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    Density of invasive western honey bee (Apis mellifera) colonies in fragmented woodlands indicates potential for large impacts on native species

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    A scientist by any other name

    Many women in science, technology, engineering and mathematics (STEM) need to make decisions about marital name change, and have to consider how this might affect their publication record and future career. Mentorship that considers race, ethnicity, culture, religion and parenting, as well as a centralized system to dynamically and retroactively streamline name change, will promote agency and choice for women navigating STEM careers, writes Bala Chaudhary.Women, whether in same-sex or heterosexual relationships, still predominantly make decisions regarding marital name change1. In science, technology, engineering and mathematics (STEM) fields, as the proportion of female researchers rises, more women are considering the potential effects of marital name change on their careers. The stakes are high, as relationship status and name discrimination contribute to gender2 and racial3 inequities in faculty hiring. The shifting demographics of students and a greater proportion of STEM undergraduates engaging in research and publishing has also led to more scientists questioning decisions around name changes. Dual-scientist couples considering sharing a last name may wonder about gendered assessments of their contributions to work. Women occasionally ask for advice on this topic using social-media platforms such as Twitter. Community members chime in with myriad options: keep your name, change your name, hyphenate, add a middle name, couples choose a new name, keep separate personal and legal names, and so on. There is no single correct approach for this personal decision, so online discussions and testimonials4 are invaluable resources for women with few immediate role models. More

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    How itchy vicuñas remade a vast wilderness

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    When mange began to kill llama-like animals called vicuñas in the high Andes, their loss reverberated through the food web to affect grasslands and, eventually, condors1.

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    doi: https://doi.org/10.1038/d41586-022-00592-8

    ReferencesMonk, J. D. et al. Ecol. Lett. https://doi.org/10.1111/ele.13983 (2022).PubMed 
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    Learning from symbioses

    Esperanza Martínez-Romero is a professor of ecological genomics and was coordinator of the undergraduate programme on genomics at Universidad Nacional Autónoma de México. Her work on plant symbioses, and outreach with local farmers has encouraged uptake of sustainable practices and the use of biofertilizers.It was during my first year as an undergraduate student that I was exposed to genetic engineering, when Dr Francisco Bolívar lectured on his development of vectors for gene cloning. I found these results fascinating, and it was listening to talks from scientists at my institute that made me realize that research was my vocation. Towards the end of my bachelor’s degree, Dr Marc von Montagu from Belgium visited and told us about plant genetic transformations — a new field within genetic engineering. Although I was accepted into his laboratory to do my doctorate, I preferred Mexico. I turned my academic journey around and instead chose to apply to a new research centre in Cuernavaca outside of Mexico City — my next turning point. I suspected that a new research centre would provide more opportunities for the development of novel areas, and would have open positions for researchers. Indeed, I was hired at this new research centre and started my own ecology group. It was there that I started working with nitrogen-fixing bacteria and plants. The effects of nitrogen-fixing bacteria on plants were outstanding. Although the scope of molecular biology was incipient to the characterization of bacterial species and populations, we were nevertheless able to make molecular characterizations of the rhizobial species that formed nitrogen-fixing nodules on beans — the most important legume for human consumption in the world. In 1991, we described a novel species, Rhizobium tropici, which could deliver high levels of nitrogen to legumes. It was then that I realized nitrogen fixation is key to the development of sustainable agriculture and could benefit farmers in Mexico and around the world. Some of the species described by my group are now used as inoculants in agriculture, reducing the use of chemical fertilizers and allowing farmers to make cost savings. To facilitate this, I published a manual on biofertilization for farmers and gave conferences and workshops to them. My group has also undertaken reforestation programmes using nitrogen-fixing legume trees inoculated with the rhizobial species that we described. More

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    Causal networks of phytoplankton diversity and biomass are modulated by environmental context

    Quantification of causal networksWe first compared the relative strengths of causal links across systems (Supplementary Fig. S3). Phytoplankton species richness was the major controlling factor for phytoplankton biomass (significant in 16 of 19 sites, Fig. 2a) in these diverse aquatic systems, consistent with experimental studies17. However, the averaged linkage strength for this effect was not significantly different from that of NO3 (i.e., BD → EF vs. NO3 → EF; permutation test P = 0.501), highlighting that nitrogen availability was equally important in affecting phytoplankton biomass in natural systems.Fig. 2: Relative strengths of various modules.Standardized linkage strengths of causal variables affecting (a) phytoplankton biomass and (b) species richness (here, BD) and loop weights for various types of (c) pairwise feedbacks and (d) triangular feedbacks. All statistics were calculated from the 19 independent sites (n = 19) and depicted as joint violins and box plots to present the empirical distribution that labels the maxima and minima at the top and bottom of the violins, respectively, and shows 25, 50, and 75% quantiles in the boxes with whiskers presenting at most 1.5 * interquartile range. The two numbers within the parentheses (S; R1) above each violin plot report the number of significant results in CCM (S; labeled blue) and the number of systems in which a particular module had the greatest strength (i.e., rank 1; R1; labeled red). Source data are provided as a Source Data file.Full size imageIn the opposite direction, phytoplankton biomass was a significant driver of phytoplankton species richness in most ecosystems (15 of 19 sites, Fig. 2b). However, NO3 more often had a stronger effect, appearing as the most important driver in 11 of 19 sites compared to phytoplankton biomass (4 of 19 sites) (Fig. 2b). Although the difference in effect strength was not significant (permutation test, P = 0.162), these results implicated nitrogen availability as an essential determinant affecting both phytoplankton diversity and biomass. As a sensitivity test, we also examined the effects of Shannon diversity. The results suggest that the importance of nutrients is robust to the use of other diversity indexes (e.g., Shannon diversity in Supplementary Fig. S4), although the causal effects from phytoplankton biomass became relatively more important compared to biomass effects on species richness (Fig. 2b). Based on these findings, we inferred that processes influencing nutrients (e.g., external loadings and internal cycling38) need to be considered when investigating aquatic biodiversity. Changes in those processes (e.g., climatic39 or anthropogenic40 driven nutrient changes) may indeed substantially impact phytoplankton biodiversity, and subsequent ecosystem functioning.The importance of NO3 uncovered in our analyses might not be a counter-intuitive result, as many systems analyzed in this study were P-rich. For instance, the average phosphate concentration was 57.5 and 41.7 μgP/L for Lake Mendota (Me) and Lake Monona (Mo) (Supplementary Table S1), respectively. In addition, there were also high total phosphorus (TP) concentrations in shallow lake systems, e.g., average TP was 106.1, 112.5, and 126.4 μgP/L in Lake Inba (Ib), Lake Kasumigaura (Ks), and Müggelsee (Mu), respectively. Phosphorus was not always a limiting factor in eutrophic and mesotrophic systems, e.g., Lake Kasumigaura41 and Lake Geneva (Gv)42. In addition, nitrogen was deficient and limited cyanobacteria bloom in Müggelsee (Mu)43. Nonetheless, we cannot exclude the possibility of colimitation44 in N and P and the possibility that P availability also depends on N45, which warrants further investigation.Apart from nutrients and temperature, the causal effects of other important drivers on phytoplankton biomass and diversity were also examined, though not in all 19 systems due to data limitation. The causal effects of physical environmental factors, such as irradiance and water column stability, were presented in Supplementary Fig. S5; the results indicated that the quantified causal strengths on average were not as strong as the effects of diversity and nutrients. Moreover, the effects of consumers (e.g., zooplankton), which have been suggested as important drivers affecting species diversity of phytoplankton communities46, were also examined. Based on our analysis of zooplankton, the causal effects of herbivorous crustaceans on phytoplankton biomass and diversity were significant in most of the analyzed systems. However, these effects were on average not as strong as the effects of phytoplankton diversity and nutrients, respectively (Supplementary Fig. S6). Nonetheless, these findings were not generalized to all 19 systems due to a lack of complete datasets as shown in Supplementary Table S3, and thus warrant more detailed investigation in future studies.In addition to individual causal effects, we investigated feedbacks across systems. Pairwise feedbacks (e.g., BD ↔ EF and NO3 ↔ EF) were common (Fig. 2c). However, the averaged linkage strength was often stronger in one direction when involving BD (Fig. 3). Specifically, the average strength of BD → EF was stronger than for the opposite direction of EF → BD (permutation test P = 0.015); BD → EF was stronger than EF → BD in 14 of the 19 systems (Fig. 3). In addition, biodiversity effects on nutrients (BD → NO3 and BD → PO4) were also stronger than their reversed effects (NO3 → BD and PO4 → BD) in 12 and 13 systems, respectively. In comparison, the interactions between nutrients and productivity were more symmetrical: nutrient effects on biomass (NO3 → EF and PO4 → EF) were stronger than biomass effects on nutrients (EF → NO3 and EF → PO4) in only 9 and 8 of 19 systems, respectively. These results supported the previous findings8 that biodiversity effects more often operate at short-term scales, which makes effects more observable in our monthly-scale analyses than feedback effects on diversity, which are expected to occur on a more prolonged timescale, e.g., through slowly changing nutrient cycling31 or decomposition47. Nevertheless, the timescale dependence of causal interactions in ecosystem networks is a topic that needs further study.Fig. 3: Directional bias in pairwise feedbacks.The difference in standardized linkage strengths between the two directions was computed for each pairwise feedback and depicted as joint violin and box plots. All statistics were calculated from the 19 independent sites (n = 19) and depicted as joint violins and box plots to present the empirical distribution that labels the maxima and minima at the top and bottom of the violins, respectively, and shows 25, 50, and 75% quantiles in the boxes with whiskers presenting at most 1.5 * interquartile range. The number above the plot indicates the number of systems with a positive difference in linkage strength. For example, BD → EF was stronger than its feedback, EF → BD, in 14 of the systems. In general, the strength of diversity effects (BD → EF, BD → NO3, BD → PO4) was usually stronger than feedback effects (EF → BD, NO3 → BD, PO4 → BD). Source data are provided as a Source Data file.Full size imageSubsequently, we quantified the strengths of pairwise feedbacks as the geometric mean of the linkage strengths in each direction, following a previous study9 (see more details in Methods). Among these feedbacks (Fig. 2c and Supplementary Fig. S7), BD ↔ NO3 had the highest median and average strength (0.78 and 0.68, respectively) across systems. However, strengths of BD ↔ NO3 were highly variable among systems (large interquartile range in Fig. 2c), and thus were only significant in 11 of 19 systems, compared to BD ↔ EF (15 of 19 systems). These findings reinforced the importance of nutrients as key determinants for aquatic biodiversity and implied that nutrient effects are context-dependent. In other words, BD ↔ NO3 was less common than BD ↔ EF across systems, despite its stronger average strength. The prevalence of BD ↔ EF indicated a need for more long-term experiments and process-based/theoretical modeling accounting for bidirectional interactions between diversity and biomass16, because bidirectional interactions and feedbacks may challenge our simple predictions for ecosystem dynamics, based on knowledge of unidirectional interactions30.Quantification of the causal network also allowed us to analyze triangular feedbacks. Within the conceptual framework of Fig. 1b, there are four kinds of triangular feedbacks involving biodiversity, ecosystem functioning, and either nitrate or phosphate (Type I: BD → EF → NO3 and BD → EF → PO4; Type II: EF → BD → NO3 and EF → BD → PO4). There was at least one significant triangular feedback in 14 of 19 sites (Fig. 2d). More specifically, NO3-associated feedbacks (Type I-N and Type II-N) were usually stronger than PO4-associated feedbacks (Type I-P and Type II-P) (Fig. 2d), although the difference in strength among the four types of feedbacks was not significant (Fig. 2d; Kruskal–Wallis test, P = 0.59). The dominance of NO3-associated feedbacks in our study was attributed to many of the sites being marine and eutrophic lakes, which are likely to be N-limited due to an imbalance in external loadings48 or strong denitrification49. Among both NO3- and PO4-associated feedbacks, there were no significant differences in strength between Type I and Type II feedbacks (Supplementary Fig. S7), suggesting that biodiversity can directly influence biomass (Type I), as well as through a pathway that involves endogenous nutrient variables (Type II) and eventually feeds back on itself.Causal networks under environmental contextsOur empirical analyses revealed state dependency of the causal links and feedbacks among biodiversity, biomass, and environmental factors in natural systems; that is, their strengths were highly dependent on the state of other variables. Based on a cross-system comparison (Methods), strengths of individual links (e.g., BD → EF), pairwise feedbacks (e.g., BD ↔ EF), and triangular feedbacks (e.g., BD → EF → NO3 → BD) varied systematically, depending on environmental characteristics (Fig. 4 and Supplementary Fig. S8). Ecosystems with higher species diversity (long-term average species richness) and lower average PO4 concentrations had stronger BD → EF links (Fig. 4a; correlation coefficient r = 0.600 and −0.513; P = 0.007 and 0.025 for species diversity and PO4, respectively). These results were further confirmed by stepwise regression, indicating that the ecosystems characterized by higher diversity, lower average temperature, and oligotrophic conditions had stronger BD → EF (best-fit regression model: BD → EF strength = 0.663 + 0.171*BD − 0.139*T − 0.096*PO4; F3, 15 = 9.958 and P  More

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    Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

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    On track to achieve no net loss of forest at Madagascar’s biggest mine

    Study site and contextAmbatovy is a very large nickel, cobalt and ammonium sulphate mine in central-eastern Madagascar owned by a consortium of international mining companies50. It represents the largest ever foreign investment in the country24 (US$8 billion by 201650) and a substantial source of fiscal income49. In 2018, the company contributed ~US$50 million in taxes, tariffs, royalties and other payments49 and employed >9,000 people (93% of whom were Malagasy)51. Commercial production began in January 201424 (Supplementary Fig. 1). As key components in batteries, supplies of nickel and cobalt are critical to the green energy transition and demand for these metals is predicted to increase notably in future52.The mining concession covers an area of 7,700 ha located in the eastern rainforests of Madagascar (Fig. 1) which have very high levels of biodiversity and endemism53,54. After avoidance and minimization measures were applied (Supplementary Methods) the mine was predicted to clear or substantially degrade 2,064 ha of high-quality natural forest at the mine footprint and upper pipeline24. Any impacts on plantations or secondary habitat are not included in this estimate. Losses at the impact site were not discounted in relation to a background rate of decline, meaning that the company took responsibility for the full area of forest lost25. Independent verification by our team (by measuring the size of the mine footprint on Google Earth) confirms the extent of forest loss at the mine footprint (Supplementary Fig. 2). Clearance of the footprint accounts for most of the forest loss associated with the mine as losses associated with the pipeline are small54.Ambatovy aims to generate biodiversity gains to offset the mine-induced losses by slowing deforestation driven by shifting agriculture elsewhere26. To this end the company designated four sites, totalling 28,740 ha, to be protected as biodiversity offsets; Ankerana, Corridor Forestier Analamay-Mantadia (CFAM), the Conservation Zone and Torotorofotsy54 (Fig. 1). The offsets are considered like-for-like30 and were selected on the basis of similarity to the impact site in terms of forest structure and type, geology, climate and altitude24. The large combined area of the offsets relative to the impacted area was designed to allow flexibility, account for uncertainty and incorporate as many of the affected biodiversity components as possible24. Ankerana is the flagship offset, selected on the basis of its size, connectivity to the Corridor Ankeniheny-Zahamena (CAZ) forest corridor and the presence of ultramafic outcrops thought to support the same rare type of azonal forest lost at the mine site54. Extensive surveys conducted within Ankerana to establish biological similarity concluded the offset to be of higher conservation significance than the forests of the mine site due to the presence of rare lowland tropical forest24.The Conservation Zone is directly managed by the company, given its location within the concession area, while the other offsets are managed in partnership with local and international NGOs24,25. Ambatovy funds the management of Ankerana by Conservation International and local NGO partners (although before 2015 Ankerana was directly managed by Ambatovy via a Memorandum of Understanding with Conservation International24), supports BirdLife partner Asity with the management of Torotorofotsy and a number of local NGOs including Voary Voakajy25 are involved in CFAM26. The company is also working to secure formal, legal protection for CFAM26 as part of a proposed Torotorofotsy–CFAM complex new protected area (although progress on this has stalled).Overview of methodsTo estimate the impact of the offsets on deforestation and determine whether this has prevented enough deforestation to offset forest loss at the mine site, we combined several complementary methods for robust impact evaluation. First, we used statistical matching to match a sample of pixels from each biodiversity offset to pixels from the wider forested landscape with similar exposure to drivers of deforestation. Then we used a site-based difference-in-differences regression for each matched offset–control sample and a fixed-effects panel regression on the pooled data, to estimate the effect of protection. We systematically explored how arbitrary modelling choices (including the statistical distance measure used in matching, caliper size, ratio of control to treated units, matching with or without replacement and which, if any, additional covariates were included) affected our inference, exploring the robustness of our results to 116 alternative model specifications.MatchingThe former province of Toamasina was selected as the geographic area from which control pixels were sampled as it encompasses forests of the same type as the concession area with varying degrees of intactness and accessibility. The four biodiversity offsets are located within this province (Fig. 1).The unit of analysis is a 30 × 30 m2 pixel that was forested in the baseline year 200045,55. It is important that the scale of analysis aligns with the scale at which the drivers of deforestation (in this case, small-scale shifting agriculture) operate56. The median agricultural plot size (from 564 measured plots) in the study region is ~36 × 36 m2 (ref. 57). We took a subsample of pixels to reduce computational effort while maintaining the capacity for robust statistical inference58,59. We used a grid-based sampling strategy ensuring a minimum distance between sample units to reduce spatial autocorrelation60 and equal coverage of the study area58. A 150 × 150 m2 resolution grid, aligned to the other 30-m resolution data layers (Fig. 1c), was overlaid on the province and the 30 × 30 m2 pixel at the centre of each grid square was extracted to produce a subsample of pixels that are 120 m away from their nearest neighbour. The 120 m is larger than the minimum distance between units used in another matching study in Madagascar (68 m; ref. 59) but smaller than that used in other studies (200 m; ref. 61) and so strikes an appropriate balance between the avoidance of spatial autocorrelation and maximizing the possible sample cells.Protected areas in the study area managed by Madagascar National Parks were excluded from our control sample as they are actively managed and therefore do not represent counterfactual outcomes for the biodiversity offsets in the absence of protection (Fig. 1). However, control pixels were sampled from within the CAZ new protected area as legal protection was only granted in 2015 and resources for management are limited and thinly spread62. Additionally, Ankerana and parts of CFAM overlap with the CAZ and would have experienced the same management, and likely trajectory, as the rest of the CAZ, had they not been designated biodiversity offsets. Areas within 10 km of an offset boundary were excluded from the control sample to reduce the chance of leakage (where pressures are displaced rather than avoided) biasing results17,29. The 10 km was selected as it is a commonly used buffer zone within the literature17,58.To test for leakage effects, we used Veronoi polygons to partition the buffer area for CFAM, the Conservation Zone and Torotorofotsy (which overlap) into three individual buffer areas according to the nearest offset centroid and took a subsample of pixels from each (Fig. 1). Areas that overlapped with the established protected areas of Mantadia National Park and Analamazotra Special Reserve were excluded from the buffer zones.The outcome variable is the annual deforestation rate sourced from the Global Forest Change (GFC) dataset34. Following Vieilledent et al.45 these data were restricted to only include pixels classed as forest in a forest cover map of Madagascar for the year 200045,55, reducing the probability of false positives (whereby tree loss is identified in pixels that were not forested). The resulting tree loss raster was snapped to the forest cover 2000 layer to align cells, resulting in a maximum spatial error of 15 m. The GFC product34 has been shown to perform reasonably well at detecting deforestation in humid tropical forests63. In the north-eastern rainforests of Madagascar, Burivalova et al.39 found that GFC data performed comparably to a local classification of very high resolution satellite imagery at detecting forest clearance for shifting agriculture (although it was not effective at detecting forest degradation from selective logging). As clearance for shifting agriculture is considered the principal agent of deforestation in the study area22 and the forests of the study area are tropical humid ( >75% canopy cover), the GFC data are an appropriate tool for quantifying forest loss. Although recent evidence suggests that GFC data may have temporal biases64, this phenomenon affects our control and treated samples equally and so is unlikely to impact our results.The choice of covariates is extremely important in matching analyses. They must include, or proxy, all important factors influencing selection to treatment and the outcome of interest so that the matched control sample is sufficiently similar to the treated sample in these characteristics to constitute a plausible counterfactual, otherwise the resulting estimates may not be valid33. On the basis of the literature and a local theory of change we selected five covariates that we believe capture or proxy for the aspects of accessibility, demand and agricultural suitability that drive deforestation in the study area22,59,65,66. These are slope, elevation, distance to main road, distance to forest edge and distance to deforestation (Supplementary Methods). These five essential covariates comprise the main matching specification and form the core set used in all alternative specifications that we tested in the robustness checks. We also defined five additional variables (annual precipitation, distance to river, distance to cart track, distance to settlement and population density) and tested the effect of including these in the robustness checks. The additional covariates were so defined because they were of poorer data quality (population density and distance to settlement), correlated with an essential variable (annual precipitation and population density) or simply considered less influential (distance to river and distance to cart track; Supplementary Methods).Statistical matching was conducted in R statistics using the MatchIt package v.4.1 (ref. 67). To improve efficiency and produce closer matches we cleaned the data before matching to remove control units with values outside the calipers of the treated sample in any of the essential covariates (see Supplementary Methods for caliper definition). Following the recommendations of Schleicher et al.68 we tested several matching specifications and selected the one that maximized the trade-off between the number of treated units matched and the closeness of matches as the main specification (Supplementary Table 7). This was 1:1 nearest-neighbour matching without replacement, using Mahalanobis distance and a caliper of 1 s.d. This specification produced acceptable matches (within 1 s.d. of the Mahalanobis distance) for all treated units within all offsets. The maximum postmatching standardized difference in mean covariate values between treated and control samples was 0.05, well below the threshold of 0.25 considered to constitute an acceptable match69. This indicates that, on average, treated and control units were very well matched across all covariates.Matching was run separately for each offset. The resulting matched datasets were aggregated by treated status (offset or control) and year to produce a matrix of the count of pixels that were deforested each year (2001–2019) in the offset and the matched control sample. Converting the outcome variable to a continuous measure of deforestation avoids the problem of attrition associated with binary measures of deforestation and is better suited to the framework of the subsequent regressions70.Robustness checksStatistical matching requires various choices to be made68, many of which are essentially arbitrary. There therefore exists a range of possible alternative specifications that are all a priori valid (although some may be better suited to the data and study objectives69) but which could influence the results20,28. We tested the robustness of our results to 116 different matching model specifications (Fig. 4). First, we tested the robustness of the estimates to the use of three alternative matching distance measures (Mahalanobis, standard propensity score matching using generalized linear model regressions with a logit distribution and propensity score matching using RandomForest), three different calipers (0.25, 0.5 and 1 s.d.), different ratios of control to treated units (one, five and ten nearest neighbours) and matching with/without replacement. Holding the choice of covariates constant (using only the essential covariates), the combination of these led to the estimation of 54 different models. Second, we tested the robustness of results to the inclusion of the five additional covariates. Holding the choice of distance measure and model parameters constant, we constructed 31 models comprising all possible combinations of additional covariates with the core set of essential covariates. Finally, we explore the robustness of results for 31 randomly selected combinations of distance measure, model parameters and additional covariates. All 116 specifications are a priori valid, assuming that the covariates capture or proxy for all important factors influencing outcomes, but may fail to satisfy the parallel trends condition or produce matches for insufficient numbers of treated observations ( More