Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus)

The explosion of online knowledge has made knowledge, paradoxically, difficult to find. A web or journal search might retrieve thousands of articles, ranked in a manner that is biased by, for example, popularity or eigenvalue centrality rather than by informed relevance to the complex query. With hundreds of thousands of articles published each year, the dense, tangled thicket of knowledge grows even more entwined. Although natural language processing and new methods of generating knowledge graphs can extract increasingly high-level interpretations from research articles, the results are inevitably biased toward recent, popular, and/or prestigious sources. This is a result of the inherent nature of human social-learning processes. To preserve and even rediscover lost scientific ideas, we employ the theory that scientific progress is punctuated by means of inspired, revolutionary ideas at the origin of new paradigms. Using a brief case example, we suggest how phylogenetic inference might be used to rediscover potentially useful lost discoveries, as a way in which machines could help drive revolutionary science.

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Complete mitochondrial genomes of Epeorus carinatus and E. dayongensis (Ephemeroptera: Heptageniidae): Genomic comparison and phylogenetic inference

Gene ◽

10.1016/j.gene.2021.145467 ◽

2021 ◽

Vol 777 ◽

pp. 145467

Author(s):

Wei Zhang ◽

Ran Li ◽

Changfa Zhou

Keyword(s):

Phylogenetic Inference ◽

Mitochondrial Genomes ◽

Genomic Comparison ◽

Complete Mitochondrial Genomes

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Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191082 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 151-179

Author(s):

L. Lee Grismer ◽

L. Wood Perry ◽

Marta S. Grismer ◽

Evan S.H. Quah ◽

Myint Kyaw Thura ◽

...

Keyword(s):

Geographic Variation ◽

Evolutionary History ◽

Phylogenetic Inference ◽

Morphological Characters ◽

Molecular Data ◽

Biodiversity Crisis ◽

Allopatric Populations ◽

Compelling Argument ◽

Historical Accuracy ◽

Molecular Phylogenetic

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.

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Parametrizations of Liquid and Ice Clouds’ Optical Properties in Operational Numerical Weather Prediction Models

Atmosphere ◽

10.3390/atmos12010089 ◽

2021 ◽

Vol 12 (1) ◽

pp. 89

Author(s):

Harel. B. Muskatel ◽

Ulrich Blahak ◽

Pavel Khain ◽

Yoav Levi ◽

Qiang Fu

Keyword(s):

Optical Properties ◽

Numerical Weather Prediction ◽

Radiation Transfer ◽

Prediction Models ◽

Weather Prediction ◽

Effective Size ◽

Asymmetry Factor ◽

Numerical Weather ◽

Numerical Weather Prediction Models ◽

Spectral Averaging

Parametrization of radiation transfer through clouds is an important factor in the ability of Numerical Weather Prediction models to correctly describe the weather evolution. Here we present a practical parameterization of both liquid droplets and ice optical properties in the longwave and shortwave radiation. An advanced spectral averaging method is used to calculate the extinction coefficient, single scattering albedo, forward scattered fraction and asymmetry factor (bext, v, f, g), taking into account the nonlinear effects of light attenuation in the spectral averaging. An ensemble of particle size distributions was used for the ice optical properties calculations, which enables the effective size range to be extended up to 570 μm and thus be applicable for larger hydrometeor categories such as snow, graupel, and rain. The new parameterization was applied both in the COSMO limited-area model and in ICON global model and was evaluated by using the COSMO model to simulate stratiform ice and water clouds. Numerical weather prediction models usually determine the asymmetry factor as a function of effective size. For the first time in an operational numerical weather prediction (NWP) model, the asymmetry factor is parametrized as a function of aspect ratio. The method is generalized and is available on-line to be readily applied to any optical properties dataset and spectral intervals of a wide range of radiation transfer models and applications.

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Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST

Systematic Biology ◽

10.1093/sysbio/syaa037 ◽

2020 ◽

Vol 70 (1) ◽

pp. 181-189

Author(s):

Guy Baele ◽

Mandev S Gill ◽

Paul Bastide ◽

Philippe Lemey ◽

Marc A Suchard

Keyword(s):

High Performance ◽

Markov Models ◽

Marginal Likelihood ◽

Likelihood Estimation ◽

Phylogenetic Inference ◽

Time Variability ◽

Substitution Process ◽

Wide Range ◽

Markov Modulated ◽

Over Time

Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.]

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Population and Conservation Genetics of Marsupials

Australian Journal of Zoology ◽

10.1071/zo9890161 ◽

1989 ◽

Vol 37 (3) ◽

pp. 161 ◽

Cited By ~ 8

Author(s):

WB Sherwin ◽

ND Murray

Keyword(s):

Population Genetics ◽

Conservation Genetics ◽

Current Knowledge ◽

Effective Size ◽

Individual Species ◽

Census Size ◽

Electrophoretic Data ◽

Marsupial Species ◽

Small Effective Size ◽

Census Number

This article summarises current knowledge of marsupial population genetics, and discusses its relevance to the conservation of marsupial species. It has been suggested that there is much lower genetic variation within marsupial populations than in eutherian mammals. This trend is not evident in the electrophoretic data summarised here. However, genetic differentiation between populations, subspecies, and species of marsupials appears to be slightly lower than comparable values for eutherians. Genetic estimates of migration between populations are scarce at present, but show values that are comparable with eutherians. Some studies of marsupial population genetics have used non-electrophoretic characteristics, or have addressed the possibility of selection on the characters analysed. Although few, these studies indicate the suitability of marsupials for such investigations. Recent debate over the theories and applications of conservation genetics has made it clear that more research is required on individual species. Given the record of extinction of marsupials in the last 200 years, it is important to test the applicability of these theories to individual marsupial species. Several examples are discussed emphasising the need for ecological studies that estimate the effective number of reproducing individuals per generation. This figure, called the effective size, is the corner- stone of conservation genetics theory, being an important determinant of both the rate of loss of variation between individuals, and the rate of inbreeding. The effective size of the mainland population of the eastern barred bandicoot, Perameles gunnii, appears to be only about one-tenth of its census number. This result is comparable with estimates made in other vertebrates, and demonstrates that many marsupial species which appear to have an adequate census size on ecological grounds may face genetic problems resulting from small effective size.

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