Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.
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We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1-2 x 10(-9) substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%-20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively. (+info)
A molecular approach to comparative phylogeography of extant Malagasy lemurs.
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The lemurs of Madagascar provide an excellent model for exploring evolutionary diversification. This study investigates genetic divergence among most extant lemur taxa in relation to potential geographical boundaries to gene flow. For this purpose, approximately 2,400 bp of mitochondrial DNA (part of the COIII gene; ND3, ND4L, and ND4 genes; and five tRNAs) were sequenced in a total of 131 lemurs from 5 families, 12 genera, 25 species, and 18 subspecies to reconstruct phylogenetic relationships among them. The comprehensive range of taxa makes this a particularly suitable molecular data set to examine lemur evolution. Those data clearly reveal that the Betsiboka River acts as an isolating barrier between populations of lemurs in north-western Madagascar. The Tsiribihina River similarly serves as a barrier to gene flow between northern and southern populations of lemurs in central western Madagascar, whereas the Mahavavy River does not seem to lead to genetic isolation of lemur populations. Several discrepancies among molecular data, current taxonomy, and geographic distribution along the western coast emerged. Examination of geographical distribution of the taxa concerned in comparison with distribution boundaries of other lemur taxa in that region yielded explanations for these inconsistencies. Eulemur fulvus and Eulemur mongoz are the only lemur taxa that also occur outside Madagascar, on the Comoro Islands. Genetic data show no significant differentiation between Malagasy and Comorian populations of these species, supporting the interpretation that both were introduced only recently to the Comoro Islands. (+info)
Pollical oblique ligament in humans and non-human primates.
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A morphological study of the oblique ligament in the thumb is presented. The ligament was consistently described in human specimens and compared with dissections of non-human primates from different species. The oblique ligament was found in some, but not all, specimens in each of the following species examined: chimpanzee, orangutan, gibbon, anubis baboon, hamadryas baboon, squirrel monkey, lemur and marmoset. A revised identity of the oblique ligament is proposed as a reinforced distal border of a fibro-osseous annular pollical flexor sheath and whose function is not independent of the flexor sheath. The constant presence and tendinous trait of the pollical oblique ligament in humans, when compared with non-human primates, supports the notion that the oblique ligament strengthens the pollical flexor sheath in humans for restraint of the flexor pollicis longus tendon during forceful precision pinching. A derivation of the pollical oblique ligament is considered as representing a vestigial radial limb of a flexor pollicis superficialis tendon in the thumb. (+info)
Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates.
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Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of pseudogenes in the OR gene family is significantly larger in humans than in other apes and significantly larger in apes than in the mouse. To investigate the process of degeneration of the olfactory repertoire in primates, we estimated the proportion of OR pseudogenes in 19 primate species by surveying randomly chosen subsets of 100 OR genes from each species. We find that apes, Old World monkeys and one New World monkey, the howler monkey, have a significantly higher proportion of OR pseudogenes than do other New World monkeys or the lemur (a prosimian). Strikingly, the howler monkey is also the only New World monkey to possess full trichromatic vision, along with Old World monkeys and apes. Our findings suggest that the deterioration of the olfactory repertoire occurred concomitant with the acquisition of full trichromatic color vision in primates. (+info)
Three-dimensional structure and evolution of primate primary visual cortex.
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In this study, three-dimensional reconstructions of primate primary visual cortex (V1) were used to address questions about its evolution. The three-dimensional shape of V1 in anthropoids is significantly longer and narrower than in strepsirrhines. This difference is an effect of clade and is not due to differences in activity pattern or V1 size. New measurements of V1 volume were also provided in order to reassess V1 size differences between strepsirrhines and anthropoids. It was found that for a given lateral geniculate nucleus (LGN) volume, anthropoids have a significantly larger V1 than strepsirrhines do. This is important since LGN is the principal source of V1's input. Finally, independent contrasts analysis was used to examine the scaling of V1 relative to LGN, the rest of cortex, and the rest of the brain. It was confirmed that V1 scales with positive allometry relative to LGN. A number of possible explanations for scaling are discussed. V1 scaling may have to do with the tendency of large brains to be more compartmentalized than small brains, or V1 scaling might reflect the geometry of information representation. (+info)
Comparative morphology of the eye in primates.
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Comparative studies of mammalian eye morphology have shown that relative cornea size is an important correlate of visual ecology. Nocturnal species tend to have large corneas relative to eye size as an adaptation for increasing visual sensitivity. By contrast, diurnal species tend to have smaller corneas relative to eye size because their eye morphology maximizes visual acuity. Although qualitative analyses suggest that activity pattern may have a similar influence on eye morphology in primates, various current hypotheses have proposed that either diurnal anthropoids or diurnal lemurs have visual systems that diverge from those of other diurnal mammals. The goal of this analysis is to quantify the relationship between eye morphology and activity pattern in primates and to determine whether primates exhibit variation in eye morphology comparable to that of other mammals. Data on eye size and cornea size were collected for 147 specimens of 55 primate species. These data reveal that, within primate suborders, diurnal species have significantly smaller relative cornea sizes than nocturnal or cathemeral species. Both haplorhines and strepsirrhines thus exhibit variation in eye morphology that is consistent with functional expectations. However, comparisons between the two primate suborders demonstrate that haplorhines and strepsirrhines differ significantly in eye morphology. Whereas strepsirrhines have relative cornea sizes that are similar to nonprimate mammals of comparable activity pattern, diurnal anthropoids have smaller relative cornea sizes than most nonprimate mammals. This derived eye morphology in anthropoids probably evolved in the anthropoid stem lineage as a result of selection for highly acute diurnal vision. (+info)
An intermediate grade of finished genomic sequence suitable for comparative analyses.
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Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of "sequence finishing" remains expensive. Near-perfect finished sequence is an appropriate goal for the human genome and a small set of reference genomes; however, such a high-quality product cannot be cost-justified for large numbers of additional genomes, at least for the foreseeable future. Here we describe the generation and quality of an intermediate grade of finished genomic sequence (termed comparative-grade finished sequence), which is tailored for use in multispecies sequence comparisons. Our analyses indicate that this sequence is very high quality (with the residual gaps and errors mostly falling within repetitive elements) and reflects 99% of the total sequence. Importantly, comparative-grade sequence finishing requires approximately 40-fold less reagents and approximately 10-fold less personnel effort compared to the generation of near-perfect finished sequence, such as that produced for the human genome. Although applied here to finishing sequence derived from individual bacterial artificial chromosome (BAC) clones, one could envision establishing routines for refining sequences emanating from whole-genome shotgun sequencing projects to a similar quality level. Our experience to date demonstrates that comparative-grade sequence finishing represents a practical and affordable option for sequence refinement en route to comparative analyses. (+info)
Assembly of lipoprotein particles containing apolipoprotein-B: structural model for the nascent lipoprotein particle.
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Apolipoprotein B (apoB) is the major protein component of large lipoprotein particles that transport lipids and cholesterol. We have developed a detailed model of the first 1000 residues of apoB using standard sequence alignment programs (ClustalW and MACAW) and the MODELLER6 package for three-dimensional homology modeling. The validity of the apoB model was supported by conservation of disulfide bonds, location of all proline residues in turns and loops, and conservation of the hydrophobic faces of the two C-terminal amphipathic beta-sheets, betaA (residues 600-763) and betaB (residues 780-1000). This model suggests a lipid-pocket mechanism for initiation of lipoprotein particle assembly. In a previous model we suggested that microsomal triglyceride transfer protein might play a structural role in completion of the lipid pocket. We no longer think this likely, but instead propose a hairpin-bridge mechanism for lipid pocket completion. Salt-bridges between four tandem charged residues (717-720) in the turn of the hairpin-bridge and four tandem complementary residues (997-1000) at the C-terminus of the model lock the bridge in the closed position, enabling the deposition of an asymmetric bilayer within the lipid pocket. (+info)