Rounding up the usual suspects: a standard target‐gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb‐weaving spiders with a new family‐rank classification (Araneae,Araneoidea)

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb‐weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb‐web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb‐web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb‐webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n. ). Araneoidea includes 17 families with the following changes: Araneidae is re‐circumscribed to include nephilines , Nephilinae rank res., Arkyidae rank n. , Physoglenidae rank n. , Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae ( syn. n. ), Holarchaeidae of Anapidae ( syn. n. ) and Sinopimoidae of Linyphiidae ( syn. n. ).     

Lanthanum from a Modified Clay Used in Eutrophication Control Is Bioavailable to the Marbled Crayfish (Procambarus fallax f. virginalis)

To mitigate eutrophication in fresh standing waters the focus is on phosphorus (P) control, i.e. on P inflows to a lake as well as a lake''s sediment as internal P source. The in-lake application of the lanthanum (La) modified clays – i.e. La modified bentonite (Phoslock) or La modified kaolinite, aim at dephosphatising the water column and at reducing the release of P from a lake''s sediment. Application of these clays raises the question whether La from these clays can become bioavailable to biota. We investigated the bioavailability of La from Phoslock in a controlled parallel groups experiment in which we measured the La in carapace, gills, ovaries, hepatopancreas and abdominal muscle after 0, 14 and 28 days of exposure to Phoslock. Expressing the treatment effect as the difference of the median concentration between the two treatment groups (Phoslock minus control group) yield the following effects, the plus sign (+) indicating an increase, concentrations in µg g⁻¹ dry weight: Day 14: carapace +10.5 µg g⁻¹, gills +112 µg g⁻¹, ovaries +2.6 µg g⁻¹, hepatopancreas +32.9 µg g⁻¹ and abodminal muscle +3.2 µg g⁻¹. Day 28: carapace +17.9 µg g⁻¹; gills +182 µg g⁻¹; ovaries +2.2 µg g⁻¹; hepatopancreas +41.9 µg g⁻¹ and abodminal muscle +7.6 µg g⁻¹, all effects were statistically significant. As La from Phoslock is bio-available to and taken up by the marbled crayfishes (Procambarus fallax f. virginalis), we advocate that the application of in-lake chemical water treatments to mitigate eutrophication should be accompanied by a thorough study on potential side effects.     

Cytochrome and alternative pathway activity in roots of thermal and non-thermal Agrostis species in response to high soil temperature

Partitioning of respiration between the cytochrome pathway (CP) and the alternative pathway (AP) may play an important role in plant adaptation to extreme environments. We examined changes in partitioning between CP and AP, and viability of roots associated with plant exposure to high soil temperature for two Agrostis species: Agrostis scabra Willd., a species adapted to high-temperature soils in geothermal areas in Yellowstone National Park, and Agrostis stolonifera L. (cv. Penncross) a heat-sensitive grass widely used in cool-climate regions. Roots of A. scabra and A. stolonifera were exposed to soil temperature of 37 or 20°C, while shoots were exposed to 20°C for 28 days. Root viability decreased, and total root respiration increased for both species at 37°C. The decline in root viability and the increase in respiration rates were less pronounced for A. scabra than for A. stolonifera . A larger proportion of total root respiration was attributed to the AP in A. scabra compared with that in A. stolonifera when both species were exposed to 37°C. At 7 and 14 days at 37°C, the relative proportion of respiration passing through AP increased by 12 and 10%, respectively, in A. scabra , whereas in A. stolonifera , AP increased by 4 and 1%, respectively. Our results suggest that maintaining a higher proportion of AP at a high soil temperature may contribute to root thermo-tolerance in A. scabra in comparison with A. stolonifera , and alternative respiration may play an important role in plant adaptation to high soil temperature.     

How do Detergents Work? A Qualitative Assay to Measure Amylase Activity

We present a practical activity focusing on two main goals: to give learners the opportunity to experience how the scientific method works and to increase their knowledge about enzymes in everyday situations. The exercise consists of determining the amylase activity of commercial detergents. The methodology is based on a qualitative assay using a colorimetric process. Quantitative results are also obtained by measuring the halo formed. This activity is suitable for and adaptable to learners at different levels of education: primary school, secondary education or even for pre-service teachers, which is the group the version described in this paper was intended for. This laboratory activity was designed to include the scientific method as a learning outcome. This was especially important in pre-service teachers, as increasing scientific literacy is one of the primary goals of science education. Through the activity, students also learn about micro-organisms and their applications in their daily lives, which is one of the tenets of Science–Technology–Society–Environment programs. A case study was conducted with a group of learners made up of 75 pre-service teachers from Universitat Rovira i Virgili in Tarragona, in order to verify whether this lab activity is well designed and can be satisfactorily implemented.     

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous ‘replacer’ gene rescues lethality caused by inactivation of a ‘target’ gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5’-phosphate (the active form of Vitamin B₆), which we validate experimentally via multicopy suppression. We perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.     

“Slash and burn” or “weed and manure”? A modelling approach to explore hypotheses of late Neolithic crop cultivation in pre-alpine wetland sites

The record of prehistoric crop cultivation in central Europe dates as far back as 5500 bc. In the pile-dwellings of the north-western pre-alpine forelands, dating roughly from 4300 to 800 bc, favourable taphonomic conditions provide evidence for the ways of cereal cultivation and consumption in unmatched detail. Based on different sets of (bio-) archaeological and palynological evidence, different hypotheses of crop husbandry methods have been developed for the wetland settlements. During the late Neolithic, two partly antithetic ideas are discussed: On one hand Shifting Cultivation assumes frequently shifted crop fields and the use of fire to provide nitrogen for plant uptake; On the other hand Permanent Cultivation reconstructs longer-ranging use of the fields, to which nitrogen may have been provided by various means. From the Bronze Age onwards, most probably some form of extensive ard cultivation was applied. In this article, we explore the implications of the different hypotheses for the socio-ecological system of the wetland sites. We combine the capability of agent-based modelling to simulate dynamic processes with the benefits provided by geographical information systems and the possibilities provided by the use of modern agro-ecosystem modelling tools. First, we used a mechanistic crop growth model, MONICA, to evaluate the influence of important factors of prehistoric crop yield formation: the climatic conditions, the soil texture and the degree of nitrogen availability. Second, we applied an agent-based model (WELASSIMO_crops) to simulate the spatial and economic implications related to the different crop husbandry methods. Our results provide quantitative information on the extent of crop husbandry activities in the wetland sites and on the effect of natural and anthropogenic factors on prehistoric crop yields. Without manure application, initial average yields of 1.0 t ha^?1 a^?1 are shown to decrease rapidly to only 50 % after 10 years. A manuring rate of 10 t ha^?1 a^?1 allows for higher yields of 1.7 t ha^?1 a^?1 and a slower rate of fertility decrease, but requires high numbers of livestock per capita. In shifting cultivation, high yields of 2.7 t ha^?1 a^?1 are reasonable, while necessitating a very large area and high labour input. Using the model results and a case study, we argue that permanent cultivation is more likely to have been the standard method, while burning of the landscape may have had different objectives than crop husbandry. We find that the combination of agent-based social and process-based biophysical modelling is a powerful tool to study the complex interdependencies in human-environment systems in the past.     

Going Cheap: Determinants of Bird Price in the Taiwanese Pet Market

BackgroundInternational wildlife trade is the largest emerging source of vertebrate invasive alien species. In order to prevent invasions, it is essential to understand the mechanics of trade and, in particular, which traded species are most likely to be released or escape into the wild. A species’ economic value is a key factor, because we expect cheaper species to be less assiduously secured against escaping, and more likely to be deliberately released. Here, we investigate determinants of the price of species in the Taiwanese bird trade. Taiwan is an international hub for bird trade, and several native species are threatened by alien bird species.MethodologyWe investigated the relationship between the traded species sale price in Taiwan and the species availability for trade (the number of birds for sale, geographic range size and their origin, conservation and CITES status) and traits (body size, coloration, song attractiveness). We used phylogenetic generalized least squares models, with multi-model inference, to assess the variables that are best related to the price of birds in the Taiwanese pet trade.

Principal Findings / Conclusions

We found that species available for sale in larger numbers, native to Taiwan, not globally endangered, and small-bodied are all relatively cheaper, as too are species lacking yellow coloration and without attractive songs. Our models of price revealed high levels of phylogenetic correlation, and hence that closely related species tended to be sold for similar prices. We suggest that, on the basis of price, native species are more likely to be deliberately or accidentally released than alien species. Nevertheless, our survey of bird shops recorded 160 species alien to Taiwan (7,631 individuals), several of which are for sale cheaply and in large numbers. Alien bird species in trade therefore present an ongoing, non-trivial invasion risk on the island.