Abstract：
:In this article, we construct a generalization of the Blum-François Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification 'potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the generating, organizing and deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the generating, organizing and deleting processes where tree topology and branch lengths are jointly modelled and provide code in SageMath/Python for these algorithms.
journal_name
R Soc Open Scijournal_title
Royal Society open scienceauthors
Sainudiin R,Véber Adoi
10.1098/rsos.160016subject
Has Abstractpub_date
2016-05-11 00:00:00pages
160016issue
5issn
2054-5703pii
rsos160016journal_volume
3pub_type
杂志文章abstract：:In the paper, the isomorphous S O 4 ...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.180919
更新日期：2019-01-23 00:00:00
abstract：:Quantum computers are expected to have a dramatic impact on numerous fields due to their anticipated ability to solve classes of mathematical problems much more efficiently than their classical counterparts. This particularly applies to domains involving integer factorization and discrete logarithms, such as public ke...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.180410
更新日期：2018-06-20 00:00:00
abstract：:The aim of this study was to compare young and adult sprinters on several biomechanical parameters that were previously highlighted as performance-related and to determine the behaviour of several muscle-tendon units (MTU) in the first stance phase following a block start in sprint running. The ground reaction force (...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.180332
更新日期：2018-06-13 00:00:00
abstract：:To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. G...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.150370
更新日期：2015-09-09 00:00:00
abstract：:Feedback is typically incorporated in word learning paradigms, in both research studies and commercial language learning apps. While the common-sense view is that feedback is helpful during learning, relatively little empirical evidence exists about the role of feedback in spoken vocabulary learning. Some work has sug...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.171496
更新日期：2018-09-05 00:00:00
abstract：:[This corrects the article DOI: 10.1098/rsos.181356.]. ...
journal_title：Royal Society open science
pub_type： 杂志文章,已发布勘误
doi：10.1098/rsos.181855
更新日期：2018-11-28 00:00:00
abstract：:This paper presents simplified finite-element analysis procedures based on geometrical nonlinearity and ductile Mohr-Coulomb-Davis plasticity for analysis of bending behaviour of steel pipes subjected to lateral soil loading. A simple, and easy to implement, user-defined subroutine to represent soil stiffness using th...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.181550
更新日期：2019-07-10 00:00:00
abstract：:We consider a directed graph model for the human brain's neural architecture that is based on small scale, directed, strongly connected sub-graphs (SCGs) of neurons, that are connected together by a sparser mesoscopic network. We assume transmission delays within neuron-to-neuron stimulation, and that individual neuro...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.160912
更新日期：2017-04-05 00:00:00
abstract：:Prior experience influences visual perception. For example, extended viewing of a moving stimulus results in the misperception of a subsequent stimulus's motion direction-the direction after-effect (DAE). There has been an ongoing debate regarding the locus of the neural mechanisms underlying the DAE. We know the mech...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.190114
更新日期：2019-03-27 00:00:00
abstract：:Leishmaniasis is a vector-borne protozoan disease; it mainly originates from the bite of sandfly and initiated when parasite is transmitted to human at metacyclic flagellated promastigote form. In the current study, a synthesis of a series of 4-substituted benzophenone ethers 1-20 was carried out in good yields and th...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.171771
更新日期：2018-05-16 00:00:00
abstract：:Hierarchical VOOH hollow spheres with low crystallinity composed of nanoparticles were prepared by a facile and template-free method, which involved a precipitation of precursor microspheres in aqueous solution at room temperature and subsequent hydrothermal reaction. Quasi-solid-state symmetric and asymmetric superca...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.171768
更新日期：2018-01-31 00:00:00
abstract：:We model radicalization in a society consisting of two competing religious, ethnic or political groups. Each of the 'sects' is divided into moderate and radical factions, with intra-group transitions occurring either spontaneously or through indoctrination. We also include the possibility of one group violently attack...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.170678
更新日期：2017-08-30 00:00:00
abstract：:The rapid rise of the CO2 level in the atmosphere has spurred the development of CO2 capture methods such as the use of biomimetic complexes that mimic carbonic anhydrase. In this study, model complexes with tris(2-pyridylmethyl)amine (TPA) were synthesized using various transition metals (Zn2+, Cu2+ and Ni2+) to cont...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.190407
更新日期：2019-08-07 00:00:00
abstract：:Due to a wide range of applications, sand casting occupies an important position in modern casting practice. The main purpose of this study was to optimize the performance parameters of sand casting based on grey relational analysis and predict the missing data using back propagation (BP) neural network. First, the in...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.181860
更新日期：2019-08-07 00:00:00
abstract：:[This corrects the article DOI: 10.1098/rsos.181295.]. ...
journal_title：Royal Society open science
pub_type： 已发布勘误
doi：10.1098/rsos.201358
更新日期：2020-09-16 00:00:00
abstract：:Social insects live in dense groups with a high probability of disease transmission and have therefore faced strong pressures to develop defences against pathogens. For this reason, social insects have been hypothesized to invest in antimicrobial secretions as a mechanism of external immunity to prevent the spread of ...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.171332
更新日期：2018-02-07 00:00:00
abstract：:Many species worldwide are impacted by habitat loss. This may result in increased competition both within species and between species. Many studies have demonstrated that when two previously non-overlapping species are forced to compete over a resource, one species is likely to become dominant over the other. This stu...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.160621
更新日期：2017-01-18 00:00:00
abstract：:Artificial microswimmers powered by magnetic fields have numerous applications, such as drug delivery, biosensing for minimally invasive medicine and environmental remediation. Recently, a Janus microdimer surface walker that can be propelled by an oscillating magnetic field near a surface was reported by Li et al. (A...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.200378
更新日期：2020-12-09 00:00:00
abstract：:Carminic acid, a natural hydrophilic dye extensively used in the food and cosmetic industries, is converted in hydrophobic dyes by acetylation or pivaloylation. These derivatives are successfully used as biocolourants for rubber objects. In this paper, spectroscopic properties of the carminic acid derivatives in dimet...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.172399
更新日期：2018-07-04 00:00:00
abstract：:The phylogenetic relationships of the recently described genus †Ticinolepis from the Middle Triassic of the Monte San Giorgio are explored through cladistic analyses of the so far largest morphological dataset for fossil actinopterygians, including representatives of the crown-neopterygian clades Halecomorphi, Ginglym...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.172337
更新日期：2018-03-21 00:00:00
abstract：:Many important data types, such as the spike trains recorded from neurons in typical electrophysiological experiments, have a natural notion of distance or similarity between data points, even though there is no obvious coordinate system. Here, a simple Kozachenko-Leonenko estimator is derived for calculating the mutu...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.140391
更新日期：2015-05-13 00:00:00
abstract：:Insect wing veins are biological composites of chitin and protein arranged in a complex lamellar configuration. Although these hierarchical structures are found in many 'venous wings' of insects, very little is known about their physical and mechanical characteristics. For the first time, we carried out a systematic c...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.160006
更新日期：2016-02-17 00:00:00
abstract：:Zeolitic-imidazole frameworks (ZIFs), as novel porous materials, are attracting much attention in several fields due to their special advantages such as large specific surface area, versatile porosity and well-connected networks. Here, we develop a porous ZIF-derived catalytic thin film, which was coated on the conduc...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.180335
更新日期：2018-05-30 00:00:00
abstract：:Exposed limestone karst landscapes, especially in the tropics, are often home to distinctive and specialized biotas. Among vertebrates, a particularly large number of karst-associated lizard taxa have been described, but for the vast majority, evidence of specific adaptions to karst is lacking. A number of studies, ho...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.170781
更新日期：2017-11-15 00:00:00
abstract：:Group living animals may eavesdrop on signalling interactions between conspecifics and integrate it with their own past social experience in order to optimize the use of relevant information from others. However, little is known about this interplay between public (eavesdropped) and private social information. To inve...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.150220
更新日期：2015-08-26 00:00:00
abstract：:The theory of evolution by natural selection can help explain why people care about other species. Building upon recent insights that morality evolves to secure fitness advantages of cooperation, we propose that conservation ethics (moral beliefs, attitudes, intuitions and norms regarding other species) could be adapt...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.181038
更新日期：2018-11-21 00:00:00
abstract：:The differences in life-history traits and processes between organisms living in the same or different populations contribute to their ecological and evolutionary dynamics. We developed mixed-effect model formulations of the popular size-at-age von Bertalanffy and Gompertz growth functions to estimate individual and g...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.192146
更新日期：2020-04-08 00:00:00
abstract：:This paper presents a study of lead zirconate titanate (PZT) films hydrothermally grown on a dome-shaped titanium diaphragm. Few articles in the literature address the implementation of hydrothermal PZT films on curved-diaphragm substrates for resonators. In this study, a 50-μm-thick titanium sheet is embossed using b...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.171363
更新日期：2017-12-20 00:00:00
abstract：:There is a long-standing interest in behavioural ecology, exploring the causes and correlates of consistent individual differences in mean behavioural traits ('personality') and the response to the environment ('plasticity'). Recently, it has been observed that individuals also consistently differ in their residual in...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.160352
更新日期：2016-10-26 00:00:00
abstract：:Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmenta...
journal_title：Royal Society open science
pub_type： 杂志文章
doi：10.1098/rsos.160239
更新日期：2016-06-22 00:00:00
