A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

Starch grains from dental calculus reveal ancient plant foodstuffs at Chenqimogou site, Gansu Province

National Natural Science Foundation of China [40771205]; National Science Fund for Distinguished Young Scholars [40625002]; Chinese Academy of Sciences [KZCX2-YW-315]

An ancient C-type lectin in Chlamys farreri (CfLec-2) that mediate pathogen recognition and cellular adhesion

C-type lectins are a superfamily of Ca2+ dependent carbohydrate-recognition proteins which play significant diverse roles in nonself-recognition and clearance of invaders. In the present study, a C-type lectin (CfLec-2) from Zhikong scallop Chlamys farreri was selected to investigate its functions in innate immunity. The mRNA expression of CfLec-2 in hemocytes was significantly up-regulated (P < 0.01) after scallops were stimulated by LPS. PGN or beta-glucan, and reached the highest expression level at 12h post-stimulation, which was 72.5-, 23.6- or 43.8-fold compared with blank group, respectively. The recombinant Cflec-2 (designated as rCfLec-2) could bind LPS, PGN, mannan and zymosan in vitro, but it could not bind beta-glucan. Immunofluorescence assay with polyclonal antibody specific for Cflec-2 revealed that CfLec-2 was mainly located in the mantle, kidney and gonad. Furthermore, rCfLec-2 could bind to the surface of scallop hemocytes, and then initiated cellular adhesion and recruited hemocytes to enhance their encapsulation in vitro, and this process could be specifically blocked by anti-rCfLec-2 serum. These results collectively suggested that CfLec-2 from the primitive deuterostome C. farreri could perform two distinct immune functions, pathogen recognition and cellular adhesion synchronously, while these functions were performed by collectins and selectins in vertebrates, respectively. The synchronous functions of pathogen recognition and cellular adhesion performed by CfLec-2 tempted us to suspect that CfLec-2 was an ancient form of C-type lectin, and apparently the differentiation of these two functions mediated by C-type lectins occurred after mollusk in phylogeny. (C) 2010 Elsevier Ltd. All rights reserved.

环境变迁在中国文明形成中的作用

The formation of civilization, one of great marks in the history of human's society development, has been remained one of the hottest topics in the world. Many theories have been put ford to explain its causes and mechanisms. Although more attentions have been paid to its development, the role of environmental change should not be ignored. In this paper, the level of ancient farming productivity was analyzed, the mechanisms and the process of Chinese ancient civilization formation was explored, and some causes why Chinese ancient civilization shows many different features from other 5 ancient civilizations of the world was analyzed. The main results and conclusions are presented as followed. 1. Compared with the productivity level of other five ancient civilizations, the productivity of ancient China characterized by a feature of extensive not intensive cultivation was lower than that of other five ancient civilizations whose agriculture were based on irrigation. 2. The 5 5000 a B.P. cold event may have facilitated the formation of Egypt and Mesopotamian ancient civilizations and also have had an influence on the development of Neolithic culture in China. 3. The 4 000 a B.P. cold event, which may be the coldest period since the Younger Dryas cold event and signifies the changes from the early Holocene Climate Optimum to late Holocene in many regions of the world, resulted in the great migration of the Indo-European peoples from north Europe to other part of the World and the collapses of ancient civilizations in Egypt, Indus and the Mesopotamian and the collapse of five Neolithic cultures around central China. More important than that is the emergence of Chinese civilization during the same period. Many theories have been put ford to explain why it was in Zhongyuan area not other places whose Neolithic cultures seem more advanced that gave rise to civilization. For now no theory could explain it satisfiedly. Archaeological evidence clearly demonstrate that war was prevailed the whole China especially during the late Longshan culture period, so it seemed war has played a very important role in the emergence of China ancient civilization. Carneiro sees two conditions as essential to the formation of complex societies in concert with warfare, i.e. population growth and environmental circumscription. It was generally through that China couldn't evolved into the environmental circumscription and population pressure because China has extensive areas to live, but that depends on situations. The environmental circumscription area was formed due to the 4000a B.P. cold event and companied flooding disasters, while the population pressure is formed due to three factors; 1) population grow rapidly because of the suitable environment provided by the Holocene Optimum and thus laid its foundations for the ancient human population; 2) population pressure is also related to the primitive agricultural level characterized by extensive not intensive cultivation; 3) population pressure was mainly related to the great migrations of people to the same areas; 4) population pressure was also related to productivity decrease due to the 4 000a B.P. cold event. 4. When population pressure is formed, war is the most possible way to solve the intensions between population and the limited cultivated land and then resulted in the formation of civilization. In this way the climate change during the 4 000a B.P. cold event may have facilitated the emergence of Chinese ancient civilization. Their detailed relations could also be further understood in this way: The first birth places of China ancient civilization could be in Changjiang areas or (and) Daihai area, Shandong province rather than in central China and the emergence time of ancient civilization formed in central China should be delayed if the 4 000a B.P. cold event and companied flooding disasters didn't occurred.

Aspects of Armageddon: An exploration of the role of volcanic eruptions in human history and civilization

Grattan, J.P. (2006) Aspects of Armageddon: An exploration of the role of volcanic eruptions in human history and civilization, Quaternary International 151, 10-18.

Analyses of patterns of copper and lead mineralisation in human skeletons excavated from an ancient mining and smelting centre in the Jordanian desert

Grattan, J.P., Al-Saad, Z., Gilbertson, D.D., Karaki, L.O., Pyatt, F.B 2005 Analyses of patterns of copper and lead mineralisation in human skeletons excavated from an ancient mining and smelting centre in the Jordanian desert Mineralogical Magazine. 69(5) 653-666.

The heavy metal content of skeletons from an ancient metalliferous polluted area in southern Jordan with particular reerence to bioaccumulation and human health

Pyatt, F.B., Pyatt, A.J., Walker, C., Sheen, T., Grattan, J.P, The heavy metal content of skeletons from an ancient metalliferous polluted area in southern Jordan with particular reerence to bioaccumulation and human health, Ecotoxicology & Environmental Safety 60, 13th August 2003, 295-300

Invertebrates of ancient heavy metal spoil and smelting tip sites in southern Jordan: Thier distribution and use as bioindicators of metalliferous pollution derived from ancient sources

Pyatt, B. Amos, D. Grattan, J. Pyatt, A. Terrell-Nield, C. Invertebrates of ancient heavy metal spoil and smelting tip sites in southern Jordan: Thier distribution and use as bioindicators of metalliferous pollution derived from ancient sources. Journal of Arid Environments. 2002. 52 pp 53-62