RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification.

Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the timing of origin of animals, yielding results consistent with early strict clock studies from the 1980s and 1990s, estimating metazoans to have a Mesoproterozoic origin-over a billion years ago. RelTime results are unexpected and disagree with the largest majority of modern, relaxed, Bayesian molecular clock analyses, which suggest animals originated in the Tonian-Cryogenian (less that 850 million years ago). Here, we demonstrate that RelTime-inferred divergence times for the origin of animals are spurious, a consequence of the inability of RelTime to relax the clock along the internal branches of the animal phylogeny. RelTime-inferred divergence times are comparable to strict-clock estimates because they are essentially inferred under a strict clock. Our results warn us of the danger of using ad hoc algorithms making implicit assumptions about rate changes along a tree. Our study roundly rejects a Mesoproterozoic origin of animals; metazoans emerged in the Tonian-Cryogenian, and diversified in the Ediacaran, in the immediate prelude to the routine fossilization of animals in the Cambrian associated with the emergence of readily preserved skeletons.This research was funded by a Marie Skłodowska-Curie Fellowship (655814 to J.L.-F.), grants from the NERC BETR (NE/P013643/1 to D.P. and P.C.J.D.), BBSRC (BB/N000919/1 to P.C.J.D.), John Templeton Foundation 43915 (D.P.) and a Royal Society Wolfson Research Merit Award (P.C.J.D.)

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution.

Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators

Diurnal sampling reveals significant variation in CO2 emission from a tropical productive lake

It is well accepted in the literature that lakes are generally net heterotrophic and supersaturated with CO2 because they receive allochthonous carbon inputs. However, autotrophy and CO2undersaturation may happen for at least part of the time, especially in productive lakes. Since diurnal scale is particularly important to tropical lakes dynamics, we evaluated diurnal changes in pCO2and CO2 flux across the air-water interface in a tropical productive lake in southeastern Brazil (Lake Carioca) over two consecutive days. Both pCO2 and CO2 flux were significantly different between day (9:00 to 17:00) and night (21:00 to 5:00) confirming the importance of this scale for CO2 dynamics in tropical lakes. Net heterotrophy and CO2 outgassing from the lake were registered only at night, while significant CO2 emission did not happen during the day. Dissolved oxygen concentration and temperature trends over the diurnal cycle indicated the dependence of CO2 dynamics on lake metabolism (respiration and photosynthesis). This study indicates the importance of considering the diurnal scale when examining CO2emissions from tropical lakes

Diurnal sampling reveals significant variation in CO2 emission from a tropical productive lake

It is well accepted in the literature that lakes are generally net heterotrophic and supersaturated with CO2 because they receive allochthonous carbon inputs. However, autotrophy and CO2undersaturation may happen for at least part of the time, especially in productive lakes. Since diurnal scale is particularly important to tropical lakes dynamics, we evaluated diurnal changes in pCO2and CO2 flux across the air-water interface in a tropical productive lake in southeastern Brazil (Lake Carioca) over two consecutive days. Both pCO2 and CO2 flux were significantly different between day (9:00 to 17:00) and night (21:00 to 5:00) confirming the importance of this scale for CO2 dynamics in tropical lakes. Net heterotrophy and CO2 outgassing from the lake were registered only at night, while significant CO2 emission did not happen during the day. Dissolved oxygen concentration and temperature trends over the diurnal cycle indicated the dependence of CO2 dynamics on lake metabolism (respiration and photosynthesis). This study indicates the importance of considering the diurnal scale when examining CO2emissions from tropical lakes

A species-level timeline of mammal evolution integrating phylogenomic data

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1-3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the deluge of new genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6 and, thus, the timescale of placental mammal evolution remains contentious7-10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Paleogene8 and show crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Paleocene/Eocene. Our new Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. As such, our approach can be used to tackle other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets

Bayesian Molecular Clock Dating Using Genome-Scale Datasets.

Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation in the branches of a phylogenetic tree and the use of flexible fossil calibration densities to describe the uncertainty in node ages. The advent of next-generation sequencing technologies has led to a flood of genome-scale datasets for organisms belonging to all domains in the tree of life. Thus, a new era has begun where dating the tree of life using genome-scale data is now within reach. In this protocol, we explain how to use the computer program MCMCTree to perform Bayesian inference of divergence times using genome-scale datasets. We use a ten-species primate phylogeny, with a molecular alignment of over three million base pairs, as an exemplar on how to carry out the analysis. We pay particular attention to how to set up the analysis and the priors and how to diagnose the MCMC algorithm used to obtain the posterior estimates of divergence times and evolutionary rates

Construindo Critérios de Julgamento em Avaliação: especialistas e satisfação dos usuários com a dispensação do tratamento do HIV/Aids Building Evaluation Criteria: experts and user satisfaction with pharmaceutical delivery services for HIV/Aids

Critério é uma ferramenta típica da avaliação e pode ser definido como uma dimensão-padrão em função da qual a realidade do objeto da avaliação receberá julgamento qualitativo e/ou quantitativo. Em uma avaliação, o procedimento de elaborar, esclarecer, negociar e aplicar critérios para determinar o valor (ou mérito) do objeto avaliado faz parte de um exercício metodológico que deve ser cuidadoso. Este artigo apresenta critérios de julgamento para avaliar a satisfação dos usuários com a dispensação dos medicamentos para o tratamento do HIV/Aids e seu processo de construção por meio de consenso entre diferentes atores sociais. Para estabelecer o consenso utilizou-se técnica de Delfos, uma técnica formal utilizada para consenso de especialistas com metodologia e processos estruturados. Neste estudo, foram considerados especialistas aqueles com experiência acadêmica e em gestão, bem como ativistas informados e comprometidos com a questão. Os achados foram sistematizados sob a forma de uma nova estrutura de satisfação, sob a qual os critérios construídos são articulados hierarquicamente. Buscou-se contribuir para o desenvolvimento de uma estratégia metodológica participativa em avaliação e ampliar o conhecimento sobre a satisfação dos usuários e a dispensação dos medicamentos para HIV/Aids.<br>A criterion is a typical tool in the evaluation field that can be defined as a standard-dimension under which the object of an evaluation receives qualitative or quantitative judgments. During an evaluation, several rigorous methodological procedures are involved in development and application of suitable criteria to determine the value of the object being evaluated. This article presents a set of criteria to evaluate user satisfaction with HIV/Aids-related pharmaceutical delivery services. The criteria construction process involved consensus amongst different experts, from academia, NGOs, management, by means of the Delphi technique. This technique prescribes a series of formal steps towards a consensus of experts, based on pre-structured methodology and processes. The findings were systematically organized in a structure under which the resulting satisfaction criteria are hierarchically organized. Results suggest the importance of developing a methodological strategy in evaluation that involves participation of different actors and of enhancing knowledge on user satisfaction and pharmaceutical delivery services for HIV/Aids