Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

Isolation and characterization of microsatellite DNA primers in Juniperus przewalskii Kom (Cupressaceae)

Juniperus przewalskii (Cupressaceae) is a dominant tree species endemic to the northeast Qinghai-Tibetan Plateau. This species plays an important role in maintaining the arid ecosystem in this region. However, natural distributions of this species have been declined. In order to develop effective conservation methods, it is important to know the distribution of the genetic diversity within and among populations. In this study, we developed nine new microsatellite loci for this species. We used the combining biotin capture method to enrich AG/CT/AC/GGT microsatellites. The polymorphisms of each locus were further assessed in 12 individuals from four geographically distant populations. The number of alleles per locus varied from three to six and expected heterozygosity ranged from 0.58 to 0.70. These loci together provide a useful tool to investigate the genetic diversity of this species. In addition, all markers have been crossly checked in the other four congeneric species.

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Origin of mitochondrial DNA diversity of domestic yaks

Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rateConclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.

Variation in mitochondrial DNA and phylogeny of six species of pikas (Ochotona)

Phylogenetic relationships of six species of Ochotona were investigated using mitochondrial DNA (mtDNA) restriction-site analysis. The phylogenetic tree constructed using PAUP was based on 62 phylogenetically informative sites with O. erythrotis designated as an outgroup. Two clades were evident. One contained O. curzoniae, O. huangensis, and O. thibetana. in the second, O. daurica was a sister taxon of O. cansus. The five species appear to come from different maternal lineages. The branching structure of the tree and sequence divergence confirm that huangensis and cansus are distinct species, and that mol-osa is a synonym of O. cansus rather than O. thibetana. Divergence time, estimated from genetic distances, indicates that the ancestors of the two maternal lineages diverged ca. 6.5 x 10(6) years ago. O. curzoniae diverged from O. huangensis, and O. daurica diverged from O. cansus, at about the same time (ca. 3.4 x 10(6) years ago). These data suggest a period of rapid radiation of the genus Ochotona in China, perhaps during the late Pliocene. These calculations correspond roughly to tectonic events and environmental changes in China throughout this period, and appear to be substantiated by the fossil record.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

细粒沉积物多组分粒度特征及其成因机制研究

By using high-resolution laser grain size instrument Mastersizer 2000, the grain size distribution of windblown depositions (loess and sandy dunes), aqueous sediments (lake, river, riverside and foreshore sand), weathering crust, sloping materials and other fine-grain sediments are systemically measured. The multimodal characteristics of grain size distribution of these sediments are carefully studied. The standard patterns and their grain size characteristics of various sediments are systemically summarized. The discrepancies of multimodal distribution among windblown depositions, aqueous sediments and other sediments are concluded and the physical mechanisms of grain size multimodal distribution of various sediments are also discussed in this paper. The major conclusions are followed: 1. The multimodal characteristic of grain size distribution is a common feature in all sediments and results from properties of transportation medium, dynamic intensity, transportation manner and other factors. 2. The windblown depositions are controlled by aerodynamic forcing, resulting in that the median size of the predominant mode gradually decreases form sandy dunes to loess. Similarly, the aqueous sediments are impacted by dynamic forces of water currents and the median grain size of the predominant mode decreases gradually from river to lake sediments. Because the kinetic viscidity of air is lower than of water, the grain size of modes of windblown depositions is usually finer than that of corresponding modes of aqueous sediments. Typical characteristics of sediments grain size distribution of various sediments have been summarized in the paper: (1) Suspended particles which diameters are less than 75μm are dominant in loess and dust. There are three modes in loess’ grain size distribution: fine, median and coarse (the median size is <1μm、1-10μm、10-75μm, respectively). The coarse mode which percentage is larger than that of others is controlled by source distance and aerodynamic intensity of dust source areas. Some samples also have a saltation mode which median size is about 300-500μm. Our analysis demonstrates that the interaction of wind, atmospheric turbulence, and dust grain gravity along the dust transportation path results in a multimodal grain size distribution for suspended dust. Changes in the median sizes of the coarse and medium modes are related to variation in aerodynamic forcing (lift force related to vertical wind and turbulence) during dust entrainment in the source area and turbulence intensity in the depositional area. (2) There is a predominant coarse saltation mode in grain size distribution of sandy dunes, which median size is about 100-300μm and the content is larger than that of other modes. The grain size distribution curve is near axis symmetric as a standard logarithm normal function. There are some suspended particles in some samples of sandy dunes, which distribution of the fine part is similar to that of loess. Comparing with sandy samples of river sediments, the sorting property of sandy dunes is better than of river samples although both they are the saltation mode. Thus, the sorting property is a criterion to distinguish dune sands and river sands. (3) There are 5~6 modes (median size are <1μm, 1-10μm, 10-70μm, 70-150μm, 150-400μm, >400μm respectively) in grain size distribution of lacustrine sediments. The former 4 modes are suspensive and others are saltated. Lacustrine sediments can be divided into three types: lake shore facies, transitional facies and central lake facies. The grain size distributions of the three facies are distinctly different and, at the same time, the transition among three modes is also clear. In all these modes, the third mode is a criteria to identify the windblown deposition in the watershed. In lake shore sediments, suspended particles are dominant, a saltation mode sometimes occurs and the fourth mode is the most important mode. In the transitional facies, the percentage of the fourth mode decreases and that of the second mode increases from lake shore to central lake. In the central lake facies, the second mode is dominant. A higher content of the second mode indicates its position more close to the central lake. (4) The grain size distribution of river sediments is the most complex. It consist of suspension, saltation and rolling modes. In most situations, the percentage of the saltation mode is larger than that of other modes. The percentage of suspension modes of river sediments is more than of sandy dunes. The grain size distribution of river sediments indicates dynamic strength of river currents. If the fourth mode is dominant, the dynamic forcing of river is weaker, such as in river floodplain. If the five or sixth mode is dominant, the water dynamic forcing of rivers is strong. (5) Sediments can be changed by later forcing in different degree to form some complicated deposition types. In the paper, the grain size distribution of aqueous sediments of windblown deposition, windblown sediments of aqueous deposition, weathering crust and slope materials are discussed and analyzed. 3. The grain size distribution characteristics of different sediments are concluded: (1) Modal difference: Usually there are suspended and saltation modes in the windblown deposition. The third mode is dominant in loess dust and the fifth mode is predominant in sandy dunes. There are suspended, saltation and rolling particles in aqueous sediments. In lacustrine sediments, the second and fourth mode are predominant for central lake facies or lake shore facies, respectively. In river sediments, the fourth, or fifth, or sixth mode is predominant. Suspended modes: the grain size of suspended particles of windblown depositions usually is less than 75μm. The content of suspended particles is lower or none in sandy dunes. However, suspended particles of aqueous sediments may reach 150μm. Difference in grain size of suspended modes represents difference between transitional mediums and the strength of dynamic forcing. Saltation modes: the median size of saltation mode of sandy dunes fluctuates less than that of river sediments. (2) Loess dust and lacustrine sediment: Their suspended particles are clearly different. There is an obvious pit between the second and the third modes in grain size distribution of lacustrine sediments. The phenomenon doesn’t occur in loess dust. In lacustrine sediments, the second mode can be a dominant mode, such as central lake facies, and contents of the second and the third modes change reversely. However, the percentage of the third mode is always the highest in loess dust. (3) Dune Sand and fluvial sand: In these two depositions, the saltation particles are dominant and the median sizes of their saltation modes overlay in distribution range. The fifth mode of dune sand fluctuates is sorted better than that of fluvial sand. (4) Lacustrine and fluvial sediments: In lacustrine sediments, there are 5-6 modes and suspended particles can be predominant. The second mode is dominant in central lake facies and the third mode is dominant in lake shore facies. Saltation or roll modes occurred in central lake facies may indicate strong precipitation events. In fluvial sediments, saltation particles (or rolling particles) usually dominant. 4. A estimation model of lake depth is firstly established by using contents of the second, the third and the fourth modes. 5. The paleoenvironmental history of the eastern part of SongLiao basin is also discussed by analyzing the grain size distribution of Yushu loess-like sediments in Jilin. It was found that there is a tectonic movement before 40ka B.P. in SongLiao basin. After the movement, loess dust deposited in Yushu area as keerqin desert developed. In recent 2000 years, the climate became drier and more deserts activated in the eastern part of Song-Liao basin.

Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific

The Quaternary cold periods in the Northwestern Pacific are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in marine fishes. To estimate the demographic history and genetic structure of Lateolabrax macula

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.

Genetic variation of fish parasite populations in historically connected habitats: undetected habitat fragmentation effect on populations of the nematode Procamallanus fulvidraconis in the catfish Pelteobagrus fulvidraco

Habitat fragmentation may have some significant effects on population genetic structure because geographic distance and physical barriers may impede gene flow between populations. In this study, we investigated whether recent habitat fragmentation affected genetic structure and diversity of populations of the nematode Procamallanus fulvidraconis in the yellowhead catfish, Pelteobagrus fin't4draco. The nematode was collected from 12 localities in 7 floodplain lakes of the Yangtze River. Using I I intersirnple sequence repeat markers, analysis of molecular variance showed that genetic diversity occurred mainly within populations (70.26%). Expected heterozygosity (He) of P. fulvidraconis was barely different between connected (0.2105) and unconnected lakes (0.2083). Population subdivision (Fst) between connected lakes (0.2177) was higher than in unconnected lakes (0. 1676). However, the connected and unconnected lakes did not Cluster into 2 clades. A Mantel test revealed significant positive correlation between genetic and geographic distances (R = 0.5335, P < 0.01). These results suggest that habitat fragmentation did not cause genetic differentiation among populations or a reduction of diversity in isolated populations of P. fulvidraconis. At least 2 factors may increase the dispersal range of the nematode, i.e., flash flooding in summer and other species of fish that may serve as the definitive hosts. Moreover, lake fragmentation is probably a recent process; population size of the nematode in these lakes is large enough to maintain Population structure.

Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai-Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi.2. Nucleotide diversities (pi) were moderate (0.0024-0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018-0.0021) in populations from Qiadam Basin. It is probable that the low intra-population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history.3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise F-ST tests were significant, with non-significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north-west of the Qinghai-Tibetan Plateau. Analysis of molecular variance (AMOVA) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems.4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai-Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations.5. The significantly large negative F-s-value (-24.91, P < 0.01) of Fu's F-s-test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement.6. The results of this study indicate that each population from the Qinghai-Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.

Embryonic stages and eye-specific gene expression of the local cyprinoid fish Anabarilius grahami in Fuxian Lake, China

Anabarilius grahami is a cyprinoid fish endemic to Fuxian Lake, Yunnan, China. In this study, a comprehensive staging series of A. grahami was produced. The embryonic development of A. grahami was divided into six main periods: zygote period, cleavage per

Fish Fauna Status in the Lugu Lake with PreliminaryAnalysis on Cause and Effect of Human Impacts

泸沽湖是位于滇西北的一个断陷湖泊，为滇川两省共有。文献记录泸沽湖原始的鱼类区系由4种鱼 类组成，隶属于裂腹鱼属和泥鳅属。于2001，2002和2004年3次考察泸沽湖，进行标本采集和鱼类区系现状调 查。查看了采自泸沽湖的鱼类标本518号，结合历史上的采集记录和大量相关文献，确定泸沽湖记录有鱼类12 种，隶属于3目4科10属；过度捕捞和毁林造成的泥石流是泸沽湖鱼类区系变化的主要原因。

Diatom community succession in the recent history of a eutrophic Yunnan Plateau lake, Lake Dianchi, in subtropical China

Fish introduction, eutrophication and disappearance of aquatic vegetation are important disturbances of aquatic ecosystems, especially in plateau lakes, which are generally considered to be very vulnerable. Fish were introduced to Lake Dianchi, a eutrophic plateau lake in southwest China, in the late 1950s and 1970s. After the introduction, invasive fish became the dominant species, and the total fish yield increased. Meanwhile, the trophic level of Lake Dianchi had a tendency to increase in the past decades because of the increases in human activities in the watershed area. In addition, the area of aquatic vegetation decreased from more than 90 to 1.8% of the lake area from the 1950s to 2000. This study investigated the effects of fish introduction, eutrophication and aquatic vegetation on the diatom community of Lake Dianchi by examining the changes of microfossil diatom assemblage and abundance. Results showed that the absolute abundance and diatom assemblages changed after fish were introduced. The endemic species, Cyclotella rohomboideo-elliptica, disappeared with the introduction of fish and increasing trophic levels after 1958. Fragilaria crotonensis entered into the lake with the introduction of fish and gradually thrived in the lake after 1958. Diatom species numbers also decreased gradually from 21 to 9 from the past to present. Epiphytic diatoms disappeared with the decrease of aquatic vegetation after 1985. Our study indicated that eutrophication was the most important process determining diatom abundance, and fish introduction was a secondary process determining diatom abundance, while aquatic vegetation had a more important role in structuring the diatom community in this eutrophic plateau lake.