Emerging semantics to link phenotype and environment

Metagenomics and biological ontology

Simple or complex: Relative impact of data availability and model purpose on the choice of model types for population viability analyses

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 17:169-178 (2012) - DOI: https://doi.org/10.3354/esr00414 Theme Section: Endangered river fish: threats and conservation options Conservation biology and management of the endangered Oxleyan pygmy perch Nannoperca oxleyana in Australia James T. Knight1,*, Angela H. Arthington2, Gabrielle S. Holder1, R. Bill Talbot1 1NSW Department of Trade and Investment, Regional Infrastructure and Services, Port Stephens Fisheries Institute, Nelson Bay, New South Wales 2315, Australia 2Australian Rivers Institute and DIVERSITAS, Griffith University, Nathan, Queensland 4111, Australia *Email: james.knight@industry.nsw.gov.au ABSTRACT: The global biodiversity crisis particularly affects freshwater fishes. Currently, 20% of Australia’s highly endemic freshwater fishes are formally recognised as being of conservation concern under national, state and territory listings. Four of the 5 described species of Nannoperca (Percichthyidae) are threatened with extinction, with N. oxleyana Whitley listed as endangered under Australian legislation and internationally by the IUCN. National recovery planning has commenced with the objective of returning this species to a position of ‘viability in nature’ in New South Wales (NSW) and Queensland. This paper describes the conservation biology of N. oxleyana, providing a case history for a small species of no commercial importance threatened by the classical triumvirate of habitat degradation and loss; small, declining and fluctuating populations driven more by environmental conditions than demographic forces; and the effects of introduced species. A process for declaring critical habitat for N. oxleyana has commenced in NSW. Habitat protection involves managing threats, including run-off originating from unsealed roads, herbicide use, fire management activities and disturbance by recreational users such as 4-wheel drivers and campers. Information on the distribution and breeding patterns of N. oxleyana has been provided to local and state government authorities to assist in managing drainage and development schemes that might impact N. oxleyana habitat. Monitoring has confirmed the persistence of many N. oxleyana populations in both jurisdictions. KEY WORDS: Endangered fishes · Conservation biology · Threat analysis · Recovery planning Full text in pdf format PreviousNextCite this article as: Knight JT, Arthington AH, Holder GS, Talbot RB (2012) Conservation biology and management of the endangered Oxleyan pygmy perch Nannoperca oxleyana in Australia. Endang Species Res 17:169-178. https://doi.org/10.3354/esr00414 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 17, No. 2. Online publication date: May 23, 2012 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2012 Inter-Research.

Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast.Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species.Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/).Contact:mah79@cam.ac.uk or vw253@cam.ac.uk

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

Summary Animal ecology could benefit from a well‐defined trait‐based framework, mostly applied in plant ecology, to further develop predictions of animal communities under various environmental conditions. We extended the functional approach to a multitrophic system by combining plant and ant traits in relation to environmental conditions to study the relationships between these three components. We sampled plant and ant abundances along an aridity gradient in grazed and ungrazed conditions in the arid steppes of eastern Morocco. We measured five plant functional traits related to water stress and grazing resistance and six ant functional traits related to body size, dispersal and behaviour. We related each component (environment, vegetation and ants) using Mantel partial correlations to uncover the causal structure between components and using a fourth‐corner analysis to describe the effects of the environment and vegetation on ant communities. Results indicated that vegetation had a direct effect on ant community composition while the environment only had an indirect effect on ant community composition through vegetation structure. This result was consistent when looking at both the taxonomic and functional composition of communities, but correlations were stronger when based on taxonomic composition. Aridity was the variable most significantly linked with ant functional traits Synthesis. The use of functional traits in animal ecology is relatively new, and an increase in trait‐based community ecology studies that include more than one trophic level would be beneficial in identifying trait‐based patterns in multitrophic communities. This new approach could become very useful in identifying mechanistic explanations of multitrophic community assembly and making predictions about their evolution under changing environmental conditions. It could also be of practical use in conservation biology in assessing habitat quality.

Since their excavation, a number of the sites listed as part of “The Megalithic Temples of Malta” inscription on the UNESCO World Heritage list have been afflicted by material and structural problems, including collapses. Therefore, three of these sites, the Ħaġar Qim, Mnajdra and Tarxien Temples, were protected by open-sided shelters, to address some of the principal causes of deterioration (e.g. direct rainfall, surface weathering, thermal stress). Environmental monitoring, condition assessments and biological surveys of the three sites took place before and after sheltering and are still in progress. To understand how the shelters are affecting these structures, a research programme has started aimed at analysing, through Computational Fluid Dynamics (CFD), the environmental data collected over a period of more than ten years. The aim of using CFD on the Temples is to provide detailed information on how different environmental conditions can affect the sites. For the CFD, macro and meso scale approaches will be used. The macroscale model represents the regional environment, including the all-terrain features around the Temples. Mesoscale modelling represents the Temple structures in a more detailed way. The final goal is to find confident correlations between CFD, and representative areas selected within the Temples showing particular deterioration patterns. All this information will be integrated with the results of in situ analyses to identify the causes of material deterioration and possibly mitigate against them.

The global ex situ conservation system reflects the collective efforts of individual genebanks, each influenced by its unique history, opportunities for acquisition and user demands. As a result, acquisition activities in most genebanks have been opportunistic rather than strategic to support representation of national crop diversity or driven by clearly identified conservation priorities. The objective of this study was to characterize the composition of national collections in 20 countries within the global ex situ conservation system. It assessed the representation of crop genetic diversity that originated nationally within the global system and evaluated the composition balance, as it relates to duplication and gaps in conservation. Across these 20 countries, numerous genebanks are conserving large number of accessions for only a few genera, while a much smaller number of genebanks are conserving fewer than 10 accessions from a broader range of genera. The findings indicate that ex situ conservation, both nationally and globally, has significant potential duplications and gaps in the genetic resource coverage. Individual institutes in the global system must carefully reconsider the composition of their collections, especially given the significant costs and limited financial and human resources available for long-term ex situ conservation. As national genebanks and the global system become increasingly important resources for the future, it will be essential for genebanks to ensure that the composition of their collections meets future demands.

Genome-wide identification and characterization of the aquaporin gene family in Sorghum bicolor (L.)

Implementing a Common Data Model in Ophthalmology: Mapping Structured EHR Ophthalmic Exam Data to Standard Vocabularies

Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity.

How can you conserve species that haven't been found?

Biological condition and population structure of benthopelagic shrimps in the Galicia Bank (NE Atlantic): Intra- and interspecific patterns

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.

The use of species distribution models (SDMs) in paleoecology enhances its contribution to ecology and conservation biology, such as estimating climate change impacts and informing conservation efforts. Acipenser sturio and A. oxyrinchus are closely related sturgeon species currently arranged in two disjunct distributions across the Atlantic Ocean. However, paleogenetic findings highlighted that both species were present in European waters over at least five millennia. Their joint European history during the Holocene period might have been driven by the thermal hypothesis, with A. oxyrinchus being a cooler-water species than A. sturio . Given their current poor state of conservation, quantifying their environmental preferences at a time when the two species were more abundant could help shape future conservation/restoration measures. Paleo-species distribution models were built for each species based on paleoclimate variables and archeozoological remains, most of which were genetically identified at the species level. Response curves for air temperature and precipitation were then applied to estimate relative continental paleohabitat suitability (HSI) in watersheds across four regions (i.e., the Baltic Sea, the Northern Seas, the South European Atlantic shelf, and the Mediterranean Sea) throughout the Holocene. The estimated niches confirmed the thermal sensitivity difference between the two species, with A. oxyrinchus having a narrower thermal range towards colder annual temperatures. Comparing HSI suitability between the two species, the four regions were globally all suitable for A. sturio but not for A. oxyrinchus , which showed much greater variability. Catchments with outlets to the Mediterranean Sea and the South European Atlantic shelf were mainly suitable for A. sturio . In contrast, those with an outlet in the Baltic Sea were slightly more suitable for A. oxyrinchus than for A. sturio . Catchments with outlets to the Northern Seas showed comparable suitability for both species. This superposition in near-past suitable habitats implied that the two species can potentially exist under the same environmental conditions and as such suggested future risks of biotic interactions which should be further acknowledged in potential stocking practices.