Genetics and modern human origins

The past decade has brought considerable debate on the subject of modern human origins. The nature of the transition from Homo erectus to archaic Homo sapiens to modern H. sapiens has been examined primarily in terms of the relative contribution of archaic populations to later moderns, both within and among geographic regions. The recent African origin model proposes that modern humans appeared first in Africa between 100,000 and 200,000 years ago, and then spread through the rest of the Old World, replacing preexisting populations.^1–6 This model has been referred to by a variety of names, including “replacement”, “Garden of Eden”, “Noah's Ark”, and “out of Africa”. The recent African origin model contrasts with the multiregional model, which proposes a species-wide transition to modern humans throughout the Old World during the past million years or more.^7–10 Indeed, some proponents of the multiregional model advocate placing Homo erectus and all subsequent species of Homo in the evolutionary species Homo sapiens.¹¹ This contrasts with the view that there were multiple hominid species during the Middle Pleistocene. The debate continues.^12,13 Although the multiregional model is often portrayed as proposing a simultaneous transition to anatomically modern humans in different geographic regions, it explicitly allows for varying degrees of continuity across time and space.¹⁰ This model, in the broad sense, does not rule out the possibility that modern human morphology appeared first in Africa and then spread through the rest of the Old World through gene flow. However, not all advocates of the multiregional model adhere to this specific subset of the general model.⁹ Comparison of the African and multiregional models is complicated by considering other, less extreme, hypotheses. Some versions of the recent African origin model imply a speciation event associated with the initial origin of modern humans. Another version, which suggests the possibility of some admixture between “moderns” leaving Africa and preexisting “archaics” elsewhere in the Old World,^14,15 is similar to some variants of the multiregional model, which also suggest that modern morphology appeared first in Africa, but involved admixture with other Old World populations.¹⁶ The major difference between these views appears to be the extent of admixture, although the exact level is never specified. A further complication is the possibility that multiple dispersals from Africa produced a more complicated pattern of worldwide variation.¹⁷     

基于DNA分子的现代人起源研究35年回顾与展望

1983年,有学者首次发表现代人线粒体DNA进化树,认为现代人可能起源自亚洲。1987年,又有学者按照分子钟假说得到线粒体在10-20万年前出自非洲的推论。随后,以分子钟为前提的Y染色体和常染色体DNA研究也支持了出非洲的结论,该结论逐渐成为分子进化领域的主流理论。2010年,对尼安德特人常染色体基因组的研究指出其对现代人有遗传贡献,这颠覆了人们先前关于现代人只来源自非洲,其他大洲的当地古人被完全取代的认知。目前,单地区起源说已经被修正为同化说。尽管学界对非洲人遗传多样性最高这一现象有共识,但是对该现象的不同解读却可以得出两种迥然不同的结果,现代人出亚洲说和出非洲说。大量研究证实基因组的大部分序列是有功能的,并处在遗传变异水平的饱和态,这质疑了中性理论以及由它推导的现代人出非洲说的合理性,而中性理论的提出恰恰是用来解释并非普遍存在的分子钟的。近年来已经有研究者从新理论的角度解读遗传多样性的饱和态和线性态,人们对现代人起源的认识将会进一步加深完善。     

Ethnic populations of India as seen from an evolutionary perspective

It is now widely accepted that (i) modern humans,Homo sapiens sapiens, evolved in Africa, (ii) migrated out of Africa and replaced archaic humans in other parts of the world, and (iii) one of the first waves of out-of-Africa migration came into India. India, therefore, served as a major corridor for dispersal of modern humans. By studying variation at DNA level in contemporary human populations of India, we have provided evidence that mitochondrial DNA haplotypes based on RFLPs are strikingly similar across ethnic groups of India, consistent with the hypothesis that a small number of females entered India during the initial process of the peopling of India. We have also provided evidence that there may have been dispersal of humans from India to southeast Asia. In conjunction with haplotype data, nucleotide sequence data of a hypervariable segment (HVS-1) of the mitochondrial genome indicate that the ancestors of the present austro-asiatic tribal populations may have been the most ancient inhabitants of India. Based on Y-chromosomal RFLP and STRP data, we have also been able to trace footprints of human movements from west and central Asia into India.     

Deep divergences of human gene trees and models of human origins

Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates--between 100,000 and 200,000 years--of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosomal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X chromosome on the other hand.     

Beringia and the global dispersal of modern humans

Until recently, the settlement of the Americas seemed largely divorced from the out‐of‐Africa dispersal of anatomically modern humans, which began at least 50,000 years ago. Native Americans were thought to represent a small subset of the Eurasian population that migrated to the Western Hemisphere less than 15,000 years ago. Archeological discoveries since 2000 reveal, however, that Homo sapiens occupied the high‐latitude region between Northeast Asia and northwest North America (that is, Beringia) before 30,000 years ago and the Last Glacial Maximum (LGM). The settlement of Beringia now appears to have been part of modern human dispersal in northern Eurasia. A 2007 model, the Beringian Standstill Hypothesis, which is based on analysis of mitochondrial DNA (mtDNA) in living people, derives Native Americans from a population that occupied Beringia during the LGM. The model suggests a parallel between ancestral Native Americans and modern human populations that retreated to refugia in other parts of the world during the arid LGM. It is supported by evidence of comparatively mild climates and rich biota in south‐central Beringia at this time (30,000‐15,000 years ago). These and other developments suggest that the settlement of the Americas may be integrated with the global dispersal of modern humans.     

魏敦瑞对北京猿人化石的研究及其人类演化理论

魏敦瑞对中国猿人（现为直立人北京亚种）,化石作了详尽而深入的描述并指出了直立人的典型特征。他正确地推测, 在从猿到人的演化过程中首先是直立姿势的采用, 跟着是头骨的变化, 脑的扩张是头骨变化的动因。本世纪前半叶, 魏敦瑞第一次用一个图将所有已知的人类化石集合在一起, 作系统排列的尝试, 来表示整个人类的演化过程。他相信所有化石人类属于一个种, 能够互相杂交, 人类不是起源于一个地方, 而是起源于几个地方。他反对南方古猿曾经参与人类进化的说法, 代之以认为人类进化的早先各期是巨人阶段, 但是他的巨人理论迄今没有化石的证据。关于现代人的起源, 多地区起源说和非洲起源说目前正在激烈争论之中。     

Global invasion history of the Mediterranean recluse spider: a concordance with human expansion

The dispersal of modern humans from their African origins to the rest of the occupied world is a topic of lively debate centering principally on single versus multiple dispersals. The Mediterranean recluse spider Loxosceles rufescens, a significant pest, has gained much of its current distribution through commensalism with humans. Therefore, the matrilineal history of this spider should reflect dispersal patterns of human females. Here, an assessment of genetic variation at mitochondrial markers in 347 colonies of L. rufescens from 104 geographic sites worldwide reveals a north African origin of the global populations of L. rufescens. This involves at least three separate events among which two involve coincidental dispersals, including one to north Africa, Europe, Asia, North America, and Australia and the other to north Africa, Europe, and Asia only. North African L. rufescens appear to have expanded initially into Israel and subsequently spread into Greece, where a subset of these populations went eastward into Iran and southeastern Asia. This corresponds to the modern human southern dispersal theory. Chinese populations appear to have expanded approximately 42 710–46 008 yr ago. The initial split between the Greek and Chinese populations dates to 41 412–44 444 yr ago, which coincides with the expansion of modern humans into Southeast and East Asia. Thus, the matrilineal history of Asian L. rufescens tracks the history of human dispersals over tens of thousands of years.     

Out of Africa with regional interbreeding? Modern human origins

A central issue in paleoanthropology is whether modern humans emerged in a single geographic area and subsequently replaced the preexisting people in other areas. Although the study of human mitochondrial DNAs supported this single-origin and complete-replacement model, a recent paper(1) argues that humans expanded out of Africa more than once and regionally interbred. However, both the genetic antiquity and the impact of the African contribution to modern Homo sapiens are so great as to view Africa as a central place of human evolution. Despite the possibility that out-of-Africa H. sapiens interbred with other populations, this evidence is more consistent with the uniregional hypothesis than the multiregional hypothesis of modern human origins.     

中更新世非洲Bodo人类头骨化石与周口店直立人的比较--中国与非洲人类头骨特征对比之三

发现于埃塞俄比亚MiddleAwash地区Bodo地点距今60万年的人类头骨化石是迄今发现的最为古老和完整的非洲中更新世人类化石。由于Bodo头骨化石在形态特征上兼有直立人与智人的特点,多年来学术界对其分类地位一直存在争议。Rightmire认为Bodo头骨化石与BrokenHill及Petralona等在分类上属于古老型智人的中更新世人类更为接近,是非洲直立人向古老型智人过渡的代表。至少在距今60万年的中更新世早期直立人向古老型智人转变的成种事件在非洲就已经发生。以Bodo头骨为代表的一批更新世中期非洲和欧洲人类化石构成了可能是后期人类祖先的人属海德堡种。这些观点导致了近年学术界对古老型智人在非洲及欧亚出现时间以及更新世中期非洲和欧亚地区古人类相互之间演化关系的关注。基于这样的背景,本文对年代与Bodo化石接近的周口店直立人头骨特征与Bodo头骨的相似及差异表现情况进行了对比研究。结果发现Bodo头骨在一系列特征上与周口店直立人相似,同时在包括颅容量在内的其它一些特征上呈现出后期智人的特点,但总体形态上似乎与直立人更为相似。作者认为尽管这种进化上的镶嵌现象在中国古人类化石记录上也广泛存在,但由于中国人类化石标本在年代上的不确定性,目前还没有可靠的证据说明这种集直立人与智人化石特征为一体的镶嵌性在中国古人类化石出现的时间接近或早于非洲。考虑到中国与非洲直立人生存年代的巨大差异及人类演化的不同步或地区间差异,具有较多后期人类特征表现的人类首先出现在非洲是完全可能的。根据这些研究对比,作者就人类演化的镶嵌现象、更新世中期非洲与亚洲地区人类演化上的差异等问题进行了讨论。     

The status of Homo heidelbergensis (Schoetensack 1908)

The species Homo heidelbergensis is central to many discussions about recent human evolution. For some workers, it was the last common ancestor for the subsequent species Homo sapiens and Homo neanderthalensis; others regard it as only a European form, giving rise to the Neanderthals. Following the impact of recent genomic studies indicating hybridization between modern humans and both Neanderthals and "Denisovans", the status of these as separate taxa is now under discussion. Accordingly, clarifying the status of Homo heidelbergensis is fundamental to the debate about modern human origins.     

The First Modern Human Dispersals across Africa

The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0’s sister clade, L1’6. We propose that the last common ancestor of modern human mtDNAs (carried by “mitochondrial Eve”) possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African “megadroughts” of MIS 5 (marine isotope stage 5, 135–75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution.     

Genetic evidence and the modern human origins debate

A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture.     

An Australasian test of the recent African origin theory using the WLH-50 calvarium

This analysis investigates the ancestry of a single modern human specimen from Australia, WLH-50 (Thorne et al., in preparation; Webb, 1989). Evaluating its ancestry is important to our understanding of modern human origins in Australasia because the prevailing models of human origins make different predictions for the ancestry of this specimen, and others like it. Some authors believe in the validity of a complete replacement theory and propose that modern humans in Australasia descended solely from earlier modern human populations found in Late Pleistocene Africa and the Levant. These ancestral modern populations are believed to have completely replaced other archaic human populations, including the Ngandong hominids of Indonesia. According to this recent African origin theory, the archaic humans from Indonesia are classified as Homo erectus, a different evolutionary species that could not have contributed to the ancestry of modern Australasians. Therefore this theory of complete replacement makes clear predictions concerning the ancestry of the specimen WLH-50. We tested these predictions using two methods: a discriminant analysis of metric data for three samples that are potential ancestors of WLH-50 (Ngandong, Late Pleistocene Africans, Levant hominids from Skhul and Qafzeh) and a pairwise difference analysis of nonmetric data for individuals within these samples. The results of these procedures provide an unambiguous refutation of a model of complete replacement within this region, and indicate that the Ngandong hominids or a population like them may have contributed significantly to the ancestry of WLH-50. We therefore contend that Ngandong hominids should be classified within the evolutionary species, Homo sapiens. The Multiregional model of human evolution has the expectation that Australasian ancestry is in all three of the potentially ancestral groups and best explains modern Australasian origins.     

Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population

Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.     

新证据下的现代人起源模型

解剖结构上的现代人是指具有近圆球形头骨、短而平的面颅、纤细的骨骼等特征的区别于其他古老人类的化石和现今的人群。支持多地区演化模型和支持近期非洲起源模型的学者,在“解剖结构上的现代人”的应用范围方面是不同的,前者以连续演化为基本思想,认为这一名词只包括智人中较进步的类群;而后者以分支系统学思想为基础,认为包括所有智人。分子古生物学研究显示,尼人、丹人和智人在遗传学水平上属于不同的人种。新近的以标本-种群为单元的系统分析,因为不是以属、种等分类学阶元进行的,因此与分类学的阶元划分无关。该系统分析的结果显示智人属于单系类群,哈尔滨人、大荔人等组成其姊妹群。尼人与智人的分异早于1百万年,与基因组水平的谱系分析相符合。多次多向的穿梭扩散是统计学上符合系统关系的模型。     

Zooarcheological evidence for the faunal exploitation behavior of Neandertals and early modern humans

The study of the origins of modern humans continues to be a dynamic, quickly changing field, as shown by the recent extraction and analysis of DNA from the Neander Valley fossils.¹ The dynamic nature of the field partly arises from the clearly defined opposing models for the origins of modern humans,² and the spirited defense of the opposing models by the main protagonists in the debate. Although the “Out-of-Africa” and “Multiregional Continuity Models” are typically argued from the perspective of biological evolution, with the debates centering on anatomical and molecular evidence, the behavioral side of the question is of equal significance. Even though the anatomical record will always be a productive avenue for behavioral reconstruction,^3,4 archeology remains the major contributor to our understanding of the behavioral side of this debate.     

The dawn of human matrilineal diversity

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000-70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.     

Middle pleistocene humans from africa

Patterns of human evolution in the Middle Pleistocene remain poorly understood. There is general consensus that by the onset of this time period, populations ofHomo erectus were dispersed from Africa into Eurasia, including the Far East. In the western part of this range (perhaps in Africa),Homo erectus then produced a daughter lineage exhibiting more advanced characters of the face, braincase and cranial base. How this new species should be defined is currently debated. In my view, fossils from sites such as Bodo and Broken Hill in Africa may be lumped with material from earlier Middle Pleistocene localities in Europe. Such a taxon is appropriately namedHomo heidelbergensis. Whether the hypodigm should be extended to include fossils from China is another question. In any case, this group of hominids is plausibly ancestral to both the specialized Neanderthals of Europe and more modern humans of the later Middle Pleistocene.     

The problem of our common mitochondrial mother

Summary It has been suggested that the mitochondrial DNA (mtDNA) of all present-day human beings stems exclusively from one woman who lived about 200000 years ago in Africa; examination of the problem by the mathematical theory of random walks supposedly renders alternatives very unlikely. However, a statistical argument first used by Fisher indicates that this hypothesis is untenable, at least if the assumptions made by previous workers are accepted. All present-day mtDNA might go back to one individual, especially if small populations and population bottlenecks with very small numbers of reproducing individuals are assumed; nevertheless, this phase in the evolution of Homo sapiens probably dates back considerably more than 200000 years.     

史前古人类之间的基因交流及对当今现代人的影响

古DNA实验技术及高通量测序技术的出现和发展,使得直接从古老化石中进行遗传物质的提取及测序成为可能,与古人类相关的基因组学研究因此取得了一系列突破性进展,已灭绝的古老型人类(如:尼安德特人和丹尼索瓦人)与非洲以外现代人之间基因的相互影响已被诸多证据所证实。研究表明,在史前时期,早期现代人向非洲以外地区扩散时,遭遇到了现已灭绝的古老型人类,他们在同一时空内长期共存,并发生了基因交流,有一部分古老型人类基因因此流向了现代人,有些基因一直流传至今,对当今现代人的基因组成产生重大影响;此外,不同古老型人类之间也存在基因交流;而早期现代人也对部分古老型人类的基因组成造成了影响。化石与古DNA信息的证据均表明,史前各种人类之间的基因交流在多个地区发生多次,他们的基因交流共同构建了当今现代人的基因库,并在生理机能、形态和疾病发生率等方面对现代人造成了深远的影响。