A neutral explanation for the correlation of diversity with recombination rates in humans

One of the most striking findings to emerge from the study of genomic patterns of variation is that regions with lower recombination rates tend to have lower levels of intraspecific diversity but not of interspecies divergence. This uncoupling of variation within and between species has been widely interpreted as evidence that natural selection shapes patterns of genetic variability genomewide. We revisited the relationship between diversity, divergence, and recombination in humans, using data from closely related species and better estimates of recombination rates than previously available. We show that regions that experience less recombination have reduced divergence to chimpanzee and to baboon, as well as lower levels of diversity. This observation suggests that mutation and recombination are associated processes in humans, so that the positive correlation between diversity and recombination may have a purely neutral explanation. Consistent with this hypothesis, diversity levels no longer increase significantly with recombination rates after correction for divergence to chimpanzee.     

Genomic analysis of common chimpanzee major histocompatibility complex class I genes

To investigate how MHC class I genes have changed in the approximately 5 million years since chimpanzees and humans diverged, we characterized six genomic fragments ranging in size from 5.1 to 6.1 kb, each containing the complete coding region, introns, and flanking regions of one of the following chimpanzee class I genes: Patr-A, Patr-E, Patr-F, Patr-G, Patr-H, and Patr-J. In humans, these genes are closely linked within the class I region and are representatives of three distinct functional categories of class I genes: the highly polymorphic Ia genes (HLA-A), the conserved Ib genes (HLA-E, HLA-F, and HLA-G), and the class I pseudogenes (HLA-H and HLA-J). Southern blot analysis of chimpanzee and human class I genes produced nearly identical patterns, suggesting that the organization and linkage of these genes differs little in the two species. Comparison of the chimpanzee fragment sequences with their human orthologues revealed structural conservation of these genes yet differences in their degree of functional constraint. This is apparent in the location and nature of the amino acid changes between species and the substantial differences in levels of divergence at functional and nonfunctional sites. Additionally, there is no correlation between patterns of divergence at these sites and intraspecific variation, an observation explained by either appreciable gene conversion or high levels of recombination, the latter unlikely given the observed strong linkage disequilibrium of these loci.     

The chimpanzee and cynomolgus monkey erythrocyte immune adherence receptors are encoded by CR1-like genes

The human erythrocyte immune adherence (IA) receptor is the Mr 220,000 type one complement receptor, or CR1. Nonhuman primate IA receptors are comprised of a family of smaller erythrocyte complement receptors (E-CRs) of unknown origin. Recently, the Mr 65,000 baboon E-CR was identified as a glycophosphatidylinositol (GPI)-linked protein encoded by a partially duplicated CR1 gene termed CR1-like. The purpose of this study was to determine the genetic origin of the Mr 75,000 chimpanzee E-CR. Two previously identified cDNAs, an alternative splice product of CR1 termed CR1a and a chimpanzee form of CR1-like, were synthesized and amplified from chimpanzee bone marrow RNA, and transiently expressed in COS-7 cells. By SDS-PAGE, the CR1a protein had a relative mobility slightly greater than chimpanzee E-CR, whereas that of the CR1-like protein was slightly less. Affinity chromatography demonstrated that little chimpanzee CR1a bound to human C3i linked to activated thiol-Sepharose (C3i-ATS), while over 50% of both chimpanzee CR1-like and chimpanzee E-CR bound to C3i-ATS. Treatment with phosphatidylinositol-specific phospholipase C (PIPLC) to assess GPI linkage released E-CR from chimpanzee erythrocytes, and E-CR from cynomolgus monkey erythrocytes. Based on size, ligand-binding specificity, and PIPLC sensitivity, we conclude that the chimpanzee E-CR is encoded by the CR1-like gene. Furthermore, based on PIPLC sensitivity, the cynomolgus monkey E-CR is also likely encoded by a CR1-like sequence. Thus, CR1-like, which is a genetic element of unknown significance in humans, is the gene that encodes the erythrocyte IA receptor of many nonhuman primates.     

X-linked,polymorphic genetic variation of thyroxin-binding globulin (TBG) in baboons and screening of additional primates

X-linked polymorphic variation of thyroxin-binding globulin (TBG) is observed in several human groups. Isoelectric focusing of plasma samples labeled in vitro with [¹²⁵I]thyroxin, followed by autoradiography, also reveals genetically determined polymorphic electrophoretic variation in baboon TBG. The protein detected by this method in baboon plasma is immunologically similar to human TBG and is distinct from the other thyroxin-binding proteins, albumin and prealbumin. The isoelectric patterns of human and baboon TBG are very similar and both have an isoelectric range of pH 4.1 to 4.5. The baboon TBG polymorphism is inherited in a two-allele X-linked fashion, with a frequency of 72% for the common allele and 28% for the slow allele. A survey of seven other primate species including African green monkey, bonnet macaque, chimpanzee, crab-eating macaque, gorilla, rhesus monkey, and spider monkey revealed no polymorphic variation in TBG, although isoelectric patterns were similar to the human and baboon patterns. In addition, samples from pregnant chimpanzees demonstrate a pronounced quantitative anodal shift in relative band densities, a shift also observed in pregnant humans. This shift was not observed in samples from pregnant baboons. TBG should prove to be a useful X-linked genetic marker in baboons and provides a model of serum protein changes in pregnancy, at least in humans and chimpanzees.This research was supported by NIH Grant 2R01-EY-02388 and a Biomedical Research Support Grant from the Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston.     

Molecular genetic divergence of orang utan (Pongo pygmaeus) subspecies based on isozyme and two-dimensional gel electrophoresis

The orang utan (Pongo pygmaeus), as currently recognized, includes two geographically separated subspecies: Pongo pygmaeus pygmaeus, which resides on Borneo, and P. p. abelii, which inhabits Sumatra. At present, there is no known route of gene flow between the two populations except through captive individuals which have been released back into the wild over the last several decades. The two subspecies are differentiated by morphological and behavioral characters, and they can be distinguished by a subspecies specific pericentric chromosomal inversion. Nei-genetic distances were estimated between orang utan subspecies, gorilla, chimpanzee and humans using 44 isozyme loci and using 458 soluble fibroblast proteins which were resolved by two-dimensional gel electrophoresis. Phenetic analysis of both data sets supports the following conclusions: the orang utan subspecies distances are approximately 10 times closer to each other than they are to the African apes, and the orang utan subspecies are approximately as divergent as are the two chimpanzee species. Comparison of the genetic distances to genetic distance estimates done in the same laboratory under identical conditions reveals that the distance between Bornean vs. Sumatran orang utans is 5-10 times the distance measured between several pairs of subspecies including lions, cheetahs, and tigers. Near species level molecular genetic distances between orang utan subspecies would support the separate management of Bornean and Sumatran orang utans as evolutionary significant units (Ryder 1987). Evolutionary topologies were constructed from the distance data using both cladistic and phenetic methods. The majority of resulting trees affirmed previous molecular evolutionary studies that indicated that man and chimpanzee diverged from a common ancestor subsequent to the divergence of gorilla from the common ancestor.     

Visual discrimination of primate species based on faces in chimpanzees

Many primate studies have investigated discrimination of individual faces within the same species. However, few studies have looked at discrimination between primate species faces at the categorical level. This study systematically examined the factors important for visual discrimination between primate species faces in chimpanzees, including: colour, orientation, familiarity, and perceptual similarity. Five adult female chimpanzees were tested on their ability to discriminate identical and categorical (non-identical) images of different primate species faces in a series of touchscreen matching-to-sample experiments. Discrimination performance for chimpanzee, gorilla, and orangutan faces was better in colour than in greyscale. An inversion effect was also found, with higher accuracy for upright than inverted faces. Discrimination performance for unfamiliar (baboon and capuchin monkey) and highly familiar (chimpanzee and human) but perceptually different species was equally high. After excluding effects of colour and familiarity, difficulty in discriminating between different species faces can be best explained by their perceptual similarity to each other. Categorical discrimination performance for unfamiliar, perceptually similar faces (gorilla and orangutan) was significantly worse than unfamiliar, perceptually different faces (baboon and capuchin monkey). Moreover, multidimensional scaling analysis of the image similarity data based on local feature matching revealed greater similarity between chimpanzee, gorilla and orangutan faces than between human, baboon and capuchin monkey faces. We conclude our chimpanzees appear to perceive similarity in primate faces in a similar way to humans. Information about perceptual similarity is likely prioritized over the potential influence of previous experience or a conceptual representation of species for categorical discrimination between species faces.     

Bayesian Inference of Shared Recombination Hotspots Between Humans and Chimpanzees

Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies.     

Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants

Hepatitis B virus (HBV) infections are widely distributed in humans, infecting approximately one third of the world's population. HBV variants have also been detected and genetically characterised from Old World apes; Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Pongo pygmaeus (orang-utan), Nomascus nastusus and Hylobates pileatus (gibbons) and from the New World monkey, Lagothrix lagotricha (woolly monkey). To investigate species-specificity and potential for cross species transmission of HBV between sympatric species of apes (such as gorillas and chimpanzees in Central Africa) or between humans and chimpanzees or gorillas, variants of HBV infecting captive wild-born non-human primates were genetically characterised. 9 of 62 chimpanzees (11.3%) and two from 11 gorillas (18%) were HBV-infected (15% combined frequency), while other Old world monkey species were negative. Complete genome sequences were obtained from six of the infected chimpanzee and both gorillas; those from P. t .ellioti grouped with previously characterised variants from this subspecies. However, variants recovered from P. t. troglodytes HBV variants also grouped within this clade, indicative of transmission between sub-species, forming a paraphyletic clade. The two gorilla viruses were phylogenetically distinct from chimpanzee and human variants although one showed evidence for a recombination event with a P.t.e.-derived HBV variant in the partial X and core gene region. Both of these observations provide evidence for circulation of HBV between different species and sub-species of non-human primates, a conclusion that differs from the hypothesis if of strict host specificity of HBV genotypes.     

A sympatric sibling species complex of Petrotilapia Trewavas from Lake Malawi analysed by enzyme electrophoresis (Pisces: Cichlidae)

The protein electromorphs of three taxa of Petrotilapia , referred to in earlier works as sibling species, were examined by starch-gel electrophoresis. The results indicated that, for the three taxa, no alternative fixed alleles occurred for any of the 25 loci (enzymes) examined. However, heterogeneous gene frequencies were indicated at seven polymorphic loci. This suggests that either the taxa are isolated 'sibling' species which recently diverged, or that they are 'incipient' species with minimal gene flow between morphs. The genetic and field data lend support to the hypothesis that sympatric splitting of morphs could be important in the explosive radiation of the cichlidae.     

Recently mobilized transposons in the human and chimpanzee genomes

Transposable genetic elements are abundant in the genomes of most organisms, including humans. These endogenous mutagens can alter genes, promote genomic rearrangements, and may help to drive the speciation of organisms. In this study, we identified almost 11,000 transposon copies that are differentially present in the human and chimpanzee genomes. Most of these transposon copies were mobilized after the existence of a common ancestor of humans and chimpanzees, approximately 6 million years ago. Alu, L1, and SVA insertions accounted for >95% of the insertions in both species. Our data indicate that humans have supported higher levels of transposition than have chimpanzees during the past several million years and have amplified different transposon subfamilies. In both species, approximately 34% of the insertions were located within known genes. These insertions represent a form of species-specific genetic variation that may have contributed to the differential evolution of humans and chimpanzees. In addition to providing an initial overview of recently mobilized elements, our collections will be useful for assessing the impact of these insertions on their hosts and for studying the transposition mechanisms of these elements.     

Habitat differentiation among three Nigeria–Cameroon chimpanzee (Pan troglodytes ellioti) populations

Ecological niche models (ENMs) are often used to predict species distribution patterns from datasets that describe abiotic and biotic factors at coarse spatial scales. Ground‐truthing ENMs provide important information about how these factors relate to species‐specific requirements at a scale that is biologically relevant for the species. Chimpanzees are territorial and have a predominantly frugivorous diet. The spatial and temporal variation in fruit availability for different chimpanzee populations is thus crucial, but rarely depicted in ENMs. The genetic and geographic distinction within Nigeria–Cameroon chimpanzee (Pan troglodytes ellioti) populations represents a unique opportunity to understand fine scale species‐relevant ecological variation in relation to ENMs. In Cameroon, P. t. ellioti is composed of two genetically distinct populations that occupy different niches: rainforests in western Cameroon and forest–woodland–savanna mosaic (ecotone) in central Cameroon. We investigated habitat variation at three representative sites using chimpanzee‐relevant environmental variables, including fruit availability, to assess how these variables distinguish these niches from one another. Contrary to the assumption of most ENM studies that intact forest is essential for the survival of chimpanzees, we hypothesized that the ecotone and human‐modified habitats in Cameroon have sufficient resources to sustain large chimpanzee populations. Rainfall, and the diversity, density, and size of trees were higher at the rainforest. The ecotone had a higher density of terrestrial herbs and lianas. Fruit availability was higher at Ganga (ecotone) than at Bekob and Njuma. Seasonal variation in fruit availability was highest at Ganga, and periods of fruit scarcity were longer than at the rainforest sites. Introduced and secondary forest species linked with anthropogenic modification were common at Bekob, which reduced seasonality in fruit availability. Our findings highlight the value of incorporating fine scale species‐relevant ecological data to create more realistic models, which have implications for local conservation planning efforts.     

Electrophoretically estimated genetic distance and divergence time between chimpanzee and man

Amount of genetic differentiation between chimpanzee and man was estimated from the result of comparative electrophoretic screening of blood protein variations at 32 independent genetic loci. TheNei's genetic distance (D) was calculated as 0.4514, and from this value the divergence time between the two species was estimated as 2.26 million years; considering the variation among amino-acid substitution rate in different proteins, the corrected figures were given as genetic distance of 0.5706 and divergence time of 2.85 million years. This genetic difference is considered too small the two species to be allocated in different families, in accordance with the results of the similar kind of analyses byKing andWilson (1975) and Bruce andAyala (1979). Discussions were made for a discrepancy between the divergence times estimated by using and not by using the splitting time recognized by paleoprimatologists as a reference, and for the difference in the estimations made in different laboratories.     

The geographic apportionment of mitochondrial genetic diversity in east African chimpanzees, Pan troglodytes schweinfurthii

This study is a geographically systematic genetic survey of the easternmost subspecies of chimpanzee, Pan troglodytes schweinfurthii. DNA was noninvasively collected in the form of shed hair from chimpanzees of known origin in Uganda, Rwanda, Tanzania, and Zaire. Two hundred sixty-two DNA sequences from hypervariable region 1 of which of the mitochondrial control region were generated. Eastern chimpanzees display levels of mitochondrial genetic variation which are low and which are similar to levels observed in humans (Homo sapiens). Also like humans, between 80% and 90% of the genetic variability within the eastern chimpanzees is apportioned within populations. Spatial autocorrelation analysis shows that genetic similarity between eastern chimpanzees decreases clinically with distance, in a pattern remarkably similar to one seen for humans separated by equivalent geographic distances. Eastern chimpanzee mismatch distributions (frequency distributions of pairwise genetic differences between individuals) are similar in shape to those for humans, implying similar population histories of recent demographic expansion. The overall pattern of genetic variability in eastern chimpanzees is consistent with the hypothesis that the subject has responded demographically to paleoclimatically driven changes in the distribution of eastern African forests during the recent Pleistocene.      

Conservation and variation in human and common chimpanzee CD94 and NKG2 genes.

To assess polymorphism and variation in human and chimpanzee NK complex genes, we determined the coding-region sequences for CD94 and NKG2A, C, D, E, and F from several human (Homo sapiens) donors and common chimpanzees (Pan troglodytes). CD94 is highly conserved, while the NKG2 genes exhibit some polymorphism. For all the genes, alternative mRNA splicing variants were frequent among the clones obtained by RT-PCR. Alternative splicing acts similarly in human and chimpanzee to produce the CD94B variant from the CD94 gene and the NKG2B variant from the NKG2A gene. Whereas single chimpanzee orthologs for CD94, NKG2A, NKG2E, and NKG2F were identified, two chimpanzee paralogs of the human NKG2C gene were defined. The chimpanzee Pt-NKG2CI gene encodes a protein similar to human NKG2C, whereas in the chimpanzee Pt-NKG2CII gene the translation frame changes near the beginning of the carbohydrate recognition domain, causing premature termination. Analysis of a panel of chimpanzee NK cell clones showed that Pt-NKG2CI and Pt-NKG2CII are independently and clonally expressed. Pt-NKG2CI and Pt-NKG2CII are equally diverged from human NKG2C, indicating that they arose by gene duplication subsequent to the divergence of chimpanzee and human ancestors. Genomic DNA from 80 individuals representing six primate species were typed for the presence of CD94 and NKG2. Each species gave distinctive typing patterns, with NKG2A and CD94 being most conserved. Seven different NK complex genotypes within the panel of 48 common chimpanzees were due to differences in Pt-NKG2C and Pt-NKG2D genes.     

Multiple origins of the octoploid Scandinavian endemic Draba cacu minum: electrophoretic and morphological evidence

The octoploid Draba cacuminum (Brassicaceae) is one of the few endemic species in Scandinavia and has frequently been considered an example supporting the glacial survival theory. Two subspecies, ssp. cacuminum in southern Norway and ssp. angusticarpa in northern Scandinavia, have been described and suggested to be geographically diverged remnants of a more continuously distributed ancestor. To test an alternative hypothesis of independent origins of similar octoploids in different areas, we investigated populations of D. cacuminum and its possible progenitors using enzyme electrophoresis and morphological analysis. Electrophoretic analysis of progeny of D. cacuminum revealed high levels of fixed heterozygosity, suggesting that the species is a genetic alloploid. Fixed electrophoretic differences among the populations and additivity of electrophoretic phenotypes indicate that the octoploid D. cacuminum has originated at least three times by alloploidizations involving different populations of the hexaploid D. norvegica and a diploid species, possibly D. fladnizensis. Electrophoretic and morphometric data suggest that populations of D. cacuminum with broad siliculae have originated from populations of D. norvegica that had broad siliculae, and that populations of D. cacuminum with narrow siliculae have originated from populations of D. norvegica that had narrow siliculae. However, the electrophoretic and morphometric variation within D. cacuminum did not correspond to the geographic origin of the populations, and the previously described subspecies could not be recognized. Draba cacuminum gives no relevant information on the glacial survival theory; the polyploidizations may have occurred in postglacial time as well as in pre-Weichselian periods.     

Detection and genetic characterization of enteroviruses circulating among wild populations of chimpanzees in Cameroon: relationship with human and simian enteroviruses

Enteroviruses (EVs), members of the family Picornaviridae, are a genetically and antigenically diverse range of viruses causing acute infections in humans and several Old World monkey (OWM) species. Despite their known wide distribution in primates, nothing is currently known about the occurrence, frequency, and genetic diversity of enteroviruses infecting apes. To investigate this, 27 chimpanzee and 27 gorilla fecal samples collected from undisturbed jungle areas with minimal human contact in Cameroon were screened for EVs. Four chimpanzee samples were positive, but none of the gorilla samples were positive. Genetic characterization of the VP1, VP4, and partial VP2 genes, the 5' untranslated region, and partial 3Dpol sequences enabled chimpanzee-derived EVs to be identified as (i) the species A type, EV76, (ii) a new species D type assigned as EV111, along with a human isolate from the Democratic Republic of Congo previously described by the International Committee on the Taxonomy of Viruses, and (iii) a new species B type (assigned as EV110) most closely related to, although a distinct type from, the SA5 isolate recovered from a vervet monkey. The identification of EVs infecting chimpanzees related to those circulating in human and OWM populations provides evidence for cross-species transmission of EVs between primates. However, the direction of transfer and the existence of primate sources of zoonotic enterovirus infections in humans require further investigation of population exposure and more extensive characterization of EVs circulating in wild ape populations.     

Revisiting protein heterozygosity in plants��nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris

Allozyme variation has been and continues to be a major source of information on the level of genetic variation among plant species. Deciphering the molecular basis of electrophoretic variation is essential for understanding the forces affecting the protein level variation. In this study, the relationship between allozyme heterozygosity and nucleotide diversity in plants is investigated among and within species. Allozyme and nucleotide diversity in 27 plant species was reviewed. At the multilocus level, the two methods are congruent: a clear correlation between the two measures of genetic diversity among plant species was observed, strengthening the view that effective population size is the major determinant of genome-wide diversity. Nucleotide diversity at six allozyme coding genes (6pgdB, aco, gdh, gotC, mdhA, and mdhB) in conifer Pinus sylvestris was investigated jointly with electrophoretic data. Single non-synonymous charge-changing mutations were found together with electrophoretic alleles that consequently were mutationally unique. Synonymous site nucleotide diversity (point estimate of θ _W—0.009 per bp) and silent site divergence from Pinus pinaster at allozyme coding loci were at comparable levels with other loci in the species. Linkage disequilibrium was extensive compared to earlier estimates from P. sylvestris and other trees, spanning several kilobases. Allozyme coding genes had an excess of closely related haplotypes whose frequency has recently increased possibly as a result of partial selective sweeps or balancing selection, but complex demographic effects cannot be excluded.     

Examination of hominid evolution by DNA sequence homology

Hominoid phylogeny was investigated in terms of unique DNA sequence homologies. In comparisons from the human standpoint the ΔTe₅₀ DNA values were Man 0, chimpanzee 0·7, gorilla 1·4, gibbon 2·7, orangutan 2·9, and African green monkey 5·7. In comparisons from the orangutan standpoint the ΔTe₅₀ DNA values were orangutan 0, chimpanzee 1·8, Man 1·9, gorilla 2·3, gibbon 2·4 and African green monkey 4·3. These results indicate that chimpanzee and gorilla are cladistically closer to Man than to orangutan and other primates, and that gorilla DNA may have diverged slightly more from the ancestral state than chimpanzee or human DNA. Comparisons from chimpanzee and gorilla DNA standpoints are needed to achieve a more definitive picture of hominoid phylogeny.