scholarly journals Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

2018 ◽  
Vol 14 (6) ◽  
pp. 20180263 ◽  
Author(s):  
Robert S. Sansom ◽  
Peter G. Choate ◽  
Joseph N. Keating ◽  
Emma Randle
Keyword(s):  
Empirical Data ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Empirical Studies ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Simulation Studies ◽  
Historic Data ◽  
Parsimony Trees ◽  
Bayesian Trees

Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here, we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking stratigraphic data as an independent benchmark indicates that parsimony analyses are more accurate for phylogenetic reconstruction of morphological data. The discrepancy between simulated and empirical studies may result from historic data peaking practices or some complexities of empirical data as yet unaccounted for.

Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽  
2015 ◽  
Vol 219 (3) ◽  
pp. 261 ◽  
Author(s):  
Julian Aguirre-Santoro ◽  
Julio Betancur ◽  
Gregory K. Brown ◽  
Timothy M. Evans ◽  
Fabiano Salgueiro ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Geographic Ranges ◽  
Dna Sequence Data ◽  
Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

scholarly journals HCPC: A New Parsimonious Clustering Method based on Hierarchical Characters for Morphological Phylogenetic Reconstruction

2021 ◽  
Author(s):  
Hongwei Feng ◽  
Meng Liu ◽  
Bei Wang ◽  
Jun Feng ◽  
Jian Han ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Simulated Annealing Algorithm ◽  
Phylogenetic Reconstruction ◽  
Poor Performance ◽  
Morphological Data ◽  
Clustering Method ◽  
Parsimonious Tree ◽  
Quantitative Basis ◽  
History Of ◽  
Two Stages

Abstract Background: Phylogenetic trees are reconstructed frequently to provide a better interpretation of the evolutionary history of species. However, most traditional methods ignore the hierarchical relationships among characters and neglect the inapplicable state that frequently exists in the morphological data, resulting in poor performance of the phylogenetic analysis.Results: In this study, we propose a phylogenetic clustering method based on hierarchical characters. Accordingly, we call our method Hierarchical Characters Parsimonious Clustering(HCPC). To combine prior phylogenetic knowledge and treat the inapplicable state more reasonably, two stages are proposed, i.e., Phylogenetic reconstruction and parsimonious tree search. During phylogenetic reconstruction, HCPC is able to infer the shared ancestral relationships among species. For the search of the parsimonious tree, we use a simulated annealing algorithm to heuristically search the phylogenetic tree based on the parsimony criterion. In addition, HCPC combines asymmetric binary relationships and character hierarchies to solve the problem of the ambiguity of the inapplicable state.Conclusion: The experimental results show that the proposed method provides better performance of phylogenetic analysis than existing methods and a scientific and quantitative basis for biologists to study species evolution.

scholarly journals Comparative Morphology, Phylogeny, Classification and Evolution of Interstitial Habits in Microcambevine Catfishes (Siluriformes: Trichomycteridae)

Taxonomy ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 313-344
Author(s):  
Wilson J. E. M. Costa ◽  
Axel M. Katz
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Trees ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Comparative Morphology ◽  
Morphological Characters ◽  
Morphological Data ◽  
High Level ◽  
Available Information

The Microcambevinae are a catfish subfamily endemic to the Brazilian Atlantic Forest, comprising rare species with interstitial habits. Microcambevines have been classified in two genera, Listrura and Microcambeva, but the relationships among included intrageneric lineages are still poorly understood. The objectives of this study are to conduct a phylogenetic analysis integrating morphological characters and a multigene dataset, and to propose a classification better reflecting morphological diversity and phylogenetic relationships. Phylogenetic analyses combining 57 morphological characters and a 2563 bp molecular dataset generated similar phylogenetic trees with high support values for most clades, including the two genera and some intrageneric groups. Six morphologically distinctive infrageneric lineages, three in Listrura and three in Microcambeva, are classified as subgenera, as well as two new species are described. The morphological diversity here recorded integrated to available information about habitat indicate high level of divergent specialisation among lineages. The analyses indicate a series of convergent morphological traits between Listrura and other teleosts sharing a fossorial lifestyle, as well as specialised traits independently occurring within Listrura lineages. Similarly, a great diversity of morphological traits occurs convergently in Microcambeva lineages and other teleosts sharing psammophilic habits. This study shows that combining molecular and morphological data yields well-supported phylogenies, making possible to unambiguously diagnose clades and to establish evolutionary hypothesis on morphological evolution.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

The role of fossils in the phylogenetic reconstruction of Echinodermata

1997 ◽  
Vol 3 ◽  
pp. 267-288 ◽  
Author(s):  
Colin D. Sumrall
Keyword(s):  
Phylogenetic Analyses ◽  
A Priori ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Character State ◽  
A Posteriori ◽  
State Transformation ◽  
Single Character ◽  
Fossil Data

Morphological data can be used effectively in phylogenetic analyses to determine relationships among echinoderm clades. These data in the form of characters are simply hypotheses that any observed morphological state among taxa results from a single character state transformation and is therefore, homologous. All such character states must be scored as potentially homologous unless the hypothesis of homology can be rejected by the tests of similarity, conjunction (a priori), or character congruence (a posteriori). Fossils are not always more incomplete than extant forms and incompleteness originates from non-preservation and long phylogenetic branches. The greatest strength of fossil data lies in its ability to effectively shorten long phylogenetic branches by occurring on the tree nearer to the nodes than extant terminal taxa and thus circumventing positively misleading results encountered in parsimony analysis under long branch conditions.

scholarly journals Estimating Genetic Similarity Matrices using Phylogenies

2020 ◽  
Author(s):  
Shijia Wang ◽  
Shufei Ge ◽  
Caroline Coljin ◽  
Liangliang Wang ◽  
Lloyd T Elliott
Keyword(s):  
Genetic Similarity ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Poor Quality ◽  
Morphological Data ◽  
Inner Product ◽  
Simulation Studies ◽  
Genetic Traits ◽  
Genetic Sequences ◽  
Similarity Matrices

AbstractGenetic similarity is a measure for the genetic relatedness among individuals. The standard method for computing similarity matrices involves the inner product of observed genetic variant matrices. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genetic sequences. We show that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. Quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, and the presence of phylogenetic trees derived from morphological data or geological dates, such analyses can be undertaken using our methods. We use simulation studies to demonstrate the advantages of our method, and we provide an application to ancient hominin data.

scholarly journals Species recognition and phylogeny of Thelotrema species in Australia (Ostropales, Ascomycota)

2008 ◽  
Vol 21 (3) ◽  
pp. 217 ◽  
Author(s):  
H. Thorsten Lumbsch ◽  
Armin Mangold ◽  
María P. Martín ◽  
John A. Elix
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Morphological Studies ◽  
Morphological Differences ◽  
Crustose Lichens

Species circumscriptions based on morphological data are difficult in crustose lichens with limited characters as they often show remarkable variability. An example is the genus Thelotrema s.str., a speciose genus of mostly tropical lichens. Morphological studies on Australian Thelotrema spp. were accompanied by a phylogenetic analysis of mt SSU rDNA sequence data of 19 species, including 25 newly obtained sequences. We performed maximum parsimony and Bayesian phylogenetic analyses of 50 samples, representing 25 species. Our results indicate that more species need to be accepted in Thelotrema than previously thought. Subtle morphological differences were found to be associated with independent lineages in the phylogenetic trees. Furthermore, monophyly of Thelotrema s.str. is strongly supported. On the basis of the corroboration of morphological evidence by molecular data, the new species Thelotrema capetribulense Mangold, T. crespoae Mangold, Lumbsch & Elix, T. oleosum Mangold, and T. pseudosubtile Mangold are described. The new combinations Chapsa phlyctidioides (Müll.Arg.) Mangold and Thelotrema defossum (Müll.Arg.) Mangold are proposed.

scholarly journals Genetic divergence and speciation within Ziziphora capitata (Lamiaceae): Molecular and micromorphological evidences

2018 ◽  
Vol 19 (2) ◽  
pp. 697-705 ◽  
Author(s):  
RAHELEH TABARIPOUR ◽  
MASOUD SHEIDAI ◽  
SEYED MEHDI TALEBI ◽  
ZAHRA NOORMOHAMMADI
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Population Substructure ◽  
Molecular Characteristics ◽  
Separate Species ◽  
Taxonomic Rank ◽  
Genetic Groups ◽  
Traditional Taxonomy

Tabaripour R, Sheidai M, Talebi SM, Noormohammadi Z. 2018. Genetic divergence and speciation within Ziziphora capitata (Lamiaceae): Molecular and micromorphological evidences. Biodiversitas 19: 697-705. Ziziphora capitata is a member of the Mint family (Lamiaceae) that naturally grows in various regions. Different subspecies have been reported for this species, from which two are recorded from Iran: Z. capitata subsp. capitata, and Z. capitata subsp. orientalis. In the present study, morphological, palynological and molecular (ISSR and cp-DNA) data were used to reveal speciation within this species and reconsider taxonomic rank of its presumed subspecies. The obtained results revealed a great difference between two presumed subsp. of Z. capitata. These taxa differed in morphological, palynological and molecular characteristics. Statistical and bioinformatics tests revealed significant genomic difference between them and phylogenetic analyses showed that they have a close affinity to some other Ziziphora species (out-groups used), then to each other. Bayesian and maximum parsimony phylogenetic trees differentiated the presumed sub-species of Z. capitata. Moreover, K-Means clustering and Bayesian analysis of genetic groups by Evanno test (optimal k) supported the presence of two distinct genetic groups within Z. capitata. This approach objectively defines a threshold separating intraspecific population substructure from interspecific divergence, which is the general aim of species delimitation studies. Therefore, the present study provides enough evidence for introducing two separate species within Z. capitata based on the traditional taxonomy as well as combination of molecular and micro-morphological data.

scholarly journals Assessing bivalve phylogeny using Deep Learning and Computer Vision approaches

2021 ◽  
Author(s):  
Steffen Kiel
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Future Directions ◽  
Classification Tasks

ABSTRACTPhylogenetic analyses using morphological data currently require hand-crafted character matrices, limiting the number of taxa that can be included. Here I explore how Deep Learning and Computer Vision approaches typically applied to image classification tasks, may be used to infer phylogenetic relationships among bivalves. A convolutional neural network (CNN) was trained on thousands of images showing species of 75 bivalve families. The predictions of the CNN on a large number of bivalve images are then interpreted as an indication of how similar these bivalves are to each other, are averaged by the families to which the species belonged, and visualized in a cluster diagram. In this cluster diagram, significantly more families clustered with members of their subclasses than expected by chance, confirming the feasibility of the approach. To address the issue of convergent evolution, two further CNNs were trained, on the same images but grouped by the orders and subclasses to which the species belonged. Combining predictions for the same images but on different taxonomic levels improved the inferred phylogenetic relationships also of families that the CNNs had not been trained on. Finally, this combined tree is merged with five published phylogenetic trees into a supertree, representing the largest single phylogeny of the Bivalvia to date, encompassing 128 families, including six exclusively fossil families and nine extant families for which presently no molecular data are available. Issues inherent to the approach and suggestions for future directions are discussed.

scholarly journals A molecular phylogenetic appraisal of the acanthostominesAcanthostomumandTimoniellaand their position within Cryptogonimidae (Trematoda: Opisthorchioidea)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4158 ◽  
Author(s):  
Andrés Martínez-Aquino ◽  
Victor M. Vidal-Martínez ◽  
M. Leopoldina Aguirre-Macedo
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Internal Transcribed Spacers ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Parasitic Infections ◽  
Larval Stages ◽  
Ecological Implications ◽  
Molecular Phylogenetic ◽  
28S Ribosomal Dna

The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae), were analysed using partial 28S ribosomal DNA (Domains 1–2) and internal transcribed spacers (ITS1–5.8S–ITS2). Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genusAcanthostomum(A.cf.americanumandA. burminis) and paraphyly of the Acanthostominae.These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages ofA.cf.americanumcercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

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