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    A new wave of marine fish invasions through the Panama and Suez canals

    1.
    Liu, X. et al. Curr. Biol. 29, 499–505.e4 (2019).
    CAS  Article  Google Scholar 
    2.
    Sardain, A. et al. Nat. Sustain. 2, 274–282 (2019).
    Article  Google Scholar 

    3.
    Review of Maritime Transport 2019 (United Nations, 2019).

    4.
    Leigh, E. G. et al. Biol. Rev. 89, 148–172 (2014).
    Article  Google Scholar 

    5.
    Seebens, H. et al. Proc. Natl Acad. Sci. USA 113, 5646–5651 (2016).
    CAS  Article  Google Scholar 

    6.
    Galil, B. et al. Manag. Biol. Invasion 8, 141–152 (2017).
    Article  Google Scholar 

    7.
    Spanier, E. & Galil, B. S. Endeavour 15, 102–106 (1991).
    Article  Google Scholar 

    8.
    Ruiz, G. M. et al. Smithson. Contrib. Mar. Sci. 38, 73–93 (2009).
    Google Scholar 

    9.
    Muirhead, J. R. et al. Divers. Distrib. 21, 75–87 (2015).
    Article  Google Scholar 

    10.
    Galil, B. S. et al. Biol. Invasion 17, 973–976 (2015).
    Article  Google Scholar 

    11.
    Azzurro, E. et al. Biol. Invasion 18, 2761–2772 (2016).
    Article  Google Scholar 

    12.
    Sharpe, D. et al. Ecology 98, 412–424 (2017).
    CAS  Article  Google Scholar 

    13.
    Salgado, J. et al. Sci. Total Environ. 729, 138444 (2020).
    CAS  Article  Google Scholar 

    14.
    Informe sobre la Aplicación y Eficiencia de Medidas de Mitigación para el Estudio de Impacto Ambiental del Proyecto “Ampliación del Canal de Panamá -Tercer Juego de Esclusas” (Panama Canal Authority, accessed 23 April 2020); https://go.nature.com/2FvcWMF

    15.
    Miller, A. W. & Ruiz, G. M. Nat. Clim. Change 4, 413–416 (2014).
    Article  Google Scholar 

    16.
    Cramer, W. et al. Nat. Clim. Change 8, 972–980 (2018).
    Article  Google Scholar 

    17.
    Ballew, N. G. et al. Sci. Rep. 6, 32169 (2016).
    CAS  Article  Google Scholar 

    18.
    Savva, I. et al. J. Fish. Biol. 97, 148–162 (2020).
    Article  Google Scholar 

    19.
    Shine, C. EPPO Bull. 37, 103–113 (2007).
    Article  Google Scholar 

    20.
    Ballast Water Management (IMO, accessed 20 May 2020); https://go.nature.com/2DUkI2t

    21.
    GloFouling (IMO, accessed 20 May 2020); https://www.glofouling.imo.org/

    22.
    Jouffray, J.-B. et al. One Earth 2, 43–54 (2020).
    Article  Google Scholar 

    23.
    Peleg, O. & Guy-Haim, T. Nature 575, 287 (2019).
    CAS  Article  Google Scholar 

    24.
    Balasingham, K. D. et al. Mol. Ecol. 27, 112–127 (2018).
    CAS  Article  Google Scholar 

    25.
    Martignac, F. et al. Fish. Fish. 16, 486–510 (2014).
    Article  Google Scholar 

    26.
    Putland, R. L. & Mensinger, A. F. Rev. Fish. Biol. Fish. 29, 789–807 (2019).
    Article  Google Scholar 

    27.
    Dennis, C. E. III et al. Biol. Invasion 21, 2837–2855 (2019).
    Article  Google Scholar 

    28.
    Sepulveda, A. J. et al. Trends Ecol. Evol. 35, 668–678 (2020).
    Article  Google Scholar 

    29.
    van Rijn, I. et al. Can. J. Fish. Aquat. Sci. 77, 752–761 (2020).
    Article  Google Scholar  More

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    American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations

    1.
    Collins, M. et al. In Climate Change 2013—The Physical Science Basis (ed. Intergovernmental Panel on Climate Change) 1029–1136 (Cambridge University Press, Cambridge, 2013).
    2.
    Ackerly, D. D. et al. The geography of climate change: implications for conservation biogeography. Divers. Distrib. 16, 476–487 (2010).
    Google Scholar 

    3.
    Bradshaw, W. E. & Holzapfel, C. M. Evolutionary response to rapid climate change. Science 312, 1477–1478 (2006).
    CAS  PubMed  Google Scholar 

    4.
    Chu, C., Mandrak, N. E. & Minns, C. K. Potential impacts of climate change on the distributions of several common and rare freshwater fishes in Canada. Divers. Distrib. 11, 299–310 (2005).
    Google Scholar 

    5.
    Princé, K. & Zuckerberg, B. Climate change in our backyards: the reshuffling of North America’s winter bird communities. Glob. Change Biol. 21, 572–585 (2015).
    ADS  Google Scholar 

    6.
    Scheffers, B. R. et al. The broad footprint of climate change from genes to biomes to people. Science 354, aaf7671 (2016).
    PubMed  Google Scholar 

    7.
    Lisiecki, L. E. & Raymo, M. E. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ 18 O records. Paleoceanography 20, PA1003 (2005).
    ADS  Google Scholar 

    8.
    Dyke, A. S. An outline of the deglaciation of North America with emphasis on central and northern Canada. Quat. Glaciat. Chronol. Part II 2b, 373–424 (2004).
    Google Scholar 

    9.
    Thompson, L. G. et al. Late glacial stage and Holocene tropical ice core records from Huascaran, Peru. Science 269, 46–50 (1995).
    ADS  CAS  Google Scholar 

    10.
    Johnsen, S. J. et al. Oxygen isotope and palaeotemperature records from six Greenland ice-core stations: camp century, dye-3, GRIP, GISP2, Renland and NorthGRIP. J. Quat. Sci. 16, 299–307 (2001).
    Google Scholar 

    11.
    Kawamura, K. et al. Northern Hemisphere forcing of climatic cycles in Antarctica over the past 360,000 years. Nature 448, 912–916 (2007).
    ADS  CAS  PubMed  Google Scholar 

    12.
    Dyke, A. S. Late quaternary vegetation history of Northern North America based on pollen, macrofossil, and faunal remains. Géogr. Phys. Quat. 59, 211–262 (2005).
    Google Scholar 

    13.
    Froese, D. et al. Fossil and genomic evidence constrains the timing of bison arrival in North America. Proc. Natl Acad. Sci. USA 114, 3457–3462 (2017).
    ADS  CAS  PubMed  Google Scholar 

    14.
    Palkopoulou, E. et al. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc. R. Soc. B Biol. Sci. 280, 20131910 (2013).
    Google Scholar 

    15.
    Debruyne, R. et al. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr. Biol. 18, 1320–1326 (2008).
    CAS  PubMed  Google Scholar 

    16.
    Shapiro, B. et al. Rise and fall of the Beringian Steppe Bison. Science 306, 1561–1565 (2004).
    ADS  CAS  PubMed  Google Scholar 

    17.
    Campos, P. F. et al. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc. Natl Acad. Sci. USA 107, 5675–5680 (2010).
    ADS  CAS  PubMed  Google Scholar 

    18.
    Chang, D. et al. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci. Rep. 7, 44585 (2017).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    19.
    Heintzman, P. D. et al. Bison phylogeography constrains dispersal and viability of the ice free corridor in western Canada. Proc. Natl Acad. Sci. USA 113, 8057–8063 (2016).
    CAS  PubMed  Google Scholar 

    20.
    Zazula, G. D. et al. American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change. Proc. Natl Acad. Sci. USA 2014, 6–11 (2014).
    Google Scholar 

    21.
    Zazula, G. D. et al. A case of early Wisconsinan “over-chill”: New radiocarbon evidence for early extirpation of western camel (Camelops hesternus) in eastern Beringia. Quat. Sci. Rev. 171, 48–57 (2017).
    ADS  Google Scholar 

    22.
    Saunders, J. J. et al. Paradigms and proboscideans in the southern Great Lakes region, USA. Quat. Int. 217, 175–187 (2010).
    Google Scholar 

    23.
    Oltz, D. F. & Kapp, R. O. Plant remains associated with Mastodon and Mammoth remains in central Michigan. Am. Midl. Nat. 70, 339–346 (1963).
    Google Scholar 

    24.
    Dreimanis, A. Extinction of Mastodons in Eastern North America: testing a new climatic-environmental hypothesis. Ohio J. Sci. 68, 257–272 (1968).
    Google Scholar 

    25.
    Shoshani, J. Understanding proboscidean evolution: a formidable task. Trends Ecol. Evol. 13, 480–487 (1998).
    CAS  PubMed  Google Scholar 

    26.
    Teale, C. L. & Miller, N. G. Mastodon herbivory in mid-latitude late-Pleistocene boreal forests of eastern North America. Quat. Res. 78, 72–81 (2012).
    Google Scholar 

    27.
    Green, J. L., DeSantis, L. R. G. & Smith, G. J. Regional variation in the browsing diet of Pleistocene Mammut americanum (Mammalia, Proboscidea) as recorded by dental microwear textures. Palaeogeogr. Palaeoclimatol. Palaeoecol. 487, 59–70 (2017).
    Google Scholar 

    28.
    Birks, H. H. et al. Evidence for the diet and habitat of two late Pleistocene mastodons from the Midwest, USA. Quat. Res. 91, 792–812 (2019).
    CAS  Google Scholar 

    29.
    Owen-Smith, N. Pleistocene extinctions: the pivotal role of megaherbivores. Paleobiology 13, 351–362 (1987).
    Google Scholar 

    30.
    Barnosky, A. D. et al. Variable impact of late-quaternary megafaunal extinction in causing ecological state shifts in North and South America. Proc. Natl Acad. Sci. USA 113, 856–861 (2016).
    ADS  CAS  PubMed  Google Scholar 

    31.
    Widga, C. et al. Late pleistocene proboscidean population dynamics in the North American midcontinent. Boreas 46, 772–782 (2017).
    Google Scholar 

    32.
    Godfrey-Smith, D., Grist, A. & Stea, R. Dosimetric and radiocarbon chronology of a pre-Wisconsinan mastodon fossil locality at East Milford, Nova Scotia, Canada. Quat. Sci. Rev. 22, 1353–1360 (2003).
    ADS  Google Scholar 

    33.
    Enk, J. et al. Mammuthus population dynamics in late pleistocene North America: divergence, phylogeogrpaphy and introgression. Front. Ecol. Evol. 4, 1–13 (2016).
    Google Scholar 

    34.
    Ishida, Y., Georgiadis, N. J., Hondo, T. & Roca, A. L. Triangulating the provenance of African elephants using mitochondrial DNA. Evol. Appl. 6, 253–265 (2013).
    CAS  PubMed  Google Scholar 

    35.
    Fernando, P., Pfrender, M. E., Encalada, S. E. & Lande, R. Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity 84, 362–372 (2000).
    CAS  PubMed  Google Scholar 

    36.
    Fisher, D. In The Proboscidea: Evolution and Paleoecology of Elephants andtheir Relatives (eds. Shoshani, J. & Tassy, P.) 296–315 (Oxford University Press, Oxford, 1996).

    37.
    Fisher, D. C. Paleobiology of pleistocene proboscideans. Annu. Rev. Earth Planet. Sci. https://doi.org/10.1146/annurev-earth-060115-012437 (2018).

    38.
    Rohland, N. et al. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol. 8, e1000564 (2010).
    CAS  PubMed  PubMed Central  Google Scholar 

    39.
    Muhs, D. R., Ager, T. A. & Begét, J. E. Vegetation and paleoclimate of the last interglacial period, central Alaska. Quat. Sci. Rev. 20, 41–61 (2001).
    ADS  Google Scholar 

    40.
    Jass, C. N. & Barrón-Ortiz, C. I. A review of quaternary proboscideans from Alberta, Canada. Quat. Int. 443, 88–104 (2017).
    Google Scholar 

    41.
    Shapiro, B. et al. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol. 28, 879–887 (2011).
    CAS  PubMed  Google Scholar 

    42.
    Drummond, A. J. & Stadler, T. Bayesian phylogenetic estimation of fossil ages. Philos. Trans. R. Soc. B Biol. Sci. 371, 20150129 (2016).
    Google Scholar 

    43.
    Plint, T., Longstaffe, F. J. & Zazula, G. Giant beaver palaeoecology inferred from stable isotopes. Sci. Rep. 9, 7179 (2019).
    ADS  PubMed  PubMed Central  Google Scholar 

    44.
    Yalden, D. W. The history of British mammals 12–27 (T & A D Poyser Ltd, Berkhamsted, 1999).

    45.
    Schreve, D. C. A new record of Pleistocene hippopotamus from River Severn terrace deposits, Gloucester, UK—palaeoenvironmental setting and stratigraphical significance. Proc. Geol. Assoc. 120, 58–64 (2009).
    Google Scholar 

    46.
    Stoffel, C. et al. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the late Pleistocene. Mol. Ecol. 24, 2507–2520 (2015).
    PubMed  Google Scholar 

    47.
    Tape, K. D., Gustine, D. D., Ruess, R. W., Adams, L. G. & Clark, J. A. Range expansion of moose in Arctic Alaska linked to warming and increased shrub habitat. PLoS ONE 11, e0152636 (2016).
    PubMed  PubMed Central  Google Scholar 

    48.
    Tape, K. D., Jones, B. M., Arp, C. D., Nitze, I. & Grosse, G. Tundra be dammed: beaver colonization of the Arctic. Glob. Change Biol. 24, 4478–4488 (2018).
    ADS  Google Scholar 

    49.
    Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
    ADS  CAS  PubMed  Google Scholar 

    50.
    Glocke, I. & Meyer, M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res. 27, 1–8 (2017).
    Google Scholar 

    51.
    Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, 1–8 (2012).
    Google Scholar 

    52.
    Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 1–10 (2010).
    Google Scholar 

    53.
    Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
    PubMed  Google Scholar 

    54.
    Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, 1–10 (2017).
    Google Scholar 

    55.
    Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. https://doi.org/10.1093/nar/gku699 (2014).

    56.
    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
    CAS  PubMed  PubMed Central  Google Scholar 

    57.
    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
    CAS  PubMed  PubMed Central  Google Scholar 

    58.
    Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9, 772–772 (2012).
    CAS  PubMed  PubMed Central  Google Scholar 

    59.
    Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
    CAS  PubMed  PubMed Central  Google Scholar 

    60.
    Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).
    CAS  PubMed  PubMed Central  Google Scholar 

    61.
    Baele, G., Lemey, P. & Suchard, M. A. Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty. Syst. Biol. 65, 250–264 (2016).
    PubMed  Google Scholar 

    62.
    Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, vey016 (2018).
    PubMed  PubMed Central  Google Scholar 

    63.
    Stuiver, M. & Reimer, P. J. Extended 14C database and revised CALIB radiocarbon calibration program. Radiocarbon 35, 215–230 (1993).
    Google Scholar 

    64.
    Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
    CAS  Google Scholar 

    65.
    Colleoni, F., Wekerle, C., Näslund, J.-O., Brandefelt, J. & Masina, S. Constraint on the penultimate glacial maximum Northern Hemisphere ice topography (≈140 kyrs BP). Quat. Sci. Rev. 137, 97–112 (2016).
    ADS  Google Scholar  More

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    The short-term costs of local content requirements in the Indian solar auctions

    Model
    An ideal experimental set-up to study the effect of LCRs on bid prices would include (at least) two identical countries, completely independent of each other, with an auction scheme identical apart from the LCR feature. Any price difference that emerged between the two auction schemes could then be fully attributed to the differences in the LCR feature. Even better would be to include additional identical countries with varying levels of stringency in the level of the LCRs (in weight, value or number of components), to study whether there are discontinuities in bid prices that seem to be attributable to increasing levels of LCR stringency. For instance, one might expect a non-linear increase in bid prices if very high levels of LCRs (say, 95%) were introduced given that the manufacturing capabilities for wafers would be near zero in India35.
    The Indian case comes close to an ideal policy experiment given that many tendered capacities were distributed between LCR and non-LCR auctions in similar geographic areas—albeit not always equally in terms of capacity. Importantly, firms were free to bid in both LCR and open auctions, and many firms submitted bids in both auction windows. However, to address the possible remaining issue of selection bias (that is, firms self-selecting into auctions with or without LCRs), we divide firms into two groups: firms that only bid in auctions without LCRs (59 firms, 134 bids) and firms that bid in both auction types, open and closed (26 firms, 143 bids). The data used in the study come from various sources from the Indian government and firm-level data from Mergent Intellect (described in more detail in the Data section).
    We considered using a multinomial selection model that would divide firms into three groups: those that only bid in auctions with LCRs, those that only bid in auctions without LCRs and those that bid in both auction types. However, since there are only seven firms in the category of ‘only LCR auctions’, we were unable to run the model. Yet we believe that the main question is whether a firm bid in an LCR auction, because it indicates whether the firm has sufficient local knowledge to either liaise with a local manufacturer or to use its own existing manufacturing facilities. Firms that only bid in the open auction, in contrast, could merely import the required parts. Hence, we expect there to be systematic differences between these two groups.
    Thus, we test whether firms that do not bid in the LCR category are different from those that do bid in the LCR category. It could be, for instance, that firms that bid in LCR auctions have more experience in local development than firms that only bid in the open auctions (where there are no restrictions in using imported material). Similarly, firms that only bid in the open auctions might be able to more effectively exploit economies of scale by producing solar PV cells and modules for several markets (for example, Canadian Solar, which has manufacturing capabilities in China).
    In addition to using standard ordinary least squares regressions, we therefore make use of a Heckman regression model, which accounts for this possible selection bias. Heckman’s 1979 seminal paper proposes a two-step statistical approach37. In the first step, an economic model is defined in which plausible factors for the probability of falling into (in our case) either Group 1 or 2 are considered. This is modelled as a probit regression,

    $${mathrm{Pr}}(G = 1|Z) = Phi (Zb)$$
    (1)

    where G indicates whether the firm belongs to Group 1 (G = 0 otherwise), Z is a vector of explanatory variables, b is a vector of unknown parameters and Φ is the cumulative distribution function of the standard normal distribution. The explanatory variables we consider are the number of employees of a given firm, whether it is a state-owned enterprise (SOE) and whether the firm is itself a manufacturer or is merely a project developer (an indication of the degree of vertical integration). We also consider whether the firm is primarily focused on energy or merely attempts to diversify from an unrelated field, indicating limited technical experience, and whether the company already bid in the NSM Phase I. The latter factor captures advantages that firms might have in the NSM Phase II due to prior experience with the auction system.
    The second stage of the Heckman model then uses the probability that a firm will self-select into Group 1, based on its characteristics, by including that probability as an explanatory variable in the ordinary least squares regression.
    For our standard ordinary least squares and Heckman regression model, we also created a number of explanatory variables that we assume influence bid price. We recognize that competition differed substantially between rounds and was on average twice as high in open auctions as in LCR auctions (as measured by our variable defined in equation (2)). Firms are likely to anticipate, or at least have beliefs about, the level of competition in an upcoming auction round, which leads them to adapt their bids accordingly (that is, to make higher bids when less competition is expected; this is well documented in the literature38). In order to exclude the possibility that bids under LCR regulation are higher solely due to this effect, we control for the degree of competition within each round. Therefore, we define the competition for each tender as follows:

    $${mathrm{Competition}}_r = frac{{mathop {sum }nolimits_{n = 1}^N B_r}}{{AC_r}}$$
    (2)

    where B is the capacity in MW of each of the bids submitted for a particular auction round r, AC is the total capacity in MW auctioned in round r and N is the overall number of bids received for each auction round r. For instance, if 20 MW are auctioned off and firms submit 100 MW in bids, the competition would be 5.
    We also include the cumulative installed capacity of each developer within the auction windows we cover to account for learning-by-doing of the developers and capacity building (for example, through greater local knowledge and connection to suppliers)39,40. Our time dummy controls for exogenous technological change, such as decrease in the cost of solar PV modules and other equipment over time, that is not directly related to the deployment in India (that is, exogenous technical progress)41. We do not include a state dummy as the variable is correlated too strongly with our time dummy (as certain states only conducted auctions in specific years, leading to high multicollinearity). We do, however, include the mean solar irradiation (annual average kWh m−2 d−1) per state to control for differences in the solar resources across different states (we also use the maximum solar irradiation for each state as a robustness check, which does not affect the results42).
    In addition, we include a dummy for the utility that purchases the electricity generated by the awarded projects. It is well documented that the financial solvency of the utility buying the electricity (that is, the offtaker) is an important factor in assessing the risk associated with a project (that is, if an offtaker is less financially stable, the risk of a default increases, making capital more expensive, which in turn increases the cost of power43). Lastly, we consider whether a PV project being in a solar park has an effect on bid price. Solar parks are designated areas where environmental impact assessment, land procurement and interconnection are already taken care of. However, these increased costs may be reflected in the land price for the solar projects. By differentiating between solar parks and normal land, we are able to capture the price differences between the two approaches.
    Thus, we use the following specification to study the effect of LCRs on bid price:

    $$begin{array}{ll}{mathrm{bid}}_i & = alpha + beta _1{mathrm{LCR}}_r + beta _2{mathrm{Competition}}_r + beta _3{mathrm{Year}} + beta _4{mathrm{Cum}}_{{mathrm{MW}}} \ & + beta _5{mathrm{Offtaker}} + beta _6{mathrm{Solar}},{mathrm{park}} + beta _7{mathrm{Sol}} + varepsilon _iend{array}$$
    (3)

    where bidi is the individual bid of each firm, r is the auction round, LCRr is the dummy for whether local content was required or not in the auction, Year is the time dummy to control for temporal shocks, CumMW is the cumulative installed capacity prior to the given auction in the NSM Phase II, Offtaker is a dummy for the utility buying the power (1 = SECI, 0 = NTPC), Solar park indicates whether the project is within a solar park, Sol refers to the annualized average solar resources (kWh m−2 d−1) in each state and εi is the error term. We also include an interaction term between LCR and our time dummy, to test whether the effect of LCRs changed over time.
    Part of the auctioned capacity was tendered under the viability gap funding (VGF) scheme, where the government fixed a base power purchase agreement (PPA) price and companies could request a top-up on the existing base price to make their project financially viable. Since price-only auctions have been implemented in India, the bidders who quoted the lowest amount of VGF were awarded the contracts until the auctioned capacity was reached (it should be noted that bidders were allowed to quote a lower PPA tariff than proposed and waive the VGF, but this rarely happened). Given that the VGF is dispensed as a capacity-based payment at the beginning of the lifetime of a power plant instead of as a constant subsidy for each unit of electricity generated, we had to levelize the amount to compare the outcomes with the generic auction results, where the payments are made across the entire lifetime of the power plant. Therefore, we applied the following method, which is based on the commonly used levelized cost of electricity (LCOE) calculation44, to calculate levelized VGF:

    $${mathrm{VGF}}_{{mathrm{levelized}}} = frac{{{mathrm{VGF}}_{{mathrm{total}}}}}{{mathop {sum }nolimits_{t = 1}^{25} frac{{E_t}}{{(1 + d)^t}}}} = frac{{C{mathrm{VGF}}}}{{mathop {sum }nolimits_{t = 1}^{25} frac{{C{mathrm{Flh}}}}{{(1 + d)^t}}}} = frac{{mathop {sum }nolimits_{t = 0}^5 frac{{{mathrm{VGF}}_t}}{{(1 + d)^t}}}}{{{mathrm{Flh}}mathop {sum }nolimits_{t = 1}^{25} frac{1}{{(1 + d)^t}}}}$$
    (4)

    In equation (4), Et is the electricity generated in year t, C is the project’s capacity in MW and Flh is its full-load hours. We assume constant, region-specific full-load hours, which can be found in ref. 45. For bids that did not indicate the project’s location in India, we assume a capacity factor of 20% and thus full-load hours of Flh = 1,752 h. Moreover, we assume a discount rate of d = 10% and a plant life of t = 25 years. With our approach, we are also able to capture the time value of money induced by the different VGF disbursement methods applied throughout Phase II (Supplementary Table 7; note that there was no VGF disbursement in Batch II). We then add the resulting levelized VGF support to the specific PPA price.
    To estimate the possible range of values for the additional cost borne directly by the Indian government due to LCRs, we used the average estimates from our Heckman regression of the additional cost of power of LCR bids when compared to the open bids. We compute this overall cost to the Indian government via an NPV model in which we discount all future payments from the Indian government to solar power plant owners and compare the cost to the clean technology budget in India. We use discount rates of 10%, 12% and 14% and a capacity factor of 20% for the solar PV plants and a 25-year running time based on REN21 (2018) data. These numbers are roughly similar (apart from possibly lower discount rates in this study) for other developing and emerging economies. These discount rates are based on information used by the Indian government for evaluating public projects46. Given the well-known challenges of choosing social discount rates (SDRs)47, we perform a sensitivity analysis by varying the discount rate between 10%, 12% and 14%. Taken together, these values for the SDRs encompass typical values of SDRs used in other developing and emerging economies, something that helps make our results more comparable to other countries46. We use the average real bid price from all open category auctions as our base price to calculate the additional cost of LCRs over the lifetime of an average solar project subject to LCRs.
    In order to analyse the possible benefits of the LCR policy, we select a small set of indicators commonly used in the innovation systems and catching-up literature to determine whether a country is ‘narrowing’ the gap between the innovation leader and itself. While there are no perfect sets of metrics, we employ three different metrics commonly used in the innovation and economics literature: (1) domestic and international patent filings in the technology of interest40, (2) domestic production versus international imports5 and (3) exports to other countries from the country of interest4.
    This analysis should be understood as correlational rather than causal, in contrast to the first part of our analysis. In addition, given how relatively recent the policy is, this analysis captures only short-term manufacturing and innovation effects. This is a limitation because some of the impacts of the policy, such as ongoing consolidation of the local industry through mergers and acquisitions, may take more time to materialize. Hence, the main contribution of this paper is the empirical assessment of the additional costs of LCRs, while the analysis of the possible benefits provides indicatory evidence of the evolution of important manufacturing and innovation metrics.
    Data
    In our analysis, we focus on the NSM Phase II auction results from 2014 to 2017. We did not include the bids and results from NSM Phase I since the majority of the projects (61% of total capacity deployed48) in the auction relied on thin film technology (as opposed to silicon panels), which was exempt from LCRs. Furthermore, we focused on the results of the PPA-based scheme and did not consider the EPC programme, which has a different focus: the auctioneer procures and owns the project and does not remunerate the electricity generated over 25 years to the project developer. The different remuneration mechanism, limited availability of data and different auction design elements, as well as different offtakers, hinder the comparability of the data. For the same reason, we neglect auctions conducted by state governments and focus solely on central government tenders conducted by either SECI or NTPC.
    Contrary to most other countries conducting auctions, the Indian government shows a high degree of transparency in terms of publishing bids in the NSM Phase II auctions—including information on firms and the bid prices of both successful and unsuccessful applicants. We collected the data about the bid prices and the respective bidders from various government sources, either directly through governmental bodies (for example, SECI) or indirectly through different industry and reputable news sites, such as Mercom India or EQ International Magazine. We include all auction rounds of Phase II that had LCR regulations in place for a total of 28 auction windows across 10 Indian states. As shown in Supplementary Fig. 5, we intentionally excluded from the analysis the state-wise utility-scale PV tenders (around 14 GW by September 2017). In addition, we exclude the central government EPC tenders (1.6 GW) as well as the ‘open category’ rounds in central government auctions in which no counterfactual LCR auction took place (around 4.6 GW), such as the 100 MW auction in Uttar Pradesh in Batch III.
    We consider our dataset with 277 bids complete in terms of auction rounds, since LCRs were abolished on 14 December 2017 due to a ruling of the WTO, with NTPC’s 250 MW Indian-wide auction being the last one under LCR regulation (the auction was later cancelled due to the negotiated phase-out of LCR). For further analysis, we consider the available submitted bids, rescale those to 2014 US dollar values to reflect inflation, and use logged bid values in our regression to normalize them. In summary, we consider bids with a total capacity of 21.7 GW, of which 18.7 GW were submitted in the open category and 3 GW under the LCR scheme.
    We also collect detailed firm data for all 85 firms within our sample. For each firm, we analyse whether it belongs to a bigger firm. Several firms are so-called special purpose vehicles, which are created merely to bid in a given auction. Given that these firms have access to the human, financial and technical capital of the bigger firm that they belong to, we use the firm characteristics of the parent company. In addition, we collect data on the employment numbers (which could be found for all firms, as opposed to sales numbers, which were unavailable for many privately owned firms), check whether the firm is an SOE and research whether the firms themselves have manufacturing capacities (that is, are vertically integrated). We analyse whether the firm had already bid in the first phase of the NSM, which might give firms a distinct advantage over newcomers due to experience with local regulations. We also check whether the main focus of the company is energy or whether it has just recently diversified its firm activities into energy. Lastly, we analyse whether the firm was founded in India or was registered abroad. We posit that all of these characteristics may influence whether a firm participates in a given auction (for example, we assume that firms that have local manufacturing capabilities are more likely to participate in LCR auctions).
    We used solar irradiation maps from the National Renewable Energy Laboratory (NREL) and converted them via QGIS (version 2.8.14) into mean, maximum and minimum values for each state. The NREL dataset provides solar resource in India for surface cells of 0.1 degrees in both latitude and longitude, or nominally 10 km in size. The NREL calculations are based on data from the Meteosat-5 and Meteosat-7 geostationary meteorological satellites42.
    Patent data were collected from the Indian Patent Database using web scraping methods (Python package Selenium), as the patent office does not offer an application programming interface (API). We employ a typology from a recent, comprehensive review of international patent classification (IPC) terms and their correspondence to PV system components published in Renewable and Sustainable Energy Reviews49. This typology covers 284 distinct IPC codes in seven groups: cells, panels, electronics, energy storage, monitoring/testing, devices and combined. Studies comparing global trends in patenting to track innovation normally rely on large patent databases such as the European patent database PATSTAT, which aggregates patent statistics across many domestic offices. However, for India the PATSTAT data are woefully incomplete, leading us to resort to web scraping techniques.
    The data on domestic production and imports in Fig. 4c are based on the Directorate General of Trade Remedies investigation on the imposition of safeguards on solar PV cells and modules on behalf of five Indian solar producers. The export data in Fig. 4d were exported from the global United Nations trade database Comtrade using the commodity code ‘HS 854140’, which describes ‘photosensitive semi-conductor devices, including photovoltaic cells whether or not assembled in modules or made up into panels’50. More

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    Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples

    1.
    Willerslev, E. et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300, 791–795 (2003).
    ADS  CAS  PubMed  Google Scholar 
    2.
    Birks, H. J. B. & Birks, H. H. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?. New Phytol. 209, 499–506 (2016).
    CAS  PubMed  Google Scholar 

    3.
    Froese, D., Westgate, J., Preece, S. & Storer, J. Age and significance of the late Pleistocene Dawson tephra in eastern Beringia. Quatern. Sci. Rev. 21, 2137–2142 (2002).
    ADS  Google Scholar 

    4.
    Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74 (2013).
    ADS  CAS  PubMed  Google Scholar 

    5.
    Poinar, H. N. et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392–394 (2006).
    ADS  CAS  PubMed  Google Scholar 

    6.
    Waters, M. R. & Stafford, T. W. Redefining the age of Clovis: implications for the peopling of the Americas. Science 315, 1122–1126 (2007).
    ADS  CAS  PubMed  Google Scholar 

    7.
    Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165 (2006).
    ADS  CAS  PubMed  Google Scholar 

    8.
    Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368 (2011).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    9.
    Nikrad, M. P., Kerkhof, L. J. & Häggblom, M. M. The subzero microbiome: microbial activity in frozen and thawing soils. FEMS Microbiol. Ecol. 92, fiw81 (2016).
    Google Scholar 

    10.
    Schuur, E. A. et al. Vulnerability of permafrost carbon to climate change: implications for the global carbon cycle. Bioscience 58, 701–714 (2008).
    Google Scholar 

    11.
    Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 345 (2017).
    ADS  CAS  PubMed  Google Scholar 

    12.
    Weyrich, L. S. et al. Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019).
    CAS  PubMed  PubMed Central  Google Scholar 

    13.
    Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl. Acad. Sci. 111, 2229–2234 (2014).
    ADS  CAS  PubMed  Google Scholar 

    14.
    Bang-Andreasen, T., Schostag, M., Priemé, A., Elberling, B. & Jacobsen, C. S. Potential microbial contamination during sampling of permafrost soil assessed by tracers. Sci. Rep. 7, 43338 (2017).
    ADS  CAS  PubMed  PubMed Central  Google Scholar 

    15.
    Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
    PubMed  PubMed Central  Google Scholar 

    16.
    Willerslev, E., Hansen, A. J. & Poinar, H. N. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol. Evol. 19, 141–147 (2004).
    PubMed  Google Scholar 

    17.
    Barbato, R. A. et al. Removal of exogenous materials from the outer portion of frozen cores to investigate the ancient biological communities harbored inside. JoVE 3, e54091 (2016).
    Google Scholar 

    18.
    D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457 (2011).
    ADS  PubMed  Google Scholar 

    19.
    Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova, L., Tutukina, M., Meyers, A., & Kondrashov, F. Metagenomic analyses of the late Pleistocene permafrost—Additional tools for reconstruction of environmental conditions. Biogeosciences 13 (2016).

    20.
    Kallmeyer, J. Contamination Control for Scientific Drilling Operations Vol. 98, 61–91 (Academic Press, London, 2017).
    Google Scholar 

    21.
    Kallmeyer, J., Mangelsdorf, K., Cragg, B. & Horsfield, B. Techniques for contamination assessment during drilling for terrestrial subsurface sediments. Geomicrobiol. J. 23, 227–239 (2006).
    CAS  Google Scholar 

    22.
    Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015).
    PubMed  Google Scholar 

    23.
    Llamas, B. et al. From the field to the laboratory: controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. STAR: Sci. Technol. Archaeol. Res. 3, 1–14 (2017).
    Google Scholar 

    24.
    Yanagawa, K., Nunoura, T., McAllister, S., Hirai, M., Breuker, A., Brandt, L., House, C., Moyer, C., Birrien, J.-L., Aoike, K., Sunamura, M., Urabe, T., Mottl, M., & Takai, K. The first microbiological contamination assessment by deep-sea drilling and coring by the D/V Chikyu at the Iheya North hydrothermal field in the Mid-Okinawa Trough (IODP Expedition 331). Front. Microbiol. 4 (2013).

    25.
    Yang, D. Y. & Watt, K. Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci. 32, 331–336 (2005).
    Google Scholar 

    26.
    Bollongino, R., Tresset, A. & Vigne, J.-D. Environment and excavation: pre-lab impacts on ancient DNA analyses. C. R. Palevol 7, 91–98 (2008).
    Google Scholar 

    27.
    Smith, D. C. Ajsmrfsahhs. Tracer-based estimates of drilling-induced microbial contamination of Deep Sea Crust. Geomicrobiol. J. 17, 207–219 (2000).
    CAS  Google Scholar 

    28.
    Krivushin, K. et al. Two metagenomes from late pleistocene Northeast Siberian Permafrost. Genome Announc. 3, e01380-e1414 (2015).
    PubMed  PubMed Central  Google Scholar 

    29.
    Vishnivetskaya, T. A. et al. Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology 6, 400–414 (2006).
    ADS  CAS  PubMed  Google Scholar 

    30.
    Wright, G. D. & Poinar, H. Antibiotic resistance is ancient: implications for drug discovery. Trends Microbiol. 20, 157–159 (2012).
    CAS  PubMed  Google Scholar 

    31.
    Kalmár, T., Bachrati, C. Z., Marcsik, A. & Raskó, I. A simple and efficient method for PCR amplifiable DNA extraction from ancient bones. Nucl. Acids Res. 28, e67–e67 (2000).
    PubMed  Google Scholar 

    32.
    Palmirotta, R. et al. Use of a multiplex polymerase chain reaction assay in the sex typing of DNA extracted from archaeological bone. Int. J. Osteoarchaeol. 7, 605–609 (1997).
    Google Scholar 

    33.
    González-Oliver, A., Márquez-Morfín, L., Jiménez, J. C. & Torre-Blanco, A. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo. Am. J. Phys. Anthropol. 116, 230–235 (2001).
    PubMed  Google Scholar 

    34.
    Kemp, B. M. & Smith, D. G. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forens. Sci. Int. 154, 53–61 (2005).
    CAS  Google Scholar 

    35.
    Rogers, S. O. et al. Comparisons of protocols for decontamination of environmental ice samples for biological and molecular examinations. Appl. Environ. Microbiol. 70, 2540–2544 (2004).
    CAS  PubMed  PubMed Central  Google Scholar 

    36.
    Salamon, M., Tuross, N., Arensburg, B. & Weiner, S. Relatively well preserved DNA is present in the crystal aggregates of fossil bones. Proc. Natl. Acad. Sci. USA 102, 13783–13788 (2005).
    ADS  CAS  PubMed  Google Scholar 

    37.
    Mackelprang, R. et al. Microbial survival strategies in ancient permafrost: insights from metagenomics. ISME 11, 2305 (2017).
    CAS  Google Scholar 

    38.
    Vishnivetskaya, T., Kathariou, S., McGrath, J., Gilichinsky, D. & Tiedje, J. M. Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 4, 165–173 (2000).
    CAS  PubMed  Google Scholar 

    39.
    Yergeau, E., Hogues, H., Whyte, L. G. & Greer, C. W. The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME 4, 1206 (2010).
    CAS  Google Scholar 

    40.
    Vishnivetskaya, T. A. et al. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol. Ecol. 87, 217–230 (2014).
    CAS  PubMed  Google Scholar 

    41.
    Braid, M. D., Daniels, L. M. & Kitts, C. L. Removal of PCR inhibitors from soil DNA by chemical flocculation. J. Microbiol. Methods 52, 389–393 (2003).
    CAS  PubMed  Google Scholar 

    42.
    Griffiths, R. I., Whiteley, A. S., O’Donnell, A. G. & Bailey, M. J. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66, 5488–5491 (2000).
    CAS  PubMed  PubMed Central  Google Scholar 

    43.
    Porter, T. M. et al. Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Mol. Ecol. Resour. 13, 798–810 (2013).
    CAS  PubMed  Google Scholar 

    44.
    Porter, T. J. et al. Recent summer warming in northwestern Canada exceeds the Holocene thermal maximum. Nat. Commun. 10, 1631 (2019).
    ADS  PubMed  PubMed Central  Google Scholar 

    45.
    Durfee, T. et al. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190, 2597–2606 (2008).
    CAS  PubMed  PubMed Central  Google Scholar 

    46.
    Guzman, L. M., Belin, D., Carson, M. J. & Beckwith, J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol. 177, 4121–4130 (1995).
    CAS  PubMed  PubMed Central  Google Scholar 

    47.
    Shaner, N. C. et al. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Methods 10, 407 (2013).
    CAS  PubMed  PubMed Central  Google Scholar 

    48.
    Cooper, A. & Poinar, H. N. Ancient DNA: do it right or not at all. Science 289, 1139–1139 (2000).
    CAS  PubMed  Google Scholar 

    49.
    Bottos, E. M., Kennedy, D. W., Romero, E. B., Fansler, S. J., Brown, J. M., Bramer, L. M., Chu, R. K., Tfaily, M. M., Jansson, J. K. & Stegen, J. C. Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. FEMS Microbiol. Ecol. 94 (2018).

    50.
    Hultman, J. et al. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521, 208 (2015).
    ADS  CAS  PubMed  Google Scholar 

    51.
    Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A. & Staudigel, H. Tracer-based estimates of drilling-induced microbial contamination of deep sea crust. Geomicrobiol J. 17, 207–219 (2000).
    CAS  Google Scholar 

    52.
    Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & D’Hondt, S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl. Acad. Sci. 109, 16213–16216 (2012).
    ADS  CAS  PubMed  Google Scholar 

    53.
    Juck, D. F. et al. Utilization of fluorescent microspheres and a green fluorescent protein-marked strain for assessment of microbiological contamination of permafrost and ground ice core samples from the Canadian High Arctic. Appl. Environ. Microbiol. 71, 1035–1041 (2005).
    CAS  PubMed  PubMed Central  Google Scholar 

    54.
    Colwell, F. S., Pryfogle, P. A., Lee, B. D. & Bishop, C. L. Use of a cyanobacterium as a particulate tracer for terrestrial subsurface applications. J. Microbiol. Methods 20, 93–101 (1994).
    Google Scholar 

    55.
    Friese, A. et al. (2017) A simple and inexpensive technique for assessing contamination during drilling operations. Limnol. Oceanogr. Methods 15, 200–211 (2017).
    CAS  Google Scholar 

    56.
    Knapp, M., Clarke, A. C., Horsburgh, K. A. & Matisoo-Smith, E. A. Setting the stage—Building and working in an ancient DNA laboratory. Ann. Anat. Anatomischer Anzeiger 194, 3–6 (2012).
    CAS  PubMed  Google Scholar 

    57.
    Eisenhofer, R. et al. Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends Microbiol. 27, 105–117 (2019).
    CAS  PubMed  Google Scholar  More

  • in

    Reconciling yield gains in agronomic trials with returns under African smallholder conditions

    Experimental design
    The trials were conducted in five regions (Boro, Ugunja, Ukwala, Wagai and Yala) of Siaya County in western Kenya. Siaya County is located at 00°08.468′ N, 34°25.378′ E, and at an altitude of 1,336 m above sea level. The experimental sites were in lower midland 1(LM1) and lower midlands 2 (LM2) agro-ecological zones, which experience bimodal rainfall with long rains (LR) starting in March to July and short Rains (SR) starting in Late August to December41 and receive average annual rainfall of 1,500 mm42. The soils are mainly Ferralsols and Acrisols in the higher areas and Vertisols in the low areas.
    Trials were conducted in 48 randomly selected villages, using stratification at the sub-county level. Half of them (randomly selected) participated in the trials in the long and short rain of 2014 and the long rain of 2015. The other half started in the short rain of 2014 and continued throughout the long and short rain of 2015. In each village 10 farmers participated in the trial. Half of them were specifically selected for participation in a community meeting. In those meetings, the researchers explained the objectives of the trials and asked the community members to nominate 5 farmers (as well as 5 potential substitutes), including two women, thought to be good farmers and interested in participating in the trials. Such non-random selection of farmers is common practice in research trials (Supplementary Table S1 online). The other half was selected randomly from the list of all the farmers in the village. All selected farmers were visited to obtain consent for the trials and identify the potential trial parcel (chosen by the farmer, conditional on fitting with some criteria for suitability to the research trials). A small number of replacements was done (but always keeping 5 selected by the community and 5 random). In each village 4 random farmers (2 random and 2 selected) were assigned to participate in the maize trial, while 3 random farmers (at least 1 random and 1 selected) were assigned to participate in the soybean trial. The other 3 farmers participated in a maize-soybean intercrop trial. During implementation, the assignment of inputs for the intercrop trial was, however, contaminated. As a result none of the plots in the intercrop trial received a best-bet input package, making the agronomic findings from that trial hard to interpret, and therefore not necessarily of interest for the decomposition proposed in this paper. Nevertheless, for completeness, results for these intercrop trials are shown in Supplementary Table S14 online.
    Researcher-designed and farmer-managed trials
    The trials would qualify as researcher-designed and farmer-managed (under the supervision of the researchers). The research team had full control over the design of the trials, from the choice of inputs to spacing and other management practices. All inputs were provided by the research team, with the exception of the local maize seed tested in two out of the six plots. A researcher (local expert agronomist) was present and led planting, gapping and thinning, all fertilizer applications, and harvesting. In these activities, labor was typically provided by the farmer. Planting dates were mostly decided by the researchers to best target the onset of rains, also responding to the farmers’ feedback on beginning of rains and availability to schedule the visit for planting. The farmer was in charge of land preparation, weeding and other management, with the researchers providing guidelines on those practices. In each village, a contact person (typically one of the ten farmers) visited the trials weekly to verify that the farmers fulfilled their responsibilities. Farmers were also asked to inform the contact person in case of any pest or disease, in which case the researcher provided the required pesticide or fungicide.
    Treatment structure and application
    Supplementary Table S2 online presents the full factorial designs of the multi-locational trials for maize and soybean, including details on crop varieties and quantity of inputs. The plot sizes were 4.5 × 5 m and the treatments were completely randomized between the six plots on each parcel. Plot sizes are of a similar order of magnitude as those found in other recently published work. A 1 m inter-plot spacing was planted with sweet potatoes to act as a buffer between plots to prevent inter-plot contamination. The sweet potatoes were planted at 50 cm from each plot, and border rows of the maize and soya plots were excluded for yield estimations to limit any edge effect. Hence the area harvested was 12.9 m2 for maize and 13.5 m2 for soybean. The experiments were repeated for three seasons, and plot layout and treatments were maintained for three seasons.
    For the soybean trials, a soybean rhizobia inoculant was tested alone, with Minjingu hyper phosphate (0-30-0 + 38CaO) or Sympal (0:23:15 + 10CaO + 4S + 1MgO + 0.1Zn) in a full factorial design. Phosphorus rate of 30 kg P ha−1 was used to determine the quantity of Sympal and Minjingu hyper phosphate to be applied. On each farm only one replicate was used; hence, 6 plots were installed on each farm. Inoculation was done at planting as a seed coating using the directions for use in the respective product labels. Each plot had 6 soybean lines of 5 m in length each spaced at 5 cm from plant to plant within row and 50 cm from row to row. Inoculation was done on all the rows. Soybean variety TGx1740-2F with medium maturity (95–100 days)43 was used as the test crop. The spatial variability of the soybean response is studied in44. The soybean trials demonstrated that the combination of rhizobia inoculant and P-source led to important yield gains44.
    The choice of inputs resulted from prior research conducted as part of the Compro project. Soybean was chosen as test crop mainly because in the prior phase of the project it had shown good response to rhizobia inoculation45 and was agro-ecologically suitable to the region. Kenya is an importer of soybean and multiple efforts are geared towards raising local production. In Compro I, the two rhizobia inoculants were tested and shown to be effective in increasing nodulation, nitrogen fixation and yield when inoculated on the tested soybean variety. Minjingu and Sympal were chosen based on their formulation with respect to the chemical characteristics of the soils in the test sites and results of earlier research46. The soils generally lack phosphorus and are acidic. A mapping study47 specifically identified Western Kenya as a potential K deficient area, and soil acidity has long been identified as a constraining factor in Western Kenya48 hence the importance of CaO. Results from soil sampling of the trial plots confirmed that more than 56.87% of soils were acidic (pH  More

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    Two potential equilibrium states in long-term soil respiration activity of dry grasslands are maintained by local topographic features

    Spatial patterns of stability proxies and background variables
    Figure 2 a, b show the spatial distribution of our two proxy variables, the average rank of Rs per position (rankRs) and of the range of the ranks per position (rangeRs) in kriged maps. The middle to southern areas were found to have the largest, whilst the north-eastern areas the smallest rankRs values, whereas a slightly different pattern was characteristic for rangeRs with some additional north-western large values. Similarly, larger average soil organic carbon content (meanSOC) and average soil water content (meanSWC) (Fig. 2 c, d) were detected at the western-middle-southern regions and smaller at the north-eastern part of the study site.
    Figure 2

    Kriged patterns of stability proxies, rankRs (a) and rangeRs (b), as well as of background factors, meanSOC (%, c) and meanSWC (%, d).

    Full size image

    Correlations between stability proxies and background variables along DEMs: entire dataset
    We investigated the potential direct effects of the different terrain attributes (local mean elevation (mALT), standard deviation of elevation (SD), topographic position index (TPI), slope (Sl), Easterness and Northness (East, North)) on the spatial distributions of our proxy variables by using the terrain attributes originating from differently smoothed DEM rasters. DEM1 was the original, 0.2 m resolution model, while DEMs 2–6 were progressively smoothed by a factor of two resulting in different resolution DEM rasters (DEM2: 0.4 m, DEM3: 0.8 m, DEM4: 1.6 m, DEM5: 3.2 m, DEM6: 6.4 m, respectively), and finally DEM7 met the resolution of the field measuring campaigns (10 m). The terrain attributes were filtered out from the rasters for the 78 measuring positions of the sampling grid.
    On the basis of the correlation analysis we found an important difference in terrain attribute features between DEM 5 and 6, especially in SD, Sl, North and East. All subsequent results are then based on DEMs 1–5, which were found to be more similar to each other and to the original DEM1. The maps of terrain attributes with the box blur kernel from DEM1-5 can be found in the Supplementary Information (SI) together with the descriptions and calculations. As we couldn’t find any of the blur kernels superior to the other when considering correlations, the results hereafter are only presented for the box blur kernel calculations for simplicity.
    When we considered the entire dataset (named hereafter: “A” dataset), we could only find significant correlation between rangeRs and TPI at less smoothed DEMs but the correlation was very weak (black symbols and line in Fig. 3).
    Figure 3

    Direct correlation between TPI and stability proxy, rangeRs at less smoothed DEMs, DEM1-2 for datasets A (black symbols and line) and S (blue symbols and line, see the information later on). The correlations were significant at p = 0.0076 and p  = 0.0172 levels, although they were weak, r2 = 0.09, r2 = 0.42 for A and S (see the information later on), respectively.

    Full size image

    Any other correlation between the proxies and the terrain attributes could only be deduced indirectly from the positive correlations between rankRs and meanSOC, meanSWC (cf. Table 1b). These correlations were scale-independent, i.e., we detected them at every DEMs. In general, the larger the soil carbon content and soil moisture at a position (cf. Figure 2c,d, showing quite similar patterns to the proxy patterns in the figure upper row), the larger the Rs activity detected and the opposite was true for lower carbon content and soil moisture positions.
    Table 1 (a) Statistically significant (p  More

  • in

    Structures spread across our seas

    1.
    Duarte, C. M. et al. Front. Ecol. Environ. 11, 91–97 (2012).
    Article  Google Scholar 
    2.
    Firth, L. B. et al. in Oceanography and Marine Biology: An Annual Review Vol. 54 (eds Hughes, R. N. et al.) 193–269 (Taylor & Francis, 2016).

    3.
    Bugnot, A. B. et al. Nat. Sustain. https://doi.org/10.1038/s41893-020-00595-1 (2020).

    4.
    Bishop, M. J. et al. J. Exp. Mar. Biol. Ecol. 492, 7–30 (2017).
    Article  Google Scholar 

    5.
    Dong, Y., Huang, X., Wang, W., Li, Y. & Wang, J. et al. Divers. Distrib. 22, 731–744 (2016).
    Article  Google Scholar 

    6.
    Nagelkerken, I., Doney, S. C. & Munday, P. L. Oceanography and Marine Biology: An Annual Review Vol. 57 (eds Hawkins, S. J. et al.) 229–264 (Taylor & Francis, 2019).

    7.
    Hawkins, S. J. et al. Mar. Pollut. Bull. 156, 111150 (2020).
    CAS  Article  Google Scholar 

    8.
    Bayraktarov, E. et al. Ecol. Appl. 26, 1055–1074 (2016).
    Article  Google Scholar 

    9.
    Jones, P. J. S., Lieberknecht, L. M. & Qiu, W. Mar. Policy 71, 256–264 (2016).
    Article  Google Scholar 

    10.
    Bracewell, S. A., Spencer, M., Marrs, R. H., Iles, M. & Robinson, L. A. PLoS ONE 7, e48863 (2012).
    CAS  Article  Google Scholar 

    11.
    Evans, A. J. et al. Environ. Sci. Policy 91, 60–69 (2019).
    Article  Google Scholar 

    12.
    Firth, L. B. et al. J. Appl. Ecol. https://doi.org/10.1111/1365-2664.13683 (2020). More

  • in

    Ecological restoration impact on total terrestrial water storage

    1.
    Bryan, B. A. et al. China’s response to a national land-system sustainability emergency. Nature 559, 193–204 (2018).
    CAS  Google Scholar 
    2.
    Ouyang, Z. et al. Improvements in ecosystem services from investments in natural capital. Science 352, 1455–1459 (2016).
    CAS  Google Scholar 

    3.
    Chen, C. et al. China and India lead in greening of the world through land-use management. Nat. Sustain. 2, 122–129 (2019).
    Google Scholar 

    4.
    Tong, X. et al. Increased vegetation growth and carbon stock in China karst via ecological engineering. Nat. Sustain. 1, 44–50 (2018).
    Google Scholar 

    5.
    Lu, F. et al. Effects of national ecological restoration projects on carbon sequestration in China from 2001 to 2010. Proc. Natl Acad. Sci. USA 115, 4039 (2018).
    CAS  Google Scholar 

    6.
    Feng, X. et al. Revegetation in China’s Loess Plateau is approaching sustainable water resource limits. Nat. Clim. Change 6, 1019 (2016).
    Google Scholar 

    7.
    Jia, X., Shao, M. A., Zhu, Y. & Luo, Y. Soil moisture decline due to afforestation across the Loess Plateau, China. J. Hydrol. 546, 113–122 (2017).
    Google Scholar 

    8.
    Chen, Y. et al. Balancing green and grain trade. Nat. Geosci. 8, 739–741 (2015).
    Google Scholar 

    9.
    Tong, X. et al. Forest management in southern China generates short term extensive carbon sequestration. Nat. Commun. 11, 129 (2020).
    CAS  Google Scholar 

    10.
    Jackson, R. B. et al. Trading water for carbon with biological carbon sequestration. Science 310, 1944–1947 (2005).
    CAS  Google Scholar 

    11.
    Li, Y. et al. Divergent hydrological response to large-scale afforestation and vegetation greening in China. Sci. Adv. 4, eaar4182 (2018).
    Google Scholar 

    12.
    Green, J. K. et al. Regionally strong feedbacks between the atmosphere and terrestrial biosphere. Nat. Geosci. 10, 410–414 (2017).
    CAS  Google Scholar 

    13.
    Branch, O. & Wulfmeyer, V. Deliberate enhancement of rainfall using desert plantations. Proc. Natl Acad. Sci. USA 116, 18841–18847 (2019).
    CAS  Google Scholar 

    14.
    Ellison, D. et al. Trees, forests and water: cool insights for a hot world. Glob. Environ. Change 43, 51–61 (2017).
    Google Scholar 

    15.
    McDonnell, J. J. et al. Water sustainability and watershed storage. Nat. Sustain. 1, 378–379 (2018).
    Google Scholar 

    16.
    Rodell, M. et al. Emerging trends in global freshwater availability. Nature 557, 651–659 (2018).
    CAS  Google Scholar 

    17.
    Mirzabaev, A. et al. in IPCC Special Report on Climate Change and Land (eds Akhtar-Schuster, M., Driouech, F. & Sankaran, M.) Ch. 3 (IPCC, Cambridge Univ. Press, 2019).

    18.
    Rodell, M., Velicogna, I. & Famiglietti, J. S. Satellite-based estimates of groundwater depletion in India. Nature 460, 999–1002 (2009).
    CAS  Google Scholar 

    19.
    Scanlon, B. R. et al. Global models underestimate large decadal declining and rising water storage trends relative to GRACE satellite data. Proc. Natl Acad. Sci. USA 115, E1080 (2018).
    CAS  Google Scholar 

    20.
    Tapley, B. D., Bettadpur, S., Ries, J. C., Thompson, P. F. & Watkins, M. M. GRACE Measurements of Mass Variability in the Earth System. Science 305, 503–505 (2004).
    CAS  Google Scholar 

    21.
    Tapley, B. D. et al. Contributions of GRACE to understanding climate change. Nat. Clim. Change 9, 358–369 (2019).
    Google Scholar 

    22.
    Tian, H. et al. Response of vegetation activity dynamic to climatic change and ecological restoration programs in Inner Mongolia from 2000 to 2012. Ecol. Eng. 82, 276–289 (2015).
    Google Scholar 

    23.
    Zhang, Z. & Huisingh, D. Combating desertification in China: monitoring, control, management and revegetation. J. Clean. Prod. 182, 765–775 (2018).
    Google Scholar 

    24.
    Huang, Y., Wang, N.-a, He, T., Chen, H. & Zhao, L. Historical desertification of the Mu Us Desert, Northern China: A multidisciplinary study. Geomorphology 110, 108–117 (2009).
    Google Scholar 

    25.
    Xu, D. Y., Kang, X. W., Zhuang, D. F. & Pan, J. J. Multi-scale quantitative assessment of the relative roles of climate change and human activities in desertification–a case study of the Ordos Plateau, China. J. Arid Environ. 74, 498–507 (2010).
    Google Scholar 

    26.
    Yan, F., Wu, B. & Wang, Y. Estimating spatiotemporal patterns of aboveground biomass using Landsat TM and MODIS images in the Mu Us Sandy Land, China. Agric. For. Meteorol. 200, 119–128 (2015).
    Google Scholar 

    27.
    Li, S. et al. Vegetation changes in recent large-scale ecological restoration projects and subsequent impact on water resources in China’s Loess Plateau. Sci. Total Environ. 569–570, 1032–1039 (2016).
    Google Scholar 

    28.
    Xu, Z. et al. Recent greening (1981–2013) in the Mu Us dune field, north-central China, and its potential causes. Land Degrad. Dev. 29, 1509–1520 (2018).
    Google Scholar 

    29.
    Poulter, B. et al. Plant functional type classification for earth system models: results from the European Space Agency’s Land Cover Climate Change Initiative. Geosci. Model Dev. 8, 2315–2328 (2015).
    Google Scholar 

    30.
    Xu, Z., Mason, J. A. & Lu, H. Vegetated dune morphodynamics during recent stabilization of the Mu Us dune field, north-central China. Geomorphology 228, 486–503 (2015).
    Google Scholar 

    31.
    Review of the Kubuqi Ecological Restoration Project: A Desert Green Economy Pilot Initiative (United Nations Environment Programme, 2015).

    32.
    Cheng, D.-h et al. Estimation of groundwater evaportranspiration using diurnal water table fluctuations in the Mu Us Desert, northern China. J. Hydrol. 490, 106–113 (2013).
    Google Scholar 

    33.
    Yu, X., Huang, Y., Li, E., Li, X. & Guo, W. Effects of rainfall and vegetation to soil water input and output processes in the Mu Us Sandy Land, northwest China. CATENA 161, 96–103 (2018).
    Google Scholar 

    34.
    Li, Q. et al. Feasibility of the combination of CO2 Geological storage and saline water development in sedimentary basins of China. Energy Proc. 37, 4511–4517 (2013).
    CAS  Google Scholar 

    35.
    Xie, X., Xu, C., Wen, Y. & Li, W. Monitoring groundwater storage changes in the Loess Plateau using GRACE satellite gravity data, hydrological models and coal mining data. Remote Sens. 10, 605 (2018).
    Google Scholar 

    36.
    Griffin-Nolan, R. J. et al. Legacy effects of a regional drought on aboveground net primary production in six central US grasslands. Plant Ecol. 219, 505–515 (2018).
    Google Scholar 

    37.
    Poulter, B. et al. Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle. Nature 509, 600–603 (2014).
    CAS  Google Scholar 

    38.
    Ahlström, A. et al. The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink. Science 348, 895–899 (2015).
    Google Scholar 

    39.
    Cho, S., Ser-Oddamba, B., Batkhuu, N.-O. & Seok Kim, H. Comparison of water use efficiency and biomass production in 10-year-old Populus sibirica and Ulmus pumila plantations in Lun soum, Mongolia. For. Sci. Technol. 15, 147–158 (2019).
    Google Scholar 

    40.
    Swenson, S. C. & Lawrence, D. M. A GRACE-based assessment of interannual groundwater dynamics in the Community Land Model. Water Resour. Res. 51, 8817–8833 (2015).
    Google Scholar 

    41.
    Guo, J., Huang, G., Wang, X., Li, Y. & Lin, Q. Investigating future precipitation changes over China through a high-resolution regional climate model ensemble. Earth’s Future 5, 285–303 (2017).
    Google Scholar 

    42.
    Gong, T., Lei, H., Yang, D., Jiao, Y. & Yang, H. Monitoring the variations of evapotranspiration due to land use/cover change in a semiarid shrubland. Hydrol. Earth Syst. Sci. 21, 863–877 (2017).
    Google Scholar 

    43.
    Feng, W. et al. Evaluation of groundwater depletion in North China using the Gravity Recovery and Climate Experiment (GRACE) data and ground-based measurements. Water Resour. Res. 49, 2110–2118 (2013).
    Google Scholar 

    44.
    Famiglietti, J. S. Satellites measure recent rates of groundwater depletion in California’s Central Valley. Geophys. Res. Lett. 38, L03403 (2011).
    Google Scholar 

    45.
    Wang, J. et al. Recent global decline in endorheic basin water storages. Nat. Geosci. 11, 926–932 (2018).
    CAS  Google Scholar 

    46.
    Chen, X. et al. Detecting significant decreasing trends of land surface soil moisture in eastern China during the past three decades (1979–2010). J. Geophys. Res. Atmos. 121, 5177–5192 (2016).
    Google Scholar 

    47.
    Peng, D. & Zhou, T. Why was the arid and semiarid northwest China getting wetter in the recent decades? J. Geophys. Res. Atmos. 122, 9060–9075 (2017).
    Google Scholar 

    48.
    Grassi, G. et al. The key role of forests in meeting climate targets requires science for credible mitigation. Nat. Clim. Change 7, 220–226 (2017).
    Google Scholar 

    49.
    Griscom, B. W. et al. Natural climate solutions. Proc. Natl Acad. Sci. USA 114, 11645 (2017).
    CAS  Google Scholar 

    50.
    Bastin, J.-F. et al. The global tree restoration potential. Science 365, 76–79 (2019).
    CAS  Google Scholar 

    51.
    Watkins, M. M., Wiese, D. N., Yuan, D.-N., Boening, C. & Landerer, F. W. Improved methods for observing Earth’s time variable mass distribution with GRACE using spherical cap mascons. J. Geophys. Res. Solid Earth 120, 2648–2671 (2015).
    Google Scholar 

    52.
    Wiese, D. N., Landerer, F. W. & Watkins, M. M. Quantifying and reducing leakage errors in the JPL RL05M GRACE mascon solution. Water Resour. Res. 52, 7490–7502 (2016).
    Google Scholar 

    53.
    Myneni, R. B., Hall, F. G., Sellers, P. J. & Marshak, A. L. The interpretation of spectral vegetation indexes. IEEE Trans. Geosci. Remote Sens. 33, 481–486 (1995).
    Google Scholar 

    54.
    Glenn, E. P., Huete, A. R., Nagler, P. L., Hirschboeck, K. K. & Brown, P. Integrating remote sensing and ground methods to estimate evapotranspiration. Crit. Rev. Plant Sci. 26, 139–168 (2007).
    Google Scholar 

    55.
    Pinzon, J. & Tucker, C. A non-stationary 1981–2012 AVHRR NDVI3g time series. Remote Sens. 6, 6929–6960 (2014).
    Google Scholar 

    56.
    Fan, X. & Liu, Y. Multisensor normalized difference vegetation index intercalibration: A comprehensive overview of the causes of and solutions for multisensor differences. IEEE Geosci. Remote Sens. Mag. 6, 23–45 (2018).
    Google Scholar 

    57.
    Huffman, G. J. et al. The TRMM multisatellite precipitation analysis (TMPA): Quasi-global, multiyear, combined-sensor precipitation estimates at fine scales. J. Hydrometeorol. 8, 38–55 (2007).
    Google Scholar 

    58.
    Harris, I., Osborn, T. J., Jones, P. & Lister, D. Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset. Sci. Data 7, 109 (2020).
    Google Scholar 

    59.
    Zhou, Y., Shi, C., Du, J. & Fan, X. Characteristics and causes of changes in annual runoff of the Wuding River in 1956–2009. Environ. Earth Sci. 69, 225–234 (2013).
    Google Scholar 

    60.
    Rodell, M. Basin scale estimates of evapotranspiration using GRACE and other observations. Geophys. Res. Lett. 31, L20504 (2004).
    Google Scholar 

    61.
    Gerten, D., Schaphoff, S., Haberlandt, U., Lucht, W. & Sitch, S. Terrestrial vegetation and water balance—hydrological evaluation of a dynamic global vegetation model. J. Hydrol. 286, 249–270 (2004).
    CAS  Google Scholar 

    62.
    Smith, B. et al. Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model. Biogeosciences 11, 2027–2054 (2014).
    Google Scholar 

    63.
    Haxeltine, A. & Prentice, I. C. BIOME3: An equilibrium terrestrial biosphere model based on ecophysiological constraints, resource availability, and competition among plant functional types. Glob. Biogeochem. Cycles 10, 693–709 (1996).
    CAS  Google Scholar 

    64.
    Prestele, R. et al. Current challenges of implementing anthropogenic land-use and land-cover change in models contributing to climate change assessments. Earth Syst. Dyn. 8, 369–386 (2017).
    Google Scholar 

    65.
    Piao, S. et al. Lower land-use emissions responsible for increased net land carbon sink during the slow warming period. Nat. Geosci. 11, 739–743 (2018).
    CAS  Google Scholar 

    66.
    Tian, H. et al. The Global N2O Model Intercomparison Project. Bull. Am. Meteorol. Soc. 99, 1231–1251 (2018).
    Google Scholar 

    67.
    Etheridge, D. M. et al. Natural and anthropogenic changes in atmospheric CO2 over the last 1000 years from air in Antarctic ice and firn. J. Geophys. Res. Atmos. 101, 4115–4128 (1996).
    CAS  Google Scholar 

    68.
    Keeling, C. D., Whorf, T. P., Wahlen, M. & van der Plichtt, J. Interannual extremes in the rate of rise of atmospheric carbon dioxide since 1980. Nature 375, 666–670 (1995).
    CAS  Google Scholar  More