scholarly journals New approaches to species delimitation and population structure of corals: two case studies using ultraconserved elements and exons

2020 ◽  
Author(s):  
Katie L. Erickson ◽  
Alicia Pentico ◽  
Andrea M. Quattrini ◽  
Catherine S. McFadden
Keyword(s):  
Population Structure ◽  
Case Studies ◽  
Species Delimitation ◽  
Conservation Status ◽  
Target Enrichment ◽  
Clustering Methods ◽  
Ecological Data ◽  
Ultraconserved Elements ◽  
New Approaches ◽  
Wide Range

AbstractAs coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,363 baits) to target-capture 3,040 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered SNPs delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using Restriction Site Associated DNA Sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow time scales in corals.

State of Conservation and Population Structure of Bird Species Inhabiting in Various Subtropical Urban Forests

2021 ◽  
Author(s):  
M. N. Rajpar ◽  
M. Zakaria
Keyword(s):  
Population Structure ◽  
Conservation Status ◽  
Distance Sampling ◽  
Bird Species ◽  
Urban Forests ◽  
Avian Species ◽  
Bird Diversity ◽  
Line Transect ◽  
Distance Analysis ◽  
Wide Range

Abstract To determine the conservation status and population structure of avian species living in various subtropical broadleaved urban forests, namely Dob Ghar, Kamal Khan, Kityari, Palamar, Seya Sar and Shahabad of Pakistan, we aimed to use the distance sampling line transect process. To avoid double counting of the same bird individual, a total of 180 counting points were set at 250 m from each other. In all, between December 2017 and November 2018, 2,879 individuals representing 53 species, 28 families and 9 orders were detected. One species was vulnerable (VU) out of 53 bird species, while the remaining 52 species were the least concerned (LC). In particular, the results of the distance analysis indicate that, in six subtropical broad-leaved forests, the bird population can vary. For eg, Palamar (0.954 ± 0.221 birds/ha) and Kityari (0.938 ± 0.162 birds/ha) were densely populated by bird species, while Kamal Khan (0.102 ± 0.178 birds/ha) was less concerm. Similarly, the CAP findings showed that bird species in Dob Ghar were more diverse (H’ = 33.92 ± 1.368) and equally distributed (E = 0.9657 ± 0.004) and that the Shahabad ecosystem was rich in bird species (R1 = 8.007 ± 0.053) compared to other habitats. In addition, the length of the twigs and topological changes in the dendrogram have shown that bird diversity may vary from habitat to habitat. The bird species were classified into eight foraging guilds. Insectivores were the most abundant bird species using all habitats in abundance. By cons, Carnivore/Piscivore/Insectivore averted to use the forest habitats Dob Ghar and Frugivore Kamal Khan and Dob Ghar. The findings of this study revealed that broad-leaved subtropical urban forests are home to a wide range of avian species. However, habitat selection among bird species varied across habitats according to vegetation structure and composition, food resources, adjoining habitats, and human settlements.

Systematics, distribution and ecological analysis of rodents in Jordan

Zootaxa ◽  
2018 ◽  
Vol 4397 (1) ◽  
pp. 1 ◽  
Author(s):  
ZUHAIR S. AMR ◽  
MOHAMMAD A. ABU BAKER ◽  
MAZIN QUMSIYEH ◽  
EHAB EID
Keyword(s):  
Eastern Mediterranean ◽  
Public Awareness ◽  
Conservation Status ◽  
Eastern Mediterranean Region ◽  
Ecological Data ◽  
African Species ◽  
Microtus Guentheri ◽  
Distribution Ranges ◽  
Wide Range ◽  
The Mediterranean

Distributional and ecological data were given to all rodents of Jordan. The rodent fauna of Jordan consists of 28 species with 20 genera in eight families (Cricetidae, Dipodidae, Gliridae, Hystricidae, Muridae, Myocastoridae, Sciuridae,and Spalacidae), including four introduced species.Keys for families and species were provided, along with diagnosis for each species and cranial illustrations for most species. Habitat preference and zoogeographic affinities of rodents in Jordan wereanalyzed, as well as their status and conservation.Threat categories and causes of threats on the rodents of Jordan were also analyzed.        The distribution of rodents in Jordan represents a reflection of their global distribution ranges and habitat preferences. Species associated with the temperate forest of northern Jordan includes Sciurus anomalus and two wood mice, Apodemus mystacinus and A. flavicollis, while non-forested areas are represented by Nannospalax ehrenbergi and Microtus guentheri. Strict sand dwellers include Gerbillus cheesmani and G. gerbillus. Petrophiles associated with sandstone or black lava deserts are exemplified by Acomys russatus, A. r. lewsi, H. indica and S. calurus. Others including: Jaculus jaculus, G. nanus, G. henleyi, Meriones crassus, and M. libycus are all desert-adapted species with wider ranges of distribution where scarce vegetation, wadibeds, and marabs with clay, loess, or gravel surfaces provide foraging grounds and shelter. A single species, Gerbillus dasyurus, exhibits a wide range of distribution over diverse habitat types.        The rodent fauna of Jordan consists of assemblages of different zoogeographical affinities. Nine, three, and seven were restricted or had most of its range within the Mediterranean, Irano-Turanian, and Saharo Arabian, respectively. Sciurus anomalus, Apodemus sp., Nannospalax ehrenbergi, and Microtus guentheri reached their most southern range of distribution in the Mediterranean regions of Jordan. The distribution of Gerbillus cheesmani extends from Asian deserts in India westwards into the Arabian Peninsula crossing Jordan as its most western range of distribution. Typical rodents of Saharo-Arabian affinities are represented by desert jerboas, gerbils, and jirds. North African species such as G. andersoni, G. gerbillus reached their most eastern distribution in southern Jordan. Both G. henleyi and G. nanus are widely-distributed species across North Africa reaching as far as India to the east, representing most northern outpost for these two species. Sekeetamys calurus is a nearly endemic to the Eastern Mediterranean region within southern Jordan and Sinai. Relicts are represented by Eliomys melanurus and Acomys russatus lewisi.        Several threats affecting the rodent biodiversity in Jordan were identified including habitat loss and degradation, human disturbance and related activity, legislative and public awareness. The global conservation status of the rodents of Jordan according to the IUCN Red List include 22 species as least concern, one as near threatened (Allactaga euphratica), and one as data deficient (Nannospalax ehrenbergi). According to the regional assessment, one species is critically endangered, three species are considered endangered, one vulnerable. 

Natural history of the New Georgia Monkey-faced Bat Pteralopex sp. nov. from the Solomon Islands

1997 ◽  
Vol 3 (2) ◽  
pp. 134 ◽  
Author(s):  
Diana Fisher ◽  
Elizabeth Tasker
Keyword(s):  
Natural History ◽  
Field Study ◽  
Small Groups ◽  
Solomon Islands ◽  
Conservation Status ◽  
Restricted Range ◽  
Ecological Data ◽  
Short Term ◽  
Wide Range ◽  
History Of

The megachiropteran bat genus Pteralopex, Monkey-faced bats, is restricted to the Solomon Islands and Fiji. No other field study has been conducted on any of the five known species. From February to May 1992, the New Georgia Monkey-faced Bat was studied to determine its distribution, assess its conservation status and to provide ecological data for management. We found New Georgia Monkey-faced Bats Pteralopex sp. nov. at four sites on the islands of Vangunu and New Georgia, but not on Kolombangara. Bats were most common around an old village site abandoned approximately 90 years ago, in undisturbed rainforest, and adjacent gardens. Pteralopex sp. nov. was absent from areas of regrowth after logging or cyclone damage. It roosts in the hollows of tall canopy or emergent trees (particularly Ficus spp.), either singly or in small groups. Like other megachiropterans, Pteralopex sp. nov. eats a wide range of fruit and flowers. Young were born throughout the study, from February to May. This species' restricted range and susceptibility to hunting make it vulnerable, especially in the short term if its habitat is affected by logging or cyclones. Old village sites may be important for Pteralopex and other wildlife in the Solomon Islands.

NEW APPROACHES TO THE ORGANIZATIONAL AND TECHNICAL SUPPORT OF THE EXAMINATION OF COMPETITIVE APPLICATIONS FOR STATE SUPPORT IN THE FORM OF GRANTS OF THE PRESIDENT OF THE RUSSIAN FEDERATION TO YOUNG RUSSIAN SCIENTISTS – DOCTORS OF SCIENCES AND PHILOSOPHY DOCTORS (DOCTORS AND Ph. D.) AND LEADING SCIENTIFIC SCHOOLS

2020 ◽  
pp. 59-67
Author(s):  
N.A. Mironov ◽  
E.A. Maryshev ◽  
N.A. Divueva
Keyword(s):  
Information System ◽  
Russian Federation ◽  
Technical Support ◽  
Examination System ◽  
State Support ◽  
New Approaches ◽  
Wide Range ◽  
Integrated Information System ◽  
The Russian Federation ◽  
Integrated Information

The article discusses the issues of improving the examination system of competitive applications for state support in the form of grants of the President of the Russian Federation on the basis of an integrated information system that includes the information support system of the Grants Council of the President of the Russian Federation and the information system of the Federal Roster of Scientific and Technological Experts and containing information about experts, applications and expert examination results. In order to improve the principles of transparency and openness of support programs and competition winners, to ensure the objectivity of the competitive selection of projects, a number of organizational and technical solutions are proposed in the application examination system based on an integrated information system. The new and proposed new approaches to the organizational and technical support of the examination of competitive applications for state support in the form of grants of the President of the Russian Federation to young Russian scientists made it possible, by attracting a wide range of scientific and technological communities, to conduct examination of more than five thousand applications with high quality and deadlines set by the Ministry of Education and Science of Russia.

Myths of the Underworld in Contemporary Culture

2019 ◽  
Author(s):  
Judith Fletcher
Keyword(s):  
Short Stories ◽  
Case Studies ◽  
Joseph Conrad ◽  
Ezra Pound ◽  
Border Crossing ◽  
First Century ◽  
Contemporary Culture ◽  
Cinematic Adaptation ◽  
Narrative Tradition ◽  
Wide Range

Stories of a visit to the realm of the dead and a return to the upper world are among the oldest narratives in European literature, beginning with Homer’s Odyssey and extending to contemporary culture. This volume examines a series of fictional works by twentieth- and twenty-first century authors, such Toni Morrison and Elena Ferrante, which deal in various ways with the descent to Hades. Myths of the Underworld in Contemporary Culture surveys a wide range of genres, including novels, short stories, comics, a cinematic adaptation, poetry, and juvenile fiction. It examines not only those texts that feature a literal catabasis, such as Neil Gaiman’s Sandman series, but also those where the descent to the underworld is evoked in more metaphorical ways as a kind of border crossing, for instance Salman Rushdie’s use of the Orpheus myth to signify the trauma of migration. The analyses examine how these retellings relate to earlier versions of the mythical theme, including their ancient precedents by Homer and Vergil, but also to post-classical receptions of underworld narratives by authors such as Dante, Ezra Pound, and Joseph Conrad. Arguing that the underworld has come to connote a cultural archive of narrative tradition, the book offers a series of case studies that examine the adaptation of underworld myths in contemporary culture in relation to the discourses of postmodernism, feminism, and postcolonialism.

Explanation Beyond Causation

2018 ◽  
Keyword(s):  
Philosophy Of Science ◽  
Case Studies ◽  
Philosophical Study ◽  
Accurate Information ◽  
Contemporary Philosophy ◽  
Causal Information ◽  
Causal Explanations ◽  
Turn On ◽  
Detailed Case ◽  
Wide Range

Explanations are very important to us in many contexts: in science, mathematics, philosophy, and also in everyday and juridical contexts. But what is an explanation? In the philosophical study of explanation, there is long-standing, influential tradition that links explanation intimately to causation: we often explain by providing accurate information about the causes of the phenomenon to be explained. Such causal accounts have been the received view of the nature of explanation, particularly in philosophy of science, since the 1980s. However, philosophers have recently begun to break with this causal tradition by shifting their focus to kinds of explanation that do not turn on causal information. The increasing recognition of the importance of such non-causal explanations in the sciences and elsewhere raises pressing questions for philosophers of explanation. What is the nature of non-causal explanations—and which theory best captures it? How do non-causal explanations relate to causal ones? How are non-causal explanations in the sciences related to those in mathematics and metaphysics? This volume of new essays explores answers to these and other questions at the heart of contemporary philosophy of explanation. The essays address these questions from a variety of perspectives, including general accounts of non-causal and causal explanations, as well as a wide range of detailed case studies of non-causal explanations from the sciences, mathematics and metaphysics.

scholarly journals Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 311
Author(s):  
Zhenqiu Liu
Keyword(s):  
Single Cell ◽  
Free Parameter ◽  
Graphical Model ◽  
Expression Patterns ◽  
Information Criterion ◽  
Log P ◽  
Rna Seq ◽  
Clustering Methods ◽  
Wide Range ◽  
Free Parameters

Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clustering (RGGC) method for scRNA-seq data. RGGC is based on high-order (partial) correlations and subspace learning, and is robust over a wide-range of a regularized parameter λ. Therefore, we can simply set λ=2 or λ=log(p) for AIC (Akaike information criterion) or BIC (Bayesian information criterion) without cross-validation. Cell subpopulations are discovered by the Louvain community detection algorithm that determines the number of clusters automatically. There is no free parameter to be tuned with RGGC. When evaluated with simulated and benchmark scRNA-seq data sets against widely used methods, RGGC is computationally efficient and one of the top performers. It can detect inter-sample cell heterogeneity, when applied to glioblastoma scRNA-seq data.

scholarly journals Ocean Emission Effects on Aerosol-Cloud Interactions: Insights from Two Case Studies

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Armin Sorooshian ◽  
Hanh T. Duong
Keyword(s):  
Case Studies ◽  
Field Experiments ◽  
Remote Sensing Data ◽  
Anthropogenic Pollution ◽  
Cloud Microphysics ◽  
Marine Aerosols ◽  
Aerosol Cloud ◽  
First Case ◽  
Wide Range ◽  
Aerosol Cloud Interactions

Two case studies are discussed that evaluate the effect of ocean emissions on aerosol-cloud interactions. A review of the first case study from the eastern Pacific Ocean shows that simultaneous aircraft and space-borne observations are valuable in detecting links between ocean biota emissions and marine aerosols, but that the effect of the former on cloud microphysics is less clear owing to interference from background anthropogenic pollution and the difficulty with field experiments in obtaining a wide range of aerosol conditions to robustly quantify ocean effects on aerosol-cloud interactions. To address these limitations, a second case was investigated using remote sensing data over the less polluted Southern Ocean region. The results indicate that cloud drop size is reduced more for a fixed increase in aerosol particles during periods of higher ocean chlorophyll A. Potential biases in the results owing to statistical issues in the data analysis are discussed.

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