Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage.

Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process.

Arthropod Distribution in a Tropical Rainforest: Tackling a Four Dimensional Puzzle.

Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004.

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information.

Urban Market Gardening and Rodent-Borne Pathogenic Leptospira in Arid Zones: A Case Study in Niamey, Niger.

Leptospirosis essentially affects human following contact with rodent urine-contaminated water. As such, it was mainly found associated with rice culture, recreational activities and flooding. This is also the reason why it has mainly been investigated in temperate as well as warm and humid regions, while arid zones have been only very occasionally monitored for this disease.

Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes.

Background: Previous cross-species painting studies with probes from chicken (Gallus gallus) chromosomes 1-10 and a paint pool of nineteen microchromosomes have revealed that the drastic karyotypic reorganization in Accipitridae is due to extensive synteny disruptions and associations. However, the number of synteny association events and identities of microchromosomes involved in such synteny associations remain undefined, due to the lack of paint probes derived from individual chicken microchromosomes. Moreover, no genome-wide homology map between Accipitridae species and other avian species with atypical karyotype organization has been reported till now, and the karyotype evolution within Accipitriformes remains unclear.

Borrelia infection in small mammals in West Africa and its relationship with tick occurrence inside burrows.

Tick-borne relapsing fever (TBRF) is a zoonotic disease caused by several Borrelia species transmitted to humans by Ornithodoros tick vectors. In West Africa, Borrelia crocidurae is a common cause of disease in many rural populations. Small mammals act as reservoirs of infection.

Assessing the Risk of Invasion by Tephritid Fruit Flies: Intraspecific Divergence Matters.

Widely distributed species often show strong phylogeographic structure, with lineages potentially adapted to different biotic and abiotic conditions. The success of an invasion process may thus depend on the intraspecific identity of the introduced propagules. However, pest risk analyses are usually performed without accounting for intraspecific diversity.

Chromosomal polymorphism in mammals: an evolutionary perspective.

Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited.

Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace.

One hundred and fifty years after Alfred Wallace studied the geographical variation and species diversity of butterflies in the Indomalayan-Australasian Archipelago, the processes responsible for their biogeographical pattern remain equivocal. We analysed the macroevolutionary mechanisms accounting for the temporal and geographical diversification of the charismatic birdwing butterflies (Papilionidae), a major focus of Wallace's pioneering work. Bayesian phylogenetics and dating analyses of the birdwings were conducted using mitochondrial and nuclear genes.

Living on the edge: timing of Rand Flora disjunctions congruent with ongoing aridification in Africa.

The Rand Flora is a well-known floristic pattern in which unrelated plant lineages show similar disjunct distributions in the continental margins of Africa and adjacent islands-Macaronesia-northwest Africa, Horn of Africa-Southern Arabia, Eastern Africa, and Southern Africa. These lineages are now separated by environmental barriers such as the arid regions of the Sahara and Kalahari Deserts or the tropical lowlands of Central Africa. Alternative explanations for the Rand Flora pattern range from vicariance and climate-driven extinction of a widespread pan-African flora to independent dispersal events and speciation in situ.

C-Nap1 mutation affects centriole cohesion and is associated with a Seckel-like syndrome in cattle.

Caprine-like Generalized Hypoplasia Syndrome (SHGC) is an autosomal-recessive disorder in Montbéliarde cattle. Affected animals present a wide range of clinical features that include the following: delayed development with low birth weight, hind limb muscular hypoplasia, caprine-like thin head and partial coat depigmentation. Here we show that SHGC is caused by a truncating mutation in the CEP250 gene that encodes the centrosomal protein C-Nap1.

Fauna europaea: Diptera - brachycera.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding the Caucasus region). The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing taxonomic specialists throughout Europe and is a unique (standard) reference suitable for many user communities in science, government, industry, nature conservation and education.

Dissecting the space-time structure of tree-ring datasets using the partial triadic analysis.

Tree-ring datasets are used in a variety of circumstances, including archeology, climatology, forest ecology, and wood technology. These data are based on microdensity profiles and consist of a set of tree-ring descriptors, such as ring width or early/latewood density, measured for a set of individual trees. Because successive rings correspond to successive years, the resulting dataset is a ring variables × trees × time datacube.

Contrasting patterns of polymorphism and selection in bacterial-sensing toll-like receptor 4 in two house mouse subspecies.

Detailed investigation of variation in genes involved in pathogen recognition is crucial for understanding co-evolutionary processes between parasites and their hosts. Triggering immediate innate response to invading microbes, Toll-like receptors (TLRs) belong presently among the best-studied receptors of vertebrate immunity. TLRs exhibit remarkable interspecific variation and also intraspecific polymorphism is well documented.

The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize.

Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.

DNA barcoding and the associated PhylAphidB@se website for the identification of European aphids (Insecta: Hemiptera: Aphididae).

Unlabelled: Aphids constitute a diverse group of plant-feeding insects and are among the most important crop pests in temperate regions. Their morphological identification is time-consuming and requires specific knowledge, training and skills that may take years to acquire. We assessed the advantages and limits of DNA barcoding with the standard COI barcode fragment for the identification of European aphids.

Genetic structure of Bemisia tabaci Med populations from home-range countries, inferred by nuclear and cytoplasmic markers: impact on the distribution of the insecticide resistance genes.

Background: Insecticide resistance management in Bemisia tabaci is one of the main issues facing agricultural production today. An extensive survey was undertaken in five Mediterranean countries to examine the resistance status of Med B. tabaci species in its range of geographic origin and the relationship between population genetic structure and the distribution of resistance genes.

'Becoming a species by becoming a pest' or how two maize pests of the genus Ostrinia possibly evolved through parallel ecological speciation events.

New agricultural pest species attacking introduced crops may evolve from pre-existing local herbivores by ecological speciation, thereby becoming a species by becoming a pest. We compare the evolutionary pathways by which two maize pests (the Asian and the European corn borers, ACB and ECB) in the genus Ostrinia (Lepidoptera, Crambidae) probably diverged from an ancestral species close to the current Adzuki bean borer (ABB). We typed larval Ostrinia populations collected on maize and dicotyledons across China and eastern Siberia, at microsatellite and mitochondrial loci.

A multilocus phylogeny of the world Sycoecinae fig wasps (Chalcidoidea: Pteromalidae).

The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades.

Increase in male reproductive success and female reproductive investment in invasive populations of the harlequin ladybird Harmonia axyridis.

Reproductive strategy affects population dynamics and genetic parameters that can, in turn, affect evolutionary processes during the course of biological invasion. Life-history traits associated with reproductive strategy are therefore potentially good candidates for rapid evolutionary shifts during invasions. In a series of mating trials, we examined mixed groups of four males from invasive and native populations of the harlequin ladybird Harmonia axyridis mating freely during 48 hours with one female of either type.

Different feeding behaviours in a single predatory mite species. 2. Responses of two populations of Phytoseiulus longipes (Acari: Phytoseiidae) to various prey species, prey stages and plant substrates.

Tritrophic studies involving several populations of the predatory mite Phytoseiulus longipes showed distinct life history traits depending on the prey offered and/or the plant substrate. In order to better understand the biology of this predator, the response to several combinations of prey species (Tetranychus evansi and Tetranychus urticae), prey stages (eggs and mobile stages) and plant substrates (bean and tomato leaf discs) has been assessed for two populations of P. longipes.

Different feeding behaviors in a single predatory mite species. 1. Comparative life histories of three populations of Phytoseiulus longipes (Acari: Phytoseiidae) depending on prey species and plant substrate.

The spider mites Tetranychus evansi and T. urticae are key pests of tomato crops, for which no sustainable practical control strategy is available yet. A Brazilian (B) and an Argentinean (A) population of a phytoseiid predatory mite species, Phytoseiulus longipes, are able to develop and reproduce on T.

Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus Cinara.

Introduction: In the past decade ecological speciation has been recognized as having an important role in the diversification of plant-feeding insects. Aphids are host-specialised phytophagous insects that mate on their host plants and, as such, they are prone to experience reproductive isolation linked with host plant association that could ultimately lead to species formation. The generality of such a scenario remains to be tested through macroevolutionary studies.

Contribution to the knowledge of the andean stonefly genus Claudioperla illies, with description of new apterous and micropterous species (Plecoptera: Gripopterygidae).

The genus Claudioperla (Plecoptera: Gripopterygidae), which has been reported from Chile and Argentina to Colombia, was until now monospecific. The study of adults from various localities of the Bolivian Altiplano has resulted in the discovery of four distinct species. Three are new and described: Claudioperla rosalesi n.