Evolutionary Timescales Research Articles

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 wildtype 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 post-insemination 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 wildtype 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 de-feminization 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.

Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila.

Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within the Drosophila simulans clade-D. simulans, D. sechellia, and D. mauritiana-and their relative, D. melanogaster. Using chromatin profiling combined with high-resolution fluorescence in situ hybridization on stretched chromatin fibers, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes in D. sechellia, where the X and fourth centromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation.

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.

Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes.

Protein complexes composed of strictly essential subunits are abundant in nature and often arise through the gradual complexification of ancestral precursor proteins. Essentiality can arise through the accumulation of changes that are tolerated in the complex state but would be deleterious for the standalone complex components. While this theoretical framework to explain how essentiality arises has been proposed long ago, it is unclear which factors cause essentiality to persist over evolutionary timescales. In this work we show that the central enzyme of photosynthesis, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), can easily start to depend on a newly recruited interaction partner through multiple, genetically distinct mechanisms that affect stability, solubility, and catalysis. We demonstrate that layering multiple mechanisms of essentiality can lead to its persistence, even if any given mechanism reverts. More broadly, our work highlights that new interaction partners can drastically re-shape which substitutions are tolerated in the proteins they are recruited into. This can lead to the evolution of multilayered essentiality through the exploration of areas of sequence space that are only accessible in the complex state.

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.

Climate change alters the future of natural floristic regions of deep evolutionary origins

Biogeographic regions reflect the organization of biotas over long evolutionary timescales but face alterations from recent anthropogenic climate change. Here, we model species distributions for 189,269 vascular plant species of the world under present and future climates and use this data to generate biogeographic regions based on phylogenetic dissimilarity. Our analysis reveals declines in phylogenetic beta diversity for years 2040 to 2100, leading to a future homogenization of biogeographic regions. While some biogeographic boundaries will persist, climate change will alter boundaries separating biogeographic realms. Such boundary alterations will be determined by altitude variation, heterogeneity of temperature seasonality, and past climate velocity. Our findings suggest that human activities may now surpass the geological forces that shaped floristic regions over millions of years, calling for the mitigation of climate impacts to meet international biodiversity targets.

Neutrino emission due to pair – annihilation in the neutron star magnetic field

In this paper, we have calculated the energy loss in terms of luminosity for neutrinos produced by the annihilation of electron–positron pair in the light of Photo – Neutrino weak interaction with an intense magnetic field. After analytical calculation, we may conclude that the neutrino luminosity increases with the magnetic field in the temperature range of 108 to 1012 Kelvins giving rise to an energy loss channel. This may provide an alternate cooling mechanism for highly magnetized neutron stars. We have also conducted a comparative study of neutrino emission from magnetized neutron stars based on both Photo–Neutrino interaction and Conventional (current – current) weak interaction. We found a remarkable similarity between the two models on temperature versus energy loss behaviour of neutron stars. However, these are found to differ from one another on the overall time scale of evolution.

Main-belt comets as contributors to the near-Earth objects population

Aims. Most studies of the dynamics of main-belt objects describing the evolution of the bodies in inner Solar System have been carried with models that include weak nongravitational forces, such as the Yarkovsky and YORP effects. Only about 19 objects exhibit cometary-type activity, with sublimation being the principal mechanism. This paper presents a study of the influence of cometary- type nongravitational forces on the dynamics of main-belt comets, and the possible paths and timescales of evolution into other Solar System regions. Methods. We used the standard Marsden model for cometary-type activity. This model was designed for elongated orbits and the continuous ejection of mass, while the main-belt comets exhibit a different mode of activity. For this reason, we propose a simple model of nongravitational force activation that is consistent with observations. The dynamical evolution of objects was studied using a fifteenth-order RADAU integrator implemented in the REBOUND package. Results. The paper presents the dynamical routes of main-belt comets in the inner Solar System when cometary-type nongravitational forces are included in calculations. The forces significantly shorten the time of transition to other regions compared to the Yarkovsky effect, shortening this time to as little as a few thousand years depending on the frequency of the activity and the A1, A2, and A3 Marsden constants. There is a large probability of a transition to near-Earth object(NEO)-type orbits for bodies with A2 &lt; 0, which means that cometary-type nongravitational forces can be a non-negligible mechanism increasing the number of bodies in that population. The forces can also deliver active main-belt objects into mean motion resonances but can equally eject bodies into outer planetary regions on far shorter timescales than the Yarkovsky and YORP effects. Cometary-type nongravitational effects should be included in dynamical studies of individual sublimating active asteroids.

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.

Analysis of control measures inducing the evolution of infectious viral diseases

With the continuation of the infectious disease, pathogens mutate and interact with the resident pathogen. In this paper, we develop an SIR model that considers the evolution of viral virulence under the regulation of different defense strengths. By using infectious disease dynamics and evolutionary adaptive dynamics, we obtain the evolutionary criteria allowing for evolutionary branching and continuously stable strategy across varying intensities of prevention and control measures. Our study finds that robust prevention and control measures can contribute to a rapid evolutionary trend toward higher virulence. We perform a critical function analysis to reveal the evolutionary consequences of trade-offs of arbitrary shape and analyze a diverse range of evolutionary dynamics. Furthermore, we investigate the coexistence of two different strains and construct an evolutionary model to obtain their invasion fitness functions and the evolutionarily singular coalition of the dimorphism. We contemplate the presence of secondary branching on a significantly extended evolutionary time scale. Last, we conduct the numerical simulations to prove our theoretical findings. This reveals the law that the evolutionary state of pathogens is affected by the intensity of prevention and control strategies. The results and methods can be used as references for studying the effects of other factors on virus evolution.

Selective expansion of motor cortical projections in the evolution of vocal novelty.

Deciphering how cortical architecture evolves to drive behavioral innovations is a long-standing challenge in neuroscience and evolutionary biology. Here, we leverage a striking behavioral novelty in the Alston's singing mouse (Scotinomys teguina), compared to the laboratory mouse (Mus musculus), to quantitatively test models of motor cortical evolution. We used bulk tracing, serial two-photon tomography, and high-throughput DNA sequencing of over 76,000 barcoded neurons to discover a specific and substantial expansion (200%) of orofacial motor cortical (OMC) projections to the auditory cortical region (AudR) and the midbrain periaqueductal gray (PAG), both implicated in vocal behaviors. Moreover, analysis of individual OMC neurons' projection motifs revealed preferential expansion of exclusive projections to AudR. Our results imply that selective expansion of ancestral motor cortical projections can underlie behavioral divergence over short evolutionary timescales, suggesting potential mechanisms for the evolution of enhanced cortical control over vocalizations-a crucial preadaptation for human language.

Evolution of Semiconvective Staircases in Rotating Flows: Consequences for Fuzzy Cores in Giant Planets

Recent observational constraints on the internal structure of Jupiter and Saturn suggest that these planets have “fuzzy” cores, i.e., gradients of the concentration of heavy elements that might span a large fraction of the planet’s radius. These cores could be composed of a semiconvective staircase, i.e., multiple convective layers separated by diffusive interfaces arising from double-diffusive instabilities. However, to date, no study has demonstrated how such staircases can avoid layer mergers and persist over evolutionary timescales. In fact, previous work has found that these mergers occur rapidly, leading to only a single convective layer. Using 3D simulations, we demonstrate that rotation prolongs the lifetime of a convective staircase by increasing the timescale for both layer merger and erosion of the interface between the final two layers. We present an analytic model for the erosion phase, predicting that rotation increases the erosion time by a factor of approximately Ro−1/2, where Ro is the Rossby number of the convective flows (the ratio of the rotation period to the convective turnover time). For Jovian conditions at early times after formation (when convection is vigorous enough to mix a large fraction of the planet), we find the erosion time to be roughly 109 yr in the nonrotating case and 1011 yr in the rotating case. If these timescales are confirmed with a larger suite of numerical simulations, the existence of convective staircases within the deep interiors of giant planets is a strong possibility, and rotation could be an important factor in the preservation of their fuzzy cores.

The Divergent Responses of Salinity Generalists to Hyposaline Stress Provide Insights Into the Colonisation of Freshwaters by Diatoms.

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long-term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage-specific environmental responses in phytoplankton have shaped marine-freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions.

Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions

BackgroundShort interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution.ResultsWe found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a “mosaic” evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions.ConclusionHere we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. Moreover, through the study of their genomic distribution in five species, we highlighted commonalities and differences with other previously studied eukaryotes, thus extending our understanding of SINE evolution across the tree of life.

Sharp habitat shifts, evolutionary tipping points and rescue: Quantifying the perilous path of a specialist species towards a refugium in a changing environment

Specialist species thriving under specific environmental conditions in narrow geographic ranges are widely recognized as heavily threatened by climate deregulation. Many might rely on both their potential to adapt and to disperse towards a refugium to avoid extinction. It is thus crucial to understand the influence of environmental conditions on the unfolding process of adaptation. Here, I study the eco-evolutionary dynamics of a sexually reproducing specialist species in a two-patch quantitative genetic model with moving optima. Thanks to a separation of ecological and evolutionary time scales and the phase-line study of the selection gradient, I derive the critical environmental speed for persistence, which reflects how the existence of a refugium impacts extinction patterns and how it relates to the cost of dispersal. Moreover, the analysis provides key insights about the dynamics that arise on the path towards this refugium. I show that after an initial increase of population size, there exists a critical environmental speed above which the species crosses a tipping point, resulting into an abrupt habitat switch. In addition, when selection for local adaptation is strong, this habitat switch passes through an evolutionary “death valley”, leading to a phenomenon related to evolutionary rescue, which can promote extinction for lower environmental speeds than the critical one.