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PubMed1995

Population genetics of dinucleotide (dC-dA)n.(dG-dT)n polymorphisms in world populations.

We have characterized eight dinucleotide (dC-dA)n.(dG-dT)n repeat loci located on human chromosome 13q in eight human populations and in a sample of chimpanzees. Even though there is substantial variation in allele frequencies at each locus, at a given locus the most frequent alleles are shared by all human populations. The level of heterozygosity is reduced in isolated or small populations, such as the Pehuenche Indians of Chile, the Dogrib of Canada, and the New Guinea highlanders. On the other hand, larger average heterozygosities are observed in large and cosmopolitan populations, such as the Sokoto population from Nigeria and German Caucasians. Conformity with Hardy-Weinberg equilibrium is generally observed at these loci, unless (a) a population is isolated or small or (b) the repeat motif of the locus is not perfect (e.g., D13S197). Multilocus genotype probabilities at these microsatellite loci do not show departure from the independence rule, unless the loci are closely linked. The allele size distributions at these (CA)n loci do not follow a strict single-step stepwise-mutation model. However, this features does not compromise the ability to detect population affinities, when these loci are used simultaneously. The microsatellite loci examined here are present and, with the exception of the locus D13S197, are polymorphic in the chimpanzees, showing an overlapping distribution of allele sizes with those observed in human populations.

Alleles↗
PubMed1993

Characterization of the patterns of polymorphism in a "cryptic repeat" reveals a novel type of hypervariable sequence.

Alternating purine and pyrimidine repeats (RY(i)) are an abundant source of polymorphism. The subset with long tandem repeats of GT or AC (GT(i)) have been studied extensively, but cryptic RY(i) (i.e., no single tandem repeat predominates) have received little attention. The factor IX gene has a polymorphic cryptic RY(i) of 142-216 bp. Previously, there were four known polymorphic alleles, of the form AB, A2B, A2B2, and A3B2, where A = (GT)(AC)3(AT)3(GT)(AT)4 and B = A with an additional 3' AT dinucleotide. To further characterize this locus, we examined more than 1,700 additional human chromosomes and determined the sequences of the homologous sites in orangutans and chimpanzees. The novel alleles found in humans expand the repertoire of A/B alleles to A0-4B1 and A1-3B2. The AnB2 series are abundant in Caucasians but are absent in blacks and Asians. Conversely, the A0B1 allele is common in blacks but is not found in more than 1,700 Caucasian chromosomes. The data are compatible with a model in which recombination is more frequent than polymerase slippage at this locus. In orangutans, the RY(i) is present, but the sequence is markedly different. An A/B-type of pattern was discerned in which B differs from A by an additional six (AT) dinucleotides at the 3' end. In chimpanzees, the size of the RY(i) locus was greatly expanded, and the sequence showed a novel pattern of hypervariability in which there are many tandem repeats of the form (GT)n(AC)o(AT)p(GT)q(AT)s, where n, o, p, q, and s are different integers. The sequences of the factor IX intron 1 cryptic RY(i) in three primates provide perspective on the range of possible patterns of polymorphism. Analysis of the patterns suggests how the RY(i) can be conserved during evolution, while the precise sequence varies.

Alleles↗
PubMed1995

Evolution and the origins of man: clues from complete sequences of hominoid mitochondrial DNA.

Dating the origins of Homo sapiens sapiens is a central problem in human population genetics and anthropology. Do we descend from a single recent ancestral population in Africa, or from multiple ancestral populations in various regions of the world which one million years ago simultaneously began developing into H.s.sapiens? The high substitution rate of mitochondrial DNA (mtDNA) makes this molecule suitable for genealogical and chronological research on closely related hominoid species. We have analyzed the complete mtDNA sequences of three humans (African, European and Japanese) and two African apes (common chimpanzee and gorilla) in an attempt to estimate more accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated at an approximately constant rate. Under the assumption, supported by the fossil record, that the orangutan and African apes diverged 13 million years ago, we have previously obtained 4.7 million years as the divergence time between humans and chimpanzees. Using this date, we calibrated the substitution rates at synonymous sites and in the displacement-loop region as 4.03 and 7.25 x 10(-8)/site/year, respectively. Based on these rates together with the observation that the African sequence presented here is most diverged from all other human sequences, we inferred the age of the last common ancestor of the human mtDNAs as 140,000 +/- 18,000 years. The result strongly supports the recent African origin of modern humans, H.s. sapiens.

Africa↗
PubMed2003

Variability of Broca's area homologue in African great apes: implications for language evolution.

The cortical circuits subserving neural processing of human language are localized to the inferior frontal operculum and the posterior perisylvian region. Functional language dominance has been related to anatomical asymmetry of Broca's area and the planum temporale. The evolutionary history of these asymmetric patterns, however, remains obscure. Although testing of hypotheses about the evolution of language areas requires comparison to homologous regions in the brains of our closest living relatives, the great apes, to date little is known about normal interindividual variation of these regions in this group. Here we focus on Brodmann's area 44 in African great apes (Pan troglodytes and Gorilla gorilla). This area corresponds to the pars opercularis of the inferior frontal gyrus (IFG), and has been shown to exhibit both gross and cytoarchitectural asymmetries in humans. We calculated frequencies of sulcal variations and mapped the distribution of cytoarchitectural area 44 to determine whether its boundaries occurred at consistent macrostructural landmarks. A considerable amount of variation was found in the distribution of the inferior frontal sulci among great ape brains. The inferior precentral sulcus in particular was often bifurcated, which made it impossible to determine the posterior boundary of the pars opercularis. In addition, the distribution of Brodmann's area 44 showed very little correspondence to surface anatomy. We conclude that gross morphologic patterns do not offer substantive landmarks for the measurement of Brodmann's area 44 in great apes. Whether or not Broca's area homologue of great apes exhibits humanlike asymmetry can only be resolved through further analyses of microstructural components.

Africa↗
PubMed2004

Mitochondrial DNA genealogy of chimpanzees in the Nimba mountains and Bossou, West Africa.

The chimpanzee populations of the Bossou and Nimba regions in West Africa were genetically surveyed to 1) reveal the genetic relationship between the Bossou and Nimba populations, and 2) elucidate the evolutionary relationship between the Bossou-Nimba and other West African populations. The chimpanzee group at Bossou is characterized by its small population size, no evidence of contact with neighboring populations, and no female immigration. It is believed that most females and adolescent males emigrate from this population. To reveal the genetic signature of these characteristics, we examined the genetic diversity of Bossou and two neighboring populations (Seringbara and Yealé) in the Nimba Mountains by sequencing approximately 605 bp of the mitochondrial DNA (mtDNA) control region. A total of 20 distinct mtDNA variants were observed from 56 sequences of noninvasively collected, anonymous samples. Nucleotide diversity in the Nimba Mountain populations was 0.03-0.04, and did not differ significantly from that in the Bossou population. Very few mitochondrial variants are shared among the sites sampled, which suggests that there is little gene flow involving mtDNA. Nevertheless, no clear population structures were revealed in either population. A comparison with published sequences from West African chimpanzees (Pan troglodytes verus) indicates that the variants observed in the Bossou and Nimba regions are scattered throughout the subspecies, rather than clustered according to geographic region. This suggests that the Bossou-Nimba populations derived only recently from the common ancestral population of the West African chimpanzees, and did not pass through a bottleneck.

Animals↗
PubMed2025

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Quercus↗
PubMed2006

Molar development in common chimpanzees (Pan troglodytes).

Numerous studies have reported on enamel and dentine development in hominoid molars, although little is known about intraspecific incremental feature variation. Furthermore, a recent histological study suggested that there is little or no time between age at chimpanzee crown completion and age at molar eruption, which is unlikely given that root growth is necessary for tooth eruption. The study presented here redefines growth standards for chimpanzee molar teeth and examines variation in incremental features. The periodicity of Retzius lines in a relatively large sample was found to be 6 or 7 days. The number of Retzius lines and cuspal enamel thickness both vary within a cusp type, among cusps, and among molars, resulting in marked variation in formation time. Daily secretion rate is consistent within analogous cuspal zones (inner, middle, and outer enamel) within and among cusp types and among molar types. Significantly increasing trends are found from inner to outer cuspal enamel (3 to 5 microns/day). Cuspal initiation and completion sequences also vary, although sequences for mandibular molar cusps are more consistent. Cusp-specific formation time ranges from approximately 2 to 3 years, increasing from M1 to M2, and often decreasing from M2 to M3. These times are intermediate between radiographic studies and a previous histological study, although both formation time within cusps and overlap between molars vary considerably. Cusp-specific (coronal) extension rates range from approximately 4 to 9 microns/day, and root extension rates in the first 5 mm of roots range from 3 to 9 microns/day. These rates are greater in M1 than in M2 or M3, and they are greater in mandibular molars than in respective maxillary molars. This significant enlargement of comparative data on nonhuman primate incremental development demonstrates that developmental variation among cusp and molar types should be considered during interpretations and comparisons of small samples of fossil hominins and hominoids.

Age Determination by Teeth↗
PubMed2001

High levels of Y-chromosome nucleotide diversity in the genus Pan.

Although some mitochondrial, X chromosome, and autosomal sequence diversity data are available for our closest relatives, Pan troglodytes and Pan paniscus, data from the nonrecombining portion of the Y chromosome (NRY) are more limited. We examined approximately 3 kb of NRY DNA from 101 chimpanzees, seven bonobos, and 42 humans to investigate: (i) relative levels of intraspecific diversity; (ii) the degree of paternal lineage sorting among species and subspecies of the genus Pan; and (iii) the date of the chimpanzee/bonobo divergence. We identified 10 informative sequence-tagged sites associated with 23 polymorphisms on the NRY from the genus Pan. Nucleotide diversity was significantly higher on the NRY of chimpanzees and bonobos than on the human NRY. Similar to mtDNA, but unlike X-linked and autosomal loci, lineages defined by mutations on the NRY were not shared among subspecies of P. troglodytes. Comparisons with mtDNA ND2 sequences from some of the same individuals revealed a larger female versus male effective population size for chimpanzees. The NRY-based divergence time between chimpanzees and bonobos was estimated at approximately 1.8 million years ago. In contrast to human populations who appear to have had a low effective size and a recent origin with subsequent population growth, some taxa within the genus Pan may be characterized by large populations of relatively constant size, more ancient origins, and high levels of subdivision.

Animals↗
PubMed2004

Influence of freezing rate on pore structure in freeze-dried collagen-GAG scaffolds.

The cellular structure of collagen-glycosaminoglycan (CG) scaffolds used in tissue engineering must be designed to meet a number of constraints with respect to biocompatibility, degradability, pore size, pore structure, and specific surface area. The conventional freeze-drying process for fabricating CG scaffolds creates variable cooling rates throughout the scaffold during freezing, producing a heterogeneous matrix pore structure with a large variation in average pore diameter at different locations throughout the scaffold. In this study, the scaffold synthesis process was modified to produce more homogeneous freezing by controlling of the rate of freezing during fabrication and obtaining more uniform contact between the pan containing the CG suspension and the freezing shelf through the use of smaller, less warped pans. The modified fabrication technique has allowed production of CG scaffolds with a more homogeneous structure characterized by less variation in mean pore size throughout the scaffold (mean: 95.9 microm, CV: 0.128) compared to the original scaffold (mean: 132.4 microm, CV: 0.185). The pores produced using the new technique appear to be more equiaxed, compared with those in scaffolds produced using the original technique.

Biocompatible Materials↗
PubMed2026

Pangenome of Streptomyces sampsonii and Relatives Highlights Horizontal Gene Transfer and Secondary Metabolism in Environmental Adaptation and Ecological Significance.

Streptomyces sampsonii is a promising biocontrol bacterium, but its genomic basis of adaptation and secondary metabolism remains unclear. Here, we present a chromosome-level genome assembly of S. sampsonii (7.20 Mb, 6015 protein-coding genes) and perform comparative analyses with 95 related Streptomyces species. Phylogenomic and synteny analyses revealed its closest relationship with S. albidoflavus, while extensive structural variations distinguished more distant lineages. Pangenome analysis uncovered 84,178 gene clusters, with pan_shell and pan_cloud genes predominantly enriched in xenobiotic biodegradation, metabolism, and antibiotic biosynthesis, highlighting their roles in ecological adaptation and biocontrol potential. Biosynthetic gene cluster (BGC) analysis identified numerous NRPS, PKS, and terpene pathways, many of which belong to pan_shell and pan_cloud regions, suggesting dynamic evolutionary origins. We further detected 66,260 horizontally transferred (HGT) genes, including 438 in BGCs, underscoring HGT as a major driver of metabolic innovation. Together, these findings provide novel insights into the genomic diversity, adaptive capacity, and secondary metabolic potential of S. sampsonii and its close relatives.

BGCs↗
PubMed1997

The tax gene sequences form two divergent monophyletic lineages corresponding to types I and II of simian and human T-cell leukemia/lymphotropic viruses.

Evolutionary associations of human and simian T-cell leukemia/lymphotropic viruses I and II (HTLV-I/II and STLV-I/II) are inferred from phylogenetic analysis of tax gene sequences. Samples studied consisted of a geographically diverse assemblage of viral strains obtained from 10 human subjects and 20 individuals representing 12 species of nonhuman primates. Sequence analyses identified distinct substitutions, which distinguished between viral types I and II, irrespective of host species. Phylogenetic reconstruction of nucleotide sequences strongly supported two major evolutionary groups corresponding to viral types I and II. With the type I lineage, clusters were composed of strains from multiple host species. A genetically diverse, monophyletic lineage consisting of eight new viral strains from several species of Asian macaques was identified. The second lineage consisted of a monophyletic assemblage of HTLV-II/STLV-II strains from Africa and the New World, including an isolate from a pygmy chimp (Pan paniscus) as an early divergence within the lineage. High levels of genetic variation among strains from Asian STLV-I macaque suggest the virus arose in Asia. Evidence of the origin of the type II virus is less clear, but diversity among HTLV-II variants from a single isolated population of Mbati villagers is suggestive but not proof of an African origin.

Amino Acid Sequence↗
PubMed2026

Nuclear mitochondrial sequences in great ape telomere-to-telomere genomes.

Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology with extant mitochondrial DNA (mtDNA), termed NUMTs, confound mtDNA sequence analysis. Here, we use great ape telomere-to-telomere (T2T) genomes to study NUMTs in bonobo, chimpanzee, human, gorilla, and Bornean and Sumatran orangutans. A phylogeny based on shared and lineage-specific NUMTs accurately recapitulates the great ape species tree topology. NUMTs are enriched at nonfunctional nonrepetitive regions of the nuclear genome and depleted within enhancers and coding sequences, suggesting negative selection. We validate the presence of a 76-kb-long heterozygous NUMT in chimpanzee, which is larger than any other NUMT observed in great apes, and find that dozens of NUMTs on the Pan Y Chromosome expanded together with palindromes. Finally, by analyzing intra-specific variation, we confirm that the vast majority of species-specific NUMTs identified in T2T assemblies are fixed or present at high frequencies in each species. Our study highlights NUMTs as a dynamic evolutionary force contributing to shaping ape genomes and is valuable for characterizing mtDNA in great apes.

Journal Article↗
PubMed1992

Identification of chimpanzee subspecies with DNA from hair and allele-specific probes.

We describe a non-invasive method of determining the subspecies identity of common chimpanzees (Pan troglodytes), based on subspecies-specific sequence differences in the mitochondrial genome. This procedure involves the extraction of DNA from hair, the amplification of a short (410 base pair (b.p.)) segment of the non-coding displacement loop (D-loop) by the polymerase chain reaction (PCR), and subspecies identification based on rapid allele-specific oligonucleotide (ASO) probe dot-blot typing. This approach will contribute to: (i) the colony-level management of captive chimpanzees by enabling managers to recognize hybrids between subspecies and minimize outbreeding depression; (ii) the recognition of inappropriately matched individuals in comparative behavioural and experimental studies; and (iii) forensic questions surrounding the origin of illegally traded animals.

Alleles↗
PubMed1999

Extensive nuclear DNA sequence diversity among chimpanzees.

Although data on nucleotide sequence variation in the human nuclear genome have begun to accumulate, little is known about genomic diversity in chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). A 10,154-base pair sequence on the chimpanzee X chromosome is reported, representing all major subspecies and bonobos. Comparison to humans shows the diversity of the chimpanzee sequences to be almost four times as high and the age of the most recent common ancestor three times as great as the corresponding values of humans. Phylogenetic analyses show the sequences from the different chimpanzee subspecies to be intermixed and the distance between some chimpanzee sequences to be greater than the distance between them and the bonobo sequences.

Animals↗
PubMed1997

Analysis of intron sequences at the class II HLA-DRB1 locus: implications for the age of allelic diversity.

Analyses of the coding sequences of HLA class II alleles have revealed high similarity between species, indicating that much of the polymorphism predates the separation of human (Homo) and chimpanzee (Pan), 4-7.4 million years ago. Recent studies of the intron sequences of alleles provide support for a much more recent origin and rapid generation of HLA alleles. At the DRB1 locus, intron analysis indicates that most of the allelic lineages have diverged from each other before the separation of Homo and Pan, consistent with the exon analysis. However, the intron sequences of alleles within lineages are almost identical, indicating that many of the alleles have been generated after the divergence of the Homo and Pan lineages.

Alleles↗
PubMed2001

Craniodental variation in Paranthropus boisei: a developmental and functional perspective.

What levels and patterns of craniodental variation among a fossil hypodigm are necessary to reject the null hypothesis that only a single species is sampled? We suggest how developmental and functional criteria can be used to predict where in the skeleton of fossil hominins we should expect more, or less, within-species variation. We present and test three hypotheses about the factors contributing to craniodental variation in extant primate taxa, and then apply these results to the interpretation of the P. boisei hypodigm. Within the comparative samples of extant Homo, Pan, Gorilla, Pongo, and Colobus, variables from the cranial base, neurocranium, and face that are not subject to high magnitudes of strain have consistently lower levels of intraspecific variation than variables from regions of the face subject to high levels of strain. Dental size variables are intermediate in terms of their reliability. P. boisei is found to have a low degree of variability relative to extant primates for variables shown to be generally useful for testing taxonomic hypotheses. Contrary to the claims of Suwa et al. ([1997] Nature 389:489-492), the recently discovered material from Konso falls within the range of variation of the "pre-Konso" hypodigm of P. boisei for available conventional metrical variables. Those aspects of the Konso material that appear to extend the range of the P. boisei hypodigm involve regions of the skull predicted to be prone to high levels of within-species variation. The approach used in this study focuses on craniodental data, but it is applicable to other regions of the skeleton.

Animals↗
PubMed2004

Expansion and divergence of the GH locus between spider monkey and chimpanzee.

Growth hormone (GH) has been previously described as showing distinct evolutionary stories between primates and other mammals. A burst of changes and successive amplification events took place in the primate lineage giving rise to a multigene family in the three Anthropoidea lineages. Polymerase chain reaction (PCR) was used to obtain the genes and the intergenic regions comprising the GH loci of the spider monkey (Ateles geoffroyi), a New-World primate, and of the chimpanzee (Pan troglodytes), an ape. The intergenic sequences of both species were screened by hybridization to detect copies of the Alu family, which have been implicated in the formation of the human GH locus. The GH locus of the spider monkey contains at least six GH-related genes, four of them were cloned. Likewise, five short intergenic sequences of approximately 3 kb were amplified and cloned. On the other hand, in the chimpanzee four new placental lactogen (PL) genes as well as four intergenic regions were amplified. Consequently, in this ape, six genes (two GHs, previously obtained, and four PLs) are clustered, separated by intergenic sequences of different lengths (two short ones of about 5 kb, and at least two long ones between 9 and 13 kb). The presence of Alu sequences within the intergenic regions of both GH loci corroborates the current hypothesis that they acted as a driving force for the locus expansion. GH sequence comparisons reveal that several gene-conversion events might have occurred during the formation of this genome region, which has undergone independent evolution in the three Anthropoidea branches. To establish the GH's evolutionary history may prove to be a difficult task due to these gene-conversion events.

Amino Acid Sequence↗