Expected impact of agriculture expansion on the world avifauna

Agriculture expansion is a major cause of the current biodiversity decline. From the knowledge of the average bird densities in the terrestrial biomes, and using forecasts of biome conversions associated to agriculture expansion between 1990 and 2050, we estimate that these conversions would reduce by 8 to 26% the global avifauna, in number of individuals, depending on socio-economic scenarios and farmland management. Then, adding these values to previous estimates, we estimate that 27-44% of the bird species could be lost due to agriculture expansion from Neolithic to 2050.     

The expanding snoRNA world

In eukaryotes, the site-specific formation of the two prevalent types of rRNA modified nucleotides, 2'-O-methylated nucleotides and pseudouridines, is directed by two large families of snoRNAs. These are termed box C/D and H/ACA snoRNAs, respectively, and exert their function through the formation of a canonical guide RNA duplex at the modification site. In each family, one snoRNA acts as a guide for one, or at most two modifications, through a single, or a pair of appropriate antisense elements. The two guide families now appear much larger than anticipated and their role not restricted to ribosome synthesis only. This is reflected by the recent detection of guides that can target other cellular RNAs, including snRNAs, tRNAs and possibly even mRNAs, and by the identification of scores of tissue-specific specimens in mammals. Recent characterization of homologs of eukaryotic modification guide snoRNAs in Archaea reveals the ancient origin of these non-coding RNA families and offers new perspectives as to their range of function.     

Ribonucleases P/MRP and the expanding ribonucleoprotein world

One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.     

Meeting water requirements of an expanding world population

Water availability in the root zone (green water) is a critical component of plant production, but is often deficient in many Third World regions. When deficient, runoff water (blue water) can be added. Focusing on ten physiographic regions in Africa and Asia, characterized by mainly or partly dry climates and rapid population growth, this study analyses whether in a 30-years'' perspective enough blue water could be provided to allow food self-sufficiency. It is assumed that for food self-sufficiency some 900 cubic metres of water per person per year has to be provided. In judging the realism it is assumed that a maximum 25 per cent increase in water mobilization rate would be manageable in a 30-year period. The study suggests that by 2025, water scarcity will make regions populated by some 55 per cent of the world''s population dependent on food imports. For water-wasting regions in Central Asia, water saving might, however, free the water needed. The paper closes by proposing some urgent measures. <br>     

Oxymoron no more: the expanding world of heterochromatic genes

Heterochromatin has been oversimplified and even misunderstood. In particular, the existence of heterochromatic genes is often overlooked. Diverse types of genes reside within regions classified as constitutive heterochromatin and activating influences of heterochromatin on gene expression in Drosophila are well documented. These properties are usually considered paradoxical because heterochromatin is commonly portrayed as "silent chromatin". In the past, studies of heterochromatic genes were limited to a few Drosophila genes. However, the recent discovery of several hundred heterochromatic genes in Drosophila, plants and mammals through sequencing projects offers new opportunities to examine the variety of ways in which heterochromatin influences gene expression. Comparative genomics is revealing diverse origins of heterochromatic genes and remarkable evolutionary fluidity between heterochromatic and euchromatic domains. These features justify a broader view of heterochromatin, one that accommodates repressive, permissive and activating effects on gene expression, and recognizes chromosomal and evolutionary transitional states between heterochromatin and euchromatin.     

Spatial turnover in the global avifauna

Despite its wide implications for many ecological issues, the global pattern of spatial turnover in the occurrence of species has been little studied, unlike the global pattern of species richness. Here, using a database on the breeding distributions of birds, we present the first global maps of variation in spatial turnover for an entire taxonomic class, a pattern that has to date remained largely a matter of conjecture, based on theoretical expectations and extrapolation of inconsistent patterns from different biogeographic realms. We use these maps to test four predictions from niche theory as to the form that this variation should take, namely that turnover should increase with species richness, towards lower latitudes, and with the steepness of environmental gradients and that variation in turnover is determined principally by rare (restricted) species. Contrary to prediction, we show that turnover is high both in areas of extremely low and high species richness, does not increase strongly towards the tropics, and is related both to average environmental conditions and spatial variation in those conditions. These results are closely associated with a further important and novel finding, namely that global patterns of spatial turnover are driven principally by widespread species rather than the restricted ones. This complements recent demonstrations that spatial patterns of species richness are also driven principally by widespread species, and thus provides an important contribution towards a unified model of how terrestrial biodiversity varies both within and between the Earth's major land masses.     

Evaluation of the non-randomness of protein compositions

A method is described for assessing the non-randomness of protein compositions, based on the chi-squared statistic for the differences between the observed numbers of residues of each type and the numbers expected for a random distribution of codons. The analysis indicates that changes in at least 30% of the residues in natural proteins are selected against.     

Old world versus new world: life-history alterations in a successful invader introduced across Europe

We examined differences in pumpkinseed (Lepomis gibbosus) life-history traits between native North American and introduced European populations, and tested three life-history predictions related to the effect of temperature, growth, waterbody size, and the presence/absence of predators on native and non-native populations. Pumpkinseed populations exhibit more ‘opportunistic’ traits (earlier maturity, smaller size at maturity, and higher reproductive allocation) in their introduced European range than those in their native range. Predictions of life-history traits were improved when indicators of juvenile growth rate (mean length at age 2), waterbody size (surface area), and thermal regime (air temperature degree-days above 10 °C) were incorporated into models along with continental location, but European pumpkinseed populations exhibit more opportunistic life-history traits than North American populations even when these factors are accounted for. Native pumpkinseed in waterbodies containing piscivores mature later and at a larger size, and have lower gonadosomatic indices than those in waterbodies lacking piscivores, whereas there is no significant difference in the same three life-history traits between European waterbodies containing or lacking piscivores. Because congeneric competitors of the pumpkinseed are absent from Europe, the apparent absence of a predator life-history effect there could also be due to the absence of the major sunfish competitors. In either case, the evolution and maintenance of more opportunistic traits in European pumpkinseed can likely be attributed to enemy release, and this may explain the successful establishment and spread of pumpkinseed in many parts of Europe.     

Real-time definition of non-randomness in the distribution of genomic events

Features such as mutations or structural characteristics can be non-randomly or non-uniformly distributed within a genome. So far, computer simulations were required for statistical inferences on the distribution of sequence motifs. Here, we show that these analyses are possible using an analytical, mathematical approach. For the assessment of non-randomness, our calculations only require information including genome size, number of (sampled) sequence motifs and distance parameters. We have developed computer programs evaluating our analytical formulas for the real-time determination of expected values and p-values. This approach permits a flexible cluster definition that can be applied to most effectively identify non-random or non-uniform sequence motif distribution. As an example, we show the effectivity and reliability of our mathematical approach in clinical retroviral vector integration site distribution.     

Patterns of non-randomness in the composition and characteristics of the Taiwanese bird trade

The invasion pathway is composed of a sequential series of stages that need to be quantified separately in order properly to understand the invasion process. Here, we examine the composition and characteristics of bird species being sold in the pet bird market in Taiwan. The bird trade in Taiwan is of high volume and financially lucrative. The identity of species in this trade is vital for informing later stages (introduction, establishment, spread) of the invasion pathway. We conducted interviews and surveys of 72 outlets selling pet birds from seven cities across Taiwan, from which we identified 247 bird species (within 34 families) for sale. Of these, 170 bird species (from 27 families) are exotic to Taiwan. Using randomization tests, we show that nine families are significantly over-represented in the pet trade (Psittacidae, Muscicapidae, Timaliidae, Sturnidae, Turdidae, Estrildidae, Chloropseidae, Zosteropidae and Fringillidae), and three after sequential Bonferroni correction (Psittacidae, Muscicapidae and Sturnidae). Species that have been identified in Taiwanese pet shops tend to have a larger native geographic range, originate further from the equator, are smaller-bodied, and have more aesthetically-pleasing songs than expected by chance. The native ranges of pet shop species are more likely to be situated in the Indo-Malay and Palearctic biogeographic realms, while fewer species than expected derive from the Neotropic, Afrotropic and Nearctic realms. Our results show that bird species for sale in Taiwan are determined by the interaction of species availability and societal demands.     

Evolution and history of the western Palaearctic avifauna

Recent data accumulated from fields as varied as avian palaeontology, palaeobotany, historical biogeography and molecular phylogenetics provide a completely renewed picture of the origin, evolution and distribution of modern birds. Although the origin of birds is still controversial, their Tertiary history is now well known. The reconstruction of palaeoenvironments and the identification of shifts in major vegetation belts and habitats during the Pliocene–Pleistocene epochs have added to these recent developments. Together they provide a new perspective on speciation and extinction rates since the late Pliocene and the establishment of modern avifaunas in the western Palaearctic.     

Extinction patterns in the avifauna of the Hawaiian islands

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.     

The modern avifauna of the Pitcairn Islands

Excluding the gadfly petrels Pterodroma spp. and the resident landbirds, this paper details the present status of bird species seen during an expedition to the Pitcairn Islands (Ducie, Henderson, Oeno and Pitcairn) in 1991 and early 1992. Ten species were recorded in the Islands for the first time. Several Southern Ocean petrels were recorded, most in the midwinter period of June and July. The populations of Christmas Island shearwaters breeding on Oeno and Ducie laid in synchrony every 9–10 months. The species is one of few with such a sub-annual, synchronized regime. The majority of other seabirds had an annual breeding cycle, laying between May and October. Around one percent of the world population of the bristle-thighed curlew passes the non-breeding season in the Pitcairn Islands.     

Evolutionary age and risk of extinction in the global avifauna

Species at high risk of extinction are not distributed at random among higher taxa. Here we demonstrate that there is a positive relationship between the proportion of species in a taxon which are considered to be threatened and the evolutionary age of that taxon, both for the global avifauna and the avifauna of the New World. The potential mechanisms and consequences of the relationship are examined.     

Factors contributing to non-randomness in species Co-occurrences on Islands

Summary There has been dispute whether patterns of species co-occurrence on islands are largely random. We present a new method for testing this question; this method lets one not only examine whether a whole fauna is non-randomly structured, but also identify in which direction and by how much each particular species combination deviates from expectations based on randomness. Application of this method to the whole Bismarck and New Hebridean avifaunas, and to two particular guilds, shows that some pairs of species have more exclusive distributions than expected for random placement of species, because of competition, differing distributional strategies, or different geographical orgins. Other pairs of species have more coincident distributions than expected, because of shared habitat, single-island endemism, shared distributional strategies, or shared geographical origins. Much of the information about non-random co-occurrence is contained in the incidence graphs for occurrence of individual species. Finally, our present understanding of assembly rules is summarized.     

Changes in native and introduced host–parasite networks

Biological Invasions - Introduced species can alter the dynamics and structure of a native community. Network analysis provides a tool to study host–parasite interactions that can help to...     

Diversity of the Bialowieza Forest avifauna in space and time

The Biaowiea Forest (BF) is an extensive and relatively little changed forest complex on the Polish-Belarussian border. Data on the structure and diversity of its breeding avifauna have mostly been collected in primeval old-growth stands, preserved within the Biaowiea National Park (BNP). Mapping censuses repeated in space (plots, replicated in riverine, oak-lime-hornbeam and coniferous stands) and time (permanent plots, 28 years) reveal that the breeding bird assemblages are rich in species (29–52/season in a 25 to 33-ha plot), but of moderate overall density (40–120 pairs/10 ha). The latter is due to low, lower than in man-transformed areas, densities of the majority of particular species. Despite marked changes in vegetation structure, the composition of the breeding bird assemblage does not vary much across different primeval forest types, with a single breeding bird community inhabiting all of them, including treefall gaps. High richness of the BF avifauna stems from the Forests geographical locality, as well as from a high level of the primeval avifauna retention. Over 95% of the 135–140 pristine species still breed there. Especially species-rich groups are birds of prey, owls, woodpeckers and Sylvinae warblers. Bird communities in the BNP and primeval tropical rain forests share many features, suggesting that natural differences between temperate and tropical forests were less pronounced in the past. The combination of high species richness with low densities of individual species is probably a feature of all pristine forests, independent of climatic zone. The BF avifauna must once have been typical of the ancient European forests and it has become so exceptional chiefly because it has preserved most of its pristine features. The BF thus constitutes an indispensable reference site for future studies of woodland bird biology. To ensure its survival should become a priority. Commercial logging, taking place over 80% of the Polish BF part, severely changes the Forests structure and strongly affects the birds, especially species which depend on dead wood (Dendrocopos leucotos, Picoides tridactylus) and on old-growth stands. The small area protected as the BNP becomes an increasingly isolated island, in which preservation of the primeval forest features seems to be impossible. In order to retain them, it is necessary to protect the whole BF area.     

Changes in the species composition of a Karoo avifauna over time: a case study from Deelfontein,South Africa

A collection of almost 830 specimens of birds and their eggs was made at Deelfontein, Northern Cape province, South Africa, in 1901 and 1902, by two soldiers who had enlisted in the Yeomanry during the South African (Boer) War. A total of 151 bird species has been recorded in the Deelfontein area in two periods, 1901–1902 and 1987–1992. There has been no apparent change in occurrence in 82 species, but 40 species were recorded only in 1901–1902, and 29 species were recorded only by observers who completed field cards for the area for the SABAP surveys in 1987–1992. It is suggested that the differences in bird species composition are most likely associated with anthropogenic influences including land-use changes and over-utilisation of shrublands as grazing for domestic livestock.