Ancestral State Reconstruction of the Apoptosis Machinery in the Common Ancestor of Eukaryotes [PDF]
G3: Genes, Genomes, Genetics, 2018 Apoptotic cell death is a type of eukaryotic cell death. In animals, it regulates development, is involved in cancer suppression, and causes cell death during pathological aging of neuronal cells in neurodegenerative diseases such as Alzheimer’s ...
Joanna Klim +4 more
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Evolutionary insights into Felidae iris color through ancestral state reconstruction. [PDF]
iScience, 2023 SummaryThere have been almost no studies with an evolutionary perspective on eye (iris) color, outside of humans and domesticated animals. Extant members of the family Felidae have a great interspecific and intraspecific diversity of eye colors, in stark contrast to their closest relatives, all of which have only brown eyes.
Tabin JA, Chiasson KA.
europepmc +3 more sources
Optimized ancestral state reconstruction using Sankoff parsimony [PDF]
BMC Bioinformatics, 2009 Background Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to ...
Valiente Gabriel +3 more
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Accuracy of ancestral state reconstruction for non-neutral traits. [PDF]
Sci Rep, 2020 AbstractThe assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection. However, the accuracy of ancestral state reconstruction for non-neutral traits is poorly understood.
Holland BR +4 more
europepmc +4 more sources
Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction. [PDF]
Genome Biol Evol, 2021 AbstractModern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells ...
Skejo J +8 more
europepmc +7 more sources
Ancestral state reconstruction of metabolic pathways across pangenome ensembles. [PDF]
Microb Genom, 2020 As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny.
Psomopoulos FE +4 more
europepmc +5 more sources
Global Alignment of Molecular Sequences via Ancestral State Reconstruction [PDF]
Stochastic Processes and their Applications, 2009 Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on substitution ...
Andoni, Alexandr +3 more
core +7 more sources
WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States [PDF]
Applications in Plant Sciences, 2016 Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage.
Gruenstaeudl, Michael
core +7 more sources
Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks. [PDF]
PLoS ONE, 2019 Ancestral state reconstruction models use genetic data to characterize a group of organisms' common ancestor. These models have been applied to salmonellosis outbreaks to estimate the number of transmissions between different animal species that share ...
Samuel Bloomfield +7 more
doaj +2 more sources
Hidden State Prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses [PDF]
Frontiers in Microbiology, 2014 Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-
Jesse Robert Zaneveld +1 more
doaj +3 more sources