Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis.

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159-160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

Is Betula carpatica genetically distinctive? A morphometric, cytometric and molecular study of birches in the Bohemian Massif with a focus on Carpathian birch.

Until recently, Czech taxonomists often treated Betula carpatica as a distinct species. Several morphological traits for distinguishing B. carpatica from B. pubescens or other birches are described in literature; however, it has been proven impossible to reliably identify B. carpatica in the field. With the use of morphological and molecular approaches, we intended to assess the position of B. carpatica in the context of other birch taxa reported from the Bohemian Massif and to find more reliable morphological traits for their identification. In our dataset, we distinguished the following birch taxa referred to in the recent Czech literature: B. pendula, B. pubescens, B. carpatica, B. oycoviensis, B. nana, B. petraea and B. ×seideliana. We complemented them with triploids and several diploid and tetraploid "working units" into which we included intermediate individuals that in terms of morphology did not unambiguously match any of the abovementioned birch taxa. Holoploid genome size was measured to determine the ploidy level. To identify genetic relationships between selected taxa and "working units", microsatellite analyses were performed. Model-based STRUCTURE analysis together with principal coordinates analysis (PCoA) based on genetic distances was performed to identify the similarities in multilocus genotype data between groups distinguished in the dataset. The applied analyses were not able clearly to distinguish any group among tetraploid individuals. In this light, it was of no use to search for any more reliable morphological traits of B. carpatica and also B. petraea. Among diploids, B. nana was always distinguished, in contrast to B. oycoviensis, which was not genetically recognized despite being usually morphologically distinct. Based on our results and a literature review, we suggest that B. carpatica and also the closely similar B. petraea should not be considered separate species. A similar conclusion seems relevant also for B. oycoviensis; however, further verification is desirable in this case.

Host plant phylogeny and geographic distance strongly structure Betulaceae-associated ectomycorrhizal fungal communities in Chinese secondary forest ecosystems.

Environmental filtering and dispersal limitation are two of the primary drivers of community assembly in ecosystems, but their effects on ectomycorrhizal (EM) fungal communities associated with wide ranges of Betulaceae taxa at a large scale are poorly documented. In this study, we examined EM fungal communities associated with 23 species from four genera (Alnus, Betula, Carpinus and Corylus) of Betulaceae in Chinese secondary forest ecosystems, using Illumina MiSeq sequencing of the ITS2 region. Effects of host plant phylogeny, soil, climate and geographic distance on EM fungal community were explored. In total, we distinguished 1738 EM fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. The EM fungal communities of Alnus had significantly lower OTU richness than those associated with the other three plant genera. The EM fungal OTU richness was significantly affected by geographic distance, host plant phylogeny, soil and climate. The EM fungal community composition was significantly influenced by host plant phylogeny (12.1% of variation explained in EM fungal community), geographic distance (7.7%), soil (4.6%) and climate (1.1%). This finding highlights that environmental filtering linked to host plant phylogeny and dispersal limitation strongly influence EM fungal communities associated with Betulaceae plants in Chinese secondary forest ecosystems.

The complete chloroplast genome of Ostrya rehderiana.

The complete chloroplast sequence of Ostrya rehderiana is 159 347 bp in length, containing 85 protein-coding genes, 8 ribosomal RNA genes, and 31 transfer RNA genes. The circular genome exhibits a typical chloroplast genome structure comprising a large single copy region of 88 552 bp, a small single copy region of 18 941 bp and a pair of inverted repeats of 25 927 bp. The overall GC content of the chloroplast genome is 36.5%. Phylogenetic analysis of O. rehderiana sequence together with 12 complete chloroplast genomes revealed a basal placement of O. rehderiana within the Fagales species.

Diploid hybrid origin of Ostryopsis intermedia (Betulaceae) in the Qinghai-Tibet Plateau triggered by Quaternary climate change.

Despite the well-known effects that Quaternary climate oscillations had on shaping intraspecific diversity, their role in driving homoploid hybrid speciation is less clear. Here, we examine their importance in the putative homoploid hybrid origin and evolution of Ostryopsis intermedia, a diploid species occurring in the Qinghai-Tibet Plateau (QTP), a biodiversity hotspot. We investigated interspecific relationships between this species and its only other congeners, O. davidiana and O. nobilis, based on four sets of nuclear and chloroplast population genetic data and tested alternative speciation hypotheses. All nuclear data distinguished the three species clearly and supported a close relationship between O. intermedia and the disjunctly distributed O. davidiana. Chloroplast DNA sequence variation identified two tentative lineages, which distinguished O. intermedia from O. davidiana; however, both were present in O. nobilis. Admixture analyses of genetic polymorphisms at 20 SSR loci and sequence variation at 11 nuclear loci and approximate Bayesian computation (ABC) tests supported the hypothesis that O. intermedia originated by homoploid hybrid speciation from O. davidiana and O. nobilis. We further estimated that O. davidiana and O. nobilis diverged 6-11 Ma, while O. intermedia originated 0.5-1.2 Ma when O. davidiana is believed to have migrated southward, contacted and hybridized with O. nobilis possibly during the largest Quaternary glaciation that occurred in this region. Our findings highlight the importance of Quaternary climate change in the QTP in causing hybrid speciation in this important biodiversity hotspot.

Ecological and genetic effects of cutting in an Alnus trabeculosa Hand.-Mazz. (Betulaceae) population.

In order to assess the ecological and genetic effects of cutting, we compared two portions of Alnus trabeculosa population at Yuda (Iwate Prefecture, Japan): one that has been cut about 30 years ago and one that has remained uncut. These portions were compared in terms of the degree of sprouting, genetic variation and gene distribution using isozyme markers. First, we determined the multilocus genotype (MLG) of all ramets, then sorted them into individuals according to the distribution of the MLGs. The average (+/- SE) of largest distance between ramets in one individual was 2.1 (+/- 0.18) m, which is consistent with the distance (2.0 (+/- 0.20) m) obtained by tracing physical connections between ramets. We found no significant differences in genetic variation between the two portions, but there were significant differences in their degree of sprouting. Furthermore, there were striking differences in gene distribution: the cut portion showed greater clustering of individuals with identical genetic components, which may be due to regeneration in the gaps made by cutting, reflecting the location of the mother trees, and seed and pollen dispersal from them.

Isozyme polymorphisms provide evidence of clinal variation with elevation in Nothofagus pumilio.

Variable physical conditions along elevational gradients strongly influence patterns of genetic differentiation in tree species. Here, the hypothesis is tested that different growth forms of Nothofagus pumilio, which characterizes the subalpine forests in the southern Andes, will display continuous genetic variation with elevation. At each of four elevational strips in three different mountain ranges, fresh leaf tissue was sampled from 30 randomly selected individuals to be analyzed by protein electrophoresis. Allelic frequencies were used to test for heterogeneity across populations and to classify populations into different elevational strips by discriminant analysis. The degree of population divergence was estimated by F(ST). Clinical variation on within-population genetic characteristics was analyzed by linear regressions against elevation. Seven enzyme systems coded for 14 putative isozyme loci, 57% of which were polymorphic in at least one population. Allele frequencies significantly varied with elevation and discriminant analysis separated populations at different elevational strips. Among-population divergence within any mountain range was small, but greater than among different mountain ranges. Overall, low-elevation populations were more variable than high-elevation populations, and regression analyses suggested continuous variation in populations of N. pumilio 100 m apart. Marked stepwise phenological differences on mountain slopes are most probably responsible for the isolation of nearby populations.

Differences in spatial autocorrelation between four sub-populations of Alnus trabeculosa Hand.-Mazz. (Betulaceae).

To investigate the spatial structure of Alnus trabeculosa Hand.-Mazz, we compared three sub-populations at Imaichi in Tochigi Prefecture and one sub-population at Juo in Ibaraki Prefecture, Japan. A total of 269 trees, covering 0.71 ha in total, were mapped and genetically analyzed using nine enzyme systems encoding 13 isozyme loci. There were no significant differences between the four sub-populations in terms of Na,Ne, H(o), H(e )and F(IS). However, according to spatial autocorrelation analysis, the Juo sub-population, which is younger than the others, showed an aggregation of multilocus genotypes, especially within 25 m radii. In contrast with the Juo sub-population, those in Imaichi showed no clear spatial structuring. In the three Imaichi sub-populations, gametic phase disequilibrium is attributable to heterogeneity of genotype frequencies, but in the Juo sub-population it seems to be due to other factors, connected with the composition of the trees in the sub-population and/or its founder population, gene flow and asexual propagation. To conserve as much as possible of the genes or genotypes in restricted areas, conservation of populations that do not show clear family structures, such as those in Imaichi, would be most effective.