Evolutionary Change in Locomotion Close to the Origin of Amniotes Inferred From Trackway Data in an Ancestral State Reconstruction Approach

Among amniote and non-amniote tetrapod trackways from late Carboniferous to early Permian deposits, certain trackway measures vary notably. Some of this variability can be attributed to evolutionary changes in trackmaker anatomy and locomotion style close to the origin of amniotes. Here we demonstrate that steps in early amniote locomotion evolution can be addressed by applying methods of ancestral state reconstruction on trackway data – a novel approach in tetrapod ichnology. Based on (a) measurements of 186 trackways referred to the Carboniferous and early Permian ichnogenera Batrachichnus, Limnopus, Hylopus, Amphisauropus, Matthewichnus, Ichniotherium, Dimetropus, Tambachichnium, Erpetopus, Varanopus, Hyloidichnus, Notalacerta and Dromopus, (b) correlation of these ichnotaxa with specific groups of amphibian, reptiliomorph, synapsid, and reptilian trackmakers based on imprint morphology and (c) known skeletal-morphology-based phylogenies of the supposed trackmakers, we infer ancestral states for functionally controlled trackway measures in a maximum likelihood approach. The most notable finding of our analysis is a concordant change in trackway parameters within a series of ancestral amniote trackmakers, which reflects an evolutionary change in locomotion: In the ancestors of amniotes and diadectomorphs, an increase in body size was accompanied by a decrease in (normalized) gauge width and glenoacetabular length and by a change in imprint orientation toward a more trackway-parallel and forward-pointing condition. In the subsequent evolution of diadectomorph, synapsid and reptilian trackmakers after the diversification of the clades Cotylosauria (Amniota + Diadectomorpha) and Amniota, stride length increased whereas gauges decreased further or remained relatively narrow within most lineages. In accordance with this conspicuous pattern of evolutionary change in trackway measures, we interpret the body size increase as an underlying factor that triggered the reorganization of the locomotion apparatus. The secondary increase in stride length, which occurred convergently within distinct groups, is interpreted as an increase in locomotion capability when the benefits of reorganization came into effect. The track-trackmaker pair of Ichniotherium sphaerodactylum and Orobates pabsti from the early Permian Bromacker locality of the Thuringian Forest, proposed in earlier studies as a suitable ancestral amniote track-trackmaker model, fits relatively well with our modeled last common ancestor of amniotes – with the caveat that the Bromacker material is younger and some of the similarities appear to be due to convergence.

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Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction

10.1101/089805 ◽

2016 ◽

Cited By ~ 1

Author(s):

Gilles Didier

Keyword(s):

Asymmetry Parameter ◽

Ancestral State Reconstruction ◽

The Body ◽

Time Dependent ◽

Compact Representation ◽

Reconstruction Method ◽

Evolutionary Trend ◽

Ancestral State ◽

State Reconstruction ◽

The Asymmetry

AbstractThe time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost).A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony.This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated to the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

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Ancestral State Reconstruction of Body Size in the Caniformia (Carnivora, Mammalia): The Effects of Incorporating Data from the Fossil Record

Systematic Biology ◽

10.1080/10635150500541698 ◽

2006 ◽

Vol 55 (2) ◽

pp. 301-313 ◽

Cited By ~ 152

Author(s):

John A. Finarelli ◽

John J. Flynn

Keyword(s):

Body Size ◽

Fossil Record ◽

Ancestral State Reconstruction ◽

Ancestral State ◽

State Reconstruction

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Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae

Applied and Environmental Microbiology ◽

10.1128/aem.01553-17 ◽

2017 ◽

Vol 84 (1) ◽

Cited By ~ 3

Author(s):

Dong-Dong Yang ◽

Gustavo M. de Billerbeck ◽

Jin-jing Zhang ◽

Frank Rosenzweig ◽

Jean-Marie Francois

Keyword(s):

Saccharomyces Cerevisiae ◽

Alcohol Dehydrogenase ◽

Lignin Degradation ◽

Molecular Mechanisms ◽

Ancestral State Reconstruction ◽

Ancestral State ◽

State Reconstruction ◽

Content Type ◽

Aryl Aldehydes ◽

Aryl Aldehyde

ABSTRACTHomology searches indicate thatSaccharomyces cerevisiaestrain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). YeastAADgenes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes,AAD4andAAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeastAADgenes are undergoing pseudogenization. The 5′ sequence ofAAD15has been deleted from the genome. Repair of anAAD3missense mutation at the catalytically essential Tyr73residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates thatAADgenes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeastAADgenes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeastAADgene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role forAADgenes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications.IMPORTANCEFunctional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the firstSaccharomyces cerevisiaegenome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-memberAADfamily. Here, we demonstrate that proteins encoded by two members of this family exhibit aliphatic and aryl-aldehyde reductase activity, and further that such activity can be recovered from pseudogenizedAADgenes via ancestral-state reconstruction. The phylogeny of yeastAADgenes suggests that these proteins may have played an important ancestral role in detoxifying aromatic aldehydes in ligninolytic fungi. However, in yeast adapted to niches rich in sugars,AADgenes become subject to mutational erosion. Our findings shed new light on the selective pressures and molecular mechanisms by which genes undergo pseudogenization.

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Ancestral state reconstruction in Peronospora provides further evidence for host jumping as a key element in the diversification of obligate parasites

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2021.107321 ◽

2021 ◽

pp. 107321

Author(s):

Sebastian Ploch ◽

Julia Kruse ◽

Young-Joon Choi ◽

Hjalmar Thiel ◽

Marco Thines

Keyword(s):

Ancestral State Reconstruction ◽

Ancestral State ◽

State Reconstruction ◽

Obligate Parasites ◽

Host Jumping

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The phylogenetic position of the solitary zoanthid genus Sphenopus (Cnidaria: Hexacorallia)

Contributions to Zoology ◽

10.1163/18759866-08101003 ◽

2012 ◽

Vol 81 (1) ◽

pp. 43-54 ◽

Cited By ~ 14

Author(s):

James D. Reimer ◽

Meifang Lin ◽

Takuma Fujii ◽

David J.W. Lane ◽

Bert W. Hoeksema

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Solid Substrate ◽

Ancestral State Reconstruction ◽

Phylogenetic Position ◽

Ancestral State ◽

State Reconstruction ◽

Unique Character ◽

The Family ◽

Southern Taiwan

The zoanthid genus Sphenopus (Cnidaria: Anthozoa: Zoantharia), like many other brachycnemic zoanthids, is found in shallow subtropical and tropical waters, but is uniquely unitary (solitary, monostomatous), azooxanthellate, and free-living. With sparse knowledge of its phylogenetic position, this study examines the phylogenetic position of Sphenopus within the family Sphenopidae utilizing specimens from southern Taiwan and Brunei collected in 1999-2011, and furthermore analyzes the evolution of its unique character set via ancestral state reconstruction analyses. Phylogenetic analyses surprisingly show Sphenopus to be phylogenetically positioned within the genus Palythoa, which is colonial (polystomatous), zooxanthellate, and attached to solid substrate. Ancestral state reconstruction strongly indicates that the unique characters of Sphenopus have evolved recently within Palythoa and only in the Sphenopuslineage. These results indicate that zoanthid body plans can evolve with rapidity, as in some other marine invertebrates, and that the traditional definitions of zoanthid genera may need reexamination.

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