Standard Evolution Models Research Articles

Phase transition in the sample complexity of likelihood-based phylogeny inference

Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical physics and that connection has led to important insights on the theoretical properties of phylogenetic reconstruction algorithms as well as the development of new inference methods. Here, we study maximum likelihood, a classical statistical technique which is perhaps the most widely used in phylogenetic practice because of its superior empirical accuracy. At the theoretical level, except for its consistency, that is, the guarantee of eventual correct reconstruction as the size of the input data grows, much remains to be understood about the statistical properties of maximum likelihood in this context. In particular, the best bounds on the sample complexity or sequence-length requirement of maximum likelihood, that is, the amount of data required for correct reconstruction, are exponential in the number, n, of tips—far from known lower bounds based on information-theoretic arguments. Here we close the gap by proving a new upper bound on the sequence-length requirement of maximum likelihood that matches up to constants the known lower bound for some standard models of evolution. More specifically, for the r-state symmetric model of sequence evolution on a binary phylogeny with bounded edge lengths, we show that the sequence-length requirement behaves logarithmically in n when the expected amount of mutation per edge is below what is known as the Kesten-Stigum threshold. In general, the sequence-length requirement is polynomial in n. Our results imply moreover that the maximum likelihood estimator can be computed efficiently on randomly generated data provided sequences are as above. Our main technical contribution, which may be of independent interest, relates the total variation distance between the leaf state distributions of two trees with a notion of combinatorial distance between the trees. In words we show in a precise quantitative manner that the more different two evolutionary trees are, the easier it is to distinguish their output.

LSPM J1314+1320: An Oversized Magnetic Star with Constraints on the Radio Emission Mechanism

Abstract LSPM J1314+1320 (=NLTT 33370) is a binary star system consisting of two nearly identical pre-main-sequence stars of spectral type M7. The system is remarkable among ultracool dwarfs for being the most luminous radio emitter over the widest frequency range. Masses and luminosities are at first sight consistent with the system being coeval at age ∼80 Myr according to standard (nonmagnetic) evolutionary models. However, these models predict an average effective temperature of ∼2950 K, which is 180 K hotter than the empirical value. Thus, the empirical radii are oversized relative to the standard models by ≈13%. We demonstrate that magnetic stellar models can quantitatively account for the oversizing. As a check on our models, we note that the radio emission limits the surface magnetic field strengths: the limits depend on identifying the radio emission mechanism. We find that the field strengths required by our magnetic models are too strong to be consistent with gyrosynchrotron emission but are consistent with electron cyclotron maser emission.

APPARENT NON-COEVALITY AMONG THE STARS IN UPPER SCORPIO: RESOLVING THE PROBLEM USING A MODEL OF MAGNETIC INHIBITION OF CONVECTION

ABSTRACT Two eclipsing binaries in the USco association have recently yielded precise values of masses and radii for four low-mass members of the association. Standard evolution models would require these dM4.5–dM5 stars to have ages which are younger than those of more massive stars in the association by factors which appear (in extreme cases) to be as large as ∼3. Are the stars in the association therefore non-coeval? We suggest that the answer is no: by incorporating the effects of magnetic inhibition of convective onset, we show that the stars in USco can be restored to coevality provided the four low-mass member stars have vertical surface fields in the range 200–700 G. Fields of such magnitude have already been measured on the surface of certain solar-type stars in other young clusters.

Massive stars in advanced evolutionary stages, and the progenitor of GW150914

AbstractThe recent discovery of a gravitational wave from the merging of two black holes of about 30 solar masses each challenges our incomplete understanding of massive stars and their evolution. Critical ingredients comprise mass-loss, rotation, magnetic fields, internal mixing, and mass transfer in close binary systems. The imperfect knowledge of these factors implies large uncertainties for models of stellar populations and their feedback. In this contribution we summarize our empirical studies of Wolf-Rayet populations at different metallicities by means of modern non-LTE stellar atmosphere models, and confront these results with the predictions of stellar evolution models. At the metallicity of our Galaxy, stellar winds are probably too strong to leave remnant masses as high as ~30 M⊙, but given the still poor agreement between evolutionary tracks and observation even this conclusion is debatable. At the low metallicity of the Small Magellanic Cloud, all WN stars which are (at least now) single are consistent with evolving quasi-homogeneously. O and B-type stars, in contrast, seem to comply with standard evolutionary models without strong internal mixing. Close binaries which avoided early merging could evolve quasi-homogeneously and lead to close compact remnants of relatively high masses that merge within a Hubble time.

The impact of rate heterogeneity on inference of phylogenetic models of trait evolution.

Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small‐scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate‐static and variable‐rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate‐heterogeneity scenarios. Our results show that rate heterogeneity is present across small‐scaled avian clades, and consequently applying only standard single‐process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable‐rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable‐rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.

The effect of pair-instability mass loss on black-hole mergers

Mergers of two stellar origin black holes are a prime source of gravitational waves and are under intensive investigations. One crucial ingredient in their modeling has so far been neglected. Pair-instability pulsation supernovae with associated severe mass loss may suppress formation of massive black holes, decreasing black hole merger rates for the highest black hole masses. The mass loss associated with pair-instability pulsation supernovae limits the Population I/II stellar-origin black hole mass to 50 Msun, in tension with earlier predictions that the maximum black hole mass could be as high as 100 Msun. Suppression of double black hole merger rates by pair-instability pulsation supernovae is negligible for our evolutionary channel. Our standard evolutionary model with inclusion of pair-instability pulsation supernovae and with pair-instability supernovae is fully consistent with the LIGO detections of black hole mergers: GW150914, GW151226 and LVT151012. The LIGO observations seem to exclude high (>400 km/s) BH natal kicks. We predict the detection of several up to 60 BH-BH mergers with total mass 10--150 Msun (most likely range: 20--80 Msun) in the forthcoming 60 effective days of LIGO O2 observations.

Spectral type, temperature, and evolutionary stage in cool supergiants

In recent years, temperature scales in cool supergiants (CSGs) have been disputed, and the possibility that spectral types (SpTs) do not depend primarily on temperature has been raised. We explore the relations between different observed parameters and the capability of deriving accurate intrinsic stellar parameters from them through the analysis of the largest spectroscopic sample of CSGs to date from SMC and LMC. We explore possible correlations between different observational parameters, also making use of near- and mid-infrared colours and literature on photometric variability. Direct comparison between the behaviour of atomic lines (Fe I, Ti I, and Ca II) in the observed spectra and synthetic atmospheric models provides compelling evidence that effective temperature is the prime underlying variable driving the SpT sequence in CSGs. However, there is a clear correlation between SpT and luminosity, with later ones tending to correspond to more luminous stars with heavier mass loss. The population of CSGs in the SMC is characterised by a higher degree of spectral variability, early spectral types (centred on type K1) and low mass-loss rates (at least as measured by dust-sensitive mid-infrared colours). The population in the LMC displays less spectroscopic variability and later spectral types. The distribution of spectral types is not single-peaked. Instead, the brightest CSGs have a significantly different distribution from less luminous objects, presenting mostly M subtypes (centred on M2), and increasing mass-loss rates for later types. In conclusion, the observed properties of CSGs in the SMC and the LMC cannot be described correctly by standard evolutionary models. The very strong correlation between spectral type and bolometric luminosity, supported by all data from the Milky Way, cannot be reproduced at all by current evolutionary tracks.

Macroscopic strength of oceanic lithosphere revealed by ubiquitous fracture-zone instabilities

The origin of plate tectonics is one of the most fundamental issues in earth and planetary sciences. Laboratory experiments indicate that the viscosity of silicate rocks is so strongly temperature-dependent that the entire surface of the Earth should be one immobile rigid plate. The rheology of oceanic lithosphere is, however, still poorly understood, and there exist few constraints on the temperature dependency of viscosity on the field scale. Here we report a new kind of observational constraint based on the geoid along oceanic fracture zones. We identify a large number of conspicuous small-scale geoid anomalies, which cannot be explained by the standard evolution model of oceanic lithosphere, and estimate their source density perturbations using a new Bayesian inversion method. Our results suggest that they are caused most likely by small-scale convection involving temperature perturbations of ∼300 K±100 K. Such thermal contrast requires the activation energy of mantle viscosity to be as low as 100±50 kJmol−1 in case of diffusion creep, and 225±112 kJmol−1 in case of dislocation creep, substantially reducing the thickness of the stiffest part of oceanic lithosphere. Oceanic lithosphere may thus be broken and bent much more easily than previously thought, facilitating the operation of plate tectonics.

Homeostasis and the physiological dimension of niche construction theory in ecology and evolution

Niche construction theory (NCT) has been represented as a new and comprehensive theory of evolution, one that breaks the constraints imposed by the dominant and largely gene-selectionist standard evolutionary model that is presently mischaracterized as “Darwinian.” I will argue that NCT is not so much a new theory, as it is a fruitful readmission of a venerable physiological perspective on adaptation, selection and evolution. This perspective is closer in spirit and philosophy to the original (and richer) Darwinian idea developed by Darwin himself, and that animated much of the rich late nineteenth century debate about evolution, heredity, adaptation and development, a debate that was largely eclipsed by the early twentieth century emergence of the Neodarwinian synthesis. I will argue that a full realization of the promise of NCT turns on a full understanding of another intellectual revolution of the nineteenth century, Claude Bernard’s conception of homeostasis, a profound statement of the nature of life that has, through the twentieth century, come to be widely misunderstood and trivialized.

Dichotomy in the population of young AGN: Optical, radio, and X‐ray properties

AbstractThere are numerous examples of radio sources with various sizes which surprisingly exhibit very similar morphology. This observational fact helped to create a standard evolutionary model in which young and small radio‐loud active galactic nuclei (AGN), called gigahertz‐peaked spectrum (GPS) sources and compact steep spectrum (CSS) sources, become largescale radio objects. However, many details of this evolutionary process are still unclear. We explored evolution scenarios of radio‐loud AGN using new radio, optical and X‐ray data of so far unstudied low luminosity compact (LLC) sources and we summarize the results in this paper. Our studies show that the evolutionary track is very “individualized” although we can mention common factors affecting it. These are interaction with the ambient medium and AGN power. The second feature affects the production of the radio jets which, if they are weak, are more vulnerable for instabilities and disruption. Thus not all GPS and CSS sources will be able to develop large scale morphologies. Many will fade away being middleaged (105 yr). It seems that only radio strong, high excitation compact AGN can be progenitors of large‐scale FRII radio sources. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

TheGaia-ESO Survey: Stellar radii in the young open clusters NGC 2264, NGC 2547, and NGC 2516

Rapidly rotating, low-mass members of eclipsing binary systems have measured radii significantly larger than predicted by standard models. It has been proposed that magnetic activity is responsible for radius inflation. By estimating the radii of low-mass stars in three young clusters (NGC 2264, NGC 2547, NGC 2516, with ages of 5, 35 and 140 Myr respectively), we aim to establish whether similar radius inflation is seen in single, magnetically active stars. We use radial velocities from the Gaia-ESO Survey (GES) and published photometry to establish cluster membership and combine GES measurements of vsini with published rotation periods to estimate average radii for groups of fast-rotating cluster members as a function of their luminosity and age. The average radii are compared with the predictions of both standard evolutionary models and variants that include magnetic inhibition of convection and starspots. At a given luminosity, the stellar radii in NGC 2516 and NGC 2547 are larger than predicted by standard evolutionary models at the ages of these clusters. The discrepancy is least pronounced and not significant ~10 percent) in ZAMS stars with radiative cores, but more significant in lower-mass, fully convective pre main-sequence cluster members, reaching 30+/-10 percent. The uncertain age and distance of NGC 2264 preclude a reliable determination of any discrepancy for its members. The median radii we have estimated for low-mass fully convective stars in the older clusters are inconsistent (at the 2-3 sigma level) with non-magnetic evolutionary models and more consistent with models that incorporate the effects of magnetic fields or dark starspots. The available models suggest this requires either surface magnetic fields exceeding 2.5 kG, spots that block about 30 per cent of the photospheric flux, or a more moderate combination of both. [Abridged]

The social evolution of genocide across time and geographic space: Perspectives from evolutionary game theory

A standard evolutionary game theory model is used to reveal the interpersonal and geographic characteristics of a population that make it vulnerable to accepting the genocidal aims of political leaders. Under conditions identified in the space-less version of the model, genocide architects can engineer the social metamorphosis of a peaceful people-group into one that supports, or does not resist, the architects’ atrocity goals. The model reveals policy interventions that prevent the social evolution of genocide among the population. The model is then extended into geographic space by analyzing interactions among peaceful and aggressive phenotypes in a Moore neighborhood. Key concepts of the analyses are applied to the onset and spread of genocide during the Holocaust (1938-1945) and to the prevention of genocide in Côte d'Ivoire (2011). [JEL codes: C73, D74]

Absolute parameters of young stars: GG Lup and μ1 Sco

New high-resolution spectroscopy and $BVR$ photometry, together with literature data, on the Gould's Belt close binary systems GG Lup and $\mu^1$ Sco are presented and analysed. In the case of GG Lup, light and radial velocity curve fittings confirm a near-Main-Sequence picture of a pair of close stars. Absolute parameters are found, to within a few percent, thus: $M_1$ = 4.16$\pm$0.12, $M_2$ = 2.64$\pm$0.12, $R_{1}$ = 2.42$\pm$0.05, $R_2$ = 1.79$\pm$0.04, ($\odot$); $T_{1}$ $\sim$13000, $T_2$ $\sim$10600 (K); photometric distance $\sim$ 160 (pc). The high eccentricity and relatively short period (105 y) of apsidal revolution may be related to an apparent `slow B-type pulsator' (SPB) oscillation. Disturbances of the outer envelope of at least one of the components then compromise comparisons to standard evolutionary models, at least regarding the age of the system. A rate of apsidal advance is derived, which allows a check on the mean internal structure constant $\bar{k_2} = 0.0058 \pm 0.0004$. This is in agreement with values recently derived for young stars of solar composition and mass $\sim$3${\odot}$. For $\mu^1$ Sco, we agree with previous authors that the secondary component is considerably oversized for its mass, implying binary (interactive) stellar evolution, probably of the `Case A' type. The primary appears relatively little affected by this evolution, however. Its parameters show consistency with a star of its derived mass at age about 13 My, consistent with the star's membership of the Sco-Cen OB2 Association. The absolute parameters are as follows: $M_1$ = 8.3$\pm$1.0, $M_2$ = 4.6$\pm$1.0, $R_{1}$ = 3.9$\pm$0.3, $R_2$ = 4.6$\pm$0.4, ($\odot$); $T_{1}$ $\sim$24000, $T_2$ $\sim$17000 (K); photometric distance $\sim$ 135 (pc).

Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.

There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.

An introduction to epigenetics as the link between genotype and environment: a personal view.

Lamarck was one of the first scientists who attempted to explain evolution, and he is especially well known for formulating the concept that acquired characteristics can be transmitted to future generations and may therefore steer evolution. Although Lamarckism fell out of favour soon after the publication of Darwin's work on natural selection and evolution, the concept of transmission of acquired characteristics has recently gained renewed attention and has led to some rethinking of the standard evolutionary model. Epigenetics, or the study of heritable (mitotically and/or meiotically) changes in gene activity that are not brought about by changes in the DNA sequence, can explain some types of ill health in offspring, which have been exposed to stressors during early development, when DNA is most susceptible to such epigenetic influences. In this review, we explain briefly the history of epigenetics and we propose some examples of epigenetic and transgenerational effects demonstrated in humans and animals. Growing evidence is available that the health and phenotype of a given individual is already shaped shortly before and after the time of conception. Some evidence suggests that epigenetic markings, which have been established around conception, can also be transmitted to future generations. This knowledge can possibly be used to revolutionize animal breeding and to increase human and animal health worldwide.

THE METAL-POOR KNEE IN THE FORNAX DWARF SPHEROIDAL GALAXY

We present alpha-element abundances of Mg, Si, and Ti for a large sample of field stars in two outer fields of the Fornax dwarf spheroidal galaxy (dSph), obtained with VLT/GIRAFFE (R~16,000). Due to the large fraction of metal-poor stars in our sample, we are able to follow the alpha-element evolution from [Fe/H]=-2.5 continuously to [Fe/H]=-0.7 dex. For the first time we are able to resolve the turnover from the Type II supernovae (SNe) dominated, alpha-enhanced plateau down to subsolar [alpha/Fe] values due to the onset of SNe Ia, and thus to trace the chemical enrichment efficiency of the galaxy. Our data support the general concept of an alpha-enhanced plateau at early epochs, followed by a well-defined "knee", caused by the onset of SNe Ia, and finally a second plateau with sub-solar [alpha/Fe] values. We find the position of this knee to be at [Fe/H]=-1.9 and therefore significantly more metal-poor than expected from comparison with other dSphs and standard evolutionary models. Surprisingly, this value is rather comparable to the knee in Sculptor, a dSph about 10 times less luminous than Fornax. Using chemical evolution models, we find that both the position of the knee as well as the subsequent plateau at sub-solar level can hardly be explained unless the galaxy experienced several discrete star formation events with a drastic variation in star formation efficiency, while a uniform star formation can be ruled out. One possible evolutionary scenario is that Fornax experienced one or several major accretion events from gas-rich systems in the past, so that its current stellar mass is not indicative of the chemical evolution environment at ancient times. If Fornax is the product of several smaller building blocks, this may also have implications of the understanding on the formation process of dSphs in general.

Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution.

Red horizontal branch stars in the Galactic field: A chemical abundance survey

A large sample survey of Galactic red horizontal-branch (RHB) stars was conducted to investigate their atmospheric parameters and elemental abundances. High-resolution spectra of 76 Galactic field stars were obtained with the 2.7 m Smith Telescope at McDonald Observatory. Only the color and the parallax were considered during the selection of the field stars. Equivalent width or synthetic spectrum analyses were used in order to determine the relative abundances of the following elements: proton-capture elements C, N, O and Li, alpha-elements Ca and Si, and neutron-capture elements Eu and La. Additionally, 12 C/ 13 C isotopic ratios were derived by using the CN features mainly located in the 7995 − 8040 spectral region. The evaluation of effective temperatures, surface gravities and 12 C/ 13 C isotopic ratios together with evolutionary stages of the candidates revealed that 18 out of 76 stars in our sample are probable RHBs. Including both kinematic and evolutionary status information, we conclude that we have five thick disk and 13 thin disk RHB stars in our sample. Although RHB stars have been regarded as thick disk members of the Galaxy, the low-velocity RHBs with a solar metallicity in our sample suggests the existence of a large number of thin disk RHBs, which cannot be easily explained by standard stellar evolutionary models.

KELT-1b: A STRONGLY IRRADIATED, HIGHLY INFLATED, SHORT PERIOD, 27 JUPITER-MASS COMPANION TRANSITING A MID-F STAR

We present the discovery of KELT-1b, the first transiting low-mass companion from the wide-field Kilodegree Extremely Little Telescope-North (KELT-North) survey. The V=10.7 primary is a mildly evolved, solar-metallicity, mid-F star. The companion is a low-mass brown dwarf or super-massive planet with mass of 27.23+/-0.50 MJ and radius of 1.110+0.037-0.024 RJ, on a very short period (P=1.21750007) circular orbit. KELT-1b receives a large amount of stellar insolation, with an equilibrium temperature assuming zero albedo and perfect redistribution of 2422 K. Upper limits on the secondary eclipse depth indicate that either the companion must have a non-zero albedo, or it must experience some energy redistribution. Comparison with standard evolutionary models for brown dwarfs suggests that the radius of KELT-1b is significantly inflated. Adaptive optics imaging reveals a candidate stellar companion to KELT-1, which is consistent with an M dwarf if bound. The projected spin-orbit alignment angle is consistent with zero stellar obliquity, and the vsini of the primary is consistent with tidal synchronization. Given the extreme parameters of the KELT-1 system, we expect it to provide an important testbed for theories of the emplacement and evolution of short-period companions, and theories of tidal dissipation and irradiated brown dwarf atmospheres.

Efficiency and stochastic stability in normal form games

Standard evolutionary game models select the risk-dominant equilibrium, even if it is not efficient. On the other hand, Robson [Robson, A.J., 1990. Efficiency in evolutionary games: Darwin, Nash and the secret handshake. J. Theoret. Biol. 144, 379–396] argues that genes can achieve efficient outcomes with a payoff-irrelevant type, even if such outcomes are not Nash. This paper follows Robsonʼs approach but assumes that a more complex mutation in both the type and the behavior is an order of magnitude less likely than a simpler mutation in only the type or the behavior. In weakly acyclic games, every long-run stable strategy profile is a strict Nash equilibrium. Meanwhile, a Pareto undominated strict Nash equilibrium is stochastically stable if for each player, the opponentsʼ equilibrium action profile uniquely maximizes his payoff given his equilibrium action. These results can be generalized to generic cyclic two-person games. In a common interests game, a strategy profile is selected if and only if it yields the unique Pareto efficient payoff vector.