scholarly journals Ancestral State Reconstruction, Rate Heterogeneity, and the Evolution of Reptile Viviparity

2015 ◽  
Vol 64 (3) ◽  
pp. 532-544 ◽  
Author(s):  
Benedict King ◽  
Michael S. Y. Lee
Keyword(s):  
Ancestral State Reconstruction ◽  
Ancestral State ◽  
Rate Heterogeneity ◽  
State Reconstruction ◽  
Reconstruction Rate

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

2017 ◽  
Vol 84 (1) ◽  
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.

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

2012 ◽  
Vol 81 (1) ◽  
pp. 43-54 ◽  
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.

Phylogenetics, ancestral state reconstruction, and a new infrageneric classification of Scleria (Cyperaceae) based on three DNA markers

Taxon ◽  
2016 ◽  
Vol 65 (3) ◽  
pp. 444-466 ◽  
Author(s):  
Kenneth Bauters ◽  
Pieter Asselman ◽  
David A. Simpson ◽  
A. Muthama Muasya ◽  
Paul Goetghebeur ◽  
...  
Keyword(s):  
Dna Markers ◽  
Ancestral State Reconstruction ◽  
Ancestral State ◽  
Infrageneric Classification ◽  
State Reconstruction
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