scholarly journals The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7430
Author(s):  
Kumiko Matsui ◽  
Takanobu Tsuihiji
Keyword(s):  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Common Ancestry ◽  
Consensus Trees ◽  
Phylogenetic Hypotheses ◽  
Aquatic Mammals ◽  
Data Matrices

Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.

Larval chaetotaxy and morphology are highly homoplastic yet phylogenetically informative in Hydrobiusini water scavenger beetles (Coleoptera: Hydrophilidae)

2020 ◽  
Author(s):  
Miguel Archangelsky ◽  
Nicolás Rafael Martínez Román ◽  
Martin Fikáček
Keyword(s):  
Phylogenetic Analyses ◽  
Head Capsule ◽  
Data Matrix ◽  
Larval Morphology ◽  
Morphometric Characters ◽  
Molecular Analyses ◽  
Adult Morphology ◽  
Phylogenetic Hypotheses

Abstract Phylogenetic analyses testing the monophyly of the tribe Hydrobiusini and the relationships among its genera are performed based on a data matrix including characters of larval morphology and morphometrics, larval chaetotaxy and adult morphology, including eight of the nine hydrobiusine genera plus 15 outgroup taxa. The head chaetotaxy of six genera of the tribe Hydrobiusini is described (Ametor, Hybogralius, Hydramara, Limnohydrobius, Limnoxenus and Sperchopsis). Morphometric characters derived from the head capsule and mouthparts are included. All characters are illustrated in detail. The analyses performed on the above datasets and their combinations reveal the monophyly of the Hydrobiusini except for Hybogralius, and reconstruct the internal topology of the tribe, largely corresponding to results of previous molecular analyses. Hybogralius groups with genera having larvae adapted to underwater feeding in all analyses. The position of the genus Tritonus within the Laccobiini is questioned by our analyses, which suggest a closer relationship with the tribes Hydrophilini or Hydrobiusini. Larval characters are revealed as highly homoplastic, with chaetotaxic characters performing slightly worse than usual larval morphology. Nonetheless, they are phylogenetically informative and useful for testing phylogenetic hypotheses resulting from analyses of molecules or adult morphology. A key to larvae of the genera of the Hydrobiusini is presented.

scholarly journals The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9808 ◽  
Author(s):  
Michela M. Johnson ◽  
Mark T. Young ◽  
Stephen L. Brusatte
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Data Matrix ◽  
Bayesian Analyses ◽  
New Family ◽  
Coastal Marine ◽  
Poor Understanding ◽  
Phylogenetic Hypotheses ◽  
One New Species ◽  
Shed Light

Teleosauroidea was a clade of ancient crocodylomorphs that were a key element of coastal marine environments during the Jurassic. Despite a 300-year research history and a recent renaissance in the study of their morphology and taxonomy, macroevolutionary studies of teleosauroids are currently limited by our poor understanding of their phylogenetic interrelationships. One major problem is the genus Steneosaurus, a wastebasket taxon recovered as paraphyletic or polyphyletic in phylogenetic analyses. We constructed a newly updated phylogenetic data matrix containing 153 taxa (27 teleosauroids, eight of which were newly added) and 502 characters, which we analysed under maximum parsimony using TNT 1.5 (weighted and unweighted analyses) and Bayesian inference using MrBayes v3.2.6 (standard, gamma and variation). The resulting topologies were then analysed to generate comprehensive higher-level phylogenetic hypotheses of teleosauroids and shed light on species-level interrelationships within the clade. The results from our parsimony and Bayesian analyses are largely consistent. Two large subclades within Teleosauroidea are recovered, and they are morphologically, ecologically and biogeographically distinct from one another. Based on comparative anatomical and phylogenetic results, we propose the following major taxonomic revisions to Teleosauroidea: (1) redefining Teleosauridae; (2) introducing one new family and three new subfamilies; (3) the resurrection of three historical genera; and (4) erecting seven new generic names and one new species name. The phylogeny infers that the Laurasian subclade was more phenotypically plastic overall than the Sub-Boreal-Gondwanan subclade. The proposed phylogeny shows that teleosauroids were more diverse than previously thought, in terms of morphology, ecology, dispersal and abundance, and that they represented some of the most successful crocodylomorphs during the Jurassic.

scholarly journals A reevaluation of the evidence supporting an unorthodox hypothesis on the origin of extant amphibians

2008 ◽  
Vol 77 (3) ◽  
pp. 149-199 ◽  
Author(s):  
David Marjanović ◽  
Michel Laurin
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Data Matrix ◽  
Small Data ◽  
Linnean Society ◽  
Original Hypothesis ◽  
The Impact ◽  
Data Matrices

The origin of frogs, salamanders and caecilians is controversial. McGowan published an original hypothesis on lissamphibian origins in 2002 (McGowan, 2002, Zoological Journal of the Linnean Society, 135: 1-32), stating that Gymnophiona was nested inside the ‘microsaurian’ lepospondyls, this clade was the sister-group of a caudate-salientian-albanerpetontid clade, and both were nested inside the dissorophoid temnospondyls. We have investigated McGowan’s data matrix and disagree with the scoring of 35% of the cells. All taxa and all but two characters are affected. In some cases, we have a different interpretation about correspondence between morphology and character states, or we delimit states differently (or use information that was unknown in 2002). In others, we report probable typographic errors. When these cells and characters are revised, the most parsimonious trees – now longer by almost 64% – support one of the three commonly advocated hypotheses, namely a monophyletic Lissamphibia nested, together with its sister-group Albanerpetontidae, within the temnospondyls (next to Doleserpeton) – even though we did not add any characters or taxa to the very small data matrix. This exemplifies the impact of errors in data matrices on the results of phylogenetic analyses. Adding the lysorophian Brachydectes, however, results in the Lissamphibia-Albanerpetontidae clade becoming the sister-group of Brachydectes and settling within the lepospondyls rather than the temnospondyls, thus supporting another of the previously published three hypotheses. This latter finding does not change if the recently described Gerobatrachus is also added. Finally, when Doleserpeton is interpreted as morphologically immature (which means scoring three characters as unknown instead of known), Lissamphibia and Albanerpetontidae are again nested within the ‘microsaurian’ lepospondyls, even though Brachydectes is not included in this analysis. This, too, does not change if Gerobatrachus is added and likewise treated as morphologically immature. Bootstrap supports are rather low under all assumptions. Such lability was to be expected from the small size of the data matrix.

An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 769-777
Author(s):  
Michael A Cantrell ◽  
Brian J Filanoski ◽  
Angela R Ingermann ◽  
Katherine Olsson ◽  
Nicole DiLuglio ◽  
...  
Keyword(s):  
Hot Spots ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Common Ancestry ◽  
Specific Element ◽  
Sine Insertion ◽  
Specific Locus ◽  
Multiple Species ◽  
Phylogenetic Character ◽  
Over Time

Abstract Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.

scholarly journals Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

2004 ◽  
Vol 73 (1-2) ◽  
pp. 3-163 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Future Research ◽  
Sister Group Relationship ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

scholarly journals Another look at matrix correlations

2019 ◽  
Vol 35 (22) ◽  
pp. 4748-4753 ◽  
Author(s):  
Ahmad Borzou ◽  
Razie Yousefi ◽  
Rovshan G Sadygov
Keyword(s):  
Matrix Decomposition ◽  
Data Matrix ◽  
Supplementary Information ◽  
Biological Processes ◽  
Single Experiment ◽  
Sample Number ◽  
The Matrix ◽  
Rv Coefficient ◽  
Systems View ◽  
Data Matrices

Abstract Motivation High throughput technologies are widely employed in modern biomedical research. They yield measurements of a large number of biomolecules in a single experiment. The number of experiments usually is much smaller than the number of measurements in each experiment. The simultaneous measurements of biomolecules provide a basis for a comprehensive, systems view for describing relevant biological processes. Often it is necessary to determine correlations between the data matrices under different conditions or pathways. However, the techniques for analyzing the data with a low number of samples for possible correlations within or between conditions are still in development. Earlier developed correlative measures, such as the RV coefficient, use the trace of the product of data matrices as the most relevant characteristic. However, a recent study has shown that the RV coefficient consistently overestimates the correlations in the case of low sample numbers. To correct for this bias, it was suggested to discard the diagonal elements of the outer products of each data matrix. In this work, a principled approach based on the matrix decomposition generates three trace-independent parts for every matrix. These components are unique, and they are used to determine different aspects of correlations between the original datasets. Results Simulations show that the decomposition results in the removal of high correlation bias and the dependence on the sample number intrinsic to the RV coefficient. We then use the correlations to analyze a real proteomics dataset. Availability and implementation The python code can be downloaded from http://dynamic-proteome.utmb.edu/MatrixCorrelations.aspx. Supplementary information Supplementary data are available at Bioinformatics online.

Phylogeny and biogeography of the South American subgenus Euschistus (Lycipta) Stål (Heteroptera: Pentatomidae: Carpocorini)

2016 ◽  
Vol 47 (4) ◽  
pp. 313-346 ◽  
Author(s):  
Luciana Weiler ◽  
Augusto Ferrari ◽  
Jocelia Grazia
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Data Matrix ◽  
South American ◽  
The South ◽  
Cladistic Analyses ◽  
Heteroptera Pentatomidae ◽  
Definition Of

Phylogenetic analyses of the 13 species of the subgenusLyciptabased on morphological characters were performed under equal and implied weighting, following the method of Mirande (2009). Species fromDichelops,Ladeaschistus,Proxys,Spinalanx,Euschistus(Euschistus) andEuschistus(Mitripus) were included as outgroups, and the tree rooted onCarpocoris. Sixty-five morphological characters were coded in the data matrix. The cladistic analyses did not recover the monophyly of the subgenusLycipta. A clade was supported based on characters of the pygophore and female ectodermal ducts strengthening a new definition ofEuschistus(Lycipta). One species,Euschistus monrosi, was excluded from the subgenus and transferred to the nominal subgenus.Euschistus(Lycipta) species are distributed in two Neotropical subregions: Brazilian (Pará, Rondônia and Yungas provinces) and Chacoan (Pampean, Atlantic, Parana andAraucariaForests and Puna provinces). Biogeographical analyses of spatial vicariance were performed employing different sets of parameters and allowed to identify five disjunctions nodes.

scholarly journals Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

2015 ◽  
Vol 2 (12) ◽  
pp. 150377 ◽  
Author(s):  
Ronald M. Clouse ◽  
Gregorio V. Linchangco ◽  
Alexander M. Kerr ◽  
Robert W. Reid ◽  
Daniel A. Janies
Keyword(s):  
Binding Sites ◽  
Body Wall ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Tissue Inhibitors Of Metalloproteinases ◽  
Multiple Sequence ◽  
Collagenous Tissue ◽  
Phylogenetic Hypotheses ◽  
Reproduction By Fission

Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies.

Phylogenetic Analysis of the Lichen Family Umbilicariaceae based on nuclear ITS1 and ITS2 rDNA Sequences

1999 ◽  
Vol 31 (5) ◽  
pp. 477-489 ◽  
Author(s):  
Natalia V. Ivanova ◽  
Paula T. Depriest ◽  
Vera K. Bobrova ◽  
Alexey V. Troitsky
Keyword(s):  
Phylogenetic Analyses ◽  
Current Treatment ◽  
Taxon Sampling ◽  
Its2 Rdna ◽  
Separate Genus ◽  
Rdna Sequences ◽  
Representative Species ◽  
Phylogenetic Hypotheses ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

AbstractThe lichen family Umbilicariaceae is accepted by most lichenologists as consisting of two genera, Lasallia and Umbilicaria. The monophyly of these two genera was examined by phylogenetic analyses of nucleotide sequences of ITS 1 and ITS2 rDNA. Sequences of these regions from three Lasallia and 17 Umbilicaria species were aligned to those of seven representatives of the outgroup taxa including Eurotiales, Onygenales and Caliciales (Mycocaliciaceae) and subjected to maximum parsimony, maximum likelihood and neighbour-joining analyses. The resulting phylogenetic hypotheses supported the monophyly of the representative species of Lasallia. However, the species of Umbilicaria did not form a monophyletic sistergroup to Lasallia due to the basal placement of other Umbilicaria species in some analyses. Based on these analyses, if Lasallia is recognized as a separate genus then Umbilicaria appears to be paraphyletic. Although further taxon sampling is required to resolve the monophyly of Umbilicaria, for the present we recommend retaining the current treatment of Lasallia as separate from Umbilicaria.

scholarly journals Common Ancestry of Borrelia burgdorferiSensu Lato Strains from North America and Europe

1999 ◽  
Vol 37 (9) ◽  
pp. 3010-3012 ◽  
Author(s):  
D. Postic ◽  
N. Marti Ras ◽  
R. S. Lane ◽  
P.-F. Humair ◽  
M. M. Wittenbrink ◽  
...  
Keyword(s):  
United States ◽  
North America ◽  
Borrelia Burgdorferi ◽  
North American ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Whole Genome ◽  
Common Ancestry ◽  
Limited Region

Ten atypical European Borrelia burgdorferi sensu lato (Borrelia spp.) strains were genetically characterized, and the diversity was compared to that encountered among relatedBorrelia spp. from North America. Phylogenetic analyses of a limited region of the genome and of the whole genome extend existing knowledge about borrelial diversity reported earlier in Europe and the United States. Our results accord with the evidence that North American and European strains may have a common ancestry.

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