Phenotypic plasticity in gut length in the planktivorous filter-feeding silver carp (Hypophthalmichthys molitrix)

Phenotypic plasticity widely exists in the external morphology of animals as well as the internal traits of organs. In the present study, we studied the gut length plasticity of planktivorous filter-feeding silver carp under different food resources in large-net cage experiments in Meiliang Bay of Lake Taihu in 2004 and 2005. There was a significant difference in stocking density between these 2 years. Under a low stocking density and abundant food resources, silver carp increased their energy intake by feeding on more zooplankton. Meanwhile, silver carp adjusted their gut length to match the digestive requirements of food when exposed to different food resources. In the main growth seasons (from April to October), silver carp significantly increased their relative gut length when feeding on more phytoplankton in 2005 (p < 0.01, 9.23 +/- 1.80 in 2004 and 10.77 +/- 2.05 in 2005, respectively). There was a nearly significant negative correlation between zooplankton proportion in the diet and the relative gut length when silver carp were stocked in a high density (p = 0.112). It appears that silver carp might have evolved plasticity to change their gut length rapidly to facilitate efficient utilization of food resources. Such resource polymorphisms in the gut may be a good indication of temporal adaptation to resource conditions. Our work provided field evidence for understanding the functional basis of resource polymorphisms and the evolution of phenotypic plasticity in planktivorous filter-feeding fish.

The change of characteristics of tidal wave in the Changjiang River mouth area since the post-glacial transgression maximum

During the period of the post-glacial transgression maximum (PGTM), there was a huge trumpet estuary in the modern Changjiang River Delta area. The location and the shape of the Paleo-Changjiang River Estuary (PCRE) were much different from those of the present Changjiang River Estuary. The study on the change of characteristics of tidal wave in the Changjiang River mouth area since the PGTM can help to understand better the dynamic development of the Changjiang River Delta. The course curves of tidal level and tidal current velocity during a single tidal cycle for 35 points are calculated, and characteristics of tidal waves in the PCRE and its adjacent area are compared with those of tidal waves in the modern Changjiang River mouth area. The results show that the tidal waves within the PCRE and in its adjacent area during the period of the PGTM belonged to standing wave or a mixture of standing wave and progressive wave. Since then, the tidal wave in the Changjiang River mouth become gradually to be progressive wave with the PCRE being filled and the Changjiang River mouth shifting southeastwards.

Phenotypic plasticity of gut structure and function during periods of inactivity in Apostichopus japonicus

Apostichopus japonicus is a common sea cucumber that undergoes seasonal inactivity phases and ceases feeding during the summer months. We used this sea cucumber species as a model in which to examine phenotypic plasticity of the digestive tract in response to food deprivation. We measured the body mass, gross gut morphology and digestive enzyme activities of A. japonicus before, during, and after the period of inactivity to examine the effects of food deprivation on the gut structure and function of this animal. Individuals were sampled semi-monthly from June to November (10 sampling intervals over 178 days) across temperature changes of more than 18 degrees C. On 5 September, which represented the peak of inactivity and lack of feeding, A. japonicus decreased its body mass, gut mass and gut length by 50%, 85%, and 70%, respectively, in comparison to values for these parameters preceding the inactive period. The activities of amylase, cellulase and lipase decreased by 77%, 98%, and 35% respectively, in comparison to mean values for these enzymes in June, whereas pepsin activity increased two-fold (luring the inactive phase. Alginase and trypsin activities were variable and did not change significantly across the 178-day experiment. With the exception of amylase and cellulase, all body size indices and digestive enzyme activities recovered and even surpassed the mean values preceding the inactive phase during the latter part of the experiment (October-November). Principal Component Analysis (PCA) utilizing the digestive enzyme activity and body size index data divided the physiological state of this cucumber into four phases: an active stage, prophase of inactivity peak inactivity, and a reversion phase. These phases are all consistent with previously suggested life stages for this species, but our data provide more defined characteristics of each phase. A. japonicus clearly exhibits phenotypic plasticity (or life-cycle staging) of the digestive tract during its annual inactive period. (C) 2008 Elsevier Inc. All rights reserved.

克隆植物对异质性环境的生态适应对策

时空异质性是生境的基本特征。几乎所有植物都是在一定尺度的时空异质性环境中完成其生活史的。在进化过程中，植物可能形成了各种有效利用环境异质性的生态适应对策。克隆生长使得克隆植物在理论上更容易适应于异质性环境。本文以匍匐茎和根状茎型草本为材料，应用实验生态学方法研究了游击型克隆植物对异质性环境的生态适应对策。 在沙丘生境（如毛乌素沙地）中，沙埋是植物常常遭遇的事件。由于沙埋在水平空间表现出非均匀性，克隆植物的基株或克隆片断常常经历局部沙埋。通过温室和野外实验，研究了克隆整合作用对鹅绒委陵菜和沙鞭沙埋分株忍受沙埋能力的影响。结果表明，克隆整合显著提高鹅绒委陵菜和沙鞭沙埋分株的存活。进一步的耗-益分析表明，克隆整合使鹅绒委陵菜沙埋分株显著受益，而对非沙埋分株却没有显著耗损，故整个克隆片断的生长得到显著提高。因此，克隆整合是沙丘生境中克隆植物对局部沙埋胁迫的生态适应对策之一。 通过2个温室实验，研究了金戴戴对光照、基质养分和盐分的克隆可塑性。结果表明：光照强度、基质养分和盐分对金戴戴克隆生长和克隆形态均有十分显著的影响。深度遮光、低养和高盐均显著削弱金戴戴的生长，其生物量、叶面积、分株数、匍匐茎长及叶柄长和根冠比对基质盐分的可塑性大小和格局显示出基株间的差异。在低养分条件下，金戴戴匍匐茎节间显著伸长，而分枝强度显著减弱。这些结果与克隆植物觅食模型相符合，表明当生长于异质性环境，金戴戴可凭借克隆可塑性实现的觅养行为来增加对养分资源的摄取。因此，克隆可塑性是克隆植物利用环境异质性的另一条途径。 在另一温室实验中，研究了三种匍匐茎克隆草本鹅绒委陵菜、金戴戴和绢毛匍匐委陵菜对光照和养分资源交互斑块性环境的反应。当置于高光低养下的分株与低光高养下的分株相连时，高光低养分株、低光高养分株以及克隆片断的生物量均得到显著提高。同时，低光高养下分株的根冠比相对增加，而高光低养下分株的根冠比相对下降。这表明，三种克隆植物发生了环境诱导的克隆内分工行为。这种环境诱导的克隆内分工行为有利于整个基株对资源交互斑块性环境的利用，是克隆植物对异质性环境的生态适应对策。

青藏高原不同构型克隆植物对资源供应的表型反应

克隆植物，尤其是丛生禾草（如紫花针茅（Stipa purpurea Griseb）、丝颖针茅（S. capillacea Keng））和根茎苔草（如青藏苔草（Carex moorcroftii Falc. ex Boott）、窄叶苔草（C. montis-everestii Kük.）），在环境条件非常特殊的青藏高原高寒草原生态系统中，作为建群种或优势种而存在。本文利用控制实验研究不同构型克隆植物对资源供应的表型反应。 源于典型草地和灌木地的窄叶苔草和丝颖针茅对养分添加和光照处理产生广泛的表型反应。植物生长型影响分株数、比叶面积和叶鞘长度对光照强度的可塑性，源生境改变分株数、植株生物量和根茎总长对光照强度的可塑性。各性状对养分水平的可塑性反应均不受生长型和源生境的影响。游击型克隆植物窄叶苔草对高度异质性的灌木生境有较强的适应能力，而密集型克隆植物丝颖针茅的生长受生境的影响较小。 青藏苔草和紫花针茅对养分供应表现出了高度的表型可塑性。种群类型对少数性状有显著影响;除生物量分配和光合特征外，其它许多性状在基因型间有显著分化;除根茎生物量分配外，没有检测出表型可塑性的遗传分化;表型性状间有着广泛的表型整合及可塑性整合，并且整合格局随养分添加范围而变化，在种间也存在整合格局的差异。青藏高原高寒草原上强烈、稳定而持续的选择压力，以及一些与适合度相关的性状间的表型整合和可塑性整合可能对表型可塑性的进化有一定的限制作用。反应规范分析显示，高寒生境的克隆植物可能具有既能利用高养分环境，又能在低养分环境下维持生长的能力，这是植物适应养分环境变化的重要对策。 青藏苔草和紫花针茅的表型反应主要受养分供应量的影响，对由等量养分不同供应频次组成的实验处理的反应并不显著。青藏苔草的分株均重、叶片长度、比根长、根茎生物量分配和紫花针茅的比根长等性状在基因型间存在遗传分化;青藏苔草的分株数和总干重，以及紫花针茅的总干重和总根长表现出表型可塑性的遗传分化。比根长、根茎生物量分配等性状的遗传变异，以及这些性状的表型可塑性和可塑性的遗传变异对于不同基因型适应不同养分供应格局可能具有适应意义。 总之，青藏高原克隆植物对资源供应表现出了高度的表型可塑性，多数表型性状在不同基因型间存在显著的遗传分化，但表型可塑性的遗传分化相对有限。克隆植物可能通过遗传变异和表型可塑性适应异质性资源分布环境。表型可塑性及其遗传变异仍需要更多的研究，以便深入理解其适应性进化。

丛枝菌根真菌对异质性环境中克隆植物的影响

克隆植物同一基株的相连克隆分株或克隆片段常常生长在资源条件不同的斑块中，分株间形成克隆整合和克隆可塑性以及克隆分工等有效地获取必需资源的生态适应对策，提高在异质性斑块生境中的适合度，适应环境的异质性变化。但在以往的克隆植物生态学的理论研究中，为了研究的简化和方便，往往忽略了土壤中微生物的作用。丛枝菌根(Arbuscular mycorrhiza, AM)真菌是自然界中广泛存在的土壤微生物之一，可与大多数的高等植物形成共生菌根，影响植物的生长、发育及其在生态系统中的作用。 本文应用实验生态学方法，以蛇莓、狗牙根和白三叶为研究对象，在温室受控条件下，对异质养分斑块中的分株对接种AM真菌，探讨AM真菌对资源斑块中克隆植物的影响。 第一个实验设计单一磷养分斑块，以蛇莓(Duchesnea indica)和摩西球囊霉(Glomus mosseae)为研究对象，探讨丛枝AM真菌对克隆整合的影响。将蛇莓相连的两个分株，即分株对，分别种植在两个隔离的花盆中，各施以高磷和低磷营养液，保持或切断分株间匍匐茎连接，即间隔子，再将菌剂接种到低磷斑块中分株。结果发现间隔子状态和接菌处理都显著影响低磷斑块中蛇莓分株的根系生物量分配。对照处理中保持间隔子连接显著减少低磷斑块中分株生物量向根系的分配，接菌后这一差异显著减小。保持间隔子连接或接菌对高磷斑块中分株的根系生物量分配不显著。保持间隔子连接和接菌都显著增加低磷斑块分株的生物量在分株对生物量中所占比例，二者无显著交互作用。 第二个实验设计光照和养分斑块，以狗牙根(Cynodon dactylon)和摩西球囊霉为研究对象，探讨AM真菌对克隆植物非局域反应的影响。将狗牙根分株对的两个分株分别种植在两个花盆中，各施以光照强度与土壤养分交互斑块性环境条件，形成高养低光和高光低养斑块，保持或切断间隔子，再将菌剂接种到目标分株。结果发现对照处理中，间隔子状态显著影响分株的局域反应。高养斑块中保持间隔子连接的分株的根长显著大于间隔子断裂的分株的根长，高光斑块中保持间隔子连接的分株的根长显著小于间隔子断裂的分株的根长。高光斑块中保持间隔子连接的分株的叶面积显著大于间隔子断裂的分株的叶面积，间隔子状态对低光高养斑块分株的叶面积无显著影响。在低光高养斑块中，相对于间隔子断裂的分株，间隔子连接的分株将更多的生物量分配到根系，而在高光斑块中的分株则相反。这些都说明，无AM真菌侵染的情况下，狗牙根分株对的两个分株在实验中各自形成的克隆部分的分株形态反应都受到了克隆整合的作用，表现为非局域反应。接种AM真菌后，高光斑块中分株的根长和高养斑块中分株的叶面积在间隔子连接和断裂处理之间的差异显著减小。生物量分配的差异不受接菌的影响。对照处理中，高养斑块中间隔子连接的分株生物量和分株数显著高于间隔子断裂的分株，但高光斑块中分株之间无显著差异。接种AM真菌显著降低高养斑块中分株的生物量和分株数，对高光斑块中分株无显著影响。 第三个实验设计光照和养分交互斑块，以白三叶(Trifolium repens)和多种AM真菌为研究对象，探讨AM真菌及其多样性对克隆分工的影响。将间隔子连接(整合)或断裂(无整合)的白三叶分株对种植于光照强度和土壤养分交互斑块性资源条件下(即，高光低养和低光高养)，向分株对接种灭菌处理、单种或五种AM真菌的菌剂。结果发现，对照处理中，间隔子连接的分株对在光养交互斑块中与间隔子断裂的分株对相比较表现出克隆分工，即高光低养斑块中的分株的根系生物量分配增加，低光高养斑块中的分株的根系生物量分配减少。单菌处理没有影响对照处理中间隔子状态对分株对生物量分配的改变；多菌处理显著减小对照中生物量分配的改变；与单菌处理比较，多菌处理能显著减小生物量分配的改变。在高光低养斑块中，多菌处理显著抑制间隔子断裂分株的根生物量分配的增加。在低光高养斑块中，多菌处理完全抑制在对照处理中间隔子连接的分株的根生物量分配的增加。在对照处理中，间隔子连接分株的单叶面积、总叶面积、叶柄长、根长都与生物量分配趋势一致，表现出对丰富资源的特化。接菌处理能显著抑制这些形态指标的改变。多菌处理显著抑制这些指标的特化，并且抑制效果显著强于单菌处理。间隔子状态和AM真菌处理显著增加高光低养、低光高养斑块中分株及整个克隆片段的生物量和分株数。多菌处理抑制间隔子连接的克隆片段生物量和分株数增加。克隆片段的生物量和分株数在对照和单菌处理间无显著差异，在多菌处理中显著高于在单菌处理中。 以上三个实验说明，(1)AM真菌对克隆植物生长的影响与非克隆植物一样，受到植物种类和环境资源水平的影响；(2)AM真菌对异质性资源环境中克隆植物的影响由于植物不同而产生不同的效应；(3)提高AM真菌的多样性可能增强菌根对克隆植物的作用。 这些研究结果揭示出AM真菌与异质性环境中克隆植物整合作用、非局域反应和克隆分工作用的交互影响，表明克隆生长在生态系统中的重要性可由生物和非生物因素共同决定。

Detecting positive darwinian selection in brain-expressed genes during human evolution

To understand the genetic basis that underlies the phenotypic divergence between human and non-human primates, we screened a total of 7176 protein-coding genes expressed in the human brain and compared them with the chimpanzee orthologs to identity genes

MicroRNA regulation and the variability of human cortical gene expression

Understanding the driving forces of gene expression variation within human populations will provide important insights into the molecular basis of human phenotypic variation. In the genome, the gene expression variability differs among genes, and at prese

Bacillus pallidus sp nov., isolated from forest soil

A Gram-positive bacterium, designated strain CW 7(T), was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30-37 degrees C and pH 7.0-8.0. The major fatty acids of strain CW 7(T) were anteiso-C-15:0, iso-C-15:0 and anteiso-C-17:0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G + C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7(T) belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5% to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7(T) represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7(T) (=KCTC 13200(T)=CCTCC AB 207188(T)=LMG 24451(T)).

Flavobacterium anhuiense sp nov., isolated from field soil

A novel strain, D3(T), isolated from a field-soil sample obtained from Anhui Province, PR China, was characterized taxonomically by using a polyphasic approach. The cells were Gram-negative, yellow-pigmented rods devoid of flagella, but showing gliding motility. The organism was able to grow at 5-37 degrees C and at pH 4.0-10.0. A comparative 16S rRNA gene sequence analysis indicated that strain D3(T) is a member of the genus Flavobacterium, sharing highest sequence similarity with the type strain of Flavobacterium defluvii (96.7 %). The major isoprenoid quinone was MK-6 and the predominant fatty acids were iso-C-15:0, summed feature 3 (C-16:1 omega 7c and/or iso-C-15:0 2-OH) and C-16:0. The DNA G + C content was 31.4 mol%. On the basis of phylogenetic and phenotypic data, strain D3(T) represents a novel species within the genus Flavobacterium, for which the name Flavobacterium anhuiense sp. nov. is proposed. The type strain is D3(T) (=KCTC 22128(T)= CGIVICC 1.6859(T)).

Identification of genes differentially expressed in wild type and Purkinje cell degeneration mice

Purkinje cell degeneration (pcd) mice are characterized by death of virtually all cerebellar Purkinje cells by postnatal day 30. In this study, we used DNA microarray analysis to investigate differences in gene expression between the brains of wild type and pcd mice on postnatal day 20, before the appearance of clear-cut phenotypic abnormalities. We identified 300 differentially expressed genes, most of which were involved in metabolic and physiological processes. Among the differentially expressed genes were several calcium binding proteins including calbindin -28k, paravalbumin, matrix gamma-carboxygluta mate protein and synaptotagamins 1 and 13, suggesting the involvement of abnormal Ca2+ signaling in the pcd phenotype.

Positive selection drives population differentiation in the skeletal genes in modern humans

During the course of evolution, the human skeletal system has evolved rapidly leading to an incredible array of phenotypic diversity, including variations in height and bone mineral density. However, the genetic basis of this phenotypic diversity and the relatively rapid tempo of evolution have remained largely undocumented. Here, we discover that skeletal genes exhibit a significantly greater level of population differentiation among humans compared with other genes in the genome. The pattern is exceptionally evident at amino acid-altering sites within these genes. Divergence is greater between Africans and both Europeans and East Asians. In contrast, relatively weak differentiation is observed between Europeans and East Asians. SNPs with higher levels of differentiation have correspondingly higher derived allele frequencies in Europeans and East Asians. Thus, it appears that positive selection has operated on skeletal genes in the non-African populations and this may have been initiated with the human colonization of Eurasia. In conclusion, we provide genetic evidence supporting the rapid evolution of the human skeletal system and the associated diversity of phenotypes.

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.