Mitochondrial DNA evidence for the spread of Pacific rats through Oceania

In the 10 years since we published our first full analysis of mitochondrial DNA (mtDNA) variation in Rattus exulans as a means for tracking human migration in Polynesia, we have extended the commensal approach through time and space with the use of ancient DNA (aDNA) and by analysing samples from across the Pacific. Not only can mtDNA phylogenies provide information regarding population origins and paths of migration, they have also provided information regarding degrees of contact and interaction between islands. An important extension of the R. exulans project is the creation and on-going development of a genetic database for the identification of Rattus species based on mtDNA sequences. The phylogenetic analysis of sequences from 18 species and 1 subspecies of Rattus thus far have raised some questions regarding species identification and species distributions in the Pacific.     

A system for sex determination from degraded DNA: a useful tool for palaeogenetics and conservation genetics of ursids

In this paper, we characterise three sex-specific genes (ZFX/Y, SRY, AMLX/Y) for all eight extant bear species and propose a new, robust and accurate molecular procedure to identify the sex of bears from non-invasive samples and fossil remains. These materials contain tiny amounts of poorly preserved deoxyribonucleic acid (DNA), leaving Polymerase Chain Reaction (PCR) amplification very prone to contamination and difficult to analyse. By taking into account the ancient DNA requirements, the duplex procedures that we developed are efficient not only on DNA extracted from bear faeces but also on ancient DNA extracted from a brown bear fossil 7,500 years old. Defined specifically for ursids, the procedure for faecal samples (co-amplification of ZFX/Y and SRY markers) appears more accurate than other published procedures, as it prevents cross-amplification of potential ingested prey and contamination (19 non-ursid species tested). This system can be applied to threatened bear populations to improve the reliability of sex-ratio and population-size estimates based on non-invasive samples. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorised users.     

藕莲种质资源形态与农艺性状的遗传变异分析(英文)

藕莲是莲(Nelumbo nucifera Gaertn.ssp.nucifera)的3种类型之一,在我国作为水生蔬菜栽培的历史愈两千年。对国家种质资源圃中来自17个省和直辖市的68份藕莲资源的19个形态和农艺性状进行了观察,并对其遗传变异进行了分析。结果发现整藕重与主藕重、主藕长和第三节粗成极显著正相关。通径分析结果表明主藕重对整藕重的正向效应最高(0.982)。主成分分析结果显示前4个成分占总变异的77.33%。结果还显示对整藕重负效应最高的是主藕重/整藕重(-0.296)。聚类分析发现所有藕莲资源可分为5组。     

花莲种质资源形态性状多样性研究(英文)

对从国家种质资源圃中选取的40份花莲种质资源的19个形态性状进行了观察。结果发现花型、花瓣数、雌蕊是否瓣化、雌蕊瓣化程度和根茎颜色与花蕾形状呈显著正相关,其中花型、花瓣数和根茎颜色与花蕾形状呈极显著高度相关。通径分析表明现蕾期对花型有显著正向效应(0.552),其次是花瓣数(0.516)和根茎颜色(0.368)。与花型呈显著负相关的性状有花瓣长(-0.801)、现花期(-0.558)和叶宽(-0.451)。主成分分析显示前四个成分累计贡献率达65.68%。聚类分析将所有材料分为四组。     

Deterioration of cichlid habitat by increased sedimentation in the rocky littoral zone of Lake Malawi

Lake Malawi has been affected by soil erosion across the catchment area. We experimentally investigated habitat preferences of cichlids in the rocky littoral zone to examine the influence of increased sedimentation on bottom-dwelling cichlids. Numbers of individuals and species, as well as the feeding rate of some of these cichlids, increased following the clearing of sediment. The results showed that these cichlids preferred sediment-free bottom and that the sedimentation causes deterioration of their habitats. Studies on the consequences of the habitat deterioration caused by increased sedimentation are needed in the management of these most diverse freshwater fish communities.     

Poly(A) tailing of ancient DNA: a method for reproducible microsatellite genotyping

Microsatellites could be of great potential use in the analysis of ancient remains, but so far such analyses have failed to be reproducible mainly because of the high degree of ancient DNA (aDNA) degradation. During PCR, annealing of the primers to the complementary sequences of microsatellites occurs together with cross-annealing of partially degraded repeated sequences. This could create chimeric alleles that do not correspond to the authentic ones. Here we report a simple method for processing aDNA fragments prior to PCR that greatly reduces the production of chimeric alleles. This approach eliminates aDNA molecules broken within the repeats as targets for Taq polymerase by adding poly(A) tails at the 3(') ends of the DNA fragments, which disrupts the homology in the region and thus prevents annealing out of register. We have analyzed one dinucleotide- (D6S337) and two trinucleotide-containing loci (IT15 and SCA1) using poly(A)-tailed and the same untreated aDNA as template. aDNAs were isolated from 28 human remains, 600 and 7000 years of age. In repeated experiments with untreated aDNAs we obtained three to five times more alleles compared to poly(A)-tailed aDNAs. According to our results, modification of aDNA by poly(A) tailing is an efficient pretreatment for accurate genotyping.     

Amplification of the ancient murine Lx family of long interspersed repeated DNA occurred during the murine radiation

We identified and characterized the relics of an ancient rodent Ll family, referred to as Lx, which was extensively amplified at the time of the murine radiation about 12 million years ago, and which we showed was ancestral to the modern L1 families in rat and mouse. Here we have extended our analysis of the Lx amplification by examining more murine and nonmurine species for Lx sequences using both blot hybridization and the polymerase chain reaction for a total of 36 species. In addition we have determined the relative copy number and sequence divergence, or age, of Lx elements in representative murine genera. Our results show that while Lx sequences are confined to murine genera, the extent of the amplification was different in the different murine lineages, indicating that the amplification of Lx did not precede, but was coincident with, the murine radiation. The implications of our findings for the evolutionary dynamics of L1 families and the utility of ancestral amplification events for systematics are discussed. Correspondence to: A.V. Furano     

Craniometric variation,genetic theory,and modern human origins

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and, the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on withingroup variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevannt to issues of human origins. Our results are in agreement with mismatch distribution analysis of mtDNA, and they support a “weak Garden o Eden” model. In this model, modern-day variation can be explained by divergence from an initial source (perhaps Africa) into a number o small isolated populations, followed by later population expansion throughout our species. The major populationn expansions of Homo sapiens during and after the late Pleistocene have had the effect of “freezing” ancient patterns of population structure. While this is not the only possible scenario, we do note the close agreement with ecent analyses of mtDNA mismatch distibutions. © 1994 Wiley-Liss, Inc.     

江西会昌发现第四纪哺乳动物化石

1990年3月上旬,会昌县水泥厂工人在开采石灰石时,发现一处石灰岩裂隙堆积,堆积物中含有种类丰富的古脊椎动物化石。我馆闻讯后,先后两次组织专业人员前往调查,并采集了一批古脊椎动物化石。 动物化石出土地点位于江西省会昌县小密乡小密村六工排万石坑,现为会昌县水泥厂的采石工地,地理坐标为115°43＇E,25°54＇N。动物化石出自一个低山丘陵的朝南向阳山坡的裂隙中,裂隙堆积物以棕红色砂质粘土为主,含少量石英和云母成分。