scholarly journals A discrete approach to the external branches of a Kingman coalescent tree. Theoretical results and practical applications

2019 ◽  
Author(s):  
Filippo Disanto ◽  
Thomas Wiehe
Keyword(s):  
Classical Model ◽  
Natural Populations ◽  
Easy Access ◽  
Practical Applications ◽  
Discrete Approach ◽  
External Branch ◽  
History Of ◽  
Tree Topologies ◽  
Coalescent Tree ◽  
Parent Node

AbstractThe Kingman coalescent process is a classical model of gene genealogies in population genetics. It generates Yule-distributed, binary ranked tree topologies—also called histories—with a finite number of n leaves, together with n −1 exponentially distributed time lengths: one for each each layer of the history. Using a discrete approach, we study the lengths of the external branches of Yule distributed histories, where the length of an external branch is defined as the rank of its parent node. We study the multiplicity of external branches of given length in a random history of n leaves. A correspondence between the external branches of the ordered histories of size n and the non-peak entries of the permutations of size n −1 provides easy access to the length distributions of the first and second longest external branch in a random Yule history and coalescent tree of size n. The length of the longest external branch is also studied in dependence of root balance of a random tree. As a practical application, we compare the observed and expected number of mutations on the longest external branches in samples from natural populations.

Update on the Boundaries of the Curly Birch Range

2020 ◽  
pp. 9-21
Author(s):  
L.V. Vetchinnikova ◽  
◽  
A.F. Titov ◽  
◽  
Keyword(s):  
Population Size ◽  
Natural Populations ◽  
Forest Tree ◽  
Published Data ◽  
Population Approach ◽  
Key Factors ◽  
History Of ◽  
Individual Trees ◽  
Karelian Birch

The article reports on the application of the best known principles for mapping natural populations of curly (Karelian) birch Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti – one of the most appealing representatives of the forest tree flora. Relying on the synthesis and analysis of the published data amassed over nearly 100 years and the data from own full-scale studies done in the past few decades almost throughout the area where curly birch has grown naturally, it is concluded that its range outlined in the middle of the 20th century and since then hardly revised is outdated. The key factors and reasons necessitating its revision are specified. Herewith it is suggested that the range is delineated using the population approach, and the key element will be the critical population size below which the population is no longer viable in the long term. This approach implies that the boundaries of the taxon range depend on the boundaries of local populations (rather than the locations of individual trees or small clumps of trees), the size of which should not be lower than the critical value, which is supposed to be around 100–500 trees for curly birch. A schematic map of the curly birch range delineated using this approach is provided. We specially address the problem of determining the minimum population size to secure genetic diversity maintenance. The advantages of the population approach to delineating the distribution range of curly birch with regard to its biological features are highlighted. The authors argue that it enables a more accurate delineation of the range; shows the natural evolutionary history of the taxon (although it is not yet officially recognized as a species) and its range; can be relatively easily updated (e.g. depending on the scope of reintroduction); should be taken into account when working on the strategy of conservation and other actions designed to maintain and regenerate this unique representative of the forest tree flora.

Animal Pain Scales in Public Policy

1990 ◽  
Vol 18 (1_part_1) ◽  
pp. 41-50
Author(s):  
F. Barbara Orlans
Keyword(s):  
Public Policy ◽  
Animal Welfare ◽  
The United States ◽  
Pain Scale ◽  
Laboratory Animals ◽  
Practical Applications ◽  
Animal Pain ◽  
Pain Scales ◽  
History Of ◽  
And Control

Pain scales classify the severity of pain inflicted on laboratory animals from little or none up to severe. A pain scale as part of public policy serves beneficial purposes that promote animal welfare. It can be used to educate people about the two alternatives of refinement and replacement, and the need to reduce animal pain. Furthermore, a pain scale has practical applications: 1) in review procedures for animal welfare concerns; 2) in developing policies on the use of animals in education; and 3) as a basis for collecting national data on animal experimentation, so that meaningful data can be collected on trends in reduction and control in animal pain. So far, only a few countries (including Sweden, the Netherlands, Canada and New Zealand) have adopted pain scales as part of their public policy. Most countries, including the United States, have not yet done so. The history of the development and adoption of pain scales by various countries is described and the case is presented for wider adoption of a pain scale in countries not currently using one.

scholarly journals Pampean lizard assemblage from subtropical Brazil: a temporal analysis

2011 ◽  
Vol 83 (4) ◽  
pp. 1345-1358 ◽  
Author(s):  
Gisele R. Winck ◽  
Tiago G. Dos Santos ◽  
Sonia Z. Cechin
Keyword(s):  
Environmental Changes ◽  
Seasonal Pattern ◽  
Natural Populations ◽  
Temporal Analysis ◽  
Natural Environments ◽  
Human Occupation ◽  
Environmental Disturbances ◽  
Pampa Biome ◽  
History Of ◽  
Recruitment Period

The increasing human occupation of natural environments is one of the greatest threats to biodiversity. To mitigate the negative anthropogenic effects, it is necessary to understand the characteristics of natural populations and the natural history of species. A study was conducted with an assemblage of lizards from a disturbed area of the Pampa biome, from February 2001 to January 2004. The assemblage showed a unimodal seasonal pattern, with the recruitment period occurring during the warmer months. The captures were seasonal for two of the three monitored years, and concentrated within warmer months. The minimum temperature explained the number of catches for the assemblage as a whole. However, when the species were analyzed individually, the temperature only explained the seasonal occurrence of Teius oculatus. The abundance of species was significantly different in the third year of study for Cercosaura schreibersii and Ophiodes striatus. This latter species was no longer registered in the study area from May 2003 until the end of the study. Therefore, O. striatus may be more sensitive to environmental changes, considering the events of change in vegetation during the study. With frequent and increasing environmental disturbances, it is necessary to take conservation measures and encourage the increase of knowledge on Pampean lizards.

A Bedouin Principle of Freedom for the Risorgimento d’Italia: Michele Amari Integrates Ibn Khaldūn with Vico’s filologia

2020 ◽  
Vol 5 (1) ◽  
pp. 76-96
Author(s):  
Markus Messling
Keyword(s):  
Nineteenth Century ◽  
State Of The Art ◽  
Classical Model ◽  
The State ◽  
Model Case ◽  
Ibn Khaldun ◽  
Giambattista Vico ◽  
New Science ◽  
Human Choice ◽  
History Of

Abstract In the New Science (1744), Giambattista Vico defined filologia as “the doctrine of all the institutions that depend on human choice” of the mondo civile. When nineteenth-century European nationalism was on the rise, supported by narratives of cultural homogeneity and specificity, philological comparatism was the state-of-the-art and it, often, legitimated the obsessions with the purity of origins and genealogies. Italy, characterized by internal plurality and its Mediterranean entanglements, is a model case. Whereas many discourses of the Risorgimento aspired to shape a new Italian nation after the classical model, Michele Amari’s History of the Muslims of Sicily (1854–1872) marked an astonishing exception. For him, going back to Islamic-Sicilian history, its literary, rhetorical and linguistic culture, meant to resume, on a higher level of incivilmento (Vico), what had been obscured by cultural decline: the spirit of freedom and equality, which Ibn Khaldūn had attributed to the Bedouins and their dynamics in history.

scholarly journals ALS-Based Detection of Past Human Activities in the Białowieża Forest—New Evidence of Unknown Remains of Past Agricultural Systems

2020 ◽  
Vol 12 (16) ◽  
pp. 2657
Author(s):  
Krzysztof Stereńczak ◽  
Rafał Zapłata ◽  
Jarosław Wójcik ◽  
Bartłomiej Kraszewski ◽  
Miłosz Mielcarek ◽  
...  
Keyword(s):  
Cultural Heritage ◽  
Human Activities ◽  
Laser Scanning ◽  
Archaeological Sites ◽  
13Th Century ◽  
Practical Result ◽  
Practical Applications ◽  
Białowieża Forest ◽  
History Of ◽  
New Evidence

The Białowieża Forest (BF), a unique ecosystem of historical significance in central Europe, has a long history of assumed human settlement, with at least 200 known archaeological sites (until 2016). This study uncovers new evidence of the cultural heritage of this unique forest area using Airborne Laser Scanning (ALS) technology combined with traditional archaeological field assessment methods to verify the ALS data interpretations and to provide additional evidence about the function and origin of the newly detected archaeological sites. The results of this study include (1) a scientific approach for an improved identification of archaeological resources in forest areas; (2) new evidence about the history of the human use of the BF based on ALS data, covering the entire Polish part of the BF; and (3) an improved remote sensing infrastructure, supporting existing GIS (Geographic Information System) systems for the BF, a famous UNESCO Heritage site. Our study identified numerous locations with evidence of past human agricultural activities known in the literature as “field systems”, “lynchets” and “Celtic fields”. The initial identification included more than 300 km of possible field boundaries and plough headlands, many of which we have verified on the ground. Various past human activities creating those boundaries have existed since the (pre-) Roman Period up to the 13th century AD. The results of this study demonstrate that past human activities in the Polish part of the Białowieża Forest had been more prevalent than previously believed. As a practical result of the described activities, a geodatabase was created; this has practical applications for the system of monument protection in Poland, as well as for local communities and the BF’s management and conservation. The more widely achieved results are in line with the implementation of the concept of a cultural heritage inventory in forested and protected areas—the actions taken specify (built globally) the forms of protection and management of cultural and environmental goods.

scholarly journals A brief history of the development of wind-profiling or MST radars

2000 ◽  
Vol 18 (7) ◽  
pp. 740-749 ◽  
Author(s):  
T. E. Van Zandt
Keyword(s):  
Gravity Waves ◽  
Weather Forecasting ◽  
Acoustic Sounding ◽  
Practical Applications ◽  
Radio Science ◽  
Meteorology And Atmospheric Dynamics ◽  
Mst Radar ◽  
History Of ◽  
Instruments And Techniques ◽  
Atmospheric Phenomena

Abstract. The history of the development of the wind-profiling or MST radar technique is reviewed from its inception in the late 1960s to the present. Extensions of the technique by the development of boundary-layer radars and the radio-acoustic sounding system (RASS) technique to measure temperature are documented. Applications are described briefly, particularly practical applications to weather forecasting, with data from networks of radars, and scientific applications to the study of rapidly varying atmospheric phenomena such as gravity waves and turbulence.Key words: Meteorology and atmospheric dynamics (instruments and techniques) · Radio science (remote sensing; instruments and techniques)

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.]

Networks and Opportunities: A Digital History of Ireland’s Great Famine Refugees in New York

2019 ◽  
Vol 124 (5) ◽  
pp. 1591-1629 ◽  
Author(s):  
Tyler Anbinder ◽  
Cormac Ó Gráda ◽  
Simone A. Wegge
Keyword(s):  
United States ◽  
New York ◽  
The United States ◽  
Electronic Version ◽  
Easy Access ◽  
Digital History ◽  
Irish Famine ◽  
Savings Bank ◽  
Large Numbers ◽  
History Of

Abstract For decades, historians portrayed the immigrants who arrived in the United States in the mid-nineteenth century fleeing the great Irish Famine as a permanent proletariat, doomed to live out their lives in America in poverty due to illiteracy, nativism, and a lack of vocational skills. Recent research, however, primarily by economic historians, has demonstrated that large numbers of Famine refugees actually fared rather well in the United States, saving surprising sums in bank accounts and making strides up the American socioeconomic ladder. These scholars, however, have never attempted to explain why some Famine immigrants thrived in the U.S. while others struggled merely to scrape by. Utilizing the unusually detailed records of New York’s Emigrant Savings Bank in conjunction with the methods of the digital humanities, this article seeks to understand what characteristics separated those Irish Famine immigrants who fared well financially from those who did not. Analysis of a database of more than 15,000 depositors suggests that networking was the key to economic advancement for the Famine immigrants. Those who lived in residential enclaves with other immigrants born in the same Irish parish saved significantly more than other immigrants, and those who created employment niches based on an Irish birthplace also amassed more wealth than those who did not. The electronic version of the article provides easy access to the database and interactive maps, allowing readers to ask their own questions of the data. The article also fleshes out the life stories of many of the immigrants found in the database, using documents found on genealogy websites such as Ancestry.com. These handwritten census records, ship manifests, and bank ledgers are hyperlinked to the electronic version of the article. That makes this essay ideal for classroom use—students can move effortlessly to the documents that underpin each paragraph and see clearly how historians use archival evidence to formulate arguments and shape historical narratives.

Genetic status of the putative hybrid swarms of mountain dwarf pine and Scots pine in contact zones of their distribution in Slovakia

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Peter Maňka ◽  
Andrej Kormuťák ◽  
Martin Galgóci ◽  
Dušan Gömöry
Keyword(s):  
Genetic Structure ◽  
Scots Pine ◽  
Molecular Level ◽  
Natural Populations ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Hybrid Swarm ◽  
Pure Species ◽  
Hybrid Swarms ◽  
History Of

AbstractGenetic structure of the mountain dwarf pine (Pinus mugo) and Scots pine (P. sylvestris) natural populations along with their 4 putative hybrid swarms in Slovakia were analyzed using 12 enzyme loci. The study aimed in evaluation of postulated hybrid status of the swarms on molecular level. Based on semidiagnostic allele frequencies of the MDH B, MDH C, 6PGDH B, ADH 1 and F-EST loci in their megagametophytes and vegetative buds, the conspicuous genetic differences were detected between P. mugo and P. sylvestris populations. The putative hybrid swarms seem to incline by their genetic structure to P. mugo rather than to P. sylvestris. Obtained results indicate independent developmental history of each of the scored hybrid swarms. The putative hybrid swarm in Sucha Hora was found to be a mixed stand consisting prevailingly of pure-species individuals of P. mugo and P. sylvestris. On the contrary, the putative hybrid swarms in Habovka, Tisovnica and Terchova are supposed to be of hybrid origin.

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