scholarly journals Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles

Genetics ◽  
1996 ◽  
Vol 144 (3) ◽  
pp. 1237-1245 ◽  
Author(s):  
O Pons ◽  
R J Petit
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Mutation Rates ◽  
Phylogeographic Structure ◽  
Published Data ◽  
Data Set ◽  
Subdivided Populations ◽  
Two Measures ◽  
The Difference ◽  
Single Data

Abstract Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Event detection of different English data sources based on transfer learning

2021 ◽  
pp. 1-11
Author(s):  
Yanan Huang ◽  
Yuji Miao ◽  
Zhenjing Da
Keyword(s):  
Transfer Learning ◽  
Event Detection ◽  
Visual Analysis ◽  
Learning Algorithm ◽  
Data Sources ◽  
Data Set ◽  
Data Source ◽  
Single Data Source ◽  
The Difference ◽  
Single Data

The methods of multi-modal English event detection under a single data source and isomorphic event detection of different English data sources based on transfer learning still need to be improved. In order to improve the efficiency of English and data source time detection, based on the transfer learning algorithm, this paper proposes multi-modal event detection under a single data source and isomorphic event detection based on transfer learning for different data sources. Moreover, by stacking multiple classification models, this paper makes each feature merge with each other, and conducts confrontation training through the difference between the two classifiers to further make the distribution of different source data similar. In addition, in order to verify the algorithm proposed in this paper, a multi-source English event detection data set is collected through a data collection method. Finally, this paper uses the data set to verify the method proposed in this paper and compare it with the current most mainstream transfer learning methods. Through experimental analysis, convergence analysis, visual analysis and parameter evaluation, the effectiveness of the algorithm proposed in this paper is demonstrated.

Development of Scales Measuring the Capacity of Community-Based Initiatives

2007 ◽  
Vol 35 (3) ◽  
pp. 298-315 ◽  
Author(s):  
Michele Lempa ◽  
Robert M. Goodman ◽  
Janet Rice ◽  
Adam B. Becker
Keyword(s):  
National Sample ◽  
Community Based ◽  
Data Set ◽  
Local Public Health ◽  
Health Initiatives ◽  
Survey Results ◽  
Two Measures ◽  
Single Data ◽  
High Degree ◽  
Public Health Initiatives

This article describes the development of two measures for the capacity of local public health initiatives. Data obtained from a qualitative study of eight community-based initiatives served as the basis for the development of a survey instrument. It was administered to a national sample of both leaders and nonleaders of 291 such initiatives. Because survey results for leaders and nonleaders differed, results could not be combined into a single data set for analysis. Results for each data set were analyzed by employing exploratory principal components and factor analyses. A 44-item, six-factor scale resulted for leaders and a 38-item, five-factor scale resulted for nonleaders. The high degree of overlap (22 items) between the two scales resulted in a combined 60-item instrument that can be administered to both leaders and nonleaders but analyzed separately.

Squamate relationships based on C-mos nuclear DNA sequences: increased taxon sampling improves bootstrap support

2001 ◽  
Vol 22 (2) ◽  
pp. 235-242 ◽  
Author(s):  
J.C. Marshall ◽  
K.A. Crandall ◽  
D.J. Harris
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Bootstrap Support ◽  
Published Data ◽  
Robust Estimate ◽  
Independent Evidence ◽  
Rapid Speciation ◽  
Mtdna Sequence

AbstractSequences of the nuclear gene C-mos from 16 new species have been combined with previously published data to produce an analysis of squamate relationships using 56 taxa, considerably more than in previous analyses. Support for many nodes is greatly increased, thus producing a more robust assessment of relationships. Sampling was concentrated within the families Iguanidae and Lacertidae, both of which have poorly supported phylogenies based on mtDNA sequence data. Our analysis supports a robust estimate of relationships within the Iguanidae. Within the Lacertidae relationships are only partially well resolved, and this provides independent evidence for rapid speciation within this family.

scholarly journals Study/Experimental/Research Design: Much More Than Statistics

2010 ◽  
Vol 45 (1) ◽  
pp. 98-100 ◽  
Author(s):  
Kenneth L. Knight
Keyword(s):  
Statistical Analysis ◽  
Research Design ◽  
Study Design ◽  
Data Gathering ◽  
Statistical Design ◽  
Data Set ◽  
Road Map ◽  
The Difference ◽  
Single Data ◽  
New Variables

Abstract Context: The purpose of study, experimental, or research design in scientific manuscripts has changed significantly over the years. It has evolved from an explanation of the design of the experiment (ie, data gathering or acquisition) to an explanation of the statistical analysis. This practice makes “Methods” sections hard to read and understand. Objective: To clarify the difference between study design and statistical analysis, to show the advantages of a properly written study design on article comprehension, and to encourage authors to correctly describe study designs. Description: The role of study design is explored from the introduction of the concept by Fisher through modern-day scientists and the AMA Manual of Style. At one time, when experiments were simpler, the study design and statistical design were identical or very similar. With the complex research that is common today, which often includes manipulating variables to create new variables and the multiple (and different) analyses of a single data set, data collection is very different than statistical design. Thus, both a study design and a statistical design are necessary. Advantages: Scientific manuscripts will be much easier to read and comprehend. A proper experimental design serves as a road map to the study methods, helping readers to understand more clearly how the data were obtained and, therefore, assisting them in properly analyzing the results.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Gül Olgun Karacan ◽  
Reyhan Çolak ◽  
Ercüment Çolak
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogeographic Structure ◽  
Field Mouse ◽  
Interphotoreceptor Retinoid Binding Protein ◽  
Aegean Islands ◽  
Mitochondrial Data ◽  
D Loop ◽  
Physical Barriers ◽  
First Time

Abstract The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

scholarly journals Thermoregulation in desert birds: scaling and phylogenetic variation in heat tolerance and evaporative cooling

2021 ◽  
Vol 224 (Suppl 1) ◽  
pp. jeb229211
Author(s):  
Andrew E. McKechnie ◽  
Alexander R. Gerson ◽  
Blair O. Wolf
Keyword(s):  
Heat Tolerance ◽  
Heat Dissipation ◽  
Arid Zone ◽  
Resting Metabolic Rate ◽  
Heat Exposure ◽  
Published Data ◽  
Evaporative Heat Loss ◽  
Evaporative Water ◽  
Data Set ◽  
The Difference

ABSTRACTEvaporative heat dissipation is a key aspect of avian thermoregulation in hot environments. We quantified variation in avian thermoregulatory performance at high air temperatures (Ta) using published data on body temperature (Tb), evaporative water loss (EWL) and resting metabolic rate (RMR) measured under standardized conditions of very low humidity in 56 arid-zone species. Maximum Tb during acute heat exposure varied from 42.5±1.3°C in caprimulgids to 44.5±0.5°C in passerines. Among passerines, both maximum Tb and the difference between maximum and normothermic Tb decreased significantly with body mass (Mb). Scaling exponents for minimum thermoneutral EWL and maximum EWL were 0.825 and 0.801, respectively, even though evaporative scope (ratio of maximum to minimum EWL) varied widely among species. Upper critical limits of thermoneutrality (Tuc) varied by >20°C and maximum RMR during acute heat exposure scaled to Mb0.75 in both the overall data set and among passerines. The slope of RMR at Ta>Tuc increased significantly with Mb but was substantially higher among passerines, which rely on panting, compared with columbids, in which cutaneous evaporation predominates. Our analysis supports recent arguments that interspecific within-taxon variation in heat tolerance is functionally linked to evaporative scope and maximum ratios of evaporative heat loss (EHL) to metabolic heat production (MHP). We provide predictive equations for most variables related to avian heat tolerance. Metabolic costs of heat dissipation pathways, rather than capacity to increase EWL above baseline levels, appear to represent the major constraint on the upper limits of avian heat tolerance.

scholarly journals Is Phylogeographic Congruence Predicted by Historical Habitat Stability, or Ecological Co-associations?

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Ryan C Garrick ◽  
Chaz Hyseni ◽  
Ísis C Arantes ◽  
Louis G Zachos ◽  
Peter C Zee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Interactions ◽  
Ecological Niche Modeling ◽  
Nuclear Dna ◽  
Abiotic Factors ◽  
Genetic Data ◽  
Phylogeographic Structure ◽  
Biotic Factors ◽  
Effective Population ◽  
Species Responses

Abstract Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community.

scholarly journals Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages

2012 ◽  
Vol 30 (2) ◽  
pp. 253-262 ◽  
Author(s):  
Martyna Molak ◽  
Eline D. Lorenzen ◽  
Beth Shapiro ◽  
Simon Y.W. Ho
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Estimation Error ◽  
Phylogenetic Analyses ◽  
Published Data ◽  
Molecular Clocks ◽  
Data Sets ◽  
Data Set ◽  
Temporal Sampling ◽  
The Impact

Abstract In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.

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