Effects of site and species characteristics on nested patterns of species composition in sedge meadows

Biotas of both geographical islands and habitat islands are often nested subsets of the biotas of successively more species-rich islands within the same system. The life history characteristics of a species may determine how that species contributes to the general pattern of species nestedness. Here, I investigate the floras of 56 sedge meadow wetlands in northern Illinois (USA) in order to characterize the degree of nestedness in these communities, determine which individual plant species contribute to the nested pattern, and investigate species characteristics that might be related to nonrandom patterns of distribution in individual plant species. The entire assemblage of species at all sedge meadows was significantly nested. Species richness and area were significantly correlated, and the nested pattern was closely related to site area, suggesting that species drop out of the assemblage in a predictable order as site area decreases. Some individual species exhibited nonrandom distributions across the sites, occurring more often in large, species-rich sites. Large sites were more likely than smaller sites to contain conservative species, i.e., those typical of pristine natural habitat, whereas nonconservative species were distributed more randomly among sites. Nested patterns of distribution of conservative species with respect to site area may result from their high probability of extinction on small sites or from a tendency for required habitats to co-occur on the same large sites. This revised version was published online in June 2006 with corrections to the Cover Date.     

CLADES: A classification‐based machine learning method for species delimitation from population genetic data

Species are considered to be the basic unit of ecological and evolutionary studies. As multilocus genomic data are increasingly available, there have been considerable interests in the use of DNA sequence data to delimit species. In this study, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes. Each pair of known populations is combined to form training samples with a label of “same species” or “different species”. We use support vector machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: “same species” or “different species”. Given multilocus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, for example with short species divergence time and gene flow.     

Assessing the diversity and distribution of Cephalothrix species (Nemertea: Palaeonemertea) in European waters by comparing different species delimitation methods

Soft‐bodied marine taxa, like ribbon worms (Nemertea), often lack clear diagnostic morphological characters impeding traditional species delimitation. Therefore, recent studies concentrated on molecular genetic methods to solve taxonomic issues. Different delimitation methods were employed to explore species boundaries and the presence of cryptic species. However, the performance of the different delimitation methods needs to be tested. A particularly promising nemertean genus in this regard is the palaeonemertean genus Cephalothrix that is commonly found in European waters. In order to gain information on the number and distribution of European cephalotrichids and to test different tree‐based and non‐tree‐based delimitation methods, we analyzed a dataset comprising the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) of 215 European Cephalothrix specimens, of which 78 were collected for this study. Our results show the presence of 12–13 European lineages of which several can be assigned to known European species. Analyzing a second dataset comprising 74 additional sequences from the Pacific and the Atlantic Oceans helped identify some of the unassigned European specimens. One resulting clade seems to represent a non‐native introduced Cephalothrix species, while another has never been recorded from Europe before. In our analysis, especially the tree‐based methods and the phylogenetic analysis proved to be a useful tool when delimiting species. It remains unclear whether the different identified clades result from cryptic speciation or from a high genetic variability of the COI gene.     

Kamala tree as an indicator of the presence of Asian elephants during the dry season in the Shivalik landscape of northwestern India

The availability of forage resources during the dry season is often a critical factor in determining the distribution and movement of large herbivores. It has long been suspected that the Kamala tree (Mallotus philippinensis) can serve as an indicator of the distribution for Asian elephants during the dry season in northwestern India. However, there is little direct evidence in support of this speculation, especially at a large landscape scale. Here, we predicted the distribution of Kamala trees in the Shivalik landscape of northwestern India based on topographic and bioclimatic variables, as well as satellite-derived vegetation indices and forest canopy height data using a presence-only ecological niche model. We used the area under the receiver operating characteristic curve (AUC) and true skill statistic (TSS) to validate the model. We then examined the relationship between the occurrence probability of Kamala trees and the presence of Asian elephants with data collected during dry seasons between 2010 and 2014 using logistic regression models. Our results showed that the probability of occurrence of Kamala trees was predicted with good accuracy (AUC = 0.88 and TSS = 0.51). The logistic regression models showed that the presence of Asian elephants can be adequately predicted by the occurrence probability of Kamala trees. This result suggests that the distribution of Kamala trees is a good indicator of the presence of Asian elephants during the dry season in the Shivalik landscape. These findings may have major implications for the conservation of Asian elephants, especially in designing wildlife corridors and mitigating human-elephant conflicts.     

International Biodiversity Observation Year in Western-Pacific and Asian regions (DIWPA-IBOY): a case report on species rarity and spatio-temporal variability of species composition in Lepidoptera and Coleoptera communities from a temperate forest of northern Japan

An international project, DIWPA-IBOY, took place for simultaneously observing biodiversity throughout the Western-Pacific and Asian regions in 2001–2003, as one of the core projects for International Biodiversity Observation Year, a crosscutting network activity of DIVERSITAS (an international programme of biodiversity science). DIWPA-IBOY provides extensive data on species diversity obtained by the standardized method. Under this project, 51,742 individuals of Lepidoptera and 11,633 of Coleoptera were collected by light traps from the Tomakomai Experimental Forest of Hokkaido University, one of the core DIWPA-IBOY sites, in the cool-temperate region of northern Japan. Based on these data, this study examined the relative abundance distribution (RAD) to evaluate the amount of rare species in the Lepidoptera and Coleoptera communities. The beta diversities between sampling seasons, forest strata, and trap sites were also assessed to evaluate the spatio-temporal variability of species composition in these communities. In the analysis of the RAD, the best-fit model was selected from the log-Normal, Zipf–Mandelbrot, and Zipf models differing in the tail length of the RAD, i.e., the proportion of rare species. To explore the beta diversity between samples, the abundance-based Jaccard index with an unseen species estimator was calculated, and then a hierarchical clustering analysis was conducted. As a result of RAD analysis, the Coleoptera community was regarded as containing a larger proportion of rare species than the Lepidoptera community. The seasonal compartmentalization of the community, deduced from the beta-diversity analysis, was finer in Lepidoptera (seven assemblages recognized) than in Coleoptera (three assemblages). The spatial (vertical and horizontal) compartmentalization was negligible in both communities. The coincidence of the larger proportion of rare species and the lower beta diversity between seasons in the Coleoptera community was explained by the longer life spans of beetles compared to moths, based on the assumption that the length of life span acts as a temporal agent for mass effect on the analogy of the migration rate as a spatial agent for mass effect.     

Assessing the conservation potential of fish and corals in aquariums globally

Aquatic ecosystems are indispensable for life on earth and yet despite their essential function and service roles, marine and freshwater biomes are facing unprecedented threats from both traditional and emerging anthropogenic stressors. The resultant species and ecosystem-level threat severity requires an urgent response from the conservation community. With their care facilities, veterinary and conservation breeding expertise, reintroduction and restoration, and public communication reach, stand-alone aquariums and zoos holding aquatic taxa have great collective potential to help address the current biodiversity crisis, which is now greater in freshwater than land habitats. However, uncertainty regarding the number of species kept in such facilities hinders assessment of their conservation value. Here we analyzed, standardized and shared data of zoological institution members of Species360, for fish and Anthozoa species (i.e. Actinopterygii, Elasmobranchii, Holocephali, Myxini, Sarcopterygii and Anthozoa). To assess the conservation potential of populations held in these institutions, we cross-referenced the Species360 records with the following conservation schemes: the Convention on the International Trade of Endangered Species of Fauna and Flora (CITES), the IUCN Red List of Threatened species, climate change vulnerability, Evolutionary Distinct and Globally Endangered (EDGE) and The Alliance for Zero Extinction (AZE). We found that aquariums hold four of the six fish species listed by the IUCN Red List as ‘Extinct in the Wild’, 31% of Anthozoa species listed by Foden et al. (2013) as vulnerable to climate change, 19 out of the 111 Anthozoa EDGE species, and none of the species prioritized by the AZE. However, it is very likely that significant additional species of high conservation value are held in aquariums that do not manage their records in standardized, sharable platforms such as Species360. Our study highlights both the great value of aquarium and zoo collections for addressing the aquatic biodiversity crisis, as well as the importance that they maintain comprehensive, standardised, globally-shared taxonomic data.     

Audio Visual Reviews

Slides/Strips,Sewage treatment and disposal, A slide pack of 40 full-frame slides and teacher's booklet in a plastic slide wallet with optional stiff binder. Compiled by Robert Gray, Director of Cleansing and Environmental Health Officer, Borough of Airdrie. Price £11.00 (plus 75p for binder). Ref. 319. Produced and distributed by Focal Point Audio Visual Ltd, 251 Copnor Road, Portsmouth, Hants P03 5EE; B. J. Purvis

Slides/Strips,Life cycle of the locust, Set of 20 35 mm colour slides, cardmounted, presented in a plastic wallet and a stiff binder, with teaching notes by Sr M. Daniel IBVM. Price £7.00. Ref 366. Available from Focal Point Audio Visual Ltd, 251 Copnor Road, Portsmouth, Hants P03 5EE; I. Fforde

Slides/Strips,A world of its own—a meadow in midsummer, Afilmstrip of 50 full-frame colour transparencies with card mounts, and leaching notes. Compiled by Sr M. Daniel, IBVM. Price £7.27. Ref. 178. Available from Focal Point Audio Visual Ltd, 251 Copnor Road, Portsmouth, Hants P03 5EE; B. J. Purvis

Slides/Strips,Living world around us, Two filmstrips in this series, each of 36 frames, in colour, in full- or half-frame format.; A. J. Williams

Slides/Strips,Exploring a field.. Photography and notes by Joan M. Clayton. Price £4.50. Ref. JC107; A. J. Williams

Slides/Strips,Exploring a garden Photography and notes by Leslie Jackman. Price £4.50. Ref. JC131. Available from Hugh Baddeley Productions, Educational Distribution Centre, 8 Brampton Road, St Albans, Herts AL1 4PW; A. J. Williams

Multi-Media,Youth and exploration, Five audiovisual packs, each containing over 30 mounted colour slides, audio cassette, commentary notes, and background information. Published as a collaborative venture by the Royal Geographical Society and BP Educational Service. Available from BP Educational Service, PO Box 5, Wetherby, West Yorkshire LS23 7EH. Price £7.50 each (available as filmstrip and notes without packaging or cassette at £1.90); Anne Heaton

Tapes,Human genetics, A one-hour taped discussion between Michael Carter of Portsmouth Polytechnic and Professor Bryan Clarke, Senior Research Fellow at Nottingham University, together with a booklet containing summaries of the discussions, a bibliography, and questions for students. Part of series ‘Sussex Tapes’ obtainable from Sussex Publications Ltd, Freepost, Poulshot, Devizes, Wilts SNIO 1BR. Reference SC3. Price £8.50 (cassette or reel); Diana Manuel

Games,The pollution game, Board game for four or five players. Price £17.41. Ref. ZRA-950-Q. Available from Griffin and George, Gerrard Biological Centre, Worthing Road, East Preston, West Sussex BN16 IAS. (Produced and distributed in the USA by Carolina Biological Supply Company, 2700 York Road, Burlington, North Carolina; ref. 44-3436); Colin Wood-Robinson

Games,Predator—the food chain game, Card game for up to 40 players. Price £5.90. Ref. ZRA-940-A. Available from Griffin and George Ltd, Gerrard Biological Centre, Worthing Road, East Preston, West Sussex BN16 IAS. (Distributed in the USA by Carolina Biological Supply Company, 2700 York Road, Burlington, North Carolina; ref 44-3425); Colin Wood-Robinson

Games,SOS—sink or swim, A card game for up to six players. Price £1.35. Produced by Dinosaur Publications for the National Trust. Obtainable from National Trust shops; P. Burdett