Microsatellites reveal high genetic diversity within colonies of Camponotus ants

In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR-products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats.     

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.     

Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream

Traditional techniques for studying the fungal community composition in streams favour the detection and identification of aquatic hyphomycetes. Our objective was to use molecular techniques to determine the presence and contributions of other fungal groups. We designed primers specific for the ITS regions in Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota and Oomycota. The primers were used to amplify DNA from linden, maple, and beech leaves, and birch wood submerged in a stream for 4 weeks in summer, autumn, winter and spring. The amplification products were separated by denaturing gradient gel electrophoresis. Ascomycota were present in large phylotype numbers (up to 21) on all substrates and all dates and represented ≥ 75 % of the fungal biomass. Basidiomycota were the second most abundant group in summer and autumn (up to 13 % on wood) and were absent only on linden and maple in spring. There were consistently large numbers of phylotypes from Chytridiomycota and their relative contribution to the microbial community peaked in winter on all substrates. Oomycota were present in summer and abundant only on wood. Zygomycota were present in low numbers and their estimated contribution to fungal biomass was ≤ 1%. Using primers to target individual groups facilitates a more balanced approach to studying fungal diversity in freshwater ecosystems.     

The role of habitat patches on mammalian diversity in cork oak agroforestry systems

Habitat patches, depending on the degree of differentiation from the matrix, can add few or many elements to the species pool of a particular landscape. Their importance to biodiversity is particularly relevant in areas with complex landscapes, where natural, naturalized, or managed habitats are interspersed by small patches of habitat types with very different biophysical characteristics; e.g., fruit orchards and riparian areas. This is the case of the montado landscape, a cork oak agroforestry system that largely covers south-western Portugal. We evaluated whether the high mammalian biodiversity found in this system is, in part, the cumulative result of the species found in the non-matrix habitats. Our results indicate that in areas where there are inclusions of orchards/olive yards and riparian vegetation in the cork oak woodland, a significantly higher number of mammalian species are present. We further detected a positive effect of low human disturbance on mammal diversity. Ultimately, our results can be used by managers to augment their management options, since we show that the inclusion and maintenance of non-matrix habitat patches in cork oak agro-silvo-forestry systems can help to maximize mammal biodiversity without compromising services associated with agriculture and forestry.     

Sexual size dimorphism in a landlocked Pacific salmon in relation to breeding habitat features

Many animal species exhibit size dimorphism between sexes. Sexual selection, whereby male–male competition favors larger body sizes, has been considered a likely cause of sexual size dimorphism. Habitat features in breeding areas could affect the outcome of male–male competition, yet few attempts have been made to relate breeding habitat features with interpopulation variation in sexual size dimorphism. In this study, we examined interpopulation variation in sexual size dimorphism by studying the landlocked amago salmon (Oncorhynchus masou ishikawae) at a microgeographic scale. We found that female body size was independent of stream size but that male body size decreased with smaller stream sizes. A likely explanation is that the relationship between reproductive success and the size of males is influenced by the availability of refuges that are only available to small-bodied males. Sexual differences in body size increased with decreasing stream sizes, supporting the hypothesis that the reproductive success of larger males is reduced in smaller streams. In contrast, the maturation-length threshold increased with stream size for both sexes. The stream-size-based interpopulation variation in sexual size dimorphism and size at maturity in landlocked amago salmon may therefore have arisen through a combination of sexual and natural selection.     

Tree diversity in primary forest and different land use systems in Central Sulawesi,Indonesia

We studied the tree communities in primary forest and three different land use systems (forest gardens, ca. 5-year-old secondary forests, cacao plantations) at 900–1200 m elevation in the environs of Lore Lindu National Park, Central Sulawesi. The primary forests had ca. 150 tree species 10 cm diameter at breast height (dbh) per hectare, which is unusually high for forests at this elevation in southeast Asia. Basal area in the primary forest was 140 m² ha^–1, one of the highest values ever recorded in tropical forests worldwide. Tree species richness declined gradually from primary forest to forest gardens, secondary forests, and cacao plantations. This decline was paralleled by shifts in tree family composition, with Lauraceae, Meliaceae, and Euphorbiaceae being predominant in primary forests, Euphorbiaceae, Rubiaceae and Myristicaeae dominating in the forest gardens and Euphorbiaceae, Urticaceae, and Ulmaceae in the secondary forests. Cacao plantations were composed almost exclusively of cacao trees and two species of legume shade trees. Forest gardens further differed from primary forests by a much lower density of understorey trees, while secondary forests had fewer species of commercial interest. Comparative studies of birds and butterflies demonstrated parallel declines of species richness, showing the importance of trees in structuring tropical forest habitats and in providing resources.     

Rapid assessments and local knowledge reveal high bird diversity in mangroves of north-west Madagascar

Although the importance of regulating and provisioning services provided by mangroves is widely recognised, our understanding of their role in the maintenance of terrestrial biodiversity is patchy globally and largely lacking for many regions, including conservation priorities such as Madagascar. We carried out the first multi-site bird inventory of mangroves in Madagascar and complemented our data with assessments of local knowledge, in order to broaden our knowledge of which species use this habitat. We directly observed 73 species across three sites in Ambanja and Ambaro Bays, while local respondents indicated the presence of 18 additional species: four observed species are globally threatened, while 37 are endemic to Madagascar or the Malagasy region. Over half the species observed are typically terrestrial, of which 22 have not previously been recorded in mangrove habitats in Madagascar. Local knowledge provided a useful complement to our observed data but we are likely to have underestimated total richness; nevertheless, our findings greatly increased our knowledge of mangrove use by Madagascar’s birds. However, further research is required to investigate the functional role of mangroves in the ecology of the observed species and provide insights into the factors influencing mangrove use.     

AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species

We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic‐alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic‐alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left‐skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were <200 years old. The oldest genets of D. octopetala, S. herbacea and V. uliginosum were found to be at least 500, 450 and 1400 years old, respectively. These results indicate that individuals in the studied populations have survived pronounced climatic oscillations, including the Little Ice Age and the postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long‐lived clonal plants in arctic‐alpine ecosystems can persist, despite considerable climatic change.     

DArTseq-derived SNPs for the genus Psidium reveal the high diversity of native species

Tree Genetics & Genomes - Climatic fluctuations and aridification have combined with the environmental heterogeneity between north and south Xinjiang to shape the spatial genetic structure and...     

Aggressiveness is associated with genetic diversity in landlocked salmon (Salmo salar)

The amount of intraindividual genetic variation has often been found to have profound effects on life history traits. However, studies concerning the relationship between behaviour and genetic diversity are scarce. Aggressiveness is an important component of competitive ability in juvenile salmonids affecting their later performance and survival. In this study, we used an experimental approach to test the prediction that juveniles with low estimated genetic diversity should be less aggressive than juveniles with high estimated genetic diversity in fry from a highly endangered population of land-locked salmon (Salmo salar). This was achieved by using a method enabling the accurate estimation of offspring genetic diversity based on parental microsatellite genotype data. This allowed us to create two groups of offspring expected to have high or low genetic diversity in which aggressive behaviour could be compared. Salmon fry with low estimated genetic diversity were significantly less aggressive than fry with high estimated genetic diversity. Closer analysis of the data suggested that this difference was due to differences in more costly acts of aggression. Our result may reflect a direct effect of genetic variation on a fitness-related trait; however, we cannot rule out an alternative explanation of allele-specific phenotype matching, where lowered aggression is expressed towards genetically more similar individuals.     

Tree diversity and phytogeographical patterns of tropical high mountain rain forests in Central Sulawesi,Indonesia

Tropical high mountain forests in Lore Lindu National Park, Sulawesi, Indonesia, were described by their floristic composition and the importance of tree families (Family importance values, FIV), based on tree inventories conducted on 4 plots (each 0.24 ha) in old-growth forest stands at c. 1800 and 2400 m a.s.l. (mid- and upper montane elevations). To identify general patterns and regional peculiarities of the forests in the SE Asian and SW Pacific context, the biogeography of the tree species was analysed using distribution records. Out of the total of 87 tree species, only 18 species were found at both elevational zones. The discovery of new species and new distribution records (28% of the data set) highlights the deficiencies in the taxonomic and distribution data for Sulawesi. Sulawesi endemism rate was 20%. In the mid-montane Fagaceae–Myrtaceae forests, Lithocarpus spp. (Fagaceae) were overall important (4 spp. occupying around half of the total basal area) and the Myrtaceae the most species rich (8 spp.), thus showing typical features of Malesian montane forests. The upper montane conifer-Myrtaceae forest contained several high mountain tree taxa and showed affinity to the forests of New Guinea. The mountain flora comprised both eastern and western Malesian elements, with the nearest neighbouring islands Borneo and Maluku both sharing species with Sulawesi, reflecting the complex palaeogeography of the island. A separate analysis showed the mid-montane forest to possess greatest biogeographical affinity to Borneo/western Malesia, and the upper montane forest had a number of typical elements of Papuasia/eastern Malesia and the Phillipines, which may be a result of historical patterns in land connection and the emergence of mountain ranges.     

Gene diversity analysis of mitochondrial DNA, microsatellites and allozymes in landlocked Atlantic salmon

This study investigates the patterns of genetic diversity detected in allozymes, mtDNA, and microsatellites, in order to assess their relative efficacy to differentiate sympatric landlocked salmon populations and to estimate changes in genetic diversity between wild and first-generation hatchery fish. Overall, the three genetic markers indicated a genetic differentiation between two sympatric populations of Lake Saint-Jean, Québec. MtDNA and microsatellites also showed significant differences between wild and first-generation hatchery fish originating from the same river. Allozyme analysis was the most limited approach due to the low genetic diversity detected and the necessity to kill specimens. Although low polymorphism was found in mtDNA, it was the most discriminant marker between wild populations. Microsatellite analysis appears to be a promising approach due to its high sensitivity in differentiating wild populations, in detecting changes in allele composition between wild and first-generation hatchery fish and its potential for increased resolution by augmenting the number of polymorphic loci. Given the benefits and disadvantages of the three methods, the combination of mtDNA and microsatellite analyses will best address our research objectives.     

Microsatellites reveal genetic diversity in Rotylenchulus reniformis populations

Rotylenchulus reniformis is the predominant parasitic nematode of cotton in the Mid South area of the United States. Although variable levels of infection and morphological differences have been reported for this nematode, genetic variability has been more elusive. We developed microsatellite-enriched libraries for R. reniformis, produced 1152 clones, assembled 694 contigs, detected 783 simple sequence repeats (SSR) and designed 192 SSR-markers. The markers were tested on six R. reniformis cultures from four states, Texas, Louisiana, Mississippi and Georgia, in the USA. Based on performance we selected 156 SSR markers for R. reniformis from which 88 were polymorphic across the six reniform nematode populations, showing as the most frequent motif the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to 0.82, and the percentage of multiallelic loci of the isolates was between 40.9 and 45.1%. An interesting finding in this study was the genetic variability detected among the three Mississippi isolates, for which 22 SSR markers were polymorphic. We also tested the level of infection of these isolates on six cotton genotypes, where significant differences were found between the Texas and Georgia isolates. Coincidentally, 62 polymorphic markers were able to distinguish these two populations. Further studies will be necessary to establish possible connections, if any, between markers and level of pathogenicity of the nematode. The SSR markers developed here will be useful in the assessment of the genetic diversity of this nematode, could assist in management practices for control of reniform nematode, be used in breeding programs for crop resistance, and help in detecting the origin and spread of this nematode in the United States.     

Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu,West Java,Indonesia

Successive microbes in solar salt ponds are essential since it is well correlated with the quality of salt produced. This research aimed to analyse the microbial diversity of the solar salt ponds in Indonesia, which use high-density polyethylene in the ponds. There are two systems, that is, an integrated open system (In-system) and a closed system (Tt-system). The In-system uses seawater while the Tt-system uses seawater from the saline artesian well. Results showed that the In-system had richer microbes than the Tt-system. Both systems shared similar halophilic microbes profile. Ponds with low salinity (3–4 Be) had very low archaea, that is, 0·2 and 0·7% for the In-system and Tt-system respectively and were dominantly inhabited by phylum Proteobacteria. In the pond with high salinity, that is, 25 Be, both systems were dominated by the phylum Euryarchaeota, family Halobacteriaceae, and genera Halorubrum was dominantly found in In25 ponds and Tt25 ponds. Even though the two systems use the same parent seawater, that is, the Java Sea and share similar microbial composition at the phylum level, we found the dominance identified microbes in both systems were different.