ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2008
Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Structures and genetic information of control region in mitogenomes of Odonata.Mitochondrial DNA. Part B, Resources · 2024Article
- Mitochondrial genome comparison reveals the evolution of cnidarians.Ecology and evolution · 2023Article
- Comparative analysis of the mitochondrial genome ofParasitology · 2023Article
- Article
- Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration.Genome biology and evolution · 2021Article
- New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves.BMC genomics · 2020Article
- Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes ofRoyal Society open science · 2020Article
- Evidence for Adaptive Selection in the Mitogenome of a Mesoparasitic Monogenean FlatwormGenes · 2019Article
- Characterization of the complete mitochondrial genome ofZooKeys · 2019Article
- Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny.Parasites & vectors · 2017Article
- MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development.Scientific reports · 2017Article
- A critical appraisal of the use of microRNA data in phylogenetics.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization.BMC genomics · 2014Article
- The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites.PloS one · 2014Article
- Cnidarian phylogenetic relationships as revealed by mitogenomics.BMC evolutionary biology · 2013Article
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- The evolution of the animals: introduction to a Linnean tercentenary celebration.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2008Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also a potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, the presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing owing to their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, thereby reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.
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