'Next generation' biogeography: towards understanding the drivers of species diversification and persistence

The drivers of species diversification and persistence are of great interest to current biogeography, especially in those global biodiversity hotspots' harbouring most of Earth's animal and plant life. Classical multispecies biogeographical work has yielded fascinating insights into broad-scale patterns of diversification, and DNA-based intraspecific phylogeographical studies have started to complement this picture at much finer temporal and spatial scales. The advent of novel next-generation sequencing (NGS) technologies provides the opportunity to greatly scale up the numbers of individuals, populations and species sampled, potentially merging intraspecific and interspecific approaches to biogeographical inference. Here, we outline these prospects and issues by using the example of an undisputed hotspot, the Cape of southern Africa. We outline the current state of knowledge on the biogeography of species diversification within the Cape, review the literature for phylogeographical evidence of its likely drivers and mechanisms, and suggest possible ways forward based on NGS approaches. We demonstrate the potential of these methods and current bioinformatic issues with the help of restriction-site-associated DNA (RAD) sequencing data for three highly divergent species of the Restionaceae, an important plant radiation in the Cape. A thorough understanding of the mechanisms that facilitate species diversification and persistence in spatially structured, species-rich environments will require the adoption of novel genomic and bioinformatic tools in biogeographical studies.

Sound objects in time, space and action

SOUND OBJECTS IN TIME, SPACE AND ACTIONThe term "sound object" describes an auditory experience that is associated with an acoustic event produced by a sound source. At cortical level, sound objects are represented by temporo-spatial activity patterns within distributed neural networks. This investigation concerns temporal, spatial and action aspects as assessed in normal subjects using electrical imaging or measurement of motor activity induced by transcranial magnetic stimulation (TMS).Hearing the same sound again has been shown to facilitate behavioral responses (repetition priming) and to modulate neural activity (repetition suppression). In natural settings the same source is often heard again and again, with variations in spectro-temporal and spatial characteristics. I have investigated how such repeats influence response times in a living vs. non-living categorization task and the associated spatio-temporal patterns of brain activity in humans. Dynamic analysis of distributed source estimations revealed differential sound object representations within the auditory cortex as a function of the temporal history of exposure to these objects. Often heard sounds are coded by a modulation in a bilateral network. Recently heard sounds, independently of the number of previous exposures, are coded by a modulation of a left-sided network.With sound objects which carry spatial information, I have investigated how spatial aspects of the repeats influence neural representations. Dynamics analyses of distributed source estimations revealed an ultra rapid discrimination of sound objects which are characterized by spatial cues. This discrimination involved two temporo-spatially distinct cortical representations, one associated with position-independent and the other with position-linked representations within the auditory ventral/what stream.Action-related sounds were shown to increase the excitability of motoneurons within the primary motor cortex, possibly via an input from the mirror neuron system. The role of motor representations remains unclear. I have investigated repetition priming-induced plasticity of the motor representations of action sounds with the measurement of motor activity induced by TMS pulses applied on the hand motor cortex. TMS delivered to the hand area within the primary motor cortex yielded larger magnetic evoked potentials (MEPs) while the subject was listening to sounds associated with manual than non- manual actions. Repetition suppression was observed at motoneuron level, since during a repeated exposure to the same manual action sound the MEPs were smaller. I discuss these results in terms of specialized neural network involved in sound processing, which is characterized by repetition-induced plasticity.Thus, neural networks which underlie sound object representations are characterized by modulations which keep track of the temporal and spatial history of the sound and, in case of action related sounds, also of the way in which the sound is produced.LES OBJETS SONORES AU TRAVERS DU TEMPS, DE L'ESPACE ET DES ACTIONSLe terme "objet sonore" décrit une expérience auditive associée avec un événement acoustique produit par une source sonore. Au niveau cortical, les objets sonores sont représentés par des patterns d'activités dans des réseaux neuronaux distribués. Ce travail traite les aspects temporels, spatiaux et liés aux actions, évalués à l'aide de l'imagerie électrique ou par des mesures de l'activité motrice induite par stimulation magnétique trans-crânienne (SMT) chez des sujets sains. Entendre le même son de façon répétitive facilite la réponse comportementale (amorçage de répétition) et module l'activité neuronale (suppression liée à la répétition). Dans un cadre naturel, la même source est souvent entendue plusieurs fois, avec des variations spectro-temporelles et de ses caractéristiques spatiales. J'ai étudié la façon dont ces répétitions influencent le temps de réponse lors d'une tâche de catégorisation vivant vs. non-vivant, et les patterns d'activité cérébrale qui lui sont associés. Des analyses dynamiques d'estimations de sources ont révélé des représentations différenciées des objets sonores au niveau du cortex auditif en fonction de l'historique d'exposition à ces objets. Les sons souvent entendus sont codés par des modulations d'un réseau bilatéral. Les sons récemment entendus sont codé par des modulations d'un réseau du côté gauche, indépendamment du nombre d'expositions. Avec des objets sonores véhiculant de l'information spatiale, j'ai étudié la façon dont les aspects spatiaux des sons répétés influencent les représentations neuronales. Des analyses dynamiques d'estimations de sources ont révélé une discrimination ultra rapide des objets sonores caractérisés par des indices spatiaux. Cette discrimination implique deux représentations corticales temporellement et spatialement distinctes, l'une associée à des représentations indépendantes de la position et l'autre à des représentations liées à la position. Ces représentations sont localisées dans la voie auditive ventrale du "quoi".Des sons d'actions augmentent l'excitabilité des motoneurones dans le cortex moteur primaire, possiblement par une afférence du system des neurones miroir. Le rôle des représentations motrices des sons d'actions reste peu clair. J'ai étudié la plasticité des représentations motrices induites par l'amorçage de répétition à l'aide de mesures de potentiels moteurs évoqués (PMEs) induits par des pulsations de SMT sur le cortex moteur de la main. La SMT appliquée sur le cortex moteur primaire de la main produit de plus grands PMEs alors que les sujets écoutent des sons associée à des actions manuelles en comparaison avec des sons d'actions non manuelles. Une suppression liée à la répétition a été observée au niveau des motoneurones, étant donné que lors de l'exposition répétée au son de la même action manuelle les PMEs étaient plus petits. Ces résultats sont discuté en termes de réseaux neuronaux spécialisés impliqués dans le traitement des sons et caractérisés par de la plasticité induite par la répétition. Ainsi, les réseaux neuronaux qui sous-tendent les représentations des objets sonores sont caractérisés par des modulations qui gardent une trace de l'histoire temporelle et spatiale du son ainsi que de la manière dont le son a été produit, en cas de sons d'actions.

Hiding the evidence: The State and spatial inequalities in health in Ireland

The Irish State has consistently reduced its production of publicly accessible disease / mortality maps over the last fifty years. State health statistics, and the small number of disease / mortality maps that have been produced in official publications, show a declining level of detail and are routinely out of date. Following a review of the production of disease / mortality maps in Ireland by the State and allied health agencies, two reasons are suggested for this decline. The first explanation relates to spatial inequalities in healthcare provision and to the absence of a health funding formulae in Ireland. The second explanation focuses on the potential politicisation of spatial inequalities in health status. Researchers in these fields are urged to disseminate information widely on spatial inequalities in healthcare provision, healthcare access and health status, both within and outside of the academic literature. Researchers in these fields are also urged to adopt an advocacy role on these issues, or to develop strategic alliances with such advocates.����

Imaging and quantifying salt-tracer transport in a riparian groundwater system by means of 3D ERT monitoring

Determining groundwater flow paths of infiltrated river water is necessary for studying biochemical processes in the riparian zone, but their characterization is complicated by strong temporal and spatial heterogeneity. We investigated to what extent repeat 3D surface electrical resistance tomography (ERT) can be used to monitor transport of a salt-tracer plume under close to natural gradient conditions. The aim is to estimate groundwater flow velocities and pathways at a site located within a riparian groundwater system adjacent to the perialpine Thur River in northeastern Switzerland. Our ERT time-lapse images provide constraints on the plume's shape, flow direction, and velocity. These images allow the movement of the plume to be followed for 35 m. Although the hydraulic gradient is only 1.43 parts per thousand, the ERT time-lapse images demonstrate that the plume's center of mass and its front propagate with velocities of 2x10(-4) m/s and 5x10(-4) m/s, respectively. These velocities are compatible with groundwater resistivity monitoring data in two observation wells 5 m from the injection well. Five additional sensors in the 5-30 m distance range did not detect the plume. Comparison of the ERT time-lapse images with a groundwater transport model and time-lapse inversions of synthetic ERT data indicate that the movement of the plume can be described for the first 6 h after injection by a uniform transport model. Subsurface heterogeneity causes a change of the plume's direction and velocity at later times. Our results demonstrate the effectiveness of using time-lapse 3D surface ERT to monitor flow pathways in a challenging perialpine environment over larger scales than is practically possible with crosshole 3D ERT.

Reaction to novelty and spatial orientation in ALPHA1B(-/-) KO mice

Knockout mice lacking alphalb noradrenergic receptors were tested in behavioural experiments to test a possible effect of the absence of this receptor in reaction to novelty and spatial orientation. Reaction to novelty was tested in two experiments. In the first one the mice' latency to exit the first part of a two compartment set-up was measured. The knockout mice were faster to emerge then their littermate controls. Then they were tested in an open-field, in which new objects were added at the second trial. In the open-field without objects (first trial), the knockout mice showed a greater locomotor activity (path length). Then the same mice showed enhanced exploration of the newly introduced objects, relative to the control. The spatial orientation experiments were done on a homing board and in the water maze. The homing board did not yield a significant difference between the knock-out and the control mice. Both groups showed impaired results when the proximal (olfactory) and distal (visual) cues were disrupted by the rotation of the table. In the water maze however, the alphalb(-/-) mice were unable to solve the task (acquisition and retention), whereas the control mice showed a good acquisition and retention behaviour. The knockout mice' incapacity to learn to reach the submerged platform was not due to an incapacity to swim, as they were as good as their control littermates to reach the platform when it was visible.

Aggravation of chronic stress effects on hippocampal neurogenesis and spatial memory in LPA₁ receptor knockout mice.

BACKGROUND The lysophosphatidic acid LPA₁ receptor regulates plasticity and neurogenesis in the adult hippocampus. Here, we studied whether absence of the LPA₁ receptor modulated the detrimental effects of chronic stress on hippocampal neurogenesis and spatial memory. METHODOLOGY/PRINCIPAL FINDINGS Male LPA₁-null (NULL) and wild-type (WT) mice were assigned to control or chronic stress conditions (21 days of restraint, 3 h/day). Immunohistochemistry for bromodeoxyuridine and endogenous markers was performed to examine hippocampal cell proliferation, survival, number and maturation of young neurons, hippocampal structure and apoptosis in the hippocampus. Corticosterone levels were measured in another a separate cohort of mice. Finally, the hole-board test assessed spatial reference and working memory. Under control conditions, NULL mice showed reduced cell proliferation, a defective population of young neurons, reduced hippocampal volume and moderate spatial memory deficits. However, the primary result is that chronic stress impaired hippocampal neurogenesis in NULLs more severely than in WT mice in terms of cell proliferation; apoptosis; the number and maturation of young neurons; and both the volume and neuronal density in the granular zone. Only stressed NULLs presented hypocortisolemia. Moreover, a dramatic deficit in spatial reference memory consolidation was observed in chronically stressed NULL mice, which was in contrast to the minor effect observed in stressed WT mice. CONCLUSIONS/SIGNIFICANCE These results reveal that the absence of the LPA₁ receptor aggravates the chronic stress-induced impairment to hippocampal neurogenesis and its dependent functions. Thus, modulation of the LPA₁ receptor pathway may be of interest with respect to the treatment of stress-induced hippocampal pathology.

Genotyping Mycobacterium bovis from cattle in the Central Pampas of Argentina: temporal and regional trends

Mycobacterium bovis is the causative agent of bovine tuberculosis (TB), a disease that affects approximately 5% of Argentinean cattle. Among the molecular methods for genotyping, the most convenient are spoligotyping and variable number of tandem repeats (VNTR). A total of 378 samples from bovines with visible lesions consistent with TB were collected at slaughterhouses in three provinces, yielding 265 M. bovis spoligotyped isolates, which were distributed into 35 spoligotypes. In addition, 197 isolates were also typed by the VNTR method and 54 combined VNTR types were detected. There were 24 clusters and 27 orphan types. When both typing methods were combined, 98 spoligotypes and VNTR types were observed with 27 clusters and 71 orphan types. By performing a meta-analysis with previous spoligotyping results, we identified regional and temporal trends in the population structure of M. bovis. For SB0140, the most predominant spoligotype in Argentina, the prevalence percentage remained high during different periods, varying from 25.5-57.8% (1994-2011). By contrast, the second and third most prevalent spoligotypes exhibited important fluctuations. This study shows that there has been an expansion in ancestral lineages as demonstrated by spoligotyping. However, exact tandem repeat typing suggests dynamic changes in the clonal population of this microorganism.

Detection of millimetric deformation using a terrestrial laser scanner: experiment and application to a rockfall event

Abstract. Terrestrial laser scanning (TLS) is one of the most promising surveying techniques for rockslope characteriza- tion and monitoring. Landslide and rockfall movements can be detected by means of comparison of sequential scans. One of the most pressing challenges of natural hazards is com- bined temporal and spatial prediction of rockfall. An outdoor experiment was performed to ascertain whether the TLS in- strumental error is small enough to enable detection of pre- cursory displacements of millimetric magnitude. This con- sists of a known displacement of three objects relative to a stable surface. Results show that millimetric changes cannot be detected by the analysis of the unprocessed datasets. Dis- placement measurement are improved considerably by ap- plying Nearest Neighbour (NN) averaging, which reduces the error (1σ ) up to a factor of 6. This technique was ap- plied to displacements prior to the April 2007 rockfall event at Castellfollit de la Roca, Spain. The maximum precursory displacement measured was 45 mm, approximately 2.5 times the standard deviation of the model comparison, hampering the distinction between actual displacement and instrumen- tal error using conventional methodologies. Encouragingly, the precursory displacement was clearly detected by apply- ing the NN averaging method. These results show that mil- limetric displacements prior to failure can be detected using TLS.

Linking life-history traits, ecology, and niche breadth evolution in north american eriogonoids (polygonaceae).

Abstract Macroevolutionary and microevolutionary studies provide complementary explanations of the processes shaping the evolution of niche breadth. Macroevolutionary approaches scrutinize factors such as the temporal and spatial environmental heterogeneities that drive differentiation among species. Microevolutionary studies, in contrast, focus on the processes that affect intraspecific variability. We combine these perspectives by using macroevolutionary models in a comparative study of intraspecific variability. We address potential differences in rates of evolution of niche breadth and position in annual and perennial plants of the Eriogonoideae subfamily of the Polygonaceae. We anticipated higher rates of evolution in annuals than in perennials owing to differences in generation time that are paralleled by rates of molecular evolution. Instead, we found that perennial eriogonoid species present greater environmental tolerance (wider climate niche) than annual species. Niche breadth of perennial species has evolved two to four times faster than in annuals, while niche optimum has diversified more rapidly among annual species than among perennials. Niche breadth and average elevation of species are correlated. Moreover, niche breadth increases more rapidly with mean species elevation in perennials than in annuals. Our results suggest that both environmental gradients and life-history strategy influence rates and patterns of niche breadth evolution.

Measuring ecological niche overlap from occurrence and spatial environmental data

1. Aim - Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data.¦2. Location - Europe, North America, South America¦3. Methods - The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with predefined distributions and amounts of niche overlap to evaluate several ordination and species distribution modeling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species.¦4. Results - We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographic space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results.¦5. Main conclusions - The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate to study niche differences between species, subspecies or intraspecific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intraspecific lineage has changed over time.

Breeding sites of drosophilids (Diptera) in the Brazilian Savanna. I. Fallen fruits of Emmotum nitens (Icacinaceae), Hancornia speciosa (Apocynaceae) and Anacardium humile (Anacardiaceae)

In this study, drosophilids that bred in fruits of three common plant species of the Brazilian Savanna were investigated: Emmotum nitens, Hancornia speciosa and Anacardium humile, along with the temporal and spatial distribution of these insects among fruits obtained from six individuals of E. nitens. Fallen fruits were collected in natural environments, placed on moist sand in individual containers and all drosophilids that emerged from these resources during 15 days were collected, counted and identified. From 3,651 fruits collected (3,435 of E. nitens, 179 of A. humile and 37 of H. speciosa) 4,541 flies emerged and were classified into 19 species of Drosophilidae. Their distribution was unequal among the three resources, also over time, and among the six individuals of E. nitens. Such fluctuations probably reflect the availability of resources in time and space and probably the action of selective factors such as larval competition.

Seasonal and spatial species richness variation of dung beetle (Coleoptera, Scarabaeidae s. str.) in the Atlantic Forest of southeastern Brazil

The knowledge on Atlantic Forest scarab beetle fauna is quite limited. This biome is strongly degraded and these insects can be used as bioindicators since they are sensitive to forest destruction and show distinct organizational patterns in forest fragments or in areas that have been deteriorated by human activity. Thus, a study of the Scarabaeidae (sensu stricto) dung beetles fauna that inhabit Serra do Japi, São Paulo, Brazil (23º12'-23º22' S and 46º53'-47º03'W) was carried out; the monthly species richness was analyzed in six areas during one year and the vegetation's structural physiognomy was described. The areas included a conserved and a degraded valley, a northward and a southward hillside, a hilltop, and an area of secondary forest growing under eucalyptus trees. The specimens were collected using four pitfall traps baited with human feces, which remained at each spot during 48 hours. Between September, 1997 and August, 1998, 3524 individuals of 39 species were collected; the most abundant were: Canthidium trinodosum, Eurysternus cyanescens, Uroxys kratochvili, Scybalocanthon nigriceps, Uroxys lata, Canthonella sp., Dichotomius assifer, Deltochilum furcatum, Canthidium sp.2, Canthon latipes, Deltochilum rubripenne, Eurysternus sp., and Dichotomius sp.1. The number of individuals and species was greater in the hot, rainy season, when there was a correlation between the number of species and the mean annual temperature [r²= 0.69; p<0.01]. The lower winter richness was most pronounced in the conserved valley, while richness remained relatively constant in the degraded valley; abundance was much higher in the degraded valley. The cluster analysis showed that the valleys and hillsides are the most similar in relation to species composition and abundance, yet different from the secondary forest with eucalypts and the hilltop.

Appraising and selecting strategies to combat and mitigate desertification based on stakeholder knowledge and globalbest practices in Cape Verde Archipelago

Cape Verde is considered part of Sahelian Africa, where drought and desertification are common occurrences. The main activity of the rural population is rain-fed agriculture, which over time has been increasingly challenged by high temporal and spatial rainfall variability, lack of inputs, limited land area, fragmentation of land, steep slopes, pests, lack of mechanization and loss of top soil by water erosion. Human activities, largely through poor farming practices and deforestation (Gomez, 1989) have accelerated natural erosion processes, shifting the balance between soil erosion and soil formation (Norton, 1987). According to previous studies, vegetation cover is one of the most important factors in controlling soil loss (Cyr et al., 1995; Hupy, 2004; Zhang et al., 2004; Zhou et al., 2006). For this reason, reforestation is a touchstone of the Cape Verdean policy to combat desertification. After Independence in 1975, the Cape Verde government had pressing and closely entangled environmental and socio-economic issues to address, as long-term desertification had resulted in a lack of soil cover, severe soil erosion and a scarcity of water resources and fuel wood. Across the archipelago, desertification was resulting from a variety of processes including poor farming practices, soil erosion by water and wind, soil and water salinity in coastal areas due to over pumping and seawater intrusion, drought and unplanned urbanization (DGA-MAAP, 2004). All these issues directly affected socio-economic vulnerability in rural areas, where about 70% of people depended directly or indirectly on agriculture in 1975. By becoming part of the Inter- State Committee for the Fight against Drought in the Sahel in 1975, the government of Cape Verde gained structured support to address these issues more efficiently. Presentday policies and strategies were defined on the basis of rational use of resources and human efforts and were incorporated into three subsequent national plans: the National Action Plan for Development (NDP) (1982–1986), the NDP (1986–1990) and the NDP (1991–1995) (Carvalho