Genotypes for 13 short tandem repeats (STRs) were used to assess the genetic diversity within and... more Genotypes for 13 short tandem repeats (STRs) were used to assess the genetic diversity within and differentiation among populations of rhesus macaques (Macaca mulatta) from mainland Asia and long-tailed macaques (M. fascicularis) from mainland and insular Southeast Asia. These animals were either recently captured in the wild or derived from wild-caught founders maintained in captivity for biomedical research.A large number of alleles is shared between the two macaque species but a significant genetic division between them persists. This distinction is more clear-cut among populations that are not, or are unlikely to have recently been, geographically contiguous. Our results suggest there has been significant interspecies nuclear gene flow between rhesus macaques and long-tailed macaques on the mainland. Comparisons of mainland and island populations of long-tailed macaques reflect marked genetic subdivisions due to barriers to migration. Geographic isolation has restricted gene flo...
Author(s): Santos, Guaciara M.; Mariana Fabr, Mariana; Laguens, Andres G.; Demarchi, Dario A.; So... more Author(s): Santos, Guaciara M.; Mariana Fabr, Mariana; Laguens, Andres G.; Demarchi, Dario A.; Southon, John R.; Taylor, R. Erv; George, Debra | Abstract: In this paper, we present an overview of 14C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountain...
The California National Primate Research Center maintains a small colony of titi monkeys (Callice... more The California National Primate Research Center maintains a small colony of titi monkeys (Callicebus cupreus) for behavioral studies. While short tandem repeat (STR) markers are critical for the genetic management of the center's rhesus macaque (Macaca mulatta) breeding colony, STRs are not used for this purpose in the maintenance of the…
The cynomolgus macaque, Macaca fascicularis, was introduced onto the island of Mauritius in the e... more The cynomolgus macaque, Macaca fascicularis, was introduced onto the island of Mauritius in the early 17 th century. The species experienced explosive population growth, and currently exists at high population densities. Anecdotes collected from nonhuman primate trappers on the island of Mauritius allege that animals from the northern portion of the island are larger in body size than and superior in condition to their conspecifics in the south. Although previous genetic studies have reported Mauritian cynomolgus macaques to be panmictic, the individuals included in these studies were either from the southern/central or an unknown portion of the island. In this study, we sampled individuals broadly throughout the entire island of Mauritius and used spatial principle component analysis to measure the fine-scale correlation between geographic and genetic distance in this population. A stronger correlation between geographic and genetic distance was found among animals in the north than in those in the southern and central portions of the island. We found no difference in body weight between the two groups, despite anecdotal evidence to the contrary. We hypothesize that the increased genetic structure among populations in the north is related to a reduction in dispersal distance brought about by human habitation and tourist infrastructure, but too recent to have produced true genetic differentiation.
The genetic structures of wild and captive rhesus macaque populations within China were compared ... more The genetic structures of wild and captive rhesus macaque populations within China were compared by analyzing the mtDNA sequences of 203 captive-bred Chinese rhesus macaques with 77 GenBank sequences from wild-caught animals trapped throughout China. The genotypes of 22 microsatellites of captive Chinese rhesus macaques were also compared with those of captive Indian animals. The Chinese population is significantly differentiated from the Indian population and is more heterogeneous. Thus, compared with Indian rhesus macaques the phenotypic variance of traits with high heritability will be inflated in Chinese animals. Our data suggest that the western Chinese provinces have more subdivided populations than the eastern and southern Chinese provinces. The southern Chinese populations are the least structured and might have been more recently established. Human-mediated interbreeding among captive Chinese populations has occurred, implying that Chinese breeding strategies can influence the interpretation of biomedical research in the USA.
Fullbred Chinese and Indian rhesus macaques represent genetically distinct populations. The Calif... more Fullbred Chinese and Indian rhesus macaques represent genetically distinct populations. The California National Primate Research Center introduced Chinese founders into its Indian-derived rhesus colony in response to the 1978 Indian embargo on exportation of animals for research and the concern that loss of genetic variation in the closed colony would hamper research efforts. The resulting hybrid rhesus now number well over a thousand animals and represent a growing proportion of the animals in the colony. We characterized the population genetic structure of the hybrid colony and compared it to that of their pure Indian and Chinese progenitors. The hybrid population contains higher genetic diversity and linkage disequilibrium than their full Indian progenitors and represents a resource with unique research applications. The genetic diversity of the hybrids indicates that the strategy to introduce novel genes into the colony by hybridizing Chinese founders and their hybrid offspring with Indianderived animals was successful.
We describe a restriction analysis that distinguishes between rhesus macaques of unmixed Indian a... more We describe a restriction analysis that distinguishes between rhesus macaques of unmixed Indian and Chinese ancestry and between western and eastern Chinese ancestry. We amplified a 254-bp fragment of mitochondrial DNA (mtDNA) that contains restriction sites hypothesized to be diagnostic of country of origin for samples from 534 and 567 individuals alleged to be of solely Indian or solely Chinese ancestry, respectively. After digestion with the MaeIII, SmlI, and BccI restriction enzymes, the polymerase chain reaction (PCR) products of only 3 of the 1101 samples exhibited restriction patterns uncharacteristic of their alleged country of origin. We genotyped a sample comprising 392 of these rhesus macaques for 24 nuclear microsatellite (STR) loci. Principal coordinates analysis confirmed marked genetic similarity of regional populations within each country but a substantial difference between Indian and Chinese rhesus macaques. Using STRUCTURE (Pritchard and Wen, 2003),we assigned probabilities of Chinese and Indian ancestry to each sample based on its STR genotypes. We assigned all the unmixed rhesus macaques to their correct countries of origin with probabilities >0.95. We constructed an artificial sample of 1st-generation hybrid Indian/Chinese rhesus macaques by randomly sampling from the genotypes of Indian and Chinese individuals. STRUCTURE assigned probabilities of Chinese and Indian ancestry to hybrids that closely corresponded with the proportions
Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites ... more Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites in South Dakota occupied between AD 1600 and 1832. The diagnostic markers of four mtDNA haplogroups to which most Native Americans belong (A, B, C, and D) were successfully identified in the extracts of 55 (87%) of the 63 samples studied. The frequencies of the four haplogroups were 42%, 29%, 22%, and 7%, respectively, and principal coordinates analysis and Fisher's exact tests were conducted to compare these haplogroup frequencies with those from other populations. Both analyses showed closer similarity among the Mohawk, Arikara, and Sioux populations than between any of these three and any other of the comparison populations. Portions of the first hypervariable segment (HVSI) of the mitochondrial genome were successfully amplified and sequenced for 42 of these 55 samples, and haplotype networks were constructed for two of the four haplogroups. The sharing of highly derived lineages suggests that some recent admixture of the Arikara with Algonquian-speaking and Siouan-speaking groups has occurred. The Arikara shared more ancient lineages with both Siouan and Cherokee populations than with any other population, consistent with the Macro-Siouan language hypothesis that Iroquoian, Siouan, and Caddoan languages share a relatively recent common ancestry.
Previous 14C determinations obtained on two segments of a single mastodon bone recovered from Mon... more Previous 14C determinations obtained on two segments of a single mastodon bone recovered from Monte Verde, Chile, were highly discordant, differing by more than 5,000 years. Because of the significance of this site in discussions concerning the earliest peopling of the Western Hemisphere, additional 14C and new δ13C values have been obtained on organic fractions isolated from both segments. The constituent amino acid profiles indicate that both bone segments retain significant amounts of protein (mostly collagen) residues. Four accelerator mass spectrometry-based 14C values obtained on total amino acids and ultrafiltered gelatin fractions—two from each segment—are statistically identical and indicate an age of 12,460 (± 30) BP for the mastodon. This value is concordant with 14C values obtained on other culturally affiliated organics associated with the MV-II levels at this site.
In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techni... more In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14 C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountains of Argentina, and b) the implication of new 14 C determinations obtained from two segments of a single mastodon bone recovered from Monte Verde, that previously differed by more than 5,000 years.
In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techni... more In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14 C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountains of Argentina, and b) the implication of new 14 C determinations obtained from two segments of a single mastodon bone recovered from Monte Verde, that previously differed by more than 5,000 years.
Genotypes for 13 short tandem repeats (STRs) were used to assess the genetic diversity within and... more Genotypes for 13 short tandem repeats (STRs) were used to assess the genetic diversity within and differentiation among populations of rhesus macaques (Macaca mulatta) from mainland Asia and long-tailed macaques (M. fascicularis) from mainland and insular Southeast Asia. These animals were either recently captured in the wild or derived from wild-caught founders maintained in captivity for biomedical research.A large number of alleles is shared between the two macaque species but a significant genetic division between them persists. This distinction is more clear-cut among populations that are not, or are unlikely to have recently been, geographically contiguous. Our results suggest there has been significant interspecies nuclear gene flow between rhesus macaques and long-tailed macaques on the mainland. Comparisons of mainland and island populations of long-tailed macaques reflect marked genetic subdivisions due to barriers to migration. Geographic isolation has restricted gene flo...
Author(s): Santos, Guaciara M.; Mariana Fabr, Mariana; Laguens, Andres G.; Demarchi, Dario A.; So... more Author(s): Santos, Guaciara M.; Mariana Fabr, Mariana; Laguens, Andres G.; Demarchi, Dario A.; Southon, John R.; Taylor, R. Erv; George, Debra | Abstract: In this paper, we present an overview of 14C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountain...
The California National Primate Research Center maintains a small colony of titi monkeys (Callice... more The California National Primate Research Center maintains a small colony of titi monkeys (Callicebus cupreus) for behavioral studies. While short tandem repeat (STR) markers are critical for the genetic management of the center's rhesus macaque (Macaca mulatta) breeding colony, STRs are not used for this purpose in the maintenance of the…
The cynomolgus macaque, Macaca fascicularis, was introduced onto the island of Mauritius in the e... more The cynomolgus macaque, Macaca fascicularis, was introduced onto the island of Mauritius in the early 17 th century. The species experienced explosive population growth, and currently exists at high population densities. Anecdotes collected from nonhuman primate trappers on the island of Mauritius allege that animals from the northern portion of the island are larger in body size than and superior in condition to their conspecifics in the south. Although previous genetic studies have reported Mauritian cynomolgus macaques to be panmictic, the individuals included in these studies were either from the southern/central or an unknown portion of the island. In this study, we sampled individuals broadly throughout the entire island of Mauritius and used spatial principle component analysis to measure the fine-scale correlation between geographic and genetic distance in this population. A stronger correlation between geographic and genetic distance was found among animals in the north than in those in the southern and central portions of the island. We found no difference in body weight between the two groups, despite anecdotal evidence to the contrary. We hypothesize that the increased genetic structure among populations in the north is related to a reduction in dispersal distance brought about by human habitation and tourist infrastructure, but too recent to have produced true genetic differentiation.
The genetic structures of wild and captive rhesus macaque populations within China were compared ... more The genetic structures of wild and captive rhesus macaque populations within China were compared by analyzing the mtDNA sequences of 203 captive-bred Chinese rhesus macaques with 77 GenBank sequences from wild-caught animals trapped throughout China. The genotypes of 22 microsatellites of captive Chinese rhesus macaques were also compared with those of captive Indian animals. The Chinese population is significantly differentiated from the Indian population and is more heterogeneous. Thus, compared with Indian rhesus macaques the phenotypic variance of traits with high heritability will be inflated in Chinese animals. Our data suggest that the western Chinese provinces have more subdivided populations than the eastern and southern Chinese provinces. The southern Chinese populations are the least structured and might have been more recently established. Human-mediated interbreeding among captive Chinese populations has occurred, implying that Chinese breeding strategies can influence the interpretation of biomedical research in the USA.
Fullbred Chinese and Indian rhesus macaques represent genetically distinct populations. The Calif... more Fullbred Chinese and Indian rhesus macaques represent genetically distinct populations. The California National Primate Research Center introduced Chinese founders into its Indian-derived rhesus colony in response to the 1978 Indian embargo on exportation of animals for research and the concern that loss of genetic variation in the closed colony would hamper research efforts. The resulting hybrid rhesus now number well over a thousand animals and represent a growing proportion of the animals in the colony. We characterized the population genetic structure of the hybrid colony and compared it to that of their pure Indian and Chinese progenitors. The hybrid population contains higher genetic diversity and linkage disequilibrium than their full Indian progenitors and represents a resource with unique research applications. The genetic diversity of the hybrids indicates that the strategy to introduce novel genes into the colony by hybridizing Chinese founders and their hybrid offspring with Indianderived animals was successful.
We describe a restriction analysis that distinguishes between rhesus macaques of unmixed Indian a... more We describe a restriction analysis that distinguishes between rhesus macaques of unmixed Indian and Chinese ancestry and between western and eastern Chinese ancestry. We amplified a 254-bp fragment of mitochondrial DNA (mtDNA) that contains restriction sites hypothesized to be diagnostic of country of origin for samples from 534 and 567 individuals alleged to be of solely Indian or solely Chinese ancestry, respectively. After digestion with the MaeIII, SmlI, and BccI restriction enzymes, the polymerase chain reaction (PCR) products of only 3 of the 1101 samples exhibited restriction patterns uncharacteristic of their alleged country of origin. We genotyped a sample comprising 392 of these rhesus macaques for 24 nuclear microsatellite (STR) loci. Principal coordinates analysis confirmed marked genetic similarity of regional populations within each country but a substantial difference between Indian and Chinese rhesus macaques. Using STRUCTURE (Pritchard and Wen, 2003),we assigned probabilities of Chinese and Indian ancestry to each sample based on its STR genotypes. We assigned all the unmixed rhesus macaques to their correct countries of origin with probabilities >0.95. We constructed an artificial sample of 1st-generation hybrid Indian/Chinese rhesus macaques by randomly sampling from the genotypes of Indian and Chinese individuals. STRUCTURE assigned probabilities of Chinese and Indian ancestry to hybrids that closely corresponded with the proportions
Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites ... more Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites in South Dakota occupied between AD 1600 and 1832. The diagnostic markers of four mtDNA haplogroups to which most Native Americans belong (A, B, C, and D) were successfully identified in the extracts of 55 (87%) of the 63 samples studied. The frequencies of the four haplogroups were 42%, 29%, 22%, and 7%, respectively, and principal coordinates analysis and Fisher's exact tests were conducted to compare these haplogroup frequencies with those from other populations. Both analyses showed closer similarity among the Mohawk, Arikara, and Sioux populations than between any of these three and any other of the comparison populations. Portions of the first hypervariable segment (HVSI) of the mitochondrial genome were successfully amplified and sequenced for 42 of these 55 samples, and haplotype networks were constructed for two of the four haplogroups. The sharing of highly derived lineages suggests that some recent admixture of the Arikara with Algonquian-speaking and Siouan-speaking groups has occurred. The Arikara shared more ancient lineages with both Siouan and Cherokee populations than with any other population, consistent with the Macro-Siouan language hypothesis that Iroquoian, Siouan, and Caddoan languages share a relatively recent common ancestry.
Previous 14C determinations obtained on two segments of a single mastodon bone recovered from Mon... more Previous 14C determinations obtained on two segments of a single mastodon bone recovered from Monte Verde, Chile, were highly discordant, differing by more than 5,000 years. Because of the significance of this site in discussions concerning the earliest peopling of the Western Hemisphere, additional 14C and new δ13C values have been obtained on organic fractions isolated from both segments. The constituent amino acid profiles indicate that both bone segments retain significant amounts of protein (mostly collagen) residues. Four accelerator mass spectrometry-based 14C values obtained on total amino acids and ultrafiltered gelatin fractions—two from each segment—are statistically identical and indicate an age of 12,460 (± 30) BP for the mastodon. This value is concordant with 14C values obtained on other culturally affiliated organics associated with the MV-II levels at this site.
In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techni... more In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14 C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountains of Argentina, and b) the implication of new 14 C determinations obtained from two segments of a single mastodon bone recovered from Monte Verde, that previously differed by more than 5,000 years.
In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techni... more In this paper, we present an overview of 14 C methods, Accelerator Mass Spectrometry (AMS) techniques, and their applications to radiocarbon dating of archaeological sites in South America. We describe sample preparation methods to be applied to archaeological bone samples as well as useful sample selection strategies to help achieve reliable AMS-based 14 C results. Application of criteria to determine bone quality (to assess lack of alteration and degradation) before and during sample preparation, and the use of a modified ultrafiltration method to extract collagen from these kinds of materials have enabled us to obtain reliable radiocarbon results. Two applications will be presented to illustrate these issues: a) Paleodietary inferences from isotopic measurements on human bone and teeth from the populations of the central mountains of Argentina, and b) the implication of new 14 C determinations obtained from two segments of a single mastodon bone recovered from Monte Verde, that previously differed by more than 5,000 years.
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