scholarly journals Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates

2011 ◽  
Vol 8 (1) ◽  
pp. 143-146 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Morphological Character ◽  
Morphological Evolution ◽  
Character Evolution ◽  
Poisson Processes ◽  
Rate Model ◽  
Testing Hypotheses ◽  
Gamma Distributions ◽  
Character Compatibility ◽  
Probabilistic Processes ◽  
Modelling Approach

Rate distributions are important considerations when testing hypotheses about morphological evolution or phylogeny. They also have implications about general processes underlying character evolution. Molecular systematists often assume that rates are Poisson processes with gamma distributions. However, morphological change is the product of multiple probabilistic processes and should theoretically be affected by hierarchical integration of characters. Both factors predict lognormal rate distributions. Here, a simple inverse modelling approach assesses the best single-rate, gamma and lognormal models given observed character compatibility for 115 invertebrate groups. Tests reject the single-rate model for nearly all cases. Moreover, the lognormal outperforms the gamma for character change rates and (especially) state derivation rates. The latter in particular is consistent with integration affecting morphological character evolution.

mvClaim : an R package for multivariate general insurance claims severity modelling

2021 ◽  
pp. 1-17
Author(s):  
Sen Hu ◽  
T. Brendan Murphy ◽  
Adrian O’Hagan
Keyword(s):  
R Package ◽  
Finite Mixture ◽  
Current Version ◽  
Mixture Of Experts ◽  
Insurance Claim ◽  
General Insurance ◽  
Gamma Distributions ◽  
Approach Theory ◽  
Modelling Approach ◽  
Model Family

Abstract The mvClaim package in R provides flexible modelling frameworks for multivariate insurance claim severity modelling. The current version of the package implements a parsimonious mixture of experts (MoE) model family with bivariate gamma distributions, as introduced in Hu et al., and a finite mixture of copula regressions within the MoE framework as in Hu & O’Hagan. This paper presents the modelling approach theory briefly and the usage of the models in the package in detail. This package is hosted on GitHub at https://github.com/senhu/.

scholarly journals The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states?

2015 ◽  
Vol 5 (6) ◽  
pp. 20150049 ◽  
Author(s):  
Jennifer F. Hoyal Cuthill
Keyword(s):  
State Space ◽  
Morphological Evolution ◽  
Character Evolution ◽  
Character State ◽  
State Spaces ◽  
Phylogenetic Constraints ◽  
Finite State ◽  
Finite States ◽  
Close Relatives ◽  
Morphological State

Biological variety and major evolutionary transitions suggest that the space of possible morphologies may have varied among lineages and through time. However, most models of phylogenetic character evolution assume that the potential state space is finite. Here, I explore what the morphological state space might be like, by analysing trends in homoplasy (repeated derivation of the same character state). Analyses of ten published character matrices are compared against computer simulations with different state space models: infinite states, finite states, ordered states and an ‘inertial' model, simulating phylogenetic constraints. Of these, only the infinite states model results in evolution without homoplasy, a prediction which is not generally met by real phylogenies. Many authors have interpreted the ubiquity of homoplasy as evidence that the number of evolutionary alternatives is finite. However, homoplasy is also predicted by phylogenetic constraints on the morphological distance that can be traversed between ancestor and descendent. Phylogenetic rarefaction (sub-sampling) shows that finite and inertial state spaces do produce contrasting trends in the distribution of homoplasy. Two clades show trends characteristic of phylogenetic inertia, with decreasing homoplasy (increasing consistency index) as we sub-sample more distantly related taxa. One clade shows increasing homoplasy, suggesting exhaustion of finite states. Different clades may, therefore, show different patterns of character evolution. However, when parsimony uninformative characters are excluded (which may occur without documentation in cladistic studies), it may no longer be possible to distinguish inertial and finite state spaces. Interestingly, inertial models predict that homoplasy should be clustered among comparatively close relatives (parallel evolution), whereas finite state models do not. If morphological evolution is often inertial in nature, then homoplasy (false homology) may primarily occur between close relatives, perhaps being replaced by functional analogy at higher taxonomic scales.

Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes

2014 ◽  
Vol 62 (3) ◽  
pp. 362-373 ◽  
Author(s):  
Anna Karnkowska ◽  
Matthew S. Bennett ◽  
Donovan Watza ◽  
Jong Im Kim ◽  
Bożena Zakryś ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Character Evolution

scholarly journals Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria

2015 ◽  
Vol 282 (1821) ◽  
pp. 20152023 ◽  
Author(s):  
Mark N. Puttick ◽  
Gavin H. Thomas
Keyword(s):  
Body Mass ◽  
Fossil Record ◽  
Morphological Character ◽  
Morphological Evolution ◽  
Evolutionary Model ◽  
The Body ◽  
Evolutionary Patterns ◽  
Size Evolution ◽  
Body Size Evolution

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns.

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