Searching for biodiversity indicators in running waters: do bryophytes, macroinvertebrates, and fish show congruent diversity patterns?

The degree to which different taxonomic groups show congruence in diversity patterns has attracted increased attention, yet such studies on stream biota are lacking. We examined environmental correlates of and congruence in the species richness patterns of bryophytes, macroinvertebrates, and fish in 101 boreal streams in Finland. Congruence in species richness among the taxonomic groups was generally low, mainly because of their differing responses to major environmental gradients. Bryophytes and macroinvertebrates showed the strongest degree of congruence, but even this relationship had a relatively weak predictive power. Bryophyte diversity showed the strongest relationship with water colour, followed by habitat stability, and stream size. Macroinvertebrate diversity increased with stream size, and further variation was accounted for by water colour and acidity. Fish species richness showed a weak and complex relationship with geographical location, stream size, and in-stream habitat characteristics. The regression models explained 23, 45, and 26% of the variation in species richness of bryophytes, macroinvertebrates, and fish, respectively. Our results suggest that indicator taxa may be of limited value in stream biodiversity inventories. Habitat-based approaches are suggested as an alternative surrogate measure in the conservation evaluation of lotic biodiversity.     

Biogeography of copepods in lakes and ponds of subarctic Québec,Canada

We aimed to determine whether the copepod assemblages in lakes and ponds of northern Québec, Canada, were closer in composition to those found in southern Québec, or to those reported from the subarctic and arctic. Six calanoid and five cyclopoid species were identified from 37 ponds and lakes located in the region between 55° N and 59° N. Species diversity was generally low, ranging from 0 to 4 species per lake. Dominant species were Leptodiaptomus minutus and Acanthocyclops vernalis. The species assemblages showed high affinity with those found in forested regions of southern Québec. Exceptions were Leptodiaptomus tyrrelli, previously only recorded west of Hudson Bay, and Hesperodiaptomus arcticus, hitherto recorded north of 58° N. Relationships between the lakes, species, and environmental variables were explored using multivariate analysis. Lakes situated along the coast and on two offshore islands clustered together and were characterised by higher conductivity and pH than those lakes located further inland. Leptodiaptomus tyrrelli was common in these coastal lakes. Canonical correspondence analysis revealed statistically significant relationships between copepod distributions and conductivity, dissolved organic carbon and pH. These three variables accounted for 70% of the variation in the species' distribution.     

Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in northern Chile: an example of geographical dispersion?

The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.     

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of alpha than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of alpha and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with alpha (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of alpha, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.     

Do microbes have macroecology? Large‐scale patterns in the diversity and distribution of marine benthic ciliates

Aim The biogeography and global distribution of protists has long been disputed, with two primary, opposing views. To test these two sets of views in greater detail, we have compiled the available data for marine benthic ciliates and assessed the general patterns of their diversity and distribution compared with Metazoa. Location World‐wide. Methods A comprehensive database (1342 species, over 350 sources) was used to analyse the diversity, distribution, species occurrences and range size distribution of free‐living ciliates that inhabit marine sediments in 17 geographical regions. Results Twenty‐five per cent of the species have been found in a single region only, whereas 18% are widespread (they occur in more than half the regions covering both hemispheres). Only 5–7% of regional faunas are endemic, which is much lower than for macroorganisms. Regional diversity depends neither on total area nor on coastline length and does not show any obvious latitudinal trends, but correlates highly with the investigation effort expended in a region and (negatively) with the average salinity. A comparison of species composition reveals distinctions between the Arctic Area (the White, Barents and Kara seas), Laurasian Area (north Atlantic, north Pacific and European seas), Gondwanian Area (Southern Ocean) and the Antarctic. No clear geographical correlations are found for faunistic composition at the genus or family levels. There is the tendency to narrow the latitudinal ranges for species found at high latitudes (reversal of Rapoport's rule). Main conclusions Undersampling and data insufficiency are the key factors affecting the observed diversity and distribution of microorganisms. Nevertheless, marine benthic ciliates demonstrate certain patterns that generally agree with the ‘moderate endemicity’ model ( Foissner, 2004, 2008 ), but consistently contradict the regularities commonly observed for multicellular taxa. Thus, ciliates do have a biogeography, but their macroecological patterns may be different in some respects from that of macroorganisms.     

Geographic patterns in fruit colour diversity: do leaves constrain the colour of fleshy fruits?

We tested for geographic patterns in fruit colour diversity. Fruit colours are thought to promote detection by seed dispersers. Because seed dispersers differ in their spectral sensitivities, we predicted that fruit colour diversity would be higher in regions with higher seed disperser diversity (i.e. the tropics). We collected reflectance data on 232 fruiting plant species and their natural backgrounds in seven localities in Europe, North and South America, and analysed fruit colour diversity according to the visual system of birds—the primary consumer types of these fruits. We found no evidence that fruit colours are either more conspicuous or more diverse in tropical areas characterised by higher seed disperser diversity. Instead, fruit colour diversity was lowest in central Brazil, suggesting that fruit colours may be more diverse in temperate regions. Although we found little evidence for geographic variation in fruit hues, the spectral properties of fruits were positively associated with the spectral properties of backgrounds. This result implies that fruit colours may be influenced by selection on the reflectance properties of leaves, thus constraining the evolution of fruit colour. Overall, the results suggest that fruit colours in the tropics are neither more diverse nor more conspicuous than temperate fruits, and that fruit colours may be influenced by correlated selection on leaf reflectance properties. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Reproduction in high altitude Aymara: physiological stress and fertility planning?

Reproductive characteristics at high altitude are described based on the reproductive histories of 720 Aymara women, collected in 1998 and 1999 in a group of twelve peasant communities at a mean altitude of 4000 m in the Bolivian Altiplano. The reproductive pattern is shaped by a late onset of childbearing, associated with a rather short reproductive span and large birth intervals. Environmental conditions could explain the particularly late age at menarche of rural girls compared with their urban counterparts, whereas the age at first birth is likely to be under cultural control. The short reproductive span appears to result from a large mean interval between last birth and menopause, which is essentially determined by cultural decisions. The birth intervals, which are longer than in many traditional societies, could be the result of a slower restoration of postpartum fecundability induced by the hard way of life inherent in the Altiplano (including poor sanitary and nutritional conditions and high workload), perhaps aggravated by hypoxia. However, a secular trend in fertility is perceptible, towards earlier menarche, earlier age at first birth, increasing reproductive span and a slight increase in live births and surviving offspring, which is probably the result of a slow improvement in living conditions. The existence of birth control on the one hand, and a total fertility rate averaging six live births among the couples who do not practise contraception on the other, are other arguments against the hypothesis of a low natural fecundity in these Aymara groups.     

Diversity assessment of benthic macroinvertebrates, yeasts, and microbiological indicators along a longitudinal gradient in Serra do Cipó, Brazil.

The main goals of this study were: 1) to evaluate the structure, diversity, and functional trophic group composition of benthic macroinvertebrate communities; 2) to characterize water quality in the headwaters of the Doce river watershed, based on physical, chemical, and biological parameters (benthic macroinvertebrates, fecal coliforms, heterotrophic bacteria, and yeasts); and 3) to contribute to the knowledge of the structure and function of longitudinal gradients in lotic ecosystems in Brazil. A total of 60 benthic macroinvertebrate taxa were identified, the dominant group being the aquatic insects, with 50 families distributed in 8 orders. The dry period presented higher values of taxonomic richness and total density of benthic macroinvertebrates. A decreasing gradient was observed in these variable values from the 3rd order stretch down to the 6th order stretch. The highest Shannon-Wiener diversity values were found in the rainy period in the 3rd order stretches, which presented well-developed riparian forest. Besides the 3rd order stretches, the Pielou evenness index values were also high in the 6th order stretch. The collectors, together with the scrapers, predominated in the benthic macroinvertebrate communities in all river stretches, except in the 2nd, 4th, and 5th order stretches in the rainy period, where communities were dominated by filterers. The shredders and predators presented low densities for all river stretches. All microbiological variables presented low levels. Due to the high counts of heterotrophic bacteria and coliforms, the studied river stretches presented inadequate potability but adequate balneability levels. The results suggest that the structure, diversity, and composition of the benthic macroinvertebrate communities are influenced by the trophic resource availability, seasonality, and sediment heterogeneity. The microbiological results of this study allow inferring that the waters from Serra do Cipó have excellent potential for recreational use and as future sources of water for human consumption.     

Distinguishing foldable proteins from nonfolders: When and how do they differ?

When a denatured polypeptide is put into refolding conditions, it undergoes conformational changes on a variety of times scales. We set out here to distinguish the fast events that promote productive folding from other processes that may be generic to any non-folding polypeptide. We have apply an ab initio folding algorithm to model the folding of various proteins and their compositionally identical, random-sequence analogues. In the earliest stages, proteins and their scrambled-sequence counterparts undergo indistinguishable reductions in the extent to which they explore conformation space. For both polypeptides, an early contraction occurs but does not involve the formation of a distinct intermediate. Following this phase, however, the naturally-occurring sequences are distinguished by an increase in the formation of three-body correlations wherein a hydrophobic group desolvates and protects an intra-molecular hydrogen bond. These correlations are manifested in a mild but measurable reduction of the accessible configuration space beyond that of the random-sequence peptides, and portend the folding to the native structure. Hence, early events reflect a generic response of the denatured ensemble to a change in solvent condition, but the wild-type sequence develops additional correlations as its structure evolves that can reveal the protein's foldability.     

The seasonal dynamics and persistence of stream macroinvertebrates in Nepal: do monsoon floods represent disturbance?

1. The monsoon causes major flood events in some Himalayan streams, but their seasonal predictability might reduce the resulting disturbance. We assessed seasonal change in the benthos of 16 streams in central Nepal over a gradient of declining rainfall and increasing altitude from 600 to 3800 m. All sites were surveyed on four occasions, two in winter (November) and two pre-monsoon (June), with additional sampling during the monsoon (August) at four low altitude sites. Invertebrate abundance, taxon richness and persistence were assessed at all sites, and density and meso-habitat distribution at the four low altitude sites only.
2. Strong seasonal variation among invertebrates was confined primarily to streams at low altitude (600–800 m) where monsoon rainfall was greatest and catchments were dominated by terraced agriculture. At these sites, a significant reduction in benthic density (on average by 77%) and taxon richness (by 20%) occurred between the winter and pre-monsoon periods, so that invertebrate numbers were already low before the monsoon. A further significant decline occurred in all meso-habitats during the monsoon, but the change in density was small in absolute terms.
3. Persistence in rank abundance was equally low at all sites, but turnover in composition was significantly lower at sites in semi-natural forest than in catchments managed for terracing or alpine pasture.
4. These data provide no evidence that monsoonal floods represent major disturbance, instead supporting the view that the ecological response might reflect an adjustment to predictable flow pattern. However, catchment land use in the Himalaya appears to be a significant source of ecosystem instability, and confounds the simple interpretation of monsoon effects.     

Local,regional and global markets: what drives the tuna fisheries?

Tuna products are amongst the most popular seafoods in the world and widely traded across the globe. Their global trade developed at a very early stage in the growth and development of tuna fisheries. In this article, recent evolutions of tuna markets in terms of products (for both sashimi and cannery-grade tuna products), market structures, and trade are introduced followed by a comprehensive study of global integration through price linkages. Most studies show a high degree of market integration and competition through prices at the world-wide level. Finally, we introduce some original results about the relationship between catches and prices (estimated coefficients of demand elasticity and flexibility), and provide answers to a few key questions for tuna fisheries and markets, including: How do consumers respond to price changes? Are fish price changes fully transmitted to consumers? Is there any economic incentive for fishers to comply with reduced catch quotas? Do fishers target particular tuna species according to the relative price of tuna species?     

Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories?

Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall F_ST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.     

Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Diatoms are a species-diverse phylum of microalgae often presenting high biomass in aquatic habitats. This makes them excellent ecological indicators in rivers and lakes. They are routinely used to assess ecological quality of rivers and lakes using microscopy, which is time consuming. An alternative is to determine species in samples based on short DNA barcodes and high-throughput sequencing (HTS). Former studies showed that community structure and water quality assessments based on diatoms deliver similar results with both methods. But, none evaluated if diversities were assessed in the same way despite the importance of this ecological metric. Based on littoral benthic samplings carried out in 56 pristine alpine lakes, we compared different diversity indices measured with microscopy and metabarcoding. Each lake was sampled in three different places of its littoral. We showed that α (diversity measured in a single sampling site of a given lake) and ? (total diversity in a lake where three independent samples were considered) diversities obtained with HTS were higher than those obtained with microscopy. This may be explained by the capacity of HTS to detect morphologically cryptic species and to better detect rare taxa. On the other hand, β diversity obtained with HTS was smaller, which may be explained by the capacity of HTS to detect very rare species and free-floating extracellular DNA. Nevertheless, diversity indices obtained with both methodologies were well correlated each other. This study validates the possibility to assess diatom diversity with HTS in a comparable way to the classical microscopic analysis.     

Benthic macroinvertebrates of tropical streams: functional and trophic diversity of the Lacantún River,Mexico

Limnology - The differences between temperate and tropical seasonality suggest that ecological models developed for temperate streams do not necessarily apply to tropical streams. While detritus is...     

Living on the edge: do central and marginal populations of plants differ in habitat suitability?

The performance of populations at the edge of specie’s distribution range may differ substantially from central populations. Here, we develop a modelling framework to estimate ecological niches (i.e. climatic) of four locally endangered plant species and measure the distance of marginal (geographically) populations to the species’ niche centroid in order to analyse whether marginal populations are outside of the optimal ecological niche of each species. Our results show that for three of the four studied species, which have their populations located at the margins of their distribution ranges, are also at the margins of their climate gradients. These results would support the hypothesis that marginality within the set of habitable conditions (i.e. ecological niche) may represent an important determinant on performance of some plant populations, as well as a plausible explanation to the degree of stagnancy or regression experienced by species in those regions where their populations are at the margin of their ecological niche and/or they are restricted to microrefugia with ecological conditions very different from those around them. Finally, this study aims to be a theoretical base from which to advance on, including other types of factors (e.g. biotic interactions, topography, human influence and population fluctuations through time), which will allow for a better understanding of the complex network of factors that occur in marginal plant populations.     

Does lake age affect zooplankton diversity in Mediterranean lakes and reservoirs? A case study from southern Italy

Zooplankton assemblages of 51 lacustrine environments located in the middle of the Mediterranean Region were analysed to evaluate the existence of an ‘age effect’ in determining their structure. The analysed datasets refer to two different geographic areas, one comprising 30 natural and artificial lakes in Sicily and the other an arrangement of 21 analogous aquatic ecosystems located at the bottom of the Italian Peninsula, a more pristine area called Southern Apennine region. Most of the natural lakes are of post-glacial origin. The artificial lakes in both datasets were built in the last century and offer the opportunity to evaluate the possible short-term effects of ageing on the structure of their zooplankton. A comparison of assemblages in the two regions by PERMANOVA and nMDS revealed that they are quite different; therefore they were analysed separately. An explorative analysis on the possible relationship between biological data and environmental data (including lake age) was performed on both datasets using DISTLM. The presence of an ‘age effect’ emerged only in the subset of artificial lakes of the Southern Apennine region; accordingly it was tested more in detail with an a posteriori PERMANOVA analysis in the subset of reservoirs that resulted positive in the first test. SIMPER allowed us to single out the main species responsible of changes in the zooplankton along the selected age groups. No age effect was evident in the Sicilian water bodies, where other variables, such as conductivity, trophic state, urbanisation and water level fluctuations proved to have a major role in shaping zooplankton assemblages. The results showed that the age effect is: (i) detectable only at a time scale of decades; (ii) masked by the human impact in the watershed.     

Population differentiation in whiskered auklets Aethia pygmaea: do diurnal and nocturnal colonies differ in genetics,morphometry and acoustics?

Despite a great number of empirical studies, the mechanisms of population differentiation and the factors that influence this process, particularly in seabirds, remain insufficiently understood. Here we analyzed population structure in the whiskered auklet Aethia pygmaea, a previously poorly studied alcid species with unusual differentiation in colony attendance rhythms (i.e. diurnal in the Sea of Okhotsk vs nocturnal in the Bering Sea), and examined the influence of it on intraspecific differentiation. For this study, we analyzed morphometric measurements, acoustic variables, mitochondrial control region fragment and five microsatellite loci from nine whiskered auklet colonies spanning the breeding range. Previous research has shown a clinal morphometric variation in this species. We build on this analysis by adding auklets from more colonies, for the first time analyzing vocalizations from different colonies and genetic structure of this species. Our data supports a clinal variation in morphometric and acoustic characters with the largest size and the lowest call frequency in western birds, and the smallest size and highest call frequency in the east. We also found two mitochondrial lineages – whiskered auklets from colonies in the Sea of Okhotsk and the Commander Is. (Bering Sea) and from the Aleutian Is. (Bering Sea), that were presumably formed during Sangamonian interglacial period (115 000–130 000 years ago). Genetic clusters found did not reflect differences in colony attendance rhythms, suggesting that they were shaped by other factors (e.g. differences in predator pressure) and are unlikely to have participated in the formation of population structure. Colony fidelity, mobility of birds, proximity of foraging grounds and location of colonies in relation to seasonal ice pack, seem to be more likely determinants of population differentiation.     

Local,cell-nonautonomous feedback regulation of myosin dynamics patterns transitions in cell behavior: a role for tension and geometry?

How robust patterns of tissue dynamics emerge from heterogeneities, stochasticities, and asynchronies in cell behavior is an outstanding question in morphogenesis. A clear understanding of this requires examining the influence of the behavior of single cells on tissue patterning. Here we develop single-cell manipulation strategies to uncover the origin of patterned cell behavior in the amnioserosa during Drosophila dorsal closure. We show that the formation and dissolution of contractile, medial actomyosin networks previously shown to underlie pulsed apical constrictions in the amnioserosa are apparently asynchronous in adjacent cells. We demonstrate for the first time that mechanical stresses and Rho1 GTPase control myosin dynamics qualitatively and quantitatively, in amplitude and direction, both cell autonomously and nonautonomously. We then demonstrate that interfering with myosin-dependent contractility in single cells also influences pulsed constrictions cell nonautonomously. Our results suggest that signals and stresses can feedback regulate the amplitude and spatial propagation of pulsed constrictions through their influence on tension and geometry. We establish the relevance of these findings to native closure by showing that cell delamination represents a locally patterned and collective transition from pulsed to unpulsed constriction that also relies on the nonautonomous feedback control of myosin dynamics.