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

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

http://science.sciencemag.org/content/sci/291/5507/1304.full.pdf

The sequence of the human genome.

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million - almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the 'Water for Life' decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as 'receivers' of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and - in the case of migrating aquatic fauna - downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management - one that has been appropriately termed 'reconciliation ecology'.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/96AA265E3D88C95FB802E7A73CCB4332/S1464793105006950a.pdf/div-class-title-freshwater-biodiversity-importance-threats-status-and-conservation-challenges-div.pdf

Freshwater biodiversity: importance, threats, status and conservation challenges

Protecting the world’s freshwater resources requires diagnosing threats over a broad range of scales, from global to local. Here we present the first worldwide synthesis to jointly consider human and biodiversity perspectives on water security using a spatial framework that quantifies multiple stressors and accounts for downstream impacts. We find that nearly 80% of the world’s population is exposed to high levels of threat to water security. Massive investment in water technology enables rich nations to offset high stressor levels without remedying their underlying causes, whereas less wealthy nations remain vulnerable. A similar lack of precautionary investment jeopardizes biodiversity, with habitats associated with 65% of continental discharge classified as moderately to highly threatened. The cumulative threat framework offers a tool for prioritizing policy and management responses to this crisis, and underscores the necessity of limiting threats at their source instead of through costly remediation of symptoms in order to assure global water security for both humans and freshwater biodiversity.

/pdf/global-threats-to-human-water-security-and-river-2hfichkqti.pdf

Global threats to human water security and river biodiversity

Summary
1. In an effort to develop quantitative relationships between various kinds of flow alteration and ecological responses, we reviewed 165 papers published over the last four decades, with a focus on more recent papers. Our aim was to determine if general relationships could be drawn from disparate case studies in the literature that might inform environmental flows science and management.

2. For all 165 papers we characterised flow alteration in terms of magnitude, frequency, duration, timing and rate of change as reported by the individual studies. Ecological responses were characterised according to taxonomic identity (macroinvertebrates, fish, riparian vegetation) and type of response (abundance, diversity, demographic parameters). A ‘qualitative’ or narrative summary of the reported results strongly corroborated previous, less comprehensive, reviews by documenting strong and variable ecological responses to all types of flow alteration. Of the 165 papers, 152 (92%) reported decreased values for recorded ecological metrics in response to a variety of types of flow alteration, whereas 21 papers (13%) reported increased values.

3. Fifty-five papers had information suitable for quantitative analysis of ecological response to flow alteration. Seventy per cent of these papers reported on alteration in flow magnitude, yielding a total of 65 data points suitable for analysis. The quantitative analysis provided some insight into the relative sensitivities of different ecological groups to alteration in flow magnitudes, but robust statistical relationships were not supported. Macroinvertebrates showed mixed responses to changes in flow magnitude, with abundance and diversity both increasing and decreasing in response to elevated flows and to reduced flows. Fish abundance, diversity and demographic rates consistently declined in response to both elevated and reduced flow magnitude. Riparian vegetation metrics both increased and decreased in response to reduced peak flows, with increases reflecting mostly enhanced non-woody vegetative cover or encroachment into the stream channel.

4. Our analyses do not support the use of the existing global literature to develop general, transferable quantitative relationships between flow alteration and ecological response; however, they do support the inference that flow alteration is associated with ecological change and that the risk of ecological change increases with increasing magnitude of flow alteration.

5. New sampling programs and analyses that target sites across well-defined gradients of flow alteration are needed to quantify ecological response and develop robust and general flow alteration–ecological response relationships. Similarly, the collection of pre- and post-alteration data for new water development programs would significantly add to our basic understanding of ecological responses to flow alteration.

https://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/exhibits/swrcb/swrcb_poff2010_2.pdf

Ecological responses to altered flow regimes: a literature review to inform the science and management of environmental flows

Les itrrdes de production se sont multipli6es ces dertlieres nnnees ut les resultuts obtenus permrtient des simplifications. Celles-ci sonf souhaitables dans lu tnesure on l’obtention des puran1Piw.s de base de la production suivant les mefhodes habituelles demande beaucoup de temps et d’effort. CTne premiere simplification importante a ete l’infroduclion du rcrpport P/U qui permet d’evaluer lu production quand la biotnasse tnoyenne est connue et traduit la vitesw de renouvellement de la biomclsse pnr unite de temps. Par ailleurs, Allen (1971) a montre que pour certaines des combinaisons des modtVes de croissance et de mortalite les plus courut&, l’expression muihematique de PI% pouvait etre tres simple. Le brrf du travail presente ici es? de rechercher, pour les tnod+les de croissutzce rt de rnortalit& les plus frequemmenl observes, des relations entre PIB et longevite (T) ; PI% et uge moyen (-J) PI~ tenant compte dr l’influence de la proportion d’individus survivants (5’) au temps T. Ceci dans le cas ideal 02 il s’agit d’une population en equilibre ngant une reproduction annuelle, un recrutetnent constant et soumise ci une mortaliit! uniforme. Deux mod?les de mortalite lineaire et exponeniielle et quatre modeles de croissance T-on Berlalanfjy, c~xponentielle negative, lineaire en poids, lineaire en longueur onf efe ufilises.

/pdf/relations-entre-le-rapport-p-b-et-la-longevite-des-289b473622.pdf

Relations entre le rapport P/B et la longévité des organismes

Il existe trois types de bassins en Côte d’ivoire; les grands bassins fluviaux s’étendant du nord au sud du puys, les bassins côtiers et les cours d’eau septentrionaux qui coulent vers le Mali. On peut dislinguer quatre régimes hydrologiques : iropical de transition, équntorial de transition atténué, équatorial de transition et régime de montagne. Les grands cours d’eau (Comoé, Bandama, Sassandra, Cavally) ont un régime mixte. La furbidiité est surtout liée au débit solide qui est maximum en début de crue; la transparence dépasse rarement un m?tre. La température de l’enu ne descend que irès rarement en dessous de 25 OC : les variutions saisonniéres sont fuibles et dans le bassin moyen du Bandama, la fempérature de l’eau se situe entre 26 et 290 pendant au moins huit mois sur douze. Les pH sont légèremeni alcalins sauf dans les cours d’eau de forêt de la zone cdlière où ils sont légèrement acides. Les rivières du centre et du nord du pays ont des conductibilités électriques en général faibles (40 8 70 micromhos en moyenne) ; les variations saisonnières sont directement liées au régime hydrologique, les plus fories teneurs en sels dissous étant observées à l’étiage, les plus faibles duranf les crues. Comme dans la plupuri des eaux douces africaines, les carbonates sont l’élément dominant parmi les unions, les sulfates viennent ensuite puis les chlorures. Les phosphates n’existent qu’à l’ébat de traces sauf en période d’étiage où ils peuvent égaler et même de’passer légèrement le poids des chlorures. Parmi les cations, calcium et sodium sont en mg/1 les éléments les mieux représentés à peu près à égal&; pofassium et magnésium viennent ensuite. Les concentrations en silice dissoute concordent avec les valeurs signnlées pour différents autres milieux d’Afrique de l’Ouest.

/pdf/caracteristiques-physico-chimiques-des-rivieres-de-cote-d-51zyo6da0y.pdf

Caractéristiques physico-chimiques des rivières de Côte d'Ivoire

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2890%2981468-4

Polypeptide components of the apamin receptor associated with a calcium activated potassium channel

/pdf/les-zones-ateliers-des-dispositifs-pour-la-recherche-sur-l-4qndz6v1c8.pdf

Les zones ateliers, des dispositifs pour la recherche sur l’environnement et les anthroposystèmes - Une action du programme « Environnement, vie et sociétés » du CNRS

Benthos consists of all those aquatic organisms which are associated in some way with the bottom sediments. We shall, therefore, consider here only the organisms and communities inhabiting the lake sediments, reserving a study of the periphyton found on higher aquatic plants for a further chapter. This periphyton was far from negligible in Lake Chad where fringing vegetation and submerged water grasses were numerous. It was usually composed of different species to the benthos although some were occasionally found among the benthos when it was sampled close to plant clumps.

Christian Lévêque

Papers

Relations entre le rapport P/B et la longévité des organismes

Caractéristiques physico-chimiques des rivières de Côte d'Ivoire

Polypeptide components of the apamin receptor associated with a calcium activated potassium channel

Les zones ateliers, des dispositifs pour la recherche sur l’environnement et les anthroposystèmes - Une action du programme « Environnement, vie et sociétés » du CNRS

The benthic fauna: ecology, biomass and communities