scholarly journals Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2968 ◽  
Author(s):  
Mauricio Diazgranados ◽  
Janet C. Barber
Keyword(s):  
Monte Carlo ◽  
Permutation Test ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Regional Scale ◽  
Herbarium Specimens ◽  
Minimum Evolution ◽  
Additional Material ◽  
Monte Carlo Permutation Test

BackgroundThe páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants.MethodsField expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny.ResultsPhylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other.ConclusionsOur data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.

scholarly journals The Bioindication Evaluation of Ground Beetles (Coleoptera: Carabidae) in Three Forest Biotopes in the Southern Part of Central Slovakia

2019 ◽  
Vol 38 (1) ◽  
pp. 25-36
Author(s):  
Vladimír Langraf ◽  
Kornélia Petrovičová ◽  
Stanislav David ◽  
Janka Nozdrovická ◽  
František Petrovič ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Permutation Test ◽  
Ground Beetle ◽  
Ground Beetles ◽  
P Value ◽  
Pitfall Traps ◽  
Flight Ability ◽  
Monte Carlo Permutation Test ◽  
Group A ◽  
Forest Habitats

AbstractGround beetles (Carabidae) were used to evaluate the bio indication environmental incidence. The ground beetle material (2,341 individuals, 30 species) was collected between 2015 and 2017 using pitfall traps in three types of forest habitats with different disturbance rates. The comparison of carabid’s sensitivity as bio indicators has been evaluated by using three methods: (i) community index of ground beetles (IKS), (ii) ellipsoid biovolume (EV) and (iii) flight ability of the carabids. Using the Monte Carlo permutation test, we did not record the statistically significant changes in IKS values, nor does a change in the representation of carabids in the bioindicative group A, E and R. On the contrary, we confirmed the statistically significant changes in the average values of ellipsoid biovolume in biotopes and between biotopes (the Friedman and Kruskal-Wallis test -ANOVA (p-value = 0.00)). A higher number of macropterous species were recorded in biotopes with high disturbance as compared to the biotopes with low disturbance.

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

2019 ◽  
Vol 69 (3) ◽  
pp. 431-444 ◽  
Author(s):  
Emily J Roycroft ◽  
Adnan Moussalli ◽  
Kevin C Rowe
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Bootstrap Support ◽  
Data Sets ◽  
Lineage Sorting ◽  
Nucleotide Sequence Data ◽  
Branch Support ◽  
Partitioning Strategy

Abstract The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

Kapcom: A Program for the Comparison of Kappa Coefficients Obtained from the Same Sample of Observations

1997 ◽  
Vol 85 (3) ◽  
pp. 899-902 ◽  
Author(s):  
Dean P. McKenzie ◽  
Andrew J Mackinnon ◽  
David M. Clarke
Keyword(s):  
Monte Carlo ◽  
Permutation Test ◽  
Statistical Significance ◽  
Monte Carlo Permutation Test ◽  
The Difference

A PC program for comparing two kappa coefficients of agreement obtained from the same sample of observations is described. The program employs a Monte Carlo permutation test to assess the statistical significance of the difference between kappa values.

scholarly journals A Monte Carlo Permutation Test for Random Mating Using Genome Sequences

PLoS ONE ◽  
2013 ◽  
Vol 8 (8) ◽  
pp. e71496 ◽  
Author(s):  
Ran Li ◽  
Minxian Wang ◽  
Li Jin ◽  
Yungang He
Keyword(s):  
Monte Carlo ◽  
Permutation Test ◽  
Random Mating ◽  
Genome Sequences ◽  
Monte Carlo Permutation Test

scholarly journals Testing the island rule: primates as a case study

2008 ◽  
Vol 276 (1657) ◽  
pp. 675-682 ◽  
Author(s):  
John J Welch
Keyword(s):  
Monte Carlo ◽  
Permutation Test ◽  
Statistical Tests ◽  
Independent Contrasts ◽  
Island Rule ◽  
Skull Length ◽  
Reduced Body ◽  
Body Sizes ◽  
Monte Carlo Permutation Test

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head–body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.

scholarly journals The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

2009 ◽  
Vol 364 (1527) ◽  
pp. 2197-2207 ◽  
Author(s):  
Peter G. Foster ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Amino Acid Sequences ◽  
Rate Variation ◽  
Molecular Sequence Data ◽  
Protein Coding ◽  
Molecular Sequence ◽  
Heterogeneous Models ◽  
Matrix Heterogeneity ◽  
Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

Phylogenetic analysis of DNA sequence data.

2021 ◽  
pp. 265-282
Author(s):  
Sergei A. Subbotin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Phylogenetic Study ◽  
Public Database ◽  
Sample Collection ◽  
Minimum Evolution ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Selection Of

Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.

Genetic variation in Trithuria inconspicua and T. filamentosa (Hydatellaceae): a new subspecies and a hypothesis of apomixis arising within a predominantly selfing lineage

2019 ◽  
Author(s):  
Rob D. Smissen ◽  
Kerry A. Ford ◽  
Paul D. Champion ◽  
Peter B. Heenan
Keyword(s):  
Genetic Variation ◽  
New Zealand ◽  
Morphological Variation ◽  
Genetic Distances ◽  
Herbarium Specimens ◽  
Minimum Evolution ◽  
The North ◽  
Genetic Groups ◽  
Morphological Differences ◽  
High Level

While examining herbarium specimens of Trithuria inconspicua Cheeseman, we observed differences in the stigmatic hairs among plants from New Zealand’s North and South Islands. This motivated us to assess genetic and morphological variation within this species and its sister T. filamentosa Rodway from Tasmania. Samples were collected from lakes in the three disjunct geographic areas where the two species occur. Genetic variation in both species was assessed with simple sequence-repeat (SSR, microsatellite) markers and analyses of genetic distances. We also compared the morphology of northern and southern New Zealand T. inconspicua using fresh material. Samples of each species clustered together in a minimum evolution tree built from genetic distances. Trithuria filamentosa had more genetic diversity than did T. inconspicua. Within T. inconspicua, plants from lakes in the North Island and the South Island formed discrete genetic groups diagnosable by subtle morphological differences. Low levels of heterozygosity in both species are consistent with a high level of selfing, as suggested for other co-sexual Trithuria species, but unusual for a putative apomict. On the basis of genetic and morphological variation, we propose recognition of the northern New Zealand and southern New Zealand lineages of T. inconspicua at subspecies rank.

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