scholarly journals Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods

2004 ◽  
Vol 10 (2) ◽  
pp. 157-166 ◽  
Author(s):  
George I. Hagstrom ◽  
Dehua H. Hang ◽  
Charles Ofria ◽  
Eric Torng
Keyword(s):  
Natural Selection ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Branch Points ◽  
Reconstruction Algorithms ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Reconstruction Methods

Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but different methods sometimes give conflicting results. Since there are few precisely known phylogenies, simulations are typically used to test the quality of reconstruction algorithms. These simulations randomly evolve strings of symbols to produce a tree, and then the algorithms are run with the tree leaves as inputs. Here we use Avida to test two widely used reconstruction methods, which gives us the chance to observe the effect of natural selection on tree reconstruction. We find that if the organisms undergo natural selection between branch points, the methods will be successful even on very large time scales. However, these algorithms often falter when selection is absent.

An annotated checklist of the chaetonotidan Gastrotricha from India

Zootaxa ◽  
2021 ◽  
Vol 5027 (3) ◽  
pp. 332-350
Author(s):  
TAPAS CHATTERJEE ◽  
M. ANTONIO TODARO
Keyword(s):  
Sequence Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
History Of Research ◽  
High Incidence ◽  
History Of ◽  
Molecular Sequencing ◽  
Annotated Checklist ◽  
Rule Out

India has a long history of research on freshwater and marine Gastrotricha. In more than 110 years of study on Order Chaetonotida, two families consisting of 11 genera and 39 species have been described. Thirty of these species are taxa originally described from other continents, while only nine species (7 freshwater, 2 marine) are only known from India. The large percentage (77%) of so-called cosmopolitan species in India has contributed to the phenomenon known as the “meiofauna paradox”. However, a careful review of the pertaining literature provides a different biogeographical picture of the chaetonotidan fauna of India. Herein we show that the high incidence of European and North American species reported from India is mainly due to a mixture of misidentification and species lumping. In fact, for only 12 species there are enough data that would make the Indian specimens morphological similar to taxa previously reported from Europe and/or North America. However, without the appropriate molecular sequence data for comparison, there is no way to rule out the possibility of cryptic speciation.We conclude that further sampling throughout India and the use of more powerful microscopical techniques (e.g., DIC optics) and molecular sequencing will reveal more species and improve the quality of re-descriptions of those (9 spp.) that so far appear to be endemic to the subcontinent. Here we recommend six species to be excluded from the fauna of India while another 11 species (non endemic to India) should be considered dubitatively present in the Indian fauna.  

scholarly journals Bayesian Estimation of Past Population Dynamics in BEAST 1.10 Using the Skygrid Coalescent Model

2019 ◽  
Vol 36 (11) ◽  
pp. 2620-2628 ◽  
Author(s):  
Verity Hill ◽  
Guy Baele
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Effective Population ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Coalescent Model ◽  
Molecular Clock Model ◽  
Past Population ◽  
Over Time

Abstract Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a nonparametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo, this coalescent model is often estimated in conjunction with a molecular clock model to produce time-stamped phylogenetic trees. We here provide a practical guide to using BEAST and its accompanying applications for the purpose of drawing inference under these models. We focus on best practices, potential pitfalls, and recommendations that can be generalized to other software packages for Bayesian inference. This protocol shows how to use TempEst, BEAUti, and BEAST 1.10 (http://beast.community/; last accessed July 29, 2019), LogCombiner as well as Tracer in a complete workflow.

The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium

Genome ◽  
2014 ◽  
Vol 57 (9) ◽  
pp. 507-511 ◽  
Author(s):  
Hamid Nikbakht ◽  
Xuhua Xia ◽  
Donal A. Hickey
Keyword(s):  
Plasmodium Falciparum ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Gc Content ◽  
Significant Degree ◽  
Malarial Parasite ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Nucleotide Content ◽  
Genus Plasmodium

The genome of the malarial parasite Plasmodium falciparum is extremely AT rich. This bias toward a low GC content is a characteristic of several, but not all, species within the genus Plasmodium. We compared 4283 orthologous pairs of protein-coding sequences between Plasmodium falciparum and the less AT-biased Plasmodium vivax. Our results indicate that the common ancestor of these two species was also extremely AT rich. This means that, although there was a strong bias toward A+T during the early evolution of the ancestral Plasmodium lineage, there was a subsequent reversal of this trend during the more recent evolution of some species, such as P. vivax. Moreover, we show that not only is the P. vivax genome losing its AT richness, it is actually gaining a very significant degree of GC richness. This example illustrates the potential volatility of nucleotide content during the course of molecular evolution. Such reversible fluxes in nucleotide content within lineages could have important implications for phylogenetic reconstruction based on molecular sequence data.

Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)

2013 ◽  
Vol 87 (2) ◽  
pp. 211-216 ◽  
Author(s):  
Bernard L. Cohen ◽  
Maria Aleksandra Bitner
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequences ◽  
Relaxed Clock

We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cannot directly illuminate the systematics of fossils, the independent, genealogical evidence and phylogenetic inferences about extant forms that they make possible are highly relevant to paleontological systematics because they highlight the limitations of evolutionary inference from morphology. Parsimony, distance, maximum likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a tree topology that disagrees strongly with the existing superfamily classification. All tested phylogenetic reconstructions agree that the taxa analyzed fall into three clades designated A1, A2, and B that reflect two major divergence events. The relaxed-clock analysis indicates that clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect Permo-Triassic (and later) events. Morphological homoplasy and possible gene co-option are suggested as the main sources for the discord between the morpho-classification, the results of cladistic analyses of morphology, and the relationships reconstructed from molecular sequences. The origin, function and evolutionary implications of the deletion-bearing rhynchonellide SSU rDNA sequences are briefly discussed in relation to pseudogenes and concerted evolution in the rDNA genomic region.

scholarly journals Compressing Streams of Phylogenetic Trees

2018 ◽  
Author(s):  
Axel Trefzer ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Branch Length ◽  
Distinct Species ◽  
Mcmc Methods ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Posterior Probability Distribution ◽  
Tree Compression

AbstractBayesian Markov-Chain Monte Carlo (MCMC) methods for phylogenetic tree inference, that is, inference of the evolutionary history of distinct species using their molecular sequence data, typically generate large sets of phylogenetic trees. The trees generated by the MCMC procedure are samples of the posterior probability distribution that MCMC methods approximate. Thus, they generate a stream of correlated binary trees that need to be stored. Here, we adapt state-of-the art algorithms for binary tree compression to phylogenetic tree data streams and extend them to also store the required meta-data. On a phylogenetic tree stream containing 1, 000 trees with 500 leaves including branch length values, we achieve a compression rate of 5.4 compared to the uncompressed tree files and of 1.8 compared to bzip2-compressed tree files. For compressing the same trees, but without branch length values, our compression method is approximately an order of magnitude better than bzip2. A prototype implementation is available at https://github.com/axeltref/tree-compression.git.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

Apertochrysa (Neuroptera: Chrysopidae): A heterogeneric phantom? 

Zootaxa ◽  
2017 ◽  
Vol 4238 (1) ◽  
pp. 58 ◽  
Author(s):  
ATSUSHI MOCHIZUKI ◽  
CHARLES S. HENRY ◽  
PETER DUELLI
Keyword(s):  
Type Species ◽  
Morphological Traits ◽  
New Genus ◽  
Sequence Data ◽  
New Combination ◽  
Wing Venation ◽  
Monophyletic Clade ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Group Relationships

The small lacewing genus Apertochrysa comprises species from Africa, Asia and Australia. All lack a tignum, but otherwise resemble distantly related genera. We show that Apertochrysa does not form a monophyletic clade, based on analyses of molecular sequence data and morphological traits such as the presence and shape of the male gonapsis, wing venation, and larval setae. Apertochrysa kichijoi forms a clade with Eremochrysa, Suarius and Chrysemosa, whereas A. albolineatoides belongs to a clade that includes Cunctochrysa. Apertochrysa albolineatoides should become a new combination as Cunctochrysa albolineatoides, while A. kichijoi will have to be transferred to a new genus. The Australian A. edwardsi, the African A. eurydera and the type species of the genus Apertochrysa, A. umbrosa, join the large Pseudomallada group. Relationships of A. umbrosa are less certain, because for it we could amplify only one of the three nuclear genes used in the overall analysis. However, in all morphological traits tested, that species strongly resembles A. edwardsi and A. eurydera and thus is very likely just another exceptional Pseudomallada lacking a tignum. The fate of the genus name Apertochrysa depends on additional molecular and morphological analyses of A. umbrosa. 

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.

Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽  
2021 ◽  
Vol 514 (3) ◽  
pp. 247-260
Author(s):  
KASUN THAMBUGALA ◽  
DINUSHANI DARANAGAMA ◽  
SAGARIKA KANNANGARA ◽  
THENUKA KODITUWAKKU
Keyword(s):  
Sri Lanka ◽  
Camellia Sinensis ◽  
Endophytic Fungi ◽  
Sequence Data ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tea Leaves ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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