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Gaynor ML, Landis JB, O'Connor TK, Laport RG, Doyle JJ, Soltis DE, Ponciano JM, Soltis PS. nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11606. [PMID: 39184199 PMCID: PMC11342224 DOI: 10.1002/aps3.11606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/01/2024] [Accepted: 05/28/2024] [Indexed: 08/27/2024]
Abstract
Premise Traditional methods of ploidal-level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site-based heterozygosity have been developed. However, these approaches may require high-coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open-source R package that addresses the main shortcomings of current methods. Methods and Results nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta-binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. Conclusions Inferring ploidy based on site-based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site-based heterozygosity method to infer ploidy.
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Affiliation(s)
- Michelle L. Gaynor
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Jacob B. Landis
- School of Integrative Plant ScienceCornell UniversityIthaca14850New YorkUSA
| | - Timothy K. O'Connor
- Department of Ecology and EvolutionUniversity of ChicagoChicago60637IllinoisUSA
| | | | - Jeff J. Doyle
- School of Integrative Plant ScienceCornell UniversityIthaca14850New YorkUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | | | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
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Cahusac PMB. Likelihood Ratio Test and the Evidential Approach for 2 × 2 Tables. ENTROPY (BASEL, SWITZERLAND) 2024; 26:375. [PMID: 38785625 PMCID: PMC11119089 DOI: 10.3390/e26050375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Categorical data analysis of 2 × 2 contingency tables is extremely common, not least because they provide risk difference, risk ratio, odds ratio, and log odds statistics in medical research. A χ2 test analysis is most often used, although some researchers use likelihood ratio test (LRT) analysis. Does it matter which test is used? A review of the literature, examination of the theoretical foundations, and analyses of simulations and empirical data are used by this paper to argue that only the LRT should be used when we are interested in testing whether the binomial proportions are equal. This so-called test of independence is by far the most popular, meaning the χ2 test is widely misused. By contrast, the χ2 test should be reserved for where the data appear to match too closely a particular hypothesis (e.g., the null hypothesis), where the variance is of interest, and is less than expected. Low variance can be of interest in various scenarios, particularly in investigations of data integrity. Finally, it is argued that the evidential approach provides a consistent and coherent method that avoids the difficulties posed by significance testing. The approach facilitates the calculation of appropriate log likelihood ratios to suit our research aims, whether this is to test the proportions or to test the variance. The conclusions from this paper apply to larger contingency tables, including multi-way tables.
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Affiliation(s)
- Peter M. B. Cahusac
- Department of Pharmacology & Biostatistics, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Department of Comparative Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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Ponciano JM, Gómez JP, Ravel J, Forney LJ. Inferring stability and persistence in the vaginal microbiome: A stochastic model of ecological dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.581600. [PMID: 38464272 PMCID: PMC10925280 DOI: 10.1101/2024.03.02.581600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The interplay of stochastic and ecological processes that govern the establishment and persistence of host-associated microbial communities is not well understood. Here we illustrate the conceptual and practical advantages of fitting stochastic population dynamics models to multi-species bacterial time series data. We show how the stability properties, fluctuation regimes and persistence probabilities of human vaginal microbial communities can be better understood by explicitly accommodating three sources of variability in ecological stochastic models of multi-species abundances: 1) stochastic biotic and abiotic forces, 2) ecological feedback and 3) sampling error. Rooting our modeling tool in stochastic population dynamics modeling theory was key to apply standardized measures of a community's reaction to environmental variation that ultimately depends on the nature and intensity of the intra-specific and inter-specific interaction strengths. Using estimates of model parameters, we developed a Risk Prediction Monitoring (RPM) tool that estimates temporal changes in persistence probabilities for any bacterial group of interest. This method mirrors approaches that are often used in conservation biology in which a measure of extinction risks is periodically updated with any change in a population or community. Additionally, we show how to use estimates of interaction strengths and persistence probabilities to formulate hypotheses regarding the molecular mechanisms and genetic composition that underpin different types of interactions. Instead of seeking a definition of "dysbiosis" we propose to translate concepts of theoretical ecology and conservation biology methods into practical approaches for the management of human-associated bacterial communities.
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Affiliation(s)
| | - Juan P. Gómez
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD
| | - Larry J. Forney
- Institute for Interdisciplinary Data Science and Department of Biological Sciences, University of Idaho, Moscow, ID
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Powell JH, Kalinowski ST, Taper ML, Rotella JJ, Davis CS, Garrott RA. Evidence of an Absence of Inbreeding Depression in a Wild Population of Weddell Seals ( Leptonychotes weddellii). ENTROPY (BASEL, SWITZERLAND) 2023; 25:403. [PMID: 36981292 PMCID: PMC10047074 DOI: 10.3390/e25030403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Inbreeding depression can reduce the viability of wild populations. Detecting inbreeding depression in the wild is difficult; developing accurate estimates of inbreeding can be time and labor intensive. In this study, we used a two-step modeling procedure to incorporate uncertainty inherent in estimating individual inbreeding coefficients from multilocus genotypes into estimates of inbreeding depression in a population of Weddell seals (Leptonychotes weddellii). The two-step modeling procedure presented in this paper provides a method for estimating the magnitude of a known source of error, which is assumed absent in classic regression models, and incorporating this error into inferences about inbreeding depression. The method is essentially an errors-in-variables regression with non-normal errors in both the dependent and independent variables. These models, therefore, allow for a better evaluation of the uncertainty surrounding the biological importance of inbreeding depression in non-pedigreed wild populations. For this study we genotyped 154 adult female seals from the population in Erebus Bay, Antarctica, at 29 microsatellite loci, 12 of which are novel. We used a statistical evidence approach to inference rather than hypothesis testing because the discovery of both low and high levels of inbreeding are of scientific interest. We found evidence for an absence of inbreeding depression in lifetime reproductive success, adult survival, age at maturity, and the reproductive interval of female seals in this population.
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Affiliation(s)
- John H. Powell
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Steven T. Kalinowski
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Mark L. Taper
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Jay J. Rotella
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Robert A. Garrott
- Department of Ecology, Montana State University, P.O. Box 173460, Bozeman, MT 59717, USA
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Taper ML, Ponciano JM, Dennis B. Entropy, Statistical Evidence, and Scientific Inference: Evidence Functions in Theory and Applications. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1273. [PMID: 36141159 PMCID: PMC9498250 DOI: 10.3390/e24091273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Scope and Goals of the Special Issue: There is a growing realization that despite being the essential tool of modern data-based scientific discovery and model testing, statistics has major problems [...].
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Affiliation(s)
- Mark L. Taper
- Department of Ecology, Montana State University, Bozeman, MT 59717, USA
| | - José Miguel Ponciano
- Biology Department, University of Florida, Gainesville, FL 32611, USA
- Mathematics Department, University of Florida, Gainesville, FL 32611, USA
| | - Brian Dennis
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, USA
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA
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Edgar A, Ponciano JM, Martindale MQ. Ctenophores are direct developers that reproduce continuously beginning very early after hatching. Proc Natl Acad Sci U S A 2022; 119:e2122052119. [PMID: 35476523 PMCID: PMC9170174 DOI: 10.1073/pnas.2122052119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/05/2022] [Indexed: 12/21/2022] Open
Abstract
A substantial body of literature reports that ctenophores exhibit an apparently unique life history characterized by biphasic sexual reproduction, the first phase of which is called larval reproduction or dissogeny. Whether this strategy is plastically deployed or a typical part of these species’ life history was unknown. In contrast to previous reports, we show that the ctenophore Mnemiopsis leidyi does not have separate phases of early and adult reproduction, regardless of the morphological transition to what has been considered the adult form. Rather, these ctenophores begin to reproduce at a small body size and spawn continuously from this point onward under adequate environmental conditions. They do not display a gap in productivity for metamorphosis or other physiological transition at a certain body size. Furthermore, nutritional and environmental constraints on fecundity are similar in both small and large animals. Our results provide critical parameters for understanding resource partitioning between growth and reproduction in this taxon, with implications for management of this species in its invaded range. Finally, we report an observation of similarly small-size spawning in a beroid ctenophore, which is morphologically, ecologically, and phylogenetically distinct from other ctenophores reported to spawn at small sizes. We conclude that spawning at small body size should be considered as the default, on-time developmental trajectory rather than as precocious, stress-induced, or otherwise unusual for ctenophores. The ancestral ctenophore was likely a direct developer, consistent with the hypothesis that multiphasic life cycles were introduced after the divergence of the ctenophore lineage.
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Affiliation(s)
- Allison Edgar
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080
| | | | - Mark Q. Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080
- Department of Biology, University of Florida, Gainesville, FL 32611
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