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Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors

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Science China(Life Sciences) 2019年第4期62卷 594-608页

作者： Jian Zu Yuexi Gu Yu Li Chentong Li Wenyu Zhang Yong E.Zhang UnJin Lee Li Zhang Manyuan Long School of Mathematics and Statistics Xi'an Jiaotong University Department of Ecology and evolution The University of Chicago Center for Systems Biology Soochow University State Key laboratory of Integrated Management of Pest Insects and Rodents & Key laboratory of the Zoological Systematics and evolution Institute of Zoology Chinese Academy of Sciences

We analyze the global structure and evolution of human gene coexpression networks driven by new gene integration. When the Pearson correlation coefficient is greater than or equal to 0.5, we find that the coexpression network consists of 334 small components and one "giant" connected subnet comprising of 6317 interacting genes. This network shows the properties of power-law degree distribution and small-world. The average clustering coefficient of younger genes is larger than that of the elderly genes(0.6685 vs. 0.5762). Particularly, we find that the younger genes with a larger degree also show a property of hierarchical architecture. The younger genes play an important role in the overall pivotability of the network and this network contains few redundant duplicate genes. Moreover, we find that gene duplication and orphan genes are two dominant evolutionary forces in shaping this network. Both the duplicate genes and orphan genes develop new links through a "rich-gets-richer"mechanism. With the gradual integration of new genes into the ancestral network, most of the topological structure features of the network would gradually increase. However, the exponent of degree distribution and modularity coefficient of the whole network do not change significantly, which implies that the evolution of coexpression networks maintains the hierarchical and modular structures in human ancestors.

关键词： Network biology gene network evolution scale-free network natural selection gene expression self-organization,gene duplication

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The broad-spectrum adaptations of hominins in the later period of Late Pleistocene of China—Perspectives from the zooarchaeological studies

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Science China Earth Sciences 2016年第8期59卷 1529-1539页

作者： ZHANG ShuangQuan ZHANG Yue LI Jing Shu GAO Xing Key laboratory of Vertebrate evolution and human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences

During the climatic fluctuations in the late Late Pleistocene, hominins in China had experienced some significant changes and adaptations in terms of subsistence strategies. Based on the zooarchaeological analyses of the faunal remains from the Shuidougou site of North China and the Ma'anshan site of South China, the present study demonstratively indicates that the broad-spectrum diet and its closely-related resource intensification for hominins were already at their places roughly at 33–35 cal ka BP. Compared to hominins of earlier period, who would have preferentially exploited large and medium-sized ungulates, hunter-gathers at later period had otherwise incorporated more small-sized animals(especially the quick ones, such as birds and hares) into their diet. Meanwhile, hominins of the later time had also greatly accelerated extractions and exploitations of the nutritional yields from the large and medium-sized animals. However, it seems clear from the current study that there was significant difference regarding the potential mechanisms for the broad-spectrum adaptations of hominins in the late Late Pleistocene of China.

关键词： Late Late Pleistocene Paleolithic Taphonomy Zooarchaeology Broad-spectrum revolution Resource intensification

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A Middle Triassic stem-neopterygian fish from China sheds new light on the peltopleuriform phylogeny and internal fertilization

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Science Bulletin 2016年第22期61卷 1766-1774页

作者： Guang-Hui Xu Xin-Ying Ma Key laboratory of Vertebrate evolution and human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences

Internal fertilization and viviparity are easily observed and well studied in living neopterygian fishes(14teleostean families), but they are difficult to identify in extinct taxa due to the limitation of the fossil record. The Peltopleuriformes from the Middle to Late Triassic of Europe and South China are a stem group of Neopterygii that may have first evolved internal fertilization and viviparity in this clade because they show a highly modified anal fin in presumed males resembling the intromittent organ in living viviparous teleosts. Until recently, Peltopleurus lissocephalus and P. rugosus from the Ladinian/Anisian boundary(*242 Ma) of Monte San Giorgio area in Switzerland and Italy represent the oldest record of Peltopleuriformes, and the phylogenetic interrelationships of this group remain controversial. Here, we report the discovery of a new peltopleuriform, Peltopleurus nitidus sp. nov., based on eleven well-preserved specimens from the early Middle Triassic(Pelsonian, Anisian, *244 Ma)of Luoping, eastern Yunnan, China. The discovery documents the oldest convincing peltopleuriform, extending the geological range of this clade by proximately two million years. Results of the phylogenetic analysis recover *** at the base of Peltopleuridae, and provide robust support for the sister-group relationships of Peltopleuridae with Thoracopteridae within the Peltopleuriformes. The male anal fin of P. nitidus shows a primitive condition unknown in other peltopleuriforms. Comparative studies of the male anal fin in P. nitidus and other peltopleuriforms shed new light on the internal fertilization in this group.

关键词： Sexual dimorphism Viviparity Peltopleuridae Thoracopteridae Triassic

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A transgenic monkey model for the study of human brain evolution

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Zoological Research 2019年第3期40卷 236-238页

作者： Lei Shi Bing Su State Key laboratory of Genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Primate Research Center Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Center for Excellence in Animal evolution and Genetics Chinese Academy of SciencesKunming Yunnan 650223China

Why humans have large brains with higher cognitive abilities is a question long asked by ***,much remains unknown,especially the underlying genetic *** the use of a transgenic mon key model,we showed that human-specific sequenee changes of a key brain development gene(Primary microcephaly 1,MCPH7)could result in detectable molecularand cognitive changes resembling human neoteny,a no table characteristic developed during human *** study was published in National Science Review(Shi et al.,2019).

关键词： human brain evolution key model

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The Jehol Biota, an Early Cretaceous terrestrial Lagerst ¨atte: new discoveries and implications

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National Science Review 2014年第4期1卷 543-559页

作者： Zhonghe Zhou Key laboratory of Vertebrate evolution and human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences

The study of the Early Cretaceous terrestrial Jehol Biota,which provides a rare window for reconstruction of a Lower Cretaceous terrestrial ecosystem,is reviewed with a focus on some of the latest progress.A newly proposed deinition of the biota based on paleoecology and taphonomy is *** the Jehol fossils are mainly preserved in two types of sedimentary rocks,there are various types of preservation with a complex mechanism that remains to be *** discoveries of signiicant taxa from the Jehol Biota,with an updated introduction of its diversity,conirm that the Jehol Biota represents one of the most diversiied biotas of the *** evolutionary signiicance of major biological groups(***,birds,mammals,pterosaurs,insects,and plants)is discussed mainly in the light of recent discoveries,and some of the most remarkable aspects of the biota are *** global and local geological,paleogeographic,and paleoenvironmental background of the Jehol Biota have contributed to the unique composition,evolution,and preservation of the biota,demonstrating widespread faunal exchanges between Asia and other continents caused by the presence of the Eurasia–North American continental mass and its link to South America,and conirming northeastern China as the origin and diversiication center for a variety of Cretaceous biological *** some progress has been made on the reconstruction of the paleotemperature at the time of the Jehol Biota,much more work is needed to conirm a possible link between the remarkable diversity of the biota and the cold intervals during the Early ***,future directions for the study of the Jehol Biota are proposed that highlight the great potential of more comprehensive and multidisciplinary studies to further our understanding of the biological and geological implications of the Jehol Lagerst¨ate.

关键词： Jehol Biota Early Cretaceous Lagerst¨ate China terrestrial ecosystem

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evolution and distribution of medullary bone: evidence from a new Early Cretaceous enantiornithine bird

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National Science Review 2020年第6期7卷 1068-1078页

作者： Min Wang Jingmai K.O'Connor Alida M.Bailleul Zhiheng Li Key laboratory of Vertebrate evolution and human Origins Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences CAS Center for Excellence in Life and Paleoenvironment

Living birds are unique among vertebrates in the formation of a female-specific bone tissue called medullary bone(MB) that is strictly associated with reproductive activity. MB is a rapidly mobilized source of calcium and phosphorus for the production of eggshell. Among living taxa, its skeletal distribution can be highly extensive such that it even exists in the ribs of some species. Due to its ephemeral nature, MB is rarely fossilized and so little is understood with regard to the origin of MB and its skeletal distribution in early *** we describe a new Early Cretaceous enantiornithine bird, Mirusavis parvus, gen. et. sp. nov., indicating that skeleton-wide distribution of MB appeared early in avian evolution. We suggest that this represents the plesiomorphic condition for the Aves and that the distribution of MB observed among extant neornithines is a product of increased pneumatization in this lineage and natural selection for more efficient distribution of MB.

关键词： Aves Cretaceous medullary bone phylogeny reproduction

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Large Tetrapod Burrows from the Permian Naobaogou Formation of the Daqingshan Area, Nei Mongol, China

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Acta Geologica Sinica(English Edition) 2013年第6期87卷 1501-1507页

作者： LIU Jun LI Lu Key laboratory of Vertebrate evolution and human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of Sciences

Two new tetrapod burrow casts from the Naobaogou Formation （Middle or Late Permian） of Nei Mongol,China are *** marks the first pre-Cenozoic tetrapod burrow from China,and one of the earliest records of tetrapod *** to other Permian and Triassic burrows suggests that these burrows were created by tetrapod slightly smaller than *** from the morphology and sizes of two burrows and known tetrapods of the Naobaogou Formation,the burrow should be the production of a therapsid,most likely a *** burrows indicate a seasonal climate and this area was semiarid or arid during that time.

关键词： burrow Naobaogou Formation dicynodon therocephalian

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Fossils of Macaca mulatta from Tianyuan Cave, with Notes on Some Previously Unpublished Specimens of Macaca from Zhoukoudian Area

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Acta Geologica Sinica(English Edition) 2014年第5期88卷 1397-1408页

作者： TONG Haowen Key laboratory of Vertebrate evolution and human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences

The recently discovered macaque fossils, including isolated teeth and mandible fragments, from Tianyuan Cave and the juvenile maxilla from Wanglaopu Cave near Zhoukoudian can be identified as Macaca mulatta; they represent the first recognized occurrence of fossil M. mulatta in the far north of China. Some previously unearthed but still unpublished Macaca specimens were also studied, including a cranium and the associated mandible from CKT Loc.13A, a maxilla and a mandible from Loc.1, a mandible from Loc.4, and a maxilla from Loc.20, as well as a mandible with complete toothrow from Zhoukoudian but without locality details, all of them can be referred to M. robusta. The study shows M. robusta is more closely related to M. mulatta than to M. anderssonL Zhoukoudian is the richest area of Macacina fossils in North China, totally 2 genera and 4 species were once recognized from 9 localities, namely, Procynocephalus wimani, M. cf. anderssoni, M. robusta and M. mulatta. The fossil records of Macacina in Zhoukoudian area were almost continuous through the Quaternary Period, and it＇s reasonable to assume that Zhoukoudian used to be an evolutionary center for macaques in North China. Therefore, the macaque population of M. mulatta once existed decades ago around Beijing probably originated from the Pleistocene ancestors in the local area, rather than being human-introduced as previously thought.

关键词： Macaca mulatta Macaca robusta Tianyuan Cave Zhoukoudian Pleistocene

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Taphonomic and paleoenvironmental issues of the Pleistocene loessic Paleolithic sites in the Qinling Mountains, central China

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Science China Earth Sciences 2016年第8期59卷 1519-1528页

作者： WANG SheJiang LU HuaYu Key laboratory of Vertebrate evolution and human Origins Institute of Vertebrate Palaeontology and PalaeoanthropologyChinese Academy of Sciences School of Geographic and Oceanographic Sciences Nanjing University

Hinterland intermountain basins and northern and southern piedmonts of the Qinling Mountains accumulated a large amount of loess during the Pleistocene. The loess strata not only record local paleogeographic and paleoenvironmental changes, but also contain rich hominin fossils and Paleolithic remains. In the northern piedmont of the Qinling Mountains and the lower valley of the South Luohe River, the loess strata have multi loess-paleosol sequences with aeolian loess continuously accumulating during glacial and interglacial cycles. In contrast to the northern piedmont, loess stratigraphy in the hinterland intermountain basins of the Qinling Mountains is relatively thin and contains finer loess particles. In this "mini" type of loess stratum, the density of Paleolithic remain generally is higher than the Loess Plateau in the north of the Qinling Mountains. Based on stratigraphic, chronological, and lithic artifacts analysis in recent years, it appears that the regional lithic assemblage belongs to the Oldowan(Mode I) lithic industry, and it is dominated by choppers, cores, flakes, and simple retouched flake tools from 1.15 to 0.6 Ma. Paleolithic open-air sites such as Gongwangling and Chenjiawo in the Lantian area, Shangbaichuan and Liuwan in the Luonan Basin, Qiaojiayao in the Lushi Basin, Longgangsi and Yaochangwan in the Hanzhong Basin, Guanmiao in the Ankang Basin, and the Yunxian Man Site in the Yunxian Basin are representative sites in the region; from 400 to 250 ka, the Longyadong cave site in the Luonan Basin inherited the characteristics of the local Mode I lithic industry, the stone assemblage is made up of cores, flakes, and small retouched flake tools, such as scrapers, points, and burins; during the period from 250 to 50 ka, bi-facially retouched Acheulean tools(Model II), such as hand-axes, picks, and cleavers, were commonly found in the Qinling Mountains region. The emergence of a large number of Model II artifacts indicates that local lithic industrie

关键词： Qinling Mountains Pleistocene Loess stratigraphy Paleoenvironment Lithic industry

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Periodicity of Retzius lines in fossil Pongo from South China

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Chinese Science Bulletin 2012年第7期57卷 790-794页

作者： HU Rong1,2,3, ZHAO LingXia1,2 & WU XinZhi2 1 Key laboratory of evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China 2 laboratory of human evolution, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China 3 Graduate University of Chinese Academy of Sciences, Beijing 100049, China laboratory of human evolution Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences Beijing 100044 China

Periodicity of Retzius lines is a key factor in dental development. In this study, we examined the periodicity of Retzius lines in fossil Pongo from South China using polarized light microscope observation of dental ground sections. The periodicities all of the 15 teeth were 9 d. Comparisons of periodicity were made with extant primates, fossil apes and hominins. Periodicity of fossil Pongo from South China was relatively long but fell within the variation of extant Pongo, Gorilla and modern human, and longer than periodicity of Pan and other extant primates. Fossil Pongo from South China was similar to Lufengpithecus and Sivapithecus, shorter than Gigantopithecus and longer than European and African fossil apes and most early hominins in periodicity. Generally, the periodicities of Asian large-body fossil apes were longer than the periodicities of European and African large-body fossil apes in Miocene. Difference among species and trend of evolution in periodicity were analyzed and discussed. We found that periodicity might gradually increase from Proconsul in early Miocene to several fossil apes in Miocene and then Gigantopithecus in Pleistocene. In addition, this study made correlate analysis between periodicity and body mass respectively in males and females of six extant apes and five fossil apes, and found that periodicity positively correlated with body mass.

关键词：周期性变化中国南方大猩猩化石灵长类动物早中新世类人猿显微镜观察

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