Estimating sexual size dimorphism in fossil species from posterior probability densities

2021 ◽  
Vol 118 (44) ◽  
pp. e2113943118
Author(s):  
Tomohiko Sasaki ◽  
Sileshi Semaw ◽  
Michael J. Rogers ◽  
Scott W. Simpson ◽  
Yonas Beyene ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Posterior Probability ◽  
Variation Method ◽  
Posterior Density ◽  
Density Peak ◽  
Fossil Species ◽  
Size Dimorphism ◽  
Probability Densities ◽  
Highest Posterior Density

Accurate characterization of sexual dimorphism is crucial in evolutionary biology because of its significance in understanding present and past adaptations involving reproductive and resource use strategies of species. However, inferring dimorphism in fossil assemblages is difficult, particularly with relatively low dimorphism. Commonly used methods of estimating dimorphism levels in fossils include the mean method, the binomial dimorphism index, and the coefficient of variation method. These methods have been reported to overestimate low levels of dimorphism, which is problematic when investigating issues such as canine size dimorphism in primates and its relation to reproductive strategies. Here, we introduce the posterior density peak (pdPeak) method that utilizes the Bayesian inference to provide posterior probability densities of dimorphism levels and within-sex variance. The highest posterior density point is termed the pdPeak. We investigated performance of the pdPeak method and made comparisons with the above-mentioned conventional methods via 1) computer-generated samples simulating a range of conditions and 2) application to canine crown-diameter datasets of extant known-sex anthropoids. Results showed that the pdPeak method is capable of unbiased estimates in a broader range of dimorphism levels than the other methods and uniquely provides reliable interval estimates. Although attention is required to its underestimation tendency when some of the distributional assumptions are violated, we demonstrate that the pdPeak method enables a more accurate dimorphism estimate at lower dimorphism levels than previously possible, which is important to illuminating human evolution.

scholarly journals Morphological characterization of Matisia cordata Bonpl. in a tropical dry forest from Antioquia, Colombia

2020 ◽  
Vol 73 (1) ◽  
pp. 9029-9038
Author(s):  
Verónica M. Álvarez-Osorio ◽  
Sandra B. Muriel-Ruíz ◽  
José M. Cotes-Torres
Keyword(s):  
Local Community ◽  
Phenotypic Diversity ◽  
Plant Genetic Resources ◽  
Scientific Information ◽  
Tropical Dry Forest ◽  
Morphological Characterization ◽  
Dry Forest ◽  
Posterior Density ◽  
Highest Posterior Density

Characterization of plant genetic resources is the first step to conserve plant diversity. Morphoagronomic characterization is a method that requires a selection of sensible descriptors, which are characteristics that define a phenotype. Sapodilla (Matisia cordata Bonpl.) is a plant genetic resource and is an important part of the agricultural tradition of the nearby western of Antioquia (Colombia). However, the lack of scientific information about this species shows that it is an underutilized fruit. The local community, in its traditional knowledge, recognizes two phenotypes of sapodilla: Creole and Ecuadorian. The phenotypic diversity of 100 trees of M. cordata was evaluated from 28 morphoagronomic descriptors. The Gower distance and UPGMA method were used to determine the diversity and make the dendrogram, respectively. The Bayes methodology was used to obtain the highest posterior density intervals of 95% probability and compare both phenotypes. Trees of the Creole phenotype had elliptical crown and acute shaped fruits, whereas the Ecuadorian phenotype presented a pyramidal crown and diverse fruit shapes. The Creole phenotype had stems with larger diameter at chest height (28.8 cm), more knots (10 cm), smaller leaves (25 cm), lighter fruits (301 g), larger peduncles (15.6 mm), smaller (40 mm) and lighter seeds (30 g), and an epicarp and a darker pulp than the Ecuadorian phenotype. The farmers’ local knowledge was partially confirmed since most of the descriptors coincided with the local perception, except descriptors of color and flavor of the pulp.

scholarly journals Sample Size Requirements for Calibrated Approximate Credible Intervals for Proportions in Clinical Trials

2021 ◽  
Vol 18 (2) ◽  
pp. 595
Author(s):  
Fulvio De Santis ◽  
Stefania Gubbiotti
Keyword(s):  
Clinical Trials ◽  
Posterior Probability ◽  
Interval Estimation ◽  
Small Sample ◽  
Sample Sizes ◽  
Posterior Density ◽  
Unknown Parameters ◽  
Credible Intervals ◽  
Small Sample Sizes ◽  
Highest Posterior Density

In Bayesian analysis of clinical trials data, credible intervals are widely used for inference on unknown parameters of interest, such as treatment effects or differences in treatments effects. Highest Posterior Density (HPD) sets are often used because they guarantee the shortest length. In most of standard problems, closed-form expressions for exact HPD intervals do not exist, but they are available for intervals based on the normal approximation of the posterior distribution. For small sample sizes, approximate intervals may be not calibrated in terms of posterior probability, but for increasing sample sizes their posterior probability tends to the correct credible level and they become closer and closer to exact sets. The article proposes a predictive analysis to select appropriate sample sizes needed to have approximate intervals calibrated at a pre-specified level. Examples are given for interval estimation of proportions and log-odds.

Some inequalities for moments and coefficients of variation for a large class of probability functions

1979 ◽  
Vol 16 (3) ◽  
pp. 665-670 ◽  
Author(s):  
Burt V. Bronk
Keyword(s):  
Large Class ◽  
Average Molecular Weight ◽  
Empirical Measure ◽  
Number Average Molecular Weight ◽  
Positive Real ◽  
Coefficients Of Variation ◽  
Probability Densities ◽  
Rigorous Bounds ◽  
Illustrative Application

Some inequalities for moments and coefficients of variation of probability densities over the positive real line are obtained by means of simple geometrical relationships. As an illustrative application rigorous bounds are obtained for the ratio of weight average to number average molecular weight for a large class of distributions of macromolecules, giving a more precise characterization of this empirical measure of heterogeneity.

scholarly journals Efeito materno e paterno sobre as taxas de fertilização e eclosão em curimba (Prochilodus lineatus)

2012 ◽  
Vol 64 (6) ◽  
pp. 1584-1590 ◽  
Author(s):  
I.B. Allaman ◽  
R.T.F. Freitas ◽  
A.T.M. Viveiros ◽  
A.F. Nascimento ◽  
G.R. Oliveira ◽  
...  
Keyword(s):  
Posterior Density ◽  
Prochilodus Lineatus ◽  
Highest Posterior Density

Avaliou-se o quanto fêmeas e machos contribuem para a variação total das taxas de fertilização e de eclosão em curimba (Prochilodus lineatus). Utilizou-se sêmen criopreservado proveniente de cinco machos para fertilizar ovócitos de seis fêmeas em um esquema fatorial cruzado 5x6, totalizando 30 famílias. Além das características reprodutivas dos machos e fêmeas, foram avaliadas as taxas de fertilização e eclosão para cômputo dos efeitos materno e paterno. Os componentes da variância foram estimados por meio da máxima verossimilhança restrita, sendo construídos intervalos Highest Posterior Density (HPD) para cada componente. Verificou-se que as fêmeas contribuíram muito mais para a variação total em relação aos machos para as taxas de fertilização e eclosão. Para a taxa de fertilização, as fêmeas contribuíram com 26,3% da variação total e os machos com 8,9%. Em relação à taxa de eclosão, as fêmeas contribuíram com 11,9% e os machos com 1,6%. Concluiu-se que houve efeito materno sobre as taxas de fertilização e eclosão e que o efeito paterno avaliado individualmente foi pouco expressivo ou até mesmo insignificante.

scholarly journals Computation of posterior distribution in Bayesian analysis – application in an intermittently used reliability system

2002 ◽  
Vol 21 (3) ◽  
pp. 78-82
Author(s):  
V. S.S. Yadavalli ◽  
P. J. Mostert ◽  
A. Bekker ◽  
M. Botha
Keyword(s):  
Posterior Distribution ◽  
Jeffreys Prior ◽  
Posterior Density ◽  
Unknown Parameters ◽  
Stationary Rate ◽  
Analysis Application ◽  
Definition Of ◽  
Hpd Intervals ◽  
Highest Posterior Density ◽  
Bayes Procedure

Bayesian estimation is presented for the stationary rate of disappointments, D∞, for two models (with different specifications) of intermittently used systems. The random variables in the system are considered to be independently exponentially distributed. Jeffreys’ prior is assumed for the unknown parameters in the system. Inference about D∞ is being restrained in both models by the complex and non-linear definition of D∞. Monte Carlo simulation is used to derive the posterior distribution of D∞ and subsequently the highest posterior density (HPD) intervals. A numerical example where Bayes estimates and the HPD intervals are determined illustrates these results. This illustration is extended to determine the frequentistical properties of this Bayes procedure, by calculating covering proportions for each of these HPD intervals, assuming fixed values for the parameters.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

A Paleoenvironmental and Archaeological Model-Based Age Estimate for the Colonization of Hawai’l

2014 ◽  
Vol 79 (1) ◽  
pp. 144-155 ◽  
Author(s):  
J. Stephen Athens ◽  
Timothy M. Rieth ◽  
Thomas S. Dye
Keyword(s):  
Bayesian Model ◽  
Depositional Model ◽  
Considerable Variability ◽  
Human Settlement ◽  
Posterior Density ◽  
Density Region ◽  
Radiocarbon Dates ◽  
The Core ◽  
Initial Settlement ◽  
Highest Posterior Density

AbstractRecent estimates of when Hawai’i was colonized by Polynesians display considerable variability, with dates ranging from about A.D. 800 to 1250. Using high resolution paleoenvironmental coring data and a carefully defined set of archaeological radiocarbon dates, a Bayesian model for initial settlement was constructed. The pollen and charcoal assemblages of the core record made it possible to identify and date the prehuman period and also the start of human settlement using a simple depositional model. The archaeological and paleoenvironmental estimates of the colonization date show a striking convergence, indicating that initial settlement occurred at A.D. 940–1130 at a 95 percent highest posterior density region (HPD), and most probably between A.D. 1000 to 1100, using a 67 percent HPD. This analysis highlights problems that may occur when paleoenvironmental core chronologies are based on bulk soil dates. Further research on the dating of the bones ofRattus exulans, a Polynesian introduction, may refine the dating model, as would archaeological investigations focused on potential early site locations.

Minimalist Biological Race

2017 ◽  
Author(s):  
Michael O. Hardimon
Keyword(s):  
Population Genetics ◽  
Evolutionary Biology ◽  
Geographic Location ◽  
Common Ancestry ◽  
Human Beings ◽  
Physical Features ◽  
Biological Race

The minimalist concept of race represents the barest characterization of the ordinary concept race possible. Minimalist races are groups of human beings distinguished by patterns of visible physical features, groups whose members are linked by a common ancestry peculiar to members of the group, and which originate from a distinctive geographic location. Minimalist races exist because there are existing human groups that satisfy the minimalist concept of race. Their existence is not precluded by the findings of population genetics. Appeal to contemporary studies in evolutionary biology and population genetics makes it possible to rebut the objection that minimalist races do not exist because they are not genetically distinct.

scholarly journals Protracted Regional Dissemination of GIM-1-Producing Serratia marcescens in Western Germany

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Andreas F. Wendel ◽  
Martin Kaase ◽  
Ingo B. Autenrieth ◽  
Silke Peter ◽  
Philipp Oberhettinger ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Gene Cassette ◽  
Recent Common Ancestor ◽  
Posterior Density ◽  
Content Type ◽  
Most Recent Common Ancestor ◽  
Bayesian Phylogenetic Analysis ◽  
Western Germany ◽  
Different Strains ◽  
Highest Posterior Density

ABSTRACT The metallo-beta-lactamase GIM-1 has been found in various bacterial host species nearly exclusively in western Germany. However, not much is known about the epidemiology of GIM-1-positive Serratia marcescens. Here we report on a surprisingly protracted regional dissemination. In-hospital transmission was investigated by using conventional epidemiological tools to identify spatiotemporal links. Strain typing was performed using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). Bayesian phylogeny was used to infer the time axis of the observed occurrence. Thirteen S. marcescens strains from 10 patients from 6 different German hospitals were investigated. Suspected in-hospital transmissions were confirmed by molecular typing at a higher resolution by WGS than by PFGE. A detailed sequence analysis demonstrated the spread of one predominant strain variant but also provided evidence for transfer of the bla GIM-1 gene cassette between different strains. A Bayesian phylogenetic analysis showed that the most recent common ancestor of the identified clonal cluster could be dated back to April 1993 (95% highest posterior density interval, January 1973 to March 2003) and that this strain might have already harbored the bla GIM-1 at that time and, therewith, years before the first detection of this resistance gene in clinical specimens. This study shows a long-standing clonal and plasmid-mediated expansion of GIM-1-producing S. marcescens that might have gone unnoticed in the absence of a standardized and effective molecular screening for carbapenemases. The systematic and early detection of resistance is thus highly advisable, especially for the prevention of potentially long-term dissemination that may progress beyond control.

scholarly journals Ontogenetic mechanisms underlying sexual size dimorphism in Urodele amphibians: An across-species approach

2013 ◽  
Vol 59 (1) ◽  
pp. 142-150 ◽  
Author(s):  
Lixia Zhang ◽  
Xin Lu
Keyword(s):  
Growth Rate ◽  
Body Size ◽  
Evolutionary Biology ◽  
Sexual Size Dimorphism ◽  
Demographic Data ◽  
High Growth ◽  
Annual Growth Rate ◽  
Size Dimorphism ◽  
Ontogenetic Trajectory ◽  
Delayed Maturation

Abstract Why do two sexes of the same species differ in body size holds a long-standing question of evolutionary biology. While many across-species comparisons have focused on ultimate causes behind sexual size dimorphism (SSD), only have a few been directed toward elucidating its ontogenetic basis. Urodeles are an amphibian group in which the direction and degree of SSD vary greatly among species. Using demographic data yielded by skeletochronology for 33 urodele species, the current study reveals a positive across-species correlation between SSD and the sex difference in mean age of adult animals, and the latter increases with the corresponding difference in age at maturity; annual growth rate does not differ between the sexes. We conclude that extended longevities in one sex, which is mediated by delayed maturation, would allow it to grow for longer and get larger, with growth rate making a weak contribution to body size. The sex-specific divergence in ontogenetic trajectory might be explained by potentially high growth costs of reproduction to females in association with stronger fecundity selection, and to males that are expected to experience stronger sexual selection.

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