Two novel species of arctic-alpine lichen-forming fungi (Ascomycota, Megasporaceae) from the Deosai Plains, Pakistan.

Members of the lichen-forming fungal genus Oxneriaria are known to occur in cold polar and high altitudinal environments. Two new species, Oxneriariacrittendenii and O.deosaiensis, are now described from the high altitude Deosai Plains, Pakistan, based on phenotypic, multigene phylogenetic and chemical evidence. Phenotypically, O.crittendenii is characterised by orbicular light-brown thalli 1.5-5 cm across, spot tests (K, C, KC) negative, apothecia pruinose, hymenium initially blue then dark orange in response to Lugol's solution. Oxneriariadeosaiensis is characterised by irregular areolate grey thalli 1.5-2 cm across, K test (light brown), KC test (dark brown), apothecia epruinose, hymenium initially blue then dark blue in response to Lugol's solution. Both species share the same characters of thalli with black margins and polarilocular ascospores. The closest previously reported species, O.pruinosa, differs from O.crittendenii and O.deosaiensis in having non-lobate margins, thin thalline exciple (45-80 µm thick), short asci (55-80 × 25-42 µm) and K positive (yellow) and KC negative tests and divergent DNA sequence in the ITS, LSU and mtSSU regions. The newly-described Oxneriaria species add to growing evidence of the Deosai Plains as a region of important arctic-alpine biodiversity.

Differentiation of Bulinus senegalensis and Bulinus forskalii Snails in West Africa Using Morphometric Analysis.

PURPOSE: Accurate identification of medically important intermediate host and vector species is crucial for understanding disease transmission and control. Identifying Bulinus snails which act as intermediate host species for the transmission of schistosomiasis is typically undertaken using conchological and genital morphology as well as molecular methods. METHODS: Here, a landmark-based morphometric analysis of shell morphology was undertaken to determine its utility to distinguish the closely related and morphologically similar sister species Bulinus senegalensis and Bulinus forskalii. The method was developed to increase the accuracy of conchological morphology methods to identify Bulinus species in the field. Both species are found in West Africa, but only B. senegalensis is implicated in the transmission of urogenital schistosomiasis. RESULTS: We found when scaled down to the same length, 3-whorl and 4-whorl (juvenile) B. senegalensis shells had a longer spire, narrower body whorl and shorter aperture than B. forskalii. In contrast, 5-whorl (adult) B. senegalensis had a shorter spire, but still had a shorter aperture and narrower body whorl than B. forskalii. Canonical Variate Analysis (CVA) showed minimal overlap between B. senegalensis and B. forskalii for 3-whorl and 4-whorl shells, with a clear separation for 5-whorl shells. Overall, B. senegalensis had a consistently shorter aperture size and narrower body whorl than B. forskalii for all development stages. Spire length was variable depending on the stage of development, with 3-whorl and 4-whorl shells having the opposite trends of adult shells. CONCLUSIONS: Our study demonstrates the applicability of landmark-based morphometrics in distinguishing the medically important, Bulinus senegalensis from its morphologically similar sister species, Bulinus forskalii. We recommend using measurements based on spire length, penultimate whorl length, body whorl width and aperture size to differentiate B. senegalensis and B. forskalii, when used with the appropriate information for each shell's development stage.

Seasonal patterns of Schistosoma mansoni infection within Biomphalaria snails at the Ugandan shorelines of Lake Albert and Lake Victoria.

Intestinal schistosomiasis is hyperendemic in many sub-Saharan African countries. In Uganda, it is endemic at both Lake Albert (LA) and Lake Victoria (LV) and caused by S. mansoni that uses Biomphalaria snails as obligatory intermediate snail hosts. To shed light on local patterns of infection, we utilised two PCR-based methods to detect S. mansoni within Biomphalaria spp. as collected at the Ugandan shorelines of Lake Albert and Lake Victoria from 2009-2010. Overall, at our Lake Albert sites, the mean infection prevalence was 12.5% (15 of 120 snails), while at our Lake Victoria sites the prevalence was 5% (3 of 60 snails). At our Lake Albert sites, the highest infection prevalence of 13.3% (8 of 60 snails) was at Walukuba, while at our Lake Victoria sites, the highest infection prevalence of 10% (2 of 20 snails) was at Lwanika. Three species of Biomphalaria, B. pfeifferi, B. stanleyi and B. sudanica, were identified at our Lake Albert collection sites, while only a single species, B. choanomphala, was identified at our Lake Victoria collection sites. Biomphalaria stanleyi (2 of 20 snails; 15%) had the highest infection prevalence, followed by B. sudanica (5 of 60 snails; 13.3%), B. pfeifferi (4 of 40 snails; 10%) and B. choanomphala (3 of 60 snails; 5%). Of the Biomphalaria species identified, B. choanomphala had the highest haplotype (gene) diversity score, followed by B. stanleyi, B. sudanica and B. pfeifferi. Sites with a higher mean prevalence of S. mansoni infection had higher intra-species haplotype diversity scores than sites with a lower mean prevalence. The wet seasons (LA: 13.3%; LV: 8.7%) had a consistently higher mean infection prevalence of S. mansoni than the dry seasons (LA: 9.5%; LV: 5%) for all species and all sites tested at both Lake Albert (n = 480) and Lake Victoria (n = 320), though the difference was not statistically significant.

Projecting the Impact of Socioeconomic and Policy Factors on Greenhouse Gas Emissions and Carbon Sequestration in U.S. Forestry and Agriculture.

Understanding greenhouse gas mitigation potential of the U.S. agriculture and forest sectors is critical for evaluating potential pathways to limit global average temperatures from rising more than 2° C. Using the FASOMGHG model, parameterized to reflect varying conditions across shared socioeconomic pathways, we project the greenhouse gas mitigation potential from U.S. agriculture and forestry across a range of carbon price scenarios. Under a moderate price scenario ($20 per ton CO2 with a 3% annual growth rate), cumulative mitigation potential over 2015-2055 varies substantially across SSPs, from 8.3 to 17.7 GtCO2e. Carbon sequestration in forests contributes the majority, 64-71%, of total mitigation across both sectors. We show that under a high income and population growth scenario over 60% of the total projected increase in forest carbon is driven by growth in demand for forest products, while mitigation incentives result in the remainder. This research sheds light on the interactions between alternative socioeconomic narratives and mitigation policy incentives which can help prioritize outreach, investment, and targeted policies for reducing emissions from and storing more carbon in these land use systems.

Species diversity and distribution of schistosome intermediate snail hosts in The Gambia.

There is a need for recent information on intermediate snail hosts of schistosomes in The Gambia; the previous studies were conducted over three decades ago. This study assessed the incidence, species diversity, distribution and infection status of schistosome intermediate snail hosts in the country. Malacological surveys were conducted in all 5 regions of The Gambia: Central River Region (CRR), Upper River Region (URR), Western Region (WR), Lower River Region (LRR) and North Bank Region (NBR). Sampling of snails was undertaken at 114 sites that included permanent water bodies such as streams (bolongs), rice fields, irrigation canals and swamps; and temporal (seasonal) laterite pools. Ecological and physicochemical factors of sites were recorded. Snails were identified morphologically and screened for schistosome infections using molecular techniques. Freshwater snails were found at more than 50% (60/114) of sites sampled. While three species of Bulinus were collected, no Biomphalaria snails were found in any of the sites sampled. Of the total 2877 Bulinus snails collected, 75.9% were identified as Bulinus senegalensis, 20.9% as Bulinus forskalii and 3.2% as Bulinus truncatus. Seasonal pools produced the largest number of snails, and CRR was the region with the largest number of snails. Bulinus senegalensis was found more in seasonal pools as opposed to permanent sites, where B. forskalii and B. truncatus were observed to thrive. Bulinus snails were more common in seasonal sites where aquatic vegetation was present. In permanent sites, the abundance of snails increased with increase in water temperature and decrease in water pH. Bulinus senegalensis was found infected with both S. haematobium and S. bovis, while B. forskalii and B. truncatus had only S. bovis infection. While the human parasite S. haematobium was restricted to just four sites, the livestock parasite S. bovis had a much more widespread geographical distribution across both CRR and URR. This new information on the distribution of intermediate snail hosts of schistosomes in The Gambia will be vital for the national schistosomiasis control initiative.

Prevalence and risk factors of schistosomiasis among primary school children in four selected regions of The Gambia.

BACKGROUND: The Gambia initiated a control programme for schistosomiasis in 2015. In light of this, recent and comprehensive data on schistosomiasis is required to effectively guide the control programme. This study aimed to evaluate the prevalence and associated risk factors of schistosomiasis among primary school children in The Gambia. METHODS: We utilised data from a previous study conducted in 2015 in 4 regions of The Gambia: North Bank Region (NBR), Lower River Region (LRR), Central River Region (CRR) and Upper River Region (URR). In the parent study, ten schools were selected randomly from each region. Urine and stool samples collected from 25 boys and 25 girls (7-14 years) in each school were examined for urinary schistosomiasis (Schistosoma haematobium infection) and intestinal schistosomiasis (Schistosoma mansoni infection) using urine filtration, dipstick and Kato-Katz methods. PRINCIPAL FINDINGS: Urinary schistosomiasis had an overall prevalence of 10.2% while intestinal schistosomiasis had a prevalence of 0.3% among the sampled school children. Prevalence of urinary schistosomiasis was significantly different among regions (χ 2 = 279.958, df = 3, p < 0.001), with CRR (27.6%) being the most endemic region, followed by URR (12.0%), then LRR (0.6%), and NBR (0.0%). Prevalence of intestinal schistosomiasis was also significantly variable among regions, with 4 of the 5 positive cases detected in CRR and 1 case in URR. Every school sampled in CRR had at least one student infected with S. haematobium, 50% of schools in URR had S. haematobium infection, and just one school in LRR had S. haematobium infection. While S. haematobium infection was significantly higher in boys (χ 2 = 4.440, df = 1, p = 0.035), no significant difference in infection rate was observed among age groups (χ 2 = 0.882, df = 2, p = 0.643). Two of the 5 students infected with S. mansoni were boys and 3 were girls. Four of these 5 students were in the 10-12 years age group and 1 was in the 7-9 years age group. Macrohaematuria and microhaematuria were found to be statistically associated with presence of S. haematobium eggs in urine. Being a male was a risk factor of S. haematobium infection. Bathing, playing and swimming in water bodies were found to pose less risk for S. haematobium infection, indicating that the true water contact behaviour of children was possibly underrepresented. CONCLUSION: The findings of this study provide invaluable information on the prevalence of schistosomiasis in The Gambia. This was useful for the schistosomiasis control efforts of the country, as it guided mass drug administration campaigns in eligible districts in the study area. More studies on S. mansoni and its intermediate snail hosts are required to establish its true status in The Gambia. As children sometimes tend to provide responses that potentially please the research or their teacher, data collection frameworks and approaches that ensure true responses in studies involving children should be devised and used.

What is Threatening Forests in Protected Areas? A Global Assessment of Deforestation in Protected Areas, 2001-2018.

The protection of forests is crucial to providing important ecosystem services, such as supplying clean air and water, safeguarding critical habitats for biodiversity, and reducing global greenhouse gas emissions. Despite this importance, global forest loss has steadily increased in recent decades. Protected Areas (PAs) currently account for almost 15% of Earth's terrestrial surface and protect 5% of global tree cover and were developed as a principal approach to limit the impact of anthropogenic activities on natural, intact ecosystems and habitats. We assess global trends in forest loss inside and outside of PAs, and land cover following this forest loss, using a global map of tree cover loss and global maps of land cover. While forests in PAs experience loss at lower rates than non-protected forests, we find that the temporal trend of forest loss in PAs is markedly similar to that of all forest loss globally. We find that forest loss in PAs is most commonly-and increasingly-followed by shrubland, a broad category that could represent re-growing forest, agricultural fallows, or pasture lands in some regional contexts. Anthropogenic forest loss for agriculture is common in some regions, particularly in the global tropics, while wildfires, pests, and storm blowdown are a significant and consistent cause of forest loss in more northern latitudes, such as the United States, Canada, and Russia. Our study describes a process for screening tree cover loss and agriculture expansion taking place within PAs, and identification of priority targets for further site-specific assessments of threats to PAs. We illustrate an approach for more detailed assessment of forest loss in four case study PAs in Brazil, Indonesia, Democratic Republic of Congo, and the United States.

Comparing PCR techniques against conventional cercarial shedding methods for detecting Schistosoma mansoni infection in Biomphalaria snails.

The detection of Schistosoma mansoni infection in both its intermediate (snail) and definitive (human) hosts is useful in providing information on the transmission of schistosomiasis. Three pairs of previously designed PCR primers (SM1-7, SMF/R & ND5) used for the detection of S. mansoni infection were tested. We assess the utility of each of these primer sets for detecting S. mansoni infection both in artificially exposed laboratory bred Biomphalaria glabrata, and field infected African Biomphalaria sudanica and Biomphalaria pfeifferi. Two of the three primer sets (SMF/R & ND5) detected S. mansoni infection in snails, but amplification of S. mansoni DNA with SM1-7 was unreliable. For the artificially exposed laboratory bred B. glabrata snails, SMF/R and ND5 both detected infection in more snails than the cercarial shedding method. Infection detection rates were 62.4% for ND5, 57.1% for SMF/R and 50.4% using traditional cercarial shedding methods. Both SMF/R and ND5 detected S. mansoni infection in 91% of snails observed shedding cercariae, increasing to 98.5% when low stringency PCR methods were used. When comparing each of the detection methods using a Bayesian latent class analysis model, ND5 had the highest detection sensitivity and negative predictive value (NPV), while SMF/R had the highest detection specificity and positive predictive value (PPV). In field collected Biomphalaria snails, ND5 detected S. mansoni infection in 21 of 24 snails categorised as shedding S. mansoni cercariae and 4 of 24 snails categorised as shedding non-S. mansoni cercariae, while SMF/R detected infection in 18 of 24 snails categorised as shedding S. mansoni cercariae and in 3 of 24 snails categorised as shedding non-S. mansoni cercariae. All SMF/R and ND5 PCR products were shown to be S. mansoni indicating that these field snails must have been infected with both S. mansoni and cercariae from other Schistosoma species. This indicates that the two primer sets are specific for S. mansoni and will not amplify non-S. mansoni species when used at their recommended annealing temperatures. Both the SMF/R and ND5 primers effectively detected S. mansoni infection in three Biomphalaria species and have improved detection sensitivity over cercarial shedding.

Resolving the basal divisions in the stylommatophoran land snails and slugs with special emphasis on the position of the Scolodontidae.

The deep divisions at the base of the stylommatophoran land snails and slugs have proved to be controversial, with the phylogenetic position of the Scolodontidae remaining unresolved. Here we present a phylogenetic analysis of 34 stylommatophoran genera based on a combined dataset (5782 sites) of four loci with the aim of resolving the position of the Scolodontidae and their relationship to the 'achatinoid' and 'non-achatinoid' clades. We also evaluate the phylogenetic utility of different genes and gene partitions. The deep phylogenetic relationships within the Stylommatophora are now clearly resolved. The Scolodontidae are shown categorically to be the sister group to all other stylommatophoran groups with robust support and with all phylogeny reconstruction methods. The 'achatinoid' and 'non-achatinoid' clades are also strongly supported in the tree. The original LSU 1-5 fragment used extensively in studies of the Stylommatophora was found to be the most informative gene fragment and works well at resolving relationships at most levels in the Stylommatophora but does not reliably resolve the deep level relationships at the very base of the clade. The concatenated dataset of four genes employed in this study is not only informative at lower levels but also resolves the deep level relationships at the base of the Stylommatophora with robust support.

Phylogenetics and species delimitations of the operculated land snail Cyclophorus volvulus (Gastropoda: Cyclophoridae) reveal cryptic diversity and new species in Thailand.

Recent conceptual and practical advances in phylogenetic species delimitation have enabled progressively robust biodiversity studies. Delimiting species in widespread taxa is an intriguing problem; the edible operculated land snail Cyclophorus volvulus (Müller, 1774) is a good example since it shows a high degree of shell and color variation along with a widespread distribution throughout Thailand. Taxonomic boundaries for C. volvulus were examined and clarified using a combined morphological and phylogenetic approach, the latter of which was based on both nuclear and mitochondrial gene sequences. Moreover, three species delimitation analyses were applied: Poisson tree processes (PTP), automatic barcode gap discovery (ABGD), and generalized mixed Yule-coalescent (GMYC). All phylogenetic trees revealed that C. volvulus was polyphyletic and comprised of three clades that coincided with their geographic distribution. The three species delimitation analyses concurred with the phylogenies and formed at least three groups. According to the results, C. volvulus s.l., as currently recognized, consists of three distinct species in Thailand: C. volvulus s.s., C. occultus sp. nov., and C. borealis sp. nov., which are described herein. Moreover, several of these highly distinct C. volvulus evolutionarily significant units (ESU) are likely to require urgent conservation attention.

Projecting the Spatial Distribution of Possible Planted Forest Expansion in the United States.

As the demand for forest products and carbon storage in standing timbers increases, intensive planting of forest resources is expected to increase. With the increased use of plantation practices, it is important to understand the influence that forest plot characteristics have on the likelihood of where these practices are occurring. Depending on the goals of a policy or program, increasing forest planting could be a desirable outcome or something to avoid. This study estimates a spatially explicit logistical regression function to assess the likelihood that forest plots will be planted based on physical, climate, and economic factors. The empirical results are used to project the potential spatial distribution of forest planting, at the intensive and extensive land-use margins, across illustrative future scenarios. Results from this analysis offer insight into the factors that have driven forest planting in the United States historically and the potential distribution of new forest planting in the coming decades under policy or market scenarios that incentivize improved forest productivity or certain ecosystem services provided by intensively managed systems (e.g., carbon sequestration).

Importance of Cross-Sector Interactions When Projecting Forest Carbon across Alternative Socioeconomic Futures.

In recent decades, the carbon sink provided by the U.S. forest sector has offset a sizable portion of domestic greenhouse gas (GHG) emissions. In the future, the magnitude of this sink has important implications not only for projected U.S. net GHG emissions under a reference case but also for the cost of achieving a given mitigation target. The larger the contribution of the forest sector towards reducing net GHG emissions, the less mitigation is needed from other sectors. Conversely, if the forest sector begins to contribute a smaller sink, or even becomes a net source, mitigation requirements from other sectors may need to become more stringent and costlier to achieve economy wide emissions targets. There is acknowledged uncertainty in estimates of the carbon sink provided by the U.S. forest sector, attributable to large ranges in the projections of, among other things, future economic conditions, population growth, policy implementation, and technological advancement. We examined these drivers in the context of an economic model of the agricultural and forestry sectors, to demonstrate the importance of cross-sector interactions on projections of emissions and carbon sequestration. Using this model, we compared detailed scenarios that differ in their assumptions of demand for agriculture and forestry products, trade, rates of (sub)urbanization, and limits on timber harvest on protected lands. We found that a scenario assuming higher demand and more trade for forest products resulted in increased forest growth and larger net GHG sequestration, while a scenario featuring higher agricultural demand, ceteris paribus led to forest land conversion and increased anthropogenic emissions. Importantly, when high demand scenarios are implemented conjunctively, agricultural sector emissions under a high income-growth world with increased livestock-product demand are fully displaced by substantial GHG sequestration from the forest sector with increased forest product demand. This finding highlights the potential limitations of single-sector modeling approaches that ignore important interaction effects between sectors.

Evaluating Potential Sources of Aggregation Bias with a Structural Optimization Model of the U.S. Forest Sector.

Structural economic optimization models of the forestry and land use sectors can be used to develop baseline projections of future forest carbon stocks and annual fluxes, which inform policy dialog and investment in programs that maintain or enhance forest carbon stocks. Such analyses vary in terms of the degree of spatial, temporal, and activity-level aggregation used to represent forest resources, land cover, and markets. While the statistical and econometric modeling communities widely discuss the effects of aggregation bias and have developed correction techniques, there is limited prior research investigating how aggregation bias may affect structural optimization models. This paper explores potential aggregation bias using the Land Use and Resource Allocation model (LURA), a detailed spatial allocation partial equilibrium model of the U.S. forest sector. We ran a series of projections representing alternative aggregation approaches including averaging forest stocks at plot, county, state, and regional levels, across one-, five, or ten-year age classes, and by two or fourteen forest types. We compared the resulting projections of forest carbon stocks and harvesting activities across each aggregation scenario. This allows us to isolate the effect of aggregation on key variables of interest (e.g., GHG emissions and supply costs), while holding all other structural characteristics of the modeling framework constant. We find that age-class and forest type aggregations have the greatest impact on modeling results, with the potential to substantially impact market and greenhouse gas projections. On the other hand, spatial aggregation has a small impact on national carbon stock projections. Importantly, regional results are greatly impacted by different aggregation approaches, with projected regional cumulative carbon stocks differing by more than 25% across scenarios.

Implications of Alternative Land Conversion Cost Specifications on Projected Afforestation Potential in the United States.

The Forestry and Agriculture Sector Optimization Model with Greenhouse Gases (FASOMGHG) has historically relied on regional average costs of land conversion to simulate land use change across cropland, pasture, rangeland, and forestry. This assumption limits the accuracy of the land conversion estimates by not recognizing spatial heterogeneity in land quality and conversion costs. Using data from Nielsen et al. (2014), we obtained the afforestation cost per county, then estimated nonparametric regional marginal cost functions for land converting to forestry. These afforestation costs were then incorporated into FASOMGHG. Three different assumptions for land moving into the forest sector (constant average conversion cost, static rising marginal costs, and dynamic rising marginal cost) were run in order to assess the implications of alternative land conversion cost assumptions on key outcomes, such as projected forest area and cropland use, carbon sequestration, and forest product output.

Seasonal and Spatial Variations of Saltmarsh Benthic Foraminiferal Communities from North Norfolk, England.

Time series foraminiferal data were obtained from samples collected from three sites at Brancaster Overy Staithe, Burnham Overy Staithe and Thornham on the North Norfolk coast over a 1-year period. At each collection point, six environmental variables-temperature, chlorophyll, sand, mud, pH and salinity-were also measured. The principle aim of this study was to examine the benthic foraminiferal fauna in regard to the temporal variability of foraminiferal abundance, seasonal trend, dominant species, species diversity and the impact of environmental variables on the foraminiferal communities in the top 1 cm of sediment over a 1-year time series. The foraminiferal assemblages at the three sites were dominated by three species: Haynesina germanica, Ammonia sp. and Elphidium williamsoni. Foraminiferal species showed considerable seasonal and temporal fluctuation throughout the year at the three investigated sites. The foraminiferal assemblage at the three low marsh zones showed a maximum abundance in autumn between September and November and a minimum abundance observed between July and August. There were two separate peaks in the abundance of Ammonia sp. and E. williamsoni, one in spring and another in autumn. In contrast, H. germanica showed a single peak in its abundance in autumn. A generalized additive modelling approach was used to explain the variation in the observed foraminiferal abundance and to estimate the significant impact of each of the environmental variables on living foraminiferal assemblages, with taxa abundance as the dependent variable. When included in the model as predictors, most of the environmental variables contributed little in explaining the observed variation in foraminiferal species abundance. However, the hypotheses for differences amongst sites, salinity and pH were significant and explained most of the variability in species relative abundance.

Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera.

Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.

Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog.

While components of the pathway that establishes left-right asymmetry have been identified in diverse animals, from vertebrates to flies, it is striking that the genes involved in the first symmetry-breaking step remain wholly unknown in the most obviously chiral animals, the gastropod snails. Previously, research on snails was used to show that left-right signaling of Nodal, downstream of symmetry breaking, may be an ancestral feature of the Bilateria [1 and 2]. Here, we report that a disabling mutation in one copy of a tandemly duplicated, diaphanous-related formin is perfectly associated with symmetry breaking in the pond snail. This is supported by the observation that an anti-formin drug treatment converts dextral snail embryos to a sinistral phenocopy, and in frogs, drug inhibition or overexpression by microinjection of formin has a chirality-randomizing effect in early (pre-cilia) embryos. Contrary to expectations based on existing models [3, 4 and 5], we discovered asymmetric gene expression in 2- and 4-cell snail embryos, preceding morphological asymmetry. As the formin-actin filament has been shown to be part of an asymmetry-breaking switch in vitro [6 and 7], together these results are consistent with the view that animals with diverse body plans may derive their asymmetries from the same intracellular chiral elements [8].

PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.

The population genetic structure of Biomphalaria choanomphala in Lake Victoria, East Africa: implications for schistosomiasis transmission.

BACKGROUND: The freshwater snail Biomphalaria acts as the intermediate host of Schistosoma mansoni, a globally important human parasite. Understanding the population structure of intermediate host species can elucidate transmission dynamics and assist in developing appropriate control methods. METHODS: We examined levels of population genetic structure and diversity in 29 populations of Biomphalaria choanomphala collected around the shoreline of Lake Victoria in Uganda, Kenya and Tanzania, where S. mansoni is hyper-endemic. Molecular markers were utilized to estimate the degree to which snail populations are genetically differentiated from one another. RESULTS: High levels of snail genetic diversity were found coupled with evidence of geographically-determined population structure but low levels of local inbreeding. The data are consistent with an effect of schistosome infection on population structure of intermediate host snails, but other factors, such as habitat and historical demographic changes, could also be important determinants of the degree of population genetic structure in Biomphalaria choanomphala. CONCLUSIONS: The low stratification of populations and high genetic diversity indicates potentially less local compatibility with intermediate snail populations than previously theorized, and highlights the importance of coordinated parasite control strategies across the region.