Mitochondrial diversity in human head louse populations across the Americas

Anthropological studies suggest that the genetic makeup of human populations in the Americas is the result of diverse processes including the initial colonization of the continent by the first people plus post‐1492 European migrations. Because of the recent nature of some of these events, understanding the geographical origin of American human diversity is challenging. However, human parasites have faster evolutionary rates and larger population sizes allowing them to maintain greater levels of genetic diversity than their hosts. Thus, we can use human parasites to provide insights into some aspects of human evolution that may be unclear from direct evidence. In this study, we analyzed mitochondrial DNA (mtDNA) sequences from 450 head lice in the Americas. Haplotypes clustered into two well‐supported haplogroups, known as A and B. Haplogroup frequencies differ significantly among North, Central and South America. Within each haplogroup, we found evidence of demographic expansions around 16,000 and 20,000 years ago, which correspond broadly with those estimated for Native Americans. The parallel timing of demographic expansions of human lice and Native Americans plus the contrasting pattern between the distribution of haplogroups A and B through the Americas suggests that human lice can provide additional evidence about the human colonization of the New World. Am J Phys Anthropol 152:118–129, 2013. © 2013 Wiley Periodicals, Inc.     

Paleobiology of the first Americans

The majority of scholars studying the human colonization of the New World agree that the first Americans, traditionally identifed as Paleoindians, entered near the end of the Pleistocene via the Bering land bridge from northeast Asia. But this is where agreement ends. Questions about the number and timing of migrations, the physical appearance of the colonists, and the manner in which they lived have been examined since the turn of the century^1–7 and still engender lively debate.^8–16 Curiously lacking from the growing body of data on the peopling of the Americas is evidence from the physical remains of the first Americans. We summarize research on the earliest human remains from North America and discuss how these remains shed new light on these unanswered questions.     

A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia

The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.     

Why we're still arguing about the Pleistocene occupation of the Americas

Although empirical issues surround the when, how, and who questions of New World colonization, much of current debate hinges on theoretical problems because it has become clear that our understanding of New World colonization is not resolute. 1 In fact, the central issues of debate have remained essentially unchanged for the last eighty years. The now classic and probably incorrect story of New World colonization begins in Late Pleistocene Siberia, with small a population of foragers migrating across Beringia (～13,500 calendar years before present (CYBP) (Box 1) through an ice‐free corridor and traveling through the interior of North America. High mobility and rapid population growth spurred southward expansion into increasingly distant unoccupied regions, culminating in the settlement of the Southern Cone of South America. Armed with the skills and weapons needed to maintain a megafauna‐based subsistence strategy, early colonists necessarily had the adaptive flexibility to colonize a diverse array of Pleistocene landscapes. For a time, this scenario seemed well substantiated. The earliest sites in South America were younger than their northern counterparts, fluted artifacts were found across the Americas within a brief temporal window, and projectile points capable of wounding elephant‐sized prey were commonly found in association with proboscidean remains. The Bering Land Bridge connecting Asia to Alaska and an ice‐free corridor providing passage between the Pleistocene ice masses of Canada seemed to provide a clear route of entry for Clovis colonists. However, recent archeological, paleoenvironmental, biological, and theoretical work largely questions the plausibility of these events.     

Emerging roles for centromeres in meiosis I chromosome segregation

Centromeres are an essential and conserved feature of eukaryotic chromosomes, yet recent research indicates that we are just beginning to understand the numerous roles that centromeres have in chromosome segregation. During meiosis I, in particular, centromeres seem to function in many processes in addition to their canonical role in assembling kinetochores, the sites of microtubule attachment. Here we summarize recent advances that place centromeres at the centre of meiosis I, and discuss how these studies affect a variety of basic research fields and thus hold promise for increasing our understanding of human reproductive defects and disease states.     

Managing consequences of climate‐driven species redistribution requires integration of ecology,conservation and social science

Climate change is driving a pervasive global redistribution of the planet's species. Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach. Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges. We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems. Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change. Species redistributions present challenges for human well‐being, environmental management and sustainable development. By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution. Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges. Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human‐centred approaches. Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions.     

The peopling of the Americas and the origin of the Beringian occupation model

The current model for peopling of the Americas involves divergence from an ancestral Asian population followed by a period of population isolation and genetic diversification in Beringia, and finally, a rapid expansion into and throughout the Americas. Studies in the 1970s sought to characterize the biological relationships between different indigenous populations and first proposed an occupation of Beringia. More recent studies using molecular genetic markers often neglect to reference early works that laid the groundwork for current colonization models. We address this matter, and briefly summarize the literature and technological advances that contributed to our current understanding of the peopling of the Americas. Furthermore, we argue that describing the process of peopling of the Americas as “migrations from Asia” minimizes the significant genetic diversification that occurred outside of Asia, and offends indigenous Americans by discounting their origin narratives and land rights. Rather than referring to the indigenous peoples of the Americas as “migrants” or “immigrants,” we recommend consistency in the language used to describe all post‐glacial expansions of people into Asia, Europe and the Americas.     

Early and Middle Holocene Hunter-Gatherer Occupations in Western Amazonia: The Hidden Shell Middens

We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region’s past and offers a new context within which the late Holocene “Earthmovers” of the Llanos de Moxos could have emerged.     

Daphnia comes of age: an ecological model in the genomic era

Scientists in various subdisciplines of biology have long relied on model organisms to push the frontiers of knowledge forward as far as possible in their specific field. Today, interdisciplinary science requires model organisms that can push our understanding on multiple frontiers and help us formulate and address more complex questions. Members of the genus Daphnia represent just such an interdisciplinary model. Daphnia are aquatic microcrustaceans (also known as waterfleas) that have long been central to the study of ecology and toxicology and have recently been developed as a genomic model. A recent survey of both nuclear and mitochondrial markers in populations of the Daphnia pulex complex from high-altitude lakes in South America ( Mergeay et al . 2008, this issue ) provides an excellent example of how genetic data and ecological information can be used to push the boundaries of our understanding in molecular ecology. In this species complex, extensive hybridization has occurred resulting in polyploidization and, consequently, asexuality. Their data reveal high levels of genetic diversity, incongruence in phylogenetic signal among genomes (nuclear and mitochondrial), cryptic species in the complex, and a new model for the historical spread of the species throughout the Americas. Their data indicate that genome-level changes have occurred in this species which have profound consequences in an ecological context, the implications of which can be more fully appreciated because of our extensive knowledge of the ecology and natural history of the genus Daphnia .     

Beringian standstill and spread of Native American founders

Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the initial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.     

Old parasites for a new world: the future of paleoparasitological research. a review

Paleoparasitological research has made important contributions to our understanding of parasite evolution and ecology since the 1960s. Since then, most studies have focused on paleoparasitological evidence from single sites or samples. With the development of high throughput sequencing techniques, new avenues of investigation for paleoparasitological material are opening up. Here, I provide an overview of recent developments and highlight how these results will broaden the scope of the field, placing paleoparasitology at the interface of a wide array of studies, including parasitology, climate change, human evolution, and evolutionary processes.     

生态系统服务功能管理研究进展

生态系统给人类提供了自然资源和生存环境两个方面的多种服务功能,这些服务功能的可持续供给是经济社会可持续发展的基础.然而,生态系统服务功能从认知走向管理实践面临着严峻挑战,包括:定量测度、多种服务功能权衡、生态系统服务功能多尺度关联、生态系统服务功能与政策设计的结合.针对这些难点,近年来生态系统服务功能管理研究主要集中在以下领域:生态系统服务功能度量;生态系统服务功能与人类福祉的关系;多种生态系统服务功能权衡;生态系统服务功能保护规划;基于生态系统服务功能的生态补偿机制.为了进一步推动生态系统服务功能管理实践,应该进一步加强生态系统服务功能供给的理论研究;增加生态系统服务研究结果表达的多样性;增加与社会学、经济学、人口统计学等领域跨学科研究;进一步探索生态系统服务功能研究的结果如何运用到管理决策中,促进在管理实践中的应用.     

Contradictions and Concordances in American Colonization Models

The traditional view of American colonization during the late Pleistocene has largely been conditioned on early conceptions of the timing and extent of continental glaciations and the age and distribution of archeological sites. A review of newer, high resolution genetic data, both from modern populations and ancient DNA samples, along with the emergence of several early archeological sites in both North and South America, and reconsiderations of the glacial dynamics in North America indicate that some aspects of the traditional view need reconsideration. It seems obvious from archeological data that a preglacial occupation of the Americas needs to be closely examined. Accumulating molecular genetic data raises new questions about the timing and population size of the initial colonization(s), while a closer examination of glacial models suggests that a number of routes into the Americas may have been available until fairly late in the last glacial cycle.     

Did pre-Columbian populations of the Amazonian biome reach carrying capacity during the Late Holocene?

The increasingly better-known archaeological record of the Amazon basin, the Orinoco basin and the Guianas both questions the long-standing premise of a pristine tropical rainforest environment and also provides evidence for major biome-scale cultural and technological transitions prior to European colonization. Associated changes in pre-Columbian human population size and density, however, are poorly known and often estimated on the basis of unreliable assumptions and guesswork. Drawing on recent developments in the aggregate analysis of large radiocarbon databases, here we present and examine different proxies for relative population change between 1050 BC and AD 1500 within this broad region. By using a robust model testing approach, our analyses document that the growth of pre-Columbian human population over the 1700 years prior to European colonization adheres to a logistic model of demographic growth. This suggests that, at an aggregate level, these pre-Columbian populations had potentially reached carrying capacity (however high) before the onset of European colonization. Our analyses also demonstrate that this aggregate scenario shows considerable variability when projected geographically, highlighting significant gaps in archaeological knowledge yet also providing important insights into the resilience of past human food procurement strategies. By offering a new understanding of biome-wide pre-Columbian demographic trends based on empirical evidence, our analysis hopes to unfetter novel perspectives on demic expansions, language diversification trajectories and subsistence intensification processes in the Amazonian biome during the late Holocene.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

Moral Horizons of Land and Place

ABSTRACT

A recent ‘moral turn’ in anthropology has cast new light on morality as a subject of ethnographic inquiry, and on the making of moral meaning and judgment. This article, and the special issue it prefaces, contribute to this emergent literature through foregrounding and examining the moral dimensions of land and place. Taking up Didier Fassin’s injunction for a critical moral anthropology – rather than an anthropology of morality – we look to land and place as groundings for moral challenges and practices that are nevertheless not place-bound. A critical moral anthropology of land and place should be directed, we argue, to the interplay of mobility and emplacement, to the dynamics of landscape and ‘dwelling’, and to the multiplicities of expectation and meaning that surround the making and exploitation of resources. In contexts of global and local change, land and place offer productive grounds from which to consider the moral horizons – both spatial and temporal – of our world and our discipline.     

Combining novel technologies with interdisciplinary basic research to enhance horticultural crops

Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.     

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.     

Genome-virome interactions: examining the role of common viral infections in complex disease

New technologies have widened our view of 'complex diseases': those with both genetic and environmental risk factors. In this Review, we explore recent genetic and virological evidence implicating host-virus interactions in three diseases: type 1 diabetes, inflammatory bowel disease and asthma. The viruses implicated in these diseases cause mucosal infections that affect most of the population but are asymptomatic or mild in many hosts. These findings place a new emphasis on common viral infections as important environmental factors in the pathogenesis of complex diseases, and they compel the field to pursue a better understanding of host interactions with the human virome.     

Molecular Views of Human Origins

Over the last half century, comparative genomics has increasingly contributed to the definition, resolution and interpretation of human evolution. Early comparisons demonstrated that African apes and humans were more closely related and diverged later than commonly thought. However, it was difficult to determine the branching between humans, chimpanzees and gorillas. By the 1990s, sufficient biomolecular data had accumulated to demonstrate that chimpanzees and humans shared a common ancestor after the divergence of the gorilla. Current reconstructions place the divergence of humans and chimpanzees at 6–8 million years. Comparative genomics from complete genome sequencing to chromosome painting provide a scenario for the origin of the human genome. Starting form the ancestral mammalian karyotype, we can determine the major steps over the last 90 million years leading to the formation of each human chromosome. Despite considerable technical problems, studies of ancient DNA now provide a direct genetic witness of human evolution and add a temporal dimension to reconstructions of our evolutionary history and phylogeny. Ancient DNA has shown that Neanderthals probably did not interbreed with anatomically modern humans and did not make a significant contribution to the gene pool of our species. Ancient DNA has also contributed to the studies of the colonization of the Americas and the Pacific Island, and the domestication of plants and animals. Understanding the genetic basis of the physical and behavioral traits that distinguish humans from other primates presents one of the great future challenges of science.     

Ancient DNA perspectives on American colonization and population history

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.