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Fulltext A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques

Smith DG, Ng J, George D, Trask JS, Houghton P, Singh B, et al.

Am J Phys Anthropol, 2014 Sep;155(1):136-48.
PMID: 24979664 DOI: 10.1002/ajpa.22564

Two subspecies of cynomolgus macaques (Macaca fascicularis) are alleged to co-exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis.
A Bayesian analysis of the temporal change of local density of proboscis monkeys: implications for environmental effects on a multilevel society

Matsuda I, Kubo T, Tuuga A, Higashi S

Am J Phys Anthropol, 2010 Jun;142(2):235-45.
PMID: 20091847 DOI: 10.1002/ajpa.21218

To understand the effects of environmental factors on a social system with multilevel society in proboscis monkey units, the temporal change of the local density of sleeping sites of monkeys was investigated along the Menanggul river from May 2005 to 2006 in Malaysia. Proboscis monkeys typically return to riverside trees for night sleeping. The sleeping site locations of a one-male unit (BE-unit) were recorded and the locations of other one-male and all-male units within 500 m of the BE-unit were verified. In addition, environmental factors (food availability, the water level of the river, and the river width) and copulation frequency of BE-unit were recorded. From the analyses of the distance from the BE-unit to the nearest neighbor unit, no spatial clumping of the sleeping sites of monkey units on a smaller scale was detected. The results of a Bayesian analysis suggest that the conditional local density around the BE-unit can be predicted by the spatial heterogeneity along the river and by the temporal change of food availability, that is, the local density of monkey units might increase due to better sleeping sites with regard to predator attacks and clumped food sources; proboscis monkeys might not exhibit high-level social organization previously reported. In addition, this study shows the importance of data analysis that considers the effects of temporal autocorrelation, because the daily measurements of longitudinal data on monkeys are not independent of each other.
Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community

Wise CA, Sullivan SG, Black ML, Erber WN, Bittles AH

Am J Phys Anthropol, 2005 Nov;128(3):670-7.
PMID: 15864813

Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.
Dental perspectives on the population history of Southeast Asia

Matsumura H, Hudson MJ

Am J Phys Anthropol, 2005 Jun;127(2):182-209.
PMID: 15558609

This article uses metric and nonmetric dental data to test the "two-layer" or immigration hypothesis whereby Southeast Asia was initially occupied by an "Australo-Melanesian" population that later underwent substantial genetic admixture with East Asian immigrants associated with the spread of agriculture from the Neolithic period onwards. We examined teeth from 4,002 individuals comprising 42 prehistoric and historic samples from East Asia, Southeast Asia, Australia, and Melanesia. For the odontometric analysis, dental size proportions were compared using factor analysis and Q-mode correlation coefficients, and overall tooth size was also compared between population samples. Nonmetric population affinities were estimated by Smith's distances, using the frequencies of 16 tooth traits. The results of both the metric and nonmetric analyses demonstrate close affinities between recent Australo-Melanesian samples and samples representing early Southeast Asia, such as the Early to Middle Holocene series from Vietnam, Malaysia, and Flores. In contrast, the dental characteristics of most modern Southeast Asians exhibit a mixture of traits associated with East Asians and Australo-Melanesians, suggesting that these populations were genetically influenced by immigrants from East Asia. East Asian metric and/or nonmetric traits are also found in some prehistoric samples from Southeast Asia such as Ban Kao (Thailand), implying that immigration probably began in the early Neolithic. Much clearer influence of East Asian immigration was found in Early Metal Age Vietnamese and Sulawesi samples. Although the results of this study are consistent with the immigration hypothesis, analysis of additional Neolithic samples is needed to determine the exact timing of population dispersals into Southeast Asia.
Metric analyses of an early holocene human skeleton from Gua Gunung Runtuh, Malaysia

Matsumura H, Zuraina M

Am J Phys Anthropol, 1999 Jul;109(3):327-40.
PMID: 10407463

A nearly complete human skeleton dating to the Early Holocene (epi-Paleolithic culture) excavated from Gua Gunung Runtuh, Malaysia, is described. Cranial, dental, and limb bone measurements are recorded on the skeleton, and compared with early and modern skeletal samples from Southeast Asia and Australia. The comparisons demonstrate that the Gua Gunung specimen is most similar to Australian Aborigines in dental and limb measurements, while the cranial measurements indicate a close affinity to Mesolithic samples from Malaysia and Flores. These findings further suggest that the Gua Gunung skeleton, as well as other fossils from Tabon and Niah, are representative of an early group of people who occupied Sundaland during the late Pleistocene, and may be the ancestors of Australian Aborigines. Some of the dental and limb bone measurements exhibited by the ancestors persist in Southeast Asian populations until the early Holocene. Differences in cranial traits have, however, accumulated since the late Pleistocene in Australian Aborigines and early Southeast Asian peoples.
Phylogeographic analysis of pigtail macaque populations (Macaca nemestrina) inferred from mitochondrial DNA

Rosenblum LL, Supriatna J, Melnick DJ

Am J Phys Anthropol, 1997 Sep;104(1):35-45.
PMID: 9331452

Mitochondrial DNA variation was surveyed in nine populations of the pigtail macaque (Macaca nemestrina), covering all three recognized subspecies in Southeast Asia. To do this, a 2,300 base pair fragment spanning the mitochondrial NAD 3 and NAD 4 genes and flanking tRNA subunits leucine and glycine was targeted for amplification and digested with a battery of 16 restriction endonucleases. Out of a total of 107 individuals, 32 unique haplotypes could be distinguished. Parsimony and neighbor-joining analyses grouped the haplotypes into five strongly supported assemblages representing China/Thailand, Malaysia, Sumatra, Borneo, and Siberut. These results indicate that the mainland and island mtDNA haplotypes are strictly and uniquely limited to the geographic ranges of the recognized morphological subspecies. Cladistic and neighbor-joining analyses indicate that inferred phylogenies of mtDNA haplotypes are congruent with subspecies designations. Furthermore, in support of morphological studies, results indicate that the Mentawai macaque is most likely not a distinct species but a subspecies of M. nemestrina.
Distribution of red cell phosphoglucomutase-1 subtypes in several Mongoloid populations of East Asia

Saha N

Am J Phys Anthropol, 1988 Sep;77(1):91-6.
PMID: 2973240

The distribution of red cell phosphoglucomutase (PGM) subtypes was determined by starch-gel electrophoresis and isoelectric focusing in a group of 2,484 unrelated individuals from ten Mongoloid populations of East Asia. The sample comprised 998 Chinese from various localities--Singapore, 325; Malaysia, 270; Taiwan, 276; Hong Kong, 67; Fouzhou, 60--as well as 342 Koreans; 252 Filipinos; 529 Thais; 336 Malays, and 27 Indonesians. Altogether 15 phenotypes controlled by four common and five rare alleles at the PGM1 locus were observed in these populations. The frequency of the most frequent allele (PGM1+) varied from 0.56 to 0.74, with the highest frequency observed in the Singapore Chinese and the lowest in the Malays. Within the Chinese from different localities a significant degree of heterogeneity was observed at the PGM1 locus. The rare allele (PGM17)6 was observed only among the Chinese, Thais, and Malays, while the PGM1 was lacking in the Filipinos. A new allele with ahigh pI (6.5) was observed in a low frequency in all the populations but the Malays.
Genetic markers of an aboriginal Taiwanese population

Chen KH, Cann H, Chen TC, Van West B, Cavalli-Sforza L

Am J Phys Anthropol, 1985 Mar;66(3):327-37.
PMID: 3857010

A group of Taiwan aborigines, the Toroko, was typed for 21 classical genetic loci. This is part of an ongoing program aimed at a comprehensive study of Taiwan aborigines. In this first paper a short summary of historical, archeological, and anthropological data in the literature is made, and results of the present survey are compared with older results from other aborigine tribes. An analysis of other neighboring populations from southeast Asia has also been carried out in order to give a preliminary answer to the question of origin of Taiwanese aborigines. Fifteen populations were studied for 13 loci by tree analysis, principal components, and isolation by distance. Tree analysis and principal component analysis gave results in fairly good agreement and indicate three major population clusters: a northeast cluster (Ainu, Korea, Japan, and Ryukyu); a southeast cluster (south China, Thailand, Vietnam, Philippines, Taiwan, and Toroko); and a third cluster including Malaya and Borneo. The positions of Polynesia, Micronesia, and Melanesia are somewhat peripheral. Analysis of the tree shows some potential cases of convergence, perhaps owing to admixture, and of divergence. The analysis of isolation by distance shows that geographic propinquity is a reasonably good predictor of general similarity in this area.
Kin groups and trait groups: population structure and epidemic disease selection

Fix AG

Am J Phys Anthropol, 1984 Oct;65(2):201-12.
PMID: 6507610

A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of extinction, individual selection, and migration and a population structure realistic in its general form, has implications for specific human polymorphisms such as hemoglobin variants and for the more general problem of the tempo of evolution as well.
Fission-fusion and lineal effect: aspects of the population structure of the Semai Senoi of Malaysia

Fix AG

Am J Phys Anthropol, 1975 Sep;43(2):295-302.
PMID: 1180359

Analysis of histories and genealogies from seven relatively unacculturated, swidden-farming Semai settlements shows that the composition of local groups fluctuates through time. This instability is similar to a pattern which Neel and his colleagues have suggested is typical of primitive society, the fission-fusion model. In addition, the individuals comprising Semai fission groups are kinsmen which implies that the number of independent genomes represented is markedly less than the number of individual migrants (the lineal effect). Fission groups may form new villages or fuse with an established settlement. In either case, the genetic effects of such migration are more pronounced than would be expected on the basis of founder effect or random migration. Despite several conspicuous differences in social organization between the Semai and the South American Indians (e.g., bilateral vs. unilineal descent) whose population structure provided the empirical basis for the fission-fusion, lineal effect model, the basic similarities are striking. The Semai case thus lends support to the proposition that this pattern may be of some generality in technologically primitive populations.
Genetic microdifferentiation in the Semai Senoi of Malaysia

Fix AG, Lie-injo LE

Am J Phys Anthropol, 1975 Jul;43(1):47-55.
PMID: 1155591

Blood samples, demographic and cultural data were collected from seven settlements of Semai Senoi, a swidden farming ethnic group of Malaysia. Three genetic loci (ABO blood group, hereditary ovalcytosis, and hemoglobin) were analyzed in a total sample of 546 individuals. These data indicate a considerable degree of genetic microdifferentiation in this area of the Semai distribution. Parent-offspring birthplace data (analyzed by means of a migration matrix) and settlement histories show that settlements are not strongly isolated. Genetic differences in the study area demonstrate a reasonable correspondence with migration and the history of the settlements. Genetic convergence also occurs through the addition of migrant groups to established populations leading to new patterns of marriage between donor and recipient groups. The genetic structure of the total Semai population through time thus comprises a mosaic of shifiting allele frequencies in a series of semi-isolated local populations.
Some anthropometric studies of the femur of the male West Malaysian Chinese

Manuel JK, Yusof Bin Mohd M

Am J Phys Anthropol, 1974 Jul;41(1):133-7.
PMID: 4843090
Multiple fetal and adult hemoglobins in Malaysian Macaca nemestrina: consequences of a-chain variation

Nute PE, Pataryas HA

Am J Phys Anthropol, 1974 Jan;40(1):17-25.
PMID: 4206325
Evidence for a genetic cline in earwax types in the Middle East and Southeast Asia

Petrakis NL, Pingle U, Petrakis SJ, Petrakis SL

Am J Phys Anthropol, 1971 Jul;35(1):141-4.
PMID: 5138849
Multivariate statistical analysis on the physical interrelationship of native tribes in Sarawak, Malaysia

Kurisu K

Am J Phys Anthropol, 1970 Sep;33(2):229-34.
PMID: 5473088
Prevalence and patterning of maxillary premolar accessory ridges (MxPARs) in several human populations

Mihailidis S, Scriven G, Khamis M, Townsend G

Am J Phys Anthropol, 2013 Sep;152(1):19-30.
PMID: 23913636 DOI: 10.1002/ajpa.22323

We present new data on the prevalence and patterning of the maxillary premolar accessory ridge (MxPAR), a common but understudied morphological dental trait that is expressed as a linear elevation extending from the buccal cusp ridge to the medial sulcus of maxillary premolar teeth. A total of 579 sets of dental casts, representing six ethnic groups, were scored using the five-grade system proposed by Burnett et al. (2010). The frequency and distribution of the MxPAR were determined by tooth type, sex, side, locus and ethnicity, and the applicability of the scoring system was assessed. The MxPAR was found in approximately two-thirds of premolar teeth, more often on second than first premolars, and more often on the distal aspect of the occlusal surface than the mesial. There was some evidence that more pronounced forms of the feature occurred more often in males than females, and that there may be some directionality in its expression between sides. Variation was also noted in the frequency of occurrence and degree of expression of the MxPAR between ethnic groups. Intra- and inter-observer concordance rates for scoring the MxPAR were low, confirming that it was difficult to score the trait identically on two different occasions. Our findings have clarified the distribution of the MxPAR within the dentition and between ethnic groups, and highlighted the need for researchers to carry out thorough replicability studies and to decide on an appropriate breakpoint for determining presence or absence of this feature before embarking on genetic studies or bio-distance analyses.
Sleep patterns, daytime predation, and the evolution of diurnal sleep site selection in lorisiforms

Svensson MS, Nekaris KAI, Bearder SK, Bettridge CM, Butynski TM, Cheyne SM, et al.

Am J Phys Anthropol, 2018 07;166(3):563-577.
PMID: 29989160 DOI: 10.1002/ajpa.23450

OBJECTIVES: Synthesize information on sleep patterns, sleep site use, and daytime predation at sleep sites in lorisiforms of Asia and Africa (10 genera, 36 species), and infer patterns of evolution of sleep site selection.
MATERIALS AND METHODS: We conducted fieldwork in 12 African and six Asian countries, collecting data on sleep sites, timing of sleep and predation during daytime. We obtained additional information from literature and through correspondence. Using a phylogenetic approach, we established ancestral states of sleep site selection in lorisiforms and traced their evolution.
RESULTS: The ancestral lorisiform was a fur-clinger and used dense tangles and branches/forks as sleep sites. Use of tree holes and nests as sleep sites emerged ∼22 Mya (range 17-26 Mya) in Africa, and use of bamboo emerged ∼11 (7-14) Mya in Asia and later in Africa. Fur clinging and some sleep sites (e.g., tree holes, nests, but not bamboo or dense tangles) show strong phylogenetic signal. Nests are used by Galagoides, Paragalago, Galago and Otolemur; tree holes by Galago, Paragalago, Sciurocheirus and Perodicticus; tangles by Nycticebus, Loris, Galagoides, Galago, Euoticus, Otolemur, Perodicticus and Arctocebus; all but Sciurocheirus and Otolemur additionally sleep on branches/forks. Daytime predation may affect sleep site selection and sleep patterns in some species of Nycticebus, Galago, Galagoides, Otolemur and Perodicticus. Most lorisiforms enter their sleep sites around sunrise and leave around sunset; several are active during twilight or, briefly, during daytime.
CONCLUSION: Variations in sleep behavior, sleep patterns and vulnerability to daytime predation provide a window into the variation that was present in sleep in early primates. Overall, lorisiforms use the daytime for sleeping and no species can be classified as cathemeral or polycyclic.
Mitochondrial genomics identifies major haplogroups in Aboriginal Australians

van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM

Am J Phys Anthropol, 2006 Oct;131(2):282-94.
PMID: 16596590

We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.

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