scholarly journals Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals

2019 ◽  
Author(s):  
Benedict King ◽  
Robin Beck
Keyword(s):  
Bayesian Methods ◽  
Prior Probability ◽  
Strong Support ◽  
Late Triassic ◽  
Evolutionary Relationships ◽  
Phylogenetic Methods ◽  
Prior Expectation ◽  
Mesozoic Mammals ◽  
History Of ◽  
Evolution Of Mammals

ABSTRACTThe incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for palaeontologists. Bayesian tip-dating (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip-dating affects the recovery of evolutionary relationships has yet to be fully explored. Here we show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip-dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip-dating have better fit to stratigraphy than trees recovered by other methods, due to trees with better stratigraphic fit being assigned a higher prior probability. Differences in stratigraphic fit and tree topology between tip-dating and other methods appear to be concentrated in parts of the tree with weaker character signal and a stronger influence of the prior, as shown by successive deletion of the most incomplete taxa from a sauropod dataset. Tip-dating applied to Mesozoic mammals firmly rejects a monophyletic Allotheria, and strongly supports diphyly of haramiyidans, with the late TriassicHaramiyaviaandThomasiaforming a clade with tritylodontids, which is distant from the middle Jurassic euharamiyidans. This result is not sensitive to the controversial age of the eutherianJuramaia. A Test of the age ofJuramaiausing a less restrictive prior reveals strong support from the data for an Early Cretaceous age. Our results suggest that tip-dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit a prior expectation that can be overturned by strong evidence from character data.

Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

2020 ◽  
Author(s):  
Benedict King
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Methods ◽  
Diversification Rate ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Tree Model ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Topologies ◽  
Birth Death

Abstract The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.]

scholarly journals The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

2019 ◽  
Author(s):  
Sebastian S Groh ◽  
Paul Upchurch ◽  
Paul M Barrett ◽  
Julia J Day
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Morphological Characters ◽  
Late Triassic ◽  
Continuous Data ◽  
Comprehensive Review ◽  
Phylogenetic Studies ◽  
History Of ◽  
First Time

Abstract Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

Provenance of Jurassic sedimentary rocks of south-central Quesnellia, British Columbia: implications for paleogeography

2004 ◽  
Vol 41 (1) ◽  
pp. 103-125 ◽  
Author(s):  
Nathan T Petersen ◽  
Paul L Smith ◽  
James K Mortensen ◽  
Robert A Creaser ◽  
Howard W Tipper
Keyword(s):  
Detrital Zircon ◽  
Middle Jurassic ◽  
Sedimentary Rocks ◽  
Source Area ◽  
Lower Jurassic ◽  
Early Jurassic ◽  
Late Triassic ◽  
Nd Isotopes ◽  
South Central ◽  
History Of

Jurassic sedimentary rocks of southern to central Quesnellia record the history of the Quesnellian magmatic arc and reflect increasing continental influence throughout the Jurassic history of the terrane. Standard petrographic point counts, geochemistry, Sm–Nd isotopes and detrital zircon geochronology, were employed to study provenance of rocks obtained from three areas of the terrane. Lower Jurassic sedimentary rocks, classified by inferred proximity to their source areas as proximal or proximal basin are derived from an arc source area. Sandstones of this age are immature. The rocks are geochemically and isotopically primitive. Detrital zircon populations, based on a limited number of analyses, have homogeneous Late Triassic or Early Jurassic ages, reflecting local derivation from Quesnellian arc sources. Middle Jurassic proximal and proximal basin sedimentary rocks show a trend toward more evolved mature sediments and evolved geochemical characteristics. The sandstones show a change to more mature grain components when compared with Lower Jurassic sedimentary rocks. There is a decrease in εNdT values of the sedimentary rocks and Proterozoic detrital zircon grains are present. This change is probably due to a combination of two factors: (1) pre-Middle Jurassic erosion of the Late Triassic – Early Jurassic arc of Quesnellia, making it a less dominant source, and (2) the increase in importance of the eastern parts of Quesnellia and the pericratonic terranes, such as Kootenay Terrane, both with characteristically more evolved isotopic values. Basin shale environments throughout the Jurassic show continental influence that is reflected in the evolved geochemistry and Sm–Nd isotopes of the sedimentary rocks. The data suggest southern Quesnellia received material from the North American continent throughout the Jurassic but that this continental influence was diluted by proximal arc sources in the rocks of proximal derivation. The presence of continent-derived material in the distal sedimentary rocks of this study suggests that southern Quesnellia is comparable to known pericratonic terranes.

L'histoire des nombres amiables: le témoignage des textes hébreux médiévaux

1996 ◽  
Vol 6 (1) ◽  
pp. 63-87 ◽  
Author(s):  
Tony Lévy
Keyword(s):  
Strong Support ◽  
Hebrew Text ◽  
17Th Century ◽  
Medieval Europe ◽  
History Of ◽  
New Material ◽  
Made In

This article analyzes new material on the history of the amicable numbers. It discusses Hebrew texts which throw new light on the diffusion in Medieval Europe of Ṯābit ibn Qurra's (9th century) work. We find Ṯābit's theorem on amicable numbers in a Hebrew translation, made in Saragossa in 1395, of an arithmetical commentary written by Abū al-Ṣalt al-Andalusī (ca. 1068–1134), and also in an original Hebrew text probably written by the Jewish Provençal scholar Qalonymos ben Qalonymos (1287 – after 1329). These texts lend strong support to the surmise that the Arabic tradition concerning amicable numbers could not have remained unknown to European mathematicians before the work of Descartes and Fermat in the 17th century.

scholarly journals Endocast of the Late Triassic (Carnian) dinosaur Saturnalia tupiniquim: implications for the evolution of brain tissue in Sauropodomorpha

2018 ◽  
Author(s):  
Mario Bronzati ◽  
Oliver W M Rauhut ◽  
Jonathas S Bittencourt ◽  
Max C. Langer
Keyword(s):  
South America ◽  
Brain Tissue ◽  
Evolutionary History ◽  
Morphological Changes ◽  
Volume Reduction ◽  
Late Triassic ◽  
History Of

The evolutionary history of dinosaurs might date back to the fist stages of the Triassic (c. 250– 240 Ma), but the oldest unequivocal records of the group come from Late Triassic (Carnian – c. 230 Ma) rocks of South America. Here, we present the fist braincase endocast of a Carnian dinosaur, the sauropodomorph Saturnalia tupiniquim, and provide new data regarding the evolution of the flccular and paraflccular lobe of the cerebellum (FFL), which has been extensively discussed in the fild of palaeoneurology. Previous studies proposed that the development of a permanent quadrupedal stance was one of the factors leading to the volume reduction of the FFL of sauropods. However, based on the new data for S. tupiniquim we identifid a fist moment of FFL volume reduction in nonsauropodan Sauropodomorpha, preceding the acquisition of a fully quadrupedal stance. Analysing variations in FFL volume alongside other morphological changes in the group, we suggest that this reduction is potentially related to the adoption of a more restricted herbivore diet. In this context, the FFL of sauropods might represent a vestigial trait, retained in a reduced version from the bipedal and predatory early sauropodomorphs.

scholarly journals The calcareous nannofossil <i>Prinsiosphaera</i> achieved rock-forming abundances in the latest Triassic of western Tethys: consequences for the δ<sup>13</sup>C of bulk carbonate

2013 ◽  
Vol 10 (5) ◽  
pp. 7989-8025 ◽  
Author(s):  
N. Preto ◽  
C. Agnini ◽  
M. Rigo ◽  
M. Sprovieri ◽  
H. Westphal
Keyword(s):  
Global Ocean ◽  
Late Triassic ◽  
Calcareous Nannofossils ◽  
Calcareous Nannofossil ◽  
Western Tethys ◽  
Carbonate Sedimentation ◽  
History Of ◽  
Calcareous Plankton ◽  
Inorganic Carbon Cycle

Abstract. The onset of pelagic biomineralization marked a milestone in the history of the long term inorganic carbon cycle: as soon as calcareous nannofossils became major limestone producers, the pH and supersaturation state of the global ocean were stabilized (the so-called Mid Mesozoic Revolution). But although it is known that calcareous nannofossils were abundant already by the end of the Triassic, no estimates exist on their contribution to hemipelagic carbonate sedimentation. With this work, we estimate the volume proportion of Prinsiosphaera, the dominant Late Triassic calcareous nannofossil, in hemipelagic and pelagic carbonates of western Tethys. The investigated Upper Triassic lime mudstones are composed essentially of microspar and tests of calcareous nannofossils, plus minor bioclasts. Prinsiosphaera became a significant component of lime mudstones since the late Norian, and was contributing up to ca. 60% of the carbonate by the late Rhaetian in periplatform environments with hemipelagic sedimentation. The increasing proportion of Prinsiosphaera in upper Rhaetian hemipelagic lime mudstones is paralleled by a increase of the δ13C of bulk carbonate. We interpreted this isotopic trend as related to the diagenesis of microspar, which incorporated respired organic carbon with a low δ13C when it formed during shallow burial. As the proportion of nannofossil tests increased, the contribution of microspar with low δ13C diminished, determining the isotopic trend. We suggest that a similar diagenetic effect may be observed in many Mesozoic limestones with a significant, but not yet dominant, proportion of calcareous plankton.

scholarly journals Petrology, mineral chemistry, and geochemistry of Late Triassic Ni–Cu ore-bearing mafic–ultramafic intrusions, Hongqiling, northeastern China: petrogenesis and tectonic implications

2019 ◽  
Vol 56 (2) ◽  
pp. 111-128
Author(s):  
Ai Li ◽  
Jian Wang ◽  
Yue Song
Keyword(s):  
Crustal Contamination ◽  
Parental Magma ◽  
Mineral Chemistry ◽  
Late Triassic ◽  
Sulfide Deposit ◽  
Chemical Compositions ◽  
Tholeiitic Magma ◽  
Average Value ◽  
Central Asian ◽  
History Of

The Hongqiling magmatic Ni–Cu sulfide deposit, situated on the southern margin of the eastern Central Asian Orogenic Belt (CAOB), is composed of over 30 mafic–ultramafic intrusions. These ore-bearing intrusions are composed mainly of harzburgite, lherzolite, websterite, orthopyroxenite, and norite (gabbro). The constituent minerals are olivine, diopside, bronzite, calcic-hornblende, plagioclase, and spinel with orthopyroxene as a dominant mineral in these intrusions. These ore-bearing intrusions are not Alaskan-type complexes. Spinel and clinopyroxene both exhibit different chemical compositions from those in the Alaskan-type complexes. The rocks that make up the intrusions have high contents of MgO (average value = 25.20 wt.%) and low TiO2 (average value = 0.58 wt.%). The high MgO contents of the minerals and the high Mg# (71) of the calculated melt in equilibrium with olivine demonstrate that the parental magma of the Hongqiling mafic–ultramafic intrusions was a high-Mg tholeiitic magma. The Hongqiling ore-bearing mafic–ultramafic intrusions and the calculated “trapped liquids” for the olivine-orthopyroxene cumulate rocks are all enriched in large-ion lithophile elements and depleted in high field strength elements. The Ce/Pb, Ta/La, Th/Yb, and (La/Sm)PM values and the depletion of Nb and Ta suggest that the magma experienced crustal contamination. The Hongqiling ore-bearing intrusions display many similarities with mafic–ultramafic intrusions that formed in a post-collisional extensional environment in the western CAOB (e.g., Huangshanxi). Common features include their whole-rock compositions and mineral chemistry. Combined with the evolutionary history of the eastern segment of the CAOB, we believe that the Late Triassic Hongqiling mafic–ultramafic intrusions formed in a post-collisional extensional environment.

Perspectives on the Evolution and Diversification of the Diatoms

2007 ◽  
Vol 13 ◽  
pp. 1-12 ◽  
Author(s):  
Matthew L. Julius
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Early Jurassic ◽  
Late Triassic ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Diatom Species ◽  
Generic Level ◽  
Existing Data

The understanding of diatom evolution has progressed greatly over the last two decades. Existing data sets have been reanalyzed, new data sets have been generated, and new tools have been employed. Hindering progress is the seemingly endless number of diatom species remaining to be described and relative small number of investigators active in the field. This problem is further confounded by the dramatic reorganization of generic level classification in the group. Despite these problems, many conclusions can be made about prior hypotheses concerning the group's development. Most notably, the origin of the diatoms can be bracketed between the Late Triassic and Early Jurassic using fossil record and molecular clock estimates. This combination of techniques has also provided consensus and clarification to the origin and duration of specific lineages enhancing our understanding of the group's diversification, early ecology, and evolutionary relationships.

scholarly journals Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

2019 ◽  
Vol 11 (9) ◽  
pp. 2531-2541 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Lucía Graña-Miraglia ◽  
Gamaliel López-Leal ◽  
Santiago Castillo-Ramírez
Keyword(s):  
Evolutionary History ◽  
Ad Hoc ◽  
Acinetobacter Calcoaceticus ◽  
Recent Attempt ◽  
Evolutionary Relationships ◽  
Closely Related Species ◽  
Acinetobacter Baumannii Complex ◽  
History Of ◽  
To Come ◽  
Clear Cases

Abstract The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

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