Population history in the 1980s: the prospects for population history.
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Demography↗
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Genetic population history relationships of the population of Bogotá, Colombia, by using the D1S80, VWA, and TH01 molecular markers.
The genetic relationships of the population of Bogotá, Colombia, was comparatively studied with regard to other populations from America, Europe, and Asia, by using the D1S80, VWA, and TH01 molecular loci. From a population history point of view, the population of Bogotá seems to be more related to a European origin, with several differential contributions coming from Amerindians rather than from African and Asian populations, when the D1S80 and TH01 markers were employed. However, the contribution was greater from African populations for the VWA marker. Several explanations are offered to resolve the genetic affiliation of this population.
Adolescent↗
Understanding population history for conservation purposes: population genetics of Saxifraga aizoides (Saxifragaceae) in the lowlands and lower mountains north of the Alps.
Several alpine species have outlying populations in the lowlands and lower mountains north of the Alps. These small, isolated populations are usually described as either (1) glacial relics, (2) descendants from populations living on forelands and moraines during the ice ages, or (3) populations founded by long-distance dispersal after glaciation. A floristic survey of the historic and present distributions and an allozyme investigation were performed on one of these relic species, Saxifraga aizoides. The species was historically more abundant and had more stations in more regions of northeastern Switzerland. The former population structures within regions, nowadays destroyed, were still reflected in distinct and high regional genetic diversity and variation. There was weak evidence of increased inbreeding in outlying populations, but populations did not deviate from Hardy-Weinberg equilibrium. No geographic pattern of genetic variation above the regional scale (>10 km) was found. Based on the spatial and genetic structures found, it was not possible to discriminate between the abovementioned hypotheses. Nevertheless, the study shows how a thorough evaluation of distribution and abundance data aids the interpretation of genetic data with respect to population history, biogeography, and conservation biology.
Journal Article↗
A population history of North America. [Review of: Haines, M.R. and Steckel, R.H., ed. A population history of North America. New York: Cambridge U. Pr., 2000].
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Demography↗
A population history of North America. [Review of: Haines, M.R. and Steckel, R.H., ed. A population history of North America. New York: Cambridge U. Pr., 2000].
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Demography↗
A population history of North America. [Review of: Haines, M.R. and Steckel, R.H., ed. A population history of North America. New York: Cambridge U. Pr., 2000].
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Demography↗
Genetics and population history of Caucasus populations.
We describe aspects of genetic diversity in several ethnic populations of the Caucasus Mountains of Daghestan using mitochondrial DNA sequences and a sample of 100 polymorphic Alu insertion loci. The mitochondrial DNA (mtDNA) sequences are like those of Europe. Principal coordinates and nearest neighbor statistics show that there is little detectable structure in the distances among populations computed from mtDNA. The Alu frequencies of the Caucasus populations suggest that they have undergone more genetic drift than most other groups since the dispersal of modern humans. Genetic differences among these populations are not large; instead, they are of the same order as distances among populations of Europe. We compare two methods of inference about the demography of ancient colonizing populations from Africa, one based on conventional FST statistics and one based on mean Alu insertion frequencies. The two approaches agree reasonably well if we assume that there was demographic growth in Africa before the diaspora of ancestors of contemporary regional human groups outside Africa.
DNA, Mitochondrial↗
A population history of North America. [Review of: Haines, M.R. and Steckel, R.H., ed. A population history of North America. New York: Cambridge U. Pr., 2000].
Explore the source record for details and available documents.
Demography↗
Inferring population history from genealogical trees.
Inference about population history from DNA sequence data has become increasingly popular. For human populations, questions about whether a population has been expanding and when expansion began are often the focus of attention. For viral populations, questions about the epidemiological history of a virus, e.g., HIV-1 and Hepatitis C, are often of interest. In this paper I address the following question: Can population history be accurately inferred from single locus DNA data? An idealised world is considered in which the tree relating a sample of n non-recombining and selectively neutral DNA sequences is observed, rather than just the sequences themselves. This approach provides an upper limit to the information that possibly can be extracted from a sample. It is shown, based on Kingman's (1982a) coalescent process, that consistent estimation of parameters describing population history (e.g., a growth rate) cannot be achieved for increasing sample size, n. This is worse than often found for estimators of genetic parameters, e.g., the mutation rate typically converges at rate under the assumption that all historical mutations can be observed in the sample. In addition, various results for the distribution of maximum likelihood estimators are presented.
DNA↗
Anthropometric variation and the population history of Ireland.
Genetic variation among human populations can reflect a combination of contemporary patterns of gene flow and genetic drift as well as long-term population relationships due to population history. We examine the likely impact of past history and contemporary structure on the patterns of anthropometric variation among 31 counties in Ireland (made up of the two nations of the Republic of Ireland and Northern Ireland). Data for 17 anthropometric measures and parent-offspring migration on 7,214 adult Irish males were taken from the large data set originally collected by Dupertuis and Dawson in the mid-1930s (Hooton et al., 1955). Patterns of genetic similarity among 31 counties were assessed using R matrix methods that allow estimation of minimum genetic distances. These distances were compared to distances reflecting history, geography, and migration using matrix permutation methods. The results indicate that among-group variation in Ireland reflects past population history to a much greater extent than contemporary patterns of migration and population size. The midland counties are distinct from other populations, and their history suggests greater genetic input from early Viking invasions. A second major pattern in biological variation is a longitudinal gradient separating western and eastern counties. This gradient appears related to patterns of early settlement and/or a concentration in the east of later immigrants, particularly from England. Comparison of regional means with published data for several other European nations confirms these hypotheses.
Adult↗
Genetic drift can obscure population history: problem and solution.
Genetic distances between populations can be derived from a wide variety of data and have been applied to studies of population structure and history ranging from local groups to an entire species. Genetic distances measure the effects of both population history (historical relations and migration) and population structure (migration and drift). Frequently, we are interested in assessing population history, and any impact of differential genetic drift is likely to confound our interpretations. I show here that when population sizes are different, differential genetic drift can obscure the underlying pattern of population history. Previous genetic distance studies have failed to take genetic drift into account when reconstructing population history. A simple method is presented here that takes into account differences in population size and differential drift. This method is illustrated using allele frequencies from Jewish and non-Jewish populations in six Old World regions. The scaled distances provide a clearer picture of population history than the traditional unscaled distances.
Bias↗
Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci.
This paper examines orangutan population history and evolution through a meta-analysis of seven loci collected from both Sumatran and Bornean orangutans. Within orangutans, most loci show that the Sumatran population is about twice as diverse as the Bornean population. Orangutans are more diverse than African apes and humans. Sumatran and Bornean populations show significant genetic differentiation from one another and their history does not differ significantly from an 'island model' (population splitting without gene flow). Two different methods support a divergence of Bornean and Sumatran orangutans at 2.7-5 million years ago. This suggests that Pleistocene events, such as the cyclical exposure of the Sunda shelf and the Toba volcanic eruption, did not have a major impact on the divergence of Bornean and Sumatran orangutans. Pairwise mismatch analyses, however, suggest that Bornean orangutans have undergone a recent population expansion (beginning 39,000-64,000 years ago), while Sumatran orangutan populations were stable. Pleistocene events may have contributed to these aspects of orangutan population history. These conclusions are applied to the debate on orangutan taxonomy.
Animals↗
Family planning in St Vincent, West Indies: a population history perspective.
St Vincent's population history, first as a slave society, then, after Emancipation, as a migration-oriented society, has strongly influenced cultural attitudes towards sexuality and fertility. In contemporary St Vincent, sexual activity and procreative ability are highly valued and linked to social status for both men and women. This paper assesses historical and contemporary factors influencing population dynamics in St Vincent, West Indies, and Vincentians' reactions to programs developed to curb population growth. The efforts of private and government programs to introduce family planning and change pronatalist attitudes are evaluated for their cultural appropriateness. Shifting migration patterns and modernization are also affecting gender roles, the social and economic value of children, and the acceptability of contraception to contribute to recent fertility declines.
Adolescent↗
Inference of population history using a likelihood approach.
We introduce an approach to revealing the likelihood of different population histories that utilizes an explicit model of sequence evolution for the DNA segment under study. Based on a phylogenetic tree reconstruction method we show that a Tamura-Nei model with heterogeneous mutation rates is a fair description of the evolutionary process of the hypervariable region I of the mitochondrial DNA from humans. Assuming this complex model still allows the estimation of population history parameters, we suggest a likelihood approach to conducting statistical inference within a class of expansion models. More precisely, the likelihood of the data is based on the mean pairwise differences between DNA sequences and the number of variable sites in a sample. The use of likelihood ratios enables comparison of different hypotheses about population history, such as constant population size during the past or an increase or decrease of population size starting at some point back in time. This method was applied to show that the population of the Basques has expanded, whereas that of the Biaka pygmies is most likely decreasing. The Nuu-Chah-Nulth data are consistent with a model of constant population.
Base Composition↗
X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations.
Linkage disequilibrium (LD) structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity -- Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) -- in 15 Eurasian populations. Demographic events predicted to increase the LD level -- genetic drift, bottleneck and admixture - had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225-DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25-40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasize the importance of understanding the history, structure and variation of a study population.
Asia↗
Human cranial anatomy and the differential preservation of population history and climate signatures.
Cranial morphology is widely used to reconstruct evolutionary relationships, but its reliability in reflecting phylogeny and population history has been questioned. Some cranial regions, particularly the face and neurocranium, are believed to be influenced by the environment and prone to convergence. Others, such as the temporal bone, are thought to reflect more accurately phylogenetic relationships. Direct testing of these hypotheses was not possible until the advent of large genetic data sets. The few relevant studies in human populations have had intriguing but possibly conflicting results, probably partly due to methodological differences and to the small numbers of populations used. Here we use three-dimensional (3D) geometric morphometrics methods to test explicitly the ability of cranial shape, size, and relative position/orientation of cranial regions to track population history and climate. Morphological distances among 13 recent human populations were calculated from four 3D landmark data sets, respectively reflecting facial, neurocranial, and temporal bone shape; shape and relative position; overall cranial shape; and centroid sizes. These distances were compared to neutral genetic and climatic distances among the same, or closely matched, populations. Results indicate that neurocranial and temporal bone shape track neutral genetic distances, while facial shape reflects climate; centroid size shows a weak association with climatic variables; and relative position/orientation of cranial regions does not appear correlated with any of these factors. Because different cranial regions preserve population history and climate signatures differentially, caution is suggested when using cranial anatomy for phylogenetic reconstruction.
Acclimatization↗
Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history.
Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.
Alleles↗
Craniometric variation and population history of the prehistoric Tewa.
Although the population history and social organization of the prehistoric Pueblo Indians of the American Southwest have received attention in the archaeological literature, little research on this topic has been conducted by biological anthropologists. Here, we examine postmarital residence at two ancestral Tewa Indian pueblos located in north-central New Mexico using determinant ratio analysis. In addition, we examine genetic relationships among pueblos, as well as levels of within-pueblo heterogeneity due to gene flow from extraregional sources, or regional aggregation. Results from determinant ratio analysis indicate greater within-pueblo male variation, consistent with matrilocal residence for at least one Tewa pueblo. Less than expected heterogeneity at two pueblos suggests that endogamy might have been practiced among some prehistoric Tewa pueblos. Gene flow from extraregional sources is indicated for two different pueblos by greater than expected within-group heterogeneity. Distance matrix correlation analyses indicate little if any relationship between phenotypic and geographic distances, suggesting that geography was not the primary basis of gene flow or mate exchange. The weak relationship between phenotypic and geographic distances may be the combined effects of endogamy at some pueblos, nonrandom extraregional gene flow or migration at other pueblos, and limited nonproximity-dependent regional gene flow or migration among pueblos, possibly structured on ritual exchange networks based on medicine society affiliation.
Anthropology↗