Taxonomic Variation Research Articles

Multiple facets of stream macroinvertebrate alpha diversity are driven by different ecological factors across an extensive altitudinal gradient.

Environmental filtering and spatial structuring are important ecological processes for the generation and maintenance of biodiversity. However, the relative importance of these ecological drivers for multiple facets of diversity is still poorly understood in highland streams. Here, we examined the responses of three facets of stream macroinvertebrate alpha diversity to local environmental, landscape‐climate and spatial factors in a near‐pristine highland riverine ecosystem. Taxonomic (species richness, Shannon diversity, and evenness), functional (functional richness, evenness, divergence, and Rao's Quadratic entropy), and a proxy of phylogenetic alpha diversity (taxonomic distinctness and variation in taxonomic distinctness) were calculated for macroinvertebrate assemblages in 55 stream sites. Then Pearson correlation coefficient was used to explore congruence of indices within and across the three diversity facets. Finally, multiple linear regression models and variation partitioning were employed to identify the relative importance of different ecological drivers of biodiversity. We found most correlations between the diversity indices within the same facet, and between functional richness and species richness were relatively strong. The two phylogenetic diversity indices were quite independent from taxonomic diversity but correlated with functional diversity indices to some extent. Taxonomic and functional diversity were more strongly determined by environmental variables, while phylogenetic diversity was better explained by spatial factors. In terms of environmental variables, habitat‐scale variables describing habitat complexity and water physical features played the primary role in determining the diversity patterns of all three facets, whereas landscape factors appeared less influential. Our findings indicated that both environmental and spatial factors are important ecological drivers for biodiversity patterns of macroinvertebrates in Tibetan streams, although their relative importance was contingent on different facets of diversity. Such findings verified the complementary roles of taxonomic, functional and phylogenetic diversity, and highlighted the importance of comprehensively considering multiple ecological drivers for different facets of diversity in biodiversity assessment.

Reverse Vaccinology Approach to Potential Vaccine Candidates Against Acinetobacter baumannii.

Acinetobacter baumannii is a rapidly evolving pathogen that largely inhabits intensive care units (ICU). This opportunistic, gram-negative organism has shown noteworthy taxonomic variations during the past three decades. A. baumannii functions as a catalase-positive, oxidase-negative obligate, aerobic, nonmotile, highly infectious, and multidrug-resistant bacterium. Therefore, the infection caused by this bacterium tends to have a fairly higher incidence rate in immune-compromised individuals ranging from 26.5% to 91%, as it colonizes in skin tissues and secretions of the respiratory tract. Recently, it has been globally labeled as a "red alert" pathogen, setting alarms throughout the medical community, arising mainly due to its widespread antibiotic resistance continuum. There is a dire need for alternative therapeutic intervention to combat A. baumannii-associated infections and the growing resistance. This chapter focuses upon the reverse vaccinology-based steps and strategies to identify novel potential vaccine candidates against this emerging pathogen.

Niche position drives interspecific variation in occupancy and abundance in a highly-connected lake system

We examined how niche position, niche breadth, biological traits and taxonomic relatedness affect interspecific variation in occupancy and abundance of two commonly-used biological indicator groups, i.e. diatoms and macroinvertebrates. We studied 291 diatom and 103 macroinvertebrate species that occupied the littoral zones of a large (305 km2) highly-connected freshwater system. We collated information on the biological traits and taxonomic relatedness of each species. Using principal coordinates analysis, we formed biological trait and taxonomic vectors describing distances between species and used the resulting vectors as predictor variables. As environmental data, we had site-specific physico-chemical variables, which were used in outlying mean index analyses to determine the niche position and niche breadth of each species. We used linear models to study if and how these two niche parameters and biological traits as well as taxonomic relatedness affected occupancy and abundance. We observed positive occupancy-abundance relationships for both diatoms and macroinvertebrates. We further found that, for both groups, occupancy was better explained by the predictor variables compared with abundance. We also observed that niche parameters, especially niche position, were the main determinants of variation in occupancy and abundance for both diatoms and macroinvertebrates. Local abundances of diatom and macroinvertebrate species were also, to a small degree, affected by biological traits or taxonomic relatedness. We further saw that the relationship between niche position and occupancy was negative, indicating that the more marginal the niche position, the rarer a species is. Our findings provide support for the use of diatoms and macroinvertebrates as ecological indicators as their occupancies and abundances were affected by niche parameters, which is not necessarily always clear in challenging study systems with high connectivity (i.e. high movement of material and species) among sites. These findings also suggest that indices using information on species’ occupancy, abundance and niche requirements are useful in environmental assessment.

Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands

There is considerable debate regarding how the taxonomic diversity of microbial communities relates to the functional diversity across space while similar questions have been explored in macro-organism communities. Here, we investigated the taxonomic and functional diversity patterns of soil microbial communities by coupling the data obtained from marker genes sequencing and functional gene surveys. Meanwhile, we evaluated the relative effects of environment and geographic distance on shaping these patterns in alpine grasslands of northern China. Although the taxonomic diversity and composition of microbial communities varied across sites, we found no consistent changes in the functional structure. Both the environmental factors and geographic distance concurrently affected the taxonomic diversity patterns but they had no effects on the spatial variations in functional genes. The functional alpha diversity was weakly correlated to the taxonomic alpha diversity across sites. Moreover, we found no significant relationship between the taxonomic and functional composition similarity among microbial communities. Together, our results provide evidence that spatial variation in microbial functions could be independent of their variations in taxonomic diversity. Even the drivers of spatial variations in the functional structure could be totally different from those of taxonomic variations such as environmental differences and dispersal limitation. Our findings suggest that spatial variations of microbial function structure within a community would not follow the variations of taxonomic structures due to different drivers between both of them over space.

Changes in multiple facets of macroinvertebrate alpha diversity are linked to afforestation in a subtropical riverine natural reserve.

Land use change is one of the major factors impacting freshwater biodiversity. Afforestation could convert new lands from agriculture or urban land uses to reduce erosion and lead to landscape alterations and biodiversity changes. Here, we examined the changes in the three facets of macroinvertebrate alpha diversity (i.e., taxonomic, functional, and phylogenetic diversity) and further explored possible mechanisms driving their variations before (2007) and after (2016) afforestation along the undammed Chishui River, the core of the National Nature Reserve of Rare and Endemic Fishes in the Upper Yangtze River. We found that taxonomic diversity measures (e.g., species richness, Shannon-Wiener index and Simpson index) increased but all measures of functional diversity (e.g., FRic, FEve, FDiv, and RaoQ) and phylogenetic diversity (e.g., indices of taxonomic distinctness) exhibited stability after the afforestation practice. We also found that only significant taxonomic diversity variation was detected and it showed a relationship to alterations of land use rather than local environmental condition changes across the 10-year afforestation practice. Moreover, hydrology and nutrients levels showed changes after afforestation, but these changes had no effect on the biodiversity changes based on multiple linear regression models. In each survey, the three facets of alpha diversity were significantly explained by natural physical factors and showed inconsistent responses to these underlying environmental variables. In addition, the biodiversity-environment relationships remained stable before and after afforestation, indicating that the inherent mechanisms that drive macroinvertebrate community variation have not changed. Our findings highlight that different alpha diversity measures of lotic macroinvertebrates provide different information about biodiversity and respond differently to various environmental variables. Thus, it is necessary to integrate them into one framework when applying routine monitoring, assessment, and conservation procedures based on lotic macroinvertebrates.

Spatial and taxonomic variation of mercury concentration in low trophic level fauna from the Mediterranean Sea.

Studies of mercury (Hg) in the Mediterranean Sea have focused on pollution sources, air-sea mercury exchange, abiotic mercury cycling, and seafood. Much less is known about methylmercury (MeHg) concentrations in the lower food web. Zooplankton and small fish were sampled from the neuston layer at both coastal and open sea stations in the Mediterranean Sea during three cruise campaigns undertaken in the fall of 2011 and the summers of 2012 and 2013. Zooplankton and small fish were sorted by morphospecies, and the most abundant taxa (e.g. euphausiids, isopods, hyperiid amphipods) analyzed for methylmercury (MeHg) concentration. Unfiltered water samples were taken during the 2011 and 2012 cruises and analyzed for MeHg concentration. Multiple taxa suggested elevated MeHg concentrations in the Tyrrhenian and Balearic Seas in comparison with more eastern and western stations in the Mediterranean Sea. Spatial variation in zooplankton MeHg concentration is positively correlated with single time point whole water MeHg concentration for euphausiids and mysids and negatively correlated with maximum chlorophyll a concentration for euphausiids, mysids, and "smelt" fish. Taxonomic variation in MeHg concentration appears driven by taxonomic grouping and feeding mode. Euphausiids, due to their abundance, relative larger size, importance as a food source for other fauna, and observed relationship with surface water MeHg are a good candidate biotic group to evaluate for use in monitoring the bioavailability of MeHg for trophic transfer in the Mediterranean and potentially globally.

Species identity matters when interpreting trophic markers in aquatic food webs.

In aquatic systems, food web linkages are often assessed using diet contents, stable isotope ratios, and, increasingly, fatty acid composition of organisms. Some correlations between different trophic metrics are assumed to be well-supported; for example, particular stable isotope ratios and fatty acids seem to reflect reliance on benthic or pelagic energy pathways. However, understanding whether the assumed correlations between different trophic metrics are coherent and consistent across species represents a key step toward their effective use in food web studies. To assess links among trophic markers, we compared relationships between major diet components, fatty acids, and stable isotope ratios in three fishes: yellow perch (Perca flavescens), round goby (Neogobius melanostomus), and spottail shiner (Notropis hudsonius) collected from nearshore Lake Michigan. Yellow perch and spottail shiner are native in this system, while round goby are a relatively recent invader. We found some evidence for agreement between different trophic metrics, especially between diet components, n-3:n-6 fatty acid ratios, and stable isotope ratios (δ13C and δ15N). However, we also observed significant variation in observed relationships among markers and species, potentially due to taxonomic variation in the specific diet items consumed (e.g., chydorid microcrustaceans and Dreissena mussels) and species-specific biochemical processes. In many of these latter cases, the invasive species differed from the native species. Understanding the effects of taxonomic variation on prey and predator signatures could significantly improve the usefulness of fatty acids in food web studies, whereas diet contents and stable isotopes appear to be reliable indicators of trophic niche in aquatic food webs.

Inventory and Assessment of theGorilla gorilla(Savage, 1847) Skeletal Collection Housed at the Yale Peabody Museum of Natural History

Museum collections are critical resources for examination of comparative anatomy, developmental biology, and life history hypotheses. Skeletal collections provide insight into spatiotemporal, species, population, and individual variation associated with environmental, social, and epidemiological history. For endangered species such as great apes, these collections provide data that are nearly impossible to replicate today. In this second in a series of articles reviewing the great ape holdings of the Peabody Museum of Natural History at Yale University, we describe the Gorilla gorilla skeletal collection, comprising 16 individuals: 13 males, 2 females, and 1 of indeterminate sex. Evidence of socioecology, interindividual violence, hunting, captive management, predation, senescence, and infectious disease are present within the skeletal material. The collection exhibits possible taxonomic diversity as well. Our evaluation of the Yale Peabody Museum collection provides a baseline for future research and testable hypotheses for alternate techniques, such as isotopic analyses of dental calculus and noninvasive genetic testing. Museum collections continue to provide new insights into taxonomic and individual variation and environmental context, and ultimately allow for comparisons between modern and historical environmental and behavioral variables.

Functional response of tropical estuarine benthic assemblages to perturbation by Polycyclic Aromatic Hydrocarbons

The potential effects of perturbations by Polycyclic Aromatic Hydrocarbons (PAHs) on nematode and macrobenthos assemblages were investigated using the Biological Traits Analysis (BTA). We sampled at tidal flats near an oil refinery and in a reference estuary. Morphological and ecological traits of benthic fauna were selected and analyzed in order to assess the contribution of PAHs concentrations, the proximity to the oil refinery, the sediment characteristics and interaction between these predictor variables on benthic fauna. Multivariate analyses (DISTLM and db-RDA), showed that a large fraction of functional and taxonomic variation of benthic assemblages was explained by the interaction between location and sediment characteristics. The interaction between ∑PAHs and sediment characteristics was relatively low but significant. The results showed that taxonomic and functional variability of benthic assemblages were driven by natural and anthropogenic variables and BTA was an important auxiliary tool for distinguishing these responses. The amount of variability explained by the model was higher for nematode assemblages than to macrofaunal assemblages, showing a potential higher sensitivity of this group to the predictor variables.

The Phylogeny of Osteopontin-Analysis of the Protein Sequence.

Osteopontin (OPN) is important for tissue remodeling, cellular immune responses, and calcium homeostasis in milk and urine. In pathophysiology, the biomolecule contributes to the progression of multiple cancers. Phylogenetic analysis of 202 osteopontin protein sequences identifies a core block of integrin-binding sites in the center of the protein, which is well conserved. Remarkably, the length of this block varies among species, resulting in differing distances between motifs within. The amino acid sequence SSEE is a candidate phosphorylation site. Two copies of it reside in the far N-terminus and are variably affected by alternative splicing in humans. Between those motifs, birds and reptiles have a histidine-rich domain, which is absent from other species. Just downstream from the thrombin cleavage site, the common motif (Q/I)(Y/S/V)(P/H/Y)D(A/V)(T/S)EED(L/E)(-/S)T has been hitherto unrecognized. While well preserved, it is yet without assigned function. The far C-terminus, although very different between Reptilia/Aves on the one hand and Mammals on the other, is highly conserved within each group of species, suggesting important functional roles that remain to be mapped. Taxonomic variations in the osteopontin sequence include a lack of about 20 amino acids in the downstream portion, a small unique sequence stretch C-terminally, a lack of six amino acids just upstream of the RGD motifs, and variable length insertions far C-terminally.

The oldest skeletal macroscopic organism Palaeopascichnus linearis

The existing problems regarding the phylogenetic resolution of Ediacaran macroscopic organisms stem from a failure to factor-in the information captured through different ‘taphonomic windows’. Here we integrate the information from sandstone- and limestone-hosted occurrences of the fossil Palaeopascichnus linearis that together show a conspicuously greater range of taxonomic and taphonomic variation. The limestone-hosted material comes from a new locality discovered on the northwestern slope of the Olenek Uplift in Arctic Siberia that characterises the uppermost Ediacaran strata of the Khatyspyt Formation, Khorbusuonka Group. Detailed taphonomic and morphodynamic studies of the fossil material revealed evidence of possible chamber wall agglutination and growth through addition of new chambers with little sideway growth. Palaeopascichnus linearis outlived the intra-Ediacaran (∼550 Myr ago) drop in species richness, the advent of bilaterians, and the increase in complexity of burrowing behaviour in metazoans. It remains to be seen whether or not the remarkable ecological success achieved by Palaeopascichnus linearis during the times of rich evolutionary experimentation has anything to do with the invention of an agglutinated test. Palaeopascichnus poses major scientific challenges, and it is now clear that such preservation as occurs in Siberia may hold the answer to what they were, how they lived and what they were related to.

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana).

Recent studies highlight that the gut mycobiota play essential roles in mammalian metabolic and immune systems, but to date we lack information on the forces that naturally shape the gut mycobiota of wild primates. To investigate the contributions of host and environmental factors in the taxonomic variation of the gut mycobiota, we examined the effects of age, sex, and season on the fecal mycobiota in wild-living Tibetan macaques (Macaca thibetana). Using next generation sequencing and a longitudinal set of fecal samples collected over 1 year, we identified a set of core fungal taxa present in the Tibetan macaque's fecal samples. The predominant genera Aspergillus and Penicillium, which promote the digestion of cellulose and hemicellulose in herbivorous mammals, were detected in this study. Similar to humans, we found age and sex effects on the macaques' fecal mycobiota. We also found that both fecal fungal composition and diversity (alpha and beta diversity) varied significantly by season. In particular, the Penicillium enriched mycobiota in summer samples may aid in the digestion of cellulose and hemicellulose present in mature leaves. The high alpha diversity detected in Tibetan macaques' winter fecal samples may facilitate a diet rich in fiber ingested during this season. We propose that the gut mycobiota play an important role in the macaques' ability to adapt to seasonal fluctuations in food availability and nutrient content.

Pioneer farming in southeast Europe during the early sixth millennium BC: Climate-related adaptations in the exploitation of plants and animals.

The Old World farming system arose in the semi-arid Mediterranean environments of southwest Asia. Pioneer farmers settling the interior of the Balkans by the early sixth millennium BC were among the first to introduce southwest Asian-style cultivation and herding into areas with increasingly continental temperate conditions. Previous research has shown that the bioarchaeological assemblages from early farming sites in southeast Europe vary in their proportions of plant and animal taxa, but the relationship between taxonomic variation and climate has remained poorly understood. To uncover associations between multiple species and environmental factors simultaneously, we explored a dataset including altitude, five bioclimatic and 30 bioarchaeological variables (plant and animal taxa) for 57 of the earliest farming sites in southeast Europe using Canonical Correspondence Analysis (CCA). An extension of correspondence analysis, CCA is widely used in applied ecology to answer similar questions of species-environment relationships, but has not been previously applied in prehistoric archaeology to explore taxonomic and climatic variables in conjunction. The analyses reveal that the changes in plant and animal exploitation which occurred with the northward dispersal of farmers, crops and livestock correlate with south-north climate gradients, and emphasize the importance of adaptations in the animal domain for the initial establishment of farming beyond the Mediterranean areas.

Splenectomy Leads to Amelioration of Altered Gut Microbiota and Metabolome in Liver Cirrhosis Patients.

Dysbiosis of gut microbiota and metabolome is a frequently encountered condition in liver cirrhosis (LC) patients. The severity of liver dysfunction was found to be correlated with the degree of microbial dysbiosis. Several clinical studies have indicated liver function improvement after therapeutic splenectomy for LC-induced hypersplenism. We sought to determine whether such post-splenectomy outcome is pertinent to modulation of the abnormal gut microenvironment in LC patients. A cross-sectional study including 12 LC patients and 16 healthy volunteers was first conducted, then a before–after study in the cohort of patients was carried out before and 6 months after splenectomy. Fecal samples were collected in hospital. Temporal bacterial (n = 40) and metabolomics (n = 30) profiling was performed using 16s rRNA gene sequencing and ultra performance liquid chromatography/mass spectrometer (UPLC/MS), respectively. Our results revealed that microbial composition in patients was clearly different from that in healthy controls (HCs), evidenced by considerable taxonomic variation. Along with improved liver function (Child–Pugh score), the patients also displayed similar gut microbiota profile and predicted metagenome function to that of HCs after splenectomy. Enterobacteriaceae and Streptococcaceae, two LC-enriched families showing positive relation with Child–Pugh score, exhibited significantly decreased abundance after splenectomy. At the genus level, 11 genera were differentially abundant between patients and HCs, but 9 genera of them restituted to normal levels by certain degree after splenectomy. PICRUSt analysis showed that the relative abundance of 17 KEGG pathways was partially restored after splenectomy. Four of them were amino acid-related pathways: lysine degradation, tryptophan degradation, amino acid metabolism, and protein digestion and absorption. These findings were supported by metabonomics results which showed that relative abundance of amino acid and corresponding catabolites changed toward normal. In addition to the variations in the relative abundances of bacteria and metabolites, the correlation between them also altered in patients after splenectomy. Dysbiosis in gut microbiome and related metabolism of LC patients was partially corrected after splenectomy. Whether the improved gut microenvironment could prevent LC-related complications and delay the progress of LC is a propitious objective for future study. Trial registration: ChiCTR-OOB-15007409. Registered November 15, 2015.

The Inocybe geophylla group in North America: a revision of the lilac species surrounding I. lilacina

ABSTRACTThe Inocybe geophylla group is circumscribed based on phylogenetic analysis of DNA sequences largely sampled from North America and Europe. Twenty-nine phylogenetic species are uncovered after analysis of combined nuc 28S rDNA (28S) and RNA polymerase II second largest subunit (rpb2) DNA sequence data. Species in the I. geophylla group share the presence of a cortina, silky-fibrillose pileus and stipe, pruinose stipe apex, spermatic odor, thick-walled hymenial cystidia, and smooth amygdaliform or elliptical basidiospores. Within the group, as many as five phylogenetic species attributable to I. lilacina and allies form a strongly supported clade based on analysis of nuc ITS1-5.8S-ITS2 rDNA (ITS [internal transcribed spacer]), 28S, and rpb2 data. However, all lilac-colored species do not form a monophyletic group. Sufficient morphological and ecological data are present to document four of the I. lilacina subgroup species, two of which are described from North America as new: I. ionocephala and I. sublilacina. Inocybe lilacina is recircumscribed based on sequencing the holotype and is distributed in the eastern United States under pines and/or hardwoods. Inocybe pallidicremea is a widespread and common conifer associate in mostly northern parts of North America, to which the name I. lilacina was previously applied. Descriptions, photographs, line drawings, and a taxonomic key to lilac species in the I. lilacina subgroup from North America are provided. Well-documented collections, especially notes on gross morphology and ecology, are needed to continue to assess and describe the high taxonomic variation in the I. lilacina subgroup and its allies worldwide.

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.

Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.

Effects of land use on zoonotic host communities: a global correlative analysis

BackgroundEnvironmental trade-offs associated with land use—for example, between food security and biodiversity conservation—are crucial dimensions of planetary health. Land use-driven biodiversity change might predictably affect disease risk if reservoir host species are consistently more likely to persist under human disturbance (ie, if ecological communities in modified habitats generally have a higher zoonotic potential than those in unmodified habitats). Such a phenomenon has been observed in specific disease systems, but with substantial change in global land use projected for this century, assessing its global and taxonomic generality would shed light on an important hypothesised driver of environmental synergies or trade-offs between conservation and public health. MethodsWe collated data on hosts of human parasites and pathogens from the published literature, and combined these with the Projecting Responses of Ecological Diversity in Changing Terrestrial Systems (PREDICTS) global database of local ecological communities and associated land use data. We analysed the effects of land use on host richness and abundance across 7330 sites globally, controlling for disease-related research effort and differences in survey methods. FindingsEcological communities in anthropogenic land uses (managed and urban ecosystems) contained a consistently higher richness and abundance of host species than did communities in nearby primary (undisturbed) sites. However, among mammal hosts of zoonotic pathogens, we found considerable taxonomic variation in host responses to land use, with abundances of rodents and bats generally increasing and those of primates and carnivores generally declining in modified landscapes. InterpretationOur results suggest that future change in global land use has the potential to drive overall increasing contact between people and ecological communities with increased shared pathogen potential (ie, more potential hosts and possible opportunities for transmission). However, the differences in host responses to modified landscapes among mammal orders suggests that these changes are unlikely to affect all zoonotic diseases consistently. This result supports arguments that, rather than expecting a consistent relationship between biodiversity change and disease, in practice, policies aiming both to conserve biodiversity and reduce human disease (eg, through establishment of protected areas) must be disease and context specific. FundingThis research was supported by a Graduate Research Scholarship from University College London (to RG), the Natural Environment Research Council (to DWR and KEJ), and a Royal Society University Research Fellowship (to TN).

Contrasting patterns of taxonomic, phylogenetic and functional variation along a Costa Rican altitudinal gradient in the plant family Melastomataceae

Abstract:The functional composition of plant communities in montane regions has been studied for decades, and most recent analyses find that environmentally favourable landscapes at lower altitudes tend to be dominated by species with resource-acquisitive traits, while more resource-conservative taxa dominate higher-altitude communities. However, it is unclear the extent to which this pattern is driven by co-gradient variation within clades or changes in clade representation across the gradient. To test for co-gradient variation, species composition, phylogenetic structure and functional traits were quantified for 97 species within the plant family Melastomataceae at five locations across a 2500-m altitudinal gradient along Volcán Barva in Costa Rica. Average melastome leaf force to punch, specific leaf area and leaf size vary with altitude, while four other functional traits do not. Taxonomic dissimilarity between communities was correlated with altitudinal difference, while phylogenetic dissimilarity was correlated with altitudinal dissimilarity only when measured with a metric that emphasizes shallow turnover of the tips of the phylogeny. These results highlight how species turnover may be more pronounced than functional or phylogenetic variation along altitudinal gradients. In addition, these results highlight the conservation value of lowland tropical forests, which here harbour a disproportionate amount of phylogenetic and functional diversity.

Function and functional redundancy in microbial systems.

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Phylogeny of highly hybridogenous Iberian Centaurea L. (Asteraceae) taxa and its taxonomic implications

Centaurea is one of the richest but less investigated genera of tribe Cardueae (Asteraceae). We reconstructed an updated phylogeny of Iberian species of Centaurea sects. Centaurea, Jacea, Lepteranthus and Phalolepis by sampling representatives from 48 taxa (~60% of the taxonomic variation). Phylogenetic trees and haplotypic networks were based on ITS and trnLF sequences, and Bayesian dating analysis on ITS data. We found two main lineages within this monophyletic group: (1) a W Mediterranean Centaurea and Phalolepis plus C. diffusa (CP) clade; and (2) an E Mediterranean – Eurosiberian Jacea and Lepteranthus (JL) clade. Our analyses provide new reconstructions for species of C. sects. Jacea and Lepteranthus that support new taxonomic circumscriptions. The inferred divergence times indicated succesive splits of the CP and JL lineages during the Miocene (e.g. CP/JL, Serravalian; Jacea/Lepteranthus, Tortonian; C. hyssopifolia, C. gr. janeri, C. gr. exarata, Messinian) and the Pliocene (C. linifolia/C. antennata). Interspecific hybridizations and polyploidizations likely took place during the Pleistocene (1.5–0.7 Ma) interglacials, when several hybrid lineages apparently originated (e.g. C. x decipiens). Allopatric speciation probably played an important role in the diversification of the Iberian Centaurea taxa, since the origins of several endemic species occurred during mid-late Pleistocene times (2.2–1.3 Ma) in several disjunct Iberian ranges.