Three nuclear protein-coding genes corroborate a recent phylogenomic model of the Branchiopoda (Crustacea) and provide estimates of the divergence times of the major branchiopodan taxa

Over the last few years, there has been an increasing amount of evidence for the de novo emergence of protein-coding genes, i.e. out of non-coding DNA. Here, we review the current literature and summarize the state of the field. We focus specifically on open questions and challenges in the study of de novo protein-coding genes such as the identification and verification of de novo-emerged genes. The greatest obstacle to date is the lack of high-quality genomic data with very short divergence times which could help precisely pin down the location of origin of a de novo gene. We conclude that, while there is plenty of evidence from a genetics perspective, there is a lack of functional studies of bona fide de novo genes and almost no knowledge about protein structures and how they come about during the emergence of de novo protein-coding genes. We suggest that future studies should concentrate on the functional and structural characterization of de novo protein-coding genes as well as the detailed study of the emergence of functional de novo protein-coding genes.

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Nuclear Protein-coding Genes in Phylogeny Reconstruction and Homology Assessment

Systematics Association Special Volumes - Molecular Systematics and Plant Evolution ◽

10.1201/9781439833278.ch12 ◽

1999 ◽

pp. 229-254 ◽

Cited By ~ 8

Author(s):

J Doyle ◽

J Doyle

Keyword(s):

Nuclear Protein ◽

Phylogeny Reconstruction ◽

Protein Coding ◽

Protein Coding Genes

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Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): An inference from nuclear protein-coding genes

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2011.07.022 ◽

2011 ◽

Vol 61 (3) ◽

pp. 628-638 ◽

Cited By ~ 82

Author(s):

Jenny Knapp ◽

Minoru Nakao ◽

Tetsuya Yanagida ◽

Munehiro Okamoto ◽

Urmas Saarma ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Nuclear Protein ◽

Protein Coding ◽

Protein Coding Genes

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Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

eLife ◽

10.7554/elife.05503 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 81

Author(s):

Christopher E Laumer ◽

Andreas Hejnol ◽

Gonzalo Giribet

Keyword(s):

Nuclear Protein ◽

Phylogenetic Signal ◽

Evolutionary Relationships ◽

Free Living ◽

Evolutionary Transitions ◽

Protein Coding ◽

Protein Coding Genes ◽

Evolutionary Innovation ◽

Genomic Signals ◽

Shed Light

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked ‘microturbellarian’ groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.

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Evaluating nuclear protein-coding genes for phylogenetic utility in beetles

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2008.05.023 ◽

2008 ◽

Vol 48 (3) ◽

pp. 877-891 ◽

Cited By ~ 125

Author(s):

Alexander L. Wild ◽

David R. Maddison

Keyword(s):

Nuclear Protein ◽

Protein Coding ◽

Protein Coding Genes

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Monophyletic blowflies revealed by phylogenomics

BMC Biology ◽

10.1186/s12915-021-01156-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Liping Yan ◽

Thomas Pape ◽

Karen Meusemann ◽

Sujatha Narayanan Kutty ◽

Rudolf Meier ◽

...

Keyword(s):

Ecosystem Services ◽

Maximum Likelihood ◽

Nuclear Protein ◽

Single Copy ◽

Phylogenomic Analysis ◽

Full Data ◽

Data Set ◽

Protein Coding ◽

Protein Coding Genes ◽

Ground Plan

Abstract Background Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. Results We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. Conclusions Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.

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