Functional and phylogenetic diversity determine woody productivity in a temperate forest

Understanding the relationships between biodiversity and ecosystem productivity has become a central issue in ecology and conservation biology studies, particularly when these relationships are connected with global climate change and species extinction. However, which facets of biodiversity (i.e. taxonomic, functional, and phylogenetic diversity) account most for variations in productivity are still not understood very well. This is especially true with regard to temperate forest ecosystems. In this study, we used a dataset from a stem‐mapped permanent forest plot in northeastern China exploring the relationships between biodiversity and productivity at different spatial scales (20 × 20 m; 40 × 40 m; and 60 × 60 m). The influence of specific environmental conditions (topographic conditions) and stand maturity (expressed by initial stand volume and biomass) were taken into account using the multivariate approach known as structural equation models. The variable “Biodiversity” includes taxonomic (Shannon), functional (FDis), and phylogenetic diversity (PD). Biodiversity–productivity relationships varied with the spatial scales. At the scale of 20 × 20 m, PD and FDis significantly affected forest biomass productivity, while Shannon had only indirect effects. At the 40 × 40 m and 60 × 60 m scales, biodiversity and productivity were weakly correlated. The initial stand volume and biomass were the most important drivers of forest productivity. The local environmental conditions significantly influenced the stand volume, biomass, biodiversity, and productivity. The results highlight the scale dependency of the relationships between forest biodiversity and productivity. The positive role of biodiversity in facilitating forest productivity was confirmed at the smaller scales. Our findings emphasize the fundamental role of environmental conditions in determining forest ecosystem performances. The results of this study provide a better understanding of the underlying ecological processes that influence specific forest biodiversity and productivity relationships.     

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.     

Northward shift in faunal diversity is a general pattern of evolution of the phanerozoic marine biota

The analysis of two global databases on spatio-temporal distribution of fossil marine animal genera (Sepkoski's compendium and The Paleobiology Database) has revealed the presence of the latitudinal diversity gradient (LDG) in the marine realm throughout the Phanerozoic. Within each time interval, LDG is characterized by two parameters: the latitudinal position of peak diversity and the steepness of monotonous decline of diversity with increasing distance from the zone of the highest diversity. During the Phanerozoic, peak diversity has drifted gradually from the tropics and subtropics of the Southern hemisphere into northern midlatitudes. The shift in peak diversity is not likely to be an artifact of incompleteness of the fossil record or uneven sampling of different regions. The shift proceeded in a stepwise manner, with periods of relatively fast changes separated by longer periods of little or no change. The latitudinal shift in peak diversity was probably due to a combination of several causes: tectonic (northward shift in the latitudinal distribution of continental shelf area), climatic (as demonstrated by the fact that peak diversity tended to occur near equator during the cold epochs and in midlatitudes during the warm epochs), and historical ("evolutionary inertia" of local faunas).     

Osteohistological analyses reveal diverse strategies of theropod dinosaur body-size evolution

The independent evolution of gigantism among dinosaurs has been a topic of long-standing interest, but it remains unclear if gigantic theropods, the largest bipeds in the fossil record, all achieved massive sizes in the same manner, or through different strategies. We perform multi-element histological analyses on a phylogenetically broad dataset sampled from eight theropod families, with a focus on gigantic tyrannosaurids and carcharodontosaurids, to reconstruct the growth strategies of these lineages and test if particular bones consistently preserve the most complete growth record. We find that in skeletally mature gigantic theropods, weight-bearing bones consistently preserve extensive growth records, whereas non-weight-bearing bones are remodelled and less useful for growth reconstruction, contrary to the pattern observed in smaller theropods and some other dinosaur clades. We find a heterochronic pattern of growth fitting an acceleration model in tyrannosaurids, with allosauroid carcharodontosaurids better fitting a model of hypermorphosis. These divergent growth patterns appear phylogenetically constrained, representing extreme versions of the growth patterns present in smaller coelurosaurs and allosauroids, respectively. This provides the first evidence of a lack of strong mechanistic or physiological constraints on size evolution in the largest bipeds in the fossil record and evidence of one of the longest-living individual dinosaurs ever documented.     

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity

Analogous to observations in RNA viruses such as human immunodeficiency virus, genetic variation associated with intrahost dengue virus (DENV) populations has been postulated to influence viral fitness and disease pathogenesis. Previous attempts to investigate intrahost genetic variation in DENV characterized only a few viral genes or a limited number of full-length genomes. We developed a whole-genome amplification approach coupled with deep sequencing to capture intrahost diversity across the entire coding region of DENV-2. Using this approach, we sequenced DENV-2 genomes from the serum of 22 Nicaraguan individuals with secondary DENV infection and captured ～75% of the DENV genome in each sample (range, 40 to 98%). We identified and quantified variants using a highly sensitive and specific method and determined that the extent of diversity was considerably lower than previous estimates. Significant differences in intrahost diversity were detected between genes and also between antigenically distinct domains of the Envelope gene. Interestingly, a strong association was discerned between the extent of intrahost diversity in a few genes and viral clade identity. Additionally, the abundance of viral variants within a host, as well as the impact of viral mutations on amino acid encoding and predicted protein function, determined whether intrahost variants were observed at the interhost level in circulating Nicaraguan DENV-2 populations, strongly suggestive of purifying selection across transmission events. Our data illustrate the value of high-coverage genome-wide analysis of intrahost diversity for high-resolution mapping of the relationship between intrahost diversity and clinical, epidemiological, and virological parameters of viral infection.     

Autopodial skeletal diversity in hystricognath rodents: Functional and phylogenetic aspects

Metapodials and phalanges of the second to fourth digital ray were measured for the hands and feet of 214 specimens belonging to 45 extant species of hystricognath rodents, encompassing members of all major clades of the radiation. Principal components analysis (PCA), the phalangeal index of the third digital ray in the hands and feet, and the relationship between second and fourth digital ray were used to investigate intrinsic autopodial proportions as well as to provide a base for comparisons between hands and feet. PCA separated cursorial Hystricognathi from arboreal ones, but lead to little distinction in other locomotory modes. Cursors have longer metapodials and shorter phalanges, particularly in their hind limb, while arboreal species have relatively longer manual and pedal phalanges. Terrestrial, scansorial, fossorial, and semi-aquatic species were not clearly distinguished, but there is a tendency towards elongated manual digits and relatively short feet in most fossorial species. Closely related species with similar locomotory habits tend to group together in PCA morphospace, and also have similar phalangeal indices. The results are in agreement with current hypotheses on locomotory adaptations of the hand and foot, and concur with many previous findings on autopodial proportions in arboreal, cursorial, and fossorial species. They also highlight the limited use of autopodial proportions for inferring systematic affinities. The lack of distinction in the majority of species is likely related to the lack of highly specialized locomotory types in Hystricognathi.     

Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales

Relationships between the four families placed in the angiosperm order Fabales (Leguminosae, Polygalaceae, Quillajaceae, Surianaceae) were hitherto poorly resolved. We combine published molecular data for the chloroplast regions matK and rbcL with 66 morphological characters surveyed for 73 ingroup and two outgroup species, and use Parsimony and Bayesian approaches to explore matrices with different missing data. All combined analyses using Parsimony recovered the topology Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). Bayesian analyses with matched morphological and molecular sampling recover the same topology, but analyses based on other data recover a different Bayesian topology: ((Polygalaceae + Leguminosae) (Quillajaceae + Surianaceae)). We explore the evolution of floral characters in the context of the more consistent topology: Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). This reveals synapomorphies for (Leguminosae (Quillajaceae + Surianaceae)) as the presence of free filaments and marginal/ventral placentation, for (Quillajaceae + Surianaceae) as pentamery and apocarpy, and for Leguminosae the presence of an abaxial median sepal and unicarpellate gynoecium. An octamerous androecium is synapomorphic for Polygalaceae. The development of papilionate flowers, and the evolutionary context in which these phenotypes appeared in Leguminosae and Polygalaceae, shows that the morphologies are convergent rather than synapomorphic within Fabales.     

Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches

Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free-living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free-living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.     

Functional and phylogenetic diversity of root-associated bacteria of Ajuga bracteosa in Kangra valley

Present study investigates the cultivable diversity of root-associated bacteria from a medicinal plant Ajuga bracteosa in the Kangra valley, in order to determine their plant growth promoting (PGP) and biotechnological potential. The plant was found to exhibit a positive rhizosphere effect of 1.3-1.5. A total of 123 morphologically different bacteria were isolated from the rhizospheric soil and roots of the plant. Medium composition was found to have significant effect on the composition of isolated bacterial populations. Majority of the rhizospheric soil isolates belonged to α- and γ-Proteobacteria, with Pseudomonas constituting the most dominant species. Endophytic bacterial community, on other hand, consisted almost exclusively of Firmicutes. Majority of the isolates showed PGP activity by producing siderophores and indole acetic acid. Several isolates were found to exhibit very high antioxidant activity in the culture medium. A significant proportion of isolates also demonstrated other ecologically important activities like phosphate solubilization, nitrogen fixation, and production of hydrolytic enzymes including amylase, protease, lipase, chitinase, cellulase, pectinase and phosphatase. Firmicutes were found to be metabolically the most versatile group and performed multiple enzyme activities. This is the first systematic study of culturable bacterial community from the rhizosphere of A. bracteosa, particularly in the Kangra valley region.     

Elevational gradients in phylogenetic structure of ant communities reveal the interplay of biotic and abiotic constraints on diversity

A central focus of ecology and biogeography is to determine the factors that govern spatial variation in biodiversity. Here, we examined patterns of ant diversity along climatic gradients in three temperate montane systems: Great Smoky Mountains National Park (USA), Chiricahua Mountains (USA), and Vorarlberg (Austria). To identify the factors which potentially shape these elevational diversity gradients, we analyzed patterns of community phylogenetic structure (i.e. the evolutionary relationships among species coexisting in local communities). We found that species at low‐elevation sites tended to be evenly dispersed across phylogeny, suggesting that these communities are structured by interspecific competition. In contrast, species occurring at high‐elevation sites tended to be more closely related than expected by chance, implying that these communities are structured primarily by environmental filtering caused by low temperatures. Taken together, the results of our study highlight the potential role of niche constraints, environmental temperature, and competition in shaping broad‐scale diversity gradients. We conclude that phylogenetic structure indeed accounts for some variation in species density, yet it does not entirely explain why temperature and species density are correlated.     

Potential functional differentiation of genome in the course of evolution and approaches to its study. II. Elucidation of diversity of phylogenetic lines]

It has been shown elsewhere (Chupov, 2001) that the branching of phylogenetical trunks goes by anisotomical way. Thus, in one of newly formed branches a possibility remains of a further evolutionary transformation, while taxa belonging to another branch sink into a prolonged evolutionary stasis. In the author's opinion, such a phenomenon is to be accompanied by distinctions in constitution of genetical cell devices of the taxa belonging to the branches with evolutionary contrasting potencies. In the article, an attempt is done to consider some other approaches relevant to this problem.     

The role of marine biota in the evolution of terrestrial biota: Gases and genes

There is greater biodiversity (in the senseof genetic distance among higher taxa) ofextant marine than of terrestrialO₂-evolvers. In addition tocontributing the genes from one group ofalgae (Class Charophyceae, DivisionChlorophyta) to produce by evolution thedominant terrestrial plants (Embryophyta),the early marine O₂-evolvers greatlymodified the atmosphere and hence the landsurface when the early terrestrialO₂-evolvers grew. The earliestterrestrial phototrophs (from geochemicalevidence) occurred 1.2 Ga ago, over 0.7 Gabefore the Embryophyta evolved, but wellafter the earliest marine (cyanobacterial)O₂ evolvers (3.45 Ga) and marineeukaryotic O₂ evolvers (2.1 Ga). Evenby the time of evolution of the earliestterrestrial O₂-evolvers the marineO₂-evolvers had modified the atmosphereand land environment in at least thefollowing five ways. Once photosyntheticO₂ paralleling organic C burial hadsatisfied marine (Fe²⁺, S^2-reductants, atmospheric O₂ built (1) upto a considerable fraction of the extantvalue (although some was consumed inoxidising terrestrial exposed Fe²⁺ and(2) provided stratospheric O₃ and thusa UV-screen. (3) CO₂ drawdown to20-30times the extant level is attributableto net production, and burial, of organic Cin the oceans (plus other geologicalprocesses). Furthermore, (4) theirproduction of volatile organic S compoundscould have helped to supply S to inland sitesbut also (5) delivered Cl and Br to thestratosphere thus lowering the O₃ leveland the extent of UV screening.     

Anatomical diversity and regressive evolution in trichomanoid filmy ferns (Hymenophyllaceae): a phylogenetic approach

To infer the anatomical evolution of the Hymenophyllaceae (filmy ferns) and to test previously suggested scenarios of regressive evolution, we performed an exhaustive investigation of stem anatomy in the most variable lineage of the family, the trichomanoids, using a representative sampling of 50 species. The evolution of qualitative and quantitative anatomical characters and possibly related growth-forms was analyzed using a maximum likelihood approach. Potential correlations between selected characters were then statistically tested using a phylogenetic comparative method. Our investigations support the anatomical homogeneity of this family at the generic and sub-generic levels. Reduced and sub-collateral/collateral steles likely derived from an ancestral massive protostele, and sub-collateral/collateral types appear to be related to stem thickness reduction and root apparatus regression. These results corroborate the hypothesis of regressive evolution in the lineage, in terms of morphology as well as anatomy. In addition, a heterogeneous cortex, which is derived in the lineage, appears to be related to a colonial strategy and likely to a climbing phenotype. The evolutionary hypotheses proposed in this study lay the ground for further evolutionary analyses that take into account trichomanoid habitats and accurate ecological preferences.     

Long‐term growth‐increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth‐increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree‐ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1_mussel) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1_discharge; r = ?0.88; P < 0.0001). PC1_mussel and PC1_discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.     

Origin and evolution of the Micronesian biota: Insights from molecular phylogenies and biogeography reveal long-distance dispersal scenarios and founder-event speciation

Micronesian islands taxa show high endemism rates, but very little is known about their biogeographical histories. The lack of systematic biogeography is mainly due to insufficient phylogenetic research in Micronesia. With the recent increase in published molecular biogeographic data, we were able to, for the first time, answer fundamental biogeography questions by reviewing and analyzing numerous geological, ecological, and evolutionary studies. This review, in addition to providing an overview of Micronesian geological history, confirmed the importance of long-distance dispersal mechanisms and founder-event speciation, and morphological and physiological adaptations of plant propagules to cross vast stretches of ocean by wind, ocean currents, bird, or bat dispersal. These adaptations to habitat and geological features, including reef types, determined colonization success as well as inland dispersal and speciation mechanisms. We further identified the source areas of the Micronesian biota and reconstructed historical dispersal scenarios: a dominant Austro-Melanesian dispersal scenario, an Indo-Malaysian connecting to the Austro-Melanesian dispersal scenario, and a Neotropical American and an African dispersal scenario toward Micronesia. Most generic origins were estimated between the Eocene and the Miocene and dispersed to Micronesia between the Miocene and the Pleistocene.