scholarly journals Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study

2020 ◽  
Vol 69 (6) ◽  
pp. 1088-1105 ◽  
Author(s):  
Oksana V Vernygora ◽  
Tiago R Simões ◽  
Erin O Campbell
Keyword(s):  
Bayesian Inference ◽  
Missing Data ◽  
Maximum Likelihood ◽  
Evolutionary Biology ◽  
False Positives ◽  
Probabilistic Methods ◽  
Morphological Data ◽  
Global Optimality ◽  
Probabilistic Algorithms ◽  
Taxonomic Sampling

Abstract Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

Taxonomic reassessment of species within the chrysaoros group of Calisto (Lepidoptera : Nymphalidae : Satyrinae)

2017 ◽  
Vol 31 (6) ◽  
pp. 747 ◽  
Author(s):  
Rayner Núñez Aguila ◽  
Antonio R. Pérez-Asso ◽  
Julio A. Genaro
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Taxonomic Status ◽  
Haplotype Network ◽  
Morphological Data ◽  
Putative Species

The taxonomic status of the Hispaniolan species of Calisto Hübner, 1823 included in the chrysaoros group is reassessed. Morphological data and COI barcode sequences were analysed through different methods: Neighbour-Joining clustering, ABGD, Median-Joining Haplotype Network, Maximum Likelihood, and Bayesian Inference. Analyses yielded two deeply separated groups or putative species: C. clydoniata and C. chrysaoros. A shallower split was found, except in the Bayesian Inference approach, among populations of southern and northern Hispaniola palaeo-islands. In light of these findings we propose the recognition of two species: C. clydoniata and C. chrysaoros. Within the latter, the populations of the southern and northern Hispaniola palaeo-islands should be recognised as different subspecies: C. chrysaoros chrysaoros Bates and C. chrysaoros galii Schwartz, respectively. Calisto clenchi, syn. nov. is a synonym of C. chrysaoros chrysaoros whereas C. galii galli, syn. nov. and C. galii choneupsilon, syn. nov. are synonyms of C. chrysaoros galii.

scholarly journals Revisiting the phylogeny of phylum Ctenophora: a molecular perspective

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2881
Author(s):  
Luis A. Arteaga-Figueroa ◽  
Valentina Sánchez-Bermúdez ◽  
Nicolás D. Franco-Sierra
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Ribosomal Rna ◽  
Single Gene ◽  
Probabilistic Methods ◽  
Data Set ◽  
Protein Coding ◽  
Rrna Sequences ◽  
Made In

The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora, are not totally understood. Previous studies have been developed on this subject, mostly based on morphology and single gene analyses (rRNA sequences). Several loci (protein coding and ribosomal RNA) from taxa belonging to this phylum are currently available on public databases (e.g. GenBank). Here we revisit Ctenophora molecular phylogeny using public sequences and probabilistic methods (Bayesian inference and maximum likelihood). To get more reliable results multi-locus analyses were performed using 5.8S, 28S, ITS1, ITS2 and 18S, and IPNS and GFP-like proteins. Best topologies, consistent with both methods for each data set, are shown and analysed. Comparing the results of the pylogenetic reconstruction with previous research, most clades showed the same relationships as the ones found with morphology and single gene analyses, consistent with hypotheses made in previous research. There were also some unexpected relationships clustering species from different orders.

Phylogenetic Patterns in Menispermaceae Based on Multiple Chloroplast Sequence Data

2009 ◽  
Vol 34 (1) ◽  
pp. 44-56 ◽  
Author(s):  
Sara B. Hoot ◽  
Herbert Zautke ◽  
David J. Harris ◽  
Peter R. Crane ◽  
Susana S. Neves
Keyword(s):  
Bayesian Inference ◽  
Missing Data ◽  
Maximum Likelihood ◽  
Northern Hemisphere ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Character Evolution ◽  
The Family ◽  
Branch Support

Menispermaceae, a dioecious, largely pantropical family of vines and lianas, consists of approximately 70 genera. In this paper, we present phylogenies (derived using maximum parsimony, maximum likelihood, and Bayesian inference) based on chloroplast atpB and rbcL sequence data for 42 Menispermaceae genera (60 species) and 15 outgroup genera representing all families in the Ranunculales. Results of this work confirm that a clade consisting of Berberidaceae and Ranunculaceae is sister to the Menispermaceae and that Menispermaceae is highly supported as monophyletic. Within Menispermaceae, Menispermum and Sinomenium, two genera with distributions in the Northern Hemisphere, are weakly to moderately supported as sister to all remaining Menispermaceae. Many of the tribes as described by previous workers are not monophyletic. To expand both the data and sampling, we combined our atpB and rbcL data with previously published ndhF data for two additional analyses: 1) for matching species and 2) for all genera available, including those with either atpB/rbcL or ndhF missing (22% missing data). All trees produced from our three analyses were highly congruent, especially where branch support was high. Four major clades were recovered from all analyses and are informally named. Superimposing our geographical distributions on our atpB/rbcL phylogeny indicates that many well supported clades have distributions on multiple continents, probably due to both vicariance and dispersal. Several previous hypotheses regarding trends in character evolution are tested; our phylogenies suggest that the following are all derived character states within the family: arborescent habit; acrodromous, peltate, compound, or lobed leaves; absence of condyle and endosperm; smooth endosperm; fused stamens; and tricolpate pollen.

scholarly journals Maximum Likelihood Estimation of the VAR(1) Model Parameters with Missing Observations

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Helena Mouriño ◽  
Maria Isabel Barão
Keyword(s):  
Stochastic Process ◽  
Missing Data ◽  
Maximum Likelihood ◽  
Moving Average ◽  
Practical Importance ◽  
Likelihood Estimation ◽  
Model Parameters ◽  
Missing Observations ◽  
Data Set ◽  
The Impact

Missing-data problems are extremely common in practice. To achieve reliable inferential results, we need to take into account this feature of the data. Suppose that the univariate data set under analysis has missing observations. This paper examines the impact of selecting an auxiliary complete data set—whose underlying stochastic process is to some extent interdependent with the former—to improve the efficiency of the estimators for the relevant parameters of the model. The Vector AutoRegressive (VAR) Model has revealed to be an extremely useful tool in capturing the dynamics of bivariate time series. We propose maximum likelihood estimators for the parameters of the VAR(1) Model based on monotone missing data pattern. Estimators’ precision is also derived. Afterwards, we compare the bivariate modelling scheme with its univariate counterpart. More precisely, the univariate data set with missing observations will be modelled by an AutoRegressive Moving Average (ARMA(2,1)) Model. We will also analyse the behaviour of the AutoRegressive Model of order one, AR(1), due to its practical importance. We focus on the mean value of the main stochastic process. By simulation studies, we conclude that the estimator based on the VAR(1) Model is preferable to those derived from the univariate context.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

scholarly journals A revised taxonomy of Asian snail-eating snakes Pareas (Squamata, Pareidae): evidence from morphological comparison and molecular phylogeny

ZooKeys ◽  
2020 ◽  
Vol 939 ◽  
pp. 45-64
Author(s):  
Ping Wang ◽  
Jing Che ◽  
Qin Liu ◽  
Ke Li ◽  
Jie Qiong Jin ◽  
...  
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Data ◽  
Multivariate Morphometrics ◽  
Cryptic Diversity ◽  
Cyt B ◽  
Morphological Comparison ◽  
The Family ◽  
Two New Species

The Asian snail-eating snakes Pareas is the largest genus of the family Pareidae (formerly Pareatidae), and widely distributed in Southeast Asia. However, potential diversity remains poorly explored due to their highly conserved morphology and incomplete samples. Here, on basis of more extensive sampling, interspecific phylogenetic relationships of the genus Pareas were reconstructed using two mitochondrial fragments (cyt b and ND4) and two nuclear genes (c-mos and Rag1), and multivariate morphometrics conducted for external morphological data. Both Bayesian Inference and Maximum Likelihood analyses consistently showed that the genus Pareas was comprised of two distinct, monophyletic lineages with moderate to low support values. Based on evidences from molecular phylogeny and morphological data, cryptic diversity of this genus was uncovered and two new species were described. In additional, the validity of P. macularius is confirmed.

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