Weighted finite population sampling to maximize entropy

Attention is drawn to a method of sampling a finite populationof N units with unequal probabilities and without replacement.The method was originally proposed by Stern & Cover (1989)as a model for lotteries. The method can be characterized asmaximizing entropy given coverage probabilities _i, or equivalentlyas having the probability of a selected sample proportionalto the product of a set of ‘weights’ w_i. We showthe essential uniqueness of the w_i given the _i. We present twomethods for stepwise selection of sampling units, and correspondingschemes for removal of units that can be used in connectionwith sample rotation. Inclusion probabilities of any order canbe written explicitly in closed form. Second-order inclusionprobabilities _ij satisfy the condition O < _ij < _ij, whichguarantees Yates & Grundy‘s variance estimator tobe unbiased, definable for all samples and always nonnegativefor any sample size.     

A diverse metaphyte assemblage from the Neoproterozoic black shales of South China

A fossil assemblage of diverse megascopic benthic algae is well preserved on bedding planes in black siliceous shales of the Neoproterozoic Lantian Formation (upper Sinian) at Lantian village, Xiunng county, Anhui Province, South China. Based on morphological differences, 12 taxa are recognized. Most specimens show both a holdfast and a vegetative thallus, some with dichotomous branching, which reveals that they are multicellular benthic algae. Each type presents a certain morphological appearance, e.g., spheroidal - Chuaria sp., filamentous - Doushantuophyton rigidulum , fan-like - Flabellophyton lantianensis. Four to six different benthic forms and more than 15 individuals are well preserved on the same bed with an area less than 150 cm². These confirm that a great morphological evolutionary radiation of seaweeds took place no later than the Lantian epoch, with an absolute age around 570 Ma. Growth cycles in Flabellophyton strigata n.sp. reveal that periodical events, such as seasonal variations, occurred in that epoch. A benthic assemblage consisting of three differentiated macroscopic remains is similar to the Miaohe Biota reported from the Doushantuo Formation of the Yangtze Gorges 1200 km away, allowing biostratigraphic correlation of both of these Neoproterozoic Formations.     

Assessment of genetic and pheromonal diversity of the Cydia strobilella species complex (Lepidoptera: Tortricidae)

Combining pheromone trapping and genetic analyses can be useful when trying to resolve complexes of closely related insect taxa that are difficult to distinguish based on morphological characters. Nearctic and Palearctic populations of the spruce seed moth, Cydia strobilella L., have been considered taxonomically synonymous since 1983, but more recent work revealing distinct sex pheromones for Canadian and Swedish moths suggest that populations in the two regions belong to different species. In order to test this hypothesis, we performed field trapping using different pheromone lures at ten sites in North America, Europe and Asia, and reconstructed phylogenetic relationships among trapped moths using mitochondrial (cytochrome oxidase subunit I) and nuclear (elongation factor 1 alpha) DNA sequence data. Trapping data and tree topologies for both genes revealed distinct pherotypes in North America and Eurasia. A genetically distinct population from China was investigated further with respect to its sex pheromone. Electrophysiological data indicated that Chinese females produce a deviant ratio of the sex pheromone components (dienic acetates) compared to Swedish females. However, trapping experiments in both areas revealed a similar broad response profile in males to a wide range of acetate ratios, and these populations should be considered taxonomically synonymous. A previous suggestion of an agonistic effect on the attraction of C. strobilella males in Sweden when adding the corresponding alcohols to the binary acetate blend was also tested in Sweden as well as in China, with no observed effect on attraction of males. In conclusion, our study demonstrates the great potential of using pheromone trapping as a tool for identification and delimitation of taxa within cryptic species complexes. Based on our data, Nearctic and Palearctic populations of C. strobilella should be considered different species, and C. youngana Kearfott stat. rev. is resurrected here as valid name for North American populations, which was the case before the revision in 1983.     

Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars

The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.     

Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.     

The evolution of social behaviour in sentinel crabs (Macrophthalmus): implications from molecular phylogeny

Crabs of the genus Macrophthalmus are known to exhibit highly developed and diverse social behaviour, such as allocleaning, fighting and waving display behaviour, the first being observed widely throughout the genus. Fighting behaviour between males has been classified previously into grasping fighting and claw‐extending fighting, and male waving display into four patterns, the vertical non‐forward‐pointing type, vertical forward‐pointing type, lateral non‐forward‐pointing type and lateral forward‐pointing type, on the basis of interspecific behaviour comparisons. To understand the evolutionary pathways of these social behavioural activities, 978‐bp nucleotide sequences from mitochondrial 16S rRNA genes of 21 species, including two outgroup taxa, were analysed and a molecular phylogeny was reconstructed. The resultant tree demonstrated striking inconsistencies with the relationships inferred from morphological features. Species with similar habitat conditions showed similar morphological features, although they were not phylogenetically close relatives. Phylogenetic analysis of allocleaning behaviour suggested that it evolved once in the early history of the lineage. The analysis of fighting behaviour demonstrated that species with claw‐extending fighting, being a more complex behaviour than grasping fighting, are found in the most ancestral part of the phylogeny. The analysis also revealed that claw‐extending fighting has evolved secondarily on two occasions, suggesting that fighting behaviour is not characterized by sufficient phylogenetic components. The superimposition of a waving pattern on to the phylogeny indicated that the lateral non‐forward‐pointing type has evolved from the vertical non‐forward‐pointing type, the lateral forward‐pointing type having evolved from the vertical forward‐pointing type. This scenario also appeared reasonable with respect to the behavioural trends of cheliped movements in waving. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88 , 45–59.     

Generation and characterization of Brassica rapa ssp. pekinensis – B. oleracea var. capitata monosomic and disomic alien addition lines

Journal of Genetics - Five monosomic alien addition lines (MAALs) of Brassica rapa ssp. pekinensis – B. oleracea var. capitata were obtained by hybridization and backcrossing between B. rapa...     

Maternal zinc deficiency impairs brain nestin expression in prenatal and postnatal mice

INTRODUCTIONZinc is essential for normal brain development,evidenced by the fact that zinc deficiency in lactating mothers is characterized by a high incidence ofneuroanatomical maiformatinns and functional abnormalities in suckling offspring[1-3]. By colltrast,relatively little is known about the relationship be{tween maternal zinc nutrition and fetal brain development[2, 4, 5]. Dvergsten et al[6-81 investigated theeffects of maternal zinc deficiency on postnatal development of the rat ce…