Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis

Paleobiology ◽  
1997 ◽  
Vol 23 (1) ◽  
pp. 1-19 ◽  
Author(s):  
William C. Clyde ◽  
Daniel C. Fisher
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Ad Hoc ◽  
Retention Indices ◽  
Significant Loss ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Phylogenetic Hypotheses ◽  
Morphologic Data

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

A phylogenetic analysis of New Zealand giant and tree weta (Orthoptera : Anostostomatidae : Deinacrida and Hemideina) using morphological and genetic characters

2001 ◽  
Vol 15 (1) ◽  
pp. 1 ◽  
Author(s):  
Mary Morgan-Richards ◽  
George W. Gibbs
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Sound Production ◽  
Morphological Characters ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Life Styles ◽  
Multiple Origins ◽  
Tree Weta ◽  
Genetic Characters

A phylogenetic analysis of New Zealand weta from the sub-family Deinacridinae is presented. Eighteen species were studied using 27 genetic characters (allozyme and cytogenetic) and 25 morphological characters. The combined data set produced a phylogenetic hypothesis with twelve well-supported nodes. Despite the great diversity of habitats and life styles exhibited by the eleven Deinacrida White species a well-supported bipartition separates them from the seven Hemideina Walker species. Six of the Hemideina species formed a monophyletic clade, with respect to H. broughi (Buller). Evolution of stridulatory ridges used for sound production in both defence and intraspecific communication appears to have occurred at least twice. Adaptation to the recent New Zealand alpine environment has also had multiple origins. Biogeographic interpretations from the phylogenetic hypothesis are discussed.

Taxonomy of Anterastes and related genera: a new synonym and a new species of Anterastes

Zootaxa ◽  
2011 ◽  
Vol 2771 (1) ◽  
pp. 41 ◽  
Author(s):  
SARP KAYA ◽  
BATTAL CIPLAK
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Genetic Data ◽  
New Combination ◽  
New Synonym ◽  
Male Calling ◽  
Phylogenetic Hypotheses ◽  
Distinct Features ◽  
A New Species

Among the Anatolian Tettigoniinae (Orthoptera, Tettigoniidae) the genera Anterastes, Koroglus, Sureyaella and Rhacocleis are distinguishable from the others by presence of one pair of spurs on the apico-ventral end of hind tibiae. The last two can be easily distinguished from the others by several distinct features, but the separation of the first two from each other is problematic. A new species described here provided opportunity of re-evaluating their taxonomy. The new species Anterastes antecessor sp. n. is described based on morphology, male calling song and genetic data. The taxonomy of Anterastes and Koroglus is rectified based on phylogentic hypotheses obtained from representative 16S rDNA haplotypes. Sureyaella bella, Parapholidoptera signata and Bolua turkiyae are used as out groups in different combinations to obtain a more stable phylogeny. Although analyses with different outgroups suggested the same topology, the phylogenetic tree with outgroups Parapholidoptera signata and Bolua turkiyae resulted with the highest bootstrap supports to the branches. Phylogenetic trees suggested the following relationships for the ingroup species; (A. antecessor sp. n. + ((Koroglus disparalatus + A. uludaghensis) + (A. turcicus + (A. niger + (A. ucari + A. babadaghi))) + ((A. tolunayi + (A. serbicus + A. antitauricus + A. burri)))). Considering the phylogenetic hypotheses and characters used in previous publications, Koroglus is put in synonymy with Anterastes, and a new combination is suggested for the only species of the former Anterastes disparalatus comb. n. A short remark is given about the characters used in the generic taxonomy of the group.

scholarly journals Comparative phylogenetic analysis of Dobrava-Belgrade virus L and S genetic segments isolated from an animal reservoir in Serbia

2014 ◽  
Vol 66 (2) ◽  
pp. 497-506 ◽  
Author(s):  
Valentina Nikolic ◽  
N. Stajkovic ◽  
Gorana Stamenkovic ◽  
R. Cekanac ◽  
P. Marusic ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Animal Reservoir ◽  
Data Set ◽  
Bunyaviridae Family ◽  
Mapping Analysis ◽  
Geographical Clustering ◽  
Segment Data ◽  
Comparative Phylogenetic Analysis ◽  
Likelihood Mapping

The Dobrava-Belgrade virus (DOBV) is a member of the Bunyaviridae family, genus Hantavirus, possessing a single-stranded RNA genome consisting of three segments, designated L (large), M (medium) and S (small). In this study, we present phylogenetic analysis of a newly detected DOBV strain isolated from Apodemus agrarius. Analysis was based on partial L and S segment sequences, in comparison to previously published DOBV sequences from Serbia and elsewhere. A phylogenetic tree based on partial S segment revealed local geographical clustering of DOBV sequences from Serbia, unrelated to host (rodent or human). The topology of the phylogenetic tree was confirmed with a high percent of completely or partially resolved quartets in likelihood-mapping analysis, whereas no evidence of possible recombination in the examined S segment data set was found.

On the Construction of “Optimal” Phylogenetic Trees

1983 ◽  
Vol 38 (1-2) ◽  
pp. 156-158 ◽  
Author(s):  
Geert De Soete
Keyword(s):  
Phylogenetic Tree ◽  
Iterative Algorithm ◽  
Phylogenetic Trees ◽  
Data Set ◽  
Dissimilarity Data

An iterative algorithm for constructing the optimal phylogenetic tree from a given set o f dissimilarity data is described. The procedure is applied for illustrative purposes an a data set com piled by Fitch and Margoliash.

scholarly journals Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3782 ◽  
Author(s):  
Daniel Madzia ◽  
Andrea Cau
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Freshwater Ecosystems ◽  
Apex Predators ◽  
Data Set ◽  
Proper Understanding ◽  
Ecological Adaptations ◽  
Adequate Knowledge ◽  
Statistical Support ◽  
Phylogenetic Hypotheses

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

scholarly journals Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction

2019 ◽  
Author(s):  
Motomu Matsui ◽  
Wataru Iwasaki
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Triosephosphate Isomerase ◽  
Rna World ◽  
Rapid Evolution ◽  
Poor Performance ◽  
Multiple Sequence ◽  
Data Set ◽  
Protein Superfamily ◽  
Tim Barrel

Abstract A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.

scholarly journals Consequences of Recombination on Traditional Phylogenetic Analysis

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 879-891 ◽  
Author(s):  
Mikkel H Schierup ◽  
Jotun Hein
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Population Data ◽  
Recent Common Ancestor ◽  
Data Sets ◽  
Data Set ◽  
Most Recent Common Ancestor ◽  
Total Branch Length ◽  
Viral Sequences

Abstract We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.

scholarly journals APRIMORAMENTOS DA SOLUÇÃO PARALELA BASEADA EM OPERAÇÕES COLETIVAS PARA O BOOTSTRAP DA RECONSTRUÇÃO DE ÁRVORES FILOGENÉTICAS NO PHYML 3.0

2021 ◽  
Vol 12 (3) ◽  
pp. 39-52
Author(s):  
Martha Ximena Torres Delgado
Keyword(s):  
Phylogenetic Tree ◽  
Statistical Method ◽  
Phylogenetic Trees ◽  
Evolutionary Relationships ◽  
Performance Tests ◽  
Memory Consumption ◽  
Data Set ◽  
Parallel Implementations ◽  
Point To Point

Phylogenetics determines the evolutionary relationships between groups of species, through a phylogenetic tree. PhyML is among the main programs for the reconstruction of phylogenetic trees. Bootstrap is a statistical method used to measure the confidence of a given data set, which is usually applied in the analysis of inferred phylogenetic trees. In PhyML this method has two MPI parallel implementations: with point-to-point operations and collective operations. The second version is more efficient than the first, however it has a limitation on the number of bootstrap to be used due to the increase in memory consumption. In order to solve this problem, three proposals were developed. The objectives of this work were to carry out the validation of these versions together with performance tests. The validation showed that the proposed solutions present results equivalent to the point-to-point version. In the performance simulations, two solutions were shown to be superior to the point-to-point version, with the best one achieving gains of 28.46% and 39.64% for 32 and 64 processes, respectively. Therefore, the enhancements allow alternatives to the point-to-point version without limitingmemory.

scholarly journals Mitogenome and Phylogenetic Analysis of Typhlocybine Leafhoppers (Hemiptera: Cicadellidae)

2021 ◽  
Author(s):  
Jia Jiang ◽  
Xiaoxiao Chen ◽  
Can Li ◽  
Yuehua Song
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Active Role ◽  
The Body ◽  
Molecular Phylogenetic Tree ◽  
Insect Phylogeny ◽  
Molecular Phylogenetic ◽  
Phylogeny And Evolution ◽  
The Relationship

Abstract Mitogenomes play an active role in determining the relationship between insect phylogeny and evolution and solve some problems encountered in traditional morphological classification. In order to increase the mitogenome data of leafhoppers the mitogenomes of Cassianeura cassiae and C. bimaculata were sequenced in this study and found to be 15,423 bp and 14,597 bp in length respectively. The gene structure was found to be similar to other published leafhopper mitogenomes, but we found the length of the control region of C. bimaculata to be the shortest in existing studies. The phylogenetic analysis of 13 PCGs resulted in a well-supported tree topology but species in Typhlocybini and Zyginellini were mixed. Meanwhile, this study also provided the phylogenetic analysis based on the body external morphology, female genitalia morphology and male genitalia morphology of 9 species of Typhlocybinae. The results showed that the female sternite VII of different species is quite different, but the female valvulae of different species in the same genus shows a certain consistency. The morphological phylogenetic tree is basically the same structure as the molecular phylogenetic tree. In the two different kinds of phylogenetic trees, Typhlocybini and Zyginellini clustered into one clade, showing a more closed relationship.

scholarly journals SeqDistK: a Novel Tool for Alignment-free Phylogenetic Analysis

2021 ◽  
Author(s):  
Xuemei Liu ◽  
Wen Li ◽  
Guanda Huang ◽  
Tianlai Huang ◽  
Qingang Xiong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Sequence Data ◽  
Ground Truth ◽  
Group Method ◽  
Metagenomic Sequence ◽  
Alignment Free

Algorithms for constructing phylogenetic trees are fundamental to study the evolution of viruses, bacteria, and other microbes. Established multiple alignment-based algorithms are inefficient for large scale metagenomic sequence data because of their high requirement of inter-sequence correlation and high computational complexity. In this paper, we present SeqDistK, a novel tool for alignment-free phylogenetic analysis. SeqDistK computes the dissimilarity matrix for phylogenetic analysis, incorporating seven k-mer based dissimilarity measures, namely d2, d2S, d2star, Euclidean, Manhattan, CVTree, and Chebyshev. Based on these dissimilarities, SeqDistK constructs phylogenetic tree using the Unweighted Pair Group Method with Arithmetic Mean algorithm. Using a golden standard dataset of 16S rRNA and its associated phylogenetic tree, we compared SeqDistK to Muscle - a multi sequence aligner. We found SeqDistK was not only 38 times faster than Muscle in computational efficiency but also more accurate. SeqDistK achieved the smallest symmetric difference between the inferred and ground truth trees with a range between 13 to 18, while that of Muscle was 62. When measures d2, d2star, d2S, Euclidean, and k-mer size k=5 were used, SeqDistK consistently inferred phylogenetic tree almost identical to the ground truth tree. We also performed clustering of 16S rRNA sequences using SeqDistK and found the clustering was highly consistent with known biological taxonomy. Among all the measures, d2S (k=5, M=2) showed the best accuracy as it correctly clustered and classified all sample sequences. In summary, SeqDistK is a novel, fast and accurate alignment-free tool for large-scale phylogenetic analysis. SeqDistK software is freely available at https://github.com/htczero/SeqDistK.

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