Climate of origin shapes variations in wood anatomical properties of 17 Picea species

BACKGROUND

Variations in hydraulic conductivity may arise from species-specific differences in the anatomical structure and function of the xylem, reflecting a spectrum of plant strategies along a slow-fast resource economy continuum. Spruce (Picea spp.), a widely distributed and highly adaptable tree species, is crucial in preventing soil erosion and enabling climate regulation. However, a comprehensive understanding of the variability in anatomical traits of stems and their underlying drivers in the Picea genus is currently lacking especially in a common garden.

RESULTS

We assessed 19 stem economic properties and hydraulic characteristics of 17 Picea species grown in a common garden in Tianshui, Gansu Province, China. Significant interspecific differences in growth and anatomical characteristics were observed among the species. Specifically, xylem hydraulic conductivity (Ks) and hydraulic diameter exhibited a significant negative correlation with the thickness to span ratio (TSR), cell wall ratio, and tracheid density and a significant positive correlation with fiber length, and size of the radial tracheid. PCA revealed that the first two axes accounted for 64.40% of the variance, with PC1 reflecting the trade-off between hydraulic efficiency and mechanical support and PC2 representing the trade-off between high embolism resistance and strong pit flexibility. Regression analysis and structural equation modelling further confirmed that tracheid size positively influenced Ks, whereas the traits DWT, D_r, and TSR have influenced Ks indirectly. All traits failed to show significant phylogenetic associations. Pearson's correlation analysis demonstrated strong correlations between most traits and longitude, with the notable influence of the mean temperature during the driest quarter, annual precipitation, precipitation during the wettest quarter, and aridity index.

CONCLUSIONS

Our results showed that xylem anatomical traits demonstrated considerable variability across phylogenies, consistent with the pattern of parallel sympatric radiation evolution and global diversity in spruce. By integrating the anatomical structure of the stem xylem as well as environmental factors of origin and evolutionary relationships, our findings provide novel insights into the ecological adaptations of the Picea genus.

Effects of UV-B radiation on pollen germination and tube growth: A global meta-analysis

Despite widespread recognition of pollen's potential sensitivity to ultraviolet-B (UV-B) radiation (280-315 nm), there remains ongoing debate surrounding the extent and mechanisms of this effect. In this study, using published data on pollen germination and tube growth including 377 pair-wise comparisons from 77 species in 30 families, we present the first global quantification of the effects of UV-B radiation on pollen germination and tube growth, along with its underlying mechanisms. Our results showed a substantial reduction in both pollen germination and tube growth in response to UV-B radiation, affecting 90.9 % and 84.2 % of species, respectively. Notably, these reductions exhibited phylogenetic constraints, highlighting the role of evolutionary history in shaping the sensitivity of pollen germination and tube growth to UV-B radiation. A negative correlation between elevation and the sensitivity of pollen tube growth was detected, suggesting that pollens from plants at higher elevations exhibit greater resistance to UV-B radiation. Our investigation also revealed that the effects of UV-B radiation on pollen germination and tube growth were influenced by a range of abiotic and biotic factors. Nevertheless, the intensity and duration of UV-B radiation exposure exhibited the highest explanatory power for the effects on both pollen germination and tube growth. This suggests that the responses of pollens to UV-B radiation are profoundly influenced by its dose, a critical consideration within the context of global change. In conclusion, our study provides valuable insights into the diverse responses of pollen germination and tube growth to UV-B radiation, highlighting the environment and species-dependent nature of pollen's susceptibility to UV-B radiation, with substantial implications for our understanding of the ecological and agricultural consequences of ongoing changes in UV-B radiation.

shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals

The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately labeled sampling times. Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences. Furthermore, while not all branches of a phylogenetic tree may exhibit a clear temporal signal, specific branches may still adhere to the assumptions, with varying evolutionary rates. Supporting a relaxed molecular clock model better aligns with the complexities of evolution. The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals. Despite its utility, there remains a lack of corresponding software implementations for broader applications. To address this gap, we present shinyTempSignal, an interactive web application implemented with the shiny framework, available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal. This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models. By extending the root-to-tip regression method to diverse signals, shinyTempSignal helps in the detection of evolving features or traits, thereby laying the foundation for deeper insights and subsequent analyses.

Woody species with higher hydraulic efficiency or lower photosynthetic capacity discriminate more against 13C at the global scale

Leaf carbon isotope composition (δ13C) provides an integrative record on the carbon and water balance of plants over long periods. Photosynthetic ability and hydraulic traits which are highly associated with stomatal behavior could affect leaf δ13C. Association between photosynthetic ability and leaf δ13C has been examined, however, how hydraulic traits influence leaf δ13C has not been fully understood. To fill this gap, we investigated the variations in leaf δ13C among 2591 woody species (547 shrub and 2044 tree species), and analyzed the link of leaf δ13C with leaf photosynthetic and xylem hydraulic traits. Our result showed that leaf δ13C was positively correlated to leaf photosynthetic ability and capacity. For hydraulic traits, leaf δ13C was negatively related to hydraulic conductivity (Ks), xylem pressure inducing 50 % loss of hydraulic conductivity (P50) and vessel diameter (Vdia). Associations of leaf δ13C with xylem hydraulic traits indicate woody species with stronger hydraulic safety discriminated less against 13C, while woody species with higher hydraulic efficiency had more negative leaf δ13C. Shrub species, which showed a lower Vdia and P50, had a significant less negative leaf δ13C than tree species. Furthermore, woody species inhabiting in dry regions discriminated less against 13C than those growing in humid regions. Moreover, leaf δ13C displayed a low phylogenetic signal based on Blomberg's K statistic. Overall, woody species with a higher leaf photosynthetic ability or stronger hydraulic safety system discriminated less against 13C and adopt the provident water use strategy.

Phylogenetic diversity and community wide-trait means offer different insights into mechanisms regulating aboveground carbon storage

Both attributes of functional traits and phylogenetic diversity influence ecosystem functions, but which of these factors is most important is still poorly understood in natural systems. Using data from West African forests and tree savannas, we analyse how (i) phylogenetic diversity complements attributes of functional traits in explaining aboveground carbon (AGC); (ii) phylogenetic diversity relates with attributes of functional traits along gradients of phylogenetic signal; and (iii) pathways between phylogenetic diversity and attributes of functional traits relate AGC to soil and climate. Phylogenetic diversity was measured as standardised effect size of Mean Pairwise Distance (sesMPD) and Mean Nearest Taxon Distance (sesMNTD). Functional dispersion (FDis) and community weighted mean (CWM) were calculated for four traits related to leaf economics spectrum and plant life-history. Functional traits-based models explained 11 % of AGC variability. With two out of the four traits being phylogenetically conserved, incorporating phylogenetic diversity in the models increased the explained variance in AGC by 15 %. The slope of phylogenetic diversity-trait relationship was more responsive to trait conservatism for FDis than CWM. AGC was positively influenced by sesMPD and CWM of plant maximum height. In turn, CWM of plant maximum height increased with higher soil nitrogen and climate moisture, whereas sesMPD was negatively related with climate moisture. Although FDis was positively associated with sesMPD, it was not as important as sesMPD and CWM of plant maximum height in influencing and relating AGC to soil nitrogen and climate moisture. Our results suggest that phylogenetic diversity is important for AGC but does not fully reflect the functional mechanisms pertaining to community-wide trait means. The study also demonstrates the role of environment in regulating AGC, which operates through differences in community fitness driven by tall plant stature, and evolutionary processes whereby closely related species are maintained in less arid environments.

Claw shape variation in oribatid mites of the genera Carabodes and Caleremaeus: exploring the interplay of habitat, ecology and phylogenetics

Background

Claws are a commonly observed biological adaptation across a wide range of animal groups. They serve different functions and their link to evolution is challenging to analyze. While there are many studies on the comparative anatomy and morphology of claws in reptiles, birds and several arthropods, knowledge about claws of soil-living oribatid mites, is still limited. Recent research on intertidal oribatid mites has shown that claw shape is strongly correlated with microhabitat and is subject to ecological selective pressures. However, the selective constraints shaping claws in terrestrial oribatid mites are still unknown.

Methods

In this study, 300 specimens from 12 different species and two genera were examined. Geometric morphometrics were used to quantify claw length and curvature, and to analyze two-dimensional claw shape. In combination with molecular phylogenetic analyses of investigated populations phylogenetic signal was quantified within genera using Blomberg's K and random replicates. Additionally, ecological information on the investigated species was gathered from previous studies and compiled into tables.

Results

The claw shapes of Carabodes species vary moderately, with the three species C. reticulatus, C. rugosior and C. tenuis deviating the most from the others. These three species are only found in a small number of habitats, which may require a more specialized claw shape. Our results show that there is a phylogenetic influence on claw shape in Carabodes but not in Caleremaeus. Additionally, habitat specificity and lifestyle were found to have ecological impact on claw shape in both genera. The present results demonstrate that characteristics of the claws of terrestrial oribatid mites are correlated with ecology, but this correlation is apparently weaker than in intertidal oribatid mites that are prone to strong external forces.

Diatom endemism and taxonomic turnover: Assessment in high-altitude alpine lakes covering a large geographical range

Diatoms are widely used as ecological indicators and show various degrees of endemism. Many studies that support the idea of endemic species integrate several climate zones, a variety of ecosystem types, and often focus on a global scale. Here, we investigated whether endemism could be detected when considering a homogeneous type of ecosystem in a single climate zone. We sampled stone biofilms at 40-50 cm depth in high-altitude lakes in the Alpine climate zone. A total of 149 samples were obtained from the French and Georgian mountains, two areas separated by ∼3000 km. Using Amplicon Sequence Variants derived from DNA metabarcoding, we assessed taxonomic turnover and Zeta-diversity (a measure of endemism). We ran haplotype networks and phylogenetic tests to measure geographical signal in the phylogenies of dominant taxa. The French and Georgian communities shared 51 % of species. Species that were not shared across both regions were mostly rare, and often not characteristic of lakes but of neighboring habitats instead. In contrast, at the sub-species level, 87 % of the genotypes showed restricted distributions. Whereas endemism was the rule at sub-species level, most species were shared across both French and Georgian lakes, suggesting that geographic barriers strongly limited dispersal at the sub-species level but not species level. Dominant species hosted higher levels of sub-specific diversity than rare species. In contrast to global-scale studies, we did not find any significant geographical structuring in the phylogeny of the investigated species. This could indicate ongoing dispersal at a frequency fast enough to prevent allopatric divergence, yet slow enough to prevent sharing most haplotypes between France and Georgia. These results have implications for biomonitoring: depending on the taxonomic level chosen, robust generic tools (species level) or tools dedicated to a region able to discriminate fine pressures differences (sub-species level) may be developed.

Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting

Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg^-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L^-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.

Detection of Microsporidia in Pollinator Communities of a Mediterranean Biodiversity Hotspot for Wild Bees

Insect pollination is crucial for the maintenance of natural and managed ecosystems but the functioning of this ecosystem service is threatened by a worldwide decline of pollinators. Key factors in this situation include the spread and interspecific transmission of pathogens worldwide through the movement of managed pollinators. Research on this field has been mainly conducted in some particular species, while studies assessing the interspecific transmission of pathogens at a community level are scarce. However, this information is pivotal to design strategies to protect pollinators. Herein, we analysed the prevalence of two common microsporidia pathogens of managed honey bees (Nosema ceranae and N. apis) in bee communities of semiarid Mediterranean areas from the Southeast of the Iberian Peninsula. Our results confirm the ability of N. ceranae to disperse across wild bee communities in semiarid Mediterranean ecosystems since it was detected in 36 Apoidea species (39% of the sampling; for the first time in nine genera). The prevalence of the pathogen did not show any phylogenetic signal which suggests a superfamily host range of the pathogen or that wild bees may be acting only as vectors of N. ceranae. In addition, N. apis was detected in an Eucera species, which is the second time it has been detected by molecular techniques in a host other than the honey bee. Our study represents the primary assessment of the prevalence of microsporidia at community level in Mediterranean areas and provides outstanding results on the ability of Nosema pathogens to spread across the landscape.

Determinants of haemosporidian single- and co-infection risks in western palearctic birds

Understanding the drivers of infection risk helps us to detect the most at-risk species in a community and identify species whose intrinsic characteristics could act as potential reservoirs of pathogens. This knowledge is crucial if we are to predict the emergence and evolution of infectious diseases. To date, most studies have only focused on infections caused by a single parasite, leaving out co-infections. Yet, co-infections are of paramount importance in understanding the ecology and evolution of host-parasite interactions due to the wide range of effects they can have on host fitness and on the evolutionary trajectories of parasites. Here, we used a multinomial Bayesian phylogenetic modelling framework to explore the extent to which bird ecology and phylogeny impact the probability of being infected by one genus (hereafter single infection) or by multiple genera (hereafter co-infection) of haemosporidian parasites. We show that while nesting and migration behaviors influenced both the probability of being single- and co-infected, species position along the slow-fast life-history continuum and geographic range size were only pertinent in explaining variation in co-infection risk. We also found evidence for a phylogenetic conservatism regarding both single- and co-infections, indicating that phylogenetically related bird species tend to have similar infection patterns. This phylogenetic signal was four times stronger for co-infections than for single infections, suggesting that co-infections may act as a stronger selective pressure than single infections. Overall, our study underscores the combined influence of hosts' evolutionary history and attributes in determining infection risk in avian host communities. These results also suggest that co-infection risk might be under stronger deterministic control than single infection risk, potentially paving the way toward a better understanding of the emergence and evolution of infectious diseases.

Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing

Different from the generally conserved plastomes (plastid genomes) of most land plants, the Selaginellaceae plastomes exhibit dynamic structure, high GC content and high substitution rates. Previous plastome analyses identified strong conflict on several clades in Selaginella, however the factors causing the conflictions and the impact on the phylogenetic inference have not been sufficiently investigated. Here, we dissect the distribution of phylogenetic signals and conflicts in Selaginella sanguinolenta group, the plastome of which is DR (direct repeats) structure and with genome-wide RNA editing. We analyzed the data sets including 22 plastomes representing all species of the S. sanguinolenta group, covering the entire geographical distribution from the Himalayas to Siberia and the Russian Far East regions. We recovered four different topologies by applying multispecies coalescent (ASTRAL) and concatenation methods (IQ-TREE and RAxML) on four data sets of PC (protein-coding genes), NC (non-coding sequences), PCN (the concatenated PC and NC), and RC (predicted RNA editing sites "C" were corrected by "T"), respectively. Six monophyletic clades, S. nummularifolia clade, S. rossii clade, S. sajanensis clade, S. sanguinolenta I clade, S. sanguinolenta II clade, and S. sanguinolenta III clade, were consistently resolved and supported by the characteristics of GC content, RNA editing frequency, and gene content. However, the relationships among these clades varied across the four topologies. To explore the underlying causes of the uncertainty, we compared the phylogenetic signals of the four topologies. We identified that the sequence types (coding versus non-coding), outlier genes (genes with extremely high |ΔGLS| values), and C-to-U RNA editing frequency in the protein-coding genes were responsible for the unstable phylogenomic relationship. We further revealed a significant positive correlation between the |ΔGLS| values and the variation coefficient of the RNA editing number. Our results demonstrated that the coalescent method performed better than the concatenation method in overcoming the problems caused by outlier genes and extreme RNA editing events. Our study particularly focused on the importance of exploring the plastid phylogenomic conflicts and suggested conducting concatenated analyses cautiously when adopting organelle genome data.

Intraspecific trait variation of woody species reduced in a savanna community, southwest China

Plants deploy various ecological strategies in response to environmental heterogeneity. In many forest ecosystems, plants have been reported to have notable inter- and intra-specific trait variation, as well as clear phylogenetic signals, indicating that these species possess a degree of phenotypic plasticity to cope with habitat variation in the community. Savanna communities, however, grow in an open canopy structure and exhibit little species diversification, likely as a result of strong environmental stress. In this study, we hypothesized that the phylogenetic signals of savanna species would be weak, the intraspecific trait variation (ITV) would be low, and the contribution of intraspecific variation to total trait variance would be reduced, owing to low species richness, multiple stresses and relatively homogenous community structure. To test these hypotheses, we sampled dominant woody species in a dry-hot savanna in southwestern China, focusing on leaf traits related to adaptability of plants to harsh conditions (year-round intense radiation, low soil fertility and seasonal droughts). We found weak phylogenetic signals in leaf traits and low ITV (at both individual and canopy-layer levels). Intraspecific variation (including leaf-, layer- and individual-scales) contributed little to the total trait variance, whereas interspecific variation and variation in leaf phenology explained substantial variance. Our study suggests that intraspecific trait variation is reduced in savanna community. Furthermore, our findings indicate that classifying species by leaf phenology may help better understand how species coexist under similar habitats with strong stresses.

Soil fertility and water availability effects on trait dispersion and phylogenetic relatedness of tropical terrestrial ferns

Analysis of plant functional traits and their phylogenetic relationships has shed light on the processes structuring the occurrence patterns of angiosperm taxa across environmental gradients. In montane tropical forests, angiosperms coexist with diverse communities of terrestrial ferns, with distinct evolutionary histories, leaf morphology, and reproductive systems. Here we examined the functional traits, functional dispersion, and phylogenetic diversity of ferns across a well-described gradient of moisture and soil nutrient availability in a premontane tropical rainforest in western Panama. We measured 15 functional traits from 33 terrestrial fern species occurring in 12 one-ha plots. We applied RLQ and fourth-corner analyses to assess relationships between trait and environmental variables and used beta regression to evaluate how functional dispersion responds to environmental factors. In addition, we analyzed trait distributions with respect to fern phylogeny. We found that functional composition was predicted by soil variables and dry season rainfall. Leaf phosphorus (P) increased and leaf carbon (C) to nitrogen (N) ratio decreased with increasing soil total N:P ratio. Functional dispersion decreased with increasing soil total N:P in wet sites and with increasing manganese in dry sites, suggesting that low soil fertility and dry season moisture stress both tend to reduce functional diversity. Traits exhibited phylogenetic clustering primarily at deep nodes associated with tree versus herbaceous fern clades. Our results indicate that environmental filtering of functional traits affects ferns in a similar way to angiosperms and highlight the association of the early tree fern clade with low fertility soils.

Linking rare and abundant phoD-harboring bacteria with ecosystem multifunctionality in subtropical forests: From community diversity to environmental adaptation

Environmental factor-driven bacterial diversity could be an indicator for evaluating ecosystem multifunctionality (EMF). However, little is known about interconnections between EMF and the community diversity of rare and abundant phoD-harboring bacteria responsible for organic phosphorus mineralization. Illumina MiSeq sequencing and multiple statistical analyses were used to evaluate diversity maintenance of rare and abundant phoD-harboring bacteria at both taxonomic and phylogenetic levels and their contributions to soil EMF in the subtropical Shennongjia primeval forest. We found that rare phoD-harboring bacteria exhibited higher community diversity and broader environmental breadths than abundant ones, while abundant phoD-harboring bacteria showed closer phylogenetic clustering and stronger phylogenetic signals of ecological preferences than rare ones. Stochastic processes dominated community assemblies of rare and abundant phoD-harboring bacteria, and temperature was an important environmental variable adjusting the balance between stochastic and deterministic processes. The taxonomic α-diversity of rare phoD-harboring bacteria showed larger contribution to soil EMF than that of abundant ones, while the phylogenetic α-diversity of abundant phoD-harboring bacteria contributed significantly more than that of rare ones. Our findings enrich knowledge of the environmental adaptation of rare and abundant phoD-harboring bacteria, and highlight linkages between soil EMF and the diversity of rare and abundant phoD-harboring bacteria at both the taxonomic and phylogenetic levels.

Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines

ETHNOPHARMACOLOGICAL RELEVANCE

Malaria remains a serious and challenging disease. Traditional antimalarial medicines are largely based on plants, and ethnopharmacological research has inspired the development of antimalarial pharmaceuticals such as artemisinin. Antimalarial drug resistance is an increasing problem in Plasmodium species, and new therapeutic strategies to combat malaria are needed. Although the number of malaria cases has been decreasing in Latin America, malaria remains a significant threat in many regions. Local people in Latin America have been using numerous plant species to treat malaria, some of which have been scientifically studied, but many others have not.

AIM OF THE STUDY

Our principal objective is to harness ethnobotanical data on species used traditionally to treat malaria, combined with phylogenetic approaches, to understand how ethnobotany could help identify plant genera as potential sources of new medicines.

MATERIALS AND METHODS

Plants used to treat malaria in Latin America were compiled from published and grey literature, unpublished data, and herbarium specimens. Initial assessment of potentially important species/genera/families included compiling the number of species used within the genus, the number of use reports per genus and species, and the geographic distribution of their use. The analysis of taxonomic distribution of species reported as antimalarial in Latin America (excluding the Southern Cone) was conducted, to determine which genera and families with reputed antimalarial properties are over-represented, and phylogenetic analyses were performed to identify if there was evidence for antimalarial species being dispersed/clustered throughout the tree or at its tips. This approach enabled 'hot-nodes' in certain families to be identified, to predict new genera with potential antimalarial properties.

RESULTS

Over 1000 plant species have been used to treat malaria in Latin America, of which over 600 species were cited only once. The genera with the highest number of antimalarial species were Aspidosperma, Solanum, Piper, Croton and Aristolochia. In terms of geographic distribution, the most widely used genera were Aspidosperma, Momordica, Cinchona, Senna and Stachytarpheta. Significant phylogenetic signal was detected in the distribution of native species used for malaria, analysed in a genus-level phylogenetic framework. The eudicot and magnoliidae lineages were over-represented, while monocots were not.

CONCLUSION

Analysis of ethnobotanical use reports in a phylogenetic framework reveals the existence of hot nodes for malaria across the Latin American flora. We demonstrate how species and genera currently lacking such reports could be pinpointed as of potential interest based on their evolutionary history. Extending this approach to other regions of the world and other diseases could accelerate the discovery of novel medicines and enhance healthcare in areas where new therapeutic strategies are needed.

Lower statistical support with larger datasets: insights from the Ochrophyta radiation

It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid, and nucleus. Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the data set size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid data set provided higher statistical support for the ochrophyte radiation than the larger nucleus data set. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear data set. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of data sets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.

Dredging alleviates cyanobacterial blooms by weakening diversity maintenance of bacterioplankton community

Disentangling ecological mechanisms behind dredging is meaningful to implement environmental policy for improving water quality. However, environmental adaptation and community assembly processes of bacterioplankton in response to dredging disturbance are poorly understood. Based on Illumine MiSeq sequencing and multiple statistical analyses, we estimated interactions, functions, environmental breadths, phylogenetic signals, phylogenetic clustering, and ecological assembly processes of bacterioplankton community before and after dredging. We found distinct change in community composition, comparable decreases in diversity, functional redundancy and conflicting interaction, relatively low phylogenetic clustering, and relatively weak environmental adaptation after dredging. The bacterioplankton community assembly was affected by both stochastic and deterministic processes before dredging, but dominated by stochasticity after dredging. Sediment total phosphorus was a decisive factor in balancing determinism and stochasticity for bacterioplankton community assembly before and after dredging. Consequently, taxonomic and phylogenetic α-diversities of bacterioplankton exhibited higher contributions to the water trophic level represented by chlorophyl α before dredging than afterwards. Our results emphasized bacterioplankton in response to environmental changes caused by dredging, with nutrient loss and ecological drift playing important roles. These findings extend knowledge of contribution of bacterioplankton diversity to water trophic level and decipher mechanisms of bacterioplankton diversity maintenance in response to dredging, which is useful for guiding mitigation of cyanobacterial blooms.

Variation of foliar silicon concentrations in temperate forbs: effects of soil silicon, phylogeny and habitat

Silicon (Si) accumulation is known to alleviate various biotic and abiotic stressors in plants with potential ecological consequences. However, for dicotyledonous plants our understanding of Si variation remains limited. We conducted a comparative experimental study to investigate (1) interspecific variation of foliar Si concentrations across 37 dicotyledonous forbs of temperate grasslands, (2) intraspecific variation in foliar Si concentration in response to soil Si availability, the influence of (3) phylogenetic relatedness, and (4) habitat association to moisture. Foliar Si differed markedly (approx. 70-fold) across the investigated forbs, with some species exhibiting Si accumulation similar to grasses. Foliar Si increased with soil Si availability, but the response varied across species: species with higher Si accumulation capacity showed a stronger response, indicating that they did not actively upregulate Si uptake under low soil Si availability. Foliar Si showed a pronounced phylogenetic signal, i.e., closely related species exhibited more similar foliar Si concentrations than distantly related species. Significant differences in foliar Si concentration within closely related species pairs nevertheless support that active Si uptake and associated high Si concentrations has evolved multiple times in forbs. Foliar Si was not higher in species associated with drier habitats, implying that in dicotyledonous forbs of temperate grasslands high foliar Si is not an adaptive trait to withstand drought. Our results demonstrated considerable inter- and intraspecific variation in foliar Si concentration in temperate forbs. This variation should have pervasive, but so far understudied, ecological consequences for community composition and functioning of temperate grasslands under land-use and climate change.

Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers

Feathers are the habitat of a myriad of organisms, from fungi and bacteria to lice and mites. Although most studies focus on specific taxa and their interaction with the bird host, anecdotal data glimpse feathers as holders of a system with its own ecology, what we call here the stylosphere. A major gap in our knowledge of the stylosphere is the ecology of the total abundance of microorganisms, being also rare to find studies that analyze abundance of more than one group of microorganisms at the bird interspecific level. Here, we quantified bacterial and fungi abundances through qPCR on the wing feathers of 144 birds from 24 passerine and one non-passerine bird species from three localities in Southern Spain. Bacteria and fungi abundances spanned three orders of magnitude among individual birds, but were consistent when comparing the right and the left wing feathers of individuals. Sampling locality explained ca. 14% of the variation in both bacteria and fungi abundances. Even when statistically controlling for sampling locality, microbial abundances consistently differed between birds from different species, but these differences were not explained by bird phylogeny. Finally, bird individuals and species having more bacteria also tended to held larger abundances of fungi. Our results suggest a quite complex explanation for stylosphere microorganisms' abundance, being shaped by bird individual and species traits, as well as environmental factors, and likely bacteria-fungi interactions.

Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters

Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

BACKGROUND

Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many studies have empirically tested and established methodology for resolving robust phylogenies, including selecting appropriate evolutionary models, identifying orthologs, or isolating partitions with strong phylogenetic signal. However, few have investigated errors that may be initiated at earlier stages of the analysis. Biases introduced during the generation of the phylogenomic dataset itself could produce downstream effects on analyses of evolutionary history. Transcriptomes are widely used in phylogenomics studies, though there is little understanding of how a poor-quality assembly of these datasets could impact the accuracy of phylogenomic hypotheses. Here we examined how transcriptome assembly quality affects phylogenomic inferences by creating independent datasets from the same input data representing high-quality and low-quality transcriptome assembly outcomes.

RESULTS

By studying the performance of phylogenomic datasets derived from alternative high- and low-quality assembly inputs in a controlled experiment, we show that high-quality transcriptomes produce richer phylogenomic datasets with a greater number of unique partitions than low-quality assemblies. High-quality assemblies also give rise to partitions that have lower alignment ambiguity and less compositional bias. In addition, high-quality partitions hold stronger phylogenetic signal than their low-quality transcriptome assembly counterparts in both concatenation- and coalescent-based analyses.

CONCLUSIONS

Our findings demonstrate the importance of transcriptome assembly quality in phylogenomic analyses and suggest that a portion of the uncertainty observed in such studies could be alleviated at the assembly stage.

Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data

Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result in incongruent topologies, but the causes of this conflict can be difficult to characterize. We examined incongruence stemming from conflict between likelihood-based signal (quantified by the difference in gene-wise log likelihood score or ΔGLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or ΔGQS) for every gene in three phylogenomic studies in animals, fungi, and plants, which were chosen because their concatenation-based IQ-TREE (T1) and quartet-based ASTRAL (T2) phylogenies are known to produce eight conflicting internal branches (bipartitions). By comparing the types of phylogenetic signal for all genes in these three data matrices, we found that 30% - 36% of genes in each data matrix are inconsistent, that is, each of these genes has higher log likelihood score for T1 versus T2 (i.e., ΔGLS >0) whereas its T1 topology has lower quartet score than its T2 topology (i.e., ΔGQS <0) or vice versa. Comparison of inconsistent and consistent genes using a variety of metrics (e.g., evolutionary rate, gene tree topology, distribution of branch lengths, hidden paralogy, and gene tree discordance) showed that inconsistent genes are more likely to recover neither T1 nor T2 and have higher levels of gene tree discordance than consistent genes. Simulation analyses demonstrate that removal of inconsistent genes from datasets with low levels of incomplete lineage sorting (ILS) and low and medium levels of gene tree estimation error (GTEE) reduced incongruence and increased accuracy. In contrast, removal of inconsistent genes from datasets with medium and high ILS levels and high GTEE levels eliminated or extensively reduced incongruence, but the resulting congruent species phylogenies were not always topologically identical to the true species trees.

Stronger environmental adaptation of rare rather than abundant bacterioplankton in response to dredging in eutrophic Lake Nanhu (Wuhan, China)

Deciphering responses of rare versus abundant bacterioplankton to environmental change, crucial for understanding and mitigating of cyanobacterial blooms, is an important but poorly investigated subject. Using MiSeq sequencing, we investigated the taxonomic and phylogenetic diversity of rare and abundant bacterioplankton in eutrophic Lake Nanhu before and after dredging. We estimated environmental breadths and phylogenetic signals of ecological preferences of rare and abundant bacterioplankton, and investigated community function and bacterioplankton assembly processes. Both taxonomic and phylogenic distances of rare and abundant bacterioplankton communities were significantly positively correlated with the dissimilarity of environmental factors. Threshold indicator taxa analysis and Blomberg's K statistic indicated that rare taxa held broader environmental thresholds and stronger phylogenetic signals for ecological traits than abundant taxa. Environmental adaptations of both rare and abundant taxa exhibited distinct changes after dredging. Higher functional redundancy occurred in the abundant compared to the rare bacterioplankton, with functions of rare bacterioplankton decreasing and for the abundant ones increasing after dredging. The null model revealed that dispersal limitation belonging to stochastic processes determined the abundant bacterioplankton community assembly, whereas variable selection belonging to deterministic processes drove the rare one. Rare bacterioplankton was more environmentally constrained than the abundant one. Dissolved oxygen was the decisive factor in determining the balance between stochasticity and determinism in both rare and abundant bacterioplankton. Our study extends our knowledge of environmental adaptation of rare versus abundant bacterioplankton to massive disturbing measures, i.e. dredging, and allows to estimate dredging performance for mitigating cyanobacterial blooms from a molecular ecology viewpoint.

A molecular phylogeny of Geotrochus and Trochomorpha species (Gastropoda: Trochomorphidae) in Sabah, Malaysia reveals convergent evolution of shell morphology driven by environmental influences

There are currently eleven Geotrochus and four Trochomorpha species in Sabah. The primary diagnostic character that separates the two genera is the intensity of sculpture on the shell upper surface. All Trochomorpha species have a coarse nodular sculpture while Geotrochus species has a non-nodular sculpture or smooth shell. However, it is known that shell characters are often evolutionary labile with high plasticity in response to environmental factors. Hence, identifying the phylogenetic and ecological determinants for the shell characters will shed light on the shell-based taxonomy. This study aims to estimate the phylogenetic relationship between Geotrochus and Trochomorpha species in Sabah based in two mitochondrial genes (COI, 16S) and one nuclear gene (ITS) and also to examine the influence of temperature, elevation and annual precipitation on the coarseness of shell upper surface sculpture and shell sizes of the species of both genera. Additionally, we also investigated the phylogenetic signal of the shell characters. The phylogenetic analysis showed that Geotrochus and Trochomorpha species are not reciprocally monophyletic. The phylogenetic signal test suggested that shell size and upper surface sculpture are homoplastic, and these shell traits are strongly influenced by elevation and annual precipitation, particularly at the cloud zone of Mount Kinabalu. The highland species of both genera have a coarser shell surface than lowland species. The shell and aperture width decrease with increasing elevation and annual precipitation. In the view of finding above, the current taxonomy of Geotrochus and Trochmorpha in this region and elsewhere that based on shell characters need to be revised with sufficient specimens throughout the distribution range of the two genera.

Timber and non-timber forest products in the northernmost Neotropical rainforest: Ecological factors unravel their landscape distribution

The benefits provided by tropical rainforests are unevenly distributed throughout the landscape and are shaped by abiotic and biotic components that influence the spatial distribution and functional traits of the species involved. We tested whether environmental stratification of the rainforest in biophysical Landscape Units (LU), defined by topography and soil, is related to the spatial distribution of diversity, abundance and productivity (standing biomass) of tree assemblages that provide potential forest products (PFP). Considering that different PFP are associated with specific plant traits, we also tested whether a phylogenetic signal exists among the species that comprise specific use categories. Non-metric multidimensional scaling ordinations and permutational analysis of variance were based on the frequency, abundance and productivity of 129 species, the PFP of which were classified as fodder, food, fuelwood, medicinal, melliferous, ornamental, plywood and timber in 15 plots of 0.5 ha each. We constructed a phylogenetic tree of the studied species and analyzed the phylogenetic signal strength (D-statistic) among them. The spatial distribution of diversity and abundance of useful species changes among the LU. Specific PFP can be provided in contrasting habitat conditions, but generally not by the same species. The PFP categories that presented a phylogenetic signal were associated with wood characteristics (fuelwood and plywood) and the palatability of the leaves and reproductive structures (fodder). The Moraceae family was significantly related to fodder and plywood, whereas Meliaceae, Myrtaceae and Sapotaceae were mostly used for fuelwood. The medicinal species presented convergent traits distributed throughout the phylogeny. However, since our study included a broad variety of plant structures, it is possible that phylogenetic dispersion can change if we consider the specific uses within each category. Our findings show that the assemblages of PFP suppliers can be clustered through biophysical units based on soil and topography, and specific categories of PFP are often supplied by phylogenetically related species. This knowledge is fundamental in order to incorporate the high diversity of tree species and their potential uses into productive reforestation and agroforestry programs.

Phylogenetic signal in floral temperature patterns

OBJECTIVES

Floral structures may be warmer than their environment, and can show thermal patterning, where individual floral structures show different temperatures across their surface. Pollinators can differentiate between artificial flowers that mimic both naturally warmed and thermally patterned ones, but it has yet to be demonstrated that these patterns are biologically meaningful. To explore the relationship between pollinators and temperature patterning, we need to know whether there is diversity in patterning, and that these patterns are not simply a by-product of floral architecture constrained by ancestry. We analysed a dataset of 97 species to explore whether intrafloral temperature differences were correlated within clades (phylogenetic signal), or whether the variation seen was diverse enough to suggest that floral temperature patterns are influenced by the abiotic or pollinator-related niches to which plant species are adapted.

RESULTS

Some phylogenetic signal was observed, with both the Asteraceae and species of Pelargonium being more similar than expected by chance, but with other species surveyed not showing signal. The Asteraceae tend to have large temperature differences across the floral surface, which may be due to floral architecture constraints within the family. Other families show no correlation, suggesting that patterning is influenced by pollinators and the environment.

Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria

The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).

The evolution of fruit scent: phylogenetic and developmental constraints

BACKGROUND

Fruit scent is increasingly recognized as an evolved signal whose function is to attract animal seed dispersers and facilitate plant reproduction. However, like all traits, fruit scent is likely to evolve in response to conflicting selective pressures and various constraints. Two major constraints are (i) phylogenetic constraints, in which traits are inherited from ancestors rather than adapted to current conditions and (ii) developmental constraints, if phenotypes are limited by the expression of other traits within the individual. We tested whether phylogenetic constraints play a role in fruit scent evolution by calculating the phylogenetic signal in ripe fruits of 98 species from three study sites. We then estimated the importance of developmental constraints by examining whether ripe fruits tend to emit compounds that are chemically similar to, and share biosynthetic pathways with, compounds emitted by conspecific unripe fruits from which they develop.

RESULTS

We show that closely related taxa are not more similar to each other than to very distinct taxa, thus indicating that fruit scent shows little phylogenetic signal. At the same time, although ripe and unripe fruits of the same species tend to emit different chemicals, they tend to employ chemicals originating from similar biosynthetic pathways, thus indicating that some developmental constraints determine ripe fruit scent.

CONCLUSIONS

Our results highlight the complex landscape in which fruit scent has evolved. On one hand, fruit scent evolution is not limited by common ancestry. On the other hand, the range of chemicals that can be employed in ripe fruits is probably constrained by the needs of unripe fruits.

Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Background

Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict.

Results

We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node.

Conclusions

Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

BACKGROUND

The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems 'Normal' (N), 'Higher Welfare' (HW) and 'Omega-3 Higher Welfare' (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence.

RESULTS

Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain.

CONCLUSIONS

Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain. Video Abstract.

Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)

The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.

Phylogenetic signals in pest abundance and distribution range of spider mites

Background

Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide.

Results

We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny.

Conclusions

The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable – including the number of known hosts and phylogenetic position of the mites – could therefore be useful in predicting future pest risk of species.

Leaf vascular architecture in temperate dicotyledons: correlations and link to functional traits

Using 227 dicotyledonous species in temperate region, we found the relationships among densities of different-order veins, creating diversity of leaf vascular architectures. Dicotyledonous angiosperms commonly possess a hierarchical leaf vascular system, wherein veins of different orders have different functions. Minor vein spacing determines leaf hydraulic efficiency, whereas the major veins provide mechanical support. However, there is limited information on the coordination between these vein orders across species, limiting our understanding of how diversity in vein architecture is arrayed. We aimed to examine the (1) relationships between vein densities at two spatial scales (lower- vs. higher-order veins and among minor veins) and (2) relationships of vein densities with plant functional traits. We studied ten traits related to vein densities and three functional traits (leaf dry mass per area [LMA], leaf longevity [LL], and adult plant height [H_adult]) for 227 phylogenetically diverse plant species that occur in temperate regions and examined the vein-vein and vein-functional traits relationships across species. The densities of lower- and higher-order veins were positively correlated across species. The minor vein density was positively correlated with the densities of both areoles and free-ending veins, and vascular networks with higher minor vein density tended to have a lower ratio of free-ending veins to areoles across species. Neither densities of lower- nor higher-order veins were related to LMA and LL. On the other hand, the densities of veins and areoles tended to be positively correlated with H_adult. These results suggest that densities of different-order veins are developmentally coordinated across dicotyledonous angiosperms and form the independent axis in resource use strategies based on the leaf economics spectrum.

The use of wing shape for characterising macroevolution in mosquitoes (Diptera: Culicidae)

The wing form of culicid mosquitoes shows considerable variation among groups: this phenomenon has been addressed by several studies through space-time analyses in mosquito populations, species, and genera. The observed variation results from a combination of two distinct factors: heredity and phenotypic plasticity. The first is usually related to wing shape, a complex character that may serve as a taxonomic marker in specific cases. We hypothesized that wing shape might be phylogenetically meaningful in Culicidae. In this study, we applied a geometric morphometrical approach based on 18 landmarks in 81 species of mosquitoes, representing 19 different genera, to investigate whether wing shape can help retrieve macroevolutionary patterns or identify any phylogenetic signals. We observed that wing shape differed considerably among groups, especially between Anophelinae and Culicinae subfamilies; thus, some wing shape elements may be synapomorphic. Comparisons among wing consensus after Procrustes superimposition revealed that landmark #1, located between the veins RS and R1, was the most variable. Sabethini tribe was distinguished from other taxa owing to a strong phylogenetic signal of its wings, whereas other culicids presented weaker signals and were not that distinguishable. Evolutionary forces such as natural selection, evolutionary limitation/constraint, or canalization mechanisms might drive the evolution of wing phenotype. These findings suggest that the wing undergoes evolution over long periods, but is not neutral enough to reconstruct the phylogenetic history of these insects. Gene-based studies should be performed to understand the driving forces in wing evolution.

Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree's terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.

Genome assembly and phylogenomic data analyses using plastid data: Contrasting species tree estimation methods

Phylogenomics has become increasingly popular in recent years mostly due to the increased affordability of next generation sequencing techniques. Phylogenomics has sparked interest in multiple fields of research, including systematics, ecology, epidemiology, and even personalized medicine, agriculture and pharmacy. Despite this trend, it is usually difficult to learn and understand how the analyses were done, how the results were obtained, and most importantly, how to replicate the study. Here we present the data and all of the code utilized to perform phylogenomic inferences using plastome data: from raw data to extensive phylogenetic inference and accuracy assessment. The data presented here utilizes plastome sequences available on GenBank (accession numbers of 94 species are available below) and the code is also available at https://github.com/deisejpg/rosids. Gonçalves et al. is the research article associated with the data analyses presented here.

Evolution of phytochemical diversity in Pilocarpus (Rutaceae)

The evolution of phytochemical diversity and biosynthetic pathways in plants can be evaluated from a phylogenetic and environmental perspective. Pilocarpus Vahl (Rutaceae), an economically important medicinal plant in the family Rutaceae, has a great diversity of imidazole alkaloids and coumarins. In this study, we used phylogenetic comparative methods to determine whether there is a phylogenetic signal for chemical traits across the genus Pilocarpus; this included ancestral reconstructions of continuous and discrete chemical traits. Bioclimatic variables found to be associated with the distribution of this genus were used to perform OLS regressions between chemical traits and bioclimatic variables. Next, these regression models were evaluated to test whether bioclimatic traits could significantly predict compound concentrations. Our study found that in terms of compound concentration, variation is most significantly associated with adaptive environmental convergence rather than phylogenetic relationships. The best predictive model of chemical traits was the OLS regression that modeled the relationship between coumarin and precipitation in the coldest quarter. However, we also found one chemical trait was dependent on phylogenetic history and bioclimatic factors. These findings emphasize that consideration of both environmental and phylogenetic factors is essential to tease out the intricate processes in the evolution of chemical diversity in plants. These methods can benefit fields such as conservation management, ecology, and evolutionary biology.

Drivers of sociality in Gobiodon fishes: An assessment of phylogeny, ecology and life-history

What drives the evolution of sociality in animals? Many robust studies in terrestrial organisms have pointed toward various kinship-based, ecological and life-history traits or phylogenetic constraint which have played a role in the evolution of sociality. These traits are not mutually exclusive and the exact combination of traits is likely taxon-specific. Phylogenetic comparative analyses have been instrumental in identifying social lineages and comparing various traits with non-social lineages to give broad evolutionary perspectives on the development of sociality. Few studies have attempted this approach in marine vertebrate systems. Social marine fishes are particularly interesting because many have a pelagic larval phase and non-conventional life-history strategies (e.g. bi-directional sex-change) not often observed in terrestrial animals. Such strategies provide novel insights into terrestrially-derived theories of social evolution. Here, we assess the strength of the phylogenetic signal of sociality in the Gobiodon genus with Pagel's lambda and Blomberg's K parameters. We found some evidence of a phylogenetic signal of sociality, but factors other than phylogenetic constraint also have a strong influence on the extant social state of each species. We then use phylogenetic generalized least squares analyses to examine several ecological and life-history traits that may have influenced the evolution of sociality in the genus. We found an interaction of habitat size and fish length was the strongest predictor of sociality. Sociality in larger species was more dependent on coral size than in smaller species, but smaller species were more social overall, regardless of coral size. Finally, we comment on findings regarding the validity of the species G. spilophthalmus which arose during the course of our research. These findings in a group of marine fishes add a unique perspective on the evolution of sociality to the excellent terrestrial work conducted in this field.

The synergistic effect of concatenation in phylogenomics: the case in Pantoea

With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.

Looking beyond the flowers: associations of stingless bees with sap-sucking insects

The main sources of food for stingless bees are the nectar and pollen harvested from flowers, whereas one important kind of nesting material (i.e. wax) is produced by their own abdominal glands. Stingless bees can, nonetheless, obtain alternative resources of food and wax from exudates released by sap-sucking insects as honeydew and waxy cover, respectively. To date, there are no comprehensive studies investigating how diversified and structured the network interactions between stingless bees and sap-sucking insects are. Here, we conducted a survey of the data on relationship between stingless bees and sap-sucking insects to evaluate: (1) which resources are collected by which stingless bee species; (2) how diverse the interaction network is, using species degree and specialisation index as a proxy; and if (3) there would be any phylogenetic signal in the species degree and specialisation indices. Our findings demonstrate that approximately 21 stingless bee species like Trigona spp. and Oxytrigona spp. have been observed interacting with 11 sap-sucking species, among which Aethalion reticulatum is the main partner. From ca. 50 records, Brazil is the country with most observations (n = 38) of this type of ecological interaction. We found also that stingless bees harvest fivefold more honeydew than waxy covers on sap-sucking insects. However, we did not find any phylogenetic signal for the occurrence of this interaction, considering species degree and specialisation indices, suggesting that both traits apparently evolved independently among stingless bee species. We suggest that specific ecological demands may drive this opportunistic behaviour exhibited by stingless bees, because major sources of food are obtained from flowers and these bees produce their own wax.

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)

Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes 'Ursidae' and 'Ursinae-Tremarctinae'. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.

Comparative reproductive dormancy differentiation in European black scavenger flies (Diptera: Sepsidae)

Seasonality is a key environmental factor that regularly promotes life history adaptation. Insects invading cold-temperate climates need to overwinter in a dormant state. We compared the role of temperature and photoperiod in dormancy induction in the laboratory, as well as winter survival and reproduction in the field and the laboratory, of 5 widespread European dung fly species (Diptera: Sepsidae) to investigate their extent of ecological differentiation and thermal adaptation. Unexpectedly, cold temperature is the primary environmental factor inducing winter dormancy, with short photoperiod playing an additional role mainly in species common at high altitudes and latitudes (Sepsis cynipsea, neocynipsea, fulgens), but not in those species also thriving in southern Europe (thoracica, punctum). All species hibernate as adults rather than juveniles. S. thoracica had very low adult winter survivorship under both (benign) laboratory and (harsh) field conditions, suggesting flexible quiescence rather than genetically fixed winter diapause, restricting their distribution towards the pole. All other species appear well suited for surviving cold, Nordic winters. Females born early in the season reproduce before winter while late-born females reproduce after winter, fulgens transitioning earliest before winter and thoracica and punctum latest; a bet-hedging strategy of reproduction during both seasons occurs rarely but is possible physiologically. Fertility patterns indicate that females can store sperm over winter. Winter dormancy induction mechanisms of European sepsids are congruent with their geographic distribution, co-defining their thermal niches. Flexible adult winter quiescence appears the easiest route for insects spreading towards the poles to evolve the necessary overwinter survival.

Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae)

The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel’s delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.

Comparative effects of the parasiticide ivermectin on survival and reproduction of adult sepsid flies

Ivermectin is a veterinary pharmaceutical widely applied against parasites of livestock. Being effective against pests, it is also known to have lethal and sublethal effects on non-target organisms. While considerable research demonstrates the impact of ivermectin residues in livestock dung on the development and survival of dung feeding insect larvae, surprisingly little is known about its fitness effects on adults. We tested the impact of ivermectin on the survival of adult sepsid dung fly species (Diptera: Sepsidae) in the laboratory, using an ecologically relevant and realistic range of 69-1978 µg ivermectin/kg wet dung, and compared the sensitivities of larvae and adults in a phylogenetic framework. For one representative, relatively insensitive species, Sepsis punctum, we further investigated effects of ivermectin on female fecundity and male fertility. Moreover, we tested whether females can differentiate between ivermectin-spiked and non-contaminated dung in the wild. Adult sepsid flies exposed to ivermectin suffered increased mortality, whereby closely related species varied strongly in their sensitivity. Adult susceptibility to the drug correlated with larval susceptibility, showing a phylogenetic signal and demonstrating systemic variation in ivermectin sensitivity. Exposure of S. punctum females to even low concentrations of ivermectin lowered the number of eggs laid, while treatment of males reduced egg-to-adult offspring survival, presumably via impairment of sperm quality or quantity. The fitness impact was amplified when both parents were exposed. Lastly, sepsid flies did not discriminate against ivermectin-spiked dung in the field. Treatment of livestock with avermectins may thus have even more far-reaching sublethal ecological consequences than currently assumed via effects on adult dung-feeding insects.

Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)

BACKGROUND

Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood.

RESULTS

Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period.

CONCLUSIONS

Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements

Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

BACKGROUND

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.

RESULTS

Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.

CONCLUSIONS

These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades

Parasites can vary in the number of host species they infect, a trait known as "host specificity". Here we quantify phylogenetic signal-the tendency for closely related species to resemble each other more than distantly related species-in host specificity of avian haemosporidian parasites (genera Plasmodium, Haemoproteus and Leucocytozoon) using data from MalAvi, the global avian haemosporidian database. We used the genetic data (479 base pairs of cytochrome b) that define parasite lineages to produce genus level phylogenies. Combining host specificity data with those phylogenies revealed significant levels of phylogenetic signal while controlling for sampling effects; phylogenetic signal was higher when the phylogenetic diversity of hosts was taken into account. We then tested for correlations in the host specificity of pairs of sister lineages. Correlations were generally close to zero for all three parasite genera. These results suggest that while the host specificity of parasite sister lineages differ, larger clades may be relatively specialised or generalised.

Leaf stable isotopes suggest shared ancestry is an important driver of functional diversity

Plant physiological strategies of carbon (C) and nitrogen (N) uptake and metabolism are often regarded as outcomes of environmental selection. This is likely true, but the role of evolutionary history may also be important in shaping patterns of functional diversity. Here, we used leaf C and N stable isotope ratios (δ¹³C, δ¹⁵N) as integrators of physiological processes to assess the relative roles of phylogenetic history and environment in a diverse group of Ericaceae species native to North America. We found strong phylogenetic signal in both leaf δ¹³C and δ¹⁵N, suggesting that close relatives have similar physiological strategies. The signal of phylogeny was generally stronger than that of the local environment. However, within some specialized environments (e.g., wetlands, sandy soils), we found environmental effects and/or niche conservatism. Phylogenetic signal in δ¹³C appears to be most closely related to the constraints on metabolic demand and supply of C, and δ¹⁵N appears to be most strongly related to mycorrhizal associations within the family.

Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny

Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.