scholarly journals Model Adequacy Tests for Probabilistic Models of Chromosome‐Number Evolution

2020 ◽  
Author(s):  
Anna Rice ◽  
Itay Mayrose
Keyword(s):  
Chromosome Number ◽  
Probabilistic Models ◽  
Model Adequacy ◽  
Chromosome Number Evolution

scholarly journals Cladogenetic and Anagenetic Models of Chromosome Number Evolution: a Bayesian Model Averaging Approach

2016 ◽  
Author(s):  
William A. Freyman ◽  
Sebastian Höhna
Keyword(s):  
Chromosome Number ◽  
Reproductive Isolation ◽  
Probabilistic Models ◽  
Chromosome Evolution ◽  
Bayesian Model Averaging ◽  
Model Averaging ◽  
Chromosomal Evolution ◽  
Parameter Estimates ◽  
Chromosome Number Evolution ◽  
Gains And Losses

AbstractChromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE’s accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.

scholarly journals Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy

2009 ◽  
Vol 59 (2) ◽  
pp. 132-144 ◽  
Author(s):  
Itay Mayrose ◽  
Michael S. Barker ◽  
Sarah P. Otto
Keyword(s):  
Chromosome Number ◽  
Probabilistic Models ◽  
Chromosome Number Evolution

scholarly journals Model Adequacy Tests for Likelihood Models of Chromosome-Number Evolution

2020 ◽  
Author(s):  
Anna Rice ◽  
Itay Mayrose
Keyword(s):  
Chromosome Number ◽  
Real Data ◽  
Central Feature ◽  
List Type ◽  
Evolutionary Patterns ◽  
Model Adequacy ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Chromosome Number Evolution ◽  
Modelling Assumptions

SummaryChromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data.Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows to determine whether the model can generate data with similar characteristics as those found in the observed ones.We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitted model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present.The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods developments.

Phylogenetic Relationships and Chromosome Number Evolution in Passiflora

2006 ◽  
Vol 31 (1) ◽  
pp. 138-150 ◽  
Author(s):  
A. Katie Hansen ◽  
Lawrence E. Gilbert ◽  
Beryl B. Simpson ◽  
Stephen R. Downie ◽  
Armando C. Cervi ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Phylogenetic Relationships ◽  
Chromosome Number Evolution

Chromosome number evolution in dalbergioid legumes (Papilionoideae, Leguminosae)

2020 ◽  
Vol 43 (3) ◽  
pp. 575-587
Author(s):  
Ana Paula Moraes ◽  
Mohammad Vatanparast ◽  
Caroline Polido ◽  
André Marques ◽  
Gustavo Souza ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Number Evolution

Chromosome number evolution, biogeography and phylogenetic relationships inSalvia(Lamiaceae)

Webbia ◽  
2015 ◽  
Vol 70 (2) ◽  
pp. 293-312 ◽  
Author(s):  
Massoud Ranjbar ◽  
Azam Pakatchi ◽  
Zahra Babataheri
Keyword(s):  
Chromosome Number ◽  
Phylogenetic Relationships ◽  
Chromosome Number Evolution
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