Patterns of Admixture and Population Structure in Native Populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.     

The emergence of obesity among indigenous Siberians

Once considered a disease of affluence and confined to industrialized nations, obesity is currently emerging as a major health concern in nearly every country in the world. Available data suggest that the prevalence rate of obesity has reached unprecedented levels in most developing countries, and is increasing at a rate that far outpaces that of developed nations. This increase in obesity has also been documented among North American circumpolar populations and is associated with lifestyle changes related to economic development. While obesity has not been well studied among indigenous Siberians, recent anthropological studies indicate that obesity and its associated comorbidities are important health problems.The present study examines recent adult body composition data from four indigenous Siberian populations (Evenki, Ket, Buriat, and Yakut) with two main objectives: 1) to determine the prevalence of overweight and obesity among these groups, and 2) to assess the influence of lifestyle and socioeconomic factors on the development of excess body fat. The results of this study indicate that obesity has emerged as an important health issue among indigenous Siberians, and especially for women, whose obesity rates are considerably higher than those of men (12% vs. 7%). The present study investigated the association between lifestyle and body composition among the Yakut, and documented substantial sex differences in lifestyle correlates of obesity. Yakut men with higher incomes and who owned more luxury consumer goods were more likely to have excess body fat while, among Yakut women, affluence was not strongly associated with overweight and obesity.     

Secular changes in craniofacial morphology of the Portuguese using geometric morphometrics

This study examines patterns of secular change in cranial morphology in the New Lisbon collection, a documented skeletal collection from Lisbon, Portugal with birth years from 1806 to 1954. This period represents a time when Lisbon was undergoing increased urbanization and population growth, as well as changes in mortality and fertility patterns. Previous studies from the U.S., Europe, and Japan have reported significant secular changes in cranial morphology over the past 200 years. In the current study, secular changes were analyzed using three-dimensional geometric morphometrics methods. The results from this study demonstrate a significant change in cranial morphology over the roughly 150-year period. Allometry was rejected as a causal factor of this change because there was no association found between temporal change and size. The pattern of temporal change is similar to that observed in other populations in the U.S., Europe, and Japan, including decreased facial breadth and a more inferiorly placed cranial base. This study, along with previous research, suggests a similar pattern of change occurs in genetically and geographically diverse populations experiencing modern environmental conditions. We argue that because the secular changes are focused in the cranial base, a region of the skull that experiences a relatively early growth curve, changes related to declines in childhood morbidity and mortality are likely important factors related to the observed changes.     

Traditional anti-malarial medicine in Roraima, Brazil

Malaria is probably the most serious health problem facing northern Amazonia, and isolated populations can benefit greatly from the knowledge of local resources which may effectively be used to control it. The results of an ethnobotanical survey of the plant species used in the treatment of malaria in the Brazilian State of Roraima are presented. Fieldwork was carried out amongst seven savanna-and forest-dwelling indigenous groups, and among the Luso-Brazilian population. Ninety-nine species, of 82 genera and 41 families, were identified as having been used for this purpose in the region. The results are discussed in the context of previously published information on anti-malarial plants of northern Latin America, which was analysed by a broad literature survey whose overall results are also presented here. Of the species collected in Roraima, only 24 appear previously to have been reported as anti-malarials, although 49% of the represented genera are known to be used in this way elsewhere. The plants are currently undergoing laboratory screening for anti-malarial activity and toxicity.     

Assessing the Potential of Indigenous-Run Demographic/Health Surveys: the 2005 Shuar Survey,Ecuador

Despite improved national censuses and “micro-demographic” studies, demographic processes and health conditions among indigenous populations in Amazonia and elsewhere in lowland Latin America are not well understood. A new source of demographic and health data has emerged in the past decade, namely meso-scale surveys initiated and administered by indigenous organizations. These surveys offer the potential for filling information gaps, shedding light on culturally specific factors that shape demographic processes and health, and empowering indigenous organizations with data that could inform health initiatives. This article assesses the indigenous-run survey “2005 Health Analysis of the Shuar and Achuar Nations” of eastern Ecuador in which the authors were involved, which reached 1,943 households in 257 communities in Morona-Santiago Province. We present findings on fertility, migration, sanitation, and health, and assess the strengths and weaknesses of the survey. We argue that despite flaws in the survey design and implementation, this survey revealed important linkages among fertility, migration, and health. Such surveys have the potential to provide much needed detail, representativeness, and cultural specificity that macro and micro data sources cannot provide. We conclude with recommendations to improve surveys of this type.     

Human population growth and the demographic transition

The world and most regions and countries are experiencing unprecedentedly rapid demographic change. The most obvious example of this change is the huge expansion of human numbers: four billion have been added since 1950. Projections for the next half century expect a highly divergent world, with stagnation or potential decline in parts of the developed world and continued rapid growth in the least developed regions. Other demographic processes are also undergoing extraordinary change: women''s fertility has dropped rapidly and life expectancy has risen to new highs. Past trends in fertility and mortality have led to very young populations in high fertility countries in the developing world and to increasingly older populations in the developed world. Contemporary societies are now at very different stages of their demographic transitions. This paper summarizes key trends in population size, fertility and mortality, and age structures during these transitions. The focus is on the century from 1950 to 2050, which covers the period of most rapid global demographic transformation.     

Rapid micro-evolution and loss of chromosomal diversity in Drosophila in response to climate warming

Concern regarding the ecological impact of rapid global warming has encouraged research on climate-induced changes in biological systems. Critical problems, still poorly understood, are the potential for rapid adaptive responses and their genetic costs to populations. The O chromosomal polymorphisms of Drosophila subobscura have been monitored at a southern Palearctic locality experiencing sustained climate warming since the mid-1970s. Observations suggest that the population is rapidly evolving in response to the new environmental conditions, and has lost a significant amount of chromosomal diversity (18.3% in 16 years). These findings are consistent with results from another population of D. subobscura, which is also undergoing climate warming, and are in accord with what would be expected from latitudinal and seasonal patterns of the various inversions. In addition, data on the O chromosomal polymorphisms from other localities throughout t he range of this species suggest that other populations vary similarly.     

Consanguinity and demography in some Chilean populations.

Spatial and temporal changes in the rates and the patterns of consanguinity are studied in some (indigenous as well as admixed) populations of Chile. Relationship between the variation of infant mortality and late fetal death rates with the degree of inbreeding is also explored. The need of a temporal study of these demographic variables is also emphasized to elucidate the influence of marriage structure or determined reproductive patterns on the genetic and demographic aspects within these populations.     

Did food increase fertility? Evaluation of !Kung and Herero history.

Low fertility among nomadic !Kung foragers of the northern Kalahari Desert of Botswana has been hypothesized to be an adaptation to scarcity of food. However, a comparison of !Kung fertility before and after a transition to a more sedentary lifestyle indicates that more food did not increase fertility. An examination of the fertility of neighboring sedentary Bantu-speaking Herero pastoralists during the same period also indicates that low female reproductive rates in this region are not unique to the !Kung. Herero fertility has increased dramatically in recent decades, probably in response to the control of sexually transmitted diseases in northwestern Botswana. More food appears to have substantially increased !Kung reproductive success by reducing infant and child mortality rates to levels observed among the Herero. These findings suggest that low !Kung fertility and mortality reflect contact with the Herero, who began expanding in large numbers into !Kung territory in the 1950s. This study emphasizes the need for a more rigorous comparative perspective in anthropology to understand better the significance of findings from restricted populations, and I suggest that evolutionary ecology would benefit from shifting some of its current focus on fertility to mortality.     

Regional variation in the age-specific natural fertility curve

This paper examines the question of whether there are consistent regional variations in the level and shape of the age-specific natural fertility curve using data for 45 less-developed countries drawn from a recent US Census Bureau compilation. The 45 countries were grouped into 4 regional categories: sub-Saharan Africa; Middle East and North Africa; South and Southeast Asia; and Latin America. In general there do not appear to be variations. A consistent age pattern of natural fertility emerges, once the rates have been normalized and an adjustment made for age at 1st exposure to the risk of pregnancy. The results strongly support Coale's original natural fertility paradigm. The differences in the absolute fertility rates among the 4 regions correspond to the differences in proportion of females aged 15 and over who are currently married. The differences among 3 of the regions are relatively small whereas sub-Saharan Africa's proportion currently married is significantly higher.     

Differential paternity in Libya

Libyan census and vital statistics data from 1973 are compared with genealogical records from Utah males born between 1830 and 1834 as representative of populations not using any method of fertility control. The Libyan vital statistics data contained 97% of paternity by age, but only 85% of maternity by age. These missing data were distributed pro rata, and all data were corrected for errors in reporting. Polygamous unions were excluded because polygamy is relatively rare in Libya. The Utah data were from 185,000 genealogies of the Genealogical Society of Utah. The Libyan child-woman ratio (number of children under age 5 per number of women aged 15-49) is 1112.9, compared to 850 in Morocco, suggesting that Libya is experiencing an increase in fertility, in child survival and probably in quality of statistics. The total fertility rates for females were 11.1 for Libya and 11.2 for Utah; the total paternity rates were 14.3 and 13.7, respectively. Male rates are higher because of remarriage after divorce or death of wives. Age-specific paternity rates are tabulated and graphed: The major difference between the 2 populations is the concave shape of the curve for Libyan men under 30. Age at marriage is late, but marriage is virtually universal for Libyan men over 30. Age-specific paternity rates by occupation show apparent lack of fertility regulation in traditional occupations like farming and sales. There is evidence of some parity-related fertility control in professional and administrative workers. Production workers have a high peak in fertility around age 27.5 and 32.5, and a dip occurring at older ages. These figures can be explained by education, since education is required for professional occupations, and older professionals were trained in the West. Production workers took advantage of rapidly expanding education in Libya late in their youth, postponing marriage. Libya's pronatalist policy forbids sale of contraceptives and provides child allowances, free education, health care, subsidized housing and social security. This paper indicates the utility of paternity data where statistics on maternity are unavailable.     

Systematic review of avian hatching failure and implications for conservation

Avian hatching failure is a widespread phenomenon, affecting around 10% of all eggs that are laid and not lost to predation, damage, or desertion. Our understanding of hatching failure is limited in terms of both its underpinning mechanisms and its occurrence across different populations. It is widely acknowledged that rates of hatching failure are higher in threatened species and in populations maintained in captivity compared to wild, non-threatened species, but these differences have rarely been quantified and any broader patterns remain unexplored. To examine the associations between threat status, management interventions, and hatching failure across populations we conducted a phylogenetically controlled multilevel meta-analysis across 231 studies and 241 species of birds. Our data set included both threatened (Critically Endangered, Endangered, and Vulnerable) and non-threatened (Near Threatened and Least Concern) species across wild and captive populations, as well as ‘wild managed’ (‘free-living’) populations. We found the mean overall rate of hatching failure across all populations to be 16.79%, with the hatching failure rate of wild, non-threatened species being 12.40%. We found that populations of threatened species experienced significantly higher mean hatching failure than populations of non-threatened species. Different levels of management were also associated with different rates of hatching failure, with wild populations experiencing the lowest rate of hatching failure, followed by wild managed populations, and populations in captivity experiencing the highest rate. Similarly, populations that were subject to the specific management interventions of artificial incubation, supplementary feeding, and artificial nest provision displayed significantly higher rates of hatching failure than populations without these interventions. The driver of this correlation between hatching failure and management remains unclear, but could be an indirect result of threatened species being more likely to have lower hatching success and also being more likely to be subject to management, indicating that conservation efforts are fittingly being focused towards the species potentially most at risk from extinction. This is the most comprehensive comparative analysis of avian hatching failure that has been conducted to date, and the first to quantify explicitly how threat status and management are associated with the rate of hatching failure in a population. We discuss the implications of our results, focusing on their potential applications to conservation. Although we identified several factors clearly associated with variation in hatching failure, a significant amount of heterogeneity was not explained by our meta-analytical model, indicating that other factors influencing hatching failure were not included here. We discuss what these factors might be and suggest avenues for further research. Finally, we discuss the inconsistency in how hatching failure is defined and reported within the literature, and propose a standardised definition to be used in future studies which will enable better comparison across populations and ensure that the most accurate information is used to support management decisions.     

Mating system affects population performance and extinction risk under environmental challenge

Failure of organisms to adapt to sudden environmental changes may lead to extinction. The type of mating system, by affecting fertility and the strength of sexual selection, may have a major impact on a population''s chances to adapt and survive. Here, we use experimental evolution in bulb mites (Rhizoglyphus robini) to examine the effects of the mating system on population performance under environmental change. We demonstrate that populations in which monogamy was enforced suffered a dramatic fitness decline when evolving at an increased temperature, whereas the negative effects of change in a thermal environment were alleviated in polygamous populations. Strikingly, within 17 generations, all monogamous populations experiencing higher temperature went extinct, whereas all polygamous populations survived. Our results show that the mating system may have dramatic effects on the risk of extinction under environmental change.     

The influence of basal metabolic rate on blood pressure among indigenous Siberians

Hypertension is an important global health issue and is currently increasing at a rapid pace in most industrializing nations. Although a number of risk factors have been linked with the development of hypertension, including obesity, high dietary sodium, and chronic psychosocial stress, these factors cannot fully explain the variation in blood pressure and hypertension rates that occurs within and between populations. The present study uses data collected on adults from three indigenous Siberian populations (Evenki, Buryat, and Yakut [Sakha]) to test the hypothesis of Luke et al. (Hypertension 43 (2004) 555-560) that basal metabolic rate (BMR) and blood pressure are positively associated independent of body size. When adjusted for body size and composition, as well as potentially confounding variables such as age, smoking status, ethnicity, and degree of urbanization, BMR was positively correlated with systolic blood pressure (SBP; P < 0.01) and pulse pressure (PP; P < 0.01); BMR showed a trend with diastolic blood pressure (DBP; P = 0.08). Thus, higher BMR is associated with higher SBP and PP; this is opposite the well-documented inverse relationship between physical activity and blood pressure. If the influence of BMR on blood pressure is confirmed, the systematically elevated BMRs of indigenous Siberians may help explain the relatively high blood pressures and hypertension rates documented among native Siberians in the post-Soviet period. These findings underscore the importance of considering the influence of biological adaptation to regional environmental conditions in structuring health changes associated with economic development and lifestyle change.     

Recent fertility trends in Suriname

A rapid decline in fertility took place in Suriname between 1962 and 1974, and then stopped. While this sudden stabilization is surprising, it is not unusual. Similar trends have occurred in some Caribbean and Latin American countries. This article analyzes the post-1960 trend in fertility in Suriname and seeks to determine whether the 1962-74 fertility decline resulted from changes in socioeconomic conditions or was caused by the activities of the Suriname Family Planning Association. The measures used are the general fertility rate, the total fertility rate by ethnic group as well as by 5-year age groups, and gross and net reproduction rates by ethnic group. All the measures point to a rapid continuing decline of fertility between 1962 and 1974, followed by a rise. The data suggest that major socioeconomic changes had already been under way for some years, when fertility started to fall in 1962. The Suriname Family Planning Association was not founded until 1968, which implies that the organization did not start the decrease. However, once the organization was founded, it continually expanded its activities and made an obvious contribution to the use of contraceptives that increased significantly in the 1970s. It is concluded that the drop in fertility resulted from the process of modernization along with the rapid increase in the use of contraceptives.     

Population responses of a conifer-dwelling aphid to seasonal changes in its host

Abstract.  1. Current evidence suggests that seasonal changes in spruce needle sap nutrients have a decisive influence on green spruce aphid ( Elatobium abietinum ) population density, but the mechanisms of population change, the roles of development rate, fertility and mortality, and the existence of density-dependent processes, are not clearly understood.
2. Experimental studies of aphid populations were conducted in controlled environments to estimate seasonal patterns in aphid mean relative growth rate, prenatal development, fertility, and mortality. Studies were also made of the effect of aphid crowding on vital rates.
3. Independent of the degree of aphid crowding, seasonal changes in the amino acid concentration of needle sap were tracked by aphid growth rate, fertility (and adult size), but not by rates of aphid mortality. The most pronounced change in vital rates, and the one most likely to drive seasonal population change, was in fertility. Prenatal development time actually became shorter in periods when nutrients were scarce, but the resulting adult aphids were smaller and less fertile than during periods of improved nutrition.
4. Density dependence of vital rates was only observed during mid-summer when nutrients were least available. Mortality, growth rate, and prenatal development were the most strongly density-dependent processes. In contrast, there was no evidence that fertility rates were likely to respond to crowding.
5. There were no important differences between populations reared on small, potted spruce trees and those on plantation trees aged 25 years. This gives confidence that demographic data from a variety of field and laboratory sources could be used to compile data appropriate for population models.     

Mortality,fertility, and the OY ratio in a model hunter–gatherer system

An agent‐based model (ABM) is used to explore how the ratio of old to young adults (the OY ratio) in a sample of dead individuals is related to aspects of mortality, fertility, and longevity experienced by the living population from which the sample was drawn. The ABM features representations of rules, behaviors, and constraints that affect person‐ and household‐level decisions about marriage, reproduction, and infant mortality in hunter–gatherer systems. The demographic characteristics of the larger model system emerge through human‐level interactions playing out in the context of “global” parameters that can be adjusted to produce a range of mortality and fertility conditions. Model data show a relationship between the OY ratios of living populations (the living OY ratio) and assemblages of dead individuals drawn from those populations (the dead OY ratio) that is consistent with that from empirically known ethnographic hunter–gatherer cases. The dead OY ratio is clearly related to the mean ages, mean adult mortality rates, and mean total fertility rates experienced by living populations in the model. Sample size exerts a strong effect on the accuracy with which the calculated dead OY ratio reflects the actual dead OY ratio of the complete assemblage. These results demonstrate that the dead OY ratio is a potentially useful metric for paleodemographic analysis of changes in mortality and mean age, and suggest that, in general, hunter–gatherer populations with higher mortality, higher fertility, and lower mean ages are characterized by lower dead OY ratios. Am J Phys Anthropol 154:222–231, 2014. © 2014 Wiley Periodicals, Inc.     

Genetic ancestry,admixture and health determinants in Latin America

Background

Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico.

Results

We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population’s genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects.

Conclusions

Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.

     

Individual state controls temperature dependence in a butterfly (Lasiommata maera)

In ectotherms there is typically a strong and positive correlation between growth rate and ambient temperature when food is not limiting. However, the exact relationship between growth rate and temperature varies among populations in many species. As a consequence, it has been suggested that selection for a rapid increase in growth rate with temperature should be stronger in populations experiencing a high degree of time-stress, compared with populations experiencing little time-stress. In the present study we take this adaptive hypothesis further and investigate if variation in time-stress among individuals of a single population may affect the relationship between growth rate and ambient temperature. Time-stress was manipulated by rearing larvae of the butterfly Lasiommata maera in different day-length regimes. The results show that individuals experiencing a higher degree of time-stress increase their growth rates more in higher temperatures compared with individuals under less time-stress. Hence, the adaptive hypothesis was supported and the relationship between growth rate and temperature was highly state dependent. These findings may be of general importance for understanding the evolution of life histories in seasonal environments.     

Changes in dispersal during species' range expansions

Explanations for rapid species' range expansions have typically been purely ecological, with little attention given to evolutionary processes. We tested predictions for the evolution of dispersal during range expansion using four species of wing-dimorphic bush cricket (Conocephalus discolor, Conocephalus dorsalis, Metrioptera roeselii, and Metrioptera brachyptera). We observed distinct changes in dispersal in the two species with expanding ranges. Recently colonized populations at the range margin showed increased frequencies of dispersive, long-winged (macropterous) individuals, compared with longer-established populations in the range core. This increase in dispersal appeared to be short-lived because 5-10 years after colonization populations showed similar incidences of macroptery to populations in the range core. These changes are consistent with evolutionary change; field patterns persisted when nymphs were reared under controlled environmental conditions, and range margin individuals reared in the laboratory flew farther than range core individuals in a wind tunnel. There was also a reproductive trade-off with dispersal in both females and males, which could explain the rapid reversion to lower rates of dispersal once populations become established. The effect of population density on wing morphology differed between populations from the range core (no significant effect of density) and expanding range margins (negative density dependence), which we propose is part of the mechanism of the changes in dispersal. Transient changes in dispersal are likely to be common in many species undergoing range expansion and can have major population and biogeographic consequences.