scholarly journals Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

2016 ◽  
Vol 12 (7) ◽  
pp. 20160237 ◽  
Author(s):  
D. W. Bapst ◽  
A. M. Wright ◽  
N. J. Matzke ◽  
G. T. Lloyd
Keyword(s):  
Model Comparison ◽  
Substantial Impact ◽  
Theropod Dinosaurs ◽  
Downstream Effects ◽  
Size Evolution ◽  
Dating Methods ◽  
Divergence Dates ◽  
Parsimony Trees ◽  
Clade Model ◽  
Evolutionary Mode

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

scholarly journals Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

2014 ◽  
Author(s):  
Guido Grimm ◽  
Pashalia Kapli ◽  
Benjamin Bomfleur ◽  
Stephen McLoughlin ◽  
Susanne S Renner
Keyword(s):  
Dna Sequences ◽  
Fossil Record ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Total Evidence ◽  
Extinction Rates ◽  
Sister Clade ◽  
Extant Species ◽  
Dating Methods ◽  
Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles

2012 ◽  
Vol 65 (3) ◽  
pp. 974-991 ◽  
Author(s):  
Daniel G. Mulcahy ◽  
Brice P. Noonan ◽  
Travis Moss ◽  
Ted M. Townsend ◽  
Tod W. Reeder ◽  
...  
Keyword(s):  
Squamate Reptiles ◽  
Mitochondrial Data ◽  
Dating Methods ◽  
Divergence Dates

scholarly journals Shared patterns in body size declines among crinoids during the Palaeozoic extinction events

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mariusz A. Salamon ◽  
Tomasz Brachaniec ◽  
Dorota Kołbuk ◽  
Anwesha Saha ◽  
Przemysław Gorzelak
Keyword(s):  
Climate Change ◽  
Body Size ◽  
Model Comparison ◽  
Abiotic Factors ◽  
Mass Extinctions ◽  
Size Evolution ◽  
Comparison Approach ◽  
Wide Range ◽  
Body Size Evolution ◽  
Extinction Events

AbstractCrinoids were among the most abundant marine benthic animals throughout the Palaeozoic, but their body size evolution has received little attention. Here, we compiled a comprehensive database on crinoid calyx biovolumes throughout the Palaeozoic. A model comparison approach revealed contrasting and complex patterns in body size dynamics between the two major crinoid clades (Camerata and Pentacrinoidea). Interestingly, two major drops in mean body size at around two mass extinction events (during the late Ordovician and the late Devonian respectively) are observed, which is reminiscent of current patterns of shrinking body size of a wide range of organisms as a result of climate change. The context of some trends (marked declines during extinctions) suggests the cardinal role of abiotic factors (dramatic climate change associated with extinctions) on crinoid body size evolution; however, other patterns (two intervals with either relative stability or steady size increase in periods between mass extinctions) are more consistent with biotic drivers.

scholarly journals Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates

2008 ◽  
Vol 5 (1) ◽  
pp. 47-50 ◽  
Author(s):  
Chris L Organ ◽  
Andrew M Shedlock
Keyword(s):  
Genome Size ◽  
Comparative Approach ◽  
Correlated Evolution ◽  
Small Genome ◽  
Theropod Dinosaurs ◽  
Phylogenetic Inertia ◽  
Estimate Genome Size ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Close Relatives

The two living groups of flying vertebrates, birds and bats, both have constricted genome sizes compared with their close relatives. But nothing is known about the genomic characteristics of pterosaurs, which took to the air over 70 Myr before birds and were the first group of vertebrates to evolve powered flight. Here, we estimate genome size for four species of pterosaurs and seven species of basal archosauromorphs using a Bayesian comparative approach. Our results suggest that small genomes commonly associated with flight in bats and birds also evolved in pterosaurs, and that the rate of genome-size evolution is proportional to genome size within amniotes, with the fastest rates occurring in lineages with the largest genomes. We examine the role that drift may have played in the evolution of genome size within tetrapods by testing for correlated evolution between genome size and body size, but find no support for this hypothesis. By contrast, we find evidence suggesting that a combination of adaptation and phylogenetic inertia best explains the correlated evolution of flight and genome-size contraction. These results suggest that small genome/cell size evolved prior to or concurrently with flight in pterosaurs. We predict that, similar to the pattern seen in theropod dinosaurs, genome-size contraction preceded flight in pterosaurs and bats.

Identifying suboptimalities with factorial model comparison

2018 ◽  
Vol 41 ◽  
Author(s):  
Wei Ji Ma
Keyword(s):  
Experimental Design ◽  
Model Comparison ◽  
Process Models ◽  
Multiple Forms ◽  
Factorial Experimental Design ◽  
Factorial Model ◽  
Multiple Components ◽  
The Many

AbstractGiven the many types of suboptimality in perception, I ask how one should test for multiple forms of suboptimality at the same time – or, more generally, how one should compare process models that can differ in any or all of the multiple components. In analogy to factorial experimental design, I advocate for factorial model comparison.

Investigation of irradiation-induced nucleation processes in silicon and germanium

1995 ◽  
Vol 53 ◽  
pp. 224-225
Author(s):  
Harry A. Atwater ◽  
C.M. Yang ◽  
K.V. Shcheglov
Keyword(s):  
Room Temperature ◽  
Crystal Size ◽  
Initial Distribution ◽  
Engineering Control ◽  
Size Evolution ◽  
Silicon And Germanium ◽  
Ge Quantum Dot ◽  
And Control ◽  
Germanium Quantum Dots ◽  
Kinetics Of

Studies of the initial stages of nucleation of silicon and germanium have yielded insights that point the way to achievement of engineering control over crystal size evolution at the nanometer scale. In addition to their importance in understanding fundamental issues in nucleation, these studies are relevant to efforts to (i) control the size distributions of silicon and germanium “quantum dots𠇍, which will in turn enable control of the optical properties of these materials, (ii) and control the kinetics of crystallization of amorphous silicon and germanium films on amorphous insulating substrates so as to, e.g., produce crystalline grains of essentially arbitrary size.Ge quantum dot nanocrystals with average sizes between 2 nm and 9 nm were formed by room temperature ion implantation into SiO2, followed by precipitation during thermal anneals at temperatures between 30°C and 1200°C[1]. Surprisingly, it was found that Ge nanocrystal nucleation occurs at room temperature as shown in Fig. 1, and that subsequent microstructural evolution occurred via coarsening of the initial distribution.

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