Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27–73%), and combined effects of seed traits and phylogeny of hardwood trees (5–55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 “global” axes of traits that were phylogenetically autocorrelated at the family and genus level and a third “local” axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30–76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.     

Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension

Genome-wide association studies (GWASs) have identified many genetic variants underlying complex traits. Many detected genetic loci harbor variants that associate with multiple—even distinct—traits. Most current analysis approaches focus on single traits, even though the final results from multiple traits are evaluated together. Such approaches miss the opportunity to systemically integrate the phenome-wide data available for genetic association analysis. In this study, we propose a general approach that can integrate association evidence from summary statistics of multiple traits, either correlated, independent, continuous, or binary traits, which might come from the same or different studies. We allow for trait heterogeneity effects. Population structure and cryptic relatedness can also be controlled. Our simulations suggest that the proposed method has improved statistical power over single-trait analysis in most of the cases we studied. We applied our method to the Continental Origins and Genetic Epidemiology Network (COGENT) African ancestry samples for three blood pressure traits and identified four loci (CHIC2, HOXA-EVX1, IGFBP1/IGFBP3, and CDH17; p < 5.0 × 10⁻⁸) associated with hypertension-related traits that were missed by a single-trait analysis in the original report. Six additional loci with suggestive association evidence (p < 5.0 × 10⁻⁷) were also observed, including CACNA1D and WNT3. Our study strongly suggests that analyzing multiple phenotypes can improve statistical power and that such analysis can be executed with the summary statistics from GWASs. Our method also provides a way to study a cross phenotype (CP) association by using summary statistics from GWASs of multiple phenotypes.     

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004–0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04–98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.     

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertilization. The responses of leaf litter bacteria and fungi to these simulated changes were significantly phylogenetically conserved. Proportional changes in abundance were highly correlated among related organisms, such that relatives with approximately 5% ribosomal DNA genetic distance showed similar responses to the treatments. A microbe''s change in relative abundance was significantly correlated between the treatments, suggesting a compromise between numerical abundance in undisturbed environments and resistance to change in general, independent of disturbance type. Lineages in which at least 90% of the microbes shared the same response were circumscribed at a modest phylogenetic depth (τ_D 0.014–0.021), but significantly larger than randomized simulations predict. In several clades, phylogenetic depth of trait consensus was higher. Fungal response to drought was more conserved than was response to nitrogen fertilization, whereas bacteria responded equally to both treatments. Finally, we show that a bacterium''s response to the manipulations is correlated with its potential functional traits (measured here as the number of glycoside hydrolase genes encoding the capacity to degrade different types of carbohydrates). Together, these results suggest that a phylogenetic, trait-based framework may be useful for predicting shifts in microbial composition and functioning in the face of global change.     

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Community assembly processes is the primary focus of community ecology. Using phylogenetic‐based and functional trait‐based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits’ variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis. Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle‐ and low‐altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large‐scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.     

Trophic convergence drives morphological convergence in marine tetrapods

Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these patterns onto phylogeny reveals coordinated evolutionary shifts in diet and morphology in different marine tetrapod lineages. Similarities in morphology between species with similar diets—even across large phylogenetic distances—are consistent with previous hypotheses that shared functional constraints drive convergent evolution in marine tetrapods.     

Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress tolerance,bamboo presence,and facilitation

AimsAmidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity, and biotic processes shaping these plant communities are largely unstudied. We characterized the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime''s CSR (C—competitor, S—stress‐tolerant, R—ruderal) scheme, what functional trade‐offs they exhibit, and how traits and functional diversity vary in response to bamboo presence/absence.MethodsTo characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e., isolated woody plants in the grasslands community). Then, we used Mann–Whitney test, t test, and variation partitioning to determine the effects of inside versus outside tree island and bamboo presence on community‐weighted means, woody species diversity, and functional diversity.ResultsWe found a general SC/S strategy with drought‐related functional trade‐offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density, and foliar water uptake were unrelated to CSR strategies, suggesting independent trait dimensions and multiple drought‐coping strategies within the predominant S strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake, and greater leaf thickness than in tree islands without bamboo.ConclusionsThe observed functional assembly hints toward large‐scale environmental abiotic filtering shaping a stress‐tolerant community strategy, and small‐scale biotic interactions driving small‐scale trait variation. We recommend experimental studies with fire, facilitation treatments, ecophysiological and recruitment traits to elucidate on future tree island expansion and community response to climate change.     

Explaining the distribution of breeding and dispersal syndromes in conifers

The evolution of plants exhibiting different sexes, or dioecy, is correlated with a number of ecological and life-history traits such as woody growth form and animal-dispersed seeds, but the underlying causes of these associations are unclear. Previous work in seed plants has suggested that the evolution of fleshy cones or seeds may favour dioecy. In this study, we use a well-sampled molecular phylogeny of conifers to show that although dioecy and fleshiness strongly co-occur at the species level, this relationship has not resulted from numerous separate origins of this trait combination or from differential rates of diversification. Instead, we suggest that two character combinations—the ancestral dry-monoecious condition and the derived fleshy-dioecious condition—have persisted in conifers longer than other combinations over evolutionary time. The persistence of these trait combinations appears to reflect differences in the rate of successful transition into and out of these character states over time, as well as the geographical restriction of species with rare combinations and their consequent vulnerability to extinction. In general, we argue that such persistence explanations should be considered alongside ‘key innovation’ hypotheses in explaining the phylogenetic distribution of traits.     

Evolutionary Sparse Learning for Phylogenomics

We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci—such as genes, proteins, genomic segments, and positions—as parameters. Using the Least Absolute Shrinkage and Selection Operator, ESL selects only the most important genomic loci to explain a given phylogenetic hypothesis or presence/absence of a trait. ESL models do not directly involve conventional parameters such as rates of substitutions between nucleotides, rate variation among positions, and phylogeny branch lengths. Instead, ESL directly employs the concordance of variation across sequences in an alignment with the evolutionary hypothesis of interest. ESL provides a natural way to combine different molecular and nonmolecular data types and incorporate biological and functional annotations of genomic loci in model building. We propose positional, gene, function, and hypothesis sparsity scores, illustrate their use through an example, and suggest several applications of ESL. The ESL framework has the potential to drive the development of a new class of computational methods that will complement traditional approaches in evolutionary genomics, particularly for identifying influential loci and sequences given a phylogeny and building models to test hypotheses. ESL’s fast computational times and small memory footprint will also help democratize big data analytics and improve scientific rigor in phylogenomics.     

The roles of environment,space, and phylogeny in determining functional dispersion of rodents (Rodentia) in the Hengduan Mountains,China

The recently described trait‐based approach is becoming widely popular for a mechanistic understanding of species coexistence. However, the greatest challenge in functional analyses is decomposing the contributions of different ecological and evolutionary processes (e.g., niche‐based process, neutral process, and evolutionary process) in determining trait structure. Taking rodents (Rodentia) in the Hengduan Mountains as our study model, we aim to (1) quantify the vertical patterns of functional structure for head–body length (HL), tail/body ratio (TR), animal component in diet (ACD), and all traits; (2) disentangle the relative importance of different assembly processes (environment, space, and phylogeny) in structuring trait dispersion; and (3) assess the feasibility of Bergmann's rule and Allen's rule along elevational gradient. Our results have suggested that the vertical functional structure pattern varied across these three traits, indicating distinct functional roles in the community assembly process. These nonrandom vertical patterns of HL, TR, and terminal ACD have demonstrated these traits were dominated by different ecological process along environmental gradient. In variance partitioning, high proportion of the spatial variations in trait dispersion was explained by environmental and spatial models, which have provided supporting strong evidence for niche‐based and neutral processes in leading species coexistence. Although the three traits all exhibited apparent phylogenetic signals, phylogenetic relationship within community failed to predict the spatial variations of functional dispersion, confirming the enormous inference of phylogenetic signals in predicting trait structure. By assessing the vertical patterns of HL and TR at order and family levels, we argued that functional adaptation along an environmental gradient is a surrogate of series of complex processes (e.g., environmental filtering, interspecific interaction, and neutral dispersal) acting on multiple functional axes, which results in inconsistence with the empirical rules along elevational gradient.     

Is It Easy to Be Urban? Convergent Success in Urban Habitats among Lineages of a Widespread Native Ant

The most rapidly expanding habitat globally is the urban habitat, yet the origin and life histories of the populations of native species that inhabit this habitat remain poorly understood. We use DNA barcoding of the COI gene in the widespread native pest ant Tapinoma sessile to test two hypotheses regarding the origin of urban populations and traits associated with their success. First, we determine if urban samples of T. sessile have a single origin from natural populations by looking at patterns of haplotype clustering from across their range. Second, we examine whether polygynous colony structure – a trait associated with invasion success – is correlated with urban environments, by studying the lineage dependence of colony structure. Our phylogenetic analysis of 49 samples identified four well supported geographic clades. Within clades, Kimura-2 parameter pairwise genetic distances revealed <2.3% variation; however, between clade genetic distances were 7.5–10.0%, suggesting the possibility of the presence of cryptic species. Our results indicate that T. sessile has successfully colonized urban environments multiple times. Additionally, polygynous colony structure is a highly plastic trait across habitat, clade, and haplotype. In short, T. sessile has colonized urban habitats repeatedly and appears to do so using life history strategies already present in more natural populations. Whether similar results hold for other species found in urban habitats has scarcely begun to be considered.     

Morphometric traits capture the climatically driven species turnover of 10 spruce taxa across China

This study explored the relative roles of climate and phylogenetic background in driving morphometric trait variation in 10 spruce taxa in China. The study further addressed the hypothesis that these variations are consistent with species turnover on climatic gradients. Nine morphometric traits of leaves, seed cones, and seeds for the 10 studied spruce taxa were measured at 504 sites. These data were analyzed in combination with species DNA sequences from NCBI GenBank. We detected the effects of phylogeny and climate through trait‐variation‐based K statistics and phylogenetic eigenvector regression (PVR) analyses. Multivariate analyses were performed to detect trait variation along climatic gradients with species replacement. The estimated K‐values for the nine studied morphometric traits ranged from 0.19 to 0.68, and the studied environmental variables explained 39–83% of the total trait variation. Trait variation tended to be determined largely by a temperature gradient varying from wet‐cool climates to dry‐warm summers and, additionally, by a moisture gradient. As the climate became wetter and cooler, spruce species tended to be replaced by other spruces with smaller needle leaves and seeds but larger cones and seed scales. A regression analysis showed that spruce species tended to be successively replaced by other species, along the gradient, although the trends observed within species were not necessarily consistent with the overall trend. The climatically driven replacement of the spruces in question could be well indicated by the between‐species variation in morphometric traits that carry lower phylogenetic signal. Between‐species variation in these traits is driven primarily by climatic factors. These species demonstrate a narrower ecological amplitude in temperature but wider ranges on the moisture gradient.     

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.     

Effect of environmental and spatial factors on the phylogenetic and functional diversity of the Mediterranean tree communities of Europe

• The tree flora of the Mediterranean Basin contains an outstanding taxonomic richness and a high proportion of endemic taxa. Contrary to other regions of the Mediterranean biome, a comprehensive phylogenetic analysis of the relationship between phylogenetic diversity, trait diversity and environmental factors in a spatial ecological context is lacking.
• We inferred the first calibrated phylogeny of 203 native tree species occurring in the European Mediterranean Basin based on 12 DNA regions. Using a set of four functional traits, we computed phylogenetic diversity for all 10,042 grid cells of 10 × 10 km spatial resolution to completely cover Mediterranean Europe. Then, we tested the spatial influence of environmental factors on tree diversity.
• Our results suggest that the nature of the relationship between traits and phylogeny varies among the different studied traits and according to the evolutionary distance considered. Phylogenetic diversity and functional diversity of European Mediterranean trees correlated strongly with species richness. High values of these diversity indices were located in the north of the study area, at high altitude, and minimum temperature of the coldest month. In contrast, the two phylogenetic indices that were not correlated with species richness (Mean Phylogenetic Distance, Phylogenetic Species Variability) were located in the south of the study area and were positively correlated with high altitude, soil organic carbon stock and sand soil texture.
• Our study provides support for the use of phylogenies in conservation biology to assess ecosystem functioning, and provides insights for the implementation of sustainable forest ecosystem management.

     

Community assembly,functional traits,and phylogeny in Himalayan river birds

Heterogeneity in riverine habitats acts as a template for species evolution that influences river communities at different spatio‐temporal scales. Although birds are conspicuous elements of these communities, the roles of phylogeny, functional traits, and habitat character in their niche use or species'' assembly have seldom been investigated. We explored these themes by surveying multiple headwaters over 3000 m of elevation in the Himalayan Mountains of India where the specialist birds of montane rivers reach their greatest diversity on Earth. After ordinating community composition, species traits, and habitat character, we investigated whether river bird traits varied with elevation in ways that were constrained or independent of phylogeny, hypothesizing that trait patterns reflect environmental filtering. Community composition and trait representation varied strongly with increasing elevation and river naturalness as species that foraged in the river/riparian ecotone gave way to small insectivores with direct trophic dependence on the river or its immediate channel. These trends were influenced strongly by phylogeny as communities became more clustered by functional traits at a higher elevation. Phylogenetic signals varied among traits, however, and were reflected in body mass, bill size, and tarsus length more than in body size, tail length, and breeding strategy. These variations imply that community assembly in high‐altitude river birds reflects a blend of phylogenetic constraint and habitat filtering coupled with some proximate niche‐based moulding of trait character. We suggest that the regional co‐existence of river birds in the Himalaya is facilitated by this same array of factors that together reflect the highly heterogeneous template of river habitats provided by these mountain headwaters.     

Variable Effects of Dispersal on Productivity of Bacterial Communities Due to Changes in Functional Trait Composition

Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate – functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B) we could thus estimate changes in functional traits in communities in experiment (A). Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal – productivity relationships. Instead, changes in trait composition with dispersal, especially the communities’ ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal – productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.     

Towards a morphological metric of assemblage dynamics in the fossil record: a test case using planktonic foraminifera

With a glance, even the novice naturalist can tell you something about the ecology of a given ecosystem. This is because the morphology of individuals reflects their evolutionary history and ecology, and imparts a distinct ‘look’ to communities—making it possible to immediately discern between deserts and forests, or coral reefs and abyssal plains. Once quantified, morphology can provide a common metric for characterizing communities across space and time and, if measured rapidly, serve as a powerful tool for quantifying biotic dynamics. Here, we present and test a new high-throughput approach for analysing community shape in the fossil record using semi-three-dimensional (3D) morphometrics from vertically stacked images (light microscopic or photogrammetric). We assess the potential informativeness of community morphology in a first analysis of the relationship between 3D morphology, ecology and phylogeny in 16 extant species of planktonic foraminifera—an abundant group in the marine fossil record—and in a preliminary comparison of four assemblages from the North Atlantic. In the species examined, phylogenetic relatedness was most closely correlated with ecology, with all three ecological traits examined (depth habitat, symbiont ecology and biogeography) showing significant phylogenetic signal. By contrast, morphological trees (based on 3D shape similarity) were relatively distantly related to both ecology and phylogeny. Although improvements are needed to realize the full utility of community morphometrics, our approach already provides robust volumetric measurements of assemblage size, a key ecological characteristic.     

Predicting microbial traits with phylogenies

Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the ‘macrobial'' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.Trait-based approaches in community ecology studies are becoming increasingly appealing for microbial ecologists partly because metagenomic sequencing allows surveying molecular functions (Green et al., 2008; Lauro et al., 2009; Burke et al., 2011; Raes et al., 2011; Brown et al., 2014; Fierer et al., 2014). Although genetic data can provide precise information on cellular processes or metabolic pathways, they are generally blind to other ecologically relevant phenotypic traits such as the tolerance to certain abiotic conditions or the specific growth rate (but see Vieira-Silva and Rocha, 2010). Unlike ‘macrobial'' ecologists, who can directly observe phenotypic characters of plants and animals, microbial ecologists usually face situations where most of the phenotypes of their study organisms are unknown. This difficulty relies on the fact that gathering phenotypic (physiological, morphological, biochemical) data requires culturing microbial species. The unbalanced growth of genotypic vs phenotypic information is currently challenging microbial ecologists to work with phylogenetic trees of increasing size (hundreds to thousands of species) in which the percentage of species with unknown traits becomes larger and larger.Recent evidence indicate that phylogeny reflects molecular functions and phenotypes in Bacteria and Archaea (Langille et al., 2013; Martiny et al., 2013). This is due to the phylogenetic conservatism of microbial traits (Martiny et al., 2013), which likely arises from microbial evolution mostly proceeding by vertical gene inheritance rather than horizontal gene transfer (Kurland et al., 2003, see Fraser et al., 2007 for theoretical models on the role of horizontal gene transfer in bacterial speciation). At present, the massive sequencing of microbes in the environment is providing a huge amount of genetic information that is extremely useful to reconstruct the phylogenetic relationships among microbial lineages. This fact has triggered the interest of microbial ecologists to apply the methods developed to predict unobserved trait values of extant taxa based on the traits observed in their evolutionary relatives (Kembel et al., 2012; Langille et al., 2013; Angly et al., 2014, see review in Zaneveld and Thurber, 2014). All these methods are based on the existence of a significant phylogenetic signal or, in other words, in the fact that close relatives have more similar traits than expected by chance. Phylogeny-based trait prediction procedures (PTP hereafter) in microbes have been mainly performed under the phylogenetic generalized least squares framework (Martins and Hansen, 1997; Garland and Ives, 2000). Specifically, the trait value (for continuous traits) or state (for binary traits) of the focal species have been reconstructed through ancestral state reconstructions after rerooting the phylogeny at the most recent common ancestor of the taxon with unobserved trait and the rest of the tree (Kembel et al., 2012). The accuracy of PTP methods has been typically assessed under ‘macrobial'' scenarios containing phylogenies of moderate size, with low-to-medium proportion of species with unknown traits and significant phylogenetic signals. For example, Fagan et al. (2013) predicted population growth rates of mammals in phylogenies of 42–65 species containing 54–64% of unknowns and a significant phylogenetic signal (Blomberg et al., 2003; Blomberg''s K) ranging from 0.68 to 1.42. However, the current microbial scenarios derived from high-throughput sequencing projects face large-sized phylogenies (hundreds to thousands tips) with a high number of species with unknown traits and varying phylogenetic signals jeopardizing the applicability of PTP methods (Zaneveld and Thurber, 2014).The extent to which phylogeny reflects phenotype is strongly dependent on the degree of conservatism with which the focal trait has evolved. For instance, complex traits that involve many genes (for example, photosynthesis or methanogenesis) show higher conservatism than simpler traits, such as the consumption of a specific carbon source (Martiny et al., 2013). Furthermore, certain traits such as those related to genes encoding antibiotic or metal resistance are particularly prone to be horizontally transferred (Bruins et al., 2000), a process that can blur their phylogenetic signal. Therefore, if phylogenetic relatedness is to be used to infer the phenotype, the phylogenetic conservatism of the target trait needs to be quantified in every case.Altogether, the abovementioned observations indicate that the possibility to estimate phenotypes from phylogenies depends on the amount of phylogenetic and phenotypic information available to predict the unobserved trait values. Here we provide a simulation exercise to test the accuracy of the most widely used PTP method in microbial ecology to predict continuous trait values and binary trait states of extant taxa with different amount of phenotypic and phylogenetic information. We simulated several situations faced by microbial ecologists, including phylogenies of different sizes in which a small (P=0.3), medium (P=0.6) or large (P=0.9) proportion of species have unknown trait values. The correlations between the actual and the predicted trait values were obtained for characters evolved under different degree of conservatism. Finally, we put these values in the context of the phylogenetic signals described in the literature for different continuous and binary microbial traits and provide some recommendations for future analyses aimed to predict microbial traits with the help of the phylogenetic information.     

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.