Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps nodes of the gene tree to the corresponding points of the species tree, and thus helps to interpret the gene family history. In this paper, we study the case when both trees are unrooted and their edge lengths are known exactly. The goal is to root them and to find a reconciliation that agrees with the edge lengths. We show a linear-time algorithm for finding the set of all possible root locations, which is a significant improvement compared to the previous O(N3logN) algorithm.

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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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Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes

BMC Evolutionary Biology ◽

10.1186/1471-2148-10-308 ◽

2010 ◽

Vol 10 (1) ◽

pp. 308 ◽

Cited By ~ 63

Author(s):

Matteo Citarelli ◽

Sachin Teotia ◽

Rebecca S Lamb

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Polymerase Gene ◽

History Of

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Evolutionary History of the 11p15 Human Mucin Gene Family

Journal of Molecular Evolution ◽

10.1007/pl00006276 ◽

1998 ◽

Vol 46 (1) ◽

pp. 102-106 ◽

Cited By ~ 51

Author(s):

Jean-Luc Desseyn ◽

Marie-Pierre Buisine ◽

Nicole Porchet ◽

Jean-Pierre Aubert ◽

Pierre Degand ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Mucin Gene ◽

History Of

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Evolutionary history of the Asr gene family

Gene ◽

10.1016/j.gene.2006.05.010 ◽

2006 ◽

Vol 378 ◽

pp. 74-83 ◽

Cited By ~ 50

Author(s):

Nicolás Frankel ◽

Fernando Carrari ◽

Esteban Hasson ◽

Norberto D. Iusem

Keyword(s):

Gene Family ◽

Evolutionary History ◽

History Of ◽

Asr Gene

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Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

Invertebrate Systematics ◽

10.1071/is16067 ◽

2017 ◽

Vol 31 (6) ◽

pp. 765 ◽

Cited By ~ 3

Author(s):

Phillip Barden ◽

Brendon Boudinot ◽

Andrea Lucky

Keyword(s):

Evolutionary History ◽

Morphological Evolution ◽

Sister Group ◽

Morphological Characters ◽

Fossil Material ◽

First Case ◽

History Of ◽

The Impact ◽

Surprising Discovery

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

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Evolutionary history of the MTG gene family in vertebrates

Proceedings of the National Academy of Sciences of Belarus Biological Series ◽

10.29235/1029-8940-2019-64-4-391-402 ◽

2019 ◽

Vol 64 (4) ◽

pp. 391-402

Author(s):

A. I. Kavaleuskaya ◽

T. V. Ramanouskaya

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Protein Sequences ◽

Stem Cell Differentiation ◽

Gene Products ◽

Functional Diversification ◽

Rates Of Evolution ◽

Different Types ◽

History Of ◽

Transcriptional Corepressors

The highly conserved MTG gene family includes three homologs in vertebrates (MTG8, MTGR1, MTG16) encoding transcriptional corepressors, which are important in haemopoiesis, neurogenesis and epithelial stem cell differentiation. These genes are of particular interest because they are involved in translocations, associated with different types of cancer. Looking at how this gene family evolved might provide insights into history of its structural and functional diversification. We have performed a phylogenetic analysis of MTG nucleotide and protein sequences to examine the evolutionary events. The domain organization of MTG gene products was clarified, the mechanism of appearance of the first MTG gene was revealed and the ancestor taxon was determined. Also the mechanism of MTG gene family emergence was established. In addition, analysis of the rates of evolution acting on individual domains was made, and conservative positions within each gene of MTG family were determined.

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Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

10.1101/043455 ◽

2016 ◽

Cited By ~ 1

Author(s):

Michael S. Barker ◽

Zheng Li ◽

Thomas I. Kidder ◽

Chris R. Reardon ◽

Zhao Lai ◽

...

Keyword(s):

Gene Family ◽

Linkage Map ◽

Evolutionary History ◽

Genome Duplication ◽

Nuclear Gene ◽

Flowering Plants ◽

The Family ◽

History Of ◽

Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

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