拟南芥基因密码子偏爱性分析

密码子偏爱性对外源基因的表达强度有一定影响,特别是编码蛋白质N端7～8个氨基酸残基的密码子.通过对拟南芥染色体中26 827个蛋白质对应的基因密码子进行分析,得到了编码氨基酸的61种密码子在拟南芥中的使用频率,并与大肠杆菌和哺乳动物进行了比较,结果表明三者间的密码子偏爱性有较大差异.这一分析结果对于动物基因在植物中的表达,及植物基因在微生物中的表达具有一定指导意义.同时提供了一种直接以XML文档为数据源解析巨型XML格式染色体数据的方法.     

Brief communication: The distribution of perikymata on Qafzeh anterior teeth

Recent studies have suggested that Neandertals and modern humans differ in the distribution of perikymata (enamel growth increments) over their permanent anterior tooth crowns. In modern humans, perikymata become increasingly more compact toward the cervix than they do in Neandertals. Previous studies have suggested that a more homogeneous distribution of perikymata, like that of Neandertals, characterizes the anterior teeth of Homo heidelbergensis and Homo erectus as well. Here, we investigated whether Qafzeh anterior teeth (N = 14) differ from those of modern southern Africans, northern Europeans, and Alaskans (N = 47–74 depending on tooth type) in the percentage of perikymata present in their cervical halves. Using the normally distributed modern human values for each tooth type, we calculated Z‐scores for the 14 Qafzeh teeth. All but two of the 14 Qafzeh teeth had negative Z‐scores, meaning that values equal to these would be found in the bottom 50% of the modern human samples. Seven of the 14 would be found in the lowest 5% of the modern human distribution. Qafzeh teeth therefore appear to differ from those of modern humans in the same direction that Neandertals do: with generally lower percentages of perikymata in their cervical regions. The similarity between them appears to represent the retention of a perikymata distribution pattern present in earlier members of the genus Homo, but not generally characteristic of modern humans from diverse regions of the world. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Was “Lucy” more human than her “child”? Observations on early hominid postcranial skeletons

Fully adult partial skeletons attributed to Australopithecus afarensis (AL 288-1, “Lucy”) and to Homo habilis (OH 62, “Lucy's child”), respectively, both include remains from upper and lower limbs. Relationships between various limb bone dimensions of these skeletons are compared to those of modern African apes and humans. Surprisingly, it emerges that OH 62 displays closer similarities to African apes than does AL 288-1. Yet A. afarensis, whose skeleton is dated more than 1 million years earlier, is commonly supposed to be the ancestor of Homo habilis. If OH 62, classified as Homo habilis by its discoverers, does indeed represent a stage intermediate between A. afarensis and later Homo, a revised interpretation of the course of human evolution would be necessary.     

Human evolution

The common ancestor of modern humans and the great apes is estimated to have lived between 5 and 8 Myrs ago, but the earliest evidence in the human, or hominid, fossil record is Ardipithecus ramidus, from a 4.5 Myr Ethiopian site. This genus was succeeded by Australopithecus, within which four species are presently recognised. All combine a relatively primitive postcranial skeleton, a dentition with expanded chewing teeth and a small brain. The most primitive species in our own genus, Homo habilis and Homo rudolfensis, are little advanced over the australopithecines and with hindsight their inclusion in Homo may not be appropriate. The first species to share a substantial number of features with later Homo is Homo ergaster, or ‘early African Homo erectus’, which appears in the fossil record around 2.0 Myr. Outside Africa, fossil hominids appear as Homo erectus-like hominids, in mainland Asia and in Indonesia close to 2 Myr ago; the earliest good evidence of ‘archaic Homo’ in Europe is dated at between 600–700 Kyr before the present. Anatomically modern human, or Homo sapiens, fossils are seen first in the fossil record in Africa around 150 Kyr ago. Taken together with molecular evidence on the extent of DNA variation, this suggests that the transition from ‘archiac’ to ‘modern’ Homo may have taken place in Africa.     

Homo erectus: Ancestor or evolutionary side branch?

Controversies in paleoanthropology wax and wane, but substantial interest is currently focused on Homo erectus. This species has traditionally been regarded as a member in good standing of the human family, where it is placed as an evolutionary intermediate between earlier Homo habilis and later Homo sapiens. Recently, however, some workers have questioned whether the species exists at all. If its populations have been transformed slowly toward the modern condition, and if continuity with living people can be demonstrated in many geographic regions, then any separation of Homo erectus from Homo sapiens must be largely arbitrary. In that case, only one species should be recognized and this slowly changing lineage would have to be called Homo sapiens. Other paleontologists adopt a different view, arguing that Homo erectus is not only anatomically distinctive but also restricted in its geographic distribution. They claim that the fossils from Java and China are so specialized in appearance that they cannot lie in the mainstream of human evolution. Homo erectus, strictly defined as limited to the Far East, probably went extinct without issue. If so, more modern populations must have evolved from another source, perhaps one outside of Asia altogether.     

Forward from Taung

The hominine grade of organization should preferably be defined by those morphological characters of the braincase and face which are first recognizable in Homo erectus. Provisionally, then, Olduvai hominid 24 and East Rudolf 1470 are regarded as protanthropine, irrespective of whether they both belong to “Homo habilis” or not. It is possible that either or both of these hominids can be considered directly prehominine, while A. africanus reflects an earlier prehominine stage.     

Homo erectus—who,when and where: A survey

The state of information bearing on Homo erectus as developed since about 1960 is surveyed, with the resulting effects on problems. Definitions of H. erectus still rest on the Far Eastern samples (Chou-k'ou-tien/Java), and thus relate to late Lower to middle Middle Pleistocene material. Numerous important individual finds, however, have expanded the total: extension of the early and very early Sangiran material; very early to later in Africa, and relatively late in Europe. Datings remain uncertain or controversial within broad limits, but with some important successes and revisions. Discussion by authors of problems concerns degree of divergence among H. erectus populations and rate of evolutionary change; both appear relatively slight, but the data are inadequate for much present judgment. The apparent zone of transition to more advanced morphology (H. sapiens, sensu lato) by the late Middle Pleistocene better reflects signs of regional divergence. Some writers—not all—believe that even the earliest European fossils known (e.g., Petralona) had already advanced to a H. sapiens basic level, with later change in the direction of Neanderthals. A separate African phylum, from OH 9, is also suggested; recent Chinese finds may provide a third different post-erectus population before the Upper Pleistocene. Taxonomic expression of all this gives some problems.     

Was Homo erectus responsible for the hand-axe culture?

This paper reviews the evidence from Africa, Asia and Europe of the cultural associations of Middle Pleistocene hominids, as well as the hominid skeletal associations of hand-axe remains.The author points out that it is possible to make a good argument—from the evidence of Steinheim, Kanjera and Swanscombe—that the hand-axes at these sites were made by Homo sapiens. On the other hand, on the basis of Fontéchevade and Vértesszöllös, it could be claimed that Middle Pleistocene Homo sapiens was responsible for primitive flake and chopper cultures. The evidence from Java is negative while that from China is directly opposed to the view that Homo erectus made hand-axes. Only from Ternifine in Algeria and Olduvai in Tanzania is there suggestive evidence that Homo erectus in those areas might have been responsible for the hand-axe culture. Thus, it is not possible at present to make any categorical statements as to the makers of either the great hand-axe culture or the flake and chopper culture, during Middle Pleistocene times.     

Sangiran 5,(“Pithecanthropus dubius”), homo erectus, “Meganthropus,” orPongo?

There are now eleven known mandibular remains from the Lower and Middle Pleistocene of Java, all but one being from the Sangiran site. All of these have been assigned toHomo erectus by most workers, while others have suggested as many as four different hominoid taxa. The author finds that the jaws cannot be a homogeneous sample. Morphologically, they are a mixture of undoubtedH. erectus, “H. meganthropus,” and possibly a pongid. If the jaws are allH. erectus then they have a sexual dimorphism exceeding that of modern gorillas. The case of“Pithecanthropus dubius” (Sangiran 5) is even less certain; even its hominid status is disputed. If it is indeedHomo it must be placed with the other“H. meganthropus” specimens. Its size and morphology are well beyond the known range anyH. erectus.     

The Indonesian Homo erectus brain endocasts revisited

New brain endocast reconstructions of Homo erectus discoveries from Indonesia since 1963 (H. erectus VI, 1963; VII, 1965; VIII, 1969) have been made and their volumes determined. In addition, older discoveries (H. erectus I, 1891; II, 1937; IV, 1937–38) have been reendocast and reconstructed, and have yielded volumes considerably different from those previously published. This is particularly so in the case of Dubois's original discovery, which yields a volume of 940 ml rather than the widely quoted volume of 750 ml. In addition, a number of morphological observations regarding hemispheric asymmetries (petalias) are provided, which suggest a condition similar to modern Homo sapiens.     

Fossil Homo femur from Berg Aukas,northern Namibia

The proximal half of a hominid femur was recovered from deep within a paleokarst feature at the Berg Aukas mine, northern Namibia. The femur is fully mineralized, but it is not possible to place it in geochrono logical context. It has a very large head, an exceptionally thick diaphyseal cortex, and a very low collodiaphyseal angle, which serve to differentiate it from Holocene homologues. The femur is not attributable to Australopithecus, Paranthropus, or early Homo (i.e., H. habilis sensu lato). Homo erectus femora have a relatively longer and AP flatter neck, and a shaft that exhibits less pilaster than the Berg Aukas specimen. Berg Aukas also differs from early modern femora in several features, including diaphyseal cortical thickness and the degree of subtrochanteric AP flattening. The massive diaphyseal cortex of Berg Aukas finds its closest similarity within archaic H. sapiens (e.g., Castel di Guido) and H. erectus (e.g., KNM-ER 736) samples. It has more cortical bone at midshaft than any other specimen, although relative cortical thickness and the asymmetry of its cross-sectional disposition at this level are comparable with those of other Pleistocene fem ora. The closest morphological comparisons with Berg Aukas are in archaic (i.e., Middle Pleistocene) H. sapiens and Neandertal samples. © 1995 Wiley-Liss, Inc.     

A deterministic model of admixture and genetic introgression: the case of Neanderthal and Cro-Magnon

There is an ongoing debate in the field of human evolution about the possible contribution of Neanderthals to the modern human gene pool. To study how the Neanderthal private alleles may have spread over the genes of Homo sapiens, we propose a deterministic model based on recursive equations and ordinary differential equations. If the Neanderthal population was large compared to the Homo sapiens population at the beginning of the contact period, we show that genetic introgression should have been fast and complete meaning that most of the Neanderthal private alleles should be found in the modern human gene pool in case of ancient admixture. In order to test/reject ancient admixture from genome-wide data, we incorporate the model of genetic introgression into a statistical hypothesis-testing framework. We show that the power to reject ancient admixture increases as the ratio, at the time of putative admixture, of the population size of Homo sapiens over that of Neanderthal decreases. We find that the power to reject ancient admixture might be particularly low if the population size of Homo sapiens was comparable to the Neanderthal population size.     

The changing face of genus Homo

Since its introduction in the 18th century, the genus Homo has undergone a number of reinterpretations, all of which have served to make it a more inclusive taxon. In this paper, we trace this trend towards greater inclusiveness, and explain how it has affected the way Homo is defined. We then demonstrate that the current criteria for identifying species of Homo are difficult, if not impossible, to operate using paleoanthropological evidence. We discuss alternative, verifiable, criteria, and show that when these new criteria are applied to Homo, two species, Homo habilis and Homo rudolfensis, fail to meet them. We contend that the lowest boundary of Homo should be redrawn so that the earliest species in the genus is Homo ergaster, or early African Homo erectus. The appearance of this species at around 1.9 Myr appears to mark a distinct shift in hominin adaptive strategy involving morphological and behavioral innovations.     

Longgupo: EarlyHomo colonizer or late plioceneLufengpithecus survivor in south China?

A fragment of mandible and a maxillary incisor of different individuals from the Longgupo Cave, China have been cited as evidence of an early dispersal ofHomo from Africa to Asia. More specifically, these specimens are said to resemble “Homo ergaster” orHomo habilis, rather than the species usually thought to be the first Asian colonizer,Homo erectus. If this supposition is correct, it calls into question which hominid (sensu stricto) first left Africa, and why hominids became a colonizing species. Furthermore, the Longgupo remains have been used to buttress the argument thatHomo erectus evolved uniquely in Asia and was not involved in the origins of modern humans. We question this whole line of argument because the mandibular fragment cannot be distinguished from penecontemporary fossil apes, especially the Late Miocene-Pliocene Chinese genusLufengpithecus, while the incisor is indistinguishable from those of recent and living east Asian people and may be intrusive in the deposit. We believe that the Longgupo mandible represents the relic survival of a Late Miocene ape lineage into a period just prior to the dispersal of hominids into southeastern Asia, with some female dental features that parallel the hominid condition. If the Longgupo mandibular fragment represents a member of theLufengpithecus clade, it demonstrates that hominoids other thanGigantopithecus and the direct ancestor of the orangutan persisted in east Asia into the Late Pliocene, while all other Eurasian large-bodied hominoids disappeared in the Late Miocene.     

A gracile hominid cranium from upper member G of the Shungura Formation,Ethiopia

A fragmentary hominid cranium with teeth, specimen L.894-1, dating from 1.84 m.y. BP in the Shungura Formation at Omo, is described. From its dental and cranial morphology and because of similarities to Olduvai Hominids 24 and 13 and Sangiran 4, among others, it is concluded that the specimen represents a member of an early species of the genus Homo (Homo habilis or Homo modjokertensis). The specimen shows approximal grooving on the premolars, pre-mortem chipping of the molar enamel, foramina ovale and spinosum divided by the sphenosquamosal suture, limited pneumatization of the mastoid region, and a possible interparietal bone. Sedimentological, ostracod, pollen, macrofloral, and taphonomic data indicate that the paleo-environmental context was a savanna/grassland or savanna woodland on the margin of a saline lake.     

Variation among early Homo crania from Olduvai Gorge and the Koobi Fora region

Fossils recognized as early Homo were discovered first at Olduvai Gorge in 1959 and 1960. Teeth, skull parts and hand bones representing three individuals were found in Bed I, and more material followed from Bed I and lower Bed II. By 1964, L.S.B. Leakey, P.V. Tobias, and J.R. Napier were ready to name Homo habilis. But almost as soon as they had, there was confusion over the hypodigm of the new species. Tobias himself suggested that OH 13 resembles Homo erectus from Java, and he noted that OH 16 has teeth as large as those of Australopithecus. By the early 1970s, however, Tobias had put these thoughts behind him and returned to the opinion that all of the Olduvai remains are Homo habilis. At about this time, important discoveries began to flow from the Koobi Fora region in Kenya. To most observers, crania such as KNM-ER 1470 confirmed the presence of Homo in East Africa at an early date. Some of the other specimens were problematical. A.C. Walker and R.E. Leakey raised the possibility that larger skulls including KNM-ER 1470 differ significantly from smaller-brained, small-toothed individuals such as KNM-ER 1813. Other workers emphasized that there are differences of shape as well as size among the hominids from Koobi Fora. There is now substantial support for the view that in the Turkana and perhaps also in the Olduvai assemblages, there is more variation than would be expected among male and female conspecifics. One way to approach this question of sorting would be to compare all of the new fossils against the original material from Olduvai which was used to characterize Homo habilis in 1964. A problem is that the Olduvai remains are fragmentary, and none of them provides much information about vault form or facial structure. An alternative is to work first with the better crania, even if these are from other sites. I have elected to treat KNM-ER 1470 and KNM-ER 1813 as key individuals. Comparisons are based on discrete anatomy and measurements. Metric results are displayed with ratio diagrams, by which similarity in proportions for several skulls can be assessed in respect to a single specimen selected as a standard. Crania from Olduvai examined in this way are generally smaller than KNM-ER 1470, although OH 7 has a relatively long parietal. In the Koobi Fora assemblage, there is variation in brow thickness, frontal flattening and parietal shape relative to KNM-ER 1470. These comparisons are instructive, but vault proportions do not help much with the sorting process. Contrasts in the face are much more striking. Measurements treated in ratio diagrams show that both KNM-ER 1813 and OH 24 have relatively short faces with low cheek bones, small orbits and low nasal openings. Also, they display more projection of the midfacial region, just below the nose. This is not readily interpreted to be a female characteristic, since in most hominoid primates the females tend to have flatter lower faces than the males. The obvious size differences among these individuals have usually been interpreted as sex dimorphism, but, in fact, two taxa may be sampled at Olduvai and in the Turkana basin at the beginning of the Pleistocene. One large-brained group made up of KNM-ER 1470, several other Koobi Fora specimens, and probably OH 7, can be called Homo habilis. If these skulls go with femora such as KNM-ER 1481 and the KNM-ER3228 hip, then this species is close in postcranial anatomy to Homo erectus. The other taxon, including small-brained individuals such as KNM-ER 1813 and probably OH 13, seems also to be Homo rather than Australopithecus. If the OH 62 skeleton is part of this assemblage, then the small hominids have postcranial proportions unlike those of Homo erectus. However, it is too early to point unequivocally to one or the other of these groups as the ancestors of later humans. Both differ from Homo erectus in important ways, and both need to be better understood before we can map the earliest history of the Homo clade. © 1993 Wiley-Liss, Inc.     

Brain endocast asymmetry in pongids and hominids: Some preliminary findings on the paleontology of cerebral dominance

Observations on petalial asymmetry for 190 hominoid endocasts are reported, and their statistical differences assessed. While all taxa of hominoids show asymmetries to various degrees, the patterns or combinations of petalial asymmetries are very different, with fossil hominids and modern Homo sapiens showing an identical pattern of left-occipital, right-frontal petalias, which contrasts with those found normally in pongids. Of the pongids, Gorilla shows the greater degree of asymmetry in left-occipital petalias. Only modern Homo and hominids (Australopithecus, Homo erectus, Neandertals) show a distinct left-occipital, right-frontal petalial pattern. Analysis by x² statistics shows the differences to be highly significant. Due to small sample size and incompleteness of endocasts, small-brained hominids, i.e., Australopithecus, are problematical. To the degree that gross petalial patterns are correlated with cognitive task specialization, we speculate that human cognitive patterns evolved early in hominid evolution and were related to selection pressures operating on both symbolic and spatiovisual integration, and that these faculties are corroborated in the archaeological record.     

嗜吞噬无形体Msp2蛋白与宿主互作靶蛋白筛选及生物信息分析

目的:筛选与嗜吞噬无形体Msp2蛋白互作的THP-1细胞靶蛋白,有助于理解病原体侵袭宿主的分子机理。方法:PCR获得无形体msp2基因克隆到pGBKT7载体上构建诱饵质粒并转化酵母菌株Y2HGold,营养缺陷培养基及蓝白斑实验验证诱饵质粒是否有自激活、毒性;抽提THP-1总RNA,经反转录、Long-distance PCR、同源重组等构建到pGADT7-Rec载体上并转化酵母菌株Y187,鉴定cDNA文库质量;酵母双杂交筛选与无形体Msp2互作的宿主细胞靶蛋白,生物信息学分析蛋白互作可能导致的信号通路变化。结果:成功构建诱饵质粒;cDNA文库容量达4×106克隆,插入片段大小100-3000 bp,且无污染;酵母双杂交获得宿主靶蛋白7个,分别是NADH脱氢酶(泛醌)1α亚体13(NDUFA13)、锌指蛋白36, C3H样2(ZFP36L2)、核糖体蛋白11(RPL11)、前胸腺素α(PTMA)、C19orf10、组织蛋白酶G(CTSG)、核糖体蛋白S25(RPS25);生物信息学分析,互作的宿主靶蛋白主要参与细胞增殖、细胞凋亡、溶酶体成熟及其它一些信号通路等生物学过程。结论:应用酵母双杂交系统初步筛选出与嗜吞噬细胞无形体表面蛋白Msp2互作的宿主细胞靶蛋白,并利用生物信息学初步分析了其参与的生物学过程,为进一步研究病原菌胞内生存分子机制奠定了基础。     

On the taxonomic affinities of the Dmanisi mandible (Georgia)

The recent discovery of unexpectedly ancient human remains has fuelled interest about the first dispersion of Homo outside Africa. The Dmanisi mandible is perhaps one of the most interesting findings, as it supposedly represents one of the oldest hominids outside of Africa. Recently, different interpretations have been published about this specimen. Our comparison of the Dmanisi mandible with a large sample of mandibles and teeth has led us to a new interpretation. In our view, the Dmanisi mandible exhibits a unique combination of traits. Some of its features, taken in isolation, may be attributed to morphological extremes within the genus Homo. The architecture of the mandible as well as the morphology and dimensions of incisors, canines, and P3s are clearly primitive. However, dental traits such as the reduction of the talonid in the P4s and a distally decreasing molar series seems to be derived. Some combinations of these traits are found in specimens of Homo ergaster and differ from those generally present in later hominids. Thus, we propose that the Dmanisi mandible might be taxonomically classified as Homo sp. indet. (aff. ergaster). Furthermore, some aspects of the dentition in Dmanisi display close similarities to Asian Homo erectus. If the 1.8–1.6 Myr dating for the Dmanisi mandible is correct, the differentiation of the Asian branch of the genus Homo could be regarded as a very ancient event. Am J Phys Anthropol 107:145–162, 1998. © 1998 Wiley-Liss, Inc.     

Quantitative and qualitative trends in human sapientization

Sapientization is envisaged as a process leading from the earliest representatives of the genus Homo to the shape and dynamism of Homo sapiens (sapiens). Taking into account the manifestation of the changes occurring in the Homo brain-case, two evolutionary trends can be distinguished: the expansion of the cranial capacity (quantitative sapientization) and the attainment of the recent shape (qualitative sapientization). Evidently, both trends cooperate towards a single objective. The writer suggests that they may come into play in an alternating way.The major changes from the psychic and ethological standpoint seem to be related to stages in qualitative change, namely, to the transition both from Australopithecus to Homo and from H. neanderthalensis to Homo sapiens (sapiens).