Towards resolving the complete fern tree of life

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.     

Towards an evolutionary ecology of life in soil

The soil-microbe system is one of the most diverse components of the terrestrial ecosystem. The origin of this diversity, and its relation to the life-sustaining processes that are mediated by the resident microbial community, is still poorly understood. The inherent complexities necessitate a theoretical framework that integrates ecological and evolutionary approaches and which embraces the physical heterogeneity of the soil environment. Such a framework is currently lacking, although recent advances in theory and experimentation are beginning to identify the essential ingredients. Here, we review and evaluate the relevance of current modelling approaches, and propose a new synthesis of an evolutionary ecology of life in soil. Key elements include an account of dispersal, horizontal gene transfer, and the consideration of the physical and biological components of soil as an integrated complex adaptive system.     

Towards writing the encyclopedia of life: an introduction to DNA barcoding

An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the 'Barcode of Life Initiative', to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g. cox1 = CO1, in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.     

An annotated list of the publications of Rupert C. Barneby

Rupert Barneby had 263 publications (two of which were published with two volumes each) during his career (including 56 book reviews), and additionally published new taxa and combinations in 16 publications by B. A. Krukoff, S. L. Welsh, and A. Lourteig. In total, these publications amount to 7676 pages. Each entry was examined, was dated as accurately as possible, and was annotated with any new nomenclauture presented in the publication. Barneby published 4 new subtribes within the legumes, 9 new genera of legumes (one based on a new combination) and 6 new genera of Menispermaceae, 621 new species (including 6 new nothospecies), 16 new subspecies, 355 new varieties, and 1 new form. Additionally, he published 238 new infrageneric taxa (subgenera, sections, or subsections). he made numerous new combinations (including nomina nova) at the infrageneric level (169), the species level (582), the subspecific level (27), and the varietal level (533), as well as a single combination at the form level.     

Towards building the tree of life: a simulation study for all angiosperm genera

Comprehensive phylogenetic trees are essential tools to better understand evolutionary processes. For many groups of organisms or projects aiming to build the Tree of Life, comprehensive phylogenetic analysis implies sampling hundreds to thousands of taxa. For the tree of all life this task rises to a highly conservative 13 million. Here, we assessed the performances of methods to reconstruct large trees using Monte Carlo simulations with parameters inferred from four large angiosperm DNA matrices, containing between 141 and 567 taxa. For each data set, parameters of the HKY85+G model were estimated and used to simulate 20 new matrices for sequence lengths from 100 to 10,000 base pairs. Maximum parsimony and neighbor joining were used to analyze each simulated matrix. In our simulations, accuracy was measured by counting the number of nodes in the model tree that were correctly inferred. The accuracy of the two methods increased very quickly with the addition of characters before reaching a plateau around 1000 nucleotides for any sizes of trees simulated. An increase in the number of taxa from 141 to 567 did not significantly decrease the accuracy of the methods used, despite the increase in the complexity of tree space. Moreover, the distribution of branch lengths rather than the rate of evolution was found to be the most important factor for accurately inferring these large trees. Finally, a tree containing 13,000 taxa was created to represent a hypothetical tree of all angiosperm genera and the efficiency of phylogenetic reconstructions was tested with simulated matrices containing an increasing number of nucleotides up to a maximum of 30,000. Even with such a large tree, our simulations suggested that simple heuristic searches were able to infer up to 80% of the nodes correctly.     

Towards a unified theory of cooperative breeding: the role of ecology and life history re-examined

We present quantitative models that unify several adaptive hypotheses for the evolution of cooperative breeding in a single framework: the ecological constraints hypothesis, the life-history hypothesis and the benefits-of-philopatry hypothesis. Our goal is to explain interspecific variation in the occurrence of cooperative breeding in terms of interspecific variation in life-history traits and ecological conditions. We analyse two models, according to whether or not helpers can inherit their parents' territory. Major results are (i) territory inheritance always promotes cooperative breeding; (ii) if territories are not inherited, neither ecological constraints nor variation in life-history traits predict interspecific variation in cooperative breeding; and (iii) if territories are inherited, the mechanism of density regulation is crucial in determining which factors promote cooperative breeding. If density dependence acts on the probability to obtain a free territory or on the survival of dispersers, variation in ecological constraints cannot explain variation in cooperative breeding. Lower adult mortality favours helping, not because it reduces the availability of free territories, but because it enhances the direct benefits of helpers. If density dependence acts on fecundity, lower probability of obtaining a free territory and lower survival of dispersers promote cooperative breeding. In this case, lower adult mortality works against the evolution of helping. We suggest that the difference between birds and social insects in the covariance between cooperative breeding and life-history traits is due to different mechanisms of density regulation that operate in these taxa, and we explain how natural selection on habitat choice might have caused these different mechanisms to operate.     

Towards social life cycle assessment of mobility services: systematic literature review and the way forward

Purpose

The main purpose of this review is to describe the state of the art of social impact assessment with a focus on mobility services. Whereas the use phase plays an important role for the assessment of services in general, the evaluation of the use phase has been underrepresented in previous social life cycle assessment studies. For that reason, particular attention has been paid to indicators, which allow the assessment of social impacts during the use phase of mobility services.

Methods

Continuous efforts to mitigate climate change and to improve quality of life in cities result in new mobility solutions based on collective use. This will have a huge impact on our society transforming the use of vehicles. In order to better understand the implications for cities, society and the automotive industry, it is essential to evaluate the social impact generated along a product life cycle with particular attention to the use phase. To reach the goal, a systematic literature review was carried out with a focus on social indicators that allow assessing use phase impacts of mobility services. The indicators were analysed and allocated to stakeholder groups. Based on the analysis, a core set of indicators is proposed under consideration of data availability.

Results and discussion

Based on the selected search strings, 51 publications were selected for the literature review, including 579 social indicators. The analysis revealed a wide variety and diversity of indicators that are trying to measure the same aspect. The allocation to the respective stakeholder groups showed that most of the indicators (36%) evaluate impacts regarding the stakeholder group local community. The majority of analysed indicators are of quantitative nature (63%). Nevertheless, a clear assessment method was often missing in the respective publications. Therefore, for the core set of indicators, an assessment method is proposed for every indicator.

Conclusions

The results from this study can help practitioners as well as researchers in the field of urban mobility assessment as it systematically analyses social sustainability aspects. The presented data gives an overview of various indicators that are suggested in other publications, and the proposed core set of indicators can be used to evaluate different mobility services in further research.

     

Towards harmonizing natural resources as an area of protection in life cycle impact assessment

Purpose

In this paper, we summarize the discussion and present the findings of an expert group effort under the umbrella of the United Nations Environment Programme (UNEP)/Society of Environmental Toxicology and Chemistry (SETAC) Life Cycle Initiative proposing natural resources as an Area of Protection (AoP) in Life Cycle Impact Assessment (LCIA).

Methods

As a first step, natural resources have been defined for the LCA context with reference to the overall UNEP/SETAC Life Cycle Impact Assessment (LCIA) framework. Second, existing LCIA methods have been reviewed and discussed. The reviewed methods have been evaluated according to the considered type of natural resources and their underlying principles followed (use-to-availability ratios, backup technology approaches, or thermodynamic accounting methods).

Results and discussion

There is currently no single LCIA method available that addresses impacts for all natural resource categories, nor do existing methods and models addressing different natural resource categories do so in a consistent way across categories. Exceptions are exergy and solar energy-related methods, which cover the widest range of resource categories. However, these methods do not link exergy consumption to changes in availability or provisioning capacity of a specific natural resource (e.g., mineral, water, land etc.). So far, there is no agreement in the scientific community on the most relevant type of future resource indicators (depletion, increased energy use or cost due to resource extraction, etc.). To address this challenge, a framework based on the concept of stock/fund/flow resources is proposed to identify, across natural resource categories, whether depletion/dissipation (of stocks and funds) or competition (for flows) is the main relevant aspect.

Conclusions

An LCIA method—or a set of methods—that consistently address all natural resource categories is needed in order to avoid burden shifting from the impact associated with one resource to the impact associated with another resource. This paper is an important basis for a step forward in the direction of consistently integrating the various natural resources as an Area of Protection into LCA.

     

Bibliography on the genus Marenzelleria and its geographical distribution, principal topics and nomenclature

A bibliography is given for the genus Marenzelleria. All together, 236 publications were found dealing with M. viridis, M. wireni and M. jonesi and their synonyms. The contents of the publications are briefly reviewed in tabular form identifying the nomenclature used, the geographical distribution and the topic of the paper in each case.     

A catalogue of Lithuanian beetles (Insecta, Coleoptera)

This paper presents the first complete and updated list of all 3597 species of beetles (Insecta: Coleoptera) belonging to 92 familiesfound and published in Lithuania until 2011, with comments also provided on the main systematic and nomenclatural changes since the last monographic treatment in two volumes (Pileckis and Monsevičius 1995, 1997). The introductory section provides a general overview of the main features of the territory of Lithuania, the origins and formation of the beetle fauna and their conservation, the faunistic investigations in Lithuania to date revealing the most important stages of the faunistic research process with reference to the most prominent scientists, an overview of their work, and their contribution to Lithuanian coleopteran faunal research.Species recorded in Lithuania by some authors without reliable evidence and requiring further confirmation with new data are presented in a separate list, consisting of 183 species. For the first time, analysis of errors in works of Lithuanian authors concerning data on coleopteran fauna has been conducted and these errors have been corrected. All available published and Internet sources on beetles found in Lithuania have been considered in the current study. Over 630 literature sources on species composition of beetles, their distribution in Lithuania and neighbouring countries, and taxonomic revisions and changes are reviewed and cited. An alphabetical list of these literature sources is presented. After revision of public beetle collections in Lithuania, the authors propose to remove 43 species from the beetle species list of the country on the grounds, that they have been wrongly identified or published by mistake. For reasons of clarity, 19 previously noted but later excluded species are included in the current checklist with comments. Based on faunal data from neighbouring countries, species expected to occur in Lithuania are matnioned. In total 1390 species are attributed to this category and data on their distribution in neighbouring countries is presented. Completion of this study provides evidence that the Lithuanian coleopteran fauna has yet to be completely investigated and it is estimated that approximately 28 % of beetle species remain undiscovered in Lithuania. More than 85% of beetle species expected for Lithuania have been found in the following families: Cerylonidae, Geotrupidae, Haliplidae, Kateridae, Lycidae, Lucanidae, Mycetophagidae, Scarabaeidae and Silphidae. In families with few species such as Alexiidae, Boridae, Byturidae, Dascilidae, Drilidae, Eucinetidae, Lampyridae, Lymexilidae, Megalopodidae, Nemonychidae, Nosodendridae, Noteridae, Orsodacnidae, Pyrochroidae, Pythidae, Psephenidae, Rhysodidae, Sphaeritidae, Sphaeriusidae, Sphindidae, Stenotrahelidae and Trogidae, all possible species have already been discovered. However in some beetle families such as Aderidae, Bothrideridae, Eucnemidae, Laemoploeidae, Mordellidae, Ptiliidae, Scraptidae and Throscidae less than 50% of all possible species are known. At present the beetle species recorded in Lithuania belong to 92 families, with species from 9 other families such as Agyrtidae, Biphylidae, Deradontidae, Mycteridae, Ochodaeidae, Phleophilidae, Phloeostichidae, Prostomidae, Trachypachidae are expected to be found.A bibliography and a index of subfamily and genus levels are provided. The information published in the monograph will serve to further faunistic and distribution research of beetles and will help to avoid confusion in the identificatation of coleopteran fauna of Lithuania.     

New records and a bibliography of the mosses of Pakistan

Abstract

Forty mosses are recorded for Pakistan, of which six appear to be new records for that country. Timmiella subintegra Dix. is reduced to synonymy under T. barbuloides (Brid.) Moenk., and there are notes on the typification of Pilotrichum pluvinii Brid. (Cryptoleptodon pluvinii (Brid.) Broth.).