Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence

Goodman, Morris; Porter, Calvin A.; Czelusniak, John; Page, Scott L.; Schneider, Horácio; Shoshani, Jeheskel; Gunnell, Gregg F.; Groves, Colin P.

doi:10.1006/mpev.1998.0495

Cited by 679 publications

(621 citation statements)

References 34 publications

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“…The third was the new branch-site model, Model D, also with k = 2 and k = 3 site categories. All models were implemented under two different tree topologies: (i) the expected species tree, derived from the literature (Goodman et al 1998;Goodman 1999;Meireles et al 1999;Page et al 1999), and (ii) the estimated gene tree. Gene trees were estimated using ML under the HKY85 substitution model (Hasegawa et al 1985) combined with a discrete gamma model of rate variation among sites (Yang 1994).…”

Section: Discussionmentioning

confidence: 99%

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

2004

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Abstract. The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (x) as a measure of selection on the protein, with x = 1, <1, and >1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in x among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different x's between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the e and c globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophilderived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the e and c globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.

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Section: Discussionmentioning

confidence: 99%

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

2004

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“…4). The RLN2 gene apparently originated between 29 and 18 mya (Goodman et al 1998;Steiper and Young 2009) in the last common ancestor of apes (Figs. 3, 4;Good-Avila et al 2009;Park et al 2008a;Wilkinson et al 2005), whereas the INSL4 gene arose from an RLN ancestor prior to the divergence of Euarchontoglires (Figs.…”

Section: Evolution Of the Rln/insl-like Genesmentioning

confidence: 99%

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

Hoffmann

Opazo

2010

J Mol Evol

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The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the relative contribution of whole genome duplications (WGDs) and tandem duplications to the observed diversity of genes is still an open question. Results from our comparative analyses favor a model of divergence post vertebrate WGDs in which a single-copy progenitor found in the last common ancestor of vertebrates experienced two rounds of WGDs before the functional differentiation that gave rise to the RLN and INSL genes. One of the resulting paralogs was subsequently lost, resulting in three proto-RLN/INSL genes on three separate chromosomes. Subsequent rounds of tandem gene duplication and divergence originated the set of paralogs found on a given cluster in extant vertebrates. Our study supports the hypothesis that differentiation of the RLN and INSL genes took place independently in each RLN/INSL cluster after the two WGDs during the evolutionary history of vertebrates. In addition, we show that INSL4 represents a relatively old gene that has been apparently lost independently in all Euarchontoglires other than apes and Old World monkeys, and that RLN2 derives from an ape-specific duplication.

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“…These five mammalian species span a total common ancestry of greater than 300 million years (Mya) 33,34 and sample three deep branches of the mammalian phylogeny (primates, rodents, and carnivores) that diverged from each other more than 80 Mya. Thus, elements showing a high degree of sequence similarity across this set of species are likely to be due to active conservation resulting from functional constraints rather than limited divergence time.…”

Section: Multispecies Comparative Genomics Of Ugt1amentioning

confidence: 99%

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster

et al. 2005

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Common polymorphisms within the human UGT1A gene locus are associated with irinotecan and tranilast toxicity. To uncover additional functional variation across this gene cluster, cross-species sequence comparisons were performed. Evolutionarily conserved segments (a total of 47.1 kb) were re-sequenced in 24 African-American, 24 European-American, and 24 Asian individuals, and 381 segregating sites (including 123 singletons) were identified. Highly conserved coding sites were less likely to be polymorphic than diverged sites (Po0.0001) but this pattern was not observed at noncoding sites (P ¼ 0.1025). Among coding variants, the distribution of those computationally predicted to affect function was skewed toward low frequencies. Some alleles occurred at similar frequencies in each population; others had wide disparities. Although strong linkage disequilibrium was detected among the hepatically expressed genes, the degree of linkage disequilibrium varied among populations. These results suggest that rare functional gene variants and inter-population variability must be considered in the interpretation of association studies between UGT1A and drug metabolism/toxicity phenotypes.

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Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence

Cited by 679 publications

References 34 publications

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster

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