The hand structure of Carnotaurus sastrei (Theropoda,Abelisauridae): implications for hand diversity and evolution in abelisaurids

Abstract: Carnotaurus sastrei is an abelisaurid dinosaur from the Late Cretaceous of Argentina that has very reduced, but robust, forelimbs and derived hands with four digits, including a large, conical‐shaped metacarpal IV lacking an articulation for a phalanx. The analysis presented in this work highlights a series of additional autapomorphies of C. sastrei. For example, the proximal phalanges are longer than the metacarpals in digits II and III, and digit III includes only one phalanx besides the ungual. The hand of Carnotaurus shares several features with those of Aucasaurus and Majungasaurus, but the hands of the latter genera also display autapomorphies, indicating that the diversity in abelisaurid hand structure is similar to the diversity of cranial protuberances of these dinosaurs.     

Molecular data and species distribution models reveal the Pleistocene history of the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)1

1. We investigated the Pleistocene and Holocene history of the rare mayfly Ameletus inopinatus EATON 1887 (Ephemeroptera: Siphlonuridae) in Europe. We used A. inopinatus as a model species to explore the phylogeography of montane, cold‐tolerant aquatic insects with arctic–alpine distributions. 2. Using species distribution models, we developed hypotheses about the species demographic history in Central Europe and the recolonisation history of Fennoscandia. We tested these hypotheses using mitochondrial cytochrome oxidase I (mtCOI) sequence data and compared our genetic results with previously generated microsatellite data to explore genetic diversity distributions of A. inopinatus. 3. We observed old lineages, deep splits and almost complete lineage sorting of mtCOI sequences among mountain ranges. These results support a periglacial survival, i.e. persistence at the periphery of Pleistocene glaciers in Central Europe. 4. There was strong differentiation between the Fennoscandian and all other populations, indicating that Fennoscandia was recolonised from a refugium not accounted for in our sampling. High degrees of population genetic structure within the northern samples suggest that Fennoscandia was recolonised by more than one lineage. However, this structure was not apparent in previously published microsatellite data, consistent with secondary contact without sexual incompatibility or with sex‐biased dispersal. 5. Our demographic analyses indicate that (i) the separation of northern and Central European lineages occurred during the early Pleistocene; (ii) Central European populations have persisted independently throughout the Pleistocene and (iii) the species extended its range about 150 000 years ago.     

Leaf‐litter colonisation and breakdown in relation to stream typology: insights from Mediterranean low‐order streams

1. Scant information is available on leaf breakdown in streams of arid and semiarid regions, including the Mediterranean, where environmental heterogeneity can be high and the relationship between stream characteristics and leaf breakdown is poorly known. We tested the hypotheses that differences in leaf breakdown metrics would be substantially higher between mountain and lowland Mediterranean streams than among streams within each subregion and that variability among streams would be substantially higher in the lowlands, because permanent reaches in the semiarid lowland streams are rare and isolated. 2. We compared leaf breakdown and associated dynamics of nutrients, fungi and invertebrates in low‐order Mediterranean streams draining sub‐humid forests in the Sierra Nevada Mountains and nearby semiarid lowlands of south‐eastern Spain. Streams differed between the two subregions mainly in water ion content, temperature and riparian tree cover. We detected higher environmental heterogeneity among streams within the lowlands compared to the Sierra Nevada mountain range. In the lowlands, breakdown coefficients (k) of alder leaves spanned almost the entire range reported for this species from temperate streams, overlapping with less variable breakdown coefficients in the Sierra Nevada. 3. The high variability of k values among the lowland sites appeared to be caused primarily by variability in the composition and abundance of a few leaf‐consuming invertebrate taxa, particularly the snail Melanopsis praemorsa. Fungal and nutrient dynamics were less variable among sites within each subregion. 4. These results indicate that the critical condition for stream functional assessment of well‐constrained breakdown rates, or related metrics, could be met at reference sites within homogenous bio‐geo‐climatic regions such as the Sierra Nevada. By contrast, in heterogeneous areas such as the semiarid lowland streams, natural variability of breakdown rates can greatly exceed the magnitude of effects expected in response to anthropogenic disturbances.     

Factors driving spatial and temporal variation in production and production / biomass ratio of stream‐resident brown trout (Salmo trutta) in Cantabrian streams

1. The objective was to identify the factors driving spatial and temporal variation in annual production (P_A) and turnover (production/biomass) ratio (P/B_A) of resident brown trout Salmo trutta in tributaries of the Rio Esva (Cantabrian Mountains, Asturias, north‐western Spain). We examined annual production (total production of all age‐classes over a year) (P_A) and turnover (P/B_A) ratios, in relation to year‐class production (production over the entire life time of a year‐class) (P_T) and turnover (P/B_T) ratio, over 14 years at a total of 12 sites along the length of four contrasting tributaries. In addition, we explored whether the importance of recruitment and site depth for spatial and temporal variations in year‐class production (P_T), elucidated in previous studies, extends to annual production. 2. Large spatial (among sites) and temporal (among years) variation in annual production (range 1.9–40.3 g m^?2 per year) and P/B_A ratio (range 0.76–2.4 per year) typified these populations, values reported here including all the variation reported globally for salmonids streams inhabited by one or several species. 3. Despite substantial differences among streams and sites in all production attributes, when all data were pooled, annual (P_A) and year‐class production (P_T) and annual (P/B_A) and year‐class P/B_T ratios were tightly linked. Annual (P_A) and year‐class production (P_T) were similar but not identical, i.e. P_T = 0.94 P_A, whereas the P/B_T ratios were 4 + P/B_A ratios. 4. Recruitment (Rc) and mean annual density (N_A) were major density‐dependent drivers of production and their relationships were described by simple mathematical models. While year‐class production (P_T) was determined (R² = 70.1%) by recruitment (Rc), annual production (P_A) was determined (R² = 60.3%) by mean annual density (N_A). In turn, variation in recruitment explained R² = 55.2% of variation in year‐class P/B_T ratios, the latter attaining an asymptote at P/B_T = 6 at progressively higher levels of recruitment. Similarly, variations in mean annual density (N_A) explained R² = 52.1% of variation in annual P/B_A, the latter reaching an asymptote at P/B_A = 2.1. This explained why P/B_T is equal to P/B_A plus the number of year‐classes at high but not at low densities. 5. Site depth was a major determinant of spatial (among sites) variation in production attributes. All these attributes described two‐phase trajectories with site depth, reaching a maximum at sites of intermediate depth and declining at shallower and deeper sites. As a consequence, at sites where recruitment and mean annual density reached minimum or maximum values, annual (P_A) and year‐class production (P_T) and annual (P/B_A) and year‐class P/B_T ratios also reached minimum and maximum values.     

Ontogenetic variation in density‐dependent growth of brown trout through habitat competition

1. Density‐dependent growth has been widely reported in freshwater fishes, but the ontogenetic evolution of competition and its subsequent effects on growth through a life span remains unclear. 2. Patterns of competition can be described by integrating population abundance data with habitat‐modelling results. Weighted usable area (WUA; m² WUA ha^?1) curves are obtained for each flow value and are then coupled with demographic data to obtain the occupancy rates (trout m^?2 WUA, the density of a given age class related to its suitable habitat) of the WUA for every age class, year and site. 3. We examined a long‐term data series searching for temporal variation in the influence of habitat occupancy rate on the growth of brown trout Salmo trutta. We tested whether (i) mean cohort mass (mean mass of the cohort during the first 3 years of life) is affected by the occupancy rate experienced across a life span; and (ii) the occupancy rate experienced at different ages influenced mean body size. 4. We observed a consistent negative power relationship between average cohort mass and mean occupancy rate through a life span, indicating that stronger cohorts were related to a reduced growth, with likely consequences for individual fitness. 5. The effects of occupancy rate on size‐at‐age were mainly detected in the size attained at the second year of life, but they were because of the competition at different times. Thus, the level of competition varied through ontogeny, in some of the rivers affecting growth since the first year of life, whereas in most of the rivers the main effects on body size resulted from the competition during the second year of life. 6. Occupancy rate appears more appropriate than density for assessing the occurrence of habitat competition in freshwater fishes, since it encompasses the differences in quantity and quality of suitable habitat for each age class. 7. Our study highlights the importance of density‐dependent growth as a key process in the dynamics of brown trout populations, its temporal variation depending on the temporal changes of density and the variation of competition associated with the habitat capacity for each life stage.     

Phylogeography of the marine isopod Stenosoma nadejda (Rezig, 1989) in North African Atlantic and western Mediterranean coasts reveals complex differentiation patterns and a new species

The transition zone between the Mediterranean and Atlantic basins has been extensively addressed in phylogeographical studies of marine species. However, biases exist towards the analysis of highly dispersive species, and there is a higher sampling effort in European coasts compared to North Africa. This may be hindering a detailed understanding of the historical and contemporary processes that shaped patterns of population genetic structure in the region. In the present study, we investigated the phylogeographical and phylogenetic patterns of mitochondrial cytochrome c oxidase subunit I sequences from a species with direct development and low dispersal abilities, Stenosoma nadejda (Rezig, 1989). The study area included 13 localities along the Atlantic and Mediterranean North African coasts, as well as the Alboran Sea. A new Stenosoma species, from the coasts of Algeria and Alboran Island, was discovered. For S. nadejda, phylogeographical analyses revealed three distinct clades: one in the Iberian Atlantic plus the Alboran Sea, one in the western Mediterranean, and another in the Atlantic coast of Africa. Haplotypes from the Alboran Island were more related to those from the western Mediterranean coast (east of the Almeria–Oran Front). Given the strong differentiation, it is probable that this species survived in multiple glacial refugia during the Pleistocenic glaciations. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 419–431.     

A collection of open source applications for mass spectrometry data mining

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front‐end graphical user interface that combines several Thermo RAW formats to MASCOT? Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode.     

Divergence in social foraging among morphs of the three‐spined stickleback,Gasterosteus aculeatus

Foraging in social groups has a number of benefits but can also increase the risk of exploitation. High tendency to shoal may be correlated with groups foraging, although facultatively social fish adjust both shoaling decisions and food resource defence based on intrinsic and extrinsic factors. The main aim of this study was to examine the relationships between shoaling, solitary foraging and aggression, forager tolerance of conspecifics joining at a discovered food patch and forager exploitation of resources discovered by others. We used two intra‐lacustrine three‐spined stickleback morph pairs, lava and mud, and monomorphic morphs from each of lava and mud habitats. The lava morph formed less cohesive shoals, was bolder during solitary foraging, approached and entered an occupied food patch less frequently than the mud morph, suggesting a link between shoaling and the propensity for social foraging. However, shoaling tendency and joiner tolerance were not correlated at a population level. Intralacustrine lava and mud morphs differed more markedly in joiner tolerance than morphs from single habitat lakes, whereas the opposite was true for shoaling tendency. We conclude that, in addition to differentiation in shoaling tendency, the lava and mud morphs differ in social foraging and these variations may act to promote population divergence. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 194–203.