scholarly journals Influence of different modes of morphological character correlation on phylogenetic tree inference

2018 ◽  
Author(s):  
Thomas Guillerme ◽  
Martin D. Brazeau
Keyword(s):  
Phylogenetic Analysis ◽  
A Priori ◽  
Probabilistic Methods ◽  
Morphological Data ◽  
Character State ◽  
Coding Schemes ◽  
Tree Inference ◽  
Character Correlation ◽  
Parsimony Trees ◽  
Character Correlations

AbstractPhylogenetic analysis algorithms require the assumption of character independence - a condition generally acknowledged to be violated by morphological data. Correlation between characters can originate from intra-organismal features, shared phylogenetic history or forced by particular character-state coding schemes. Although the two first sources can be investigated by biologists a posteriori and the third one can be avoided a priori with good practices, phylogenetic software do not distinguish between any of them.In this study, we propose a new metric of raw character difference as a proxy for character correlation. Using thorough simulations, we test the effect of increasing or decreasing character differences on tree topology. Overall, we found an expected positive effect of reducing character correlations on recovering the correct topology. However, this effect is less important for matrices with a small number of taxa (25 in our simulations) where reducing character correlation is not more effective than randomly drawing characters. Furthermore, in bigger matrices (350 characters), there is a strong effect of the inference method with Bayesian trees being consistently less affected by character correlation than maximum parsimony trees.These results suggest that ignoring the problem of character correlation or independence can often impact topology in phylogenetic analysis. However, encouragingly, they also suggest that, unless correlation is actively maximised or minimised, probabilistic methods can easily accommodate for a random correlation between characters.

Currhaeus, a new genus of net-winged beetles and phylogenetic analysis of Eurrhacini (Coleoptera: Lycidae: Lycinae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (3) ◽  
pp. 387-403
Author(s):  
ELYNTON ALVES DO NASCIMENTO ◽  
TAMIRES DINIZ BRESSAN ◽  
MILADA BOCAKOVA
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Species Identification ◽  
Male Genitalia ◽  
New Genus ◽  
Morphological Data ◽  
Key To Species ◽  
Diagnostic Characters ◽  
Parsimony Trees

A new genus of Neotropical Lycidae, Currhaeus gen. nov., is herein proposed as the second Eurrhacini genus lacking parameres in male genitalia. Seven new species are described: Currhaeus striatus sp. nov., C. nigroapicalis sp. nov., C. championi sp. nov., C. tabascensis sp. nov., C. ruschii sp. nov., C. polegattoi sp. nov., and C. paranaensis sp. nov. Illustrations of diagnostic characters and a key to species identification are presented. Parsimony and maximum likelihood analyses of morphological data demonstrated that Currhaeus gen. nov. belongs in the crown Eurrhacini. Implied weighting parsimony trees recovered Currhaeus as sister to Eurrhacus Waterhouse. 

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.

Cephalotrichella echinicola, sp. nov. (Palaeonemertea : Cephalotrichellidae), a new nemertean associated with sea urchins from Nha Trang Bay (South China Sea)

2019 ◽  
Author(s):  
Alexei V. Chernyshev ◽  
Neonila Polyakova ◽  
Temir A. Britayev ◽  
Olga A. Bratova ◽  
Elena S. Mekhova
Keyword(s):  
Phylogenetic Analysis ◽  
South China Sea ◽  
South China ◽  
Sea Urchins ◽  
Laser Scanning Microscopy ◽  
Morphological Data ◽  
28S Rrna ◽  
Gene Markers ◽  
China Sea ◽  
Nha Trang Bay

About 50 nemertean species have been reported to live in symbiotic relationships with other invertebrates, but only two hoplonemertean species are associated with echinoderms (starfish). The palaeonemertean Cephalotrichella echinicola, sp. nov. is described from samples collected in Nha Trang Bay, Vietnam, South China Sea. The species is the first known nemertean associated with sea urchins (Metalia sternalis and M. spatagus), living on both the oral and the aboral surfaces of the host and freely moving among its spines. The internal morphology of the new species is described based on histological sections and confocal laser scanning microscopy with phalloidin and antibody labelling. Sequences of three nuclear gene markers (18S rRNA, 28S rRNA, and histone H3) and two mitochondrial gene markers (16S rRNA and COI) were compared with those of other palaeonemertean species, and a phylogenetic analysis suggested that C. echinicola is closest to the free-living Cephalotrichella alba Gibson & Sundberg, 1992. Both the morphological data and the phylogenetic analysis provide additional evidence for distinguishing the families Cephalotrichidae and Cephalotrichellidae and support the rejection of Cephalotrichella as a junior synonym of Cephalothrix. A new diagnosis of the genus Cephalotrichella is given. http://zoobank.org/urn:lsid:zoobank.org:pub:091B5D56-71B2-4F4C-9AD8-F666B4610DE2

scholarly journals Primula sunhangii (Primulaceae): a new species from Hubei, Central China

PhytoKeys ◽  
2020 ◽  
Vol 156 ◽  
pp. 103-112
Author(s):  
Jiao Sun ◽  
Dai-Gui Zhang ◽  
Xian-Han Huang ◽  
Komiljon Tojibaev ◽  
Jing-Yuan Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Hubei Province ◽  
Central China ◽  
Morphological Data ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
A New Species

This report provides a description of Primula sunhangii from the Shennongjia Forestry District, Hubei Province in Central China, which is categorized as a new species of the primrose family. Primula sunhangii is morphologically similar to P. involucrata Wall. ex Duby in terms of its simple umbel, efarinose, and prolonged bracts. However, P. sunhangii is distinguished by its glabrous sepal, short petiole (compare with blade) and cylindrical calyx and capsule. Molecular phylogenetic analysis based on nuclear and cpDNA genes demonstrates that P. sunhangii and P. involucrata are closely related. Combining genetic and morphological data, the recognition of P. sunhangii as a unique new species is supported.

scholarly journals Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China

ZooKeys ◽  
2019 ◽  
Vol 851 ◽  
pp. 27-69
Author(s):  
Rong Yang ◽  
Zhenzhen Wang ◽  
Yanshuang Zhou ◽  
Zongqing Wang ◽  
Yanli Che
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Species ◽  
Species Delimitation ◽  
Female Genitalia ◽  
Morphological Data ◽  
Coi Sequences ◽  
First Time

This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

Integrative Taxonomy of Australian Metopia (Sarcophagidae: Miltogramminae) Reveals a New Species and Challenges Traditional Phylogeny

2020 ◽  
Vol 4 (6) ◽  
Author(s):  
Nikolas P Johnston ◽  
James F Wallman ◽  
Thomas Pape
Keyword(s):  
Phylogenetic Analysis ◽  
Species Complex ◽  
Molecular Phylogenetics ◽  
Taxonomic Revision ◽  
Integrated Approach ◽  
Integrative Taxonomy ◽  
Morphological Data ◽  
Australian Species ◽  
A New Species ◽  
Generic Relationships

Abstract A taxonomic revision of all Australian species of Metopia Meigen (Sarcophagidae: Miltogramminae) is completed using an integrated approach combining molecular and morphological data. Metopia nudibasis (Malloch) is redescribed as a species complex and a new endemic Australian species, Metopia sputnik sp. n., is described. Evidence is presented that Metopia sauteri (Townsend) is absent from Australia and this species is therefore removed from the known Australian fauna. Molecular phylogenetics is used to reconstruct interspecific and generic relationships and support morphology-based species hypotheses. Phylogenetic analysis splits Metopia Meigen into two clades, separated by Aenigmetopia Malloch, rendering the former genus nonmonophyletic. The implications of this are discussed.

Selected Ordovician Trilobites from the Lake St. John District of Quebec and Their Bearing on Systematics

1995 ◽  
Vol 69 (S42) ◽  
pp. 1-19 ◽  
Author(s):  
Pierre J. Lespérance ◽  
Sylvain Desbiens
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Minimal Length ◽  
Large Data Sets ◽  
Morphological Data ◽  
Eye Position ◽  
Data Sets ◽  
Close Relationship ◽  
The Status

The thorax of Hypodicranotus has ten segments and a spine on the eighth. The ages of Erratencrinurus s.l. spicatus and Erratencrinurus (Erratencrinurus?) vigilans in the Lake St. John district do not confirm their temporal roles leading to subgenera of Erratencrinurus, as has been recently suggested. Phylogenetic analyses of large data sets of species previously referred to Encrinuroides and Physemataspis yield a minimal length cladogram containing 18 species. Encrinuroides is restricted to four species, two of which have biogeographic affinities with Iapetus. These results lead to three clades, named the Walencrinuroides n. gen. clade, Frencrinuroides n. gen. clade, and finally the Physemataspis clade, with an enlarged concept of the genus with the erection of Physemataspis (Prophysemataspis) n. subgen. These last three clades are restricted to North America and Scotland, with alternating predominance of one region. Walencrinuroides s.l. gelaisi n. gen. n. sp. is described. New morphological data on Erratencrinurus s.l. spicatus confirm its close relationship with the clades discussed above. Data are insufficient for phylogenetic analysis of selected cheirurine species here surveyed. Eye position, glabellar segmentation, and pygidial shape differentiate the genera Ceraurus and Gabriceraurus; emended diagnoses of these genera are presented. Ceraurus globulobatus and C. matranseris are distinct, but morphologically close to one another. The status of Gabriceraurus dentatus can be stabilized on its extant types.

scholarly journals A molecular method for a qualitative analysis of potentially coding sequences of DNA

2004 ◽  
Vol 64 (3a) ◽  
pp. 383-398
Author(s):  
M. L. Christoffersen ◽  
M. E. Araújo ◽  
M. A. M. Moreira
Keyword(s):  
Amino Acid ◽  
Phylogenetic Analyses ◽  
A Priori ◽  
Morphological Data ◽  
Computer Algorithms ◽  
Protein Coding ◽  
Tree Topologies ◽  
Alternative Amino Acid ◽  
Cladistic Analyses ◽  
Transformation Series

Total sequence phylogenies have low information content. Ordinary misconceptions are that character quality can be ignored and that relying on computer algorithms is enough. Despite widespread preference for a posteriori methods of character evaluation, a priori methods are necessary to produce transformation series that are independent of tree topologies. We propose a stepwise qualitative method for analyzing protein sequences. Informative codons are selected, alternative amino acid transformation series are analyzed, and most parsimonious transformations are hypothesized. We conduct four phylogenetic analyses of philodryanine snakes. The tree based on all nucleotides produces least resolution. Trees based on the exclusion of third positions, on an asymmetric step matrix, and on our protocol, produce similar results. Our method eliminates noise by hypothesizing explicit transformation series for each informative protein-coding amino acid. This approaches qualitative methods for morphological data, in which only characters successfully interpreted in a phylogenetic context are used in cladistic analyses. The method allows utilizing character information contained in the original sequence alignment and, therefore, has higher resolution in inferring a phylogenetic tree than some traditional methods (such as distance methods).

scholarly journals Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  
Keyword(s):  
Character State ◽  
Ancestral Character State ◽  
Wide Range ◽  
Tree Inference ◽  
Ancestral Character State Reconstruction ◽  
Inference Methods ◽  
Genome Scale ◽  
The Impact ◽  
Rock Inhabiting Fungi ◽  
Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

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