OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

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Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed ≈6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage.

“…We used OCPAT (26) 1). If no homologous gene sequence was identified for a given species, this species was not included in the gene alignment.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Goodman

Sterner

Islam

et al. 2009

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“…Genes positively selected during human ancestry were determined with the assistance of OCPAT (54). Subsequent analyses were conducted using codeml (55), under the free-ratio model.…”

Section: Methodsmentioning

confidence: 99%

Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution

Uddin¹,

Goodman

Erez

et al. 2008

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The human genome evolution project seeks to reveal the genetic underpinnings of key phenotypic features that are distinctive of humans, such as a greatly enlarged cerebral cortex, slow development, and long life spans. This project has focused predominantly on genotypic changes during the 6-million-year descent from the last common ancestor (LCA) of humans and chimpanzees. Here, we argue that adaptive genotypic changes during earlier periods of evolutionary history also helped shape the distinctive human phenotype. Using comparative genome sequence data from 10 vertebrate species, we find a signature of human ancestry-specific adaptive evolution in 1,240 genes during their descent from the LCA with rodents. We also find that the signature of adaptive evolution is significantly different for highly expressed genes in human fetal and adult-stage tissues. Functional annotation clustering shows that on the ape stem lineage, an especially evident adaptively evolved biological pathway contains genes that function in mitochondria, are crucially involved in aerobic energy production, and are highly expressed in two energy-demanding tissues, heart and brain. Also, on this ape stem lineage, there was adaptive evolution among genes associated with human autoimmune and aging-related diseases. During more recent human descent, the adaptively evolving, highly expressed genes in fetal brain are involved in mediating neuronal connectivity. Comparing adaptively evolving genes from pre-and postnatal-stage tissues suggests that different selective pressures act on the development vs. the maintenance of the human phenotype.fetal ͉ human disease ͉ mitochondria ͉ placenta ͉ thyroid

“…The tool is available at http://homopan.wayne.edu/Pise/ ocpat.html. Details of the analysis pipeline are provided at http://homopan.wayne.edu/ocpat/index.html (54). Taxa included in the study were Homo sapiens (human) (36), Pan troglodytes (chimpanzee) (37), Macaca mulatta (Rhesus monkey) (38), Mus musculus (mouse) (39), Rattus norvegicus (rat) (40), Oryctolagus cuniculus (rabbit), Canis familiaris (dog) (41), Bos taurus (cow), Dasypus novemcinctus (armadillo), Loxodonta africana (African elephant), Echinops telfairi (tenrec), Monodelphis domestica (gray short-tailed opossum) (42), Gallus gallus (chicken) (43), and Xenopus tropicalis (Western clawed frog).…”

Section: Methodsmentioning

confidence: 99%

Genomics, biogeography, and the diversification of placental mammals

Wildman

Uddin²,

Opazo

et al. 2007

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161

128

Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively resolved the basal branching order within Placentalia. Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of crown placental mammals. Focusing on Ϸ1,700 conserved gene loci, those that have the more slowly evolving coding sequences, and using maximum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree reconstruction methods, we find from almost all results that a clade (the southern Atlantogenata) composed of Afrotheria and Xenarthra is the sister group of all other (the northern Boreoeutheria) crown placental mammals, among boreoeutherians Rodentia groups with Lagomorpha, and the resultant Glires is close to Primates. Only the NJ tree for nucleotide sequences separates Rodentia (murids) first and then Lagomorpha (rabbit) from the other placental mammals. However, this nucleotide NJ tree still depicts Atlantogenata and Boreoeutheria but minus Rodentia and Lagomorpha. Moreover, the NJ tree for amino acid sequences does depict the basal separation to be between Atlantogenata and a Boreoeutheria that includes Rodentia and Lagomorpha. Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.Atlantogenata ͉ Eutheria ͉ Notolegia ͉ phylogeny ͉ vicariance