Genotoxicity biomarkers in aquatic bioindicators

Pollution of the aquatic environment is an ever-growing problem, as waters are the ultimate sink for the large number of xenobiotics from multiple sources. DNA damaging agents have a significant ecological relevance since they are implicated in many pathological processes and exert effects beyond that of individual being active through following generations. A large number of methods have been applied to evaluate genotoxic damage in different aquatic species. Comet assay, as method for de- tecting DNA alterations, and micronucleus test, as an index of chromosomal damage are the most widely applied and validated methods in field studies. These methods were applied in different vertebrate and invertebrate aquatic species, but only mollusk and fish species have been employed in routine biomonitoring programs. Mussels, due to their widely geographical distribution and the suitability for caging represent the bioindicator of choice in field studies. Mytilus species is the most used marine mussel. The use of fish is limited to specific geographic areas. The present review mainly focuses on the application of comet assay and micronucleus test in mussels. A number of biomonitoring studies in mussels, using comet assay or micronucleus test, revealed exposure to different classes of genotoxic compounds with a good discrimination power. The different evidence from the two as- says, reflects different biological mechanisms for the two genetic endpoints, DNA damage and chromosomal damage, suggesting their combined application in the field. Different endogenous and exogenous factors have been shown to modulate the genotoxic responses in mussels, acting as confounding factors in environmental monitoring. The use of standardized protocol for caging, sampling and genotoxity evaluation is critical in biomonitoring studies. The use of a multimarker approach coupling genotoxicity biomarkers with physiological and biochemical factors allows to have a complete picture of the environmental pollution [Current Zoology 60 （2）： 273-284, 2014].     

Mesenchymal stem cells for cartilage regeneration in dogs

Articular cartilage damage and osteoarthritis (OA) are common orthopedic diseases in both humans and dogs. Once damaged, the articular cartilage seldom undergoes spontaneous repair because of its avascular, aneural, and alymphatic state, and the damage progresses to a chronic and painful situation. Dogs have distinctive characteristics compared to other laboratory animal species in that they share an OA pathology with humans. Dogs can also require treatment for naturally developed OA;therefore, effective treatment methods for OA are desired in veterinary medicine as well as in human medicine. Recently, interest has grown in regenerative medicine that includes the use of mesenchymal stem cells (MSCs). In cartilage repair, MSCs are a promising therapeutic tool due to their self-renewal capacity, ability to differentiate into cartilage, potential for trophic factor production, and capacity for immunomodulation. The MSCs from dogs (canine MSCs;cMSCs) share various characteristics with MSCs from other animal species, but they show some deviations, particularly in their differentiation ability and surface epitope expression. In vivo studies of cMSCs have demonstrated that intraarticular cMSC injection into cartilage lesions results in excellent hyaline cartilage regeneration. In clinical situations, cMSCs have shown great therapeutic effects, including amelioration of pain and lameness in dogs suffering from OA. However, some issues remain, such as a lack of regulations or guidelines and a need for unified methods for the use of cMSCs. This review summarizes what is known about cMSCs, including their in vitro characteristics, their therapeutic effects in cartilage lesion treatment in preclinical in vivo studies, their clinical efficacy for treatment of naturally developed OA in dogs, and the current limitations of cMSC studies.     

Comparative ecogenotoxicology： Monitoring the DNA of wildlife

Ecogenotoxicology is the study of interactions between genetic material and DNA-damaging agents of anthropogenic origin in wild populations, in relation to subsequent effects on the health of organisms （Shugart and Theodorakis, 1994）. Traditionally, biomarkers for genetic toxicology can be classified in ＂biomarkers of exposure＂ and ＂biomarkers of effect＂, depending whether the aim is to monitor and quantify the exposure to genotoxicants,     

Evolutionary Genomics of Weedy Rice in the USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.     

Diversity Suppression-Subtractive Hybridization Array for Profiling Genomic DNA Polymorphisms

Genomlc DNA polymorphlsms are very useful for tracing genetic traits end studying biological diversity among species. Here, we present a method we call the ＂diversity suppresslon-subtractlve hybridization array＂ for effectively profiling genomlc DNA polymorphisms. The method first obtains the subtracted gDNA fragments between any two species by suppression subtraction hybridization （SSH） to establish e subtracted gDNA library, from which diversity SSH arrays are created with the selected subtracted clones. The diversity SSH array hybridizes with the DIG-labeled genomlc DNA of the organism to be assayed. Six closely related Dendrobium species were studied as model samples. Four Dendrobium species as testers were used to perform SSH. A total of 617 subtracted positive clones were obtained from four Dendrobium species, and the average ratio of positive clones was 80.3%. We demonstrated that the average percentage of polymorphlc fragments of palrwlse comparisons of four Dendrobium species was up to 42.4%. A dendrogram of the relatedness of six Dendrobium species was produced according to their polymorphic profiles. The results revealed that the diversity SSH array Is a highly effective platform for profiling genomlc DNA polymorphlsms and dendrograms.     

A meta-analysis of the effects of geolocator application on birds

An increasing trend in use of tracking devices such as geolocators is based on the assumption that the information gathered from such devices provides reliable information about the migratory behavior of free-living birds. This underlying as- sumption is rarely tested, as evidenced by the absence in many studies of controls, in particular treated controls, and so far never with a reasonable statistical power. Published studies have shown reduced survival prospects or delayed breeding in some species, suggesting that there may be reason to doubt that tracking devices provide unbiased information. Therefore, we conducted a meta-analysis of studies applying geolocators to wild birds to determine whether geolocators affected fitness components. Ge- olocators had an overall negative effect on fitness components, in particular survival, and ecological variables. Effect size was larger for aerial foragers than for other species. Moreover the leg band attachment method was more detrimental for birds than the leg-loop backpack harness. A meta-regression model of effect size showed independent negative effects of geolocators on ae- rial foragers, smaller species, species with smaller migration distances and in studies where geolocators were attached with a ring. These results suggest that geolocator studies should be interpreted with caution, but also raise questions whether it is ethically defensible to use geolocators on aerial foragers or small species without carrying out robust pilot studies.     

Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats

In the face of ongoing habitat fragmentation,many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity,population bottlenecks,and inbreeding depression,including golden snub-nosed monkeys Rhinopithecus roxellana.Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band,which is followed by one or more bachelor groups composed of juvenile,subadult,and adult male members.In this research,we examine the continuous landscape resistance surface,the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains,China.Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands.Although these conditions are expected to result in reduced gene flow,reduced genetic diversity,and an increased opportunity for a genetic bottleneck,based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band,we found high levels of genetic diversity but low levels of genetic divergence,as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands.Our results indicate that the movement of bachelor males across the landscape,along with their association with several different breeding bands,appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.     

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis)

The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.     

Genomic regions underlying agronomic traits in linseed （Linum usitatissimum L.） as revealed by association mapping

The extreme climate of the Canadian Prairies poses a major chal enge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core col ection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bol s per area, 1,000 seed weight, seeds per bol , start of flowering, end of flowering, plant height, plant branching, and lodging col ected from up to eight environments was used for association mapping. Based on a mixed model （principal component analysis （PCA） t kinship matrix （K））, 12 significant marker-trait associations for six agronomic traits were identi-fied. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable al eles have additive effects. None of the modern cultivars carried the five favorable al eles and the maximum number of four observed in any accessions was mostly in＆amp;nbsp;breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while il ustrating the potential for improvement through marker-assisted selection.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei （Primulaceae）： implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% （percentage of polymorphic bands） and Hsp=0.1762 （total genetic diversity）. However, a high level of genetic differentiation among populations was detected based on different measures （Nei＇s genetic diversity analysis： Gst=0.6038; AMOVA analysis： Fst=0.6797）. Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Nonlinear maternal effects on personality in a rodent species with fluctuating densities

Consistent among individual variation in behavior,or animal personality,is present in a wide variety of species.This behavioral variation is maintained by both genetic and environmental factors.Parental effects are a special case of environmental variation and are expected to evolve in populations experiencing large fluctuations in their environment.They represent a non-genetic pathway by which parents can transmit information to their offspring,by modulating their personality.While it is expected that parental effects contribute to the observed personality variation,this has rarely been studied in wild populations.We used the multimammate mouse Mastomys natalensis as a model system to investigate the potential effects of maternal personality on offspring behavior.We did this by repeatedly recording the behavior of individually housed juveniles which were born and raised in the lab from wild caught females.A linear correlation,between mother and offspring in behavior,would be expected when the personality is only affected by additive genetic variation,while a more complex relationship would suggests the presence of maternal effects.We found that the personality of the mother predicted the behavior of their offspring in a non-linear pattern.Exploration behavior of mother and offspring was positively correlated,but only for slow and average exploring mothers,while this correlation became negative for fast exploring mothers.This may suggests that early maternal effects could affect personality in juvenile M.natalensis,potentially due to density-dependent and negative frequency-dependent mechanisms,and therefore contribute to the maintenance of personality variation.     

Global comparisons of beta diversity among mammals, birds, reptiles, and amphibians across spatial scales and taxonomic ranks

Beta diversity is the change in species composition among areas in a geographic region. The proportion of species shared between two areas often decreases when the distance separating them increases, leading to an increase in beta diversity. This study compares beta diversity among four classes of terrestrial vertebrates （mammals, birds, reptiles, and amphibians） at both regional （biogeographic realm） and global extents, using the same sets of faunal sample units for all four groups in each comparison. Beta diversity is lower for the two endothermic taxa （birds and mammals） than for the two ectothermic taxa （reptiles and amphibians） in all six biogeographic realms examined. When the four taxa in the six biogeographic realms are combined, beta diversity at the species rank is higher than that of the genus rank by a factor of 1.24, and is higher than that of the family rank by a factor of 1.85. The ratio of beta diversity at the genus rank to that at the family rank is 1.50. Beta diversity is slightly higher for ecoregions of 5000-99,999 km^2 than for ecoregions of 100,000-5,000,000 km^2.     

Do assortative mating and immigrant inviability help maintain population genetic structuring of an herbivore on a crop and a wild relative?

Population genetic structuring is common among herbivorous insects and frequently is associated with divergent host plants, such as crops and their wild relatives. Previous studies showed population genetic structuring in corn leafhopper Dulbulus maidis in Mexico, such that the species consists of two sympatric, host plant-associated populations: an abundant and widespread "pestiferous” population on maize (Zea mays mays), and a small and localized "wild" population on perennial teosinte (Zea diploperennis). a maize wild relative with a limited distribution. This study addressed whether assortative mating and immigrant inviability mediate genetic structuring of corn leafliopper by comparing the mating and reproductive successes of pestiferous and wild females that colonize their nonassociated host plants against the successes of females colonizing their associated host plants. Assortative mating was assessed by comparing mating frequencies and premating and mating times among females of each population on each host plant: immigrant inviability was assessed by comparing, across two generations, the fecundity, survival, development time, sex ratio, and population growth rate among leafhopper populations and host plants. Our results showed that on maize, and compared to resident, pestiferous females, wild females were more likely to mate, and greater proportions of their offspring survived to adult stage and were daughters;consequently, the per-generation population growth rate on maize was greater for immigrant, wild leafhoppers compared to resident, pestiferous leafhoppers. Our results suggested that wild leafhoppers emigrating to maize have a fitness advantage over resident, pestiferous leafhoppers, while immigrant pestiferous and resident wild leafhoppers on teosinte have similar fitnesses.     

Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes

Allopolyploidy accelerates genome evolution in wheat in two ways： 1） allopolyploidization triggers rapid genome alterations （revolutionary changes） through the instantaneous generation of a variety of cardinal genetic and epigenetic changes, and 2） the allopolyploid condition facilitates sporadic genomic changes during the life of the species （evolutionary changes） that are not attainable at the diploid level. The revolutionary alterations, occurring during the formation of the allopolyploid and leading to rapid cytological and genetic diploidization, facilitate the successful establishment of the newly formed allopolyploid in nature. On the other hand, the evolutionary changes, occurring during the life of the allopolyploids, increase the intra-specific genetic diversity, and consequently, increased fimess, adaptability and competitiveness. These phenomena, emphasizing the dynamic plasticity of the allopolyploid wheat genome with regards to both structure and function, are described and discussed in this review.     

Aphids as models for ecological and evolutionary studies

Aphids （Hemiptera： Aphididae） are a group of phloemfeeding insects numbering more than 5 000 extant species（Favret, 2014a）. Most species have complex life cycles that include both asexual （viviparous parthenogenesis）and sexual reproduction. They display a high degree of intraspecific polyphenism with multiple phenotypes froman identical genotype, and they have specialized associations with their host plants （Blackman ＆ Eastop, 2000）.Some aphid species are gall-makers and even have evolved sociality with division of labor （Aoki, 1977; Stern ＆Foster, 1996）. Many aphid species are agricultural and forestry pests. They incur damage to plants and carryvector plant viruses （Blackman ＆ Eastop, 2000）. Due to their fascinating biological character and economic importance, aphids have long been popular animals for research in basic and applied biology, and are becominguseful research models for studying important questions in ecology and evolution, especially in the genomic era（Brisson ＆ Stem, 2006; Huang ＆ Qiao, 2006; Srinivasan ＆ Brisson, 2012）.     

Species diversification and phylogeographical patterns of birds in response to the uplift of the Qinghai-Tibet Plateau and Quaternary glaciations

The Qinghai-Tibet Plateau （QTP） is well known for being of great importance in the evolution of montane species due to its unique geological history and landform configuration, climate complexity, and diversified habitats. The effect of environmental changes since the Quaternary on species diversification, population genetic structure, and demography under environmental change can be studied using phylogenetic and phylogeographieal approaches. Birds are the most well-studied group of all terrestrial vertebrates with regard to their response to climatic changes over time. Herein, we briefly review the species diversification of birds in response to the uplift of the QTP, focusing on summarizing the different phylogeographical patterns of birds on the Plateau, its southeastern margin, and the Eastern Himalayas and the reasons underlying these patterns. Speciation was found to be closely related to the uplift of the QTP, with different patterns of intraspecific processes： （1） no divergence within a single refuge was identified in a restricted semi-continuous area of the eastern margin of the Plateau; （2） two divergent lineages with separated refugia were located at the south-eastern and north-eastern margins of the plateau; and （3） multiple divergent lineages within subregions were found in the Eastern Himalayas. Glacial movements and induced climate change are considered to be key factors in shaping these different patterns. The species distributed mainly in the heavily ice-covered platform regions of the Plateau experienced population expansion following the retreat of the extensive glaciations, whereas the species distributed on the ice-free edges of the plateau maintained their population size at a stable level. Demographic stresses on the edge species might have been mitigated by the milder climate in comparison to their platform-distributed counterparts. Various behavioral and ecological characteristics, including dispersal capacity, habitat preference, and elevation specificity, along with evolutionary history might have helped to shape these different phylogeographical patterns [Current Zoology 60 （2）： 149-161, 2014].     

An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

The environmental risks associated with genetically-engineered （GE） organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment （ERA） model that follows the 1998 USEPA guidelines, focusing on potential adverse effects to biological diversity. The approach starts by （ 1 ） identifying the local environmental values so the ERA addresses specific concerns associated with local biological diversity. The model simplifies the indicator endpoint selection problem by （2） classifying biological diversity into ecological functional groups and selecting those that deliver the identified environmental values. （3） All of the species or ecosystem processes related to the selected functional groups are identified and （4） multi-criteria decision analysis （MCDA） is used to rank the indicator endpoint entities, which may be spe- cies or ecological processes. MCDA focuses on those species and processes that are critical for the identified ecological functions and are likely to be highly exposed to the GE organism. The highest ranked indicator entities are selected for the next step. （5） Rele- vant risk hypotheses are identified. Knowledge about the specific transgene and its possible environmental effects in other countries can be used to assist development of risk hypotheses. （6） The risk hypotheses are ranked using MCDA with criteria related to the severity of the potential risk. The model emphasizes transparent, expert-driven, ecologically-based decision-making and provides formal methods for completing a screening level-ERA that can focus ERA on the most significant concerns. The process requires sub- stantial human input but the human capital is available in most countries and regions of the world.     

The foraging behavior of Japanese macaques Macaca fuscata in a forested enclosure: Effects of nutrient composition,energy and its seasonal variation on the consumption of natural plant foods

<正> In the wild, primate foraging behaviors are related to the diversity and nutritional properties of food, which are affectedby seasonal variation. The goal of environmental enrichment is to stimulate captive animals to exhibit similar foraging behaviorof their wild counterparts, e.g. to extend foraging time. We conducted a 12-month study on the foraging behavior of Japanesemacaques in a semi-naturally forested enclosure to understand how they use both provisioned foods and naturally availableplant foods and what are the nutritional criteria of their consumption of natural plants. We recorded time spent feeding on provisionedand natural plant foods and collected the plant parts ingested of their major plant food species monthly, when available.We conducted nutritional analysis (crude protein, crude lipid, neutral detergent fiber-'NDF', ash) and calculated totalnon-structural carbohydrate - 'TNC' and total energy of those food items. Monkeys spent 47% of their feeding time foraging onnatural plant species. The consumption of plant parts varied significantly across seasons. We found that leaf items were consumedin months when crude protein, crude protein-to-NDF ratio, TNC and total energy were significantly higher and NDF was significantlylower, fruit/nut items in months when crude protein and TNC were significantly higher and crude lipid content was significantlylower, and bark items in months when TNC and total energy were higher and crude lipid content was lower. This preliminaryinvestigation showed that the forested enclosure allowed troop members to more fully express their species typical flexiblebehavior by challenging them to adjust their foraging behavior to seasonal changes of plant item diversity and nutritional content,also providing the possibility for individuals to nutritionally enhance their diet     

Genetic diversity of the endangered species Rosa rugosa Thunb. in China and implications for conservation strategies

Rosa rugosa Thunb. is one of the dominant and important shrub species in estuary dunes and shingle beaches of northern China. However, its area of distribution, the number of populations, and the size of each population have decreased rapidly in the past two decades because of habitat degradation and loss. Random amplified polymorphic DNA markers were used to determine the genetic diversity of four remaining large natural populations of R. rugosa and to discuss an effective conservation strategy for this endangered species in China. High genetic variations were detected in R. rugosa populations in China. The mean percentage of polymorphic loci （P%） within four local populations was 57.99%, with the P% of the total population being 75.30%. Mean Shannon＇s information index （H0） was 0.2826, whereas total Ho was 0.3513. The genetic differentiation among populations was 0.1878, which indicates that most genetic diversity occurs within populations. Population Tumenjiang （TMJ） showed the highest genetic diversity （P% = 66.27%; H0 = 0.3117） and contained two exclusive bands. Population Changshandao （CSD） showed higher genetic diversity （P% =59.04%; H0 = 0.3065）. Populations TMJ and CSD contained 95.33% and 99.33%, respectively, of loci with moderate to high frequency （P〉0.05） of the total population. These results indicate that populations TMJ and CSD should be given priority for in situ conservation and regarded as seed or propagule sources for ex situ conservation. The results of the present study also suggest that R. rugosa in China has become endangered as a result of human actions rather than genetic depression of populations; thus, human interference should be absolutely forbidden in R. rugosa habitats.     

SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF SUCKING LICE IN YUNNAN, CHINA

On the basis of investigating 9 counties (towns) in Yunnan Province of China, the species diversity and community structure of sucking lice on the body surface of small mammal hosts are studied in the paper. Species richness (S) is used to stand for the species diversity. The calculation of community diversity index and evenness are based on Shannon-Wiener‘s method. 2745 small mammals captured from the investigated sites belong to 10 families, 25 genera and 41 species in 5 orders (Rodentia, Insectivora, Scandentia, Logomorpha and Carnivora) while 18165 individuals of sucking lice collected from the body surface of the small mammal hosts are identified into 4 families, 6 genera and 22 species. The species of sucking lice are much less than the species of their hosts. Most species of small mammals have their fixed sucking lice on their body surface. One species of small mammals usually have few species of sucking lice (1 to 4 species). The close species of the hosts in the taxonomy are found to have the same or similar dominant species of sucking lice on their body surface. The results reveal that the species diversity of sucking lice on small mammals is very low with a very simple community structure. The results also imply there may be a close co-evolution relationship between the lice and the hosts.