The human phylome

Huerta-Cepas, Jaime; Dopazo, Hernán; Dopazo, Joaquín; Gabaldón, Toni

doi:10.1186/gb-2007-8-6-r109

Cited by 154 publications

(202 citation statements)

References 93 publications

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“…They have also played a central role in the development of our understanding of how gene families evolve (38). Similar to results found in other amniote lineages (39, 40), genes associated with olfactory perception were over-represented among duplicated genes in crocodilians. Crocodilians possess a diverse olfactory receptor (OR) repertoire, and each species has approximately 1,000 ORs, half of which are likely functional (Table S21) (17) which is not unusual for a tetrapod genome.…”

Section: Gene Family Evolution Suggests Retention Of Ancestral Ortholsupporting

confidence: 83%

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green

Braun

Armstrong

et al. 2014

Science

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To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

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Section: Gene Family Evolution Suggests Retention Of Ancestral Ortholsupporting

confidence: 83%

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green

Braun

Armstrong

et al. 2014

Science

Self Cite

307

326

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“…Phylogenetic analyses performed on a limited number of Hydra sequences identified through RBHs indeed confirmed the orthology of these sequences (Wenger and Galliot 2013). Two types of methods are generally used to assign orthology: tree-based when relying on building phylogenetic trees (Page and Holmes 1998; Huerta-Cepas et al 2007; Hejnol et al 2009) and graph-based when relying on pairwise comparisons of large data sets (Overbeek et al 1999; Altenhoff and Dessimoz 2012). Building trees from large data sets is computationally intensive and requires supervision to include meaningful outgroups.…”

Section: Discussionmentioning

confidence: 99%

“…This approach detects the first occurrence in macroevolutionary times of proteins harboring similar domains but not necessarily orthologs. To systematically trace the origins of all human orthologs, Huerta-Cepas et al (2007) established a genomewide pipeline to derive the human phylome defined as a complete collection of all gene phylogenies of the human genome. To detect orthology, they automatized many steps of a “classical” phylogenetic analysis using phylogenetic tree and developed pipelines to reduce computing requirements.…”

Section: Introductionmentioning

confidence: 99%

“…Previous phylostratigraphic analyses (Domazet-Loso et al 2007; Huerta-Cepas et al 2007) rely on the idea that the coordinated emergence of genes sharing an involvement in a particular phenotype represents a “footprint” of the emergence of this phenotypic trait. Here, we used the inferences on human ortholog origins with the detailed annotation of the human proteome and the grouping of its proteins into biological processes (BPs) (Ashburner et al 2000) to quantify the most significant protein enrichments for BPs active in humans (huBPs) at specific evolutionary steps.…”

Section: Introductionmentioning

confidence: 99%

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Punctuated Emergences of Genetic and Phenotypic Innovations in Eumetazoan, Bilaterian, Euteleostome, and Hominidae Ancestors

Wenger

Galliot

2013

Genome Biology and Evolution

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Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans, bilaterians, euteleostomi (bony vertebrates), and hominidae, largely specific to each epoch, whereas early branching deuterostome and chordate phyla show very few innovations. Interestingly, groups of proteins that act together in their modern human functions often originated concomitantly, although the corresponding human phenotypes frequently emerged later. For example, the three cnidarians Acropora, Nematostella, and Hydra express a highly similar protein inventory, and their protein innovations can be affiliated either to traits shared by all eumetazoans (gut differentiation, neurogenesis); or to bilaterian traits present in only some cnidarians (eyes, striated muscle); or to traits not identified yet in this phylum (mesodermal layer, endocrine glands). The variable correspondence between phenotypes predicted from protein enrichments and observed phenotypes suggests that a parallel mechanism repeatedly produce similar phenotypes, thanks to novel regulatory events that independently tie preexisting conserved genetic modules.

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“…Examples of such tree collections are the phylomes that encompass trees for all sufficiently widespread genes in a given genome (1-4) or the “Forest of Life” (FOL) that consists of all trees for widespread genes in a representative set of organisms (5). It has been known since the early days of phylogenetics that trees built on the same set of species often have different topologies, especially when the set includes distant species, most notably, in prokaryotes (6, 7).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

Puigbò

Wolf

Koonin

2012

Methods in Molecular Biology

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Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a ‘species tree’.

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The human phylome

Abstract: The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.

Cited by 154 publications

References 93 publications

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Punctuated Emergences of Genetic and Phenotypic Innovations in Eumetazoan, Bilaterian, Euteleostome, and Hominidae Ancestors

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

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