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This book presents a history of microbial evolutionary biology from the 19th century to the present. It follows the research of molecular evolutionists who explore the origins of the genetic system and the primary life forms: three domains and multiple kingdoms, created by mechanisms very unlike those considered by Darwin and his followers.

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate.

BackgroundIndwelling pleural catheters (IPCs) offer symptom relief from pleural effusions. Usage is complicated by infection in ~5% of cases.1 IPCs can be colonised when bacteria grow from pleural fluid without infective features.2 The causes of colonisation are undescribed and its relationship with infection unexplored.AimsDescribe the incidence and microbiology of IPC colonisation.Identify clinical features associated with IPC colonisation.Compare asymptomatically colonising bacteria with those from infection.MethodsAll infected and non-infected IPCs were collected from four sites, along with associated metadata. Infected IPCs were identified clinically and non-infected IPCs categorised as ‘colonised’ if bacteria was cultured from them, and ‘clean’ if not. The genomes of all cultured organisms were sequenced, assembled and taxonomically classified. For Staphylococcus aureus isolates, a maximum likelihood phylogenetic tree was constructed from Snippy-core alignment using IQ-Tree, with S. aureus NCTC8325 as reference.ResultsOf 108 IPCs, 54 were ‘clean’, 34 colonised and 20 infected. Infected and colonised IPCs had longer mean insertion durations (197.6 and 181.3 days) compared with ‘clean’ ones (98 days).Of 34 colonised IPCs, 17 were colonised by multiple species. The most common causes were Coagulase-negative Staphylococci (CoNS n=18), Enterobacteriaceae (n=18), Corynebacteria spp (n=4) & S. aureus (n=4).Two of 20 infected IPCs were culture negative. We retrieved the same organism causing infection from 14/18 IPCs. The most common pathogens were S. aureus (n=8), Pseudomonas aeruginosa (n=3), Enterococcus spp (n=2) and Enterobacter cloacae (n=2). Figure 1 demonstrates clustering of S. aureus isolates from deep and superficial infection.Abstract S149 Figure 1Phylogenetic tree of Staphylococcus aureus isolates from colonised and infected IPCs. S. aureus NCTC8325 is the reference strain[Image Omitted. See PDF.]ConclusionA significant proportion of IPCs are colonised. Colonisation and infection are associated with longer insertion duration. Enterobacteriaceae and CoNS are the most common causes of colonisation, whereas S. aureus and Pseudomonas aeruginosa commonly cause infection. S. aureus isolates causing deep infection show higher genetic similarity versus colonising strains. This, and our phylogenetic analysis, suggests colonisation does not cause infection, but rather there is a virulent subset of isolates causing infection. Ongoing work will identify genes and markers associated with infection.ReferencesSundaralingam, et al. Chest 2022;161(5):1407–1425.Sethi, et al. Clinical & Translational Science 2023:1287–1288.

ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate and introduces several new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions. ModelTest-NG is available under a GNU GPL3 license at https://github.com/ddarriba/modeltest, last accessed September 2, 2019.

Tumour clones consist of cancerous cells with shared ancestry. The study of cancer evolution has been further advanced by the introduction of mathematical algorithms to reconstruct the phylogenetic tree within the tumour. Bulk sequencing data pro- vides not only the VAF and ploidy information that most established methods now use to infer tumour subclonal structure, but also another equally important piece of information, namely phasing information. Phasing information from sequencing reads can be used to find the most likely phylogenetic trees. During my Ph.D, I proposed a generative model of SNVs distribution in next-gen sequencing reads, PhaDPClust, which utilises phasing information and constructs complete phylogenetic trees automatically. This method builds on the DPClust framework, and can be applied to both single sample and multiple sample analysis. On single sample analysis, PhaDPClust outperformed other established methods in subclone reconstruction, measured by several metrics from the SMC-HET Chal- lenge. The performance of PhaDPClust was constrained by the abundance of phase information, as evidenced by results on real tumour samples. Then, PhaDPClust was extended to multisample analysis. PhaDPClust succeeded in reconstructing phylogenetic trees in similar topology automatically, but failed to split some clusters, implying some work still needs to be done in the future.

Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community-weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect those analyses. On one hand, phylogenetic signal might indicate niche conservatism along clade evolution, reinforcing the environmental signal in trait assembly patterns. On the other hand, it might introduce phylogenetic autocorrelation to mean trait variation among communities. Under this latter scenario, phylogenetic signal might inflate type I error in analysis relating CWM variation to environmental gradients. We explore multiple ways phylogenetic history may influence analysis relating CWM to environmental gradients. We propose the concept of neutral trait diffusion, which predicts that for a functional trait x, CWM variation among local communities does not deviate from the expectation that x evolved according to a neutral evolutionary process. Based on this framework we introduce a graphical tool called neutral trait diffusion representation (NTDR) that allows for the evaluation of whether it is necessary to carry out phylogenetic correction in the trait prior to analyzing the association between CWM and environmental gradients. We illustrate the NTDR approach using simulated traits, phylogenies and metacommunities. We show that even under moderate phylogenetic signal in both the trait used to define CWM and species distribution across communities, OLS models relating CWM variation to environmental gradients lead to inflated type I error when testing the null hypothesis of no association between CWM and environmental gradient. To overcome this issue, we propose a phylogenetic correction for OLS models and evaluate its statistical performance (type I error and power). Phylogeny-corrected OLS models successfully control for type I error in analysis relating CWM variation to environmental gradients but may show decreased power. Combining the exploratory tool of NTDR and phylogenetic correction in traits, when necessary, guarantees more precise inferences about the environmental forces driving trait-mediated species sorting across metacommunities.

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confdently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.

[This corrects the article DOI: 10.1371/journal.pone.0217050.].

Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. Despite a wealth of studies exploring trait relationships across the entire plant kingdom, the dominant traits underpinning these unique aspects of tree form and function remain unclear. Here, by considering 18 functional traits, encompassing leaf, seed, bark, wood, crown, and root characteristics, we quantify the multidimensional relationships in tree trait expression. We find that nearly half of trait variation is captured by two axes: one reflecting leaf economics, the other reflecting tree size and competition for light. Yet these orthogonal axes reveal strong environmental convergence, exhibiting correlated responses to temperature, moisture, and elevation. By subsequently exploring multidimensional trait relationships, we show that the full dimensionality of trait space is captured by eight distinct clusters, each reflecting a unique aspect of tree form and function. Collectively, this work identifies a core set of traits needed to quantify global patterns in functional biodiversity, and it contributes to our fundamental understanding of the functioning of forests worldwide.