Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data

Background  

The association-rules discovery (ARD) technique has yet to be applied to gene-expression data analysis. Even in the absence of previous biological knowledge, it should identify sets of genes whose expression is correlated. The first association-rule miners appeared six years ago and proved efficient at dealing with sparse and weakly correlated data. A huge international research effort has led to new algorithms for tackling difficult contexts and these are particularly suited to analysis of large gene-expression matrices. To validate the ARD technique we have applied it to freely available human serial analysis of gene expression (SAGE) data.     

The socio-economic importance of wild vegetable resources and their conservation: a case study from China

In the Xiangxi region of western Hunan province, China, 335 taxa belonging to 87 families and 119 genera are utilised as wild vegetables. In order to take advantage of this naturally occurring resource we examined the horticultural and the associated socio-economic aspects of these taxa. Wild vegetables, as the mainstay of human diet and Chinese traditional medicines, have played an important role in the daily life and income of local ethnic groups for centuries. We examine candidate species for their prevalence and their potential to offer returns, for example in cereal production and tourism, and indicate horticultural management and processing technologies which may exploit wild vegetable availability.     

The importance of defining the geographic distribution of species for conservation: The case of the Bearded Wood-Partridge

Delimitation of the distribution areas of species has fundamental implications for the understanding of biodiversity and for decision-making in conservation. This is illustrated by the case of the Bearded Wood-Partridge (Dendrortyx barbatus), which is endemic to Mexico and was classified as threatened by the IUCN. Recently the discovery of this species in new locations caused an increase in the known distribution area whereupon it was reclassified in a lower risk category. In our study, delimitation and comparison of the Bearded Wood-Partridge distribution area is carried out utilising five different methods: minimum convex polygon; areographic; cartographic; ecological niche modeling; and, “free hand”. A number of locality records are also used to demonstrate the chronological order of appearance. The results show that the size and shape of the distribution area of this species vary depending on the number of records and on their spatial and environmental location, as well as on the particular delimitation method used. However, ecological niche modeling provides the best results in terms of spatial and numerical sensitivity as well as lower values of omission and a moderate extent of predicted areas. We suggest that decisions related to species conservation (categories of risk, areas of endemism, etc.), particularly those species of high geographical restriction, should be contingent on the formalised delimitation of distribution areas based on ecological niche modeling methods.     

Awareness of a conservation unit: a Brazilian case study

The range of uses of a conservation area by a nearby population was quantified by questionnaires applied to residents of Santa Helena county, Brazil. Of the 312 responses compiled, 71.2% of the residents acknowledged the presence of a conservation unit within the county limits while only 59.3% of the respondents had participated in some recreational or leisure outdoor activity within the unit. Activities cited by respondents included games (11.7%), beach visits (11.4%), cross-country walks (9.4%), and fishing (8.3%). A possible visitor fee to improve infrastructure within the area was approved by 64.9% of the interviewees. Suggested visitor fee varied from 50 cents to two dollars.     

Genomics for conservation: a case study of behavioral genes in the Tasmanian devil

The increased availability of genomic resources for many species has expanded perspectives on problems in conservation by helping to design management strategies for threatened species. Tasmanian devils (Sarcophilus harrisii) are an iconic and endangered marsupial with an intensively managed breeding program aimed at preventing extinction in the wild caused by devil facial tumour disease. Between 2015 and 2017, 85 devils from this program were released to three sites in Tasmania to support wild populations. Of these, 26 were known to have been killed by vehicles shortly after release. A previous analysis indicated that increased generations in captivity was a positive predictor of vehicle strike, with possible behavioural change hypothesised. Here we use 39 resequenced devil genomes to characterise diversity at 35 behaviour-associated genes, which contained 826 single nucleotide polymorphisms (24 were non-synonymous). We tested for a predictor of survival by examining three genes (AVPR1B, OXT and SLC6A4) in 62 released devils with known fates (survived, N?=?39; died, N?=?23), and genome-wide associations via reduced-representation sequencing (1727 single nucleotide polymorphisms [SNPs]), in 55 devils with known fates (survived, N?=?38; died, N?=?17). Overall, there was little evidence of an association between genetic profile and probability of being struck by a vehicle. Despite previous evidence of low genetic diversity in devils, the 35 behaviour-associated genes contained variation that may influence their functions. Our dataset can be used for future research into devil behavioural ecology, and adds to the increasing body of research applying genomics to conservation problems.

     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.     

The importance of urban reserves for conserving beetle communities: a case study from New Zealand

Urban reserves provide a major opportunity for conservation of indigenous biodiversity in the heavily urbanised landscape of Waitakere City (Auckland), New Zealand. However, there is little documented information on what indigenous fauna survives in these reserves. Beetle (Coleoptera) communities associated with two small, isolated urban reserves and two sites in a larger forest area within the Waitakere Ranges were sampled using pitfall traps and analysed. A total of 887 beetles, from 23 families and 89 recognisable taxonomic units were caught. The urban reserves had a marked reduction in species richness and abundance of beetles compared with the sites within the larger forest areas. Various environmental factors influencing the distribution of beetles across the sites were investigated. The most important factors were size of fragment, local forest cover and soil moisture. Common species (>5 specimens in the total dataset) found in the Waitakere Ranges and small urban reserves, were either endemic or indigenous to New Zealand. Therefore, even though these reserves may be isolated from a larger, more continuous forest tract, they have considerable potential as reservoirs of beetle diversity in highly modified landscapes and the contribution of urban reserves to the local sustainability of beetle assemblages emphasises the importance of maintaining green areas in and around cities.     

The importance of disturbance for the conservation of a low-competitive herb in mesotrophic grasslands

For the protection or re-establishment of species-rich grasslands, the limiting factors controlling species richness have increasingly become of scientific interest. This study aims to analyze the role of disturbance for the occurrence of a low-competitive herb, Centaurium erythraea Rafn, in mesotrophic, lowland grasslands in NW Germany. We sampled a total of 38 plots with presence of C. erythraea and 24 control (random) plots in semi-natural grasslands. As a proxy for disturbance, we estimated the cover of bare ground and Ellenberg flooding indicator species and measured the distance between the plot and the nearest path. Moreover, we counted the number of C. erythraea individuals within each plot. In the GLM analyses the distance from path was the only predictor; both the presence of the species and the number of individuals decreased with the distance from path. The grasslands at the path edges had the highest disturbance intensity. Here horse riding, military-vehicle traffic and regular sod-cutting directly create bare ground. In general, disturbance creating bare ground seems to be the key factor enabling germination and growth of C. erythraea in mesotrophic grasslands and other low-competitive short-lived species. Disturbance enhances the expression of the seed bank, favours the development of the shade-avoiding and low-growing rosettes and oppresses tall-growing competitors. Therefore we suggest grazing as the best management method.     

The effectiveness of botanic garden collections in supporting plant conservation: a European case study

Europe has the greatest concentration of botanic gardens in the world, they cultivate extensive collections of plants that include samples of European threatened plant species. This study looks at the effectiveness of these collections in supporting species conservation. A three part study is presented: (1) the results of a survey and assessment of threatened plants in botanic gardens, as defined by the Bern Convention; (2) case studies illustrating current issues in the ex situ management of European threatened plant species; and (3) presentation of policy recommendations on further improving botanic garden contributions to European plant conservation. The survey indicated that of 119 European botanic gardens in 29 European countries, 105 are cultivating 308 of the 573 threatened plant species listed by the Bern Convention. The survey identified 25 botanic gardens in 14 countries undertaking 51 conservation projects focused on 27 Bern listed species. In particular this survey has established that the majority of taxa are held in a small number of collections, dominated by non-wild origin accessions, and are not adequately documented. The majority of specimens in botanic gardens are cultivated out of the range country and not contributing to a specific conservation project. We review the genetic representation and documentation of origin in collections. Existing plant collections contain representatives of populations, now lost in the wild and maintain samples of at least nine European plant taxa identified as 'Extinct in the Wild'. However, inadequate standards of record keeping has compromised the conservation value of many collections. We highlight the dangers of hybridisation and disease in ex situ collections. The results suggest that botanic garden collections are skewed towards horticulturally robust and ornamental species and do not fully reflect priorities as defined by the Bern Convention. Recognising the limitations of traditional botanic garden collections we propose that botanic gardens more effectively utilise their two core competencies, namely scientific horticulture and public display and interpretation. The unique horticultural skills resident in European botanic gardens could be more effectively utilised through the application of horticulture to the management of wild populations.Journal of the Royal Horticultural Society     

The utility of repeated presence data as a surrogate for counts: a case study using butterflies

Abundance data are widely used to monitor long-term population trends for management and conservation of species of interest. Programs that collect count data are often prohibitively expensive and time intensive, limiting the number of species that can be simultaneously monitored. Presence data, on the other hand, can often be collected in less time and for multiple species simultaneously. We investigate the relationship of counts to presence using 49 butterfly species across 4 sites over 9 years, and then compare trends produced from each index. We also employed simulated datasets to test the effect of reduced sampling on the relationship of counts to presence data and to investigate changes in each index’s power to reveal population trends. Presence and counts were highly correlated for most species tested, and population trends based on each index were concordant for most species. The effect of reduced sampling was species-specific, but on a whole, sensitivity of both indices to detect population trends was reduced. Common and rare species, as well as those with a range of life-history and behavioral traits performed equally well. The relationship between presence and count data may break down in cases of very abundant and widespread species with extended flight seasons. Our results suggest that when used cautiously, presence data has the potential to be used as a surrogate for counts. Collection of presence data may be useful for multi-species monitoring or to reduce the duration of monitoring visits without fully sacrificing the ability to infer population trends.