scholarly journals Bayesian phylogenetic analysis of linguistic data using BEAST

2021 ◽  
Author(s):  
Konstantin Hoffmann ◽  
Remco Bouckaert ◽  
Simon J Greenhill ◽  
Denise Kühnert
Keyword(s):  
Phylogenetic Analysis ◽  
Language Evolution ◽  
Software Tool ◽  
Theoretical Background ◽  
Linguistic Data ◽  
Bayesian Phylogenetic Analysis ◽  
Phylogenetic Methods ◽  
History Of ◽  
Set Up ◽  
Clock Models

Abstract Bayesian phylogenetic methods provide a set of tools to efficiently evaluate large linguistic datasets by reconstructing phylogenies—family trees—that represent the history of language families. These methods provide a powerful way to test hypotheses about prehistory, regarding the subgrouping, origins, expansion, and timing of the languages and their speakers. Through phylogenetics, we gain insights into the process of language evolution in general and into how fast individual features change in particular. This article introduces Bayesian phylogenetics as applied to languages. We describe substitution models for cognate evolution, molecular clock models for the evolutionary rate along the branches of a tree, and tree generating processes suitable for linguistic data. We explain how to find the best-suited model using path sampling or nested sampling. The theoretical background of these models is supplemented by a practical tutorial describing how to set up a Bayesian phylogenetic analysis using the software tool BEAST2.

Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

2020 ◽  
Author(s):  
Benedict King
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Methods ◽  
Diversification Rate ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Tree Model ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Topologies ◽  
Birth Death

Abstract The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.]

scholarly journals Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages

2011 ◽  
Vol 278 (1725) ◽  
pp. 3662-3669 ◽  
Author(s):  
Sean Lee ◽  
Toshikazu Hasegawa
Keyword(s):  
Linguistic Diversity ◽  
Language Evolution ◽  
Global Scale ◽  
Striking Similarity ◽  
Agricultural Expansion ◽  
Bayesian Phylogenetic Analysis ◽  
The People ◽  
History Of ◽  
Linguistic Evolution ◽  
Lexical Data

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.

Mande

2020 ◽  
pp. 173-183
Author(s):  
Henning Schreiber
Keyword(s):  
Linguistic Data ◽  
Phylogenetic Methods ◽  
Genealogical Relationship ◽  
Theoretical Assumptions ◽  
History Of ◽  
Linguistic Classification ◽  
Methodological Aspects ◽  
Relationship Of ◽  
The Impact

The chapter surveys the history of classification of Mande languages from the first attempts in 1849 to the most recent ones on the basis of quantitative approaches to language classification, linguistic reconstruction, and theories on language stability. It discusses various proposals for the internal genealogical relationship of Mande languages and examines their advances and differences in the light of methodological aspects and availability of reliable linguistic data. Special emphasis is laid on the historical tan/fu dichotomy and its revision. Typological issues are treated in the discussion of Mande-specific typological obstacles for lexicostatistic classification. The problem of internal convergence for the linguistic classification of Mande is exemplified in particular in accounting the impact of Greater Manding. The effect of changes in classification methodology by the introduction of phylogenetic methods and theoretical assumptions about language stability are addressed in the final discussion of a revised classification of Mande.

Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families

2019 ◽  
Vol 4 (2) ◽  
pp. 108-123 ◽  
Author(s):  
Andrew M Ritchie ◽  
Simon Y W Ho
Keyword(s):  
Evolutionary Biology ◽  
Language Evolution ◽  
Model Parameters ◽  
Data Sets ◽  
Cultural Groups ◽  
Phylogenetic Methods ◽  
History Of ◽  
Erroneous Estimate ◽  
Coalescent Tree ◽  
Lexical Data

Abstract Bayesian phylogenetic methods derived from evolutionary biology can be used to reconstruct the history of human languages using databases of cognate words. These analyses have produced exciting results regarding the origins and dispersal of linguistic and cultural groups through prehistory. Bayesian lexical dating requires the specification of priors on all model parameters. This includes the use of a prior on divergence times, often combined with a prior on tree topology and referred to as a tree prior. Violation of the underlying assumptions of the tree prior can lead to an erroneous estimate of the timescale of language evolution. To investigate these impacts, we tested the sensitivity of Bayesian dating to the tree prior in analyses of four lexical data sets. Our results show that estimates of the origin times of language families are robust to the choice of tree prior for lexical data, though less so than when Bayesian phylogenetic methods are used to analyse genetic data sets. We also used the relative fit of speciation and coalescent tree priors to determine the ability of speciation models to describe language diversification at four different taxonomic levels. We found that speciation priors were preferred over a constant-size coalescent prior regardless of taxonomic scale. However, data sets with narrower taxonomic and geographic sampling exhibited a poorer fit to ideal birth–death model expectations. Our results encourage further investigation into the nature of language diversification at different sampling scales.

Formation and Development of the Pre-Professional Training System of Foreign Medical Applicants in Ukraine (Historical and Educational Aspect)

2014 ◽  
Vol 4 (3) ◽  
pp. 95-98
Author(s):  
Iana Proskurkina
Keyword(s):  
Foreign Students ◽  
Professional Training ◽  
Training System ◽  
Further Education ◽  
Effective System ◽  
History Of ◽  
Set Up ◽  
The University ◽  
History Of Formation ◽  
Educational Aspect

Abstract The growing number of foreign applicants looking forward to getting education in Ukrainian medical universities makes us find the ways how to improve and make effective the pre-professional training system of foreign medical applicants for further education. The article deals with the issues of the history of formation and development of the preprofessional training system of foreign medical applicants in Ukraine. On the ground of the electronic databases of the official websites of higher educational establishments, the data on years of opening first offices of the dean, departments and preparatory faculties for foreign medical applicants in Ukrainian medical universities are analyzed and systematized. Also the data on the setting up preparatory faculties at other universities who carry out licensed training of foreign students of the medical profile are presented. The data on the operating and management of such institutions in the system of the University administration are generalized. It’s revealed that during the years of its functioning the pre-professional training has changed, in particular the system was commercialized and the institutions involved in training foreign applicants have been reorganized. The modern trends in teaching foreign medical students at the preparatory faculties of the Ukrainian medical universities are displayed. Based on the analysis of the data it is concluded that the system of the pre-professional training of foreign medical applicants was set up in the 50s-60s years of the twentieth century. During this time, some positive experience in the preparation of future international medical specialists has been gained. The system of the pre-professional training of foreign medical applicants has been comprehensively improved and an effective system of managing foreign medical applicants has been created.

Отцейхгаузадомузеяизисториивоенно-историческогомузеяартиллерии,инженерныхвойскивойсксвязи

2019 ◽  
pp. 134-197
Author(s):  
V.E. . Sergei
Keyword(s):  
18Th Century ◽  
Military History ◽  
Peter The Great ◽  
General Field ◽  
Signal Corps ◽  
History Of ◽  
Set Up ◽  
The 1960S ◽  
Military Engineering ◽  
The Military

The article is dedicated to the history of the Military Historical Museum of Artillery, Engineering and Signal Corps. The author examines the main stages of the museums formation, starting with the foundation of the Arsenal, established in St. Petersburg at the orders of Peter the Great on August 29th 1703 for the safekeeping and preservation of memory, for eternal glory of unique arms and military trophies. In 1756, on the base of the Arsenals collection, the General Inspector of Artillery Count P.I. created the Memorial Hall, set up at the Arsenal, on St. Petersburgs Liteyny Avenue. By the end of the 18th century the collection included over 6,000 exhibits. In 1868 the Memorial Hall was transferred to the New Arsenal, at the Crownwork of the Petropavlovsky Fortress, and renamed the Artillery Museum (since 1903 the Artillery Historical Museum). A large part of the credit for the development and popularization of the collection must be given to the historian N.E. Brandenburg, the man rightly considered the founder of Russias military museums, who was the chief curator from 1872 to 1903. During the Civil and Great Patriotic Wars a significant part of the museums holdings were evacuated to Yaroslavl and Novosibirsk. Thanks to the undying devotion of the museums staff, it not only survived, but increased its collection. In the 1960s over 100,000 exhibits were transferred from the holdings of the Central Historical Museum of Military Engineering and the Military Signal Corps Museum. In 1991 the collection also received the entire Museum of General Field Marshal M.I. Kutuzov, transferred from the Polish town of Bolesawjec. The Military Historical Museum of Artillery, Engineering and Signal Coprs is now one of the largest museums of military history in the world. It holds an invaluable collection of artillery and ammunition, of firearms and cold steel arms, military engineering and signal technology, military banners, uniforms, a rich collection of paintings and graphic works, orders and medals, as well as extensive archives, all dedicated to the history of Russian artillery and the feats of our nations defenders.Статья посвящена истории создания ВоенноИсторического музея артиллерии, инженерных войск и войск связи. Автор рассматривает основные этапы становления музея, начиная с основания Арсенала, созданного в СанктПетербурге по приказу Петра I 29 августа 1703 года для хранения и сохранения памяти, во имя вечной славы уникального оружия и военных трофеев. В 1756 году на базе коллекции Арсенала генеральный инспектор артиллерии граф П. И. создал мемориальный зал, установленный при Арсенале, на Литейном проспекте СанктПетербурга. К концу 18 века коллекция насчитывала более 6000 экспонатов. В 1868 году Мемориальный зал был перенесен в Новый Арсенал, на венец Петропавловской крепости, и переименован в Артиллерийский музей (с 1903 года Артиллерийский Исторический музей). Большая заслуга в развитии и популяризации коллекции принадлежит историку Н.Е. Бранденбургу, человеку, по праву считавшемуся основателем российских военных музеев, который был главным хранителем с 1872 по 1903 год. В годы Гражданской и Великой Отечественной войн значительная часть фондов музея была эвакуирована в Ярославль и Новосибирск. Благодаря неусыпной преданности сотрудников музея, он не только сохранился, но и пополнил свою коллекцию. В 1960х годах более 100 000 экспонатов были переданы из фондов Центрального исторического военноинженерного музея и Музея войск связи. В 1991 году коллекцию также получил весь музей генералфельдмаршала М. И. Кутузова, переданный из польского города Болеславец. Военноисторический музей артиллерии, инженерных войск и войск связи в настоящее время является одним из крупнейших музеев военной истории в мире. Здесь хранится бесценная коллекция артиллерии и боеприпасов, огнестрельного и холодного оружия, военной техники и сигнальной техники, военных знамен, обмундирования, богатая коллекция живописных и графических работ, орденов и медалей, а также обширные архивы, посвященные истории русской артиллерии и подвигам защитников нашего народа.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 28
Author(s):  
Umaru Bangura ◽  
Jacob Buanie ◽  
Joyce Lamin ◽  
Christopher Davis ◽  
Gédéon Ngiala Bongo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sierra Leone ◽  
Small Mammal ◽  
Hemorrhagic Fever ◽  
Lassa Fever ◽  
Lassa Virus ◽  
Sierra Leonean ◽  
Bayesian Phylogenetic Analysis ◽  
Prevalent Species ◽  
Lineage Iv

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

scholarly journals Case of Human Infestation with Dermanyssus gallinae (Poultry Red Mite) from Swallows (Hirundinidae)

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 299
Author(s):  
Georgios Sioutas ◽  
Styliani Minoudi ◽  
Katerina Tiligada ◽  
Caterina Chliva ◽  
Alexandros Triantafyllidis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Clinical Symptoms ◽  
Skin Lesions ◽  
Coi Gene ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Human Form ◽  
Bayesian Phylogenetic Analysis

Dermanyssus gallinae (the poultry red mite, PRM) is an important ectoparasite in the laying hen industry. PRM can also infest humans, causing gamasoidosis, which is manifested as skin lesions characterized by rash and itching. Recently, there has been an increase in the reported number of human infestation cases with D. gallinae, mostly associated with the proliferation of pigeons in cities where they build their nests. The human form of the disease has not been linked to swallows (Hirundinidae) before. In this report, we describe an incident of human gamasoidosis linked to a nest of swallows built on the window ledge of an apartment in the island of Kefalonia, Greece. Mites were identified as D. gallinae using morphological keys and amplifying the Cytochrome C oxidase subunit I (COI) gene by PCR. Bayesian phylogenetic analysis and median-joining network supported the identification of three PRM haplogroups and the haplotype isolated from swallows was identical to three PRM sequences isolated from hens in Portugal. The patient was treated with topical corticosteroids, while the house was sprayed with deltamethrin. After one week, the mites disappeared and clinical symptoms subsided. The current study is the first report of human gamasoidosis from PRM found in swallows’ nest.

The Unfinished Sexual Revolution

1971 ◽  
Vol 3 (4) ◽  
pp. 473-492 ◽  
Author(s):  
Laurie Taylor
Keyword(s):  
Sexual Revolution ◽  
Editorial Note ◽  
Memorial Lecture ◽  
Human Welfare ◽  
The World ◽  
Control Clinic ◽  
History Of ◽  
Set Up ◽  
The Uk ◽  
The University

Editorial note. March 17th, 1971 was the fiftieth anniversary of the opening by Marie Stopes of her birth control clinic in Holloway, London, the first of its kind in the UK and possibly in the world. In recognition of this notable event, the Board of the Marie Stopes Memorial Foundation, in conjunction with the University of York, has established a Marie Stopes Memorial Lecture to be given annually for a term of years. The first of the series was delivered on 12th March in the Department of Sociology, University of York, by Mr Laurie Taylor of that department. In introducing the speaker, Dr G. C. L. Bertram, the Chairman, emphasized the great contribution made by Marie Stopes to human welfare and gave a brief history of the clinic, which was soon moved to Whitfield Street. On Marie Stopes' death in 1958 the Memorial Foundation was set up to manage the clinic, still in Whitfield Street, and as a working monument to a great women.Mr Taylor's script is printed below as delivered and it will be seen that the lecture was a notable one. Not only that, but it was delivered with the verve of a Shakespearean actor and the members of the large and appreciative audience will not readily forget the occasion.

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