scholarly journals Unbiased clade age estimation using a Bayesian Brownian Bridge

2021 ◽  
Author(s):  
Daniele Silvestro ◽  
Christine D. Bacon ◽  
Wenna Ding ◽  
Qiuyue Zhang ◽  
Philip C. J. Donoghue ◽  
...  
Keyword(s):  
Age Estimation ◽  
Fossil Record ◽  
High Probability ◽  
Brownian Bridge ◽  
New Model ◽  
Fossil Evidence ◽  
Wide Range ◽  
Fossil Data ◽  
Simplistic Model ◽  
Age Estimates

AbstractIn a recent paper1 we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2 critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.

scholarly journals The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

2021 ◽  
Vol 288 (1959) ◽  
Author(s):  
G. P. Fournier ◽  
K. R. Moore ◽  
L. T. Rangel ◽  
J. G. Payette ◽  
L. Momper ◽  
...  
Keyword(s):  
Fossil Record ◽  
Surface Oxidation ◽  
Oxygenic Photosynthesis ◽  
Evolutionary Models ◽  
Crown Group ◽  
Relative Dating ◽  
Wide Range ◽  
Rapid Diversification ◽  
Oxygenic Phototrophs ◽  
Age Estimates

The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.

Palaeophysiology of terrestrialisation in the Chelicerata

1989 ◽  
Vol 80 (3-4) ◽  
pp. 303-310 ◽  
Author(s):  
Paul A. Selden ◽  
Andrew J. Jeram
Keyword(s):  
Fossil Record ◽  
Sensory Perception ◽  
Lower Carboniferous ◽  
Book Lungs ◽  
Fossil Evidence ◽  
Wide Range ◽  
Continuous Record

ABSTRACTThe wide range of organs of respiration (book-gills, book-lungs, sieve- and tube-tracheae), reproduction, sensory perception, etc., among the chelicerates indicates that the major groups made the transition to land life independently. The fossil record is patchy for most chelicerate groups, certain intervals (e.g. Westphalian) being particularly rich in chelicerate bearing Lagerstatten while in others (e.g. Mesozoic) they are sparse. Due, apparently, to their unusual hyaline exocuticle, scorpions are better preserved than other arthropods, and show a fairly continuous record from fully aquatic forms in the Silurian, to both aquatic and terrestrial faunas in the Carboniferous. In particular, new and well-preserved material of the earliest demonstrably terrestrial scorpions from the Lower Carboniferous of East Kirkton, West Lothian, suggests that book-lungs, at least in the scorpions, developed directly from book-gills by suturing of the covering plate (Blattfuss of the related eurypterids) to leave stigmata for diffusion of air. This evidence supports the ideas of early authors that the scorpion mesosomal ‘sternites’ are fused plates, contra Kjellesvig-Waering (1986) who envisaged the plates being lost to reveal true sternites beneath. The fossil evidence also indicates that by the Triassic at least two scorpion lineages had evolved intra-‘sternite’ stigmata.

scholarly journals Fossil data do not support a long pre-Cretaceous history of flowering plants

2021 ◽  
Author(s):  
Graham E. Budd ◽  
Richard P. Mann ◽  
James A. Doyle ◽  
Mario Coiro ◽  
Jason Hilton
Keyword(s):  
Fossil Record ◽  
Brownian Bridge ◽  
Temporal Distribution ◽  
Rapid Rise ◽  
Crown Group ◽  
Bridge Model ◽  
History Of ◽  
Origin Of Angiosperms ◽  
Fossil Data ◽  
Molecular Clock Dating

AbstractThe origin of angiosperms is a classic macroevolutionary problem, because of their rapid rise in the Early Cretaceous fossil record, beginning about 139 Ma ago, and the conflict this creates with older crown-group ages based on molecular clock dating1. Silvestro et al.2 use a novel methodology to model past angiosperm diversity based on a Bayesian Brownian Bridge model of fossil finds assigned to extant families, concluding that a Cretaceous origin is vanishingly unlikely. However, their results strongly conflict with the known temporal distribution of angiosperm fossils, and, while we agree that statistical analysis aids interpretation of the fossil record, here we show the conclusions of Silvestro et al.2 are unsound.

scholarly journals A New Cost Function Combining Deep Neural Networks (DNNs) and l2,1-Norm with Extraction of Robust Facial and Superpixels Features in Age Estimation

2018 ◽  
Vol 8 (10) ◽  
pp. 1943
Author(s):  
Arafat Abu Mallouh ◽  
Zakariya Qawaqneh ◽  
Buket Barkana
Keyword(s):  
Neural Networks ◽  
Cost Function ◽  
Age Estimation ◽  
Deep Neural Networks ◽  
New Model ◽  
Age Related ◽  
Wide Range ◽  
Deep Learning Network ◽  
High Level ◽  
Facial Images

Automatic age estimation from unconstrained facial images is a challenging task and it recently has gained much attention due to its wide range of applications. In this paper, we propose a new model based on convolutional neural networks (CNNs) and l2,1-norm to select age-related features for the age estimation task. A new cost function is proposed. To learn and train the new model, we provide the analysis and the proof for the convergence of the new cost function to solve minimization problem of deep neural networks (DNNs) and the l2,1-norm. High-level features are extracted from the facial images by using transfer learning, since there are currently not enough large age databases that can be used to train a deep learning network. Then, the extracted features are fed to the proposed model to select the most efficient age-related features. In addition, a new system that is based on DNN to jointly fine-tune two different DNNs with two different feature sets is developed. Experimental results show the effectiveness of the proposed methods and achieved the state-of-art performance on a public database.

Mortality Estimation: Biased Results from Unbiased Ages

1984 ◽  
Vol 41 (12) ◽  
pp. 1843-1847 ◽  
Author(s):  
Jay Barlow
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Age Estimation ◽  
Age Determination ◽  
Mortality Rates ◽  
Age Classes ◽  
Estimation Errors ◽  
Mortality Estimation ◽  
Age Estimates

Estimates of mortality rates from age distributions are biased by imprecision in age estimation, even if age estimates are unbiased. I have derived a method for predicting the magnitude of this bias from information on the precision of age determination. Monte Carlo simulations show that bias can be accurately predicted. The commonly used Chapman–Robson mortality estimator is shown to be robust to imprecision in age determination if all age-classes are included. Errors are likely, however, if one or more age-classes are excluded or if other mortality estimators are used. Biases can be corrected if the distribution of age-estimation errors is known.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

scholarly journals More Than Names: The role of updated taxonomy in palaeontology collections

2019 ◽  
Vol 3 ◽  
Author(s):  
Ricardo Paredes
Keyword(s):  
Fossil Record ◽  
Marine Invertebrate ◽  
Research Community ◽  
Type Material ◽  
Museum Collections ◽  
Web Based ◽  
2D Imaging ◽  
Visual Impact ◽  
Fossil Data

The accuracy on taxonomic determinations of palaeontology collections may have significant consequences in estimations of organism diversity through time. This justifies the need of taxonomic standardization of palaeontological collections. The perception of palaeodiversity through Phanerozoic time has significantly improved since the Sepkoski showed the marine invertebrate taxonomic data in diversity graphs, organized in orders (Sepkoski 1978) and families (Sepkoski 1979, Sepkoski 1984). The visual impact of these graphs engaged palaeontologists into gathering quantitative macroevolution in order to better understand marine palaeodiversity. Alroy et al. (2008) presented a rebuilt diversity curve based on genus-level in a large sample record. These and other statistically sound and standardized datasets of fossil occurrences have combined sources as literature, databases, and museum collections data as a foundation. Integration of these datasets with the entire fossil record based on individual specimens in space and time would be the ideal approach to species-level taxonomy standards determinations. An example showing how this approach may be achieved is the use of initiatives such as the Web-based data facility Palaeontology Database (PdB) which includes a large amount of fossil record data from throughout the world. The major advantage of that is to gather institucional and also private palaeontological collections with taxonomy experts validation. The core of these datasets is the taxon, with the species as the expected most reliable unit. Taxonomy is therefore the discipline enrolled in the process with the taxonomist at the centre of the process. Updated taxonomy is crucial to create reliable datasets and a careful approach should prevent biased data due to under- or overestimation of diversity. Palaeontological museum collections are known to be one of the largest repositories of fossil data. Taxonomic standardization of palaeontology collections in the context of a museum should: Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. These practices are valuable complements to current methodologies adopted to improve the taxonomy of collections, resulting in more reliable data which further enables museum-based research focusing on palaeodiversity estimations.

scholarly journals Professional characteristics of an educator: A survey of literature

2013 ◽  
Vol 25 (1) ◽  
pp. 1-22
Author(s):  
J. Anitha ◽  
R. Krishnaveni
Keyword(s):  
Student Outcome ◽  
Wide Scope ◽  
Review Of Literature ◽  
New Model ◽  
Professional Characteristics ◽  
Wide Range ◽  
Made In ◽  
Comprehensive Study

Literature has shown that various studies have dealt with different professional features of teaching and they have focused on one or few professional characteristics of educators. In spite of the immense amount of literature on educator characteristics, a comprehensive study that would encompass the vital professional characteristics of an educator in total is lacking. This has instigated the researcher to take up the study to identify the professional characteristics of an educator. An attempt was made in identifying the educators' characteristics using student outcome as a boundary criterion to select the characteristics from among several that are available in the literature. Therefore, a new model of professional characteristics of educators was proposed. This paper discusses in detail, the characteristics of a profession in general and the wide range of educator’s characteristics as studied in previous researches. The paper presents a wide scope for the models developed to be studied in depth to appreciate and investigate more about the professional characteristics identified through this review of literature. The models may also be tested empirically for further accumulation of knowledge in the field.

scholarly journals Major features of protistan evolution: controversies, problems and a few answers

2006 ◽  
Vol 29 (1) ◽  
pp. 55-80
Author(s):  
Jere H Lipps
Keyword(s):  
Fossil Record ◽  
Molecular Data ◽  
Trophic Levels ◽  
Early Earth ◽  
Huge Number ◽  
Geologic Time ◽  
Earth History ◽  
Important Development ◽  
Fossil Evidence

The major features of protist evolution are fraught with controversies, problems and few answers, especially in early Earth history. In general they are based on molecular data and fossil evidence that respectively provide a scaffold and details of eukaryotic phylogenetic and ecologic histories. 1. Their origin, inferred from molecular sequences, occurred very early (>;3Ga). They are a chimera of different symbiont-derived organelles, including possibly the nucleus. 2. The initial diversification of eukaryotes may have occurred early in geologic time. Six supergroups exist today, each with fossils known from the Proterozoic and Phanerozoic. 3. Sex, considered an important development, may have been inherited from bacteria. 4. Precambrian protists were largely pelagic cyst-bearing taxa, but benthic forms were probably quite diverse and abundant. 5. Protists gave rise to animals long before 600 Ma through the choanoflagellates, for which no fossil record exists. 6. Acritarchs and skeletonized protists radiated in the Cambrian (544-530 my). From then on, they radiated and became extinct at all the major events recorded in the metazoan fossil record. 7. Protists dominated major environments (shelves and reefs) starting with a significant radiation in the Ordovician, followed by extinctions and other radiations until most died out at the end of the Permian. 8. In the Mesozoic, new planktic protozoa and algae appeared and radiated in pelagic environments. 9. Modern protists are important at all trophic levels in the oceans and a huge number terrestrial, parasitic and symbiotic protists must have existed for much of geologic time as well. 10. The future of protists is likely in jeopardy, just like most reefal, benthic, and planktic metazoans. An urgent need to understand the role of protists in modern threatened oceans should be addressed soon.

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