Identification of the Oligocene to early Miocene loricariid catfish †Taubateia paraiba as a member of the Rhinelepinae

2021 ◽  
pp. 1-5
Author(s):  
Jonathan W. Armbruster ◽  
Nathan K. Lujan
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Clock ◽  
Early Miocene ◽  
Primary Sources ◽  
Correct Identification ◽  
Circular Reasoning ◽  
Time Calibration ◽  
Molecular Phylogenies ◽  
Taxonomic Groups

Correct identification of fossil taxa is immensely important for dating molecular phylogenies and understanding when and how quickly modern biodiversity evolved. Fossils that are available for a clade of interest and can be directly incorporated in the phylogenetic analysis are considered primary sources of time calibration, whereas calibrations inferred from other studies are secondary (Arroyave et al., 2013). Studies of taxonomic groups that lack fossils must either expand their analyses to include fossilized outgroup lineages, use secondary calibrations, or use more problematic primary calibrations, e.g., vicariant geologic events. The use of vicariant geologic events to calibrate phylogenies poses the risk of circular reasoning, because the goal of many such studies is to determine how geologic events have affected diversification. Near et al. (2012) argued that fossil calibrations external to clades of interest, but still within the broader Actinopterygian (ray-finned fishes) tree, could be used as means of calibrating a generalized molecular clock, but internal calibrations are still valuable for refining such inferences (Arroyave et al., 2013).

scholarly journals History of earthquake studies in Russia

2009 ◽  
Vol 47 (2-3) ◽  
Author(s):  
R. Tatevossian
Keyword(s):  
Seismic Hazard Assessment ◽  
Historical Seismicity ◽  
Primary Sources ◽  
Original Form ◽  
Correct Identification ◽  
Tectonic Earthquake ◽  
Time Period ◽  
Long Time ◽  
History Of ◽  
Modern Knowledge

To evaluate the completeness of modern knowledge on historical seismicity it is necessary to know the general geopolitical and socio-cultural background in the country. It determines the possibility to record the evidence of an earthquake and conserve the record in original form for a long time-period. The potential duration of historical earthquake study in Russia is assessed based on these considerations. Certain stages of earthquake study in Russia have been detected. Specific problems of seismicity studies of low active areas are discussed as an example of Russian platform. The value of each (even moderate magnitude) event becomes crucial for seismic hazard assessment in such territories. A correct identification of event nature (tectonic earthquake or exogenous phenomena - landslides, karsts, etc.) is practically impossible without using primary sources with detailed descriptions. Occurrence of modern earthquakes can be used to assess the accuracy of historical seismicity knowledge.

scholarly journals A New Cypselomorph Bird from the Middle Eocene of Germany and the Early Diversification of Avian Aerial Insectivores

The Condor ◽  
2005 ◽  
Vol 107 (2) ◽  
pp. 342-352 ◽  
Author(s):  
Gerald Mayr
Keyword(s):  
Phylogenetic Analysis ◽  
Middle Eocene ◽  
Sister Group ◽  
Food Competition ◽  
Early Miocene ◽  
New Taxon ◽  
Insectivorous Birds ◽  
Dominant Group ◽  
Early Diversification ◽  
Aerial Insectivores

Abstract A new taxon of the Cypselomorphae—the clade including nightjars, potoos, owlet-nightjars, and apodiform birds—is described from the middle Eocene of Messel in Germany. Phylogenetic analysis of 49 characters shows Protocypselomorphus manfredkelleri gen. et sp. nov. to be the sister group of all other cypselomorph taxa, although this placement was not robust to bootstrapping. As evidenced by its swift-like beak, long forearm, and reduced feet, P. manfredkelleri was hawking insects on the wing. Thus it adds a distinctive new taxon to the already diverse assemblage of Paleogene aerial insectivores, all of which belong to the Cypselomorphae. This strongly contrasts with the extant avifauna where many aerial insectivores belong to songbirds, and among the insectivorous cypselomorph taxa only swifts and nightjars are species rich and widely distributed. The diversity of aerial insectivores among the Cypselomorphae may have been reduced by food competition with songbirds, which do not become the dominant group of insectivorous birds before the early Miocene. Una Nueva Ave Cipselomorfa del Eoceno Medio de Alemania y la Diversificación Temprana de las Aves Insectívoras Aéreas Resumen. Se describe un nuevo taxón de Cypselomorphae, el clado que incluye a las familias Caprimulgidae, Nyctibiidae, Aegothelidae y a las aves apodiformes, del Eoceno medio de Messel en Alemania. Un análisis filogenético de 49 caracteres muestra que Protocypselomorphus manfredkelleri gen. et sp. nov. es el grupo hermano de los demás taxa de cipselomorfos, aunque esta posición no fue apoyada por el análisis de bootstrap. Como lo evidencia su pico tipo vencejo, antebrazo largo y patas pequeñas, P. manfredkelleri cazaba insectos al vuelo. Así, este hallazgo añade un nuevo taxón al grupo ya diverso de los insectívoros aéreos del Paleógeno, todos los cuales pertenecen al grupo de los cipselomorfos. Esto contrasta fuertemente con la avifauna actual, en que muchos insectívoros aéreos pertenecen al grupo de los paseriformes, mientras que de los taxa de insectívoros cipselomorfos sólo los apodiformes y caprimúlgidos presentan alta diversidad específica y se encuentran ampliamente distribuidos. La diversidad de los insectívoros aéreos en los cipselomorfos pude haberse reducido debido a la competencia por alimento con las aves paseriformes, las cuales no se transforman en el grupo dominante de aves insectívoras sino hasta el Mioceno temprano.

scholarly journals Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4349 ◽  
Author(s):  
Aristóteles Góes-Neto ◽  
Marcelo V.C. Diniz ◽  
Daniel S. Carvalho ◽  
Gilberto C. Bomfim ◽  
Angelo A. Duarte ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Phylogenetic Analysis ◽  
Complex Networks ◽  
Complex Network ◽  
Bootstrap Method ◽  
Molecular Data ◽  
Data Sets ◽  
Fungal Cell ◽  
Taxonomic Groups ◽  
Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

Reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) and the problems of using ribosomal DNA at the lowest taxonomic levels

2013 ◽  
Vol 26 (3) ◽  
pp. 233 ◽  
Author(s):  
Alexander N. Schmidt-Lebuhn
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Species Tree ◽  
Gene Trees ◽  
Species Relationships ◽  
Reciprocal Monophyly ◽  
Molecular Phylogenies

The reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) is tested, with a phylogenetic analysis of ribosomal and chloroplast DNA. Although one species of the latter genus was not sampled, the results of the present study indicated that it is most likely monophyletic as opposed to paraphyletic with respect to Craspedia. Within Craspedia, deeper sampling results in the appearance of several species (C. aurantia, C. coolaminica, C. glabrata and C. variabilis) in both major Australian rDNA clades, indicating that the available molecular phylogenies have to be considered gene trees instead of species phylogenies. Additional studies using more independent loci and species-tree approaches are needed to resolve species relationships in the genus.

Pronival (protalus) ramparts: a review of forms, processes, diagnostic criteria and p alaeoenvi ronmental implications

1997 ◽  
Vol 21 (3) ◽  
pp. 394-418 ◽  
Author(s):  
R.A. Shakesby
Keyword(s):  
Diagnostic Criteria ◽  
Critical Review ◽  
Correct Identification ◽  
Circular Reasoning ◽  
Constituent Material ◽  
Mechanisms Of Formation ◽  
Rock Glaciers

Most of the literature on pronival (protalus) ramparts deals with supposed fossil examples with very few studies devoted to active features and/or observed processes. Not surprisingly, this has led to circular reasoning and assumptions about typical rampart form, constituent material and genesis that have been shown to be inadequate or spurious from the few detailed investigations of actively forming ramparts so far carried out. Nevertheless, reliance continues to be placed on the characteristics of fossil features in the search for previously unidentified fossil examples. This article provides a critical review of rampart terminology, morphology and sedimentology, mechanisms, 'diagnostic' criteria, position in a continuum of talus-derived landforms and palaeoclimatic significance. It is suggested that the descriptor pronival is preferable to the widely used protalus, as the latter is misleadingly restrictive in terms of the known range of possible locations. Greater variability in terms of form and mechanisms of formation than most workers assume is indicated by recent studies of active features, with multiple as well as single ridges, fines and edge-worn as well as coarse angular clasts being found, and a variety of supranival and also subnival processes regarded as possibly contributing to rampart formation. It is concluded that only when further investigations of actively forming ramparts have been carried out, will it be possible to compile a reliable list of criteria for dist inguishing ramparts from moraines, protalus rock glaciers and other bedrock cliff-foot deposi tional forms. Correct identification of fossil ramparts may then lead to a better understanding of 1) their place in a continuum of talus-derived landforms; and 2) their potential as palaeoclimatic indicators.

scholarly journals The phylogenetic position of Gallinuloides Eastman (Aves: Galliformes) from the Tertiary of North America

Zootaxa ◽  
2003 ◽  
Vol 199 (1) ◽  
pp. 1 ◽  
Author(s):  
GARETH J. DYKE
Keyword(s):  
Phylogenetic Analysis ◽  
North America ◽  
Molecular Clock ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Calibration Point ◽  
Fossil Calibration ◽  
Evolutionary Radiation ◽  
Fossil Bird

I have extended a recent phylogenetic analysis of morphological characters for galliform birds (pheasants, grouse, partridges and allies) to investigate the placement of the enigmatic fossil Gallinuloides wyomingensis Eastman. This analysis shows that, contrary to most previous interpretations, the fossil Gallinuloides is a basal member of the ‘phasianoid’ assemblage within Galliformes—not basal within the order as has been previously proposed. This conclusion is supported by several clear osteological features preserved on the holotype and only currently described specimen of this enigmatic fossil bird. Resolving the evolutionary relationships of Gallinuloides is of importance because this fossil taxon has proved a key player in debates regarding the timing of the diversification of all modern birds (Neornithes)—Gallinuloides has been used as both an internal and external fossil calibration point for molecular clock hypotheses dealing with the pattern and timing of the neornithine evolutionary radiation.

Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups

Genetica ◽  
2005 ◽  
Vol 124 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Edward J. Smith ◽  
Li Shi ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analysis ◽  
Gallus Gallus ◽  
Taxonomic Groups

scholarly journals Root Digger: a root placement program for phylogenetic trees

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ben Bettisworth ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Model ◽  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Markov Models ◽  
Root Position ◽  
Clock Analysis ◽  
Confidence Value ◽  
Root Location ◽  
Molecular Clock Analysis

Abstract Background In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. Results We present a software called which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement. We find that is successful at finding roots when compared to similar tools such as IQ-TREE and MAD, and will occasionally outperform them. Additionally, we find that the exhaustive mode of is useful in quantifying and explaining uncertainty in rooting positions. Conclusions can be used on an existing phylogeny to find a root, or to asses the uncertainty of the root placement. is available under the MIT licence at https://www.github.com/computations/root_digger.

scholarly journals Phylogenetic analysis of different Artemisia species based on chloroplast gene rps11

2011 ◽  
Vol 63 (3) ◽  
pp. 661-665 ◽  
Author(s):  
Tariq Mahmood ◽  
Nadia Hassan ◽  
Nazia Nazar ◽  
Ishrat Naveed
Keyword(s):  
Phylogenetic Analysis ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
Restriction Enzymes ◽  
The Family ◽  
Artemisia Species ◽  
The Subject ◽  
Analysis System ◽  
Mixed Pattern ◽  
Taxonomic Groups

Artemisia L. of the family Astereacae is a genus with enormous economical and medicinal importance. As a result, the genus Artemisia has been the subject of diversity-focused studies. In the present study, phylogenetic analysis based on restriction fragment length polymorphism of the chloroplast rps11 gene was conducted on eight species of Artemisia that represent the major morphological subgroups. After digestion of the rps11 gene that was amplified from eight species, with six different restriction enzymes, each restriction site was observed and scored on a 12% polyacrylamide gel. The data were analyzed using the Numerical Taxonomy and Multivariate Analysis System to infer the phylogenetic relationship within the genus. A mixed pattern was observed among the species belonging to various taxonomic groups of Artemisia.

Late Miocene eastwards transatlantic dispersal of flightless anchonine weevils (Coleoptera: Curculionidae: Molytinae)

Zootaxa ◽  
2021 ◽  
Vol 4952 (1) ◽  
pp. 55-70
Author(s):  
VASILY V. GREBENNIKOV ◽  
ROBERT S. ANDERSON
Keyword(s):  
Phylogenetic Analysis ◽  
Atlantic Ocean ◽  
Molecular Clock ◽  
Molecular Data ◽  
West African ◽  
The West ◽  
Incertae Sedis ◽  
Clock Analysis ◽  
Morphological And Molecular Data ◽  
Molecular Clock Analysis

The weevil genera Aethiopacorep Voisin and Titilayo Cristóvão & Lyal are the only native African members of the nearly pantropical and poorly known tribe Anchonini. All Anchonini are flightless, a trait likely limiting dispersal, yet these weevils are found on both sides of the Atlantic Ocean. A phylogenetic analysis of 79 terminals and 3248 aligned positions from one mitochondrial and two nuclear ribosomal fragments supports a clade of West African Anchonini nested within American Anchonini. As suggested by previous authors, the Asian genera Himalanchonus Zherikhin and Otibazo Morimoto do not form a clade with the tribe’s core, and along with Cycloterinus Kolbe, Euthycodes Pascoe, Leptanchonus Morimoto, Nepalanchonus Zherikhin, and Tanyomus Champion, are here removed from Anchonini and placed as Molytinae incertae sedis. So defined, the monophyletic tribe Anchonini contains 36 genus-group names, all but two denoting American taxa. Using molecular clock analysis, we estimate the separation of the West African Anchonini from its American sister at 9.5–5.2 million years ago (Ma). This date greatly postdates the Cretaceous opening of the Atlantic Ocean (about 100 Ma) and, therefore, evokes a single transatlantic dispersal to West Africa, likely by over-water rafting, leading to subsequent diversification. We postulate this to be the first documented eastwards crossing of the Atlantic Ocean by terrestrial non-volant arthropods based on morphological and molecular data. 

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