Global knowledge about the spatial distribution of species is orders of magnitude coarser in resolution than other geographically-structured environmental datasets such as topography or land cover. Yet such knowledge is crucial in deciphering ecological and evolutionary processes and in managing global change. In this review, we propose a conceptual and cyber-infrastructure framework for refining species distributional knowledge that is novel in its ability to mobilize and integrate diverse types of data such that their collective strengths overcome individual weaknesses. The ultimate aim is a public, online, quality-vetted 'Map of Life' that for every species integrates and visualizes available distributional knowledge, while also facilitating user feedback and dynamic biodiversity analyses. First milestones toward such an infrastructure have now been implemented.

Integrating biodiversity distribution knowledge: toward a global map of life

Why the impact factor of journals should not be used for evaluating research

The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface. In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements.

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The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

/pdf/sequence-based-classification-and-identification-of-fungi-4swk2mlkgb.pdf

Sequence-based classification and identification of Fungi

Ghost forests created by the submergence of low-lying land are one of the most striking indicators of climate change along the Atlantic coast of North America. Although dead trees at the margin of estuaries were described as early as 1910, recent research has led to new recognition that the submergence of terrestrial land is geographically widespread, ecologically and economically important, and globally relevant to the survival of coastal wetlands in the face of rapid sea level rise. This emerging understanding has in turn generated widespread interest in the physical and ecological mechanisms influencing the extent and pace of upland to wetland conversion. Choices between defending the coast from sea level rise and facilitating ecosystem transgression will play a fundamental role in determining the fate and function of low-lying coastal land. A review of the phenomenon of low-lying ‘ghost forests’, and the physical and ecological mechanisms that control their occurrence in the context of sea level rise, with a focus on the Atlantic Coast of North America.

/pdf/sea-level-driven-land-conversion-and-the-formation-of-ghost-3rkwkyr05z.pdf

Sea-level driven land conversion and the formation of ghost forests

Stimulated in large part by the advent of the Internet, research productivity in many academic disciplines has changed dramatically over the last two decades. However, the assessment system that governs professional success has not kept pace, creating a mismatch between modes of scholarly productivity and academic assessment criteria. In this article, we describe the problem and present ideas for solutions. We argue that adjusting assessment criteria to correspond to modern scholarly productivity is essential for the success of individual scientists and of our discipline as a whole. The authors and endorsers of this article commit to a number of actions that constitute steps toward ensuring that all forms of scholarly productivity are credited. The emphasis here is on systematic biology, but we are not alone in experiencing this mismatch between productivity and assessment. An additional goal in this article is to begin a conversation about the problem with colleagues in other subdisciplines of biology.

https://bioone.org/journals/bioscience/volume-61/issue-8/bio.2011.61.8.8/Biology-Needs-a-Modern-Assessment-System-for-Professional-Productivity/10.1525/bio.2011.61.8.8.pdf

Biology Needs a Modern Assessment System for Professional Productivity

We took a two-tiered approach to test monophyly of Nelsonioideae and place the group within Lamiales, and to determine relationships among taxa within the group. Phylogenetic analysis of a molecula ...

Phylogenetic placement, delimitation, and relationships among genera of the enigmatic Nelsonioideae (Lamiales: Acanthaceae).

Modern agricultural practices pose serious threats to biodiversity worldwide Species losses from habitat conversion are well documented, but indirect impacts such as reduced water availability to adjacent ecosystems are less known San Quintin is an important agricultural valley in the mediterranean climate region of Baja California, Mexico The region is also a hotspot of plant species richness and endemism Plant species in the region are here analyzed by comparison of the contemporary flora to historical botanical collections to identify extirpations Historical collections indicate that habitat loss to agriculture has been a direct cause of species losses As importantly, the unsustainable extraction of groundwater has apparently led to salt water intrusion, resulting in the loss of 22 native plant taxa, including 13 rare plants Seventy-eight percent of all the vernal pool taxa have been lost from the flora (including 85 % of the rare taxa) and 11 % of plants of riparian and pond habitat (including 25 % of the rare taxa) are no longer found in the region Unsustainable agricultural practices continue to threaten fragile coastal ecosystems and are a serious challenge to current and future conservation efforts Ironically, these same practices frequently result in abandonment of cultivated areas Owing to indirect impacts, conservation of biodiversity and large-scale agricultural operations are even less compatible on a regional scale than indicated by direct impacts It is vital that sustainable agricultural practices be adopted locally and globally to avoid further losses of biodiversity

Lucinda A. McDade

Papers

Biology Needs a Modern Assessment System for Professional Productivity

Phylogenetic placement, delimitation, and relationships among genera of the enigmatic Nelsonioideae (Lamiales: Acanthaceae).

Conservation challenges in a threatened hotspot: agriculture and plant biodiversity losses in Baja California, Mexico

Vegetation patterns in the mediterranean-desert ecotone of baja california, mexico