Neural network for female mate preference,trained by a genetic algorithm

In some animals, males evolve exaggerated traits (e.g. the peacock''s conspicuous tail and display) because of female preference. Recently Enquist and Arak presented a simple neural network model for a visual system in female birds that acquires the ability to discriminate males of the correct species from those of the wrong species by training. They reported that the trained networks were attracted by ''supernormal stimuli'' where there was a greater response to an exaggerated form than to the images used as the correct species for training. They suggested that signal recognition mechanisms have an inevitable bias in response, which in turn causes selection on signal form. We here examine the Enquist and Arak model in detail. A three-layered neural network is used to represent the female''s mate preference, which consists of 6 by 6 receptor cells arranged on a regular square lattice, ten hidden cells, and one output cell. Connection weights of the network were modified by a genetic algorithm, in which the female''s fitness increases if she accepts a conspecific male but decreases if she accepts a male of a different species or a random image. We found that: (i) after the training period the evolved network was able to discriminate male images. Female preference evolves to favour unfamiliar patterns if they are similar to the images of the correct species (generalization); (ii) the speed and the final degree of learning depended critically on the choice of the random images that are rejected. The learning was much less successful if the random images were changed every generation than if 20 random images were fixed throughout the training period; (iii) the male of the same species used for training achieved the highest probability of being accepted by the trained network. Hence, contrary to Enquist and Arak, the evolved network was not attracted by supernormal stimuli.     

Bayesian networks as a novel tool to enhance interpretability and predictive power of ecological models

In today's world, it is becoming increasingly important to have the tools to understand, and ultimately to predict, the response of ecosystems to disturbance. However, understanding such dynamics is not simple. Ecosystems are a complex network of species interactions, and therefore any change to a population of one species will have some degree of community level effect. In recent years, the use of Bayesian networks (BNs) has seen successful applications in molecular biology and ecology, where they were able to recover plausible links in the respective systems they were applied to. The recovered network also comes with a quantifiable metric of interaction strength between variables. While the latter is an invaluable piece of information in ecology, an unexplored application of BNs would be using them as a novel variable selection tool in the training of predictive models. To this end, we evaluate the potential usefulness of BNs in two aspects: (1) we apply BN inference on species abundance data from a rocky shore ecosystem, a system with well documented links, to test the ecological validity of the revealed network; and (2) we evaluate BNs as a novel variable selection method to guide the training of an artificial neural network (ANN). Here, we demonstrate that not only was this approach able to recover meaningful species interactions networks from ecological data, but it also served as a meaningful tool to inform the training of predictive models, where there was an improvement in predictive performance in models with BN variable selection. Combining these results, we demonstrate the potential of this novel application of BNs in enhancing the interpretability and predictive power of ecological models; this has general applicability beyond the studied system, to ecosystems where existing relationships between species and other functional components are unknown.     

Scale dependence of plant species richness in a network of protected areas

Despite the widely recognised importance of reserve networks, their effectiveness in encompassing and maintaining biodiversity is still debated. Species diversity is one of the most affordable measures of biodiversity, but it is difficult to survey such data over large scales. This research aimed to perform a sample-based assessment of species richness of groups of plants with different conservation value (alien species, protected species, and all species) within a reserve network, testing the use of partitioning as a tool for assessing diversity at different spatial scales, from the plot to the entire network. Plant diversity patterns differed for the groups of species for most of the investigated spatial scales. Despite these patterns assumed divergent tendencies when different species groups were considered, most of the species richness within the network was given by larger scale β-diversity for both alien and protected species, as well for all species. Diversity partitioning proved an effective tool to quantify the role of spatial scales in structuring the total species richness of the network, and is helpful in planning reserve networks.     

Solubilization of Membrane-Bound Acetyicholinesterase by a Phosphatidylinositol-Specific Phospholipase C

Phosphatidylinositol-specific phospholipase C (PIPLC) quantitatively solubilizes acetylcholinesterase (AChE) from purified synaptic plasma membranes and intact synaptosomes of Torpedo ocellata electric organ. The solubilized AChE migrates as a single peak of sedimentation coefficient 7.0S upon sucrose gradient centrifugation, corresponding to a subunit dimer. The catalytic subunit polypeptide of AChE is the only polypeptide detectably solubilized by PIPLC. This selective removal of AChE does not affect the amount of acetylcholine released from intact synaptosomes upon K+ depolarization. PIPLC also quantitatively solubilizes AChE from the surface of intact bovine and rat erythrocytes, but only partially solubilizes AChE from human and mouse erythrocytes. The AChE released from rat and human erythrocytes by PIPLC migrates as a approximately 7S species on sucrose gradients, corresponding to a catalytic subunit dimer. PIPLC does not solubilize particulate AChE from any of the brain regions examined of four mammalian species. Several other phospholipases tested, including a nonspecific phospholipase C from Clostridium welchii, fail to solubilize AChE from Torpedo synaptic plasma membranes, rat erythrocytes, or rat striatum.     

Towards a small animal model for hepatitis C

Hepatitis C virus (HCV) causes chronic liver disease and affects an estimated 3% of the world's population. Options for the prevention or therapy of HCV infection are limited; there is no vaccine and the nonspecific, interferon‐based treatments now in use are frequently ineffective and have significant side effects. A small‐animal model for HCV infection would significantly expedite antiviral compound development and preclinical testing, as well as open new avenues to decipher the mechanisms that underlie viral pathogenesis. The natural species tropism of HCV is, however, limited to humans and chimpanzees. Here, we discuss the prospects of developing a mouse model for HCV infection, taking into consideration recent results on HCV entry and replication, and new prospects in xenotransplantation biology. We highlight three independent, but possibly complementary, approaches towards overcoming current species barriers and generating a small‐animal model for HCV pathogenesis.     

A comparative anatomical and biochemical analysis in salsola (Chenopodiaceae) species with and without a Kranz type leaf anatomy: a possible reversion of C4 to C3 photosynthesis

Leaf anatomy was studied by light and electron microscopy and the leaf activities of RUBP carboxylase, PEP carboxylase, and malic enzyme were assayed in: Salsola australis and S. oreophila grown on the West Pamirs at 1800 m altitude; in S. australis grown on the East Pamirs at 3860 m; and in S. arbusculiformis grown in the Kisil-Kum desert in Middle Asia near 500 m. Carbon isotope fractionation ratio values also were measured on whole leaf tissue for 18 Salsola species field collected in these and other regions of the former USSR. S. australis leaves are cylindrical and in cross section exhibit a peripheral ring of mesophyll and then an inner ring of bundle sheath type cells; and its biochemical characteristics and deltaC values are typical of a C4 species of the NADP-malic enzyme malate-forming group. These traits were expressed independent of the plant growth altitude up to 4000 m. C4 type deltaC values were obtained in 14 of the Salsola species. Anatomical, structural, and biochemical features typical of the C4 syndrome were absent in S. oreophila and S. arbusculiformis. Four Salsola species, including these two, had C3-type deltaC values. Their cylindrical leaves in cross section exhibited two to three peripheral rings as layers of palisade parenchyma. Although their vascular bundles were surrounded by green bundle sheath cells, their organelle numbers were comparable to those in mesophyll cells. Neither bundle sheath cell wall thickenings nor dimorphic chloroplasts in two leaf cell types were observed. In S. oreophila, there was a high activity of RuBP carboxylase, but a low activity of C4 cycle enzymes. Interpretation of these data lends evidence to the hypothesis that a small group of C3 Salsola species, including S. oreophila, S. arbusculiformis, S. montana, and S. pachyphylla, arose as the result of a reversion of a C4 to a C3 type of photosynthetic CO2 fixation in the cooler climates of Middle Asia.     

Complement Activation Products C3a and C4a as Endogenous Antimicrobial Peptides

All vertebrate species are constantly challenged by infectious agents and pathogens. In order to fight these infectious agents the human host has developed a sophisticated and powerful immune defense. The complement system, which represents the first defense line of innate immunity is activated immediately, within seconds. The activated immune system recognizes and damages an invading microbe, coordinates the host immune response and further orchestrates the adaptive immune response. Activation of the complement system leads to a rapid and amplified response which includes the generation of small peptides like C3a and C4a that display antimicrobial, anti-fungal and anaphylactic activity. Here we report how these antimicrobial peptides are generated during the immune response and summarize the functional mechanisms of these intrinsically generated anti microbial peptides.     

大气污染胁迫下9种植物幼苗叶片热值、C/N和灰分含量比较

用氧弹热值仪测定了生长在硫和氟复合污染环境和相对洁净环境下的9种木本植物幼苗叶片热值。结果表明,植物叶片的基础干重热值、灰分含量因种类不同而有差异,其中热值较高的(大于19．00kJ g^-1)植物有铁冬青(Ilex rotunda)、华润楠(Machilus chinensis)和仪花(Lysidice rhodostegia),热值中等的(介于18．00-19．00kJ g^-1)植物有复羽叶栾树(Koelreuteria bipinnata)、环榕(Ficus annulata)、乐昌含笑(Michelia chapensis)、小叶榕(Ficus microcarpa)和红花油茶(Camellia semiserrata),热值低的(低于18．00kJ g^-1)种类有火焰木(Spathodea campanulata)。大气污染导致复羽叶栾树、华润楠和铁冬青幼苗叶片基础干重热值增加,仪花、含笑、小叶榕、火焰木和红花油茶幼苗叶片基础干重热值下降,环榕基础干重热值则维持相对稳定。Pearson相关系数分析表明,9种植物幼苗叶片去灰分热值与叶片自身C／N比、叶片灰分含量的相关性均不显著,但污染胁迫下植物幼苗叶片热值相对波动程度与其对污染物的抗性有关,提示叶片热值可以作为植物幼苗对硫和氟复合污染的敏感性指标。     

Growing of a Fuzzy Recurrent Artificial Neural Network (FRANN) for pattern classification

This paper describes a method for growing a recurrent neural network of fuzzy threshold units for the classification of feature vectors. Fuzzy networks seem natural for performing classification, since classification is concerned with set membership and objects generally belonging to sets of various degrees. A fuzzy unit in the architecture proposed here determines the degree to which the input vector lies in the fuzzy set associated with the fuzzy unit. This is in contrast to perceptrons that determine the correlation between input vector and a weighting vector. The resulting membership value, in the case of the fuzzy unit, is compared with a threshold, which is interpreted as a membership value. Training of a fuzzy unit is based on an algorithm for linear inequalities similar to Ho-Kashyap recording. These fuzzy threshold units are fully connected in a recurrent network. The network grows as it is trained. The advantages of the network and its training method are: (1) Allowing the network to grow to the required size which is generally much smaller than the size of the network which would be obtained otherwise, implying better generalization, smaller storage requirements and fewer calculations during classification; (2) The training time is extremely short; (3) Recurrent networks such as this one are generally readily implemented in hardware; (4) Classification accuracy obtained on several standard data sets is better than that obtained by the majority of other standard methods; and (5) The use of fuzzy logic is very intuitive since class membership is generally fuzzy.     

Structure of a plant-pollinator network on a pahoehoe lava desert of the Galápagos Islands

Plant-pollinator interactions are important for the evolution and survival of the species involved. Plant-pollinator networks on oceanic islands are often small in size and as a consequence the connectance is high suggesting a substantial generalisation level. Further, linkage level for insular plants is shown to be lower than on mainland. The present study investigates a plant-pollinator network on the Galápagos Islands that is unique because of its very small size. We recorded pollinator visits to plant species as well as pollen grains on insect bodies. The combination of these data increased the observed number of interactions. The values for connectance and linkage level for plants were found to be consistent with similar values found in other network studies. There were no relation between the abundance of plant species and the number of pollinating species. The dominating pollinator species was the Galápagos carpenter bee Xylocopa darwini . Specimens of the shorthorned grasshopper Halmenus cuspidatus turned out to carry pollen from five plant species out of twelve and are probably functioning as pollinator. Bagging experiments revealed dependency on insect visits for a high seed set for most of the plant species, but only one species Plumbago scandens seemed to possess a pollen limited seed set. The network showed an asymmetric pattern of number of interactions per species with a few species having several interactions and many species a few. This pattern is supposed to result in a rather robust community, but is also fairly sensitive if the dominant species are threatened. The high connectance value found could, however, counteract this vulnerability.     

The Chromodorididae (Opisthobranchia: Mollusca) of the Indo-West Pacific: Chromodoris epicuria, C. aureopurpurea, C. annulata, C. coi and Risbecia tryoni colour groups

Twenty-five species of chromodorid nudibranchs from the Indo-West Pacific are described including nine which are new to science. There are six new species of Chromodoris , two of Nounea and a new species which forms the type of a new monotypic genus. Of the other species discussed in this paper, ten are species of Chromodoris , five Risbecia and one Digidentis. Species with the following colour patterns are discussed: white with orange or yellow spots; white with yellow (or orange) and purple spots; white with purple spots or patches and mantle border; white with a sinuous submarginal brown band. A full review of the relevant literature is included as is a discussion on Indian Ocean and West Pacific species pairs.     

A Flow Cytometric Analysis of the Nuclear 2C DNA Content in 17 Phaseolus Species (53 Genotypes)

The genus Phaseolus is characterized by a highly stable karyotype of 2n = 22. Despite this constancy, the size of the chromosomes varies, and crossing of species is possible only in a few cases. We determined the 2C nuclear DNA content of a number of Phaseolus species, cultivars and genotypes by flow cytometry, in order to realize the interspecific and intraspecific variation of the 2C value. The data range from 1.03 pg to 2.18 pg without any clear correlation to systematic relationships. The mean DNA values of wild and cultivated forms, as well as those of Andean and Mesoamerican genotypes, do not differ significantly. The variation is interpreted in terms of some nucleotypic adaptations. The data may be useful for molecular biological analyses, as well as for biotechnological and classical breeding programmes.     

小叶、中间和柠条三种锦鸡儿的分布式样及其生态适应

确定了小叶锦鸡儿、中间锦鸡儿和柠条锦鸡儿3种植物的分布式样:小叶锦鸡儿为蒙古高原东部-F松辽平原西部-华北山地分布种,中间锦鸡儿为东戈壁-鄂尔多斯高原-黄土高原北部分布种,柠条锦鸡儿为南阿拉善-西鄂尔多斯分布种。小叶锦鸡儿适应分布于蒙古高原典型草原带和森林草原带以及华北山地落叶阔叶林带,在草原带高平原上可形成灌丛化草原的景观,在草原带的沙地上可形成以小叶锦鸡儿为建群种的沙地灌丛植被;中间锦鸡儿适应分布于蒙古高原的荒漠化草原及草原化荒漠带、鄂尔多斯高原的典型草原和荒漠化草原带的沙地及梁地上、黄土高原北部的黄土丘坡上,常形成以中间锦鸡儿为建群种的沙地灌丛植被;柠条锦鸡儿则适应分布于草原化荒漠和典型荒漠带的固定和半固定沙地上。近缘的3种锦鸡儿的地带性分布从东至西或从北向南形成明显的有规律的地理替代分布格局。     

The photosynthetic response of C3 and C4 bioenergy grass species to fluctuating light

Bioenergy grass species are a renewable energy source, but their productivity has not been fully realized. Improving photosynthetic efficiency has been proposed as a mechanism to increase the productivity of bioenergy grass species. Fluctuating light, experienced by all field grown crops, is known to reduce photosynthetic efficiency. This experiment aimed to evaluate the photosynthetic performance of both C₃ and C₄ bioenergy grass species under steady state and fluctuating light conditions by examining leaf gas exchange. The fluctuating light regime used here decreased carbon assimilation across all species when compared to expected steady state values. Overall, C₄ species assimilated more carbon than C₃ species during the fluctuating light regime, with both photosynthetic types assimilating about 16% less carbon than expected based on steady state measurements. Little diversity was observed in response to fluctuating light among C₃ species, and photorespiration partially contributed to the rapid decreases in net photosynthetic rates during high to low light transitions. In C₄ species, differences among the four NADP-ME species were apparent. Diversity observed among C₄ species in this experiment provides evidence that photosynthetic efficiency in response to fluctuating light may be targeted to increase C₄ bioenergy grass productivity.     

Identifying areas of high importance for orchid conservation in east Macedonia (NE Greece)

The establishment of a network of reserves is of fundamental importance to the loss of biodiversity. Seven different area selection methods for the establishment of a reserve network were applied in the present study: (a) 5% cut-off value of the grid cells with the highest species richness or conservation value, (b) complementarity analysis using as criteria species richness or conservation value or rarest species richness, and (c) mixed complementarity analysis using as criteria species richness or conservation value. These methods were applied in the orchid taxa of east Macedonia. The conservation values of taxa were estimated on the basis of regional rarity, broad-scale rarity, and species specialization. The spatial overlap between the resulting networks and the Natura 2000 network of the study area was assessed. Furthermore, the efficiency of the latter network to protect the orchid taxa of the study area was examined. Our results suggest that: (a) a multiscale estimation of rarity is necessary for the unbiased estimation of species conservation values; (b) species specialization adds valuable ecological information to the assessment of taxa conservation values; (c) complementarity and mixed complementarity analyses on species richness or conservation value safeguard all the taxa of the region; (d) complementarity analysis on the basis of the richness of the rarest species safeguards all the rarest taxa, but not the total number of the remaining taxa; (e) the 5% cut-off value on species richness or conservation value fails to protect all the taxa of the region, including a large number of the rarest taxa; and (f) the Natura 2000 network, despite its large coverage in the study area, fails to safeguard all the taxa, including some of the rarest.     

Training radial basis function neural networks: effects of training set size and imbalanced training sets

Obtaining training data for constructing artificial neural networks (ANNs) to identify microbiological taxa is not always easy. Often, only small data sets with different numbers of observations per taxon are available. Here, the effect of both size of the training data set and of an imbalanced number of training patterns for different taxa is investigated using radial basis function ANNs to identify up to 60 species of marine microalgae. The best networks trained to discriminate 20, 40 and 60 species respectively gave overall percentage correct identification of 92, 84 and 77%. From 100 to 200 patterns per species was sufficient in networks trained to discriminate 20, 40 or 60 species. For 40 and 60 species data sets an imbalance in the number of training patterns per species always affected training success, the greater the imbalance the greater the effect. However, this could be largely compensated for by adjusting the networks using a posteriori probabilities, estimated as network output values.     

Mesophyll cells of C4 plants have fewer chloroplasts than those of closely related C3 plants

The evolution of C₄ photosynthesis from C₃ ancestors eliminates ribulose bisphosphate carboxylation in the mesophyll (M) cell chloroplast while activating phosphoenolpyruvate (PEP) carboxylation in the cytosol. These changes may lead to fewer chloroplasts and different chloroplast positioning within M cells. To evaluate these possibilities, we compared chloroplast number, size and position in M cells of closely related C₃, C₃–C₄ intermediate and C₄ species from 12 lineages of C₄ evolution. All C₃ species had more chloroplasts per M cell area than their C₄ relatives in high‐light growth conditions. C₃ species also had higher chloroplast coverage of the M cell periphery than C₄ species, particularly opposite intercellular air spaces. In M cells from 10 of the 12 C₄ lineages, a greater fraction of the chloroplast envelope was pulled away from the plasmalemma in the C₄ species than their C₃ relatives. C₃–C₄ intermediate species generally exhibited similar patterns as their C₃ relatives. We interpret these results to reflect adaptive shifts that facilitate efficient C₄ function by enhancing diffusive access to the site of primary carbon fixation in the cytosol. Fewer chloroplasts in C₄ M cells would also reduce shading of the bundle sheath chloroplasts, which also generate energy required by C₄ photosynthesis.     

Leaf anatomy and subgeneric affiliations of C3 and C4 species of Suaeda (Chenopodiaceae) in North America

The halophytic genus Suaeda (Chenopodiaceae) includes species with the C3 and C4 photosynthetic pathways. North American species of this genus were investigated to determine whether C3 and C4 leaf anatomy are consistent within the two sections of Suaeda, Chenopodina and Limbogermen, present on this continent. All species from section Chenopodina were found to possess C3 anatomy, whereas all species from section Limbogermen were found to be C4 species. Characteristics of leaf anatomy and chloroplast ultrastructure are similar to those reported from C3 and C4 species, respectively, from the Eastern Hemisphere. All species from section Limbogermen have the suaedoid type of leaf anatomy, characterized by differentiation of the mesophyll into palisade parenchyma and a chlorenchymatous sheath surrounding central water-storage tissue, as well as leaf carbon isotope ratios (_13C) of above -20. All species from section Chenopodina have austrobassioid leaf anatomy without a chlorenchymatous sheath and _13C values of below -20. According to our literature review, the photosynthetic pathway has now been reported for about half (44) of the Suaeda species worldwide. The C3 and C4 photosynthetic syndromes are with few exceptions distributed along sectional or subsectional lines. These findings throw new light on the infrageneric taxonomy of this genus.     

Evolutionary implications of C3–C4 intermediates in the grass Alloteropsis semialata

C₄ photosynthesis is a complex trait resulting from a series of anatomical and biochemical modifications to the ancestral C₃ pathway. It is thought to evolve in a stepwise manner, creating intermediates with different combinations of C₄‐like components. Determining the adaptive value of these components is key to understanding how C₄ photosynthesis can gradually assemble through natural selection. Here, we decompose the photosynthetic phenotypes of numerous individuals of the grass Alloteropsis semialata, the only species known to include both C₃ and C₄ genotypes. Analyses of δ¹³C, physiology and leaf anatomy demonstrate for the first time the existence of physiological C₃–C₄ intermediate individuals in the species. Based on previous phylogenetic analyses, the C₃–C₄ individuals are not hybrids between the C₃ and C₄ genotypes analysed, but instead belong to a distinct genetic lineage, and might have given rise to C₄ descendants. C₃ A. semialata, present in colder climates, likely represents a reversal from a C₃–C₄ intermediate state, indicating that, unlike C₄ photosynthesis, evolution of the C₃–C₄ phenotype is not irreversible.     

刘承钊教授生前发表的两栖动物新种

本文介绍刘承钊教授生前本人或与合作者描述发表的两栖动物66个新种,分隶2目9科,计有尾目2科9种,无尾目7科57种(名单见附表)。其中,刘承钊和胡淑琴(1961)《中国无尾两栖类》将以下4种列为同物异名:108页:ＡｅｌｕｒｏｐｈｒｙｎｅｂｒｅｖｉｐｅｓＬｉｕ=胸腺猫眼蟾ＡｇｌａｎｄｕｌａｔｕｓＬｉｕ[后改属名,称为胸腺齿突蟾Ｓｃｕｔｉｇｅｒｇｌａｎｄｕｌａｔｕｓ(Ｌｉｕ)]。265页:胡氏树蛙ＲｈａｃｏｐｈｏｒｕｓｈｕｉＬｉｕ=杜氏树蛙ＲｈａｃｏｐｈｏｒｕｓｄｕｇｒｉｔｅｉＤａｖｉｄ[后改属名,称为杜氏泛树蛙Ｐｏｌｙｐｅｄａｔｅｓｄ…