dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR-RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (GST= 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south-eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.     

Evolutionary ecology of mast-seeding in temperate and tropical oaks (Quercus spp.)

Mast-seeding is the synchronous production of large seed crops within a population or community of species every two or more years. This paper addresses three non-mutually exclusive hypotheses explaining the evolution of mast-seeding in temperate tree species, especially the genus Quercus: (1) mast-seeding is a consequence of mast-flowering which evolves to increased pollination efficiency in mast-flowering years; (2) mast-seeding has evolved as an anti-predator adaptation by which large seed crops during mast years satiate the seed predators and allow survival of some of the seeds; (3) selection on seed size by habitat can indirectly affect the evolution of masting if trees with large seeds require more time to accumulate reserves to mature those seeds. I find support for the pollination hypothesis in several wind-pollinated temperate tree species but not oaks. However, oaks show evidence favoring the predation and seed size hypotheses. I then develop a model to illustrate the relationships among the three hypotheses in their effects on the evolution of masting. Finally, using data from herbaria and Floras, the influence of selection via flowering, fruiting, and seed size in the evolution of masting in tropical oaks is discussed. I conclude that the need for a supra-annual cue to synchronize flowering and fruiting as well as the larger seed size found in many tropical oak species should contribute to the evolution of masting to a greater extent than seen among temperate oaks.     

Contrasting seasonal patterns of fine root production for blue oaks (Quercus douglasii) and annual grasses in California oak woodland

In a blue oak woodland in NE California, we used root ingrowth cores to study seasonal patterns of fine root (< 2 mm diameter) production (FRP) for annual grasses and blue oaks (Quercus douglasiiHook and Arn.). At each of three sites (River, Upland and Hilltop) there were three studies: a short-term seasonal study, a long-term cumulative study and a core nutrient enrichment study. In the short-term study, ingrowth cores were installed and harvested in 3-month intervals. Grass and oak FRP dominated in different seasons. Grass FRP was greater in fall (Oct–Dec, 26.0 g m^–2 month^–1(gmm)) and winter (Jan–Mar, 18.1 gmm), lower in spring (Apr–Jun, 2.9 gmm) and negligible in summer (July–Sep). In contrast, oak FRP was greater in spring (6.1 gmm) with lower, but significant summer growth (2.9 gmm). Grass FRP declined steadily with soil depth (0–40 cm) in all seasons. Oak FRP changed little with soil depth, except in the summer, when production was greatest at lower soil depths. In the long-term study, ingrowth cores were installed and harvested after 3, 6, 9 and 12 months. Oak annual FRP was greater in the long-term study than in the short-term study at the River and Upland sites. Thus production in the short-term study may be an underestimate, due to disturbance effects. Nutrient enrichment of cores with N-P-K increased grass FRP, but surprisingly, decreased oak FRP, suggesting that annual grasses may have competitive advantages in nutrient enriched soil.     

Genetic variation and differentiation within a natural community of five oak species (Quercus spp.)

Chloroplast DNA and two categories of nuclear markers - isozymes and microsatellites - were used to examine a very rich natural community of oaks (Quercus spp.) situated in west-central Romania. The community consists of five oak species: Q. robur, Q. petraea, Q. pubescens, and Q. frainetto - that are closely related -, and Q. cerris. A total of five chloroplast haplotypes was identified. Q. cerris was fixed for a single haplotype. The other four species shared the two most common haplotypes. One haplotype was confined to Q. robur and a very rare one was restricted to Q. petraea. Both types of nuclear markers revealed a larger genetic variation for Q. pubescens and Q. petraea than for Q. frainetto and Q. robur, although the differences between species are in most cases not significant. At the nuclear level, Q. cerris could be clearly separated from the other four oak species confirming the taxonomic classification. Regardless of the estimate used, the levels of polymorphism revealed by microsatellites were much higher than those based on isozymes. For the four closely related species the overall genetic differentiation was significant at both categories of nuclear markers. Several loci, such as Acp-C for isozymes, and ssrQpZAG36 and ssrQrZAG96 for microsatellites were very useful to discriminate among species. However, the level of differentiation varied markedly between pairs of species. The genetic affinities among the species may reflect different phylogenetic distances and/or different rates of recurrent gene flow at this site.     

Chloroplast DNA polymorphisms provide evidence for postglacial re-colonisation of oaks (Quercus spp.) across the Swiss Alps

The spatial pattern of chloroplast DNA (cpDNA) variation in Quercus robur, Quercus petraea and Quercus pubescens was studied in 1036 trees from 181 locations throughout the Swiss Alps and adjacent regions in order to gain a deeper insight into the postglacial history of these species. A total of ten different cpDNA types (haplotypes) were identified, six of which are described for the first time. The genetic variation was mainly found between collection sites (G _ST =0.881). Spatial autocorrelation indicated that the two dominant haplotypes had a structured, non-random distribution. The spatial pattern of these two haplotypes, which are associated with different ice-age refugia, reveals: (1) that oaks did not immigrate into regions of the Swiss Alps together, rather they immigrated separately in space and/or time, and (2) that the spatial mixing of haplotypes as a consequence of seed dispersal was low. Furthermore, the geographic distribution of the haplotypes suggests that the Alps only partially blocked the re-colonisation of oaks: Quercus species, which originated after range expansion from a refugium in Italy, have most likely crossed the Swiss Alps. Previously proposed postglacial migration pathways are reviewed and possible re-colonisation routes are discussed. Received: 1 March 2000 / Accepted: 14 April 2000     

How did an annual plant react to Pleistocene glaciations? Postglacial history of Rhinanthus angustifolius in Europe

The impact of climate fluctuations during the Pleistocene on the geographic structure of genetic variation in plant populations is well documented, but there is a lack of studies of annual species at the European scale. The present study aimed to infer the history of the widespread European annual Rhinanthus angustifolius C. C. Gmelin (Orobanchaceae). We explored variation in chloroplast DNA (cpDNA) sequences and amplified fragment length polymorphism (AFLP) in twenty-nine populations covering the entire distribution area of the species. Five AFLP groups were identified, suggesting at least two glacial refugial areas: one area in southwestern Europe and one large eastern area in the Balkan/Caucasus. Recolonization of previously glaciated areas mainly took place from the east of Europe. Despite the difference in life-history traits, the patterns found for the annual R. angustifolius show similarities with those of perennial species in terms of genetic diversity and geographic organization of genetic variation. Although organelle markers have typically been preferred in phylogeographic studies, the cpDNA variation in R. angustifolius did not show any clear geographic structure. The absence of geographic structure in the cpDNA variation may reflect persistence of ancestral polymorphisms or hybridization and introgression with closely-related species.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 1–13.     

Glacial-induced altitudinal migrations in Armeria (Plumbaginaceae) inferred from patterns of chloroplast DNA haplotype sharing

In contrast to northern European areas where large-scale migrations occurred to recolonize territories after glacial periods, species in southern regions survived and diverged without large geographical displacements. As a result of the importance of orography in much of the southern areas, such displacements must have involved populations ascending or descending mountains. The present study provides support for glacial-induced altitudinal migrations from chloroplast phylogeographic patterns in Armeria (Plumbaginaceae) in southeast Spain. One hundred and five sequences of the trnL-F spacer were obtained from seven species. Fifteen different haplotypes were recognized, their genealogy was inferred, and associations with geography were explored using nested clade analysis. Seven instances were detected in which the same haplotype is shared by two or three species within a particular massif. In all the cases, at least one of the species involved displayed different haplotypes in other areas; in most, the haplotype shared is predominant either in one of the species involved or in the massif. These patterns of haplotype sharing strongly suggest horizontal transfer between species. In one of the massifs (Sierra Nevada) the three species involved in haplotype sharing (A. splendens, A. filicaulis ssp. nevadensis, A. villosa ssp. bernisii) occur at markedly different altitudinal belts. It is argued that altitudinal migrations within the contraction-expansion model provide the best explanation for the current pattern, and that at least in one case it resulted in the formation of a new hybrid taxon, A. filicaulis ssp. nevadensis.     

Glacial history of high alpine Ranunculus glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context

There is considerable controversy concerning the fate of Alpine plants during Pleistocene glaciations. While some studies have found evidence for nunatak survival, others have explained the present genetic patterns by survival only in peripheral refugia. We investigated 75 populations of high alpine Ranunculus glacialis from its entire Alpine distribution. Phylogeographical analyses of AFLP data revealed four groups of populations. Two of them, located in the western Alps, were genetically isolated from each other and from the eastern groups, whereas the two eastern Alpine groups were genetically more similar to each other. This suggests longer isolation and/or lower levels of gene flow in the two western groups. As all groups are close to, or overlap with, presumed glacial refugia, invoking glacial survival on nunataks is unnecessary to explain the present genetic pattern. Similar to the phylogeographical patterns of R. glacialis , the previously investigated alpine Phyteuma globulariifolium and Androsace alpina , which are also confined to siliceous bedrock, showed strong geographical affinities to peripheral refugial areas and there were large-scale congruencies in the location of these refugia for all three species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 183–195.     

Multiple introgression events and range shifts in Schizocodon (Diapensiaceae) during the Pleistocene

Range shifts during the Pleistocene shaped the unique phylogeographical structures of numerous species. Accompanying species migration, sister taxa may have experienced multiple introgression events. Here, we report the signature of introgression events in multiple areas in Schizocodon, herbs endemic to Japan, using amplified fragment length polymorphism (AFLP) fingerprinting and plastid DNA haplotyping in 48 populations. Although the present distributions of S. soldanelloides and S. ilicifolius are mainly allopatric, the species share plastid DNA haplotypes in each region (north‐eastern, north‐central, south‐central and south‐western Japan); in contrast, the specific groups were highly supported by AFLP analyses. These results support the occurrence of multiple introgression events in Schizocodon. Notably, the disjunct plastid haplotypes found only in S. ilicifolius var. intercedens suggest complete plastid DNA replacement at local areas from S. soldanelloides into S. ilicifolius var. ilicifolius. Furthermore, we found that S. soldanelloides experienced range contraction and expansion during glacial and interglacial cycles based on mismatch distribution analysis and ecological niche modelling. Based on several pieces of evidence, our study supports the idea that historical range shifts associated with Pleistocene climatic oscillations favoured multiple and regional introgression events in Schizocodon. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 46–63.     

Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions

Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested whether >3500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate and soil characteristics. In the analysis including all species, the most frequently associated environmental factors were those best describing the habitats of the species. In the species‐specific analyses, the most important environmental factors and associated SNPs greatly differed among species. However, we identified one SNP and seven genes that were associated with the same environmental factor across all species. We finally used regressions of allele frequencies of the most strongly associated SNPs along environmental gradients to predict the risk of nonadaptedness (RONA), which represents the average change in allele frequency at climate‐associated loci theoretically required to match future climatic conditions. RONA is considerable for some populations and species (up to 48% in single populations) and strongly differs among species. Given the long generation time of oaks, some of the required allele frequency changes might not be realistic to achieve based on standing genetic variation. Hence, future adaptedness requires gene flow or planting of individuals carrying beneficial alleles from habitats currently matching future climatic conditions.     

Xylophagous entomofauna in branches of oaks (Quercus spp.) and its significance for oak health in the Karst region of Slovenia

Samples of dying branches from 121 trees of Quercus pubescens, Q. cerris, and Q. petraea were taken from 102 sites in Seslerio autumnalis-Quercetum petraeae and Ostryo-Quercetum pubescentis forests. After nine months’ rearing in eclectors, branches were cut to 20-cm sections, and signs of infestation as well as larvae and adult insects were noted. We analysed 395 sections of branches from Q. pubescens, 125 sections from Q. cerris, and 85 sections from Q. petraea. We found 44 adult insects: 45% were from the Cerambycidae family (Callimus angulatus ssp. angulatus, Poecilium alni, and Exocentrus adspersus), 18% were from the Scolytinae subfamily (Scolytus intricatus, Xyleborus dispar), 4% from the Buprestidae family (Coraebus florentinus), 4.5% from the Cleridae family (Tilloidea unifasciata), and 28.5% from other families. In addition, 145 larvae were found: 50% from the Cerambycidae family, 39% from the Buprestidae family, 4% from the Scolytinae subfamily, and 7% from other families. Significant difference in the abundance of adult insects and larvae with regard to the diameter of branch sections and the host species were found. 78% of dying branches showed signs of infestation. Species of the Buprestidae, Scolytinae, and Cerambycidae represent important factors in the decline in oak vitality in the lower Karst region of Slovenia.     

Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.     

Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.)

Multiplex PCR is a fast and cost‐effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q. robur, a 12‐plex of EST‐SSRs (eSSRs) and an 8‐plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.     

Influence of host species on ectomycorrhizal communities associated with two co-occurring oaks (Quercus spp.) in a tropical cloud forest

Interactions between host tree species and ectomycorrhizal fungi are important in structuring ectomycorrhizal communities, but there are only a few studies on host influence of congeneric trees. We investigated ectomycorrhizal community assemblages on roots of deciduous Quercus crassifolia and evergreen Quercus laurina in a tropical montane cloud forest, one of the most endangered tropical forest ecosystems. Ectomycorrhizal fungi were identified by sequencing internal transcribed spacer and partial 28S rRNA gene. We sampled 80 soil cores and documented high ectomycorrhizal diversity with a total of 154 taxa. Canonical correspondence analysis indicated that oak host was significant in explaining some of the variation in ectomycorrhizal communities, despite the fact that the two Quercus species belong to the same red oak lineage (section Lobatae ). A Tuber species, found in 23% of the soil cores, was the most frequent taxon. Similar to oak-dominated ectomycorrhizal communities in temperate forests, Thelephoraceae, Russulaceae and Sebacinales were diverse and dominant.