Many ways to die, one way to arrive: how selection acts through pregnancy.

When considering selective forces shaping human evolution, the importance of pregnancy to fitness should not be underestimated. Although specific mortality factors may only impact upon a fraction of the population, birth is a funnel through which all individuals must pass. Human pregnancy places exceptional energetic, physical, and immunological demands on the mother to accommodate the needs of the fetus, making the woman more vulnerable during this time-period. Here, we examine how metabolic imbalances, infectious diseases, oxygen deficiency, and nutrient levels in pregnancy can exert selective pressures on women and their unborn offspring. Numerous candidate genes under selection are being revealed by next-generation sequencing, providing the opportunity to study further the relationship between selection and pregnancy. This relationship is important to consider to gain insight into recent human adaptations to unique diets and environments worldwide.

Genomic and evolutionary analyses of asymmetrically expressed genes in human fetal left and right cerebral cortex.

In the human brain, the left and right hemispheres are anatomically asymmetric and have distinctive cognitive function, although the molecular basis for this asymmetry has not yet been characterized. We compared gene expression levels in the perisylvian regions of human left-right cortex at fetal weeks 12, 14, and 19 using serial analysis of gene expression (SAGE). We identified dozens of genes with evidence of differential expression by SAGE and confirmed these by quantitative reverse transcriptase-polymerase chain reaction. Most genes with differential levels of expression in the left and right hemispheres function in signal transduction and gene expression regulation during early cortical development. By comparing genes differentially expressed in left and right fetal brains with those previously reported to be differently expressed in human versus chimpanzee adult brains, we identified a subset of genes that shows evidence of asymmetric expression in humans and altered expression levels between chimps and humans. We also compared the coding sequences of genes differentially expressed between left and right hemispheres and found genes that show both asymmetric expression and evidence of positive evolutionary selection in the primate lineage leading to humans. Our results identify candidate genes involved in the evolution of human cerebral cortical asymmetry.

The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans (Pongo pygmaeus).

The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5' of alpha-2 globin. The alpha-globin-type gene is notable for having four amino acid replacements relative to the orangutan's alpha-1 and alpha-2 globin genes, with no synonymous differences. Pairwise K(a)/K(s) methods and likelihood ratio tests (LRTs) revealed that the evolutionary history of the alpha-globin-type gene has been marked by either neutral or positive evolution, but not purifying selection. A comparative analysis of the amino acid replacements of the alpha-globin-type gene with human hemoglobinopathies and hemoglobin structure showed that two of the four replaced sites are members of the same molecular bond, one that is crucial to the proper functioning of the hemoglobin molecule. This suggested an adaptive evolutionary change. Functionally, this locus may result in a thalassemia-like phenotype in orangutans, possibly as an adaptation to combat Plasmodium.

The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus).

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.

Comparative primate genomics: the year of the chimpanzee.

This is the year of the chimpanzee genome. Chimpanzee chromosome 22 has been sequenced and soon will be followed by the whole genome, and thousands of chimpanzee cDNA sequences are available for comparative analysis. Not only does this genomic information allow us to identify human-specific changes in particular genes that are potentially under selection, but also to understand molecular evolutionary dynamics characterizing the two most closely related mammalian genomes sequenced so far. Studies comparing gene expression in chimpanzees and other closely related primates reveal significant species differences in brain, liver and fibroblasts. New empirical data, in combination with models of speciation, are giving insight into how humans and chimpanzees speciated.

Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome.

Joubert syndrome is a congenital brain malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioral disturbances. Here we identified a locus associated with Joubert syndrome, JBTS3, on chromosome 6q23.2-q23.3 and found three deleterious mutations in AHI1, the first gene to be associated with Joubert syndrome. AHI1 is most highly expressed in brain, particularly in neurons that give rise to the crossing axons of the corticospinal tract and superior cerebellar peduncles. Comparative genetic analysis of AHI1 indicates that it has undergone positive evolutionary selection along the human lineage. Therefore, changes in AHI1 may have been important in the evolution of human-specific motor behaviors.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of the cerebral cortex in mammals and especially primates. Mutations in ASPM, which encodes the human homologue of a fly protein essential for spindle function, are the most common known cause of MCPH. Here we have isolated large genomic clones containing the complete ASPM gene, including promoter regions and introns, from chimpanzee, gorilla, orangutan, and rhesus macaque by transformation-associated recombination cloning in yeast. We have sequenced these clones and show that whereas much of the sequence of ASPM is substantially conserved among primates, specific segments are subject to high Ka/Ks ratios (nonsynonymous/synonymous DNA changes) consistent with strong positive selection for evolutionary change. The ASPM gene sequence shows accelerated evolution in the African hominoid clade, and this precedes hominid brain expansion by several million years. Gorilla and human lineages show particularly accelerated evolution in the IQ domain of ASPM. Moreover, ASPM regions under positive selection in primates are also the most highly diverged regions between primates and nonprimate mammals. We report the first direct application of TAR cloning technology to the study of human evolution. Our data suggest that evolutionary selection of specific segments of the ASPM sequence strongly relates to differences in cerebral cortical size.

New World monkey phylogeny based on X-linked G6PD DNA sequences.

The Platyrrhini, or New World monkeys, are an infraorder of Primates comprised of 16 genera. Molecular phylogenetic analyses have consistently sorted these genera into three groups: the Pitheciidae (e.g., saki and titi monkeys), Atelidae (e.g., spider and howler monkeys), and Cebidae (e.g., night monkeys, squirrel monkeys, and tamarins). No consensus has emerged on the relationships among the three groups or within the Cebidae. Here, approximately 0.8 kb of newly generated intronic DNA sequence data from the X-linked glucose-6-phosphate dehydrogenase (G6PD) locus have been collected from nine New World monkey taxa to examine these relationships. These data are added to 1.3 kb of previously generated G6PD intronic DNA sequence data [Mol. Phylogenet. Evol. 11 (1999) 459]. Using distance and parsimony-based techniques, G6PD sequences provide support for an initial bifurcation between the Pitheciidae and the remaining platyrrhines, linking Atelidae and Cebidae as sister taxa. Bayesian methods provided a conflicting phylogeny with Atelidae as outgroup. Within the Cebidae, a sister relation between Aotus and the Cebus/Saimiri clade is favored by parsimony analysis, but not by other analyses. Potential reasons for the difficulty in resolving family level New World monkey phylogenetics are discussed.

Genetic sex identification in orangutans.

To date, no established protocol for genetic sex identification in orangutans (Pongo pygmaeus) exists. In nearly all apes (gibbons, gorillas, chimpanzees, and humans), genetic sex identification is possible using the amelogenin gene because copies located on X and Y chromosomes have different sizes. Here we report that orangutan sex identification can be resolved through multiplex polymerase chain reaction (PCR) of the Y-linked SRY locus and the amelogenin locus. PCR amplifications of orangutan amelogenin produces one fragment size in both sexes, while SRY amplifies only in males. This protocol will allow primatologists to identify the sex of orangutans through genetic analysis.

The Tre2 (USP6) oncogene is a hominoid-specific gene.

Gene duplication and domain accretion are thought to be the major mechanisms for the emergence of novel genes during evolution. Such events are thought to have occurred at early stages in the vertebrate lineage, but genomic sequencing has recently revealed extensive amplification events during the evolution of higher primates. We report here that the Tre2 (USP6) oncogene is derived from the chimeric fusion of two genes, USP32 (NY-REN-60), and TBC1D3. USP32 is an ancient, highly conserved gene, whereas TBC1D3 is derived from a recent segmental duplication, which is absent in most other mammals and shows rapid amplification and dispersal through the primate lineage. Remarkably, the chimeric gene Tre2 exists only in the hominoid lineage of primates. This hominoid-specific oncogene arose as recently as 21-33 million years ago, after proliferation of the TBC1D3 segmental duplication in the primate lineage. In contrast to the broad expression pattern of USP32 and TBC1D3, expression of Tre2 is testis-specific, a pattern proposed for novel genes implicated in the emergence of reproductive barriers. The sudden emergence of chimeric proteins, such as that encoded by Tre2, may have contributed to hominoid speciation.

Chorionic gonadotropin has a recent origin within primates and an evolutionary history of selection.

Chorionic gonadotropin (CG) is a critical signal in establishing pregnancy in humans and some other primates, but this placentally expressed hormone has not been found in other mammalian orders. The gene for one of its two subunits (CG beta subunit [CGbeta]) arose by duplication from the luteinizing hormone beta subunit gene (LHbeta), present in all mammals tested. In this study, 14 primate and related mammalian species were examined by Southern blotting and DNA sequencing to determine where in mammalian phylogeny the CGbeta gene originated. Bats (order Chiroptera), flying lemur (order Dermoptera), strepsirrhine primates, and tarsiers do not have a CGbeta gene, although they possess one copy of the LHbeta gene. The CGbeta gene first arose in the common ancestor of the anthropoid primates (New World monkeys, Old World monkeys, apes, and humans), after the anthropoids diverged from tarsiers. At least two subsequent duplication events occurred in the catarrhine primates, all of which possess multiple CGbeta copies. The LHbeta-CGbeta family of genes has undergone frequent gene conversion among the catarrhines, as well as periods of strong positive selection in the New World monkeys (platyrrhines). In addition, newly generated DNA sequences from the promoter of the CG alpha subunit gene indicate that platyrrhine monkeys use a different mechanism of alpha gene expression control than that found in catarrhines.