Subfossil diatoms from Hann Park pond,Dakar, Senegal: floristic inventory and palaeoenvironmental reconstruction

Diatoms in a 100 cm-long core from a pond in Hann Forest Park, western Senegal, were studied with the aim of reconstituting this interdune depression’s history, particularly the human influence, during the last century. Sixty-three species and varieties of diatoms belonging to 32 genera were identified, of which twelve are reported for the first time in Senegambia. The genera most represented were Nitzschia (10 species), Eunotia (9 species) and Pinnularia (6 species). The microflora was characterised by a dominance of epipelic, epiphytic and aerophilic species. Diatom assemblage analyses, combined with lithological core data, showed that the pond has remained very shallow throughout its evolution. The disappearance of acidophilic species and the development of mesosaprobes and mesoeutrophic alkaliphilic species in the upper part of the core can be attributed to organic pollution caused by human activities, which resulted in eutrophication of the pond waters since the beginning of the 20th century.     

Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites

Given their large population sizes and presumed high dispersal capacity, protists are expected to exhibit homogeneous population structure over large spatial scales. On the other hand, the fragmented and short‐lived nature of the lentic freshwater habitats that many protists inhabit promotes strong population differentiation. We used microsatellites in two benthic freshwater diatoms, Eunotia bilunaris ‘robust’ and Sellaphora capitata, sampled from within a pond and connected ponds, through isolated ponds from the same region to western Europe to determine the spatial scale at which differentiation appears. Because periods of low genotypic diversity contribute to population differentiation, we also assessed genotypic diversity. While genotypic diversity was very high to maximal in most samples of both species, some had a markedly lower diversity, with up to half (Eunotia) and over 90% (Sellaphora) of the strains having the same multilocus genotype. Population differentiation showed an isolation‐by‐distance pattern with very low standardized F_ST values between samples from the same or connected ponds but high values between isolated ponds, even when situated in the same region. Partial rbcL sequences in Eunotia were consistent with this pattern as isolated ponds in the same region could differ widely in haplotype composition. Populations identified by Structure corresponded to the source ponds, confirming that ‘pond’ is the main factor structuring these populations. We conclude that freshwater benthic diatom populations are highly fragmented on a regional scale, reflecting either less dispersal than is often assumed or reduced establishment success of immigrants, so that dispersal does not translate into gene flow.     

Gogorevia,a New Monoraphid Diatom Genus for Achnanthes exigua and Allied Taxa (Achnanthidiaceae) Described on the Basis of an Integrated Molecular and Morphological Approach

A new diatom genus, Gogorevia, is described on the basis of an integrated molecular and morphological investigation. Two species are described from Vietnam: the generitype, G. rinatii sp. nov., and G. ovalis sp. nov. These species share many morphological features with Achnanthes exigua and allied taxa that were previously transferred to the genera Achnanthidium or Lemnicola. Our current molecular investigation shows that Gogorevia is distinct and phylogenetically removed from the above-mentioned genera. Morphologically, Gogorevia differs from Achnanthidium and Lemnicola by the shape of the valves, possessing uniseriate striae, raphe morphology, and the presence of an evident sternum. The recently described species Lemnicola uniseriata is transferred to Gogorevia on the basis that it possesses the same morphological features and phylogenetic position as other members of the genus.     

Huia caspica gen. & comb. nov., a dinoflagellate species that recently crossed the marine‐freshwater boundary

The dinoflagellate subfamily Diplopsalidoideae encompasses 11 genera whose plate patterns show a large diversity. In a recently published molecular phylogeny (Liu et al. 2015) some of these genera (e.g. Diplopsalis, Diplopelta) are polyphyletic, suggesting that further subdivision of these genera is needed. Here we established the cyst‐theca relationship of Diplopsalis caspica by incubating cysts collected from the East China Sea. Cells of D. caspica display a plate formula of Po, X, 3′, 1a, 6″, 3c+t, ?4s, 5″′, 1″″, characterized by a small, parallelogrammic anterior intercalary plate (1a) located in the middle of the dorsal part of the epitheca. The cysts are spherical and smooth‐walled with a theropylic archeopyle. In addition, we obtained four large subunit ribosomal DNA (LSU rDNA) sequences from the germinated motile cells by single‐cell polymerase chain reaction. Strains of D. caspica from the marine environment of the East China Sea differ at 0–2 positions of LSU rDNA sequences from that of lacustrine strains from NE China. In the molecular phylogeny, D. caspica was close to Lebouraia pusilla but distant from D. lenticula, the type species of Diplopsalis. Our results support the systematic importance of plate 1a, and therefore D. caspica was transferred to a new genus, Huia. The conservative LSU rDNA sequences in H. caspica suggest that the marine‐freshwater transition occurred recently.     

Land‐use Change Dynamics,Soil Type and Species Forming Mono‐dominant Patches: the Case of Pteridium aquilinum in a Neotropical Rain Forest Region

Deforestation and agricultural land degradation in tropical regions can create conditions for growth of perennial plant species forming mono‐dominated patches (MDP). Such species might limit forest regeneration, and their proliferation forces the abandonment of fields and subsequent deforestation to establish new fields. Therefore, identifying factors fostering MDP species is critical for biodiversity conservation in human‐modified landscapes. Here, we propose a conceptual framework to identify such factors and apply it to the case of Pteridium aquilinum (bracken fern), a light‐demanding species, tolerant of low soil fertility and fire. We hypothesize that bracken proliferation is promoted by land‐use changes that increase light availability, especially in sites with low soil fertility and land uses involving fire. We assessed this idea using agricultural fields in southeastern Mexico with different land‐use change histories and quantifying prevalence and cover of bracken. Five different land‐use change histories resulted from transitions among forest, crop, pasture, and fallow field stages. Of the 133 fields sampled, 71 percent had P. aquilinum; regression tree analysis indicated that 65 percent of inter‐field variation in prevalence and 90 percent in cover was explained by land‐use change history and soil type. Maximum prevalence, cover, and rates of increase in bracken were found on fields with low fertility sandy/clay soils, which had been used for crops and pasture, were frequently burned, and had high levels of light. Fields on fertile alluvial soil never used for pasture were bracken‐free. Agriculture promoting high light environments on less fertile soils is a major cause of bracken proliferation and likely that of other MDP species.     

Structure of a pond community in Central Mexico

The community structure of a tropical pond located in Mexico City was described. Primary producers were diverse and abundant and macrophyte components provide a broad habitat diversity. Major biotic components in the water column were algae of the genera Microcystis, Scenedesmus and Chlamydomonas. Mats of Cyclotella were located in deeper, shaded areas associated with the bottom. Three species of emergent macrophytes characterize the large primary producers. The zooplankton was dominated by protozoa, which were more abundant than rotifers and Crustacea. Dominant invertebrate species of the pond bottom were insect larvae, gastropod mollusks, oligochaete annelids and nematodes. Vertebrates (fish, amphibians, reptiles) feed on this variety of biotic components. A flow diagram depicted the major biological interactions and suggested a complex trophic structure.     

Pathways of ornamental and aquarium fish introductions into urban ponds of Epping Forest (London,England): the human vector*

To examine the role of humans in the non‐native fish introductions, we measured the frequency of occurrence and density of non‐native fishes in ponds (Epping Forest, Essex, England) that had been restored (drained of water and voided of fish or treated with rotenone) on a known date and into which no piscivorous or non‐native fishes had subsequently been stocked intentionally. For each pond, the period of time since pond restoration, pond area, distance to nearest residential housing, distance to nearest footpath, distance to nearest water body or stream, and the proportion of pond vegetated were measured. The occurrence of both non‐native and unexpected native fish species was non‐random, and the number of ornamental varieties was found to increase as pond distance from the nearest road decreased. Variety richness of each of three categories of fish (non‐native, goldfish Carassius auratus and native) was significantly correlated with at least two of the following variables: distance from nearest road, nearest footpath and nearest pond. The rate of non‐native fish introductions (adjusted variety richness per year) could also be estimated from pond distance to the nearest road, being about 3.5 ornamental varieties introduced per year in ponds adjacent to roads, but the rate appears to be much greater in ponds that had recently (<1.5 years) undergone restoration. Implications for conservation and management, as well as the potential role of societal issues such as recreational activities, cultural and religious practices, are discussed.     

Wind‐driven thermocline movements affect the colonisation and growth of Achnanthidium minutissimum,a ubiquitous benthic diatom in lakes

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The relative roles of contemporary and ancient processes in shaping genetic variation of a generalist fish in a catchment dominated by agriculture

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Timing matters: species‐specific interactions between spawning time,substrate quality,and recruitment success in three salmonid species

Substratum quality and oxygen supply to the interstitial zone are crucial for the reproductive success of salmonid fishes. At present, degradation of spawning grounds due to fine sediment deposition and colmation are recognized as main factors for reproductive failure. In addition, changes in water temperatures due to climate change, damming, and cooling water inlets are predicted to reduce hatching success. We tested the hypothesis that the biological effects of habitat degradation depend strongly on the species‐specific spawning seasons and life‐history strategies (e.g., fall‐ vs. spring‐spawners, migratory vs. resident species) and assessed temperature as an important species‐specific factor for hatching success within river substratum. We studied the species‐specific differences in their responses to such disturbances using egg‐to‐fry survival of Danube Salmon (Hucho hucho), resident brown trout (Salmo trutta fario), and migratory brown trout (Salmo trutta lacustris) as biological endpoint. The egg incubation and hatching success of the salmonids and their dependence on temperature and stream substratum quality were compared. Hatching rates of Danube salmon were lower than of brown trout, probably due to higher oxygen demands and increased interstitial respiration in spring. Increases in maximum water temperature reduced hatching rates of resident and migratory brown trout (both fall‐spawners) but were positively correlated with hatching rates of Danube salmon (a spring‐spawner). Significantly longer incubation periods of resident and migratory brown trout coincided with relatively low stream substratum quality at the end of the egg incubation. Danube salmon seem to avoid low oxygen concentrations in the hyporheic zone by faster egg development favored by higher water temperatures. Consequently, the prediction of effects of temperature changes and altered stream substratum properties on gravel‐spawning fishes and biological communities should consider the observed species‐specific variances in life‐history strategies to increase conservation success.     

Comparative landscape genetics of pond‐breeding amphibians in Mediterranean temporal wetlands: The positive role of structural heterogeneity in promoting gene flow

Comparative landscape genetics studies can provide key information to implement cost‐effective conservation measures favouring a broad set of taxa. These studies are scarce, particularly in Mediterranean areas, which include diverse but threatened biological communities. Here, we focus on Mediterranean wetlands in central Iberia and perform a multi‐level, comparative study of two endemic pond‐breeding amphibians, a salamander (Pleurodeles waltl) and a toad (Pelobates cultripes). We genotyped 411 salamanders from 20 populations and 306 toads from 16 populations at 18 and 16 microsatellite loci, respectively, and identified major factors associated with population connectivity through the analysis of three sets of variables potentially affecting gene flow at increasingly finer levels of spatial resolution. Topographic, land use/cover, and remotely sensed vegetation/moisture indices were used to derive optimized resistance surfaces for the two species. We found contrasting patterns of genetic structure, with stronger, finer scale genetic differentiation in Pleurodeles waltl, and notable differences in the role of fine‐scale patterns of heterogeneity in vegetation cover and water content in shaping patterns of regional genetic structure in the two species. Overall, our results suggest a positive role of structural heterogeneity in population connectivity in pond‐breeding amphibians, with habitat patches of Mediterranean scrubland and open oak woodlands (“dehesas”) facilitating gene flow. Our study highlights the usefulness of remotely sensed continuous variables of land cover, vegetation and water content (e.g., NDVI, NDMI) in conservation‐oriented studies aimed at identifying major drivers of population connectivity.     

Shifts in leaf litter breakdown along a forest–pasture–urban gradient in Andean streams

Tropical montane ecosystems of the Andes are critically threatened by a rapid land‐use change which can potentially affect stream variables, aquatic communities, and ecosystem processes such as leaf litter breakdown. However, these effects have not been sufficiently investigated in the Andean region and at high altitude locations in general. Here, we studied the influence of land use (forest–pasture–urban) on stream physico‐chemical variables (e.g., water temperature, nutrient concentration, and pH), aquatic communities (macroinvertebrates and aquatic fungi) and leaf litter breakdown rates in Andean streams (southern Ecuador), and how variation in those stream physico‐chemical variables affect macroinvertebrates and fungi related to leaf litter breakdown. We found that pH, water temperature, and nutrient concentration increased along the land‐use gradient. Macroinvertebrate communities were significantly different between land uses. Shredder richness and abundance were lower in pasture than forest sites and totally absent in urban sites, and fungal richness and biomass were higher in forest sites than in pasture and urban sites. Leaf litter breakdown rates became slower as riparian land use changed from natural to anthropogenically disturbed conditions and were largely determined by pH, water temperature, phosphate concentration, fungal activity, and single species of leaf‐shredding invertebrates. Our findings provide evidence that leaf litter breakdown in Andean streams is sensitive to riparian land‐use change, with urban streams being the most affected. In addition, this study highlights the role of fungal biomass and shredder species (Phylloicus; Trichoptera and Anchytarsus; Coleoptera) on leaf litter breakdown in Andean streams and the contribution of aquatic fungi in supporting this ecosystem process when shredders are absent or present low abundance in streams affected by urbanization. Finally, we summarize important implications in terms of managing of native vegetation and riparian buffers to promote ecological integrity and functioning of tropical Andean stream ecosystems.     

DIATOMS LIVING INSIDE THE THALLUS OF THE GREEN ALGAL LICHEN COENOGONIUM LINKII IN NEOTROPICAL LOWLAND RAIN FORESTS1

Coenogonium linkii Ehrenb. is a very common filamentous lichen, growing on stems, hanging roots, and lianas in the understory of neotropical lowland rain forests. We investigated several thalli of this species from locations in Panama and French Guiana. All thalli were inhabited by various species of terrestrial diatoms, which were found between the thallus filaments on extracellular material of the mycobiont. We identified 18 species of diatoms belonging to nine genera: Diadesmis, Eunotia, Hantzschia, Luticola, Melosira, Nitzschia, Orthoseira, Pinnularia, and Stauroneis. The potential benefits both diatoms and lichens could derive from symbiosis in relation to water, irradiance, and nitrogen availability are discussed.     

Molecular phylogeny of hinge‐beak shrimps (Decapoda: Caridea: Rhynchocinetes and Cinetorhynchus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny

The Rhynchocinetidae (‘hinge‐beak’ shrimps) is a family of marine caridean decapods with considerable variation in sexual dimorphism, male weaponry, mating tactics, and sexual systems. Thus, this group is an excellent model with which to analyse the evolution of these important characteristics, which are of interest not only in shrimps specifically but also in animal taxa in general. Yet, there exists no phylogenetic hypothesis, either molecular or morphological, for this taxon against which to test either the evolution of behavioural traits within the Rhynchocinetidae or its genealogical relationships with other caridean taxa. In this study, we tested (1) hypotheses on the phylogenetic relationships of rhynchocinetid shrimps, and (2) the efficacy of different (one‐, two‐, and three‐phase) methods to generate a reliable phylogeny. Total genomic DNA was extracted from tissue samples taken from 17 species of Rhynchocinetidae and five other species currently or previously assigned to the same superfamily (Nematocarcinoidea); six species from other superfamilies were used as outgroups. Sequences from two nuclear genes (H3 and Enolase) and one mitochondrial gene (12S) were used to construct phylogenies. One‐phase phylogenetic analyses (SATé‐II) and classical two‐ and three‐phase phylogenetic analyses were employed, using both maximum likelihood and Bayesian inference methods. Both a two‐gene data set (H3 and Enolase) and a three‐gene data set (H3, Enolase, 12S) were utilized to explore the relationships amongst the targeted species. These analyses showed that the superfamily Nematocarcinoidea, as currently accepted, is polyphyletic. Furthermore, the two major clades recognized by the SATé‐II analysis are clearly concordant with the genera Rhynchocinetes and Cinetorhynchus, which are currently recognized in the morphological‐based classification (implicit phylogeny) as composing the family Rhynchocinetidae. The SATé‐II method is considered superior to the other phylogenetic analyses employed, which failed to recognize these two major clades. Studies using more genes and a more complete species data set are needed to test yet unresolved inter‐ and intrafamilial systematic and evolutionary questions about this remarkable clade of caridean shrimps. © 2014 The Linnean Society of London     

Factors affecting the distribution and abundance of Cloeon and Caenis (Ephemeroptera) larvae in a tropical impounded river, Nigeria

Impoundment of rivers affects the mayfly (Ephemeroptera) fauna inhabiting such water bodies, especially with respect to their distribution and abundance. A two‐year study of the mayfly fauna and some of the physicochemical parameters of the Opa stream–reservoir revealed that there are two mayfly genera inhabiting it, Cloeon and Caenis. The number of Cloeon larvae collected was 10,930 while the number of Caenis larvae was 450. It was observed that although both genera occurred at all the sampling stations, their numbers were reduced in the stream below the dam due to increased water current velocity. There were significant differences in the abundance of Cloeon among the stations, but none for Caenis. Submerged aquatic plants and water current velocity were found to be the major factors responsible for the significant differences. There were significant correlations between the number of Cloeon larvae and pH as well as between dissolved oxygen concentration and Caenis. These findings are discussed with reference to inter‐specific differences in patterns of response to environmental parameters. A species‐specific approach is suggested for studies on the strategies that enable mayfly species maintain their populations in stressed and unstable aquatic ecosystems.     

Using species distribution models to select species resistant to climate change for ecological restoration of bowé in West Africa

Bowalization is a particular form of land degradation and leads to lateral expansion of ferricrete horizons. The process occurs only in tropical regions. In this study, the most adapted and resistant species towards climate change were identified on bowé. The 15 most common bowé species of the subhumid and semi‐arid climate zones of Benin were submitted together with significant environmental variables (elevation, current bioclimatic variables, soil types) to three ecological niche modelling programmes (Maxent, Domain and GARP). For future prediction (2050), IPCC4/CIAT and IPCC5/CMIP5 climate data were applied. Asparagus africanus, Andropogon pseudapricus and Combretum nigricans were identified as the most resistant species for ecological restoration of bowé in the semi‐arid climate zone and Asparagus africanus, Detarium microcarpum and Lannea microcarpa in the subhumid climate zone. The ‘Pull’ strategies were identified as appropriate for ecological restoration of bowé in Benin.     

Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach

The genera Elliptochloris and Pseudochlorella were erected for Chlorella‐like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS‐2 Barcodes using the ITS‐2/CBC approach.