Convergent rates of protein evolution identify novel targets of sexual selection in primates.

Sexual selection is the differential reproductive success of individuals, resulting from competition for mates, mate choice, or success in fertilization. In primates, this selective pressure often leads to the development of exaggerated traits which play a role in sexual competition and successful reproduction. In order to gain insight into the mechanisms driving the development of sexually selected traits, we used an unbiased genome-wide approach across 21 primate species to correlate individual rates of protein evolution to relative testes size and sexual dimorphism in body size, 2 anatomical hallmarks of sexual selection in mammals. Among species with presumed high levels of sperm competition, we detected strong conservation of testes-specific proteins responsible for spermatogenesis and ciliary form and function. In contrast, we identified accelerated evolution of female reproductive proteins expressed in the vagina, cervix, and fallopian tubes in these same species. Additionally, we found accelerated protein evolution in lymphoid tissue, indicating that adaptive immune functions may also be influenced by sexual selection. This study demonstrates the distinct complexity of sexual selection in primates revealing contrasting patterns of protein evolution between male and female reproductive tissues.

Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes.

The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2ß gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.

Admixture between historically isolated mitochondrial lineages in captive Western gorillas: recommendations for future management.

Although captive populations of western gorilla have been maintained in the United States for over a century, little is known about the geographic origins and genetic composition of the current zoo population. Furthermore, although previous mitochondrial analyses have shown that free-range gorilla populations exhibit substantial regional differentiation, nothing is known of the extent to which this variation has been preserved in captive populations. To address these questions, we combined 379 pedigree records with data from 52 mitochondrial sequences to infer individual haplogroup affiliations, geographical origin of wild founders and instances of inter-breeding between haplogroups in the United States captive gorilla population. We show that the current captive population contains all major mitochondrial lineages found within wild western lowland gorillas. Levels of haplotype diversity are also comparable to those found in wild populations. However, the majority of captive gorilla matings have occurred between individuals with different haplogroup affiliations. Although restricting crosses to individuals within the same haplogroup would preserve the phylogeographic structure present in the wild, careful management of captive populations is required to minimize the risk of drift and inbreeding. However, when captive animals are released back into the wild, we recommend that efforts should be made to preserve natural phylogeographic structure.

Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography.

The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives.

Glycerophosphocholine utilization by Candida albicans: role of the Git3 transporter in virulence.

Candida albicans contains four ORFs (GIT1,2,3,4) predicted to encode proteins involved in the transport of glycerophosphodiester metabolites. Previously, we reported that Git1, encoded by ORF 19.34, is responsible for the transport of intact glycerophosphoinositol but not glycerophosphocholine (GroPCho). Here, we report that a strain lacking both GIT3 (ORF 19.1979) and GIT4 (ORF 19.1980) is unable to transport [(3)H]GroPCho into the cell. In the absence of a GroPCho transporter, C. albicans can utilize GroPCho via a mechanism involving extracellular hydrolysis. Upon reintegration of either GIT3 or GIT4 into the genome, measurable uptake of [(3)H]GroPCho is observed. Transport assays and kinetic analyses indicate that Git3 has the greater transport velocity. We present evidence that GDE1 (ORF 19.3936) codes for an enzyme with glycerophosphodiesterase activity against GroPCho. Homozygous deletion of GDE1 results in a buildup of internal GroPCho that is restored to wild type levels by reintegration of GDE1 into the genome. The transcriptional regulator, Pho4, is shown to regulate the expression of GIT3, GIT4, and GDE1. Finally, Git3 is shown to be required for full virulence in a mouse model of disseminated candidiasis, and Git3 sequence orthologs are present in other pathogenic Candida species. In summary, we have characterized multiple aspects of GroPCho utilization by C. albicans and have demonstrated that GroPCho transport plays a key role in the growth of the organism in the host.

A reference map of the membrane proteome of Enterococcus faecalis.

Enterococcus faecalis is a gram-positive bacterium that is part of the indigenous microbiotica of humans and animals as well as an opportunistic pathogen. In this study, we have fractionated the membrane proteome of E. faecalis and identified many of its constituents by mass spectrometry. We present blue native-/SDS-PAGE reference maps that contain 102 proteins. These proteins are important for cellular homeostasis, virulence, and antibiotic intervention. Intriguingly, many proteins with no known function were also identified, indicating that there are substantial gaps in the knowledge of this organism's biology. On a more limited scale, we also provide insight into the composition of membrane protein complexes. This study is a first step toward elucidating the membrane proteome of E. faecalis, which is critical for a better understanding of how this bacterium interacts with a host and with the extracellular milieu.

Hominoid seminal protein evolution and ancestral mating behavior.

Hominoid mating systems show extensive variation among species. The degree of sexual dimorphism in body size and canine size varies among primates in accordance with their mating system, as does the testes size and the consistency of ejaculated semen, in response to differing levels of sperm competition. To investigate patterns of evolution at hominoid seminal proteins and to make inferences regarding the mating systems of extinct taxa, we sequenced the entire coding region of the prostate-specific transglutaminase (TGM4) gene in human, chimpanzee, bonobo, western lowland gorilla, eastern lowland gorilla, orangutan, and siamang, including multiple humans, chimps, and gorillas. Partial DNA sequence of the coding regions was also obtained for one eastern lowland gorilla at the semenogelin genes (SEMG1 and SEMG2), which code for the predominant proteins in semen. Patterns of nucleotide variation and inferred protein sequence change were evaluated within and between species. Combining the present data with previous studies demonstrates a high rate of amino acid substitutions, and low intraspecific variation, at seminal proteins in Pan, presumably driven by strong sperm competition. Both gorilla species apparently possess nonfunctional TGM4, SEMG1, and SEMG2 genes, suggesting that gorillas have had low sperm competition, and therefore their current polygynous mating system, for a long time before their divergence. Similarly, orangutans show longstanding stasis at TGM4, which may be interpreted as evidence for an unchanging mating system for most of their evolution after their divergence from African apes. In contrast to the great apes, the data from humans could be interpreted as evidence of fluctuations between different mating systems or alternatively as a relaxed functional constraint in these proteins. It is our hope that this study is a first step toward developing a model to predict ancestral mating systems from extant molecular data to complement interpretations from the fossil record.

Stalking metal-linked dimers.

Protein dimerization is essential for cellular processes including regulation and biosignalling. While protein-protein interactions can occur through many modes, this review will focus on those interactions mediated through the binding of metal ions to the proteins. Selected techniques used to study protein-protein interactions, including size exclusion chromatography, mass spectrometry, affinity chromatography, and frontal zone chromatography, are described as applied to the characterization of the Enterococcus hirae protein CopY. CopY forms a homodimer to control the expression of proteins involved in the homeostasis of cellular copper levels. At the center of the CopY dimerization interaction lies a metal binding motif, -CxCxxxxCxC-, capable of binding Zn(II) or Cu(I). The binding of metal to this cysteine hook motif, one within each monomer, is critical to the dimerization interaction. The CopY dimer is also stabilized by hydrophobic interactions between the two monomers. The cysteine hook metal binding motif has been identified in numerous other uncharacterized proteins across the biological spectrum. The prevalence of the motif gives evidence to the biological relevance of this motif, both as a metal binding domain and as a dimerization motif.

Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains.

Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. Although the genomic sequence has generated much interest, only three complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307-16,315 bp) from 10 inbred rat strains (that are standard laboratory models around the world) and 2 wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (nonsynonymous substitutions) in 12 of the 13 protein coding genes within the mitochondrial genome. There were 11 single nucleotide polymorphisms within the tRNA genes, six in the 12S rRNA, and 12 in the 16S rRNA including 3 insertions/deletions. We found 14 single nucleotide polymorphisms and 2 insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, whereas the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.

Nuclear integrations of mitochondrial DNA in gorillas.

Great ape systematics, particularly at the species level and below, is currently under debate, due in part to the recent influx of molecular data. The phylogenies of previously published mitochondrial control region (or D-loop) DNA sequences in gorillas show deep splits within West African gorillas (Gorilla gorilla gorilla), and very high levels of nucleotide diversity in this subspecies. Here we demonstrate that several previously reported D-loop haplotypes from West African gorillas are in all likelihood nuclear integrations of mitochondrial DNA. Revised estimates of the amount and pattern of mitochondrial DNA diversity in gorillas are provided, revealing two reciprocally monophyletic and highly divergent groups of gorillas, concurrent with their geographic distribution.

Nucleotide diversity in gorillas.

Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (pi) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that pi in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated pi to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA pi values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.

Comparative recombination rates in the rat, mouse, and human genomes.

Levels of recombination vary among species, among chromosomes within species, and among regions within chromosomes in mammals. This heterogeneity may affect levels of diversity, efficiency of selection, and genome composition, as well as have practical consequences for the genetic mapping of traits. We compared the genetic maps to the genome sequence assemblies of rat, mouse, and human to estimate local recombination rates across these genomes. Humans have greater overall levels of recombination, as well as greater variance. In rat and mouse, the size of the chromosome and proximity to telomere have less effect on local recombination rate than in human. At the chromosome level, rat and mouse X chromosomes have the lowest recombination rates, whereas human chromosome X does not show the same pattern. In all species, local recombination rate is significantly correlated with several sequence variables, including GC%, CpG density, repetitive elements, and the neutral mutation rate, with some pronounced differences between species. Recombination rate in one species is not strongly correlated with the rate in another, when comparing homologous syntenic blocks of the genome. This comparative approach provides additional insight into the causes and consequences of genomic heterogeneity in recombination.

Identification of candidate disease genes by EST alignments, synteny, and expression and verification of Ensembl genes on rat chromosome 1q43-54.

We aligned Incyte ESTs and publicly available sequences to the rat genome and analyzed rat chromosome 1q43-54, a region in which several quantitative trait loci (QTLs) have been identified, including renal disease, diabetes, hypertension, body weight, and encephalomyelitis. Within this region, which contains 255 Ensembl gene predictions, the aligned sequences clustered into 568 Incyte genes and gene fragments. Of the Incyte genes, 261 (46%) overlapped 184 (72%) of the Ensembl gene predictions, whereas 307 were unique to Incyte. The rat-to-human syntenic map displays rearrangement of this region on rat chr. 1 onto human chromosomes 9 and 10. The mapping of corresponding human disease phenotypes to either one of these chromosomes has allowed us to focus in on genes associated with disease phenotypes. As an example, we have used the syntenic information for the rat Rf-1 disease region and the orthologous human ESRD disease region to reduce the size of the original rat QTL to only 11.5 Mb. Using the syntenic information in combination with expression data from ESTs and microarrays, we have selected a set of 66 candidate disease genes for Rf-1. The combination of the results from these different analyses represents a powerful approach for narrowing the number of genes that could play a role in the development of complex diseases.

BAC resources for the rat genome project.

Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male Brown Norway (BN/SsNHsd) rat as a DNA source long before plans for rat genome sequencing had been launched. The second library was prepared from a highly inbred female (BN/SsNHsd/MCW) rat in support of the rat genome sequencing project. The use of an inbred rat strain is essential to avoid problems with genome assembly resulting from the difficulty of distinguishing haplotype variation from variation among duplicons. We have demonstrated the suitability of the library by using a detailed quality assessment of large insert sizes, narrow size distribution, consistent redundancy for many markers, and long-range continuity of BAC contig maps. The widespread use of the two libraries as an integral part of the rat genome project has led to the database annotations for many clones, providing rat researchers with a rich resource of BAC clones that can be screened in silico for genes of interest.

Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen.

The hominoid primates (apes and humans) exhibit remarkable diversity in their social and sexual behavioral systems. This is reflected in many ways in their anatomy and physiology. For example, the testes and seminal vesicles are relatively large in species with high sperm competition like the chimpanzee and small in species with low or no sperm competition like the gorilla. Additionally, the chimpanzee is the only hominoid primate known to produce a firm copulatory plug, which presumably functions in sperm competition by blocking insemination of subsequent males. Here we examine the molecular evolution of the semenogelin genes (SEMG1 and SEMG2), which code for the predominant structural proteins in human semen. High molecular weight complexes of these proteins are responsible for the viscous gelatinous consistency of human semen; their rodent homologs are responsible for the formation of a firm copulatory plug. Chimpanzees have an expanded SEMG1 gene caused by duplications of tandem repeats, each encoding 60 amino acids, resulting in a protein nearly twice as long as that of humans. In contrast, at both SEMG1 and SEMG2 we observed several gorilla haplotypes that contain at least one premature stop codon. We suggest that these structural changes in the semenogelin proteins that have arisen since the human-chimpanzee-gorilla split may be responsible for the physiological differences between these species ejaculated semen that correlate with their sociosexual behavior.

Low nucleotide diversity in chimpanzees and bonobos.

Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (pi) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the pi value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The pi values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (N(e)) in the human lineage after the human-chimpanzee divergence, because a reduction in N(e) has a stronger effect on mtDNA diversity than on nuclear DNA diversity. Sequence data from this article have been deposited with the GenBank Data libraries under accession nos. AY 275957-AY 277244.