Evolutionary history of the UCP gene family: gene duplication and selection

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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Functional evolutionary history of the mouseFgf gene family

Developmental Dynamics ◽

10.1002/dvdy.21388 ◽

2007 ◽

Vol 237 (1) ◽

pp. 18-27 ◽

Cited By ~ 242

Author(s):

Nobuyuki Itoh ◽

David M. Ornitz

Keyword(s):

Gene Family ◽

Evolutionary History ◽

History Of

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Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

10.1101/288530 ◽

2018 ◽

Author(s):

Mónica Lopes-Marques ◽

André M. Machado ◽

Raquel Ruivo ◽

Elza Fonseca ◽

Estela Carvalho ◽

...

Keyword(s):

Gene Family ◽

Metabolic Pathways ◽

Evolutionary History ◽

Gene Families ◽

Gene Repertoire ◽

Physiological Processes ◽

Complex Lipid ◽

History Of ◽

Enzyme Families ◽

Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

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Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

10.1101/766360 ◽

2019 ◽

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis Enrique Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Common Ancestor ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Common Ancestry ◽

Demethylation Pathway ◽

History Of ◽

New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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