evolutionary models
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2022 ◽  
Author(s):  
Michael Sennett ◽  
Douglas Theobald

Ancestral sequence reconstruction (ASR) has become widely used to analyze the properties of ancient biomolecules and to elucidate the mechanisms of molecular evolution. By recapitulating the structural, mechanistic, and functional changes of proteins during their evolution, ASR has been able to address many fundamental and challenging evolutionary questions where more traditional methods have failed. Despite the tangible successes of ASR, the accuracy of its reconstructions is currently unknown, because it is generally impossible to compare resurrected proteins to the true ancient ancestors that are now extinct. Which evolutionary models are the best for ASR? How accurate are the resulting inferences? Here we answer these questions by applying cross-validation (CV) to sets of aligned extant sequences. To assess the adequacy of a chosen evolutionary model for predicting extant sequence data, our column-wise CV method iteratively cross-validates each column in an alignment. Unlike other phylogenetic model selection criteria, this method does not require bias correction and does not make restrictive assumptions commonly violated by phylogenetic data. We find that column-wise CV generally provides a more conservative criterion than the AIC by preferring less complex models. To validate ASR methods, we also apply cross-validation to each sequence in an alignment by reconstructing the extant sequences using ASR methodology, a method we term extant sequence reconstruction (ESR). We can thus quantify the accuracy of ASR methodology by comparing ESR reconstructions to the corresponding true sequences. We find that a common measure of the quality of a reconstructed sequence, the average probability of the sequence, is indeed a good estimate of the fraction of the sequence that is correct when the evolutionary model is accurate or overparameterized. However, the average probability is a poor measure for comparing reconstructions, because more accurate phylogenetic models typically result in reconstructions with lower average probabilities. In contrast, the entropy of the reconstructed distribution is a reliable indicator of the quality of a reconstruction, as the entropy provides an accurate estimate of the log-probability of the true sequence. Both column-wise CV and ESR are useful methods to validate evolutionary models used for ASR and can be applied in practice to any phylogenetic analysis of real biological sequences.


2022 ◽  
Vol 924 (2) ◽  
pp. 44
Author(s):  
Erin Aadland ◽  
Philip Massey ◽  
D. John Hillier ◽  
Nidia Morrell

Abstract We present a spectral analysis of four Large Magellanic Cloud (LMC) WC-type Wolf–Rayet (WR) stars (BAT99-8, BAT99-9, BAT99-11, and BAT99-52) to shed light on two evolutionary questions surrounding massive stars. The first is: are WO-type WR stars more oxygen enriched than WC-type stars, indicating further chemical evolution, or are the strong high-excitation oxygen lines in WO-type stars an indication of higher temperatures. This study will act as a baseline for answering the question of where WO-type stars fall in WR evolution. Each star’s spectrum, extending from 1100 to 25000 Å, was modeled using cmfgen to determine the star’s physical properties such as luminosity, mass-loss rate, and chemical abundances. The oxygen abundance is a key evolutionary diagnostic, and with higher resolution data and an improved stellar atmosphere code, we found the oxygen abundance to be up to a factor of 5 lower than that of previous studies. The second evolutionary question revolves around the formation of WR stars: do they evolve by themselves or is a close companion star necessary for their formation? Using our derived physical parameters, we compared our results to the Geneva single-star evolutionary models and the Binary Population and Spectral Synthesis (BPASS) binary evolutionary models. We found that both the Geneva solar-metallicity models and BPASS LMC-metallicity models are in agreement with the four WC-type stars, while the Geneva LMC-metallicity models are not. Therefore, these four WC4 stars could have been formed either via binary or single-star evolution.


2021 ◽  
Vol 163 (1) ◽  
pp. 26
Author(s):  
K. L. Luhman ◽  
T. L. Esplin

Abstract We present spectroscopy of 285 previously identified candidate members of populations in the Sco-Cen complex, primarily Ophiuchus, Upper Sco, and Lupus. The spectra are used to measure spectral types and diagnostics of youth. We find that 269 candidates exhibit signatures of youth in our spectra or previous data, which is consistent with their membership in Sco-Cen. We have constructed compilations of candidate members of Ophiuchus, Upper Sco, and Lupus that have spectral classifications and evidence of youth, which contain a total of 2274 objects. In addition, we have used spectra from previous studies to classify three sources in Ophiuchus that have been proposed to be protostellar brown dwarfs: ISO Oph 70, 200, and 203. We measure spectral types of early M from those data, which are earlier than expected for young brown dwarfs based on evolutionary models (≳M6.5) and instead are indicative of stellar masses (∼0.6 M ⊙).


2021 ◽  
Author(s):  
Nhan Ly-Trong ◽  
Suha Naser-Khdour ◽  
Robert Lanfear ◽  
Bui Quang Minh

Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programs exist, but the most feature-rich programs tend to be rather slow, and the fastest programs tend to be feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly-used rate matrix and probability matrix approach. AliSim takes 1.3 hours and 1.3 GB RAM to simulate alignments with one million sequences or sites, while popular software Seq-Gen, Dawg, and INDELible require two to five hours and 50 to 500 GB of RAM. We provide AliSim as an extension of the IQ-TREE software version 2.2, freely available at www.iqtree.org, and a comprehensive user tutorial at http://www.iqtree.org/doc/AliSim.


2021 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Michael T. Monaghan

Our understanding of the eukaryote tree of life is continually improving, although the branching events at some of the deepest nodes remain elusive. The fungi are an ancient group of eukaryotes with a wide range of morphologies, life-history strategies, and ecological roles. While several recent phylogenomic analyses have been shown to be a powerful tool for uncovering even earliest diversifications, no study has yet examined the entire tree of fungi using a taxonomically comprehensive data set and suitable models of evolution. Here, we assembled a data set of 299 proteins from all recognised fungal groups for which genomic/transcriptomic data were available and subjected this to a battery of analyses, including tree inferences using site-heterogeneous mixture models and the Multi-Species Coalescent model. Tree topology was highly congruent and well supported, and any incongruence was found to result from an inability of some frequently used evolutionary models to model fast-evolving and heterogeneous sites. Our results provide higher resolution among early-branching lineages than previous studies, and shed light on hitherto highly contested evolutionary origins of the major fungal groups.


Author(s):  
Иван Игоревич Волков

Несмотря на многообразие современных научных знаний проблема человека и его эволюции остается актуальной в интердисциплинарной перспективе. Анализ одной из таких эволюционных моделей, созданной французским философом Пьером Тейяром де Шарденом в его труде «Феномен Человека», является целью статьи. В ее формате рассмотрены философские, теологические и научные идеи, позволившие этому автору создать собственное оригинальное видение феномена человека, до сих пор оживленно обсуждаемое представителями различных научных дисциплин, философами и теологами. Despite the diversity of contemporary scientific knowledge, the problem of man and his evolution remains relevant in an interdisciplinary perspective. The analysis of one of such evolutionary models created by the French philosopher Pierre Teilhard de Chardin in his work «The Phenomenon of Man» is the aim of this article. In its format, philosophical, theological and scientific ideas that allowed this author to create his own original vision of the human phenomenon are considered. They are still actively discussed by representatives of various scientific disciplines, philosophers and theologians.


2021 ◽  
Author(s):  
Juan Afonso ◽  
Walid Ben Mansour ◽  
Suzanne O’Reilly ◽  
William Griffin ◽  
Farshad Salajeghegh ◽  
...  

The thermochemical structure of the subcontinental mantle holds crucial information on its origin and evolution that can inform energy and mineral exploration strategies, natural haz-ard mitigation and evolutionary models of the Earth1−4. However, imaging the fine-scale thermochemical structure of continental lithosphere remains a major challenge. Here we combine multiple land and satellite datasets via thermodynamically-constrained inversions to obtain a high-resolution thermochemical model of central and southern Africa. Results reveal diverse structures and compositions for cratons, indicating distinct evolutions and responses to geodynamic processes. While much of the Kaapvaal lithosphere retained its cra-tonic features, the western Angolan-Kasai shield and the Rehoboth block have lost their cra-tonic keels. The lithosphere of the Congo Craton has been affected by metasomatism, increas-ing its density and inducing its conspicuous low-topography, geoid and magnetic anomalies. Our results reconcile mantle structure with the causes and location of volcanism within and around the Tanzanian Craton, whereas the absence of volcanism towards the north is the result of local asthenospheric downwellings, not to a previously-proposed lithospheric root connecting with the Congo Craton. Our study offers greatly improved integration of man-tle structure, magmatism and the evolution and destruction of cratonic lithosphere and lays the groundwork for new evolutionary models and exploration frameworks for the Earth and other terrestrial planets.


2021 ◽  
Author(s):  
Ignacio Quintero ◽  
Marc A. Suchard ◽  
Walter Jetz

How and why lineages evolve along niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a comprehensive empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of external episodic and biotic factors remains poorly understood. Here we characterize species' two-dimensional temperature and precipitation niche space occupied (i.e., species niche envelope) as complex geometries and assess their evolution across a large vertebrate radiation (all Aves) using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the K-Pg boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution as lineages diversify, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings share the limitations of all work based purely on extant taxa but highlight the growing ecological and conservation insights arising from the model-based integration of increasingly comprehensive and robust environmental and phylogenetic information.


2021 ◽  
Vol 923 (2) ◽  
pp. 177
Author(s):  
Javier Serna ◽  
Jesus Hernandez ◽  
Marina Kounkel ◽  
Ezequiel Manzo-Martínez ◽  
Alexandre Roman-Lopes ◽  
...  

Abstract We present a large-scale study of stellar rotation for T Tauri stars in the Orion star-forming complex. We use the projected rotational velocity ( v sin ( i ) ) estimations reported by the APOGEE-2 collaboration as well as individual masses and ages derived from the position of the stars in the HR diagram, considering Gaia-EDR3 parallaxes and photometry plus diverse evolutionary models. We find an empirical trend for v sin ( i ) decreasing with age for low-mass stars (0.4M ⊙ < M * < 1.2M ⊙). Our results support the existence of a mechanism linking v sin ( i ) to the presence of accreting protoplanetary disks, responsible for regulating stellar rotation on timescales of about 6 Myr, which is the timescale in which most of the T Tauri stars lose their inner disk. Our results provide important constraints to models of rotation in the early phases of evolution of young stars and their disks.


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