Genetic diversity among Mycoplasma species bovine group 7: clonal isolates from an outbreak of polyarthritis, mastitis, and abortion in dairy cattle

A comprehensive genetic analysis of 60 Mycoplasma sp. bovine group 7 isolates from different geographic origins and epidemiological settings is presented. Twenty-four isolates were recovered from the joints of calves during sporadic episodes of polyarthritis in geographically distinct regions of Queensland and New South Wales, Australia, including two clones of the type strain PG5O. A further three Australian isolates were also recovered from the tympanic bulla, retropharyngeal lymph node and the lung and another three isolates had unconfirmed histories. Six isolates originated from Germany, Portugal, Nigeria, and France. Twenty-four epidemiologically related isolates of Mycoplasma sp. bovine group 7 were recovered from multiple tissue sites and body fluids of infected calves with polyarthritis, mastitic milk, and from the stomach contents, lung and liver from aborted foetuses in three large, centrally managed dairy herds in New South Wales, Australia. Restriction endonuclease analysis (REA) of genomic DNA differentiated 29 Cfol profiles among these 60 isolates and grouped all 24 epidemiologically related isolates in a defined pattern showing a clonal origin. Three isolates of this clonal cluster were recovered from mastitic milk and the synovial exudate of clinically-affected calves and appeared sporadically for periods up to 18 months after the initial outbreak of polyarthritis indicating a persistent, close association of the organism with cattle in these herds. The Cfol profile representative of the clonal cluster was distinguishable from profiles of isolates recovered from multiple, unrelated cases of polyarthritis in Queensland and New South Wales and from other countries. All 24 isolates from the clonal cluster possessed a plasmid (pBG7AU) with a molecular size of 1022 bp. DNA sequence analysis of pBG7AU identified two open reading frames sharing 81 and 99% DNA sequence similarity with hypothetical replication control proteins A and B respectively, previously described in plasmid pADB201 isolated from M. mycoides subspecies mycoides. Other isolates of bovine group 7, epidemiologically unrelated to the clonal cluster, including two clones of the type strain PG5O, possessed a similar-sized plasmid. These data confirm that Mycoplasma sp. bovine group 7 is capable of migrating to, and multiplying within, different tissue sites within a single animal and among different animals within a herd.

Opportunities and limits of the ecosystem services framework in capturing the cultural dimension of sustainable regional and landscape development in protected areas

With regard to protected areas, the concepts of ecosystem services and the cultural dimension of sustainable development (SD) are increasingly under debate. This contribution analyses the role of cultural aspects within the ecosystem services framework using the Millennium Ecosystem Assessment classification as a reference. The limits of the ecosystem services framework in capturing the cultural dimension are highlighted. Potential ways of strengthening the position of cultural values within this framework are discussed.

Genetic diversity in the modern horse illustrated from genome-wide SNP data.

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Genetic diversity, phenotypic variation and local adaptation in the alpine landscape: case studies with alpine plant species

Plant survival in alpine landscapes is constantly challenged by the harsh and often unpredictable environmental conditions. Steep environmental gradients and patchy distribution of habitats lead to small size and spatial isolation of populations and restrict gene flow. Agricultural land use has further increased the diversity of habitats below and above the treeline. We studied the consequences of the highly structured alpine landscape for evolutionary processes in four study plants: Epilobium fleischeri, Geum reptans, Campanula thyrsoides and Poa alpina. The main questions were: (1) How is genetic diversity distributed within and among populations and is it affected by altitude, population size or land use? (2) Do reproductive traits such as allocation to sexual or vegetative reproduction vary with altitude or land use? Furthermore, we studied if seed weight increases with altitude. Within-population genetic diversity of the four species was high and mostly not related to altitude and population size. Nevertheless, genetic differentiation among populations was pronounced and strongly increasing with distance. In Poa alpina genetic diversity was affected by land use. Results suggest considerable genetic drift among populations of alpine plants. Reproductive allocation was affected by altitude and land use in Poa alpina and by succession in Geum reptans. Seed weight was usually higher in alpine species than in related lowland species. We conclude that the evolutionary potential to respond to global change is mostly intact in alpine plants, even at high altitude. Phenotypic variability is shaped by adaptive as well as by random evolutionary processes; moreover plastic responses to growth conditions seem to be crucial for survival of plants in the alpine landscape.

Prevalence, genetic diversity and antimicrobial susceptibility of Listeria monocytogenes isolated from open-air food markets in Greece

A total of 210 food samples originating from milk products, ready-to-eat salads, raw meat and raw meat products purchased in ten open-air market places in Thessaloniki, Greece, were analyzed for the presence of Listeria monocytogenes. Thirty (14.3%) contained L. monocytogenes with the highest prevalence in raw meat (27.5%), raw meat products (18%) and cheese (8%). The strains were susceptible to 16 antimicrobials as determined by microbroth dilution, except one strain which displayed resistance to tetracycline (MIC > 32 μg/ml). This strain carried the tetracycline resistance gene tet(M). Pulsed-field gel electrophoresis (PFGE) revealed a low genetic diversity among the isolates, irrespective of their origin. This suggests that dominant L. monocytogenes clones are widespread in different food product types in open-air food markets in Greece. The high prevalence of L. monocytogenes in these products indicates that appropriate hygienic measures and periodic bacteriological controls are also necessary in open-air food markets to reduce contamination with food-borne pathogens. Greek specialties made with raw meat and raw milk may contain L. monocytogenes and should not be consumed by persons at risk.

Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]

Tef Eragrostis tef (Zucc.) Trotter is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n=4x=40), belongs to the Family Poaceae and, together with finger millet (Eleusine coracana Gaertn), to the Subfamily Chloridoideae. It was believed to have originated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

Genetic diversity of bovine Neospora caninum determined by microsatellite markers

Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed.

People, protected areas and ecosystem services: a qualitative and quantitative analysis of local people's perception and preferences in Côte d'Ivoire

The long-term integrity of protected areas (PAs), and hence the maintenance of related ecosystem services (ES), are dependent on the support of local people. In the present study, local people's perceptions of ecosystem services from PAs and factors that govern local preferences for PAs are assessed. Fourteen study villages were randomly selected from three different protected forest areas and one control site along the southern coast of Côte d'Ivoire. Data was collected through a mixed-method approach, including qualitative semi-structured interviews and a household survey based on hypothetical choice scenarios. Local people's perceptions of ecosystem service provision was decrypted through qualitative content analysis, while the relation between people's preferences and potential factors that affect preferences were analyzed through multinomial models. This study shows that rural villagers do perceive a number of different ecosystem services as benefits from PAs in Côte d'Ivoire. The results based on quantitative data also suggest that local preferences for PAs and related ecosystem services are driven by PAs' management rules, age, and people's dependence on natural resources.

Long distance dispersal shaped patterns of human genetic diversity in Eurasia

Most previous attempts at reconstructing the past history of human populations did not explicitly take geography into account, or considered very simple scenarios of migration and ignored environmental information. However, it is likely that the Last Glacial Maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite dataset genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion, or to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM-contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

Genetic composition, genetic diversity, and small-scale environmental variation matter for the experimental reintroduction of a rare plant

Aims Reintroduction has become an important tool for the management of endangered plant species. We tested the little-explored effects of small-scale environmental variation, genotypic composition (i.e. identity of genotypes), and genotypic diversity on the population survival of the regionally rare clonal plant Ranunculus reptans. For this species of periodically inundated lakeshores genetic differentiation had been reported between populations and between short-flooded and long-flooded microsites within populations.Methods We established 306 experimental test populations at a previously unoccupied lake shore, comprising either monocultures of 32 genotypes, mixtures of genotypes within populations or mixtures of genotypes between populations. In 2000, three years after planting out at the experimental site, a long-lasting flood caused the death of half of the experimental populations. In 2003, an extreme drought resulted in the lowest summer water levels ever measured.Important findings Despite these climatic extremes, 27 of the established populations survived until the end of the experiment in December 2003. The success of experimental populations largely differed between microsites. Moreover, the success of genotype monocultures depended on genotype and source population. Genetic differentiation between microsites played a minor role for the success of reintroduction. After the flood, populations planted with genotypes from different source populations increased in abundance, whereas populations with genotypes from single source populations and genotype monocultures decreased. We conclude that sources for reintroductions need to be selected carefully. Moreover, mixtures of plants from different populations appear to be the best choice for successful reintroduction, at least in unpredictably varying environments.