The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci.

Bayesian methods provide a powerful way to estimate species divergence times by combining information from molecular sequences with information from the fossil record. With the explosive increase of genomic data, divergence time estimation increasingly uses data of multiple loci (genes or site partitions). Widely used computer programs to estimate divergence times use independent and identically distributed (i.i.d.) priors on the substitution rates for different loci. The i.i.d. prior is problematic. As the number of loci (L) increases, the prior variance of the average rate across all loci goes to zero at the rate 1/L. As a consequence, the rate prior dominates posterior time estimates when many loci are analyzed, and if the rate prior is misspecified, the estimated divergence times will converge to wrong values with very narrow credibility intervals. Here we develop a new prior on the locus rates based on the Dirichlet distribution that corrects the problematic behavior of the i.i.d. prior. We use computer simulation and real data analysis to highlight the differences between the old and new priors. For a dataset for six primate species, we show that with the old i.i.d. prior, if the prior rate is too high (or too low), the estimated divergence times are too young (or too old), outside the bounds imposed by the fossil calibrations. In contrast, with the new Dirichlet prior, posterior time estimates are insensitive to the rate prior and are compatible with the fossil calibrations. We re-analyzed a phylogenomic data set of 36 mammal species and show that using many fossil calibrations can alleviate the adverse impact of a misspecified rate prior to some extent. We recommend the use of the new Dirichlet prior in Bayesian divergence time estimation. [Bayesian inference, divergence time, relaxed clock, rate prior, partition analysis.].This work was supported by Biotechnology and Biological Sciences Research Council (BBSRC), UK, grant BB/J009709/1. Z.Y. is a Royal Society Wolfson Merit award holder. T.Z. is supported by Natural Science Foundation of China (NSF) grants (31301093, 11301294 and 11201224)

Bayesian estimation of species divergence times using correlated quantitative characters

Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times

This work was supported by UCL Impact studentship to K.A.; and Biotechnological and Biological Sciences Research Council (BBSRC) [BB/N000609/1 to Z.Y.]

Molecular Clocks without Rocks: New Solutions for Old Problems.

Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods

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

Características físico-químicas de extratos de arroz integral, quirera de arroz e soja.

Extratos hidrossolúveis são bebidas de origem vegetal, que possuem apelo comercial nutricional, quanto aos aspectos de saúde, como ausência de gorduras animais e altos teores de minerais. O objetivo deste trabalho foi comparar as características físico-químicas de extratos hidrossolúveis de arroz integral, quirera de arroz e soja. As análises (em triplicata) foram: pH, teor de sólidos solúveis, umidade, cinzas, proteínas, lipídeos, carboidratos totais, cálcio, magnésio, cobre, manganês, ferro, zinco e valor energético. O extrato de quirera de arroz apresentou o maior teor de carboidratos (3,17 g 100 g-1) e o menor teor de cinzas (0,58 g 100 g-1), proteínas (0,73 g 100 g-1), lipídeos (0,41 g 100 g-1) e valor energético (17,28 kcal 100 g-1), enquanto o extrato de arroz integral apresentou o maior valor de pH (6,77) e valores intermediários de cálcio (1,2 mg 100 g-1) e magnésio (1,69 mg 100 g-1). O extrato de soja se destacou com maiores valores de todos os minerais, cinzas (0,84 g 100 g-1), proteínas (2,51 g 100 g-1), lipídeos (1,05 g 100 g-1) e valor energético (68,34 kcal 100 g-1), porém, menor valor de carboidratos (2,62 g 100 g-1). Apesar do menor valor nutricional, quando comparado ao extrato de soja, os extratos de arroz integral ou de quirera de arroz são alternativas alimentares viáveis à substituição do leite ou do extrato de soja, para pessoas que possuam intolerância à lactose e/ou alergia às proteínas da soja

Qualidade de biscoitos formulados com diferentes teores de farinha de casca de pequi.

O objetivo deste estudo foi avaliar a qualidade de biscoitos tipo cookie, formulados com diferentes níveis de farinha de casca de pequi (FCP), em substituição à farinha de trigo (FT). Utilizou-se um delineamento inteiramente casualizado, com controle mais quatro tratamentos (12,5%; 25%; 37,5%; e 50% de substituição de FT por FCP), e quatro repetições. Foram analisados: aceitabilidade, cor (luminosidade), composição centesimal, valor energético e teores de alguns minerais de cada amostra

Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic counting methods and the maximum-likelihood (ML) method based on a codon substitution model are widely used for such analysis. However, these methods do not have nice statistical properties, as the estimates can be zero or infinity in some data sets, so that their means and variances are infinite. In large genome-scale comparisons, such extreme estimates (either 0 or ∞) of ω and sequence distance (t) are common. Here, we implement a Bayesian method to estimate ω and t in pairwise sequence comparisons. Using a combination of computer simulation and real data analysis, we show that the Bayesian estimates have better statistical properties than the ML estimates, because the prior on ω and t shrinks the posterior of those parameters away from extreme values. We also calculate the posterior probability for ω > 1 as a Bayesian alternative to the likelihood ratio test. The new method is computationally efficient and may be useful for genome-scale comparisons of protein-coding gene sequences

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genusDaubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-a and V1Rstrep-b. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available