Systematics,the scientific basis for inventories of biodiversity

A taxonomic inventory strategy is proposed for the planetary exploration of biological diversity. Such inventories result in comprehensive collections, our only insurance against bio-ignorance; meet needs for basic taxonomic and phylogenetic research; make full use of limited taxonomic resources; and provide credible, verifiable data associated with museum and herbarium specimens. Decisive efforts to meet the biodiversity crisis need not compromise advances in taxonomic theory and practice in the interest of expediency. Inventories provide data for understanding the origin and history of diversification of life on Earth, while gathering scientific evidence to inform decisions related to conservation and resource management.     

National forest inventories and biodiversity monitoring in Australia

Abstract

Forests currently cover over 20% of the Australian continent and are an important resource, subject to a wide range of economic and environmental pressures. These lands support substantial numbers of forest-dependent species with national forest inventories providing important information on biodiversity. National scale information on these forests has been collected or collated since 1988 under the National Forest Inventory (NFI) programme, but substantial problems with the ‘snap shot’ approach have been recognized, particularly with respect to monitoring change and a consequent move towards a permanent and sample-based continental forest monitoring framework (CFMF) has been proposed. CFMF is proposed to consist of three Tiers: (1) satellite imagery of the continent to identify forest and change in forest cover; (2) systematic high-resolution remotely sensed data and (3) permanent ground points at 20×20 km grid interception points. The CFMF approach is in line with the international trend of national forest inventories in developed countries although the Tier 2 approach offers a useful extension. An alternative inventory approach is provided by the National Carbon Accounting System (NCAS) which models the mass of carbon and nitrogen in seven separate living and dead biomass pools for any point under forest or agriculture land use since 1970. The NCAS approach allows fine spatial and temporal monitoring of changes in these carbon and nitrogen biomass pools, and predictions of changes that result from policy or management decisions. This paper briefly reviews NFI, NCAS and the proposed CFMF, with particular emphasis on issues of use and potential for monitoring biodiversity in this biologically very diverse country.     

Use of extensive habitat inventories in biodiversity studies

Large monitoring programs exist in many countries and are necessary to assess present and past biodiversity status and to evaluate the consequences of habitat degradation or destruction. Using such an extensive data set of the floristic richness in the Paris Ile-de-France region (France), we compared different sampling efforts and protocols in different habitat units to highlight the best methods for assessing the actual plant biodiversity. Our results indicate that existing data can be used for a general understanding of site differences, but analysts should be aware of the limitations of the data due to non-random selection of sites, inconsistent observer knowledge, and inconsistent sampling period. The average species diversity recorded in a specific habitat does not necessarily reflect its actual diversity, unless the monitoring effort was very strong. Overall, increasing the sampling effort in a given region allows improvement of the (1) number of habitats visited, (2) the total sampled area for a given habitat type, (3) the number of seasons investigated. Our results indicate that the sampling effort should be planned with respect to these functional, spatial and temporal heterogeneities, and to the question examined. While the effort should be applied to as many habitats as possible for the purpose of capturing a large proportion of regional diversity, or comparing different regions, inventories should be conducted in different seasons for the purpose of comparing species richness in different habitats.     

Awareness and use of biodiversity collections by fish biologists

A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.     

Linking land use inventories to biodiversity impact assessment methods

The International Journal of Life Cycle Assessment - There is generally a mismatch in the land use classification of life cycle inventory (LCI) databases and life cycle impact assessment (LCIA)...     

Sampling the rarest: threatened beetles in boreal forest biodiversity inventories

Presence or absence of threatened species in samples is information that is widely used in designing and implementing conservation actions. We explored the effectiveness of beetle (Coleoptera) inventories and contribution of different sampling methods in revealing occurrences of threatened and near threatened species in boreal forests. The number of species caught using traps in a particular area proved to be a useful indicator of the representativeness of data, the relationship between total number of species and the number of threatened and near threatened species being almost exponential. Samples containing less than 200 trapped species (or 2000 individuals) are almost useless in surveying threatened and near threatened species. The probability of finding such species increases considerably when the number of trapped species exceeds 400. Window traps attached directly on the trunks of dead trees proved to be the most efficient sampling method in trapping threatened beetles, whereas many other standard methods gave relatively poor results. We suggest that the best alternative in surveying threatened species in boreal forests is a combination of intensive direct searching and trunk window traps. Finding threatened beetles with rigorous probability requires very large sample sizes, even if the most effective sampling methods are used. For example, ranking 10 boreal forest areas to be protected according to the occurrence of threatened species with some reliability may require trapping of over 100000 beetle individuals. Collecting and identifying these large samples routinely in conservation actions is not feasible, which means that shortcuts (indicators etc.) are necessary. However, a lot of good-quality inventories with appropriate sampling efforts are needed before these shortcuts can be identified and elaborated. Such inventories are also crucial for the improvement of the classification of threatened species and full assessment on how past forest management has eventually affected the biota.     

Linking inventories and impact assessment models for addressing biodiversity impacts: mapping rules and challenges

The International Journal of Life Cycle Assessment - An adequate matching between the nomenclature of elementary flows in life cycle inventory (LCI) databases and life cycle impact assessment...     

A pervasive denigration of natural history misconstrues how biodiversity inventories and taxonomy underpin scientific knowledge

Embracing comparative biology, natural history encompasses those sciences that discover, decipher and classify unique (idiographic) details of landscapes, and extinct and extant biodiversity. Intrinsic to these multifarious roles in expanding and consolidating research and knowledge, natural history endows keystone support to the veracity of law-like (nomothetic) generalizations in science. What science knows about the natural world is governed by an inherent function of idiographic discovery; characteristic of natural history, this relationship is exemplified wherever an idiographic discovery overturns established wisdom. This nature of natural history explicates why inventories are of such epistemological importance. Unfortunately, a Denigration of Natural History weakens contemporary science from within. It expresses in the prevalent, pervasive failure to appreciate this pivotal role of idiographic research: a widespread disrespect for how natural history undergirds scientific knowledge. Symptoms of this Denigration of Natural History present in negative impacts on scientific research and knowledge. One symptom is the failure to appreciate and support the inventory and monitoring of biodiversity. Another resides in failures of scientiometrics to quantify how taxonomic publications sustain and improve knowledge. Their relevance in contemporary science characteristically persists and grows; so the temporal eminence of these idiographic publications extends over decades. This is because they propagate a succession of derived scientific statements, findings and/or conclusions - inherently shorter-lived, nomothetic publications. Widespread neglect of natural science collections is equally pernicious, allied with disregard for epistemological functions of specimens, whose preservation maintains the veracity of knowledge. Last, but not least, the decline in taxonomic expertise weakens research capacity; there are insufficient skills to study organismal diversity in all of its intricacies. Beyond weakening research capacities and outputs across comparative biology, this Denigration of Natural History impacts on the integrity of knowledge itself, undermining progress and pedagogy throughout science. Unprecedented advances in knowledge are set to follow on consummate inventories of biodiversity, including the protists. These opportunities challenge us to survey biodiversity representatively—detailing the natural history of species. Research strategies cannot continue to ignore arguments for such an unprecedented investment in idiographic natural history. Idiographic shortcuts to general (nomothetic) insights simply do not exist. The biodiversity sciences face a stark choice. No matter how charismatic its portrayed species, an incomplete ‘Brochure of Life’ cannot match the scientific integrity of the ‘Encyclopedia of Life’.     

Retrieving taxa names from large biodiversity data collections using a flexible matching workflow

In the domain of biological classification there are several taxon name matching services that can search for a species scientific name in a large collection of taxonomic names. Many of these services are available online, and many others run on computers of individual scientists. While these systems may work very well, most suffer from the fact that the list of names used as a reference, and the criteria to decide on a match, are hard-coded in the engine that performs the name matching. In this paper we present BiOnym, a taxon name matching system that separates reference namelists, search criteria and matching engine. The user is offered a choice of several taxonomic reference lists, including the option to upload his/her own list onto the system. Furthermore, BiOnym is a flexible workflow, which embeds and combines techniques using lexical matching algorithms as well as expert knowledge. It is also an open platform allowing developers to contribute with new techniques. In this paper we demonstrate the benefits brought by this approach in terms of the efficiency and effectiveness of the information retrieval process with respect to other solutions.     

The types ofScelionidae [Hymenoptera: Proctotrupoidea] in some Italian collections (Museums of Genoa and Florence,Institute of Portici)

A large number ofScelionidae have been described byKieffer who, unfortunately, did not keep a private collection so that the types of his species are scattered and often not recognized in many museums. This contribution gives information on the types of species described byKieffer, besides a few other authors, on material collected by Italian entomologists. The finding and the study of old species is fundamental to subsequent revisions and reliable identifications, mostly in this group ofParasitica in which so often new species of economic importance are described.

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Résumé Ce travail est consacré aux types deScelionidae de quelques collections italiennes parmi lesquelles on a trouvé 60 holotypes: 50 dans le Museum civil d'histoire naturelle de Gênes, 6 dans le Musée zoologique La Specola de Florence et 4 à l'Institut d'entomologieF. Silvestri à Portici. Il y a 51 espèces décrites parKieffer, 5 parFouts et 1 parMasi, Rondani, Sarra etSilvestri, respectivement. Ces espèces proviennent de plusieurs régions et en particulier de la Méditerranée. On donne en outre des informations sur des espèces non types, intéressantes au point de vue taxonomie.

     

Museum collections, species distributions, and rarefaction

Biological specimens in museums and herbaria are sometimes used to compare the geographical distribution of different species. In doing so, it is necessary to account for differences in the numbers of specimens. We show how rarefaction can be used for this purpose. Rarefaction is a simple mathematical method originally designed to compare species richness in communities that differed in the number of sampled individuals. We present an example involving two Phragmipedium orchid species. In this case, rarefaction suggests that the apparent difference in range can be explained by the difference in the numbers of specimens.     

居群、物种与生物多样性

正受《生物多样性》主编之邀,我对洪德元先生(2016)的"生物多样性事业需要科学、可操作的物种概念"一文谈一点体会。鉴于在学术声望上我只能望洪先生之项背以及"可操作性的物种概念"之复杂性,我后悔轻率答应了撰文。但为了引起我国植物分类与系统植物学界关注这一重要问题的讨论,我不得不勉为其难。1三个目的我理解,洪先生撰写此文有三个非常明确的目的:第一,他以熟知的芍药属(Paeonia)植物为例,指出科学认识物种是有效保护我国珍稀濒危物种     

Assessing biodiversity with species accumulation curves; inventories of small reptiles by pit‐trapping in Western Australia

Abstract We examined 11 non‐linear regression models to determine which of them best fitted curvilinear species accumulation curves based on pit‐trapping data for reptiles in a range of heterogeneous and homogenous sites in mesic, semi‐arid and arid regions of Western Australia. A well‐defined plateau in a species accumulation curve is required for any of the models accurately to estimate species richness. Two different measures of effort (pit‐trapping days and number of individuals caught) were used to determine if the measure of effort influenced the choice of the best model(s). We used species accumulation curves to predict species richness, determined the trapping effort required to catch a nominated percentage (e.g. 95%) of the predicted number of species in an area, and examined the relationship between species accumulation curves with diversity and rarity. Species richness, diversity and the proportion of rare species in a community influenced the shape of species accumulation curves. The Beta‐P model provided the best overall fit (highest r²) for heterogeneous and homogeneous sites. For heterogeneous sites, Hill, Rational, Clench, Exponential and Weibull models were the next best. For homogeneous habitats, Hill, Weibull and Chapman–Richards were the next best models. There was very little difference between Beta‐P and Hill models in fitting the data to accumulation curves, although the Hill model generally over‐estimated species richness. Most models worked equally well for both measures of trapping effort. Because the number of individuals caught was influenced by both pit‐trapping effort and the abundance of individuals, both measures of effort must be considered if species accumulation curves are to be used as a planning tool. Trapping effort to catch a nominated percentage of the total predicted species in homogeneous and heterogeneous habitats varied among sites, but even for only 75% of the predicted number of species it was generally much higher than the typical effort currently being used for terrestrial vertebrate fauna surveys in Australia. It was not possible to provide a general indication of the effort required to predict species richness for a site, or to capture a nominated proportion of species at a site, because species accumulation curves are heavily influenced by the characteristics of particular sites.     

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case. Digitization is an activity that museums and academic institutions increasingly recognize, though many still do not embrace, as a means to boost the impact of collections to research and society through improved access. The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health. This paper examines new opportunities to design and implement infrastructure that will support not just mass digitization efforts, but also a broad range of research on biological diversity and physical sciences in order to make scientific collections increasingly relevant to societal needs and interest.     

Destination Culture: Tourism, Museums, and Heritage

Destination Culture: Tourism, Museums, and Heritage. Barbara Kirshenblatt-Gimblett. Berkeley: University of California Press. 1998.xviii. 326pp.