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On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas  [PDF]
Jody Hey
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0030193
Abstract: The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.
On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas  [PDF]
Jody Hey
PLOS Biology , 2005, DOI: 10.1371/journal.pbio.0030193
Abstract: The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.
Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure  [PDF]
Pongsakorn Wangkumhang, Philip James Shaw, Kridsadakorn Chaichoompu, Chumpol Ngamphiw, Anunchai Assawamakin, Manit Nuinoon, Orapan Sripichai, Saovaros Svasti, Suthat Fucharoen, Verayuth Praphanphoj, Sissades Tongsima
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079522
Abstract: There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects.
Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions  [PDF]
Ryan M. Ames, Daniel Money, Simon C. Lovell
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099480
Abstract: The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.
Genetic Variability and Population Structure of Ark Shell in Japan  [PDF]
Tomomi Tanaka, Futoshi Aranishi
Open Journal of Marine Science (OJMS) , 2014, DOI: 10.4236/ojms.2014.41002
Abstract:

Ark shell Scapharca kagoshimensis is one of the commercially important bivalve resources in East Asia. In Japan, the mass production method for its natural seedlings was developed in the 1880s, and they had been transplanted to an array of the major fishing areas. It has been therefore concerned with its genetic disturbance among not only current but also former fishing areas in Japan. This study was undertaken to ascertain its genetic diversity and population structure in East Asia by means of nucleotide sequence analysis of a 555-bp portion of the mitochondrial DNA COI gene. Of 225 individuals collected from 8 populations and 1 population in Japan and Korea, respectively, a total of 59 haplotypes, including 14 common haplotypes, were found, and Japan and Korea shared 3 common haplotypes. In Japan, the haplotype diversity and nucleotide diversity ranged from 0.65 to 0.93 and from 0.22% to 0.59%, respectively, reflecting relatively high levels of genetic diversity. The values in Korea were determined to be 0.45% and 0.19%, respectively, indicating significantly lower genetic diversity compared with that in Japan. Mismatch distribution analysis and neutrality tests showed a recent history of multiple types of reproduction and signals of demographic change in each population. These results suggest that S. kagoshimensis has experienced rapid population growth or reduction in population size such as a bottleneck in a short period.

Inferring the Composition of a Trader Population in a Financial Market  [PDF]
Nachi Gupta,Raphael Hauser,Neil F. Johnson
Physics , 2007, DOI: 10.1007/978-88-470-0665-2_7
Abstract: We discuss a method for predicting financial movements and finding pockets of predictability in the price-series, which is built around inferring the heterogeneity of trading strategies in a multi-agent trader population. This work explores extensions to our previous framework (arXiv:physics/0506134). Here we allow for more intelligent agents possessing a richer strategy set, and we no longer constrain the estimate for the heterogeneity of the agents to a probability space. We also introduce a scheme which allows the incorporation of models with a wide variety of agent types, and discuss a mechanism for the removal of bias from relevant parameters.
Elderly Population Projection and Their Health Expenditure Prospects in Japan  [PDF]
Tetsuo Fukawa
Modern Economy (ME) , 2017, DOI: 10.4236/me.2017.811085
Abstract: By using a dynamic micro-simulation model named INAHSIM-II, we conducted a population-household projection in Japan (INAHSIM 2017) for the period of 2015-2065. Due to rapid aging of the population, the distribution of the elderly (65 years old or older) by dependency level has a profound impact on health expenditure (namely medical expenditure and long-term care expenditure) of the elderly. In this paper, we estimated health expenditure of the elderly in 2025-2065, using the results of the projection of the elderly by dependency level.
Genomic view on the peopling of India  [cached]
Tamang Rakesh,Thangaraj Kumarasamy
Investigative Genetics , 2012, DOI: 10.1186/2041-2223-3-20
Abstract: India is known for its vast human diversity, consisting of more than four and a half thousand anthropologically well-defined populations. Each population differs in terms of language, culture, physical features and, most importantly, genetic architecture. The size of populations varies from a few hundred to millions. Based on the social structure, Indians are classified into various caste, tribe and religious groups. These social classifications are very rigid and have remained undisturbed by emerging urbanisation and cultural changes. The variable social customs, strict endogamy marriage practices, long-term isolation and evolutionary forces have added immensely to the diversification of the Indian populations. These factors have also led to these populations acquiring a set of Indian-specific genetic variations responsible for various diseases in India. Interestingly, most of these variations are absent outside the Indian subcontinent. Thus, this review is focused on the peopling of India, the caste system, marriage practice and the resulting health and forensic implications.
GM and KM immunoglobulin allotypes in the Galician population: new insights into the peopling of the Iberian Peninsula
Rosario Calderón, Rosa Lodeiro, Tito A Varela, José Fari?a, Beatriz Ambrosio, Evelyne Guitard, Antonio González-Martín, Jean M Dugoujon
BMC Genetics , 2007, DOI: 10.1186/1471-2156-8-37
Abstract: Galician population shows a genetic profile for GM haplotypes that is defined by the high presence of the European Mediterranean GM*3 23 5* haplotype, and the relatively high incidence of the African marker GM*1,17 23' 5*. Data based on comparisons between Galician and other Spanish populations (mainly from the north of the peninsula) reveal a poor correlation between geographic and genetic distances (r = 0.30, P = 0.105), a noticeable but variable genetic distances between Galician and Basque subpopulations, and a rather close genetic affinity between Galicia and Valencia, populations which are geographically separated by a long distance and have quite dissimilar cultures and histories. Interestingly, Galicia occupies a central position in the European genetic map, despite being geographically placed at one extreme of the European continent, while displaying a close genetic proximity to Portugal, a finding that is consistent with their shared histories over centuries.These findings suggest that the population of Galicia is the result of a relatively balanced mixture of European populations or of the ancestral populations that gave rise to them. This would support the importance of the migratory movements that have taken place in Europe over the course of recent human history and their effects on the European genetic landscape.Galicia is located at the north-west tip of the Iberian Peninsula and covers an area of 29 424 km2, 5.8% of the total area of Spain. It forms part of the Cantabrian mountain range, which extends along the coast of the Cantabrian Sea from Cape Finisterre to the western limit of the Pyrenees. The territory is bordered to the north and west by the Atlantic Ocean, to the south by Portugal and to the east by the regions of Asturias and Leon (Figure 1).Galicia is currently divided into four provinces: La Coru?a, Lugo, Orense and Pontevedra. Its economy has traditionally been based on agriculture and fishing. The population of Galicia has a high leve
Updated Three-Stage Model for the Peopling of the Americas  [PDF]
Connie J. Mulligan, Andrew Kitchen, Michael M. Miyamoto
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003199
Abstract: Background We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. ~40,000 years ago) expansion signal we had proposed for the proto-Amerind population. Methodology/Findings Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World. Conclusions/Significance The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.
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