Evolutionary Timescales Research Articles

Dating the bacterial tree of life based on ancient symbiosis.

Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within Proteobacteria. The expanded mitochondria-bacterial tree allows the node age constraints of eukaryotes established by their abundant fossils to be propagated to ancient co-evolving bacterial symbionts and across the bacterial tree of life. Importantly, we formulate a new probabilistic framework that considers uncertainty in inference of the ancestral lifestyle of modern symbionts to apply 19 relative time constraints (RTC) each informed by host-symbiont association to constrain bacterial symbionts no older than their eukaryotic host. Moreover, we develop an approach to incorporating substitution mixture models that better accommodate substitutional saturation and compositional heterogeneity for dating deep phylogenies. Our analysis estimates that the last bacterial common ancestor (LBCA) occurred approximately 4.0-3.5 billion years ago (Ga), followed by rapid divergence of major bacterial clades. It is generally robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The obtained timetree serves as a foundation for testing hypotheses regarding bacterial diversification and its correlation with geobiological events across different timescales.

Analysis of Synonymous Codon Usage bias of Lassa virus.

Lassa virus genome consists of two single-stranded, negative-sense RNA segments that lie in the genus Arenavirus. The disease associated with the Lassa virus is distributed all over the world, with approximately 3,000,000-5,000,000 infections diagnosed annually in West Africa. It shows high health risks to the human being. Previous research used the evolutionary time scale and adaptive evolution to describe the Lassa virus population pattern. However, it is still unclear how the Lassa virus takes advantage of synonymous codons. In this study, we analyzed the codon usage bias in 162 Lassa virus strains by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results disclosed that LASV strains are rich in A/T. The average ENC value indicated a low codon usage bias in LASVs. The ENC-plot, neutrality plot and parity rule 2 plot demonstrated that, besides mutational pressure, other factors like natural selection also contributed to codon usage bias. This study is significant because it described the pattern of codon usage in the genomes of the Lassa viruses and provided the information needed for a fundamental evolutionary study of them.

An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.

Transcriptional activation of the embryonic genome (EGA) is a major developmental landmark enabling the embryo to become independent from maternal control. The magnitude and control of transcriptional reprogramming during this event across mammals remains poorly understood. Here, we developed Smart-seq+5' for high sensitivity, full-length transcript coverage and simultaneous capture of 5' transcript information from single cells and single embryos. Using Smart-seq+5', we profiled 34 developmental stages in 5 mammalian species and provide an extensive characterization of the transcriptional repertoire of early development before, during, and after EGA. We demonstrate widespread transposable element (TE)-driven transcription across species, including, remarkably, of DNA transposons. We identify 19,657 TE-driven genic transcripts, suggesting extensive TE co-option in early development over evolutionary timescales. TEs display similar expression dynamics across species and species-specific patterns, suggesting shared and divergent regulation. Our work provides a powerful resource for understanding transcriptional regulation of mammalian development.

Exploring freshwater soundscapes of tropical marshland habitats in Southeast Asia: insights into auditory sensory adaptation of wild Siamese fighting fish Betta splendens.

While soundscapes shape the structure and function of auditory systems over evolutionary timescales, there is limited information regarding the adaptation of wild fish populations to their natural acoustic environments. This is particularly relevant for freshwater ecosystems, which are extremely diverse and face escalating pressures from human activities and associated noise pollution. The Siamese fighting fish Betta splendens is one of the most important cultured species in the global ornamental fish market and is increasingly recognized as a model organism for genetics and behavioural studies. This air-breathing species (Anabantoidei), characterized by the presence of a suprabranchial labyrinth organ that enhances auditory sensitivity, is native to Southeast Asia and inhabits low flow freshwater ecosystems that are increasingly threatened due to habitat destruction and pollution. We characterized the underwater soundscape, along with various ecological parameters, across five marshland habitats of B. splendens, from lentic waterbodies to small canals near a lake in Chiang Rai province (Thailand). All habitats exhibited common traits of low dissolved oxygen and dense herbaceous vegetation. Soundscapes were relatively quiet with Sound Pressure Level (SPL) around 102-105 dB re 1 µPa and most spectral energy below 1,000 Hz. Sound recordings captured diverse biological sounds, including potential fish vocalizations, but primarily insect sounds. Hearing thresholds were determined using auditory evoked potential (AEP) recordings, revealing best hearing range within 100-400 Hz. Males exhibited lower hearing thresholds than females at 400 and 600 Hz. This low-frequency tuning highlights the potential susceptibility of B. splendens to anthropogenic noise activities. This study provides first characterization of the auditory sensitivity and natural soundscape of B. splendens, establishing an important ground for future hearing research in this species. The information provided on the auditory sensory adaptation of B. splendens emphasizes the importance of preserving quiet soundscapes from lentic freshwater ecosystems.

Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer.

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent, and in most cases not statistically significant. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, for shorter evolutionary timescales, frequent co-acquisition of MGE and defense systems results in a net positive association of the latter with HGT. Given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by their strong linkage with MGE. These findings help explain the contradictory conclusions of previous research by pointing at mobility and within-host retention times as key factors that determine the impact of defense systems on genome plasticity.

Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years

Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.

Cycles of Change: Long and Short Term Aeolian Evolution at the Olympus Maculae, Mars

The low-dust Olympus Maculae are a unique geologic window to the local volcanic and aeolian stratigraphy on Mars. The Maculae display dust-cover changes associated with the 2018 global dust storm and dust devils confined to the dark maculae. Regional yardangs and sand patches indicate erosion and deposition and thus strong wind, yet we have not observed meter-scale ripple movement within the dark sand deposits nor decameter-scale ripple movement more regionally. On longer timescales, yardangs along a continuum of morphologies point to cycles of abrasion, infilling, lithification, and re-abrasion. Together, the dust changes and yardang evolution bracket the timescales for landscape evolution in and around the Maculae.

Astronomical time scale and Paleo-water depth evolution of the Miocene in the Pearl River Mouth Basin

Astronomical time scale and Paleo-water depth evolution of the Miocene in the Pearl River Mouth Basin

Ecological trait divergence over evolutionary time underlies the origin and maintenance of tropical spider diversity

Relative to its size, tropical Asia is likely to be the richest region in terms of biodiversity. However, the factors of species diversity formation and maintenance in Southeast (SE) Asia and neighboring regions remain poorly understood. Here we infer the evolutionary relationships within psilodercid spiders by incorporating fossil information into a robust, unprecedentedly complete species‐level phylogeny of 202 extant species to explore potential abiotic drivers and ecological features underlying their stable diversification history. The combination of extant and extinct historical biogeographic data indicates that in situ speciation is the predominant form of diversification in tropical Asia but diverse Cretaceous psilodercids in Myanmar ambers were replaced by other biogeographical lineages during the northward movements of the Burma Terrane. Furthermore, our diversification analyses show no diversification rate changes through time and across geographic space in this family, but the genus Althepus displays an accelerated rate of species diversification driven by the remarkable expansion of leg length. Trait evolution analysis shows that ecological trait divergence contributes to the diversification and accumulation of tropical spiders by facilitating species coexistence. These findings provide empirical evidence that the ecological trait divergence over evolutionary time scales is key to forming species diversity hotspots in SE Asia. Thus, this study integrating molecular evidence and paleontological interpretation provides a new framework for understanding the evolution of tropical species diversity.

Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation.

Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems, chromosomal fusion with an autosome may be one way that sex chromosomes can "refresh" their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the most complete reference assembly for treehoppers to date for Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution.

Tubulin sequence divergence is associated with the use of distinct microtubule regulators.

Diverse eukaryotic cells assemble microtubule networks that vary in structure and composition. While we understand how cells build microtubule networks with specialized functions, we do not know how microtubule networks diversify across deep evolutionary timescales. This problem has remained unresolved because most organisms use shared pools of tubulins for multiple networks, making it difficult to trace the evolution of any single network. In contrast, the amoeboflagellate Naegleria expresses distinct tubulin genes to build distinct microtubule networks: while Naegleria builds flagella from conserved tubulins during differentiation, it uses divergent tubulins to build its mitotic spindle. This genetic separation makes for an internally controlled system to study independent microtubule networks in a single organismal and genomic context. To explore the evolution of these microtubule networks, we identified conserved microtubule-binding proteins and used transcriptional profiling of mitosis and differentiation to determine which are upregulated during the assembly of each network. Surprisingly, most microtubule-binding proteins are upregulated during only one process, suggesting that Naegleria uses distinct component pools to specialize its microtubule networks. Furthermore, the divergent residues of mitotic tubulins tend to fall within the binding sites of differentiation-specific microtubule regulators, suggesting that interactions between microtubules and their binding proteins constrain tubulin sequence diversification. We therefore propose a model for cytoskeletal evolution in which pools of microtubule network components constrain and guide the diversification of the entire network, so that the evolution of tubulin is inextricably linked to that of its binding partners.

Quantum state preparation in Jaynes-Cummings lattices

Abstract One of the key questions in quantum information is the preparation of desired multipartite quantum states with high fidelity. Adiabatic evolution has been widely explored to achieve state preparation in quantum many-body systems. However, in noisy quantum systems, the adiabatic approach faces a dilemma: either extending the evolution timescales to reduce diabatic transitions or shortening the timescales to mitigate decoherence effects. Various quantum control approaches have been studied to resolve this dilemma. In a few recent works, we utilized Jaynes-Cummings (JC) lattices as a platform to investigate the potential of several quantum control techniques in preparing quantum many-body states, including the optimized adiabatic evolution approach, the quantum optimal control technique, and quantum shortcuts to adiabaticity. Here we first give an overview of our previous results on utilizing quantum optimal control in JC lattices with unit filling and utilizing local counterdiabatic driving in JC lattices with a single excitation. Then we present our results on the energy costs and energy fluctuations in these approaches. Our studies give insights into the implementation of different approaches in practical quantum devices and the connection between the energy costs and the quantum speed limit in preparing desired quantum many-body states for quantum simulation and quantum computation.

Evolution of Cataclysmic Variables with Binary-driven Mass Loss during Nova Eruptions

The discrepancies between observations and theoretical predictions of cataclysmic variables (CVs) suggest that there exists unknown angular-momentum-loss mechanism(s) besides magnetic braking and gravitational radiation. Mass loss due to nova eruptions belongs to the most likely candidates. While standard theory assumes that mass is lost in the form of radiation-driven, optically thick wind (fast wind), recent numerical simulations indicate that most of the mass loss is initiated and shaped by binary interaction. We explore the effect of this binary-driven mass loss (BDML) on the CV evolutions assuming a major fraction of the lost mass leaves the system from the outer Lagrangian point. Different from the traditional continuous wind picture, we consider the mass loss process to be instantaneous because the duration of nova eruptions is much shorter than the binary evolutionary timescale. Our detailed binary evolution calculations reveal the following results. (1) BDML seems able to provide extra angular momentum loss below the period gap. The mass transfer rates at a given orbital period occupy a large range, in agreement with the observed secular mass transfer rate distribution in CVs. (2) The enhanced mass transfer rates do not lead to a runaway mass transfer process and allow the white dwarfs to grow mass ≲0.1 M ☉. (3) BDML can cause both positive and negative variations in the orbital period induced by nova eruptions, in line with observations, and can potentially explain the properties of some peculiar supersoft X-ray sources likely CAL 87, 1E 0035.4−7230, and RX J0537.7−7034.

The function(s) of consciousness: an evolutionary perspective.

The functions of consciousness, viewed from an evolutionary standpoint, can be categorized as being either general or particular. There are two general functions, meaning those that do not depend on the particulars of how consciousness influences behavior or how and why it first evolved: of (1) expanding the behavioral repertoire of the individual through the gradual accumulation of neurocircuitry innovations incorporating consciousness that would not exist without it, and (2) reducing the time scale over which preprogrammed behaviors can be altered, from evolutionary time, across generations, to real-time. But neither answers Velmans' question, of why consciousness is adaptive in a proximate sense, and hence why it would have evolved, which depends on identifying the particular function it first performed. Memory arguably plays a role here, as a strong case can be made that consciousness first evolved to make motivational control more responsive, though memory, to the past life experiences of the individual. A control mechanism of this kind could, for example, have evolved to consciously inhibit appetitive behaviors, whether consciously instigated or not, that would otherwise expose the individual to harm. There is then the question of whether, for amniote vertebrates, a role in memory formation and access would have led directly to a wider role for consciousness in the way the brain operates, or if some other explanation is required. Velmans' question might then have two answers, the second having more to do with the advantages of global oversight for the control of behavior, as in a global workspace, or for conferring meaning on sensory experience in a way that non-conscious neural processes cannot. Meaning in this context refers specifically to the way valence is embodied in the genomic instructions for assembling the neurocircuitry responsible for phenomenal contents, so it constitutes an embodied form of species memory, and a way of thinking about the adaptive utility of consciousness that is less concerned with real-time mechanistic events than with information storage on an evolutionary time scale.

Distributional Semantics: Meaning Through Culture and Interaction.

Mastering how to convey meanings using language is perhaps the main challenge facing any language learner. However, satisfactory accounts of how this is achieved, and even of what it is for a linguistic item to have meaning, are hard to come by. Nick Chater was one of the pioneers involved in the early development of one of the most successful methodologies within the cognitive science of language for discovering meaning: distributional semantics. In this article, we review this approach and discuss its successes and shortcomings in capturing semantic phenomena. In particular, we discuss what we dub the "distributional paradox:" how can models that do not implement essential dimensions of human semantic processing, such as sensorimotor grounding, capture so many meaning-related phenomena? We conclude by providing a preliminary answer, arguing that distributional models capture the statistical scaffolding of human language acquisition that allows for communication, which, in line with Nick Chater's more recent ideas, has been shaped by the features of human cognition on the timescale of cultural evolution.

Transcriptomic Sexual Conflict at Two Evolutionary Timescales Revealed by Experimental Evolution in Caenorhabditis elegans.

Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wild-type expression state and potentially impact many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans, we explore the coupling of direct sexual selection on males with the transcriptomic response in males and females over microevolutionary timescales to uncover the extent to which postinsemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression evolved in a sex-specific manner in males, while in females, indirect selection causes an evolved response. Almost all differentially expressed genes were downregulated in both evolved males and females. Moreover, 97% of significantly differentially expressed genes in males and 69% of significantly differentially expressed genes in females have wild-type female-biased expression profile. Changes in gene expression profiles were likely driven through trans-acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together, these data suggest a defeminization of the male transcriptome and masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales, sexual selection can generate putative sexual conflict in expression space.

The Variability of Persistent Radio Sources of Fast Radio Bursts

Over 700 bright millisecond-duration radio transients, known as fast radio bursts (FRBs), have been identified to date. Nevertheless, the origin of FRBs remains unknown. Two repeating FRBs (FRB 20121102A and FRB 20190520B) have been verified to be associated with persistent radio sources (PRSs), making them the best candidates to study the nature of FRBs. Monitoring the variability in PRSs is essential for understanding their physical nature. We conducted 22 observations of the PRSs linked to FRB 20121102A and FRB 20190520B using the Karl G. Jansky Very Large Array, to study their variability. We have observed significant flux variability for the PRSs of FRB 20121102A and FRB 20190520B, with a confidence level exceeding 99.99%, based on the observations covering the longest timescale recorded to date. The observed variability of the two PRSs exhibits no significant difference in amplitude across both short and long timescales. We found that the radio-derived star formation rates of the two FRB hosts are significantly higher than those measured by the optical H α emissions, indicating that their host galaxies are highly obscured or most radio emissions are not from star formation processes. The observed timescale of PRS flux evolution constrained the magnetic field of FRB 20121102A with B ∥ ≳ 1 mG and FRB 20190520B with B ∥ ≳ 0.1 mG.

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids.

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations.

New stellar age estimates using SPInS based on Gaia DR3 photometry and LAMOST DR8 abundances

Reliable stellar age estimates are fundamental for testing several problems in modern astrophysics, in particular since they set the timescales of Galactic dynamical and chemical evolution. In this study, we determine ages using only photometry and parallaxes, in combination with interstellar extinction maps, and spectroscopic metallicities and alpha abundances from the latest data release (DR8) of the LAMOST survey. In contrast with previous age estimates, we do not use spectroscopic effective temperatures or surface gravities, and thus we rely on the excellent precision and accuracy of the Gaia photometry. We use a new version of the publicly available SPInS code with improved features, including the on-the-fly computation of the autocorrelation time and the automatic convergence evaluation. We determine reliable age estimates for 35,096 and 243,768 sub-giant and main-sequence turn-off stars in the LAMOST DR8 low- and medium-resolution surveys with typical uncertainties smaller than 10&lt;!PCT!&gt;. In addition, we successfully test our method on more than 4,000 stars of 14 well-studied open and globular star clusters covering a wide range of ages, confirming the reliability of our age and uncertainty estimates.

Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal.

Our understanding of the evolution of many microbes has been revolutionised by the molecular clock, a statistical tool to infer evolutionary rates and timescales from analyses of biomolecular sequences. In all molecular clock models, evolutionary rates and times are jointly unidentifiable and 'calibration' information must therefore be used. For many organisms, sequences sampled at different time points can be employed for such calibration. Before attempting to do so, it is recommended to verify that the data carry sufficient information for molecular dating, a practice referred to as evaluation of temporal signal. Recently, a fully Bayesian approach, BETS (Bayesian Evaluation of Temporal Signal), was proposed to overcome known limitations of other commonly used techniques such as root-to-tip regression or date randomisation tests. BETS requires the specification of a full Bayesian phylogenetic model, posing several considerations for untangling the impact of model choice on the detection of temporal signal. Here, we aimed to (i) explore the effect of molecular clock model and tree prior specification on the results of BETS and (ii) provide guidelines for improving our confidence in molecular clock estimates. Using microbial molecular sequence data sets and simulation experiments, we assess the impact of the tree prior and its hyperparameters on the accuracy of temporal signal detection. In particular, highly informative priors that are inconsistent with the data can result in the incorrect detection of temporal signal. In consequence, we recommend: (i) using prior predictive simulations to determine whether the prior generates a reasonable expectation of parameters of interest, such as the evolutionary rate and age of the root node, (ii) conducting prior sensitivity analyses to assess the robustness of the posterior to the choice of prior, and (iii) selecting a molecular clock model that reasonably describes the evolutionary process.