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Thread: New Guinean populations: possible early human migration from Africa

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    Post New Guinean populations: possible early human migration from Africa

    Original Investigation
    DNA sequence variation of the human ABO-secretor locus (FUT2) in New Guinean populations: possible early human migration from Africa
    Yoshiro Koda1 , Takafumi Ishida2, Hidenori Tachida3, Baojie Wang1, 4, Hao Pang1, 4, Mikiko Soejima1, Augustinus Soemantri5 and Hiroshi Kimura1

    (1) Division of Human Genetics, Department of Forensic Medicine, Kurume University School of Medicine, 830-0011 Kurume, Japan
    (2) Department of Anthropology, Unit of Human Biology and Genetics, Faculty of Science, University of Tokyo, Hongo, 113-0033 Tokyo, Japan
    (3) Department of Biology, Faculty of Sciences, Kyushu University, 812-8581 Fukuoka, Japan
    (4) Department of Serology, Faculty of Forensic Medicine, China Medical University, 11001 Shenyang, China
    (5) Faculty of Medicine, Diponegoro University, Semarang, Indonesia


    Yoshiro Koda
    Email: ykoda@med.kurume-u.ac.jp
    Fax: +81-942-317700

    Received: 30 June 2003 Accepted: 30 July 2003 Published online: 3 September 2003

    Abstract We have investigated the allelic polymorphism of the human ABO-secretor locus (FUT2) in 90 unrelated Papuan-speaking New Guineans (Dani group), 101 admixed New Guineans from Irian Jaya, Indonesia, and 32 New Guineans from Papua New Guinea by DNA sequencing analysis. Whereas the total frequency of various nonfunctional alleles at the FUT2 locus in the worldwide populations so far examined is around 0.5, we have found only one individual heterozygous for a nonfunctional allele in the 90 Dani group members and a frequency of nonfunctional alleles of 0.1–0.2 in the admixed New Guineans. Admixed New Guineans had the Asian-specific null allele se385 and the characteristic nonfunctional allele sedel2 found in Polynesians. In addition, both New Guinean populations had unique functional alleles (Se375 and Se400) with high frequencies (0.11–0.37); these are absent in other populations of the world except for African and Samoan populations. The Se375 allele had G and C at positions 1009 and 1011 of the 3' untranslated region, respectively, whereas all other FUT2 alleles found so far in the world, except for se428, have 1009A and 1011T. The Se375 allele found in Africans has 1009G and 1011T, or 1009A and 1011T. Corresponding positions of nonhuman primates have G and C, suggesting that the Se375 allele is one of the ancestral alleles, reflecting the early human migration from Africa to New Guinea and the long isolation of Dani populations from neighboring populations.

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    Introduction
    The human ABO-secretor locus (FUT2) encodes an (1,2)fucosyltransferase (Se enzyme) that is responsible for the production of the H antigen of the ABO histo-blood group in gastrointestinal mucosa and body fluids but not on red blood cells. A secretor has the H antigen in saliva and other body fluids, whereas a nonsecretor does not. Since the H substance is essential for synthesis of A and B histo-blood group substances, a nonsecretor also fails to express ABH antigens in saliva and other body fluids. A secretor has at least one functional allele (Se), and a nonsecretor is homozygous for a nonfunctional allele (se).

    Recent molecular analyses have revealed interesting ethnic differences in the FUT2 polymorphism (Kelly et al. 1995; Koda et al. 1996, 2001a; Liu et al. 1998, 1999; Pang et al. 2000, 2001). The total frequency of nonfunctional alleles of FUT2 is approximately 0.5 in most human populations of the world. The se428 allele with the nonsense mutation G428A is a prevalent null allele in Africans, Iranians, and Europeans (Kelly et al. 1995; Liu et al. 1998; Koda et al. 2001b), whereas the se385 allele with the missense A385T substitution has to date been found in east and southeast Asian populations but not in African, Iranian, and European populations, suggesting that se428 has disappeared in Asians and that Asians have produced a new null allele se385 that has expanded to a frequency of about 0.5. Of other nonfunctional alleles, se302 has been found in individuals of south Asia, and se571 has been identified in Pacific islanders at a relatively high frequency (Henry et al. 1996a, 1996b, 1996c; Chang et al. 1999; Peng et al. 1999; Pang et al. 2000). The functional Se40 allele has been found in African individuals at a high frequency and is absent in the other populations (Liu et al. 1998). In addition, we have reported three recombinant FUT2 alleles as nonfunctional alleles. One is the fusion gene (sefus) consisting of the 5' region of a pseudogene of FUT2 (Sec1) and the 3' region of FUT2 in Japanese individuals (Koda et al. 1996; Liu et al. 1999), and the other two are distinct complete deletions of FUT2 (sedel and sedel2) generated by an Alu-Alu recombination (Koda et al. 1997, 2000a; Pang et al. 2000, 2001). The sedel allele was originally identified in Indian individuals with the classic Bombay phenotype (Koda et al. 1997; Fernandez-Mateos et al. 1998) and was found in a Bangladeshi population with a high frequency (0.074; Pang et al. 2001). The sedel2 allele has been found in Samoans with a high frequency (0.104; Pang et al. 2000).

    The se428 allele has seven base differences relative to the reference allele (Se), which was first cloned by Kelly et al. (1995), in the 984-bp coding and 30-bp 3' untranslated regions of exon 2, and the era of the most recent common ancestor of the Se and se428 alleles was estimated to be about 3 million years ago (Koda et al. 2000b). In addition, polymorphic patterns at the FUT2 locus of the European and Iranian populations do not fit the expectations of the equilibrium neutral model with an infinite number of sites, because of the high frequency of the null allele se428 (Koda et al. 2001b). These results suggest that the polymorphism of this locus is generated by some kind of selection.

    The frequency of the nonsecretor phenotype in New Guinean populations is extremely low (Cavalli-Sforza et al. 1994). However, DNA sequence analysis of FUT2 is not yet available in New Guinean populations. It is thus of interest to study the FUT2 polymorphism, which shows a high ethnic specificity in worldwide populations, because Redd and Stoneking (1999) have suggested a close relationship of New Guinean and African populations. In this study, we have investigated the polymorphism of FUT2 in New Guinean populations of Irian Jaya, the western half of the New Guinea island, and of Papua New Guinea.


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    Materials and methods
    Sample preparation
    The study protocol was approved by the Ethics Committee of Kurume University School of Medicine. Oral informed consent was obtained from all subjects. Blood samples were randomly collected from New Guinean individuals. There were apparently no related individuals; however, inbreeding could not be excluded. The numbers of individuals studied in the present study in respective populations were: 57 Papuan-speaking individuals from Nabire (NB, Dani group), 33 Papuan-speaking individuals from Wamena (WA, Dani group), 101 admixed New Guineans from several villages of Irian Jaya, Indonesia (IJ, divided into 75 Papuan-speaking individuals, 19 Austronesian-speaking individuals, and seven individuals unclassified by self-declaration), and 32 admixed individuals from highland and coastal Papua New Guinea (LAE). Genomic DNA was prepared from leukocytes by SDS-proteinase K treatment and the phenol/chloroform extraction method. Substitutions of nucleotides in the FUT2 sequences shown in this article describe changes from the reference Se allele first cloned by Kelly et al. (1995).

    Polymerase chain reaction amplification and DNA sequencing
    The 1014-bp region containing the 984-bp FUT2 coding region and the 30-bp 3' untranslated region were amplified from genomic DNA by the polymerase chain reaction (PCR; Koda et al. 1996). The purified PCR products (20–30 ng) were used for direct DNA sequencing as described previously (Liu et al. 1998). The FUT2 fusion gene (sefus) was amplified by using a pair of primers located in the 5' flanking region of Sec1 for the upper primer and in the 3' flanking region of FUT2 for the lower primer (Koda et al. 1996). Another set of primers was used for the amplification of the two alleles with deletions, sedel and sedel2 (Koda et al. 2000a; Pang et al. 2000). Three recombinants were identified by electrophoresis of the PCR products on 1.0% agarose gel and then staining with ethidium bromide.

    Haplotype determination and measurement of (1,2)fucosyltransferase activity
    For determination of haplotypes, purified PCR products were ligated into plasmid pGEM-T (Promega, Madison, Wis.) and sequenced (Koda et al. 1996). Each clone containing a newly identified missense mutation was then subcloned into mammalian expression vector pRc/CMV (Invitrogen, San Diego, Calif.) for transient expression study. Transient expression of plasmid DNA into COS7 cells and measurement of (1,2)fucosyltransferase activity were performed as described previously (Koda et al. 1996).

    Statistical analysis within and between populations
    To measure diversity within a population, the values of and were calculated; is based on the average number of nucleotide differences per site between two sequences randomly drawn from a population, and is based on the proportion of segregating sites in a population (Hartl and Clark 1997). Under the equilibrium neutral model, values and provide alternative estimators of 4Ne, where Ne is the effective population size and is the mutation rate per site per generation (Watterson 1975; Nei and Tajima 1981). From the two estimates of and , a test statistic, D, proposed by Tajima (1989) was computed. In addition, the number of singleton sites s was employed to calculate the test statistics D* proposed by Fu and Li (1993) and Fu's Fs statistics (Fu 1997). FST between populations was estimated from the sequence data by using the method of Hudson et al. (1992). All calculations were performed by using the DnaSP 3.50 software package (Rozas and Rozas 1999). We also calculated the Snn statistic from Hudson (2000) to detect genetic differentiation across subpopulations. In addition, the haplotype frequency and the Hardy-Weinberg estimation were calculated by using the statistical program "Arlequin" (Schneider et al. 2000).


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    Results
    Nucleotide substitutions of FUT2 in the New Guinean populations
    We examined the allelic polymorphism of the 1014-bp region containing the 984-bp coding region (from 16 bp to 999 bp) and the 30 bp of the 3' untranslated region (from 1000 bp to 1029 bp) of FUT2, by using direct DNA sequencing in 223 New Guineans. We found 15 single-nucleotide polymorphisms (SNPs; Fig. 1), of which 12 sites had previously been reported in various populations (Henry et al. 1996a, 1996b, 1996c; Kelly et al. 1995; Yu et al. 1995, 1996, 1999; Koda et al. 1996, 2001a, 2001b; Liu et al. 1998; Chang et al. 1999; Pang et al. 2000, 2001). The additional three sites of nonsynonymous base substitutions, viz., 664C to T (Arg to Cys), 760G to A (Asp to Asn), and 868G to A (Gly to Arg), were first identified in the present study. Extracts of COS7 cells transfected with a plasmid containing the wildtype FUT2 allele (Se) was shown to have enzyme activity by using lacto-N-biose I as acceptor (23.8±3.8 nmol/mg per hour, n=4), whereas those with a plasmid containing the allele with 664T, 760A, or 868A showed no detectable enzyme activity (less than 0.1 nmol/mg per hour). The results suggested that the se664 (from Se375), se760 (from Se400), and se868 (from Se357) alleles were nonsecretor alleles. Five of the 13 sites of a base substitution in the coding region of FUT2 were synonymous, and the other eight were nonsynonymous. Eight of the 15 single-nucleotide substitutions (singleton, s) were identified, viz., 171A to G, 216C to T, 428G to A, 739G to A and 960A to G (all substitutions on se428) in an IJ population (unclassified group), 571C to T and 760G to A in an LAE (Papua New Guineans) population, and 868G to A in an NB (Dani group) population. In addition to the 15 SNPs, complete gene deletion (sedel2) was found in admixed New Guinean (IJ) and LAE populations and was absent in Dani (NB and WA) populations.

    Fig. 1. Polymorphic base substitutions in 11 FUT2 alleles. Numbers in parentheses Number of chromosomes examined, Se functional alleles, se nonfunctional alleles. Top Positions of nucleotides of human FUT2 are given vertically. Sites are also classified depending on whether the change is a replacement (R) or synonymous (S), or in the noncoding region (N). Asterisks Sequence matched the reference allele (Se) at that position, – deletion at that position. The frequencies of alleles are expressed in %. Nucleotides of corresponding positions of FUT2 homologs of orangutan, gorilla, and chimpanzee are shown for reference. WA Wamena, Dani group, IJ Irian Jaya, (pap) Papuan-speaking individuals, (aus) Austronesian-speaking individuals, LAE highland and coastal Papua New Guineans

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    To compare the distributions of base substitutions of the FUT2 locus in four New Guinean populations, we analyzed the nucleotide diversity, and , by using the DnaSP 3.50 software package (Table 1). We divided the IJ population into three groups by self-declaration (75 Papuan-speaking individuals, 19 Austronesian-speaking individuals, and seven unclassified individuals). The value of was similar in all populations (0.19%–0.20%), whereas the variation in (%) varied between 0.11, 0.10, 0.21, and 0.19 in NB, WA, IJ, and LAE populations, respectively. However, was smaller in the Austronesian-speaking group (0.09%) than in the other populations (0.19%–0.20%). The nucleotide diversity of the 1014-bp region at FUT2 in four New Guinean populations (=0.195±0.007) was two-fold less than that in five representative populations from the rest of the world (African, European, Iranian, Chinese, and Japanese populations; =0.410±0.007; (Koda et al. 2001b). The nucleotide diversity of replacement sites was 0.060 (%), whereas that of synonymous and noncoding sites was 0.557 (%). Consistent with previous observations (Koda et al. 2001b), the high nucleotide diversity was attributable to a large silent-site variation and not to less constraint on replacement changes at the FUT2 locus. Tajima's D values were calculated to be –0.16 to 1.82 in four New Guinean populations, and Fu and Li's D* values were calculated to be between –2.01 and 1.07 (Table 1). We could not reject the null hypothesis of neutrality at FUT2 in any of the four New Guinean populations. In addition, Fu's Fs values were not significantly positive.
    Table 1. Population genetic statistics for FUT2 variation. NB Nabire, Dani group, WA Wamena, Dani group, IJ Irian Jaya, (Pap) Papuan-speaking individuals, (Aus) Austronesian-speaking individuals, LAE highland and coastal Papua New Guineans
    Population
    n
    Sa
    b

    s
    Tajima's D
    Fu and Li's D*
    Fu's Fs

    NB
    114
    6
    0.11
    0.20
    1
    1.77
    0.14
    4.72

    WA
    66
    5
    0.10
    0.19
    0
    1.82
    1.07
    3.43

    IJ
    183
    12
    0.21
    0.19
    5
    –0.16
    –2.01
    1.89

    (Pap)
    139
    7
    0.13
    0.20
    0
    1.37
    1.17
    2.67

    (Aus)
    33
    6
    0.15
    0.09
    4
    –1.01
    –1.96
    –0.68

    LAE
    63
    9
    0.19
    0.19
    2
    –0.04
    –0.04
    –0.31

    Total
    426
    15
    0.22
    0.20
    8
    –0.30
    –3.86
    0.86


    aS is the number of segregating sites
    b
    Haplotype diversity of FUT2 in four New Guinean populations
    From the results of sequencing after the subcloning of some heterozygous alleles, we determined the haplotypes and estimated the frequencies of probable alleles. As shown in Fig. 1, 11 alleles were encountered in the four populations. We found four alleles in the NB, four in the WA, eight in the IJ, and nine in the LAE populations. The functional alleles were composed of three prevalent alleles of Se357 (with a synonymous mutation at 357C to T), Se375, and Se400 in all populations. The 375A to G substitution was first reported as the functional Se375 allele in an African (Xhosa) population with a low frequency (0.015; Liu et al. 1998). Nucleotide positions 1009 and 1011 are located in the 3' untranslated region. The Se375 allele found in Xhosa individuals has 1009G and 1011T (Koda et al. 2001b), whereas the New Guinean Se375 allele has 1009G and 1011C. All FUT2 alleles so far examined except the se428 allele have 1009A and 1011T. As shown in Fig. 1, nonhuman primates have G and C at the corresponding positions, suggesting Se375 is one of the ancestral alleles of FUT2 alleles.

    To analyze FUT2 phylogenetically, a neighbor-joining tree was drawn by using orangutan sequences (DDBJ accession no. AB015636) as a outgroup (Fig. 2). Human alleles are monophyletic, although the se428 allele seems to be very old (Koda et al. 2000b, 2001b). This analysis supports the idea that the Se375 is the most ancient ancestral allele of FUT2 alleles, except for se428.

    Fig. 2. Neighbor-joining tree constructed from human FUT2 alleles and ape FUT2 homologs (chimpanzee, gorilla, and orangutan: DDBJ accession nos. AB015634, AB015635, and AB015636, respectively). Numbers on branches Percentage of 1,000 bootstrap samples supporting the branch

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    Of the nonfunctional alleles, se385 and sedel2 were observed in admixed New Guinean (IJ) and Papua New Guinean (LAE) populations. One individual heterozygous for the se428 allele was found in the unclassified group of the IJ population, and one individual heterozygous for the se571 allele was identified in the LAE population. However, we found neither sefus nor sedel in the four populations. Three alleles, viz., se664, se760 and se868, were novel nonfunctional alleles first identified in this study. The frequency of the null allele in Dani populations (NB and WA) was low (0.0056). We found only one null allele (se868), which probably emerged from Se357 in the NB population.

    The genotype frequencies in the IJ population deviated significantly from the Hardy-Weinberg expectation because of an excess of homozygosity (Table 2). Deviation from the Hardy-Weinberg expectation was also observed in the Papuan-speaking group of the IJ population. Although we cannot rule out the possibility that we have been unable to detect unknown null alleles generated by a rearrangement other than sefus, sedel, and sedel2, deviation from the Hardy-Weinberg expectation in the Papuan-speaking group of the IJ population is likely to be attributable to the population structure, such as the recent admixture between New Guineans and Austronesian-speaking populations, population substructure, or inbreeding.
    Table 2. Hardy-Weinberg equilibrium at the FUT2. NB Nabire, Dani group, WA Wamena, Dani group, IJ Irian Jaya, (Pap) Papuan-speaking individuals, (Aus) Austronesian-speaking individuals, LAE highland and coastal Papua New Guineans
    Number.
    Homozygosity

    Observed
    Expected
    Probability

    NB
    57
    0.35
    0.34
    0.86

    WA
    33
    0.42
    0.44
    0.91

    IJ
    101
    0.41
    0.28
    0.001

    (Pap)
    75
    0.38
    0.29
    0.005

    (Aus)
    19
    0.50
    0.39
    0.18

    LAE
    32
    0.38
    0.26
    0.10


    FST values within the New Guinean populations and among other populations
    In order to quantify the population differentiation, we computed FST values pairwise among the four New Guinean populations (Table 3). When following the qualitative guidelines proposed by Wright (1978), there was little genetic differentiation among the New Guinean populations. However, FST values between the Austronesian-speaking group in the IJ population and Dani groups were higher than those between the Papuan-speaking group in the IJ population and Dani groups. The Hudson Snn statistical analysis showed significant genetic differentiation between the Austronesian-speaking group in the IJ population and Dani groups, but not in the LAE population (Table 3; Hudson 2000). In addition, the NB population was genetically different from other New Guinean populations. The results may reflect reduced gene flow between the NB population and other Dani populations. On the other hand, large to very large genetic differentiation was observed between the New Guinean populations and other worldwide populations, suggesting no significant admixture between New Guineans and any populations, including neighboring Indonesians.
    Table 3. FSTs in all pairs of populations estimated from sequence diversity and P values of the Snn test within the New Guinean populations at FUT2. P values of the Snn tests are shown in parentheses. NB Nabire, Dani group, WA Wamena, Dani group, IJ (Pap) Irian Jaya, Papuan-speaking individuals, IJ (Aus) Irian Jaya, Austronesian-speaking individuals
    NB
    WA
    IJ (Pap)
    IJ (Aus)
    LAE

    NB
    0.045 (0.000700)
    0.013 (0.001700)
    0.133 (0.000000)
    0.039 (0.000000)

    WA
    –0.001 (0.122400)
    0.101 (0.003500)
    0.012 (0.000800)

    IJ (Pap)
    0.097 (0.025300)
    0.008 (0.023300)

    IJ (Aus)
    0.026 (0.276400)

    Africans
    0.275
    0.276
    0.268
    0.361
    0.288

    Caucasians
    0.320
    0.303
    0.303
    0.387
    0.319

    Japanese
    0.352
    0.292
    0.293
    0.238
    0.203

    Indonesians
    0.382
    0.328
    0.328
    0.307
    0.250

    Samoans
    0.242
    0.197
    0.194
    0.139
    0.113



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    Discussion
    In this study, we analyzed the population structure of inhabitants in Irian Jaya and Papua New Guinea by using the polymorphism of FUT2. The frequency of nonfunctional alleles in Dani populations was surprisingly low (0.0056; only one individual among 90 heterozygous for the se868 allele). The frequency of nonsecretors was roughly calculated to be 1 in 32,400 in Dani populations. We did not find the se385 and se428 alleles (prevalent in east and southeast Asian populations and in European, Iranian, and African populations, respectively) in Dani populations. Although our present result was anticipated to a great extent from a phenotype study (Cavalli-Sforza et al. 1994), it was also surprising, because the total frequency of null alleles of FUT2 is approximately 0.5 in all Old World populations. However, se385 was found in the admixed New Guinean populations (0.025 in IJ and 0.094 in LAE) at low frequencies compared with those in Indonesians (0.631) and Samoans (0.396; Pang et al. 2000, 2001). In addition, sedel2, found at a frequency of 0.104 in a Samoan population but not at all in an Indonesian population, was also observed in the admixed New Guinean populations (0.094 in IJ and 0.016 in LAE). The se571 allele, which was found at a relatively high frequency (0.167) in a Samoan population, but was rare in an Indonesian population (0.012), was found in one LAE individual. The nonfuctional allele frequency was similar between the Papuan-speaking group and the Austronesian-speaking group.

    Although the FUT2 locus has null alleles with high frequencies (about 0.5) in most populations of the world and has prevalent null alleles (se428 and se385; Kelly et al. 1995; Koda et al. 1996, 2001b; Liu et al. 1998), the mutational character in the null allele of Dani populations is similar to that observed in FUT1, in which null alleles of the FUT1 locus (h alleles, the Bombay or para-Bombay phenotype in the ABO histo-blood group system) are rare and generated by different mutational events without prevalent null alleles (Kelly et al. 1994; Koda et al. 1997; Wagner and Flegel 1997; Wang et al. 1997; Fernandez-Mateos et al. 1998; Wagner et al. 2001).

    Of two New Guinean-specific functional alleles (Se400 and Se375), Se400 was found at low frequencies in Samoan and Indonesian populations (0.021 and 0.012, respectively; Pang et al. 2000, 2001), and Se375 was also observed at a low frequency (0.021) in Samoans but not in Indonesians. The Se400 allele has one base substitution, G to A, at position 400 compared with the reference Se allele first cloned by Kelly et al. (1995). The reference Se allele is very rare in Dani populations (0.0056), whereas the Se400 allele found in New Guineans with high frequencies (0.11–0.37) is nearly absent in other populations of the world, suggesting that the base substitution at position 400 emerged in the Papuan-speaking population. The Se375 found in New Guineans with a high frequency (0.13-0.27) was present in African and Samoan populations at low frequencies (0.015 and 0.021, respectively). The frequency of Se375 was also much lower in the Austronesian-speaking group than in the Papuan-speaking group in IJ populations, although, except for Se375, the functional allele frequencies were similar between the two groups. However, this allele is absent in Asians, Iranians, and Europeans (Liu et al. 1998; Pang et al. 2000, 2001; Koda et al. 2001b). The New Guinean Se375 allele has 1009G and 1011C in the 3' noncoding region, whereas the African Se375 allele has 1009G and 1011T (Koda et al. 2001b). In addition, we have found another Se375 allele, which has 1009A and 1011T, in an African population (unpublished). All other FUT2 functional and nonfunctional alleles except for the se428 allele have 1009A and 1011T, whereas nonhuman primate FUT2 homologs contain G and C at corresponding positions, respectively (Fig. 1; Koda et al. 2000b). Although the chimpanzee FUT2 homolog contains A at position 375, gorilla, orangutan, and green monkey FUT2 homologs have G at position 375. Therefore, the Se375 (A375G) allele found in Papuan-speaking populations is thought to be an ancestral allele of functional alleles, including the African Se375 allele. Accordingly, the Se375 allele probably came directly from Africa to New Guinea, and a base substitution at position 1011 (C to T) and then at position 1009 (G to A) might have occurred in Africa but not in New Guinea. The presence of the New-Guinean-specific functional alleles (Se400 and Se375) suggests that the Papuan-speaking populations have a different evolutional history at the FUT2 locus.

    FST analysis between four New Guinean populations and two neighboring populations (Samoans and Indonesians) indicated that Dani populations showed marked genetic differentiation from the Indonesian population (Table 3). On the other hand, a closer relationship between Samoan and admixed New Guinean populations, particularly with the Austronesian-speaking group, than Dani populations was observed. In addition, a close relationship between Dani and admixed New Guinean populations, particularly with the Papuan-speaking group, was seen. These results support the hypothesis that, whereas some Papuan-speaking populations have been separated from neighboring populations for a long time, coastal New Guinean populations are recently admixed with Austronesian-speaking populations and that New Guineans possibly migrated to Polynesia.

    In our previous study (Koda et al. 2001b), FST estimated from the sequence diversity of FUT2 showed a peculiar pattern. First, FSTs between any pair of African, European, and Iranian populations were small. Second, the FST between the African/European/Iranian and Asian populations was large (>0.42). This is attributable to the high frequency of the se428 allele, which has seven base substitutions relative to the reference Se allele, in African, European, and Iranian populations and to the presence of the se385 allele instead of the se428 allele in Asian populations. As shown in Table 3, a large genetic differentiation of New Guinean populations from other representative populations of the world was observed by FST analysis. This can be explained by the high frequency of the Se375 allele, which has three base substitutions relative to the reference Se allele, only in New Guinean populations. However, the presence of the Se375 allele only in Africans and New Guineans and the absence of the Asian-specific se385 allele in New Guineans suggest that, at least in part, ancient and independent migrations occurred from Africa to New Guinea, and that whereas the New Guineans have been isolated for a long time, extensive expansion of the number of Asians has occurred in southeast Asia.

    In a previous study, we speculated that a high frequency of null alleles may have an unknown advantage for human survival (Koda et al. 2001b). However, the nonprevalent character of the FUT2-inactivating mutations in New Guinea suggests that the Dani populations may have been subjected to different selective pressures, although we cannot imagine the selective force acting on the FUT2 locus at present. Alternatively, the nonfunctional alleles, such as se385 and/or se428, were swept into a population bottleneck during the early colonization of Sahul (the combined Australia-New Guinea landmass during the Ice Age when sea levels were lower), and the frequency of the population-specific functional alleles (Se375 and Se400) has been increased by genetic drift and subsequent population expansion in the Papuan-speaking populations.

    Although Tajima's D , Fu and Li's D*, and Fu's Fs values in Dani populations (NB and WA) are not significant, these values are positive. This is attributable to the presence of three functional alleles (Se357, Se375, and Se400) with high frequencies. From these results, we cannot rule out the possibility that the polymorphism of FUT2 in New Guinean populations has been generated by some kind of selection, such as balancing selection. However, three prevalent functional allele (Se357, Se375, and Se400)-encoded enzymes show similar activities (Pang et al. 2000), and low genetic diversity of hemoglobin haplotypes was observed in the Papua New Guinea populations (Roberts-Thomson et al. 1996). Thus, the positive D value of New Guinean populations may be explained by a population bottleneck and subsequent population expansion in the Papuan-speaking population, rather than as a result of a selection.

    The indigenous people of New Guinea belong to the Melanesian race and are related to the people inhabiting the islands of Melanesia. The common ancestors of Australians and New Guineans are believed to have settled on Sahul probably some 50,000 years ago. The Dani populations still maintain their ancestral customs and traditions and are virtually untouched by alien influences. Most of the changes have so far taken place among the coastal people, who are being subjected to ever-increasing contacts with the world outside. To estimate the origin of the Papuan-speaking population genetically, several genetic marker systems including autosomal chromosomes, Y chromosome, and mtDNA have been investigated (Jorde et al. 2000; Kayser et al. 2001a, 2001b; Hurles et al. 1998; Redd and Stoneking 1999; Tishkoff et al. 2000; Roberts-Thomson et al. 1996; Tsintsof et al. 1990). These studies also suggest that Dani populations have been isolated for a long period from neighboring populations, whereas coastal New Guineans seem to have been involved in considerable admixture with Austronesian-speaking populations who originated from southeast Asia and who colonized coastal New Guinea during the past 5,000 years (Kayser et al. 2001a, 2001b; Hurles et al. 1998; Redd and Stoneking 1999; Tishkoff et al. 2000). In addition, some studies of Y chromosome polymorphism have indicated ancient ties between Papua New Guinean and African populations and suggested that the Papua New Guinea highland populations seem to be descendants of the earliest migration into this region from Africa (Redd and Stoneking 1999; Tishkoff et al. 2000). However, some analyses have not found evidence for a closer relationship of Papua New Guinean to African populations than to non-Africans (Cavalli-Sforza et al. 1994). The high frequency of Se375, supposed to be the most ancestral allele of FUT2 in New Guineans, supports a close relationship of New Guineans and African populations, although a large genetic differentiation between New Guinean and African populations has been demonstrated by FST analysis.

    The genetic relationship of Aboriginal Australian and New Guinean populations is controversial. Some studies support a common origin of both populations (Roberts-Thomson et al. 1996), whereas other studies support an independent origin of these populations (Kayser et al. 2001a; Redd and Stoneking 1999). Although we have not yet examined the FUT2 polymorphism in Aboriginal Australian populations, and despite the analysis of only the single locus (FUT2) in this study not being sufficient, the characteristic distributions of both the functional and nonfunctional FUT2 alleles may provide useful information for the genetic origin(s) of Aboriginal Australian populations and Papuan-speaking populations.

    Acknowledgements This work was supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Science, Culture and Sports of Japan. H. T. was supported by a Grant-in-Aid for Scientific Research on Priority Areas ''Medical Genome Science'' no. 15012239. We thank Mr. S. Kamimura and Miss Y. Noguchi for technical assistance.


    --------------------------------------------------------------------------------

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    Post Re: New Guinean populations: possible early human migration from Africa

    C Loring Brace also found that Africans group with the people of the Sahul. He was using craniometry, but he also mentioned some genetic evidence.

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