Ancient split of major genetic lineages of European Black Pine: evidence from chloroplast <Emphasis>DNA</Emphasis>

The European Black Pine (Pinus nigra Arn.) has a long and complex history. Genetic distance and frequency analyses identified three differentiated genetic groups, which corresponded to three wide geographical areas: Westerns Mediterranean, Balkan Peninsula and Asia Minor. These groups shared common ancestors (14.75 and 10.72 Ma). The most recent splits occurred after the Messinian Salinity Crisis (4.37 Ma) and the Early–Middle Pleistocene Transitions (0.93 Ma). The posterior ancestral population size (Na) is 260,000–265,000 individuals. Each pool is further fragmented, with evidence of a phylogeographic structure (N _st  > G _st ) typically observed in some natural populations from the Western Mediterranean region and the Balkan Peninsula. The laboratory analysis was performed by fragment analysis—i.e. electrophoretic sizing of polymerase chain reaction fragments, combined with the sequencing analysis of 33 % of all individuals as a control. Intense sampling of chloroplast DNA polymorphisms (3154 individuals and 13 markers: SNPs and SSRs) over the full area of the species’ natural distribution indicated moderate among-population variability (G _st(nc) ≤ 0.177) in various parts of its range. These results indicate that the natural populations have long migration histories that differ from one another and that they have been strongly phylogeographically affected by complex patterns of isolation, speciation and fragmentation. Long and varying climatic fluctuations in the region of the principal genetic group have been the probable cause of different forest community associations with different successional patterns resulting in interglacial refugia vs. macro long-term refugia.     

Relationship between density and ultrasonic velocity in Brazilian tropical woods

In this study, the effect of density on the velocity of an ultrasonic wave in wood is investigated. The aim of the present study was to analyze the influence of density on the longitudinal velocity of an ultrasonic wave, propagated in the longitudinal direction. Experiments were conducted on 5cm x 5cm x 5cm wood specimens selected from the following species: pinus caribea (Pinus caribea var. caribea), eucalyptus citriodora (Eucalyptus citriodora), eucalyptus grandis (Eucalyptus grandis), cupiúba (Goupia glabra) and jatobá (Hymenaea sp.). The relationship between density and velocity was analyzed in two different manners: between and within species. The results obtained between species indicated that ultrasonic velocity tends to increase with increasing density. The results obtained within species also showed an increasing trend in ultrasonic velocity as density increased, but the relationship was not as significant as it was for between species.     

Beech versus spruce deadwood as forest microhabitat: does it make any difference to bryophytes?

The presence data of 153 bryophyte species, recorded on beech (BDW) and spruce (SDW) deadwood in the managed forests within a montane watershed, were analysed by controlling for different plot size, substrate pH and elevation. Only three pleurocarpous species, which were probably remnant epiphytes from live wood, showed relative specificity for BDW, but none to SDW. The few species displaying preference for BDW or SDW were generally true epixylic, mosses and hepatics, respectively. The chances of occurrence of epiphytic (early successional) and epixylic (mid-late successional) taxa on either deadwood species increased and respectively, decreased with the substrate pH. There was no consistent relationship between bryophyte preference to BDW/SDW and elevation. Neither total nor threatened species richness was related to deadwood species identity. However, at 100 cm² resolution and within certain extension range, the cumulative number of bryophyte species was significantly higher on BDW than on SDW, despite no significant difference in species pool size. Threatened species richness increased monotonically towards lower elevations, suggesting that valley bottoms might act as refugia with high air humidity. The number of threatened species and in particular, the presence of Lophozia ascendens, were good predictors of total bryophyte richness regardless of deadwood species identity.     

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well‐supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.     

Species‐delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis,including a new species from Brazil

Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI‐5P and rbcL) and performed several DNA‐based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods.     

Species trait syndrome drives the leaves’ functional variations of dominant grasses to modifications in summer water supply

Climate change models predict a strong reduction of average precipitation, especially of the summer rainfall, and an increase in intensity and frequency of drought events in the Mediterranean region. The research aim was to understand how four dominant grass species (Arrhenatherum elatius, Cynosurus cristatus, Elymus repens, and Lolium perenne) in sub-Mediterranean meadows (central Apennines, Italy) modulate their resource acquisition and conservation strategies to short-term variation of the pattern of summer water supply. During summer 2016, using a randomized block design, we tested the effect of three patterns of summer water supply, differing in water amount and watering frequency, on leaf area, leaf dry mass, specific leaf area (SLA), leaf senescence, and plant height. Our results showed that dominant grass species can modulate their strategies to variation of the pattern of summer water supply, but the response of leaf traits and plant height is mediated by the set of functional characteristics of the species. E. repens and A. elatius, with summer green leaves, lower SLA, later flowering period, and deeper roots, were less influenced by changes in water amount. C. cristatus and L. perenne, which display acquisitive strategies (persistent leaves, higher SLA values), earlier flowering, and shallower roots were more influenced by changes in the pattern of summer water supply. Our results suggest that a short-term decrease in water availability might affect primarily species with trait syndromes less adapted to face summer drought.

     

Enzymatic properties of 8-bromoadenine nucleotides.

8-Bromoadenine nucleotides were tested as potential substrates and/or inhibitors of mitochondrial processes in intact or disrupted organelles, as substrates of various phosphotransferases, and as allosteric effectors in the reactions catalyzed by phosphofructokinase, isocitrate dehydrogenase, glutamate dehydrogenase, and fructose-1,6-bisphosphatase. 8-BrATP and 8-BrADP are not recognized by the translocase system located in the inner mitochondrial membrane and cannot be used as usbstrates in oxidative phosphorylation and related reactions catalyzed be beef heart submitochondrial membranes. This confirms the high specificity for adenine nucleotides of the mammalian systems involved in energy-yielding and energy-requiring reactions. However, 8-BrATP and 8-BrADP are able to substitute for the natural adenine nucleotides in reactions catalyzed by many phosphotransferases, although their capacity as phosphate donors and acceptors is generally much reduced. On the other hand, in almost all investigated cases, the 8-bromoadenine nucleotides have lost the capability of the natural adenine nucleotides to act as allosteric effectors, indicating that the structural requirements for allosteric activity are more stringent than those for catalytic activity.     

Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae,Rhodophyta) using molecular and morphological data

Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single‐marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae.     

Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists

Recent studies show that soil eukaryotic diversity is immense and dominated by micro‐organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro‐organisms. Major diversification events in multicellular organisms have often been attributed to long‐term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum‐dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro‐organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.