scholarly journals Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

2012 ◽  
Vol 279 (1743) ◽  
pp. 3678-3686 ◽  
Author(s):  
Jacob A. Esselstyn ◽  
Ben J. Evans ◽  
Jodi L. Sedlock ◽  
Faisal Ali Anwarali Khan ◽  
Lawrence R. Heaney
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Simulated Data ◽  
Interspecific Variation ◽  
The Philippines ◽  
Effective Population ◽  
Current Estimate ◽  
Echolocation Call ◽  
Biologically Relevant ◽  
Additional Information

Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule–coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats ( Hipposideros ) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size ( N e ) and speciation rate (SR; per lineage per million years) was less than or equal to 10 5 , while interspecific variation in N e was twofold or less. However, at higher but also biologically relevant values of N e × SR and when N e varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N e , SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

scholarly journals Species delimitation and phylogeny estimation under the multispecies coalescent

2014 ◽  
Author(s):  
Graham R Jones
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
A Priori ◽  
Simulated Data ◽  
Species Trees ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Multiple Loci ◽  
Population Sizes ◽  
Phylogeny Estimation

This article describes a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using DNA sequences from multiple loci. The focus here is on species delimitation with no a priori assignment of individuals to species, and no guide tree. The method uses a new model for the population sizes along the branches of the species tree, and three new operators for sampling from the posterior using the Markov chain Monte Carlo (MCMC) algorithm. The correctness of the moves is demonstrated both by proofs and by tests of the implementation. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al, 2014). The same simulated data set is used to demonstrate the accuracy and efficiency of the present method. The method is implemented in a package called STACEY for BEAST2.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals Development of Instant Sinigang Powder from Katmon Fruit (Dillenia philippinensis)

2019 ◽  
Vol 7 (1) ◽  
pp. 367-383
Author(s):  
Marchelita Beverly Tappy ◽  
Sophiya Celine Dellosa ◽  
Teejay Malabonga
Keyword(s):  
High School Students ◽  
Nutritional Value ◽  
Nutrient Content ◽  
The Philippines ◽  
Iodized Salt ◽  
School Students ◽  
Additional Information ◽  
The Cost ◽  
Online Software ◽  
Senior High School Students

INTRODUCTION:Katmon Fruit (Dillenia Philippinensis) is a fruit tree commonly use in the rural area in the Philippines. Katmon is eaten as fruit but is not very popular because of the unacceptable taste that resembles a green sour apple. The purpose of this study is to develop an instant sinigang powder as a base ingredients of sinigang and using the natural sour taste for sinigang dish.   METHOD:This study use katmon fruit, shiitake mushroom, garlic, iodized salt, and sugar to develop an instant sinigang mix powder. It were dehydrated using the Multi-Commodity Heat Pump Dryer for 13 hours. These were powdered using a grinder mixed with iodized salt and sugar. The nutrient content was computed using iFNRI online software. Thirty participants comprising: 10 faculty, 10 dormitory students,10 senior high school students did the taste test.   RESULTS:The results revealed that the product was liked very much in terms of color, texture, taste, aroma, and appearance. The instant sinigang powder is stored in a polyethylene metalized zip lock packaging 8.5 x 14cm. The cost per serving is PhP 37.5 .It is cheaper and has more nutritional value compared to other products.   DISCUSSION AND RECOMENDATION: The study recommend for more enhancement in terms of flavour of instant sinigang powder from katmon additional ingredient from natural sources to have more tasty and more nutritional content. This study also can help future researchers to have additional information about the katmon fruit.

Distribution of a Secale cereale DNA repeat sequence among 25 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (3) ◽  
pp. 383-388 ◽  
Author(s):  
P. K. Gupta ◽  
G. Fedak ◽  
S. J. Molnar ◽  
Roger Wheatcroft
Keyword(s):  
Dna Sequences ◽  
Secale Cereale ◽  
Dna Hybridization ◽  
Interspecific Variation ◽  
Repeat Sequence ◽  
Species Variation ◽  
Repeated Dna ◽  
Repeat Units ◽  
Dna Repeat ◽  
Hordeum Species

DNA of 61 accessions representing 25 Hordeum species was tested for homology to a highly repeated 120-bp sequence from Secale cereale (rye). Homology to the probe (pSC119) was detected in dot blots of all species except H. vulgare (cultivated barley) and its related species, H. agriocrithon and H. spontaneum. Hybridization patterns of Southern blots of restriction fragments demonstrated both intraspecific and interspecific variation in the organization of complex units of DNA having homology to the probe. For eight species, digestion of the DNA with BamHI gave ladder patterns characteristic of tandem arrays of 120-bp repeat units. For EcoRI, HindIII, and SacI digests, the hybridization patterns appeared to be highly conserved in the section Hordeum, except those for H. bulbosum, which were unique. A further set of patterns for these three enzymes was common among the remaining species of the genus. Thus, DNA hybridization with pSC119 generally gave patterns consistent with the current taxonomy of Hordeum species, except that H. bulbosum and H. vulgare were not shown to be closely related.Key words: Hordeum, repeated DNA sequences, pSC119, species variation.

Selection intensity for codon bias.

Genetics ◽  
1994 ◽  
Vol 138 (1) ◽  
pp. 227-234 ◽  
Author(s):  
D L Hartl ◽  
E N Moriyama ◽  
S A Sawyer
Keyword(s):  
Amino Acids ◽  
Dna Sequences ◽  
Codon Bias ◽  
Enteric Bacteria ◽  
Average Intensity ◽  
Ancestral State ◽  
Selection Intensity ◽  
Coding Region ◽  
Effective Population ◽  
Synonymous Codons

Abstract The patterns of nonrandom usage of synonymous codons (codon bias) in enteric bacteria were analyzed. Poisson random field (PRF) theory was used to derive the expected distribution of frequencies of nucleotides differing from the ancestral state at aligned sites in a set of DNA sequences. This distribution was applied to synonymous nucleotide polymorphisms and amino acid polymorphisms in the gnd and putP genes of Escherichia coli. For the gnd gene, the average intensity of selection against disfavored synonymous codons was estimated as approximately 7.3 x 10(-9); this value is significantly smaller than the estimated selection intensity against selectively disfavored amino acids in observed polymorphisms (2.0 x 10(-8)), but it is approximately of the same order of magnitude. The selection coefficients for optimal synonymous codons estimated from PRF theory were consistent with independent estimates based on codon usage for threonine and glycine. Across 118 genes in E. coli and Salmonella typhimurium, the distribution of estimated selection coefficients, expressed as multiples of the effective population size, has a mean and standard deviation of 0.5 +/- 0.4. No significant differences were found in the degree of codon bias between conserved positions and replacement positions, suggesting that translational misincorporation is not an important selective constraint among synonymous polymorphic codons in enteric bacteria. However, across the first 100 codons of the genes, conserved amino acids with identical codons have significantly greater codon bias than that of either synonymous or nonidentical codons, suggesting that there are unique selective constraints, perhaps including mRNA secondary structures, in this part of the coding region.

Quantifying genetic variation at the molecular level

2019 ◽  
pp. 34-66
Author(s):  
Asher D. Cutter
Keyword(s):  
Genetic Variation ◽  
Dna Sequences ◽  
Migration Rate ◽  
Population Genetic ◽  
Quantitative Methods ◽  
Molecular Level ◽  
Effective Population ◽  
Fundamental Properties ◽  
Site Frequency Spectrum ◽  
Population Genetic Variation

Chapter 3, “Quantifying genetic variation at the molecular level,” introduces quantitative methods for measuring variation directly in DNA sequences to help decipher fundamental properties of populations and what they can tell us about evolution. It provides an overview of the evolutionary factors that contribute to genetic variation, like mutational input, effective population size, genetic drift, migration rate, and models of migration. This chapter surveys the principal ways to measure and summarize polymorphisms within a single population and across multiple populations of a species, including heterozygosity, nucleotide polymorphism estimators of θ‎, the site frequency spectrum, and F ST, and by providing illustrative natural examples. Populations are where evolution starts, after mutations arise as the spark of population genetic variation, and Chapter 3 describes how to quantify the variation to connect observations to predictions about how much polymorphism there ought to be under different circumstances.

scholarly journals Use of Correlated Data for Nonparametric Prediction of a Spatial Target Variable

Mathematics ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 2077
Author(s):  
Pilar García-Soidán ◽  
Tomás R. Cotos-Yáñez
Keyword(s):  
Spatial Data ◽  
Lead Level ◽  
Simulated Data ◽  
Auxiliary Variable ◽  
Correlated Data ◽  
Dependence Structure ◽  
Nonparametric Approach ◽  
Additional Information ◽  
Squared Prediction Error ◽  
Kernel Approach

The kriging methodology can be applied to predict the value of a spatial variable at an unsampled location, from the available spatial data. Furthermore, additional information from secondary variables, correlated with the target one, can be included in the resulting predictor by using the cokriging techniques. The latter procedures require a previous specification of the multivariate dependence structure, difficult to characterize in practice in an appropriate way. To simplify this task, the current work introduces a nonparametric kernel approach for prediction, which satisfies good properties, such as asymptotic unbiasedness or the convergence to zero of the mean squared prediction error. The selection of the bandwidth parameters involved is also addressed, as well as the estimation of the remaining unknown terms in the kernel predictor. The performance of the new methodology is illustrated through numerical studies with simulated data, carried out in different scenarios. In addition, the proposed nonparametric approach is applied to predict the concentrations of a pollutant that represents a risk to human health, the cadmium, in the floodplain of the Meuse river (Netherlands), by incorporating the lead level as an auxiliary variable.

Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea

2020 ◽  
Vol 86 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Jun Liu ◽  
Dan Cui ◽  
Hui Wang ◽  
Jiawei Chen ◽  
Helu Liu ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Species Delimitation ◽  
Strong Support ◽  
Hainan Island ◽  
The Philippines ◽  
Nominal Species ◽  
Cryptic Diversity ◽  
China Sea ◽  
Giant Clams

Abstract Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences from Hainan Island in the South China Sea and previously published ones from Japan, Taiwan, Singapore, the Philippines, Indonesia, Australia, the Solomon Islands and the Red Sea. Three nominal species, Tridacna crocea, T. squamosa and T. noae, were recognized at Hainan Island on the basis of distance-based DNA barcoding, with mean interspecific K2P distances of 10.6–24.7% for seven Tridacna species (T. crocea, T. squamosa, T. noae, T. maxima, T. mbalavuana, T. derasa and T. gigas). The most abundant species, T. noae, represents the first record of this species from Hainan Island. Using a combination of phylogenetic and DNA-based species delimitation analyses (automatic barcode gap discovery, generalized mixed Yule coalescent and Bayesian Poisson tree processes), we found strong support for a total of 13 operational taxonomic units (OTUs) for the seven nominal Tridacna species. These results, coupled with the fact that each OTU occupies different regions in the Indo-Pacific, strongly suggest multiple cryptic species of giant clams. Our findings point to the need for taxonomic revisionary work on giant clams throughout the Indo-Pacific; such work will have important conservation implications.

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 62 (1) ◽  
pp. 427-446 ◽  
Author(s):  
Susana Schönhuth ◽  
David M. Hillis ◽  
David A. Neely ◽  
Lourdes Lozano-Vilano ◽  
Anabel Perdices ◽  
...  
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
The North
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