scholarly journals Avoiding potential biases in ses.PD estimations with the Picante software package

2019 ◽  
Author(s):  
Rafael Molina-Venegas
Keyword(s):  
Species Richness ◽  
Software Package ◽  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
R Package ◽  
List Type ◽  
Routine Procedure ◽  
Phylogenetic Structure ◽  
Simulation Exercise ◽  
Simple Simulation

AbstractFaith’s phylogenetic diversity (PD) is one of the most widespread used indices of phylogenetic structure in the eco-phylogenetic literature. The metric became notably popular with the publication of the function pd as part of the Picante R package, which is nowadays a reference software for phylogenetic analyses.Because PD is not statistically independent of species richness, the routine procedure is to standardize the observed PD values for unequal richness across samples. The function ses.pd, which is also implemented in the Picante R package, is the reference function to conduct such standardization.Unfortunately, I have detected an anomaly in the function that may result in biased estimations of standardized PD values, particularly in communities with low species richness (i.e. less than four species) and unbalanced phylogenies.I conduct a simple simulation exercise to illustrate the issue and propose two alternative and easy to implement solutions to go around the problem.

scholarly journals Species richness, phylogenetic diversity and phylogenetic structure patterns of exotic and native plants along an elevational gradient in the Himalaya

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kumar Manish
Keyword(s):  
Species Richness ◽  
Exotic Species ◽  
Native Species ◽  
Phylogenetic Diversity ◽  
Elevational Gradient ◽  
Species Assemblages ◽  
Native Plant ◽  
Phylogenetic Structure ◽  
Phylogenetic Overdispersion ◽  
The Himalaya

Abstract Background So far, macroecological studies in the Himalaya have mostly concentrated on spatial variation of overall species richness along the elevational gradient. Very few studies have attempted to document the difference in elevational richness patterns of native and exotic species. In this study, this knowledge gap is addressed by integrating data on phylogeny and elevational distribution of species to identify the variation in species richness, phylogenetic diversity and phylogenetic structure of exotic and native plant species along an elevational gradient in the Himalaya. Results Species distribution patterns for exotic and native species differed; exotics tended to show maximum species richness at low elevations while natives tended to predominate at mid-elevations. Native species assemblages showed higher phylogenetic diversity than the exotic species assemblages over the entire elevational gradient in the Himalaya. In terms of phylogenetic structure, exotic species assemblages showed majorly phylogenetic clustering while native species assemblages were characterized by phylogenetic overdispersion over the entire gradient. Conclusions The findings of this study indicate that areas with high native species richness and phylogenetic diversity are less receptive to exotic species and vice versa in the Himalaya. Species assemblages with high native phylogenetic overdispersion are less receptive to exotic species than the phylogenetically clustered assemblages. Different ecological processes (ecological filtering in case of exotics and resource and niche competition in case of natives) may govern the distribution of exotic and native species along the elevational gradient in the Himalaya.

scholarly journals Local-Scale Environmental Filtering Shape Plant Taxonomic and Phylogenetic Diversity in the Isolated Amazonian Tepui (Tepequém Table Mountain)

2021 ◽  
Author(s):  
Prímula Campos ◽  
Carlos Ernesto Schaefer ◽  
Vanessa Pontara ◽  
Márcio Xavier ◽  
José Frutuoso Vale Júnior ◽  
...  
Keyword(s):  
Species Richness ◽  
Soil Properties ◽  
Community Assembly ◽  
Altitudinal Gradient ◽  
Phylogenetic Diversity ◽  
Local Scale ◽  
Environmental Drivers ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Table Mountain

Abstract Understanding how environmental drivers induce changes in plant composition and diversity across evolutionary time can provide important insights into the mechanisms of community assembly. We evaluated how taxonomic and phylogenetic diversity and structure of plant communities change along a local-scale edaphic and topographic gradient in the Tepequém table mountain, Brazilian Amazon. We selected three phytophysiognomies along the altitudinal gradient: Open Rupestrian Grassland, Shrubby Rupestrian Grassland, and Forest. We compared community composition and taxonomic and phylogenetic diversity between phytophysiognomies, and we tested regression linear effect models to investigate the effect of altitude and soil properties on taxonomic and phylogenetic diversity. The highest species richness and phylogenetic diversity were found at lower elevation for Forest. Mean pairwise phylogenetic distance, mean nearest taxon phylogenetic distance, and all standardised phylogenetic metrics were significantly lower in Shrubby Rupestrian Grassland. This phytophysiognomy showed phylogenetic clustering. Forest showed a cluster pattern when only terminal nodes are considered and random dispersion to deep phylogenetic nodes. Open Rupestrian Grassland also showed random phylogenetic structure. The regression analyses showed that species richness and different phylogenetic diversity metrics were explained by altitude and soil properties. However, standardised metrics were not explained by these environmental variables. Comprehensive studies including the role of environmental drivers in plant evolutionary history along the altitudinal gradient are necessary for explaining community assembly patterns and provide additional information for conservation planning.

scholarly journals DETECTING PHYLODIVERSITY-DEPENDENT DIVERSIFICATION WITH A GENERAL PHYLOGENETIC INFERENCE FRAMEWORK

2021 ◽  
Author(s):  
Francisco Richter ◽  
Ernst C. Wit ◽  
Rampal S. Etienne ◽  
Thijs Janzen ◽  
Hanno Hildenbrandt
Keyword(s):  
Species Richness ◽  
Expectation Maximization ◽  
Phylogenetic Diversity ◽  
R Package ◽  
Inference Method ◽  
Likelihood Methods ◽  
Species Diversification ◽  
As Species ◽  
Monte Carlo Expectation Maximization ◽  
Phylogenetic Divergence

Diversity-dependent diversification models have been extensively used to study the effect of ecological limits and feedback of community structure on species diversification processes, such as speciation and extinction. Current diversity-dependent diversification models characterise ecological limits by carrying capacities for species richness. Such ecological limits have been justified by niche filling arguments: as species diversity increases, the number of available niches for diversification decreases. However, as species diversify they may diverge from one another phenotypically, which may open new niches for new species. Alternatively, this phenotypic divergence may not affect the species diversification process or even inhibit further diversification. Hence, it seems natural to explore the consequences of phylogenetic diversity-dependent (or phylodiversity-dependent) diversification. Current likelihood methods for estimating diversity-dependent diversification parameters cannot be used for this, as phylodiversity is continuously changing as time progresses and species form and become extinct. Here, we present a new method based on Monte Carlo Expectation-Maximization (MCEM), designed to perform statistical inference on a general class of species diversification models and implemented in the R package emphasis. We use the method to fit phylodiversity-dependent diversification models to 14 phylogenies, and compare the results to the fit of a richness-dependent diversification model. We find that in a number of phylogenies, phylogenetic divergence indeed spurs speciation even though species richness reduces it. Not only do we thus shine a new light on diversity-dependent diversification, we also argue that our inference framework can handle a large class of diversification models for which currently no inference method exists.

scholarly journals Distribution and Community Assembly of Trees Along an Andean Elevational Gradient

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 326
Author(s):  
Samantha J. Worthy ◽  
Rosa A. Jiménez Paz ◽  
Álvaro J. Pérez ◽  
Alex Reynolds ◽  
Jennifer Cruse-Sanders ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Phylogenetic Analyses ◽  
Elevation Gradient ◽  
Elevational Gradient ◽  
Pairwise Distance ◽  
Phylogenetic Structure ◽  
Tree Ferns ◽  
Fern Species ◽  
Standardized Effect Sizes ◽  
Angiosperm Species

Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440–3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon–Weaver diversity, Simpson’s Dominance, Simpson’s Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.

scholarly journals Climate change impacts on the phylogenetic diversity of the world’s terrestrial birds: more than species numbers

2020 ◽  
Author(s):  
Alke Voskamp ◽  
Christian Hof ◽  
Matthias F. Biber ◽  
Thomas Hickler ◽  
Aidin Niamir ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Richness ◽  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Climate Change Impacts ◽  
Climate Impact ◽  
Species Assemblages ◽  
Potential Threat ◽  
Phylogenetic Structure ◽  
Species Numbers

AbstractOngoing climate change is a major threat to biodiversity and impacts on species distributions and abundances are already evident. Heterogenous responses of species due to varying abiotic tolerances and dispersal abilities have the potential to further amplify or ameliorate these impacts through changes in species assemblages. Here we investigate the impacts of climate change on terrestrial bird distributions and, subsequently, on species richness as well as on different aspects of phylogenetic diversity of species assemblages across the globe. We go beyond previous work by disentangling the potential impacts on assemblage phylogenetic diversity of species gains vs. losses under climate change and compare the projected impacts to randomized assemblage changes.We show that climate change might not only affect species numbers and composition of global species assemblages but could also have profound impacts on assemblage phylogenetic diversity, which, across extensive areas, differ significantly from random changes. Both the projected impacts on phylogenetic diversity and on phylogenetic structure vary greatly across the globe. Projected increases in the evolutionary history contained within species assemblages, associated with either increasing phylogenetic diversification or clustering, are most frequent at high northern latitudes. By contrast, projected declines in evolutionary history, associated with increasing phylogenetic over-dispersion or homogenisation, are projected across all continents.The projected widespread changes in the phylogenetic structure of species assemblages show that changes in species richness do not fully reflect the potential threat from climate change to ecosystems. Our results indicate that the most severe changes to the phylogenetic diversity and structure of species assemblages are likely to be caused by species range shifts rather than range reductions and extinctions. Our findings highlight the importance of considering diverse measures in climate impact assessments and the value of integrating species-specific responses into assessments of entire community changes.

scholarly journals Linking morphological and molecular sources to disentangle the case of Xylodon australis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier Fernández-López ◽  
M. Teresa Telleria ◽  
Margarita Dueñas ◽  
Mara Laguna-Castro ◽  
Klaus Schliep ◽  
...  
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
R Package ◽  
Molecular Data ◽  
Historical Collections ◽  
Close Relationship ◽  
Kinship Relations ◽  
History Of ◽  
Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

scholarly journals Conspicuousness, phylogenetic structure, and origins of Müllerian mimicry in 4000 lycid beetles from all zoogeographic regions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michal Motyka ◽  
Dominik Kusy ◽  
Michal Masek ◽  
Matej Bocek ◽  
Yun Li ◽  
...  
Keyword(s):  
Simple Model ◽  
Phylogenetic Diversity ◽  
Single Species ◽  
Visual Signals ◽  
South East Asia ◽  
Phylogenetic Information ◽  
Phylogenetic Structure ◽  
Chemical Defences ◽  
Single Region ◽  
General Appearance

AbstractBiologists have reported on the chemical defences and the phenetic similarity of net-winged beetles (Coleoptera: Lycidae) and their co-mimics. Nevertheless, our knowledge has remained fragmental, and the evolution of mimetic patterns has not been studied in the phylogenetic context. We illustrate the general appearance of ~ 600 lycid species and ~ 200 co-mimics and their distribution. Further, we assemble the phylogeny using the transcriptomic backbone and ~ 570 species. Using phylogenetic information, we closely scrutinise the relationships among aposematically coloured species, the worldwide diversity, and the distribution of aposematic patterns. The emitted visual signals differ in conspicuousness. The uniform coloured dorsum is ancestral and was followed by the evolution of bicoloured forms. The mottled patterns, i.e. fasciate, striate, punctate, and reticulate, originated later in the course of evolution. The highest number of sympatrically occurring patterns was recovered in New Guinea and the Andean mountain ecosystems (the areas of the highest abundance), and in continental South East Asia (an area of moderate abundance but high in phylogenetic diversity). Consequently, a large number of co-existing aposematic patterns in a single region and/or locality is the rule, in contrast with the theoretical prediction, and predators do not face a simple model-like choice but cope with complex mimetic communities. Lycids display an ancestral aposematic signal even though they sympatrically occur with differently coloured unprofitable relatives. We show that the highly conspicuous patterns evolve within communities predominantly formed by less conspicuous Müllerian mimics and, and often only a single species displays a novel pattern. Our work is a forerunner to the detailed research into the aposematic signalling of net-winged beetles.

scholarly journals Simulation Studies as a Tool to Understand Bayes Factors

2021 ◽  
Vol 4 (1) ◽  
pp. 251524592097262
Author(s):  
Don van Ravenzwaaij ◽  
Alexander Etz
Keyword(s):  
Simulation Study ◽  
Prior Distribution ◽  
Bayes Factor ◽  
R Package ◽  
Bayes Factors ◽  
Simulation Studies ◽  
Social Scientists ◽  
Simple Simulation ◽  
Set Up

When social scientists wish to learn about an empirical phenomenon, they perform an experiment. When they wish to learn about a complex numerical phenomenon, they can perform a simulation study. The goal of this Tutorial is twofold. First, it introduces how to set up a simulation study using the relatively simple example of simulating from the prior. Second, it demonstrates how simulation can be used to learn about the Jeffreys-Zellner-Siow (JZS) Bayes factor, a currently popular implementation of the Bayes factor employed in the BayesFactor R package and freeware program JASP. Many technical expositions on Bayes factors exist, but these may be somewhat inaccessible to researchers who are not specialized in statistics. In a step-by-step approach, this Tutorial shows how a simple simulation script can be used to approximate the calculation of the Bayes factor. We explain how a researcher can write such a sampler to approximate Bayes factors in a few lines of code, what the logic is behind the Savage-Dickey method used to visualize Bayes factors, and what the practical differences are for different choices of the prior distribution used to calculate Bayes factors.

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

scholarly journals Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yushan Liu ◽  
Yizhou Wang ◽  
Jiabo Pei ◽  
Yadong Li ◽  
Haiyue Sun
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Lignin Content ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Land Plant ◽  
Phylogenetic Structure ◽  
Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

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