In the strong LD region (SL region; ~4.4 kb) of the sequenced region, I found that two allelic lineages (V and M) have been in the human population for 2.4 ± 0.4 million years (my) enforced. Furthermore, signs of positive Darwinian selection for haplotypes belonging to the V lineage have been detected from the pattern and level of polymorphism of the two lineages. The V-lineage haplotypes are predominant (62%), but show small nucleotide diversity (π = 0.05%), recent TMRCA thousand years) and strong LD in the SL region.
Diversity is significantly lower in the SL region than the other regions, but this reduction in diversity is not seen in M-lineage haplotypes. These observations are consistent with the rapid expansion of V-lineage haplotypes under positive selection. It is essential to the elucidation of human evolution that understanding the demographic history leading to modern humans and the human-specific evolution of genes associated with mental activity.
CHAPTER
INTRODUCTION
- Mental activity of modern humans
- Lipid storage diseases
- Sphingolipids and ceramides
- Ceramidase
This membrane domain serves to bind intracellular signaling molecules and receptors, thus facilitating signal transduction (Bollinger et al. 2005). In addition, SLs are enriched in neuronal plasma membranes and are highly associated with neuronal development such as neurite outgrowth (Schwarz and Futerman 1997; Buccoliero et al. 2002; Buccoliero and Futerman 2003; Ruvolo 2003). Acid ceramidase product ceramides and sphingosines are important cell signaling molecules (Spiegel et al. 1998; Pyne 2002; Ruvolo 2003).
An inherited deficiency leads to the accumulation of ceramides in various tissues, resulting in Farber disease, also known as Farber lipogranulomatosis (Sugita et al. 1972). Null mutants of ASAH2 in mice have a normal lifespan but show limited abnormalities in the intestinal breakdown of ceramides (Kono et al. 2006). This suggests that ASAH2-encoded neutral ceramidase is a key enzyme for the catabolism of dietary ceramides (Kono et al.
MATERIALS AND METHODS
- The long-range haplotype test
- DNA samples, PCR and sequencing
- Population genetic analyses
- Computer simulations
- Phylogenetic and dot-matrix analyses
Chromosome numbers and SNPs used in the LRH assay of eight LSD-related genes. The average nucleotide difference between the root haplotype and each individual in the sample was calculated in each of lineages V and M. To trace a particular lineage (lineage N) in a subpopulation, a single marker mutation is introduced into a single gene in popN.
Then the π values within the S and N line and in the entire population were measured in each replication and ~ 100 such π values were collected. At any segregating site, the line with a nucleotide of its frequency ~ 0.7 is defined as the S-line, while if the frequency is ~ 0.3, the line with the nucleotide is defined as the N-line. The π-values within the S or N line and in the entire population were calculated in the same way for the case of selection, and ~1000 π-values within each line were collected.
THE LONG-RANGE HAPLOTYPE TEST FOR THE LSD-ASSOCIATED GENES
- The purpose of the long-range haplotype test
- The result of the long-range haplotype test
In selection, the red allele is beneficial to other alleles and then spreads rapidly in a population. For the application of the LRH test, the core region of each of the eight LSD-associated genes is selected separately in YRI, CEU, CHB and JPT. For each gene, the core region appears to be nearly the same in the four populations, or the pattern of LD does not differ between populations.
Both EHH and REHH of each haplotype in the core region (core haplotype) were measured either in the region ~200 kb upstream or downstream from the core region and compared to data simulated under a neutral model without recombination (Materials and Methods). However, the significant core haplotype sequences of ASAH1 are the same and show strong LD in all four populations (Figures 3-3B and 3-4). The most parsimonious explanation for the separation of ASAH1 scores across Africans and non-Africans is that selective sweeps occurred in the region prior to the dispersal of modern humans from Africa.
Brown dots indicate simulation results, and blue dots represent the observations of each four populations. Blue rectangles indicate genes in the ~200 kb downstream region of ASAH1, with the official symbol of the gene shown on the rectangles. Below the genes, blue bars indicate the SNPs used for the LRH assay and dark blue bars represent SNPs in the core region.
The black bar in the light blue rectangle shows the location of the SNPs used for the LD analysis, with the reference SNP ID indicated below each SNP. The haplotype of number 1 shows the significantly high EHH and REHH in Figure 3-2. The root of each diagram is a haplotype in the core region, identified by a dark blue circle.
Blue lines indicate haplotypes in the ~200 kb region, and the thickness of each corresponds to the number of chromosomes.
COALESCENCE ANALYSES OF ASAH1 IN THE HUMAN
- Two distinct lineages at ASAH1
- Coalescence simulations under various demographic models
In the distribution, the TMRCA of 6 loci out of 16 loci of autosomes excluding ASAH1 is older than 2 my. The null hypothesis of the HKA test is that the level of genetic variations will be the same within and between species between loci under neutral evolution. The number above the sequence indicates the bp position of each site, and sites in the coding region are represented by the larger font size than the others.
These nucleotide sequence data appear in the DDBJ/EMBL/GenBank nucleotide sequence databases with the accession numbers AB371370 – AB371406. Since the nucleotide at the 32nd position (Figure 4-1) in M080 is the same as that in the chimpanzee, parallel substitution was thought to have occurred at this site; the site is incompatible with others and therefore excluded from the tree. The first column shows the haplotype name in the SL region corresponding to that in Figure 4-1.
The first two numbers in Figure 4-1 indicate the haplotype number in the SL region indicated in this table. From the second to the last column, the number of chromosomes in the samples is shown. The TMRCA of ASAH1 was estimated from the π value of the SL region (Nei and Li 1979).
Then, the results of 50,000 replications showed that the probability was lower than 0.03 except for the ancient population structure model (Table 4-4). As a result, however, the observed π value of CMAH rejects the ancient model of population structure even though ancient TMRCA is observed for the gene. Sachidanandam et al. 2001) and results from a low level of sequence differences (π = 0.02%) in the non-African sample.
The results suggest that human diversity can be explained by the ancient demographic history of population structure.
- The human demographic history
- ASAH1 POLYMORPHISM OF THE HUMAN POPULATION
- Signatures of Darwinian positive selection
- Lineage-specific amino acid changes
- Theoretical considerations of positive selection operating on ASAH1
- Biological significances of ASAH1 in the evolution of human mental activity The pattern and level of genetic variability at ASAH1 cannot be explained by
- PHYLOGENETIC ANALYSES OF CERAMIDASE GENES
- The phylogeny of ceramidase family
- The blast and dot-matrix analyses for ASAH2
- Human specific ASAH2 paralogous genes
- Number of sites: 15797 (Complete deletion)
- Number of sites: 7828 (Complete deletion)
- Number of sites: 6983 (Complete deletion)
- SUMMARY AND SIGNIFICANCE
The reason for rejecting the population structure model is that other loci in the human genome did not show a similar pattern of genealogy to that observed for MCPH. In addition, the number of haplotypes in lineage V is only six, and lineage M is 11. As mentioned earlier, the frequency of lineage V in the entire sample is higher (0.62) than that of lineage M (0.38).
Alignment of avian and mammalian ASAH1 orthologs in the SL region (A) and the NJ tree obtained based on nonsynonymous substitutions throughout ASAH1 of these orthologs (B). Bold letters indicate amino acid substitutions in the human lineage compared to birds and mammals. Thus, neutrality cannot explain the observed reduction in nucleotide diversity in lineage V in the SL region.
As modern humans spread out of Africa, mixing of the various V and M lineages occurred, and the advantageous V lineage has since spread throughout the population (Figure 5-3). This figure represents a representation of subpopulation distributions in Africa during the period of modern human migrations from Africa. In the previous chapters, the development of ASAH1, which codes for acid ceramidase, and human development were described.
The conservations may suggest that five groups of genes have achieved specific roles in the evolution of ceramidase. This suggests that the gene may be involved in brain or central nervous systems in the fruit fly. The tree and divergence in the R1 region reveal that the human ASAH2 gene was duplicated after the ASAH2B gene in a human and chimpanzee ancestor, and after the divergence of humans and chimpanzees to ASAH2C.
It is likely that human ASAH2B acquired new nucleotide sequences in the human lineage and ASAH2B is human specific. In this chapter, two ASAH2 paralogs, ASAH2B and ASAH2C, are identified in the human genome. I expect that the findings in the diploma thesis are definitely valuable for understanding especially the evolution of man, the evolution of modern man.
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Tribolo et al, 2002 Emergence of modern human behavior: Middle Stone Age carvings from South Africa. Bernardo et al, 1996 Molecular cloning and characterization of a full-length complementary DNA encoding human acid ceramidase. Kalkofen et al, 2006 Neutral ceramidase encoded by the Asah2 gene is essential for the intestinal breakdown of sphingolipids.
Chen et al, 1999 The human acid ceramidase gene (ASAH): structure, chromosomal location, mutational analysis and expression. Clarke et al, 2005 Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Nishigaki et al, 2002 Mutational analysis of the acid ceramidase gene in Japanese patients with Farber disease.
Hudson et al, 2005 Interrogating multiple facets of variation in a complete sequencing dataset to infer changes in human population size. Liao et al, 2005 Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origins. Nielsen et al, 2005 Simultaneous inferences of selection and population growth from patterns of variation in the human genome.
Fry et al, 2005 Positive selection of the CAG repeat of the human SCA2 gene prior to expansion.
