Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.     

Tree functional diversity affects litter decomposition and arthropod community composition in a tropical forest

Disturbance can alter tree species and functional diversity in tropical forests, which in turn could affect carbon and nutrient cycling via the decomposition of plant litter. However, the influence of tropical tree diversity on forest floor organisms and the processes they mediate are far from clear. We investigated the influence of different litter mixtures on arthropod communities and decomposition processes in a 60‐year‐old lowland tropical forest in Panama, Central America. We used litter mixtures representing pioneer and old growth tree species in experimental mesocosms to assess the links between litter types, decomposition rates, and litter arthropod communities. Overall, pioneer species litter decomposed most rapidly and old growth species litter decomposed the slowest but there were clear non‐additive effects of litter mixtures containing both functional groups. We observed distinct arthropod communities in different litter mixtures at 6 mo, with greater arthropod diversity and abundance in litter from old growth forest species. By comparing the decay of different litter mixtures in mesocosms and conventional litterbags, we demonstrated that our mesocosms represent an effective approach to link studies of litter decomposition and arthropod communities. Our results indicate that changes in the functional diversity of litter could have wider implications for arthropod communities and ecosystem functioning in tropical forests.     

Genetic diversity among accessions of an ancient olive variety of Cyprus.

To evaluate germplasm variability and to discriminate between accessions of 'Ladolia', an ancient olive variety of Cyprus, different accessions from a germplasm collection were screened with 11 selected oligonucleotide primers in RAPD-PCRs. A total of 49 polymorphic markers were scored, the combination of which resulted in 70 distinct electrophoretic patterns. Based on either unique or combined patterns, all accessions were identified. Seven genotype-specific markers were detected. One RAPD marker could distinguish accessions according to fruit size. Genetic similarities between accessions, estimated using the Dice similarity coefficient, indicated a high degree of genetic diversity among 'Ladolia' accessions. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA) and principal components analysis (PCA). Three main groups of accessions were detected. The first group was generally composed of accessions with small-sized fruits and could be further divided into two subgroups. According to PCA, most accessions with medium- or large-sized fruits were clustered together. Our results support previous observations suggesting that 'Ladolia' is actually a highly variable mixture of genetically distinct landraces.     

The influence of habitat structure on arthropod diversity in Argentine semi-arid Chaco forest

Abstract. The Argentine Chaco is a mosaic of grassland and open forest habitats maintained by natural disturbance activities such as fire. Since the introduction of domestic livestock and other human activities, the balance of this mosaic has been significantly altered, both in plant species and structural composition. This study focuses on the impact of such changes on the diversity of ground-dwelling arthropods within semi-arid Chaco forest. Quantitative measures of habitat structure and arthropod diversity were taken in forest areas previously subjected to grazing, logging and ploughing. Results indicated that arthropod diversity was smaller on sites with reduced structural complexity, with marked changes in arthropod family composition. The habitat components relating to plant architectural and vertical diversity were particularly influential on arthropod diversity. The guild size ratio of predatory to non-predatory arthropods also differed significantly between habitats suggesting a change in the resource base available to some groups. The latter suggests a shift in the functional organisation of the forest ecosystem which could have important repercussions for the diversity of other trophic levels.     

鼎湖山季风常绿阔叶林及针阔叶混交林节肢动物群落多样性调查

20 0 1年 5月和 10月在自然保护区鼎湖山季风常绿阔叶林和针阔叶混交林的灌木层和草本 -苗木层对节肢动物多样性进行了调查。结果表明 ,5月份的灌木层 ,季风常绿阔叶林的节肢动物物种数和个体数 >针阔叶混交林 ,相反 ,在草本 -苗木层 ,针阔叶混交林的物种数和个体数 >季风常绿阔叶林。 10月份 ,针阔叶混交林节肢动物物种数和个体数与季风常绿阔叶林间无明显差异。两林分中 ,天敌占总物种数的 2 7.5 0 %～ 87.5 0 % ,蜘蛛类群占总物种数的 18.18%～ 6 6 .6 7%、占天敌物种数的 5 3.33%～ 90 .91%。除 5月份的草本 -苗木层外 ,节肢动物的丰富度指数、多样性指数均是季风常绿阔叶林 >针阔叶混交林 ,优势集中性指数则是针阔叶混交林 >季风常绿阔叶林。     

Primary and secondary vegetation patches as contributors to floristic diversity in a tropical deciduous forest landscape

The floristic diversity of Mexican tropical deciduous forests (TDF) is of critical importance given the high species richness (alpha diversity), species turnover (beta diversity), and the intense deforestation rates. Currently, most TDF landscapes are mosaics of agricultural land, secondary vegetation, and patches of relatively undisturbed primary vegetation. Here we illustrate how both primary forest remnants and secondary vegetation patches contribute to the floristic diversity of TDF in a landscape of volcanic origin in central Veracruz, Mexico. Our objectives were to assess sampling efficiency and inventory completeness, to compare mean and cumulative species richness between primary forest and secondary vegetation sites, and to analyze beta diversity between vegetation types. In an area of 12,300 m2 we recorded 105 families, 390 genera, and 682 species. Species inventories for both vegetation types were about 80% complete. Secondary vegetation is more alpha diverse than primary forest, both in terms of cumulative and mean species richness. We found a remarkably high beta diversity between vegetation types (75% of complementarity, 91.60% of mean dissimilarity). We also identified the species that contribute the most to similarity within vegetation types and to dissimilarity between vegetation types. Our results support the idea that assessing biodiversity on the landscape scale is an appropriate way to ascertain the impact of human activities. For this land mosaic, conservation of the flora would not be possible by focusing solely on primary forest remnants. We propose the implementation of a network of small conservation areas with a flexible structure, following the “archipelago reserve” model.     

Grass abundance maintains positive plant–arthropod diversity relationships in maize fields and margins in South Africa

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King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times

Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.     

Vegetation structure and diversity of an ancient temperate deciduous forest in SW Denmark

Bolderslev Skov (113 ha) is the largest contiguous ancient forest remnant in Denmark. The forest has been preserved since 1998 as a strict non-intervention forest reserve. We studied vegetation structure, floristic gradients, and diversity of the forest in 50 plots of 100 m² placed according to a restricted random sampling design. Dominant tree species were Fagus sylvatica, Fraxinus excelsior, Tilia cordata and Quercus robur, which in most parts of the forest form a mixed canopy. Most stands appeared to be of moderate age, 55-80 years old, and large old trees were rare. pH in association with light and thickness of the litter layer were the most important factors in explaining floristic gradients in the forest. Soil moisture (dry to mesic) was not strongly correlated with DCA axes for neither tree nor field layer, but had a significant effect on the distribution of a number of herb species. Forest structure was not important in explaining species distributions. Field layer species richness showed a positive relationship with the pH-gradient. At the scale of 1m² plots we also found a highly significant negative relationship between field layer species richness and the plot-wise Ellenberg indicator value for nitrogen availability. Structure of the tree layer had little effect on field layer species richness. The mixed composition, long continuity, and presence of a high proportion of the regional species pool assigns a high conservation value to Bolderslev Skov and makes it an important site for future studies of the dynamic properties, niche preferences, and inter-specific competition of temperate deciduous forest species. This revised version was published online in June 2006 with corrections to the Cover Date.     

Selection maintains MHC diversity through a natural population bottleneck

A perceived consequence of a population bottleneck is the erosion of genetic diversity and concomitant reduction in individual fitness and evolutionary potential. Although reduced genetic variation associated with demographic perturbation has been amply demonstrated for neutral molecular markers, the effective management of genetic resources in natural populations is hindered by a lack of understanding of how adaptive genetic variation will respond to population fluctuations, given these are affected by selection as well as drift. Here, we demonstrate that selection counters drift to maintain polymorphism at a major histocompatibility complex (MHC) locus through a population bottleneck in an inbred island population of water voles. Before and after the bottleneck, MHC allele frequencies were close to balancing selection equilibrium but became skewed by drift when the population size was critically low. MHC heterozygosity generally conformed to Hardy-Weinberg expectations except in one generation during the population recovery where there was a significant excess of heterozygous genotypes, which simulations ascribed to strong differential MHC-dependent survival. Low allelic diversity and highly skewed frequency distributions at microsatellite loci indicated potent genetic drift due to a strong founder affect and/or previous population bottlenecks. This study is a real-time examination of the predictions of fundamental evolutionary theory in low genetic diversity situations. The findings highlight that conservation efforts to maintain the genetic health and evolutionary potential of natural populations should consider the genetic basis for fitness-related traits, and how such adaptive genetic diversity will vary in response to both the demographic fluctuations and the effects of selection.     

不同经营管理方式对锥栗林节肢动物群落结构与多样性的影响

通过对不同经营管理方式下锥栗林节肢动物群落的调查,研究了生产上典型的5种经营管理方式对锥栗林节肢动物群落结构与多样性的影响.结果表明:5种不同经营管理方式下锥栗林节肢动物群落结构和多样性有较大差别,管理精细未用药型的锥栗林物种多样性和稳定性最高,植食性集团的多样性指数最高,天敌功能集团的相对丰盛度最高,对害虫的自然控制效能高,不利于优势害虫的暴发;相比管理撂荒型,精细的经营管理会提高林冠层物种多样性,而化学农药的使用降低了各功能集团的物种多样性、均匀度,提高了植食性集团的相对丰盛度.     

Relationships between spatial configuration of tropical forest patches and woody plant diversity in northeastern Puerto Rico

The destruction and fragmentation of tropical forests are major sources of global biodiversity loss. A better understanding of anthropogenically altered landscapes and their relationships with species diversity and composition is needed in order to protect biodiversity in these environments. The spatial patterns of a landscape may control the ecological processes that shape species diversity and composition. However, there is little information about how plant diversity varies with the spatial configuration of forest patches especially in fragmented tropical habitats. The northeastern part of Puerto Rico provides the opportunity to study the relationships between species richness and composition of woody plants (shrubs and trees) and spatial variables [i.e., patch area and shape, patch isolation, connectivity, and distance to the Luquillo Experimental Forest (LEF)] in tropical forest patches that have regenerated from pasturelands. The spatial data were obtained from aerial color photographs from year 2000. Each photo interpretation was digitized into a GIS package, and 12 forest patches (24–34 years old) were selected within a study area of 28 km². The woody plant species composition of the patches was determined by a systematic floristic survey. The species diversity (Shannon index) and species richness of woody plants correlated positively with the area and the shape of the forest patch. Larger patches, and patches with more habitat edge or convolution, provided conditions for a higher diversity of woody plants. Moreover, the distance of the forest patches to the LEF, which is a source of propagules, correlated negatively with species richness. Plant species composition was also related to patch size and shape and distance to the LEF. These results indicate that there is a link between landscape structure and species diversity and composition and that patches that have similar area, shape, and distance to the LEF provide similar conditions for the existence of a particular plant community. In addition, forest patches that were closer together had more similarity in woody plant species composition than patches that were farther apart, suggesting that seed dispersal for some species is limited at the scale of 10 km.     

转基因玉米对田间节肢动物群落多样性的影响

通过对转基因耐除草剂(EPSPS)抗虫(Cry1Ab)玉米转化体‘DBN9936’、受体玉米‘DBN318’、常规玉米‘先玉335’和喷施除草剂的转化体‘DBN9936’玉米田中节肢动物种类及数量的调查, 评价转基因玉米对田间节肢动物群落多样性的影响。2015年和2017年我们采用直接观察法、陷阱调查法和剖秆法对田间节肢动物进行调查, 采用聚类分析、物种累积曲线等方法对数据进行分析, 并比较了4个处理玉米田节肢动物群落的Margalef丰富度指数、Shannon-Wiener多样性指数、Simpson多样性指数、Pielou均匀度指数、优势集中性指数和群落相似性指数的差异及其随时间变化的规律。调查期间共记录节肢动物20目80科; 转化体玉米‘DBN9936’ (2015: 10.3 ± 2.6头, 2017: 3.3 ± 1.7头)和喷施除草剂的转化体玉米‘DBN9936’ (2015: 6.0 ± 1.5头, 2017: 17.0 ± 0.6头)上鳞翅目昆虫的数量明显低于受体‘DBN318’ (2015: 20.0 ± 3.2头, 2017: 24.0 ± 6.0头)和‘先玉335’ (2015: 21.0 ± 8.9头, 2017: 26.7 ± 2.0头); 物种累积曲线呈典型的抛物线, 各类玉米田间总体物种丰富度差异较小; 玉米生育期节肢动物调查结果累计数量的功能团组成及其丰富度、多样性、均匀度、优势集中性间均无明显的差异, 各类指数随时间变化的动态趋于一致, 群落间相似性程度较高。转基因玉米‘DBN9936’对鳞翅目害虫有明显的抗性, 对非靶标节肢动物无显著的影响, 对田间节肢动物的群落多样性、均匀度、丰富度、优势集中性等没有明显的影响。     

Pollination and reproduction of a self-incompatible forest herb in hedgerow corridors and forest patches

Habitat-corridors are assumed to counteract the negative impacts of habitat loss and fragmentation, but their efficiency in doing so depends on the maintenance of ecological processes in corridor conditions. For plants dispersing in linear habitats, one of these critical processes is the maintenance of adequate pollen transfer to insure seed production within the corridor. This study focuses on a common, self-incompatible forest herb, Trillium grandiflorum, to assess plant–pollinator interactions and the influence of spatial processes on plant reproduction in hedgerow corridors compared to forests. First, using pollen supplementation experiments over 2 years, we quantified the extent of pollen limitation in both habitats, testing the prediction of greater limitation in small hedgerow populations than in forests. While pollen limitation of fruit and seed set was common, its magnitude did not differ between habitats. Variations among sites, however, suggested an influence of landscape context on pollination services. Second, we examined the effect of isolation on plant reproduction by monitoring fruit and seed production, as well as pollinator activity and assemblage, in small flower arrays transplanted in hedgerows at increasing distances from forest and from each other. We detected no difference in the proportion of flowers setting fruit or in pollinator activity with isolation, but we observed some differences in pollinator assemblages. Seed set, on the other hand, declined significantly with increasing isolation in the second year of the study, but not in the first year, suggesting altered pollen transfer with distance. Overall, plants in hedgerow corridors and forests benefited from similar pollination services. In this system, plant–pollinator interactions and reproduction seem to be influenced more by variations in resource distribution over years and landscapes than by local habitat conditions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

车八岭山地常绿阔叶林冰灾后土壤节肢动物群落的多样性

2008年初车八岭山地常绿阔叶林受到中国南方80年一遇的冰灾的重创。为了揭示灾后林冠开度的梯度对土壤节肢动物多样性与分布的影响, 在受冰灾影响的车八岭山地常绿阔叶林设置2 ha固定样地, 按照冠层受损程度选取17个20 m×20 m的样方, 用半球面影像技术获取林冠开度, 并分凋落物层、0–10 cm和10–20 cm的矿质土层采集凋落物及土壤样品, 分析土壤节肢动物多样性。利用双向聚类分析(two-way cluster analysis)对凋落物层的土壤节肢动物和样地进行聚类, 以典范对应分析(canonical correspondence analysis)研究冠层开度、土壤有机质、电导率以及自然含水量与0–10 cm表土层土壤节肢动物的关系。结果表明土壤节肢动物的多度、丰富度和多样性随土壤层的加深而下降, 具有明显的表聚性; 林冠开度与凋落物层的土壤节肢动物类群数量呈负相关; 甲螨亚目、中气门亚目和前气门亚目动物对光照的适应范围广; 膜翅目、鞘翅目幼虫、综合纲和伪蝎目动物具有明显的避光性; 土壤节肢动物类群的分布与林冠开度、土壤自然含水量、电导率和有机质关系密切。因此可以推论, 冰灾对车八岭山地常绿阔叶林冠层的破坏及土壤因子的变化会进一步影响土壤节肢动物群落的组成和分布。本项研究还表明, 土壤节肢动物群落能有效地表征它们所栖息的生态系统的特点, 可用于监测冰灾后森林恢复和演替动态。而双向聚类分析和典范对应分析对于揭示土壤节肢动物的空间异质性及其与环境因子的相互关系具有理想的效果。     

Clonal diversity and genetic differentiation in Ilex leucoclada M. patches in an old-growth beech forest

We investigated clonal diversity within patches of Ilex leucoclada and genetic variation within and among patches using random amplified polymorphic DNA (RAPD) markers in a 1-ha plot within an old-growth beech forest. We found 38 patches that exhibited a clumped distribution in the middle of the plot. We identified a total of 166 RAPD phenotypes among the 215 stems sampled from 27 patches that were completely within the plot. The population showed high clonal diversity within patches (mean number of genets relative to number of stems = 0.79; mean Simpson's D = 0.89). Variation in RAPD phenotypes among patches was highly significant (PhiST in the molecular variance analysis = 0.316, P < 0.001), indicating genetic differentiation among patches. Pairwise genetic distances, PhiST, among patches did not correlate with geographical distances among patches. The cluster analysis based on the genetic distances showed few clear clusters of patches, indicating no spatial genetic structure among patches. High levels of clonal diversity both within patches and within the population may be explained by multiple founders, seedling recruitment during patch-formation, and somatic mutation. The significant genetic differentiation among patches may be caused by separate founding events and/or kin structuring within patches.     

Experimental tests of the dependence of arthropod diversity on plant diversity

ABSTRACT Because a diversity of resources should support a diversity of consumers, most models predict that increasing plant diversity increases animal diversity. We report results of a direct experimental test of the dependence of animal diversity on plant diversity. We sampled arthropods in a well-replicated grassland experiment in which plant species richness and plant functional richness were directly manipulated. In simple regressions, both the number of species planted ([Formula: see text] transformed) and the number of functional groups planted significantly increased arthropod species richness but not arthropod abundance. However, the number of species planted was the only significant predictor of arthropod species richness when both predictor variables were included in ANOVAs or a MANOVA. Although highly significant, arthropod species richness regressions had low [Formula: see text] values, high intercepts (24 arthropod species in monocultures), and shallow slopes. Analyses of relations among plants and arthropod trophic groups indicated that herbivore diversity was influenced by plant, parasite, and predator diversity. Furthermore, herbivore diversity was more strongly correlated with parasite and predator diversity than with plant diversity. Together with regression results, this suggests that, although increasing plant diversity significantly increased arthropod diversity, local herbivore diversity is also maintained by, and in turn maintains, a diversity of parasites and predators.     

Patch size of forest openings and arthropod populations

Summary Five sizes of canopy openings (0.016 ha to 10 ha) were established in the Southern Appalachian Mountains in early 1982 to examine the initial patterns of plant and arthropod establishment across a size range of forest disturbances. Vegetation standing crop after the first growing season was considerably higher in large than small openings in apparent response to greater resource release (e.g., sunlight) in larger openings. Woody stump and root sprouts were the dominant mode of revegetation in each patch size. Forest dominants such as Quercus rubra, Q. prinus and Carya spp. were less important as sprouters in openings than several minor forest components (e.g., Robinia pseudo-acacia, Acer rubrum, Halesia carolina and Cornus florida). Arthropod abundance and community composition varied across the size range of forest openings. Arthropods from the surrounding forest readily utilized the smallest canopy openings (0.016 ha). All feeding guilds were well represented in these small openings and herbivore biomass and load (mg of herbivores/g of foliage) were much higher than in larger patches. In contrast, arthropod abundance and species richness were significantly lower in mid-size than smaller patches. The relatively sparse cover and high sunlight in mid-size openings may have promoted surface heat buildups or soil surface/litter moisture deficits which restricted arthropod entry from the surrounding forest. Arthropod abundance and species richness were higher in large than mid-size patches. The greater vegetation cover in larger openings may have minimized the deleterious effects on arthropod populations. However, the absence of population increases among these arthropod species maintained herbivore loads at very low levels in large patches. Our results suggest that arthropod abundance and diversity in sprout-dominated forest openings are highly dependent on the extent of environmental differences between patch and surrounding forest.     

Effects of large herbivores on grassland arthropod diversity

Both arthropods and large grazing herbivores are important components and drivers of biodiversity in grassland ecosystems, but a synthesis of how arthropod diversity is affected by large herbivores has been largely missing. To fill this gap, we conducted a literature search, which yielded 141 studies on this topic of which 24 simultaneously investigated plant and arthropod diversity. Using the data from these 24 studies, we compared the responses of plant and arthropod diversity to an increase in grazing intensity. This quantitative assessment showed no overall significant effect of increasing grazing intensity on plant diversity, while arthropod diversity was generally negatively affected. To understand these negative effects, we explored the mechanisms by which large herbivores affect arthropod communities: direct effects, changes in vegetation structure, changes in plant community composition, changes in soil conditions, and cascading effects within the arthropod interaction web. We identify three main factors determining the effects of large herbivores on arthropod diversity: (i) unintentional predation and increased disturbance, (ii) decreases in total resource abundance for arthropods (biomass) and (iii) changes in plant diversity, vegetation structure and abiotic conditions. In general, heterogeneity in vegetation structure and abiotic conditions increases at intermediate grazing intensity, but declines at both low and high grazing intensity. We conclude that large herbivores can only increase arthropod diversity if they cause an increase in (a)biotic heterogeneity, and then only if this increase is large enough to compensate for the loss of total resource abundance and the increased mortality rate. This is expected to occur only at low herbivore densities or with spatio‐temporal variation in herbivore densities. As we demonstrate that arthropod diversity is often more negatively affected by grazing than plant diversity, we strongly recommend considering the specific requirements of arthropods when applying grazing management and to include arthropods in monitoring schemes. Conservation strategies aiming at maximizing heterogeneity, including regulation of herbivore densities (through human interventions or top‐down control), maintenance of different types of management in close proximity and rotational grazing regimes, are the most promising options to conserve arthropod diversity.