从霍凯特的语言设计特征到语言的“进化-发育”观

比较语言学家霍凯特在二十世纪五、六十年代提出的语言设计特征迄今仍然是比较动物交流和人类语言的颇具影响力的方法,尽管他试图把"语言"与"进化"相联系,但专注于言语行为与语码本身。之后塞格达尔等提出"原语言"的设计特征,强调了语言的文化实现。近二十年来生物语言学家从"进化-发育"的角度看待语言,把语言视为一套生物体获得和使用的感觉运动、认知和社交能力,研究语言形成的核心要素与外围条件,从而发现人类语言系统的延续性与独特性。

THE EVOLUTION IN THE HIGHER TAXA OF THE CERAMBYCIDAE (COLEOPTERA)

Summary Five subfamilies of the Cerambycidate: Lamiinae, Cerambycinae, Lepturinae (including Necydalini and Apatophysis), Aseminae (including S pondylis), and Prioninae (including Parandra) are recognized in this paper, All the evolutionary evidences provided in the present research indicate that these subfamilies may be arranged in order from the oldest to the youngest as follows: (1) Lamiinae, Prioninae, Cerambycinae, Lepturinae, Aseminae; or (2) Lamiinae, Cerambycinae, Prioninae, Lepturinae, Aseminae. The possible phylogenetic relationships among the subfamilies are also given.

A New Sampling Approach to Obtain Genomic DNA of Marine Shellfish

[Objective] The aim was to explore a new sampling approach to obtain genomic DNA of marine shellfish,as well as to provide reference for the molecular biology research on precious shellfish.[Method] Meretrix meretrix,Atrina pectinata,Perna viridis,Crassostrea hongkongensis and Scapharca kagoshimensis were used as experimental materials and the genomic DNA of adductor muscle was taken as reference to extract the genomic DNA of shell cavity fluids with the conventional phenol-chloroform method.And then biophotometer,agarose gel electrophoresis,amplification and sequencing of the target fragments were used to examine the quality of genomic DNA.At the same time,the phylogenic tree was constructed to verify the reality of source contributions.[Result] The quality of genomic DNA of shell cavity fluids extracted by the phenol-chloroform method was better than the genomic of adductor muscle.The genomic DNA extracted by this method showed less content of protein,polyphenol and pigment,which could completely meet the demands of amplification and sequencing of the target fragments.Through the phylogenic tree,it was verified that the source contributions of shell cavity fluids were not come from foreign pollutions.[Conclusion] It is completely feasible to obtain the genomic DNA from shell cavity fluids,which could be applied in the target fragments amplification.

Pattern and Significance of Seedling Development in Titanotrichum oldhamii (Gesneriaceae)

The seedling development of Titanotrichum oldhamii (Hemsl.) Solereder has been investigated to provide insight into the evolution and systematic position of Titanotrichum. In T. oldhamii, the size differentiation of the two cotyledons begins while the hypocotyl grows. However, both of the two cotyledons develop normally and locate at the same level. Finally, the two cotyledons are almost equal in size. The aerial shoot (including stem and leaves) is produced from the permanent activity of the apical meristem in the plumular bud. Even though the seedling development in Titanotrichum basically conforms to the general growth pattern of the seedling in the Cyrtandroideae, it is remarkably different from that of other Cyrtandroideae. Based on the revealed evidence in seedling development in Titanotrichum and other comparative data, the authors have evaluated the possible evolutionary pathway of Titanotrichum and further discussed the familial placement of this genus.

Evolution of 5S rRNA Genes in Ophiopogon xylorrhizus Wang et Dai and O. sylvicola Wang et Tang (Convallariaceae)

To reveal how a large gene family evolved in the highly organized genome, the present study sequenced 294 copies of 5S rRNA genes from six individuals of three populations of Ophiopogon xylorrhizus Wang et Dai, and 45 copies from its closest species, O. sylvicola Wang et Tang. Based on the sequences the gene-phylogeny was inferred through PAUP. The sequences were highly diversified. Of the 339 randomly cloned copies, only 13 pairs (3.8%) were identical, with length varied between 307 - 548 bp (average 438.6 bp). The sequence differentiation index (SDI) in O. xylorrhints was 0.078, in O. sylvicola was 0.032, and between these two species was 0.149. In the most parsimonious tree reconstructed, all of the 294 copies of O. xylorrhizus were grouped into one clade, and those of O. sylvicola were grouped into another clade with 100% bootstrap support. The result demonstrated that the copies of 5S rRNA genes originated from just one progenitor copy, 'founder copy', in both of the species respectively, followed by a series of proliferation, and little, if any, homogenization ever occurred in the copies. As the common ancestor of the two species must have home multiple copies of the genes, all the other copies were lost during or after the speciation. Additionally, the phylogeny clearly showed that the founder copy was proliferated continuously through time, not just once. O. xylorrhizus is an extremely endangered species in which high genetic diversity, selfing and depression on seedlings were observed previously. In our study the sequences from different populations or different individuals were mixed in the branches of the O. xylorrhizus clade, although they evolved independently. It is assumed that gene flow of the species happened much more frequently in the past, making the proliferated copies dispersed to different populations, and the species maintained an amount of genetic diversity. Therefore, the selfing and seedling depression would be the result of a recent event. We suggest that some changes in outer mechanisms, such as the pollinators or seed-dispersers, might cause the species selfed, depressed and, finally, endangered.

A brief review on the strategy for selection of orthology prediction methods in phylogenomic studies

With the development and decreasing cost of sequencing techniques, it is possible for scientists to conduct deeper research in phylogenomics. During the procedure of phylogenomic analysis, the mostimportant and vitalest step is orthology prediction, for that the prerequisite to phylogenetic reconstruction is that the genes being compared are orthologous. Here we briefly review the related concept of orthology anddifferent methods for orthology prediction. We also provide recommendations to give some advice for better selection of orthology prediction methods.

Dental Variation Among Asian Colobines, with Specific Reference to the Macaques on the Same Continent

In order to discern dental morphometric variations among the Asian colobines, residuals of the colobines, derived from allometric baselines formed by the Asian macaques （Macaca）, were analyzed with Principal Components Analysis and Euclidean Distances. Results indicated that the widely accepted view that the colobines possess relatively smaller front teeth than the macaques is only the case for the first incisors. The colobines show relatively smaller molars than the macaques. Such profiles may be related to the differences in dietary preferences between the two major groups of the Asian Old World monkeys. The magnitude of such differences is not as great as usullay assumed for the two groups that contain both African and Asian taxa. In other words, the two Asian cercopithecoid groups may have homogenously been shaped by the tectonic modifications and climate alterations in the past five million years. There exist marked differences among the Asian colobines when each of the genera is compared with macaques; the dental profile reflects not only the variation in geographic distribution but also in phylogenetic divergence. Thus, the snub-nosed monkeys （Rhinopithecus） and the gray langurs （Semnopithecus） are characterized by relatively larger molars than the other colobines - larger even than those of the macaques. The differences among Asian colobines, depicted by Euclidean Distances, seems to reflect the relationship of the phylogeny and evolution between colobines and cercopithecines.

Tumor： Life Retrogression？

Cancer emerged in human history for centuries. It seems that while human beings are evolving, tumors are always on their heels. In order to explain and study the mechanism of tumor progression, we proposed a new hypothesis that the tumor is a retrogression of life evolution, in other word, a resurgence of some past fragments in human development history. Our inference was based on the fact that tumors are not foreign diseases, but use of human inherent developmental genes to achieve self-improvement. Characteristics and biological behavior of tumor cells are similar to human normal stem cell to some degree. Thus, studying the process of human evolution could speculate and analyze the occurrence and development of tumors. The latest research showed that many cancer treatment were also taking advantages of those features about retrogression. Continuous in-depth analysis about tumor environmental characteristics and internal law of human evolution may produce new approaches to promote cancer prevention and treatment. Our hypothesis, for the first time, proposed that taking advantage of the evolution laws to reverse the tumor progression as a path of life retrogression is better than exterminating them completely as outside enemies. Some new studies on tumor induced differentiation had also demonstrated the clinical significance of our hypothesis

Diversity and Evolution of Inflorescences in Celastrales

Inflorescences structures in context of their evolution have been conducted for 60 genera and 170 species of Celastrales （according to APG （Angiosperm Phylogeny Group） III 2009, almost 60% of genera and 15% of species from this taxon of the world flora）. There are two big groups of inflorescences in Celastrales-intercalary （more often） and terminal. For many genera of Celastrales both types of inflorescences can be observed, although the frequency of their occurrence varies. There is an important difference between two types of inflorescences： character of completion of the main axis （the terminal flower present or absent）. Flower opening can be in basipetal （Celastraceae, Brexia） or acropetal （Stackhousiaceae） order. Partial inflorescence types included： simple, compound or umbrellate dichasia, spike, raceme, thyrse. Simple flowers of Parnassia are large, nested on long reproductive shoots, emerging from a rosette, with amplexicaule leaf.

Close Relationship between the 2009 H1N1 Virus and South Dakota AIV Strains

Although previous publications suggest the 2009 pandemic influenza A (H1N1) virus was reassorted from swine viruses of North America and Eurasia,the immediate ancestry still remains elusive due to the big evolutionary distance between the 2009 H1N1 virus and the previously isolated strains. Since the unveiling of the 2009 H1N1 influenza,great deal of interest has been drawn to influenza,consequently a large number of influenza virus sequences have been deposited into the public sequence databases. Blast analysis demonstrated that the recently submitted 2007 South Dakota avian influenza virus strains and other North American avian strains contained genetic segments very closely related to the 2009 H1N1 virus,which suggests these avian influenza viruses are very close relatives of the 2009 H1N1 virus. Phylogenetic analyses also indicate that the 2009 H1N1 viruses are associated with both avian and swine influenza viruses circulating in North America. Since the migrating wild birds are preferable to pigs as the carrier to spread the influenza viruses across vast distances,it is very likely that birds played an important role in the inter-continental evolution of the 2009 H1N1 virus. It is essential to understand the evolutionary route of the emerging influenza virus in order to find a way to prevent further emerging cases. This study suggests the close relationship between 2009 pandemic virus and the North America avian viruses and underscores enhanced surveillance of influenza in birds for understanding the evolution of the 2009 pandemic influenza.

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

We compared the numbers of nucleotide substitutions occurring in the non-coding regions and coding regions of Ebola virus genomes and found that non-coding regions contain indispensable phylogenetic and evolutionary information. The omission of genetic data from non-coding regions can lead to unreliable phylogenies and inaccurate estimates of evolutionary parameters.

The genetic equidistance result:misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later

In 1963,Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species.This finding,together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962,directly inspired the ad hoc molecular clock hypothesis.Unfortunately,however,many biologists have since mistakenly viewed the molecular clock as a genuine reality,which in turn inspired Kimura,King,and Jukes to propose the neutral theory of molecular evolution.Many years of studies have found numerous contradictions to the theory,and few today believe in a universal constant clock.What is being neglected,however,is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery.In recent years,we fortuitously rediscovered the equidistance result,which remains unknown to nearly all researchers.Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity,we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena.The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology.

Phylogeny and evolutionary history of the silkworm

The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecular methods.In this study,DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives.All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm.Domestication was estimated to have occurred about 4100 years ago(ya),and the radiation of the different geographic strains of B.mori about 2000 ya.The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya.These estimates are in good agreement with the fossil evidence and historical records.In addition,we show that the domesticated silkworm experienced a population expansion around 1000 ya.The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics,in the genetic analysis of domestic animals,and for understanding the spread of human civilizations.

Referential alarm calling behaviour in New World primates

There is relatively good evidence that non-human primates can communicate about objects and events in their envi- ronment in ways that allow recipients to draw inferences about the nature of the event experienced by the signaller. In some spe- cies, there is also evidence that the basic semantic units are not individual calls, but call sequences and the combinations gener- ated by them. These two findings are relevant to theories pertaining to the origins of human language because of the resemblances of these phenomena with linguistic reference and syntactic organisation. Until recently, however, most research efforts on the primate origins of human language have involved Old World species with comparatively few systematic studies on New World monkeys, which has prevented insights into the deeper phylogenetic roots and evolutionary origins of language-relevant capaci- ties. To address this, we review the older primate literature and very recent evidence for functionally referential communication and call combinations in New World primates. Within the existing literature there is ample evidence in both Callitrichids and Ce- bids for acoustically distinct call variants given to external disturbances that are accompanied by distinct behavioural responses. A general pattern is that one call type is typically produced in response to a wide range of general disturbances, often on the ground but also including inter-group encounters, while another call type is produced in response to a much narrower range of aerial threats. This pattern is already described for Old World monkeys and Prosimians, suggesting an early evolutionary origin. Second, recent work with black-fronted tiff monkeys has produced evidence for different alarm call sequences consisting of acoustically distinct call types. These sequences appear to encode several aspects of the predation event simultaneously, notably predator type and location. Since meaningful call sequences have already been described in Old World primates, we suggest that basic combi- natorial vocal communication has evolved in the primate lineage long before the advent of language. Moreover, it is possible that some of these communicative abilities have evolved even earlier, or independently, as there is comparable evidence in other taxonomic groups. We discuss these findings in an attempt to shed further light on the primate stock from which human language has arisen [Current Zoology 58 （5）： 680-697, 2012].