scholarly journals randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

2022 ◽  
Author(s):  
Ignacio Ramos-Gutierrez ◽  
Herlander Lima ◽  
Rafael Molina-Venegas
Keyword(s):  
R Package ◽  
Phylogenetic Information ◽  
Extant Species ◽  
Generalized Framework ◽  
Molecular Phylogenetic ◽  
Long Time ◽  
Molecular Information ◽  
Molecular Phylogenies ◽  
To Come ◽  
Backbone Tree

The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Here, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package "randtip", a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the "blind" expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Western Education and Rural Productivity in Tropical Africa

Africa ◽  
1962 ◽  
Vol 32 (4) ◽  
pp. 313-323 ◽  
Author(s):  
P. C. C. Evans
Keyword(s):  
Rural Life ◽  
Tropical Africa ◽  
African Countries ◽  
Western Education ◽  
Political Independence ◽  
White Collar Workers ◽  
Long Time ◽  
Complete Rejection ◽  
To Come ◽  
Opening Paragraph

Opening ParagraphFor many years British administrators and others concerned with the developing countries of tropical Africa have criticized Western-type schooling introduced there for what they believe to have been its bad effects on the life of rural peoples. They have complained that such schooling is prejudicial to rural life, since it produces a distaste for agriculture and leads to a drift from the land. They say it promotes in schoolchildren a desire to be clerks or white-collar workers and, because of their schooling, they develop a strong dislike for manual work and a reluctance to soil their hands with physical labour. They assert that these values inculcated by Western schooling lead finally to an almost complete rejection of rural life, a contempt for agriculture, and therefore to a decrease in rural productivity. Finally, they maintain that this is particularly serious in view of the fact that, as far as we can see at present, many African countries will have to depend on agriculture and the land for a long time to come, for it is only through such dependence that it seems likely that they will achieve economic viability which will be an important factor in making a success of political independence.

Using Old Photographs in Interviews: Some Cautionary Notes About Silences in Fieldwork

1990 ◽  
Vol 17 ◽  
pp. 327-334 ◽  
Author(s):  
Bill Bravman
Keyword(s):  
Power Relations ◽  
Men And Women ◽  
Cultural Assumptions ◽  
The People ◽  
Taita Hills ◽  
National Archives ◽  
Long Time ◽  
Photo Collection ◽  
Image Production ◽  
To Come

In September 1987, early in my research at the Kenya National Archives, I came across a collection of photographs taken by a British missionary during the 1920s and early 1930s. The collection contained nearly 250 photos of the terrain and people of Kenya's Taita Hills, where I would soon be going for my fieldwork. I pored over the photo collection for a long time, and had reproductions made of twenty-five shots. The names of those pictured had been recorded in the photo album's captions. Many of the names were new to me, though a few WaTaita of the day who had figured prominently in the archival records were also captured on film. When I moved on to Taita in early 1988,1 took the photographs with me. Since I would be interviewing men and women old enough either to remember or be contemporaries of the people in the pictures, I planned to show the photos during the interviews. At first I was simply curious about who some of the people pictured were, but my curiosity quickly evolved into a more ambitious plan. I decided to try using the photographs as visual prompts to get people to speak more expansively than they otherwise might about their lives and their experiences.In the event, I learned that using the photographs in interviews involved many more complexities than I had envisaged in my initial enthusiasm. I found that I had to alter the expectations and techniques I took to Taita, and feel out some of the limitations of working with the photographic medium. I had to recognize the power relations embedded in my presence as a researcher in Taita, in my position as bearer of images from peoples' pasts, and in the photos themselves. I found, too, that I needed to come to grips with a number of issues about the politics of image production, and the historical product of those politics: the bounded, selected images that are photographs. Finally, I had to address some of my own cultural assumptions about photography and how people respond to pictures, assumptions that my informants did not necessarily share.

scholarly journals Physical Properties of Thermoplastic Starch Derived from Natural Resources and Its Blends: A Review

Polymers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1396
Author(s):  
Z. N. Diyana ◽  
R. Jumaidin ◽  
Mohd Zulkefli Selamat ◽  
Ihwan Ghazali ◽  
Norliza Julmohammad ◽  
...  
Keyword(s):  
Thermoplastic Starch ◽  
Natural Fibre ◽  
Polymer Materials ◽  
Secondary Pollution ◽  
Wide Range ◽  
Potential Applications ◽  
Long Time ◽  
To Come ◽  
Main Component ◽  
Significant Attention

Thermoplastic starch composites have attracted significant attention due to the rise of environmental pollutions induced by the use of synthetic petroleum-based polymer materials. The degradation of traditional plastics requires an unusually long time, which may lead to high cost and secondary pollution. To solve these difficulties, more petroleum-based plastics should be substituted with sustainable bio-based plastics. Renewable and natural materials that are abundant in nature are potential candidates for a wide range of polymers, which can be used to replace their synthetic counterparts. This paper focuses on some aspects of biopolymers and their classes, providing a description of starch as a main component of biopolymers, composites, and potential applications of thermoplastics starch-based in packaging application. Currently, biopolymer composites blended with other components have exhibited several enhanced qualities. The same behavior is also observed when natural fibre is incorporated with biopolymers. However, it should be noted that the degree of compatibility between starch and other biopolymers extensively varies depending on the specific biopolymer. Although their efficacy is yet to reach the level of their fossil fuel counterparts, biopolymers have made a distinguishing mark, which will continue to inspire the creation of novel substances for many years to come.

Secrecy, State-Private Networks and Operational Effectiveness in Cold War Europe

2016 ◽  
Vol 25 (3) ◽  
pp. 551-560
Author(s):  
ERIC PULLIN
Keyword(s):  
Central Intelligence Agency ◽  
Unintended Consequences ◽  
Freedom Of Information ◽  
Public Attention ◽  
Operational Effectiveness ◽  
Intelligence Agency ◽  
The Us ◽  
Long Time ◽  
To Come ◽  
Us Senate

Secrecy has unintended consequences. The release on 9 December 2014 of the US Senate Intelligence Committee's report on the torture of terrorism detainees focused public attention on the secret activities of the Central Intelligence Agency (CIA). Regrettably, lost amidst debate over justifying or condemning state-sponsored torture is a more basic concern, the issue of state secrecy, which underlies the discussion of how governments promote national ends. Only two days after the issuance of the Senate Intelligence Committee's report, the US House of Representatives adjourned without taking action on the Freedom of Information Act reform bill – despite receiving unanimous approval in both houses. This bill would not have required complete openness, but it would have eliminated many of the arbitrary mechanisms that enable the CIA and other governmental agencies to suppress requests for information. Although the House Republican leadership failed to put the act on the legislative calendar, the Obama administration's Department of Justice also deserves opprobrium for surreptitiously opposing the act behind the scenes. The US government's disregard for establishing reasonable rules of transparency virtually guarantees that the CIA will continue to suppress its records, and thus public scrutiny of its unchecked activities, for a very long time to come.

scholarly journals The Case of Windy Lake by M. Hutchinson

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Kaia MacLeod
Keyword(s):  
Indigenous People ◽  
Large City ◽  
Historical Trauma ◽  
Critical Discussion ◽  
University Of Alberta ◽  
Wide Range ◽  
Long Time ◽  
To Come ◽  
Fitting In ◽  
The City

Hutchinson, Michael. The Case of Windy Lake. Second Story Press, 2019. Micheal Hutchinson is a citizen of the Misipawistik Cree Nation in the Treaty 5 territory and is no stranger to the Canadian media. He’s worked as a print reporter for The Calgary Straight and Aboriginal Times and became the host of APTN national news. Somehow in his busy life, he has found time to write two amazing children’s books. The Case of the Missing Auntie is Hutchinson’s second Mighty Muskrat Mystery book. It follows the cousins Chickadee, Otter, Samuel, and Atim (the Mighty Muskrats) of the Windy Lake First Nation. It takes place after the first book, but this time the Muskrats are leaving their reserve to spend time with family in the city. By setting the book in the city, the topic of urban Indigenous people arises. Hutchinson depicts a wide range of Indigenous people: nurses, students, musicians, and bullies. He doesn’t romanticize Indigenous people, opting to focus on realism and making the characters lifelike. The book makes sure to mention potential issues with moving/travelling from a reserve to a large city such as not fitting in and racism. The story has the same style as the previous Mighty Muskrat Mystery book with clear goals for the Muskrats to obtain: visit the Exhibition Fair, get Otter a ticket to see the band Wavoka’s Wail, and look for Auntie Charlotte who was taken during the 60’s scoop. One of the best parts is how realistic the story is, not everything goes the Mighty Muskrats way. This isn’t your typical “everything is going to work out just fine” story but that makes it a solid read—they need to come up with a plan B. It opens a dialogue on residential schools, the 60’s scoop, and the Truth and Reconciliation Commission. It felt like a good introduction to those tough topics, explaining what they are without dismissing them as something that happened a long time ago or minimizing their modern impacts. Instead, the story shows the aftermath, and how it affects the younger generation without limiting characters’ identities to only be their relationship to historical trauma. As such, this book could work as a discussion starter between children and adults on these topics and could be used to promote critical discussion around themes like Indigenous identities and experiences. Highly recommended: 4 out of 4 starsReviewer: Kaia MacLeod Reviewers BiographyKaia MacLeod, a member of the James Smith Cree Nation, is an MLIS candidate at the University of Alberta. Her bachelor’s degree was in Film Studies, which she sometimes likes to call a degree in “movie watching,” she enjoys exploring how folklore is represented on film and in online content.

China's Urbanization: Migration by the Millions

2016 ◽  
Keyword(s):  
Dual Language ◽  
New World ◽  
Full Range ◽  
The United States ◽  
Registration System ◽  
Land System ◽  
Chinese Characteristics ◽  
Long Time ◽  
Urbanization In China ◽  
To Come

Joseph Eugene Stiglitz, laureate of the Nobel Prize in Economic Sciences, once named urbanization in China and the new technical revolution led by the United States as the two great events shaping the world of the 21st century. British specialist Tom Miller refers to China’s urbanization as “the greatest migration in human history.” China's Urbanization: Migration by the Millions is a full-range description of how millions of farmers in China became urban citizens in different periods of history. It further explores the deep-rooted issues of the country’s land system and household registration system, issues that will be confronted by urbanization for a long time to come. China is the world’s largest single-country population transfer and urbanization country. Its urbanization is faced with ever more stringent constraints on resources and environment. This means China has to take a brand new path of urbanization with Chinese characteristics. Through this book, readers can get both the ropes of official and mainstream views on the new urbanization initiative and get familiar with multi-directional probes on this issue in academic circles so they may gain a comprehensive and balanced understanding of the whole picture. This book was first published by New World Press in 2014, and republished jointly by New World Press and Global Century Press in 2016. This joint publication is the first volume in the ‘China Urbanization Studies’ series. We have retained the original typesetting, but we have added DOI numbers for the book, Series Editors’ Prefaces and all chapters, as well as a section of dual language additions from Global Century Press in English and Chinese.

PENERAPAN ESTETIKA VISUAL ARSITEKTUR MODEREN PADA REDESAIN BANGUNAN & FASAD HOTEL KOTA TEPIAN DI SAMARINDA

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Nur Husniah Thamrin ◽  
Maulana Refindo Dhuhur
Keyword(s):  
Economic Potential ◽  
Architectural Style ◽  
Natural Lighting ◽  
Public Facilities ◽  
East Kalimantan ◽  
Building Facades ◽  
Strategic Location ◽  
Long Time ◽  
To Come ◽  
The City

ABSTRACTThe development of the city of Samarinda is increasing and is still sustainable for a long time, especially in terms of suppressing administrative areas. The city of Samarinda as a province of East Kalimantan still has economic potential to continue to grow, this is triggered by increasing population and economic growth in the city of Samarinda. Hotel Kota Tepian have been around for a long time around 1990, Hotel Kota Tepian are included in the class of 2 star hotels that have various facilities such as 25 rooms to stay with various types of superior, premium, and standard. Hotel Kota Tepian also provides facilities for meetings, restaurants and SPA.The advantages of the Hotel Kota Tepian are its strategic location and is located in the middle of the city close to public facilities, offices and shopping centers such as Segiri Market, Mall Plaza Mulia, and Lembuswana while the shortcomings and problems of the Hotel Kota Tepian are designing the City Edge Hotel with emphasis on building facades using a modern architectural style, then designing natural lighting and artificial redesign on the interior of the Hotel Kota Tepian. Therefore, Kota Tepian hotel really needs to be redesigned to restore the image of the hotel in terms of visual aesthetic facade so that it becomes an attraction for visitors to come and feel comfortable while Kota Tepian Hotel.Keywords: Hotel, Kota Tepian, Redesign, Building, Facade. ABSTRAKPerkembangan kota Samarinda semakin meningkat dan masih berkelanjutan dalam waktu yang lama, khususnya dalam hal penekanan wilayah administrasi. Kota Samarinda sebagai provinsi dari Kalimantan Timur masih memiliki potensi ekonomi untuk terus berkembang, hal ini dipicu oleh semakin meningkatnya pertumbuhan penduduk dan ekonomi di kota Samarinda.Hotel Kota Tepian telah berdiri sejak lama sekitar tahun 1990, Hotel Kota Tepian termasuk dalam kelas hotel berbintang 2 yang memiliki berbagai macam fasilitas seperti 25 kamar tempat menginap dengan berbagai tipe yaitu superior, premium, dan standart.Pada Hotel Kota Tepian juga menyediakan fasilitas untuk pertemuan, restorant, dan SPA. Kelebihan dari Hotel Kota Tepian adalah lokasi yang strategis dan terletak di tengah kota dekat dengan falitas umum, perkantoran dan pusat perbelanjaan seperti pasar segiri, mall plaza mulia, dan lembuswana sedangkan kekurangan dan menjadi permasalahan dan penekanan dari Hotel Kota Tepian yaitu meredesain Hotel Kota Tepian dengan penekanan pada fasad bangunan dengan memakai gaya arsitektur modern. Maka dari itu Hotel Kota Tepian sangat perlu untuk di redesain untuk mengembalikan citra hotel dari segi estetika visual fasad sehingga menjadi daya tarik bagi pengunjung untuk datang dan merasa nyaman saat berada di Hotel Kota Tepian.Kata Kunci: Hotel, Kota Tepian, Redesain, Fasad, Bangunan.

New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges

Zootaxa ◽  
2021 ◽  
Vol 5052 (3) ◽  
pp. 353-379
Author(s):  
JULIO C.C. FERNANDEZ ◽  
MARIANELA GASTALDI ◽  
GERMÁN ZAPATA-HERNÁNDEZ ◽  
LUIS M. PARDO ◽  
FABIANO L. THOMPSON ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Southern Chile ◽  
Deep Waters ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenies ◽  
Taxonomic Studies ◽  
Phylogenetic Affinities

Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.  

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