Challenges in Assembling the Dated Tree of Life.

The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available.

A time-calibrated phylogeny of the diversification of Holoadeninae frogs.

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification.

Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.

Relaxing the molecular clock using models of how substitution rates change across lineages has become essential for addressing evolutionary problems. The diversity of rate evolution models and their implementations are substantial, and studies have demonstrated their impact on divergence time estimates can be as significant as that of calibration information. In this review, we trace the development of rate evolution models from the proposal of the molecular clock concept to the development of sophisticated Bayesian and non-Bayesian methods that handle rate variation in phylogenies.

Bioactive Compounds and Antioxidant Capacity of Pulp, Peel and Seeds from Jeriva ().

Jeriva () is a fruit from palm trees of the Arecaceae family, widely distributed in tropical and subtropical areas of Latin America. It has low production costs and high productivity throughout the year; however, its consumption is very low, and the production goes almost entirely to feed animals or to waste. To improve its consumption, a good characterization of the whole fruit is necessary.

The role of cue salience in prospective memory commission errors in nonperformed nonfocal tasks.

Prospective memory (PM) refers to the ability to remember to execute an intention in the future without having a permanent reminder. These intentions can be performed when they are not relevant or become no-longer needed, the so-called "commission errors". The present study aims to understand the effect of cue salience on PM commission errors with unperformed intentions and on the ongoing task performance-associated costs.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites.

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P.

Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments.

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive.

Bats (Mammalia: Chiroptera) in urban-rural interfaces: community structure associated with pathogen screening in São Paulo-the largest metropolitan region in Brazil.

Little is known about the influence of the urban environments on bat species 'ecology. The urbanization process potentially lead to critical ecological changes in bat communities' intra and interspecific pathogenic transmissions dynamics. To date, the monitoring of pathogens in bats in Brazil has only been done with bats found dead or alive in households, from rabies surveillance systems.

Remembering to whom we transmit information during pandemics: the effect of face masks on destination memory.

Considering the global pandemic we currently experience, face masks have become standard in our daily routine. Even though surgical masks are established as a safety measure against the dissemination of COVID-19, previous research showed that their wearing compromises face recognition. Consequently, the capacity to remember to whom we transmit information-destination memory-could also be compromised.

Assessing the relative performance of fast molecular dating methods for phylogenomic data.

Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues.

Modeling Alzheimer's Disease Using Human Brain Organoids.

Alzheimer's disease (AD) is the primary cause of dementia, to date. The urgent need to understand the biological and biochemical processes related to this condition, as well as the demand for reliable in vitro models for drug screening, has led to the development of novel techniques, among which stem cell methods are of utmost relevance for AD research, particularly the development of human brain organoids. Brain organoids are three-dimensional cellular aggregates derived from induced pluripotent stem cells (iPSCs) that recreate different neural cell interactions and tissue characteristics in culture.

Prediction and reasons for COVID-19 second dose vaccine hesitation: a cross-sectional study in a municipality of Brazil.

Background: Hesitation and refusal to take a second dose of the vaccine for coronavirus disease 19 (COVID-19) are prevalent.

Objectives: We aimed to identify predictive factors for hesitation or refusal and describe groups with higher rates of vaccine hesitancy.

Design And Setting: A cross-sectional study in Assis City, Brazil.

The performance of outgroup-free rooting under evolutionary radiations.

Tree rooting implies a temporal dimension to phylogenies. Only after defining the position of the root node is that the ancestral-descendant relationship between branches can be fully deduced. Rooting has been usually carried out by employing evolutionarily close outgroup lineages, which is a drawback when these lineages are unavailable or unknown.

Molecular dating of the blood pigment hemocyanin provides new insight into the origin of animals.

The Neoproterozoic included changes in oceanic redox conditions, the configuration of continents and climate, extreme ice ages (Sturtian and Marinoan), and the rise of complex life forms. A much-debated topic in geobiology concerns the influence of atmospheric oxygenation on Earth and the origin and diversification of animal lineages, with the most widely popularized hypotheses relying on causal links between oxygen levels and the rise of animals. The vast majority of extant animals use aerobic metabolism for growth and homeostasis; hence, the binding and transportation of oxygen represent a vital physiological task.

Evolution of a key enzyme of aerobic metabolism reveals Proterozoic functional subunit duplication events and an ancient origin of animals.

The biological toolkits for aerobic respiration were critical for the rise and diversification of early animals. Aerobic life forms generate ATP through the oxidation of organic molecules in a process known as Krebs' Cycle, where the enzyme isocitrate dehydrogenase (IDH) regulates the cycle's turnover rate. Evolutionary reconstructions and molecular dating of proteins related to oxidative metabolism, such as IDH, can therefore provide an estimate of when the diversification of major taxa occurred, and their coevolution with the oxidative state of oceans and atmosphere.

A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly.

Background: The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp).

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches.

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences.

Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times.

Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs.

The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis.

The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist.

Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda.

The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time.

Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data.

The use of discrete morphological data in Bayesian phylogenetics has increased significantly over the last years with the proposal of total evidence analysis and the treatment of fossils as terminal taxa in Bayesian molecular dating. Both approaches rely on the assumption that probabilistic Markov models reasonably accommodate all the complexity of morphological evolution of discrete traits. The performance of such morphological models used in Bayesian phylogenetics has been thoroughly investigated, but conclusions so far were based mostly on simulated data.

Estimating TimeTrees with MEGA and the TimeTree Resource.

The main outcome of molecular dating, the timetree, provides crucial information for understanding the evolutionary history of lineages and is a requirement of several evolutionary analyses. Although essential, the estimation of divergence times from molecular data is frequently regarded as a complicated task. However, establishing biological timescales can be performed in a straightforward manner, even with large, genome-wide data sets.

Impact of long-term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages.

Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage.

Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites.

Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium.

Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases.

Glycoside hydrolases (GHs) are carbohydrate-active enzymes that assist the hydrolysis of glycoside bonds of complex sugars into carbohydrates. The current standard GH family classification is available in the CAZy database, which is based on the similarities of amino acid sequences and curated semi-automatically. However, with the exponential increase in data availability from genome sequences, automated classification methods are required for the fast annotation of coding sequences.