ArticleBMC evolutionary biology2011
Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer.
Article in BMC evolutionary biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Mitochondrial genome ofFrontiers in plant science · 2026Article
- Secondary Plastids of Euglenids and Chlorarachniophytes Function with a Mix of Genes of Red and Green Algal Ancestry.Molecular biology and evolution · 2018Article
- Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.Scientific reports · 2016Article
- Article
- The evolution of photosynthesis in chromist algae through serial endosymbioses.Nature communications · 2014Article
- The eukaryotic tree of life from a global phylogenomic perspective.Cold Spring Harbor perspectives in biology · 2014Review
- Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates.Eukaryotic cell · 2014Article
- Computational approaches to species phylogeny inference and gene tree reconciliation.Trends in ecology & evolution · 2013Review
- Analysis of horizontal genetic transfer in red algae in the post-genomics age.Mobile genetic elements · 2013Article
- The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis.BMC genomics · 2013Article
- Next-generation phylogenomics.Biology direct · 2013Article
- Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.Genome biology and evolution · 2013Article
- Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates.Genome biology and evolution · 2013Article
- ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().Journal of phycology · 2012Article
- Algal genes in aplastidic eukaryotes are not necessarily derived from historical plastids.Mobile genetic elements · 2012Article
- Endosymbiotic and horizontal gene transfer in microbial eukaryotes: Impacts on cell evolution and the tree of life.Mobile genetic elements · 2012Article
- Controversies in modern evolutionary biology: the imperative for error detection and quality control.BMC genomics · 2012Article
- Article
- An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.Genome biology and evolution · 2012Article
- Interkingdom gene transfer may contribute to the evolution of phytopathogenicity in botrytis cinerea.Evolutionary bioinformatics online · 2012Article
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Abstract
A growing number of phylogenomic investigations from diverse eukaryotes are examining conflicts among gene trees as evidence of horizontal gene transfer. If multiple foreign genes from the same eukaryotic lineage are found in a given genome, it is increasingly interpreted as concerted gene transfers during a cryptic endosymbiosis in the organism's evolutionary past, also known as "endosymbiotic gene transfer" or EGT. A number of provocative hypotheses of lost or serially replaced endosymbionts have been advanced; to date, however, these inferences largely have been post-hoc interpretations of genomic-wide conflicts among gene trees. With data sets as large and complex as eukaryotic genome sequences, it is critical to examine alternative explanations for intra-genome phylogenetic conflicts, particularly how much conflicting signal is expected from directional biases and statistical noise. The availability of genome-level data both permits and necessitates phylogenomics that test explicit, a priori predictions of horizontal gene transfer, using rigorous statistical methods and clearly defined experimental controls.
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