RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Stamatakis, Alexandros

doi:10.1093/bioinformatics/btl446

Cited by 14,382 publications

(10,585 citation statements)

References 10 publications

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“…ProtTest (Darriba et al ., 2011) was then run on the trimmed concatenated alignment to determine the best amino acid substitution matrix to generate a phylogenetic tree based on the Bayesian Information Criterion score. The identified model was employed to generate the phylogenetic tree using a maximum likelihood and a Bayesian approach employing RA x ML and M r B ayes (Stamatakis, 2006). In both approaches, Blastocystis hominis was used as outgroup.…”

Section: Methodsmentioning

confidence: 99%

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

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Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo‐nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics.We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex‐related genes. We also identified a small number of conserved noncoding elements.Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein‐coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis‐related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient‐replete conditions.The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.

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Section: Methodsmentioning

confidence: 99%

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

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“…Specifically, we used RAxML version 7.2.8 to infer the ML topology, branch lengths, and evolutionary rates (Stamatakis, 2006). We exported this ML phylogeny to another software package, PhyML (Guindon et al., 2010), in order to calculate statistical support for branches as approximate likelihood ratios.…”

Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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“…The species recorded are listed in Appendix S1. The phylogeny was assembled using RAxML (Stamatakis, 2006) based on the DNA barcodes rbc L, mat K, trn H– psb A, and ITS (the original sequences have been reported in Huang, Ci, Conran, & Li, 2015). A semiparametric method based on a penalized likelihood in the R statistical software package “ape” was used to generate an ultrametric phylogenetic tree (Paradis, Claude, & Strimmer, 2004; R Core Team, 2015; Figure 2, Appendix S2).…”

Section: Methodsmentioning

confidence: 99%

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest

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et al. 2016

Ecology and Evolution

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The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty‐nine plots of 400 m2 (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract: icwww.epfl.ch/~stamatak

Cited by 14,382 publications

References 10 publications

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest

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