To what extent did Neanderthals and modern humans interact?

Neanderthals represent an extinct hominid lineage that existed in Europe and Asia for nearly 400,000 years. They thrived in these regions for much of this time, but declined in numbers and went extinct around 30,000 years ago. Interestingly, their disappearance occurred subsequent to the arrival of modern humans into these areas, which has prompted some to argue that Neanderthals were displaced by better suited and more adaptable modern humans. Still others have postulated that Neanderthals were assimilated into the gene pool of modern humans by admixture. Until relatively recently, conclusions about the relationships between Neanderthals and contemporary humans were based solely upon evidence left behind in the fossil and archaeological records. However, in the last decade, we have witnessed the introduction of metagenomic analyses, which have provided novel tools with which to study the levels of genetic interactions between this fascinating Homo lineage and modern humans. Were Neanderthals replaced by contemporary humans through dramatic extinction resulting from competition and/or hostility or through admixture? Were Neanderthals and modern humans two independent, genetically unique species or were they a single species, capable of producing fertile offspring? Here, we review the current anthropological, archaeological and genetic data, which shed some light on these questions and provide insight into the exact nature of the relationships between these two groups of humans.     

基因组时代的新视野: 东南亚哺乳动物类群在第四纪冰河时期多样性的起源与分化

东南亚地区东起菲律宾群岛, 西至印度次大陆, 北及中国中部, 南至巽他群岛, 涵盖了世界上25个最重要的生物多样性热点地区之中的6个, 具有极其重要的全球生物多样性保护的战略意义。该地区复杂的地质地貌和气候历史使其动植物的种类和数量都极为丰富。经典的生物地理分界线华莱士线和克拉地峡将该地区进一步划分出包括部分巽他群岛和马来半岛在内的南部巽他区和北部印度支那区两个生物多样性热点地区。主要基于形态学的生物地理学研究认为巽他区和印度支那区通过马来半岛陆地相连, 并且第四纪大部分时间海平面下降形成大陆桥, 直到一万年前该地区的众多岛屿仍与大陆连接, 促进了哺乳动物的种群迁徙与基因交流, 因此物种种群间的差别将很细微。然而近来分子遗传学研究表明, 由于其他生态因素制约, 哺乳动物的迁移能力可能比以往认为的低, 大陆桥的存在并不一定导致迁徙的发生, 许多种群的隔离早在200万年前便已形成, 并且没有因为后来冰川期海平面降低而恢复种群交流, 而距今7.3万年前发生的苏门答腊多巴超级火山爆发也可能进一步影响了物种间和物种内多样性的形成和分化。通过已有的东南亚哺乳动物种群遗传学研究结果, 我们认为物种间或种群间的差异主要表现为三个层次: 巽他区种群与印度支那区种群间约百万年尺度的分化, 巽他区不同岛屿种群间约数十万年尺度的分化, 以及发生于晚更新世的分化事件。已有的东南亚种群遗传学研究主要采用线粒体及核基因多位点数据进行分析, 而种群基因组学分析则使得获得详尽的种群历史动态成为可能, 并使我们可以进一步了解东南亚哺乳动物类群所经历的物种形成过程。     

History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae)

The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.     

The Projection of a Test Genome onto a Reference Population and Applications to Humans and Archaic Hominins

We introduce a method for comparing a test genome with numerous genomes from a reference population. Sites in the test genome are given a weight, w, that depends on the allele frequency, x, in the reference population. The projection of the test genome onto the reference population is the average weight for each x, w¯(x). The weight is assigned in such a way that, if the test genome is a random sample from the reference population, then w¯(x)=1. Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture, and changes in past population size. The projection is sensitive to small amounts of past admixture, the direction of admixture, and admixture from a population not sampled (a ghost population). We compute the projections of several human and two archaic genomes onto three reference populations from the 1000 Genomes project—Europeans, Han Chinese, and Yoruba—and discuss the consistency of our analysis with previously published results for European and Yoruba demographic history. Including higher amounts of admixture between Europeans and Yoruba soon after their separation and low amounts of admixture more recently can resolve discrepancies between the projections and demographic inferences from some previous studies.