Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

Trabajo presentado en el 39th CIESM Congress, celebrado en Venecia, Italia, del 10 al 14 de mayo de 2010

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Biodiversity of the Mediterranean Sea: estimates, patterns and threats

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.

This abstract has been translated to other languages (File S1).

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The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

Ulva, one of the first Linnaean genera, was later circumscribed to consist of green seaweeds with distromatic blades, and Enteromorpha Link was established for tubular forms. Although several lines of evidence suggest that these generic constructs are artificial, Ulva and Enteromorpha have been maintained as separate genera. Our aims were to determine phylogenetic relationships among taxa currently attributed to Ulva, Enteromorpha, Umbraulva Bae et I.K. Lee and the monotypic genus Chloropelta C.E. Tanner, and to make any nomenclatural changes justified by our findings. Analyses of nuclear ribosomal internal transcribed spacer DNA (ITS nrONA) (29 ingroup taxa including the type species of Ulva and Enteromorphat, the chloroplast-encoded rbcL gene (for a subset of taxa) and a combined data set were carried out. All trees had a strongly supported clade consisting of all Ulva, Enteromorpha and Chloropelta species, but Ulva and Enteromorpha were not monophyletic. The recent removal of Vmbraulva olivascens (PJ.L...

Linnaeus was right all along: Ulva and Enteromorpha are not distinct genera

A goal of phylogeography is to relate patterns of genetic differentiation to potential historical geographic isolating events. Quaternary glaciations, particularly the one culminating in the Last Glacial Maximum ;21 ka (thousands of years ago), greatly affected the distributions and population sizes of temperate marine species as their ranges retreated southward to escape ice sheets. Traditional genetic models of glacial refugia and routes of recolonization include these predictions: low genetic diversity in formerly glaciated areas, with a small number of alleles/haplotypes dominating disproportionately large areas, and high diversity including ''private'' alleles in glacial refugia. In the Northern Hemisphere, low diversity in the north and high diversity in the south are expected. This simple model does not account for the possibility of populations surviving in relatively small northern periglacial refugia. If these periglacial populations experienced extreme bottlenecks, they could have the low genetic diversity expected in recolonized areas with no refugia, but should have more endemic diversity (private alleles) than recently recolonized areas. This review examines evidence of putative glacial refugia for eight benthic marine taxa in the temperate North Atlantic. All data sets were reanalyzed to allow direct comparisons between geographic patterns of genetic diversity and distribution of particular clades and haplotypes including private alleles. We contend that for marine organisms the genetic signatures of northern periglacial and southern refugia can be distinguished from one another. There is evidence for several periglacial refugia in northern latitudes, giving credence to recent climatic reconstructions with less extensive glaciation.

Evaluating signatures of glacial refugia for north atlantic benthic marine taxa

Marine aliens are non-native species that have been transported across major geographical barriers by human activities, involving vectors that move propagules along pathways. Species may also be newly observed in a geographical area due to range shifts, generally in association with climate change. Artificial structures are considered to be either man-made materials or natural materials shaped or displaced to serve a specific function for human activities. All types of artificial structures are currently increasing dramatically in coastal zones due to increasing human populations on coastlines. Most of the significant marine vectors and pathways involve mobile artificial structures and are reviewed here. These include shipping (ballast water and hull fouling) and aquaculture, including stock transfer and unintentional introductions, all of which can move species into new biogeographical provinces. Some types of structures frequently move long distances but have low fouling loads (e.g., commercial shipping), whereas others (e.g., barges and pontoons) can be hyperfouled due to long stationary periods such that when moved they transport mature fouling communities. We also examine the presence of alien marine species on static (immobile) artificial structures, which support different communities from those on natural hard substrata. We consider the role of these structures, such as coastal defences, artificial reefs, and offshore platforms, in the dispersal and abundance of alien species. Marinas include both mobile and immobile structures and are apparently particularly favourable habitats for many aliens. For example, in coastal North America approximately 90% of the alien species inhabiting hard substrata have been reported from docks and marinas. Detailed case studies of alien marine species (two seaweeds and four invertebrates) are provided, with an analysis of their origin, vectors of transport, habitat in the introduced range, and potential impact. Although there are exceptions, a large majority of marine alien species seem to be associated, at least for some of the time, with artificial structures. It is clear that artificial structures can pave the way and act as stepping stones or even corridors for some marine aliens, as do urban areas, roads and riparian environments in terrestrial ecosystems. The observed acceleration of spread rates for marine invasions over the course of the last two centuries may partly be a result of the increase of artificial structures in coastal environments coupled with greater activity of vectors.

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Christine A. Maggs

Papers

Linnaeus was right all along: Ulva and Enteromorpha are not distinct genera

Evaluating signatures of glacial refugia for north atlantic benthic marine taxa

Changing coasts: marine aliens and artificial structures

Environmental tolerances of free-living coralline algae (maerl): implications for European marine conservation

Seaweeds of the British Isles. Volume 1 Rhodophyta, Part 3A Ceramiales.