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    How diverse ecosystems remain stable

    May, R. M. Nature 238, 413–414 (1972).CAS 
    Article 
    PubMed 

    Google Scholar 
    Yonatan, Y., Amit, G., Friedman, J. & Bashan, A. Nat. Eco. Evo., https://doi.org/10.1038/s41559-022-01745-8 (2022).Yodzis, P. Nature 289, 674–676 (1981).Article 

    Google Scholar 
    Winemiller, K. O. Am. Nat. 134, 960–968 (1989).Article 

    Google Scholar 
    James, A. et al. Am. Nat. 185, 680–692 (2015).Article 
    PubMed 

    Google Scholar 
    Schmid-Araya, J. M. et al. J. Anim. Ecol. 71, 1056–1062 (2002).Article 

    Google Scholar 
    Bashan, A. et al. Nature 534, 259–262 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Human Microbiome Project Consortium. Nature 486, 207–214 (2012).Article 

    Google Scholar 
    Moitinho-Silva, L. et al. Gigascience 6, 1–7 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Dunne, J. A., Williams, R. J. & Martinez, N. D. Proc. Natl Acad. Sci. USA 99, 12917–12922 (2002).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grilli, J., Barabás, G., Michalska-Smith, M. J. & Allesina, S. Nature 548, 210–213 (2017).CAS 
    Article 
    PubMed 

    Google Scholar  More

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    Large size in aquatic tetrapods compensates for high drag caused by extreme body proportions

    Drag coefficients of plesiosaurs, ichthyosaurs and modern cetaceansAt equal Reynolds numbers (same body length and same flow velocity), the total drag coefficients of plesiosaurs (Cd) are higher than the estimated values for ichthyosaurs and modern cetaceans (Fig. 1a). The limbless bodies, however, display similar Cd in all three groups and are even lower-than-average in the long-necked plesiosaurs, indicating that the limbs are responsible for the observed high Cd. The limbs of plesiosaurs contribute to more than 20% of their total drag coefficient: up to 32.2% in the basal Meyerasaurus and averaging 25% in derived plesiosaurs, with no major differences between plesiosaur morphotypes. In parvipelvian ichthyosaurs the contribution of the limbs to Cd is 11.2–15.6%, compared to 8.7–14.3% in modern cetaceans. Some of the living taxa we include provide a functional reference for this analysis. Our computed drag coefficient for the bottlenose dolphin model (Cd = 0.00413 at Re = 107) for example, is consistent with the estimates from a gliding living dolphin33 (Cd = 0.0034 at Re = 9.1 × 106) and other static CFD simulations34 (Cd = 0.00413 at Re = 107). It is worth noting that these values are, as expected, lower than estimates obtained from kinematic models, as motion is not accounted for35. In a former study, drag coefficients for a plesiosaur (Cryptoclidus), two ichthyosaurs and various cetaceans were obtained from rigid models in water tanks36. However, the pressure drag component (Cp) was likely overestimated due to the proximity of the models to the air–water interface, and thus are not directly comparable to ours.Fig. 1: Comparison of the drag coefficient of derived plesiosaurs, ichthyosaurs and cetaceans.a Total drag coefficient computed for the full models including the limbs (‘body + limbs’, circles) and the limbless models (‘body’, squares). Average (point) and range (bar) shown for calculations at Re = 5 × 106–107. The derived short-necked plesiosaurs are highlighted in orange; the parvipelvian ichthyosaurs in blue and the extant cetaceans in red. A basal plesiosaur included as a reference is highlighted in purple. b Representative two-dimensional plots of the flow velocity magnitude at Re = 5 × 106 (inlet velocity of 5 ms−1) in lateral view. For dorsal view see Supplementary Fig. 1. Images of Tursiops and the three ichthyosaurs modified from Gutarra et al.29.Full size imageIn all models across the various clades, velocity plots display a stagnation point at the anterior tip of the model, a thin velocity gradient along the body corresponding to the boundary layer, an area of higher velocity around the greatest diameter and a low velocity wake behind the body, characteristic features of a fully developed external flow (Fig. 1b, Supplementary Fig. 1). The acceleration of flow results in areas of low pressure (Supplementary Fig. 2), while high pressure areas are observed where stagnation occurs. Our CFD methodology has been previously validated against experimental data from slender torpedo-like shapes26 and has been shown to provide a reliable distribution of internal drag components29 essential when dealing with streamlined bodies35. In all our simulations, the proportion of frictional and pressure drag was consistent with the expected values for slender geometries31: most of the drag originated from skin friction with a minor pressure drag component (Supplementary Fig. 2). The relatively larger limbs of plesiosaurs (Supplementary Table 1) produce a small increase in skin friction (Supplementary Fig. 2a), but a large increase in the pressure drag coefficient (Supplementary Fig. 2b), indicating that the latter largely explains differences in total drag coefficient between the groups. These effects might be explained by the low local Reynolds number of the flippers (resulting from a small chord length) producing high local Cd relative to the rest of the body31, alongside interference drag (i.e. drag caused by the interaction of flow fields where limbs and body meet), which might be higher for larger flippers.Effect of body shape and body size on drag-related costs of steady swimmingWhen comparing morphologies at the same volume (proxy for body mass) and the same velocity, to focus on the effect of shape alone, derived plesiosaurs produce on average 30% more drag than parvipelvian ichthyosaurs and modern cetaceans (Fig. 2a, Supplementary Table 3; two-sample t-tests p  0.05). In these conditions, the drag-related costs of steady swimming of plesiosaurs fall within the range observed in both modern cetaceans and ichthyosaurs. Normalised against a 2.85 m-long Tursiops, the COTdrag for derived plesiosaurs ranges from 0.42, estimated for the large elasmosaur Thalassomedon, to 1.41 in the medium-sized Dolichorhynchops. In the parvipelvians, COTdrag spans from 0.33 estimated for the large Temnodontosaurus, to 1.76 in a 2.5 m-long Stenopterygius. Cetaceans show a smaller lower limit, because they include the largest animal in our sample, a 16 m-long humpback whale, with a COTdrag of 0.13 compared to Tursiops. The estimated cetacean upper COTdrag limit is 1.54 for a 1.9 m Tursiops. On the other hand, comparisons of the total drag power (Pdrag, i.e., the non-mass normalised version of COTdrag) for the same speed of 1 ms−1 (Fig. 3), show a different trend. Pdrag is highest for Megaptera, higher than in any fossil taxa included in this study, and is lowest in Tursiops. Thalassomedon is comparable both in total drag power and COTdrag to the killer whale. Similarly, the thalassophonean pliosaurid Liopleurodon matches the elasmosaurian Hydrotherosaurus in having a similarly low mass-normalised COTdrag but requiring about 4× more total drag power than Tursiops. Smaller forms like the polycotylid Dolichorhynchops and the thunnosaurian Ophthalmosaurus resemble the extant bottlenose dolphin in having a relatively high COTdrag and low total power.Fig. 3: Comparative plot of mass-normalised drag power and total drag power.Values of mass-normalised drag power (i.e., drag per unit of volume or COTdrag calculated as in Fig. 2b) in grey, and non-mass-normalised total drag power, in black, for an array of derived plesiosaurs, parvipelvian ichthyosaurs and modern cetaceans compared at the same inlet velocity of 1 ms−1. Error bars represent minimum and maximum values accounting for taxon body size variation (see Supplementary Data). Values are normalised to the results for Tursiops.Full size imageThus, in contrast to the volume-normalised simulations, differences between animals at their life-size scale are mainly influenced by size. For example, medium-sized plesiosaurs and ichthyosaurs, such as Dolichorhynchops and Ophthalmosaurus, have values of COTdrag close to that of a dolphin, while large plesiosaurs like Thalassomedon are more like the parvipelvian ichthyosaur Temnodontosaurus and a modern Orcinus. It is worth noting that the inflow velocity of 1 ms−1, is a reference velocity used for comparative purposes, and is not equivalent to the optimal cruising speed (i.e. speed at which COT is minimum16). This parameter is known to vary little in nature, with most vertebrates displaying values of preferred speed between 1–2 ms−1 regardless of body size40,41,42, which means it is reasonable to assume all tested taxa, regardless of their size, were able to swim at this velocity. Using a different reference velocity (2 ms−1) has no effect on the relative values of drag per unit of volume and the mass-normalised drag power (Supplementary Fig. 3; Supplementary Data). A reduction of mass-normalised drag-related costs of cruising as body size increases is selectively advantageous, as energy savings can be used to extend foraging and mating range, increase swimming speed and fuel other activities42,43.Our analysis shows that for highly aquatic tetrapods, size dominates over shape in affecting the drag-related costs of steady locomotion. This is because COTdrag (i.e., the balance of drag to volume) is highly sensitive to surface/volume proportion (Fig. 2f), and so is much influenced by isometry in streamlined animals.Interplay between neck anatomy and body size in plesiosaur dragSimulations at constant Reynolds number (i.e., comparing models at same total length and same flow velocity), show that necks up to 5× the length of the trunk do not increase substantially the total drag coefficient. Longer neck ratios up to 7× were found to impact the drag coefficient by as little as 3% (Fig. 4a). We estimated a 4–10% increase in skin friction drag coefficient for neck ratios of 3–7×, but also a comparable reduction in pressure drag resulting in almost no change in the total drag coefficient. A previous CFD-based study also found no differences in drag coefficient between plesiosaur models with variable neck proportions20, but further comparison is not possible because of great differences in the order of magnitude of Cd, the use of a different scaling reference area and the lack of information on skin and pressure drag20. Here, we have shown that long necks produce only a small increase in skin friction, although not as great as previously speculated25,30, and this is nullified by reduced pressure drag.Fig. 4: Influence of neck length and its interaction with body size on the drag-related costs of swimming in plesiosaurs.a Total drag coefficient and skin friction drag coefficient for an array of hypothetical plesiosaurs with varying neck ratios computed at Re = 5 × 106 (same total length and inflow velocity). b Drag per unit of trunk volume computed for the same array of models scaled at the same trunk length and tested at the same speed of 1 ms−1. The hypothetical models were created by modifying the length in the model of the basal plesiosaur Meyerasaurus victor which has a neck ratio of 0.87×. The limits of the trunk (which extends along the torso and includes the edges of the pectoral and pelvic girdles) are shown in red in the rendered models. c Three-dimensional models of a wide array of plesiosaurs, in dorsal view, at their life-size dimensions, showing the differences in body proportions and sizes. The limits of the trunk in the models (defined as in b) are coloured by group. Basal plesiosaurs are highlighted in purple. Among the derived groups, thalassophonean plesiosaurs (derived pliosaurid plesiosaurs) are highlighted in light orange, polycotylid plesiosaurs in dark orange and elasmosaurid plesiosaurs in green. d Scatterplot of trunk length (cm) and neck ratio showing the relative drag per unit of trunk volume as a gradient of colour for each taxon analysed and for the plot area in between (contour lines represent the interpolated values of drag per unit of volume). e Plot of the relative drag per unit of trunk volume versus the trunk length showing results highlighted by group. Line plots at the right-hand side show the range for each group. The D/Vtr and the trunk length show a significant negative correlation (Pearson’s correlation coefficient calculated with log-transformed variables, p = 2.28 × 10−7, R2 = −0.92). A small version of the fitted power curve (regression equation (y=69.76{x}^{-0.94})) is shown on the right upper corner. The grey area around the curve represents a confidence interval of 95%. All values in b, d and e are normalized to the results for the Meyerasaurus model.Full size imageNext, we explored the impact of neck proportions on drag-related costs of swimming in simulations where the size factor is removed. We found that if trunk dimensions are kept constant while the neck is enlarged, the drag per unit of trunk volume does not change appreciably for neck ratios up to 2×. However, longer neck proportions did impact resistive forces. This was moderate for a 3× ratio, with 12% more drag per unit of trunk volume, but became more substantial for longer necks, with 22%, 35% and 59% excess drag for necks of 4×, 5× and 7× respectively (Fig. 4b). This means that elasmosaurine elasmosaurs, with necks commonly 3–4× the length of the trunk23 might have experienced higher drag than other plesiosaurs of similar trunk dimensions.To test if the ‘long neck effect’ remains when body size is accounted for, we compared the relative amount of drag-per-unit-trunk-volume (D/Vtr) in a wide sample of plesiosaurs (Fig. 4c) at life-size scale for a constant velocity of 1 ms−1, including three species with neck ratios above 2×: Styxosaurus (2.76×), Hydrotherosaurus (3.18×) and Albertonectes (3.72×), the last being the elasmosaur with the longest reported neck44. Our results show great variability in D/Vtr. Small-bodied plesiosaurs such as Plesiosaurus, Meyerasaurus and Dolichorhynchops generated up to six times more D/Vtr than the largest plesiosaurs, Kronosaurus and Aristonectes (Fig. 4d, e). Comparisons per group show that both basal plesiosaurs and derived polycotylids, the groups with the smallest specimens, produced generally higher D/Vtr. Moreover, we did not find substantial differences between elasmosaurs and thalassophonean pliosauroids (Fig. 4e, Supplementary Table 4; all two-sample t-tests p  > 0.05). Both groups had similarly low ranges of D/Vtr regardless of neck length, lower on average than in polycotylids. These results stand even if we exclude Aristonectes, which belongs to the aristonectines, an elasmosaur subfamily with reduced neck length23,45. Further comparisons by morphotype show no significant differences between short-necked pliosauromorphs (here arbitrarily including plesiosaurs with neck ratios below 2×) and long-necked plesiosauromorphs (Supplementary Table 4, all two-sample t-tests p  > 0.05). The highest values of D/Vtr occur in animals with trunk lengths of 100 cm or less, followed by a steep decrease between 100–150 cm and a steadier decrease in longer trunks. This indicates a strong negative correlation between trunk dimensions and D/Vtr (Pearson’s product-moment correlation between the log-transformed variables, adjusted r2 = −0.92, p = 2.28 × 10−7). The curve that best describes this relationship is the power equation, D/Vtr = 69.76 × Trunk length−0.944 (Fig. 4e), an almost inversely proportional relationship, consistent with the streamlined nature of these animals for which skin friction drag is dominant.Polycotylids and thalassophonean pliosaurs, both derived pliosauromorph plesiosaurs9,21, share the same general body proportions9,21,46, but the latter had larger bodies and therefore needed less power in relation to their muscles to move at the same speed. Elasmosaurs on the other hand, despite their disparate morphologies, were no different from thalassophonean pliosaurs in their drag-related costs of forward swimming (Fig. 4c–e) and therefore they were likely to have been equally efficient cruisers.Earlier research suggested that, even if long necks did not add extra drag during forward swimming, speed in elasmosaurs would have been limited to avoid added drag when their necks bent20. However, when the neck is bent in living forms, the course of swimming changes, as does the flow direction, but the body remains streamlined in the direction of incoming flow. For example, sea lions perform non-powered turns initiated by the head in which the body glides smoothly in a curved position, limiting deceleration47. Further biomechanical research is needed to understand the role of plesiosaur necks in manoeuvrability and other aspects of swimming performance, as well as how these were influenced by shape and flexibility. The well-established idea that long-necked plesiosaurs were sluggish, slow swimmers7,30 is thus not supported here, not because long necks did not increase drag20, but because body size overrode this drag excess.Long necks evolved in large-bodied plesiosaurs: implications for dragWe analysed trends of body size and neck proportion in a wider sample of sauropterygians, including plesiosaurian and non-plesiosaurian Triassic sauropterygians. Long necks (neck ratio > 3×) occur in taxa with trunk lengths > 150 cm, whereas most sauropterygians had neck ratios of ≤ 2× (Fig. 5a). The great plasticity of body proportions of sauropterygians before and after their transition to a pelagic lifestyle after the Triassic has been well documented21,23,46, but this is the first time that neck and body size have been explored in the context of swimming performance for such a wide sample. We show that overall, sauropterygians and particularly plesiosaurs, mainly explored neck morphologies with little or no effect on drag costs and did not enter morphospaces that were suboptimal for aquatic locomotion (i.e., corresponding to small trunks with long necks; Fig. 5a). In fact, ancestral state reconstruction for trunk length shows that the ancestor of elasmosaurs was likely around 180 cm long and had a relatively short neck with a ratio smaller than 2× (Fig. 5b, c). This indicates that large trunks preceded neck elongation in elasmosaurs and suggests that extreme proportions might have been favoured by a release of hydrodynamic constraints.Fig. 5: Evolutionary trends of neck proportions and body size in Sauropterygia and their implications for the drag-related costs of swimming.a Bivariate plot of the length of trunk and the neck ratio of 79 sauropterygian taxa. Polygons in different colours show area occupied by the main sauropterygian groups. The functional trends describing the effect of each axis are based on results from flow simulations. On the top of this graph, a univariate plot shows the distribution and mean values of trunk length for each group. b, c Phenograms showing the disparity of trunk length (b) and neck ratio (c) in sauropterygians through time. The branches corresponding to basal Plesiosauria (including Rhomaleosauridae and Plesiosauridae), thalassophonean pliosaurs, polycotylids and elasmosaurs are highlighted (colour coding as in a). d, e Sauropterygian trees showing the evolutionary rates for trunk length (d) and neck ratio (e) represented by colour gradient (see Supplementary Fig. 5 for an alternative analysis to 5d using the log10-transformed trunk length). Consensus trees show average results from analyses of 20 cal3-dated trees (see Supplementary Figs. 4 and 6 for analysis on Hedman-dated trees). Rates are based on the mean scalar evolutionary rate parameter.Full size imageWe next explored evolutionary rates of relative neck length and trunk length in sauropterygians. The pattern of trunk length evolution is consistent with a heterogeneous rates model, not a homogeneous Brownian motion model (log Bayes Factor48 (BF)  > 5 in 100% of the sampled trees and > 10 in 92.5%, Supplementary Table 5). Analysis of non-transformed trunk data shows that through the evolution of Sauropterygia, there was a general increase in trunk length with some higher rates, in Triassic nothosauroids, Jurassic rhomaleosaurids and Cretaceous aristonectine elasmosaurs (Fig. 5d; Supplementary Fig. 4a). Additionally, analysis of the log10-transformed trunk data highlights variation in the small-to-medium size ranges and reveals high rates in Triassic eosauropterygians (Supplementary Figs. 5 and 6). The largest trunks evolved independently in two groups, thalassophonean pliosaurids and elasmosaurid plesiosauroids, with no evidence of high rates in the former. In the plesiosauroids, rates are not particularly high in the basal branches, but they are very high in derived aristonectines, and rates for the whole clade were significantly higher than the background rate in 40% of randomisation tests (Supplementary Fig. 7 and Table 6). A progressive increase in body mass over evolutionary time has been described for various clades of aquatic mammals49 and seems to be a common hallmark of the aquatic adaptation to marine pelagic lifestyles in secondarily aquatic tetrapods44. Whether body size reaches a plateau as is the case in cetaceans49 and what constraints influence the evolutionary patterns of size in plesiosaurs remains unexplored. Against this general trend, some derived plesiosaurs, such as polycotylids, saw a reduction in body size, which might have been related to pressures on niche selection, such as adaptation to specific prey, the need for higher manoeuvrability or other ecological factors. As shown earlier, small sizes require lower amounts of total power for a given speed, and therefore would be favoured if for example food resources were limited. This suggests that, in spite of the energy advantages of large size in terms of reduced mass-specific drag29 and metabolic rates49,50, which make it a common adaptation to the pelagic mode of life, other constraints limiting very large sizes were also at work50,51.A heterogeneous evolutionary rates model for neck proportion is also strongly supported (log BF  > 5 in 100% of the sampled trees and > 10 in 45%, Supplementary Table 5). Fast rates are consistently seen at the base of Pistosauroidea (including some Triassic forms and plesiosaurs) and, interestingly, also within elasmosaurs (Fig. 5e; Supplementary Fig. 4b). The neck proportions of elasmosaurs were found to evolve at a faster pace than the background rate in 90% of analyses (randomisation test p-value < 0.001 in 80% and < 0.01 in 10% of the sampled trees; Supplementary Fig. 7 and Table 6). Very fast rates in elasmosaurs are concentrated in the most derived branches (i.e., Euelasmosauridia from the late Upper Cretaceous52) and represent both rapid neck elongation in elasmosaurines and rapid neck shortening in weddellonectians (i.e., aristonectines and closely related taxa52). Additionally, various other independent instances of relative shortening of the neck occurred during the evolution of Sauropterygia, most notably in placodonts, pliosaurs and polycotylids, but these are not associated with high rates.Our findings contrast with a previous study23 which did not identify any significant evolutionary rate shifts in the neck ratio across Sauropterygia. Here we use a larger number of taxa and a different model fitting approach, which might account for these discrepancies. The association between very long necks and large trunks, along with our flow simulations results and the evidence of high rates in the elongation of necks in elasmosaurines (Fig. 5e), suggests that neck elongation was facilitated by large body sizes. The question remains why neck ratios did not evolve longer than 4×. According to our data, hydrodynamic constraints might have operated against the selection of such long necks. However, it is possible that the primary function for which they were selected, which is still debated30,53, did not require necks with those characteristics. Neck anatomy is likely to be the result of a compromise between different functions/constraints, one of them being hydrodynamic, as shown by the results presented herein. More

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    The relationship between ecosystem services and human modification displays decoupling across global delta systems

    Cumming, G. S. et al. Implications of agricultural transitions and urbanization for ecosystem services. Nature 515, 50–57 (2014).CAS 
    Article 

    Google Scholar 
    Cumming, G. S. & Von Cramon-Taubadel, S. Linking economic growth pathways and environmental sustainability by understanding development as alternate social-ecological regimes. Proc. Natl. Acad. Sci.115, 9533–9538 (2018).CAS 
    Article 

    Google Scholar 
    Costanza, R. et al. The value of the world’s ecosystem services and natural capital. Nature 387, 253–260 (1997).CAS 
    Article 

    Google Scholar 
    de Groot, R. S., Alkemade, R., Braat, L., Hein, L. & Willemen, L. Challenges in integrating the concept of ecosystem services and values in landscape planning, management and decision making. Ecol. Complex. 7, 260–272 (2010).Article 

    Google Scholar 
    Clapp, J. Financialization, distance and global food politics. J. Peasant Stud. 41, 797–814 (2014).Article 

    Google Scholar 
    Crona, B. I. et al. Masked, diluted and drowned out: how global seafood trade weakens signals from marine ecosystems. Fish Fish. 17, 1175–1182 (2016).Article 

    Google Scholar 
    United Nations Environment Programme International Resource Panel. Decoupling Natural Resource Use and Environmental Impacts from Economic Growth (2011).Srinivasana, U. T. et al. The debt of nations and the distribution of ecological impacts from human activities. Proc. Natl. Acad. Sci. 105, 1768–1773 (2008).Article 

    Google Scholar 
    Rist, L. et al. Applying resilience thinking to production ecosystems. Ecosphere 5, 1–11 (2014).Article 

    Google Scholar 
    Dermody, B. J. et al. A virtual water network of the Roman world. Hydrol. Earth Syst. Sci. 18, 5025–5040 (2014).Article 

    Google Scholar 
    Maskell, L. C. et al. Exploring the ecological constraints to multiple ecosystem service delivery and biodiversity. J. Appl. Ecol. 50, 561–571 (2013).Article 

    Google Scholar 
    Potschin, M. B. & Haines-Young, R. H. Ecosystem services: Exploring a geographical perspective. Prog. Phys. Geogr. 35, 575–594 (2011).Article 

    Google Scholar 
    Peng, J. et al. Ecosystem services response to urbanization in metropolitan areas: Thresholds identification. Sci. Total Environ. 607–608, 706–714 (2017).Article 
    CAS 

    Google Scholar 
    Millennium Ecosystem Assessment. Ecosystems and human well-being: Biodiversity synthesis (2005). https://doi.org/10.1057/9780230625600Díaz, S. et al. Assessing nature’s contributions to people: Recognizing culture, and diverse sources of knowledge, can improve assessments. Science 359, 270–272 (2018).Article 

    Google Scholar 
    Wallace, K. J. Classification of ecosystem services: Problems and solutions. Biol. Conserv. 139, 235–246 (2007).Article 

    Google Scholar 
    Lee, H. & Lautenbach, S. A quantitative review of relationships between ecosystem services. Ecol. Indic. 66, 340–351 (2016).Article 

    Google Scholar 
    Bennett, E. M., Peterson, G. D. & Gordon, L. J. Understanding relationships among multiple ecosystem services. Ecol. Lett. 12, 1394–1404 (2009).Article 

    Google Scholar 
    Saidi, N. & Spray, C. Ecosystem services bundles: Challenges and opportunities for implementation and further research. Environ. Res. Lett. 13, 113001 (2018).Cord, A. F. et al. Towards systematic analyses of ecosystem service trade-offs and synergies: Main concepts, methods and the road ahead. Ecosyst. Serv. 28, 264–272 (2017).Article 

    Google Scholar 
    Mitsch, W. J. & Gosselink, J. G. The value of wetlands: importance of scale and landscape setting. Ecol. Econ. 35, 25–33 (2000).Article 

    Google Scholar 
    Raudsepp-Hearne, C., Peterson, G. D. & Bennett, E. M. Ecosystem service bundles for analyzing tradeoffs in diverse landscapes. Proc. Natl. Acad. Sci. 107, 5242–5247 (2010).CAS 
    Article 

    Google Scholar 
    Hamann, M., Biggs, R. & Reyers, B. Mapping social-ecological systems: Identifying ‘green-loop’ and ‘red-loop’ dynamics based on characteristic bundles of ecosystem service use. Glob. Environ. Change 34, 218–226 (2015).Article 

    Google Scholar 
    Macklin, M. G. & Lewin, J. The rivers of civilization. Quat. Sci. Rev. 114, 228–244 (2015).Article 

    Google Scholar 
    Barbier, E. B. et al. The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193 (2011).Article 

    Google Scholar 
    Stanley, D. J. & Warne, A. G. Sea level and initiation of Predynastic culture in the Nile delta. Nature 363, 435–438 (1993).Article 

    Google Scholar 
    Costanza, R. et al. Changes in the global value of ecosystem services. Glob. Environ. Change 26, 152–158 (2014).Article 

    Google Scholar 
    Edmonds, D. A., Caldwell, R. L., Brondizio, E. S. & Siani, S. M. O. Coastal flooding will disproportionately impact people on river deltas. Nat. Commun. 11, 1–8 (2020).Article 
    CAS 

    Google Scholar 
    Renaud, F. G. et al. Tipping from the Holocene to the Anthropocene: How threatened are major world deltas? Curr. Opin. Environ. Sustain. 5, 644–654 (2013).Article 

    Google Scholar 
    Santos, M. J. & Dekker, S. C. Locked‑in and living delta pathways in the Anthropocene. Sci. Rep. 10, 19598 (2020).Tessler, Z. D. et al. Profiling risk and sustainability in coastal deltas of the world. Science 349, 638–643 (2015).CAS 
    Article 

    Google Scholar 
    Kennedy, C. M., Oakleaf, J. R., Theobald, D. M., Baruch-Mordo, S. & Kiesecker, J. Managing the middle: A shift in conservation priorities based on the global human modification gradient. Glob. Change Biol. 25, 811–826 (2019).Article 

    Google Scholar 
    Seto, K. C. Exploring the dynamics of migration to mega-delta cities in Asia and Africa: Contemporary drivers and future scenarios. Glob. Environ. Change 21, S94–S107 (2011).Article 

    Google Scholar 
    Carpenter, S. R., Stanley, E. H. & Vander Zanden, M. J. State of the World’s Freshwater Ecosystems: Physical, Chemical, and Biological Changes. Annu. Rev. Environ. Resour. 36, 75–99 (2011).Article 

    Google Scholar 
    Dugan, P. J. et al. Fish migration, dams, and loss of ecosystem services in the mekong basin. Ambio 39, 344–348 (2010).Article 

    Google Scholar 
    Notebaert, B., Broothaerts, N. & Verstraeten, G. Evidence of anthropogenic tipping points in fluvial dynamics in Europe. Glob. Planet. Change 164, 27–38 (2018).Article 

    Google Scholar 
    Vörösmarty, C. J. et al. Global threats to human water security and river biodiversity. Nature 467, 555–561 (2010).Article 
    CAS 

    Google Scholar 
    Haberl, H. et al. Quantifying and mapping the human appropriation of net primary production in earth’s terrestrial ecosystems. Proc. Natl. Acad. Sci. 104, 12942–12947 (2007).CAS 
    Article 

    Google Scholar 
    Minderhoud, P. S. J. et al. The relation between land use and subsidence in the Vietnamese Mekong delta. Sci. Total Environ. 634, 715–726 (2018).CAS 
    Article 

    Google Scholar 
    Venter, O. et al. Global terrestrial Human Footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).Article 

    Google Scholar 
    FAO. AQUASTAT Database. (2022). Available at: https://www.fao.org/aquastat/statistics/query/index.html. (Accessed: 14th February 2022)Chau, N. D. G., Sebesvari, Z., Amelung, W. & Renaud, F. G. Pesticide pollution of multiple drinking water sources in the Mekong Delta, Vietnam: evidence from two provinces. Environ. Sci. Pollut. Res. 22, 9042–9058 (2015).CAS 
    Article 

    Google Scholar 
    Phien-wej, N., Giao, P. H. & Nutalaya, P. Land subsidence in Bangkok, Thailand. Eng. Geol. 82, 187–201 (2006).Article 

    Google Scholar 
    Käkönen, M. Mekong Delta at the crossroads: more control or adaptation? Ambio 37, 205–212 (2008).Article 

    Google Scholar 
    Smajgl, A. et al. Responding to rising sea levels in the Mekong Delta. Nat. Clim. Change 5, 167–174 (2015).Article 

    Google Scholar 
    Schneider, P. & Asch, F. Rice production and food security in Asian Mega deltas—A review on characteristics, vulnerabilities and agricultural adaptation options to cope with climate change. J. Agron. Crop Sci. 206, 491–503 (2020).Article 

    Google Scholar 
    Gibson, L. et al. Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478, 378–381 (2011).CAS 
    Article 

    Google Scholar 
    Davis, M., Faurby, S. & Svenning, J. C. Mammal diversity will take millions of years to recover from the current biodiversity crisis. Proc. Natl. Acad. Sci. 115, 11262–11267 (2018).CAS 
    Article 

    Google Scholar 
    Arowolo, A. O., Deng, X., Olatunji, O. A. & Obayelu, A. E. Assessing changes in the value of ecosystem services in response to land-use/land-cover dynamics in Nigeria. Sci. Total Environ. 636, 597–609 (2018).CAS 
    Article 

    Google Scholar 
    Lang, Y. & Song, W. Quantifying and mapping the responses of selected ecosystem services to projected land use changes. Ecol. Indic. 102, 186–198 (2019).Article 

    Google Scholar 
    Tilman, D., Reich, P. B. & Isbell, F. Biodiversity impacts ecosystem productivity as much as resources, disturbance, or herbivory. Proc. Natl. Acad. Sci. 109, 10394–10397 (2012).CAS 
    Article 

    Google Scholar 
    Liang, J. et al. Positive biodiversity-productivity relationship predominant in global forests. Science 354, aaf8957 (2016).Diaz, R. J. & Rosenberg, R. Spreading dead zones and consequences for marine ecosystems. Science 321, 926–929 (2008).CAS 
    Article 

    Google Scholar 
    Dalin, C., Konar, M., Hanasaki, N., Rinaldo, A. & Rodriguez-Iturbe, I. Evolution of the global virtual water trade network. Proc. Natl. Acad. Sci. 109, 5989–5994 (2012).CAS 
    Article 

    Google Scholar 
    Van Asselen, S., Verburg, P. H., Vermaat, J. E. & Janse, J. H. Drivers of wetland conversion: A global meta-analysis. PLoS One 8, e81292 (2013).Davidson, N. C., Fluet-Chouinard, E. & Finlayson, C. M. Global extent and distribution of wetlands: trends and issues. Mar. Freshw. Res. 69, 620–627 (2018).Article 

    Google Scholar 
    Gordon, L. J., Finlayson, C. M. & Falkenmark, M. Managing water in agriculture for food production and other ecosystem services. Agric. Water Manag. 97, 512–519 (2010).Article 

    Google Scholar 
    Syvitski, J. P. M. & Kettner, A. J. Sediment flux and the anthropocene. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 369, 957–975 (2011).Article 

    Google Scholar 
    Nienhuis, J. H. et al. Global-scale human impact on delta morphology has led to net land area gain. Nature 577, 514–518 (2020).CAS 
    Article 

    Google Scholar 
    Cinner, J. E. et al. Bright spots among the world’s coral reefs. Nature 535, 416–419 (2016).CAS 
    Article 

    Google Scholar 
    Stott, I., Soga, M., Inger, R. & Gaston, K. J. Land sparing is crucial for urban ecosystem services. Front. Ecol. Environ. 13, 387–393 (2015).Article 

    Google Scholar 
    Caldwell, R. L. et al. A global delta dataset and the environmental variables that predict delta formation. Earth Surf. Dyn. Discuss. 7, 773–787 (2019).Article 

    Google Scholar 
    Lehner, B., Verdin, K. & Jarvis, A. New global hydrography derived from spaceborne elevation data. Eos (Washington DC) 89, 93–94 (2008).USGS. HYDRO1k Elevation Derivative Database. https://doi.org/10.5066/F77P8WN0 (2000).CIESIN – Center for International Earth Science Information Network Columbia University. Gridded Population of the World, Version 4 (GPWv4): Population Density, Revision 11. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC) https://doi.org/10.7927/H4JW8BX5 (2018).Venter, O. et al. Last of the Wild Project, Version 3 (LWP-3): 2009 Human Footprint, 2018 Release. NASA Socioeconomic Data and Applications Center https://doi.org/10.7927/H46T0JQ4 (2018).Venter, O. et al. Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation. Nat. Commun. 7, 1–11 (2016).Article 
    CAS 

    Google Scholar 
    Zeileis, A., Leisch, F., Hornik, K. & Kleiber, C. strucchange: An R package for testing for structural change in linear regression models. J. Stat. Softw. 7, 1–38 (2002).Article 

    Google Scholar 
    Monti, S., Tamayo, P., Mesirov, J. & Golub, T. Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52, 91–118 (2003).Article 

    Google Scholar 
    Reader, M. O. et al. Zenodo. https://doi.org/10.5281/zenodo.6346472 (2022).QGIS Development Team. QGIS Geographic Information System. Open Source Geospatial Foundation Project. (2019).R Core Team. R: A language and environment for statistical computing. (2020). More

  • in

    Evolution of coastal forests based on a full set of mangrove genomes

    He, Z. et al. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. Natl Sci. Rev. 6, 275–288 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhou, R. et al. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol. Biol. Evol. 24, 2746–2754 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    Xu, S. et al. Genome-wide convergence during evolution of mangroves from woody plants. Mol. Biol. Evol. 34, 1008–1015 (2017).CAS 
    PubMed 

    Google Scholar 
    He, Z. et al. Convergent adaptation of the genomes of woody plants at the land–sea interface. Natl Sci. Rev. 7, 978–993 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lyu, H., He, Z., Wu, C.-I. & Shi, S. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. New Phytol. 217, 428–438 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Xu, S. et al. The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. Natl Sci. Rev. 4, 721–734 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Feng, X. et al. Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC Plant Biol. 20, 178 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Feng, X. et al. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. New Phytol. 231, 2346–2358 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Angelini, C. et al. A keystone mutualism underpins resilience of a coastal ecosystem to drought. Nat. Commun. 7, 12473 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Atwood, T. B. et al. Global patterns in mangrove soil carbon stocks and losses. Nat. Clim. Change 7, 523–528 (2017).CAS 
    Article 

    Google Scholar 
    Barbier, E. B. et al. Coastal ecosystem-based management with nonlinear ecological functions and values. Science 319, 321–323 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Barbier, E. B. et al. The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193 (2011).Article 

    Google Scholar 
    Hensel, M. J. S. & Silliman, B. R. Consumer diversity across kingdoms supports multiple functions in a coastal ecosystem. Proc. Natl Acad. Sci. USA 110, 20621–20626 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tomlinson, P. B. The Botany of Mangroves 2nd edn (Cambridge Univ. Press, 2016).Rovai, A. S. et al. Global controls on carbon storage in mangrove soils. Nat. Clim. Change 8, 534–538 (2018).CAS 
    Article 

    Google Scholar 
    Alongi, D. M. Carbon sequestration in mangrove forests. Carbon Manag. 3, 313–322 (2012).CAS 
    Article 

    Google Scholar 
    Grant, K. M. et al. Sea-level variability over five glacial cycles. Nat. Commun. 5, 5076 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Guo, Z. et al. Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses. Glob. Change Biol. 24, 1741–1748 (2018).Article 

    Google Scholar 
    Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sollars, E. S. A. et al. Genome sequence and genetic diversity of European ash trees. Nature 541, 212–216 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhao, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat. Genet. 45, 67–71 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Duke, N. C. in Mangrove Ecosystems: A Global Biogeographic Perspective (eds Rivera-Monroy, V. H. et al.) 17–53 (Springer, 2017).Ellison, A. M., Farnsworth, E. J. & Merkt, R. E. Origins of mangrove ecosystems and the mangrove biodiversity anomaly. Glob. Ecol. Biogeogr. 8, 95–115 (1999).
    Google Scholar 
    Gee, C. T. The mangrove palm Nypa in the geologic past of the new world. Wetl. Ecol. Manag. 9, 181–203 (2001).Article 

    Google Scholar 
    Germeraad, J. H., Hopping, C. A. & Muller, J. Palynology of tertiary sediments from tropical areas. Rev. Palaeobot. Palynol. 6, 189–348 (1968).Article 

    Google Scholar 
    Graham, A. Paleobotanical evidence and molecular data in reconstructing the historical phytogeography of Rhizophoraceae. Ann. Missouri Bot. Gard. 93, 325–334 (2006).Article 

    Google Scholar 
    Mazer, S. J. & Tiffney, B. H. Fruits of Wetherellia and Palaeowetherellia (?Euphorbiaceae) from Eocene sediments in Virginia and Maryland. Brittonia 34, 300–333 (1982).Muller, J. Fossil pollen records of extant angiosperms. Bot. Rev. 47, 1–142 (1981).Article 

    Google Scholar 
    Srivastava, J. & Prasad, V. Evolution and paleobiogeography of mangroves. Mar. Ecol. 40, e12571 (2019).Hu, M.-J. et al. Chromosome-scale assembly of the Kandelia obovata genome. Hortic. Res. 7, 75 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jin, Y. & Qian, H. V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography 42, 1353–1359 (2019).Article 

    Google Scholar 
    Zachos, J. C., Dickens, G. R. & Zeebe, R. E. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451, 279–283 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Handley, L., Crouch, E. M. & Pancost, R. D. A New Zealand record of sea level rise and environmental change during the Paleocene–Eocene Thermal Maximum. Palaeogeogr. Palaeoclimatol. Palaeoecol. 305, 185–200 (2011).Article 

    Google Scholar 
    Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Saintilan, N. et al. Thresholds of mangrove survival under rapid sea level rise. Science 368, 1118–1121 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Lu, J. & Wu, C.-I. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc. Natl Acad. Sci. USA 102, 4063–4067 (2005).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lynch, M. et al. Perspective: spontaneous deleterious mutation. Evolution 53, 645–663 (1999).Article 
    PubMed 

    Google Scholar 
    Ohta, T. Slightly deleterious mutant substitutions in evolution. Nature 246, 96–98 (1973).CAS 
    Article 
    PubMed 

    Google Scholar 
    Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23, 263–286 (1992).Article 

    Google Scholar 
    Liu, X. & Fu, Y. X. Exploring population size changes using SNP frequency spectra. Nat. Genet. 47, 555–559 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Liu, X. & Fu, Y.-X. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Krauss, K. W. et al. How mangrove forests adjust to rising sea level. New Phytol. 202, 19–34 (2014).Article 
    PubMed 

    Google Scholar 
    Lovelock, C. E. et al. The vulnerability of Indo-Pacific mangrove forests to sea-level rise. Nature 526, 559–563 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Frederiksen, N. O. Review of Early Tertiary Sporomorph Paleoecology (American Association of Stratigraphic Palynologists Foundation, 1985).Smith, D. E., Harrison, S., Firth, C. R. & Jordan, J. T. The early Holocene sea level rise. Quat. Sci. Rev. 30, 1846–1860 (2011).Article 

    Google Scholar 
    Bouillon, S. et al. Mangrove production and carbon sinks: a revision of global budget estimates. Glob. Biogeochem. Cycles 22, GB2013 (2008).Article 
    CAS 

    Google Scholar 
    Donato, D. C. et al. Mangroves among the most carbon-rich forests in the tropics. Nat. Geosci. 4, 293–297 (2011).CAS 
    Article 

    Google Scholar 
    Hamilton, S. E. & Friess, D. A. Global carbon stocks and potential emissions due to mangrove deforestation from 2000 to 2012. Nat. Clim. Change 8, 240–244 (2018).CAS 
    Article 

    Google Scholar 
    Hutchison, J., Manica, A., Swetnam, R., Balmford, A. & Spalding, M. Predicting global patterns in mangrove forest biomass. Conserv. Lett. 7, 233–240 (2014).Article 

    Google Scholar 
    Ouyang, X. & Lee, S. Y. Improved estimates on global carbon stock and carbon pools in tidal wetlands. Nat. Commun. 11, 317 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bauer, J. E. et al. The changing carbon cycle of the coastal ocean. Nature 504, 61–70 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Richards, D. R., Thompson, B. S. & Wijedasa, L. Quantifying net loss of global mangrove carbon stocks from 20 years of land cover change. Nat. Commun. 11, 4260 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sanders, C. J. et al. Are global mangrove carbon stocks driven by rainfall? J. Geophys. Res. Biogeosci. 121, 2600–2609 (2016).Article 

    Google Scholar 
    Alongi, D. M. Carbon cycling and storage in mangrove forests. Ann. Rev. Mar. Sci. 6, 195–219 (2014).Article 
    PubMed 

    Google Scholar 
    Valiela, I., Bowen, J. L. & York, J. K. Mangrove forests: one of the world’s threatened major tropical environments. Bioscience 51, 807–815 (2001).Article 

    Google Scholar 
    Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
    Google Scholar 
    Yang, G., Zhou, R., Tang, T. & Shi, S. Simple and efficient isolation of high-quality total RNA from Hibiscus tiliaceus, a mangrove associate and its relatives. Prep. Biochem. Biotechnol. 38, 257–264 (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Wang, O. et al. Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res. 29, 798–808 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Liu, B. et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Preprint at https://arxiv.org/abs/1308.2012v2 (2013).Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chin, C.-S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xiao, C.-L. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods 14, 1072–1074 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M. & Jaffe, D. B. Direct determination of diploid genome sequences. Genome Res. 27, 757–767 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 4, 30 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6, 11 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tarailo‐Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 25, 4.10.1–4.10.14 (2009).Article 

    Google Scholar 
    Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997).CAS 
    Article 
    PubMed 

    Google Scholar 
    Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).CAS 
    Article 
    PubMed 

    Google Scholar 
    Birney, E. Genewise and genomewise. Genome Res. 14, 988–995 (2004).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kent, W. J. BLAT—The BLAST-Like Alignment Tool. Genome Res. 12, 656–664 (2002).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188–196 (2007).Article 
    CAS 
    PubMed 

    Google Scholar 
    Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. Methods Mol. Biol. 1962, 227–245 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Katoh, K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).CAS 
    Article 
    PubMed 

    Google Scholar 
    Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    Reis, M. Dos & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).Article 
    CAS 
    PubMed 

    Google Scholar 
    Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. GGTREE: an package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).Article 

    Google Scholar 
    Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003).CAS 
    Article 
    PubMed 

    Google Scholar 
    Smith, S. A. & Brown, J. W. Constructing a broadly inclusive seed plant phylogeny. Am. J. Bot. 105, 302–314 (2018).Article 
    PubMed 

    Google Scholar 
    Zanne, A. E. et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1053–1055 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Liang, Y. et al. Chromosome level genome assembly of Andrographis paniculata. Front. Genet. 11, 701 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, L. et al. The water lily genome and the early evolution of flowering plants. Nature 577, 79–84 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967 (2010).CAS 
    Article 
    PubMed 

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

    Google Scholar 
    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Miller, K. G. et al. The Phanerozoic record of global sea-level change. Science 310, 1293–1298 (2005).CAS 
    Article 
    PubMed 

    Google Scholar 
    Marçais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Narasimhan, V. et al. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32, 1749–1751 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hudson, R. R. Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18, 337–338 (2002).CAS 
    Article 
    PubMed 

    Google Scholar  More

  • in

    Complexity–stability trade-off in empirical microbial ecosystems

    May, R. M. Will a large complex system be stable? Nature 238, 413–414 (1972).CAS 
    Article 
    PubMed 

    Google Scholar 
    May, R. M. & Mac Arthur, R. H. Niche overlap as a function of environmental variability. Proc. Natl Acad. Sci. USA 69, 1109–1113 (1972).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    May, R. M. Stability and Complexity in Model Ecosystems (Princeton Univ. Press, 2019).Sinha, S. Complexity vs. stability in small-world networks. Phys. A 346, 147–153 (2005).Article 

    Google Scholar 
    Thébault, E. & Fontaine, C. Stability of ecological communities and the architecture of mutualistic and trophic networks. Science 329, 853–856 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Mougi, A. & Kondoh, M. Diversity of interaction types and ecological community stability. Science 337, 349–351 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Allesina, S. & Tang, S. Stability criteria for complex ecosystems. Nature 483, 205–208 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Allesina, S. & Tang, S. The stability–complexity relationship at age 40: a random matrix perspective. Popul. Ecol. 57, 63–75 (2015).Article 

    Google Scholar 
    Qian, J. J. & Akçay, E. The balance of interaction types determines the assembly and stability of ecological communities. Nat. Ecol. Evol. 4, 356–365 (2020).Article 
    PubMed 

    Google Scholar 
    Landi, P., Minoarivelo, H. O., Brännström, Å., Hui, C. & Dieckmann, U. in Systems Analysis Approach for Complex Global Challenges (eds Mensah, P. et al.) 209–248 (Springer, 2018).Townsend, S. E., Haydon, D. T. & Matthews, L. On the generality of stability–complexity relationships in Lotka–Volterra ecosystems. J. Theor. Biol. 267, 243–251 (2010).Article 
    PubMed 

    Google Scholar 
    Pimm, S. L., Lawton, J. H. & Cohen, J. E. Food web patterns and their consequences. Nature 350, 669–674 (1991).Article 

    Google Scholar 
    Yodzis, P. The stability of real ecosystems. Nature 289, 674–676 (1981).Article 

    Google Scholar 
    Winemiller, K. O. Must connectance decrease with species richness? Am. Naturalist 134, 960–968 (1989).Article 

    Google Scholar 
    Warren, P. H. Variation in food-web structure: the determinants of connectance. Am. Nat. 136, 689–700 (1990).Article 

    Google Scholar 
    de Ruiter, P. C., Neutel, A.-M. & Moore, J. C. Energetics, patterns of interaction strengths, and stability in real ecosystems. Science 269, 1257–1260 (1995).Article 
    PubMed 

    Google Scholar 
    Schmid-Araya, J. M. et al. Connectance in stream food webs. J. Anim. Ecol. 71, 1056–1062 (2002).Article 

    Google Scholar 
    Neutel, A.-M. et al. Reconciling complexity with stability in naturally assembling food webs. Nature 449, 599–602 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    James, A. et al. Constructing random matrices to represent real ecosystems. Am. Nat. 185, 680–692 (2015).Article 
    PubMed 

    Google Scholar 
    Jacquet, C. et al. No complexity–stability relationship in empirical ecosystems. Nat. Commun. 7, 12573 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thompson, L. R. et al. A communal catalogue reveals earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207 (2012).CAS 
    Article 

    Google Scholar 
    Fricker, A. M., Podlesny, D. & Fricke, W. F. What is new and relevant for sequencing-based microbiome research? A mini-review. J. Adv. Res. 19, 105–112 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sander, E. L., Wootton, J. T. & Allesina, S. Ecological network inference from long-term presence-absence data. Sci. Rep. 7, 7154 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Steinway, S. N., Biggs, M. B., Loughran Jr, T. P., Papin, J. A. & Albert, R. Inference of network dynamics and metabolic interactions in the gut microbiome. PLoS Comput. Biol. 11, e1004338 (2015).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bucci, V. et al. Mdsine: microbial dynamical systems inference engine for microbiome time-series analyses. Genome Biol. 17, 121 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9, e1003388 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fisher, C. K. & Mehta, P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PloS ONE 9, e102451 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gerber, G. K., Onderdonk, A. B. & Bry, L. Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput. Biol. 8, e1002624 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cao, H.-T., Gibson, T. E., Bashan, A. & Liu, Y.-Y. Inferring human microbial dynamics from temporal metagenomics data: pitfalls and lessons. BioEssays 39, 1600188 (2017).Article 

    Google Scholar 
    David, L. A. et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, R89 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Buffie, C. G. et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to clostridium difficile-induced colitis. Infect. Immun. 80, 62–73 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Dohlman, A. B. & Shen, X. Mapping the microbial interactome: statistical and experimental approaches for microbiome network inference. Exp. Biol. Med. 244, 445–458 (2019).CAS 
    Article 

    Google Scholar 
    Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jiang, D. et al. Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities. Front. Genet. 10, 995 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Faust, K. Open challenges for microbial network construction and analysis. ISME J. 15, 3111–3118 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bashan, A. et al. Universality of human microbial dynamics. Nature 534, 259–262 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vila, J. C., Liu, Y.-Y. & Sanchez, A. Dissimilarity–overlap analysis of replicate enrichment communities. ISME J. 14, 2505–2513 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Moitinho-Silva, L. et al. The sponge microbiome project. Gigascience 6, gix077 (2017).Article 
    PubMed Central 

    Google Scholar 
    Swierts, T., Cleary, D. & de Voogd, N. Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny. FEMS Microbiol. Ecol. 94, fiy194 (2018).CAS 
    Article 
    PubMed Central 

    Google Scholar 
    Jost, L. Entropy and diversity. Oikos 113, 363–375 (2006).Article 

    Google Scholar 
    Suweis, S., Grilli, J., Banavar, J. R., Allesina, S. & Maritan, A. Effect of localization on the stability of mutualistic ecological networks. Nat. Commun. 6, 10179 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Grilli, J., Barabás, G., Michalska-Smith, M. J. & Allesina, S. Higher-order interactions stabilize dynamics in competitive network models. Nature 548, 210–213 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Butler, S. & O’Dwyer, J. P. Stability criteria for complex microbial communities. Nat. Commun. 9, 2970 (2018).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Allesina, S. & Grilli, J. in Theoretical Ecology: Concepts and Applications (eds McCann, K. & Gellner, G.) Ch. 6 (Oxford Univ. Press, 2020).Jayant, P. & Shnerb, N. M. How temporal environmental stochasticity affects species richness: destabilization neutralization and the storage effect. J. Theor. Biol. 539, 111053 (2022).Article 

    Google Scholar 
    Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52–132ra52 (2012).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Van der Maaten, L. & Hinton, G. Visualizing data using t-sne. J. Mach. Learn. Res. 9, 2579–2605 (2008).
    Google Scholar 
    Bunin, G. Ecological communities with Lotka-Volterra dynamics. Phys. Rev. E 95, 042414 (2017).Article 
    PubMed 

    Google Scholar  More

  • in

    Assessment of acute toxicity and developmental transformation impacts of polyethylene microbead exposure on larval daggerblade grass shrimp (Palaemon pugio)

    Sharma, S. & Chatterjee, S. Microplastic pollution, a threat to marine ecosystem and human health: A short review. Environ. Sci. Pollut. Res. 24(27), 21530–21547 (2017).Article 

    Google Scholar 
    Gray, A. D., Wertz, H., Leads, R. R. & Weinstein, J. E. Microplastic in two South Carolina Estuaries: Occurrence, distribution, and composition. Mar. Pollut. Bull. 128, 223–233 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Weinstein, J. E., Dekle, J. L., Leads, R. R. & Hunter, R. A. Degradation of bio-based and biodegradable plastics in a salt marsh habitat: Another potential source of microplastics in coastal waters. Mar. Pollut. Bull. 160, 111518 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Robin, R. S. et al. Holistic assessment of microplastics in various coastal environmental matrices, southwest coast of India. Sci. Total Environ. 703, 134947 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Kwon, O. Y., Kang, J. H., Hong, S. H. & Shim, W. J. Spatial distribution of microplastic in the surface waters along the coast of Korea. Mar. Pollut. Bull. 155, 110729 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Fendall, L. S. & Sewell, M. A. Contributing to marine pollution by washing your face: Microplastics in facial cleansers. Mar. Pollut. Bull. 58(8), 1225–1228 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hantoro, I., Löhr, A. J., Van Belleghem, F. G., Widianarko, B. & Ragas, A. M. Microplastics in coastal areas and seafood: Implications for food safety. Food Addit. Contam. Part A 36(5), 674–711 (2019).CAS 
    Article 

    Google Scholar 
    Retama, I. et al. Microplastics in tourist beaches of Huatulco Bay, Pacific coast of southern Mexico. Mar. Pollut. Bull. 113(1–2), 530–535 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Frias, J. P. G. L., Otero, V. & Sobral, P. Evidence of microplastics in samples of zooplankton from Portuguese coastal waters. Mar. Environ. Res. 95, 89–95 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hosseini, R., Sayadi, M. H., Aazami, J. & Savabieasfehani, M. Accumulation and distribution of microplastics in the sediment and coastal water samples of Chabahar Bay in the Oman Sea, Iran. Mar. Pollut. Bull. 160, 111682 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Andrady, A. L. Persistence of Plastic Litter in the Oceans. Marine Anthropogenic Litter 57–72 (Springer, 2015).Leads, R. R. & Weinstein, J. E. Occurrence of tire wear particles and other microplastics within the tributaries of the Charleston Harbor Estuary, South Carolina, USA. Mar. Pollut. Bull. 145, 569–582 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Nor, N. H. M. & Obbard, J. P. Microplastics in Singapore’s coastal mangrove ecosystems. Mar. Pollut. Bull. 79(1–2), 278–283 (2014).PubMed 

    Google Scholar 
    Plastics Europe. Plastics—The Facts 2017. (Plastics Europe, 2017).Lusher, A. L., Welden, N. A., Sobral, P., & Cole, M. Sampling, isolating and identifying microplastics ingested by fish and invertebrates. In Analysis of Nanoplastics and Microplastics in Food 119–148. (CRC Press, 2020).Murray, F. & Cowie, P. R. Plastic contamination in the decapod crustacean Nephrops norvegicus (Linnaeus, 1758). Mar. Pollut. Bull. 62(6), 1207–1217 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gray, A. D. & Weinstein, J. E. Size-and shape-dependent effects of microplastic particles on adult daggerblade grass shrimp (Palaemonetes pugio). Environ. Toxicol. Chem. 36(11), 3074–3080 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Au, S. Y., Bruce, T. F., Bridges, W. C. & Klaine, S. J. Responses of Hyalella azteca to acute and chronic microplastic exposures. Environ. Toxicol. Chem. 34(11), 2564–2572 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cole, M. et al. Microplastic ingestion by zooplankton. Environ. Sci. Technol. 47(12), 6646–6655 (2013).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Woods, M. N., Stack, M. E., Fields, D. M., Shaw, S. D. & Matrai, P. A. Microplastic fiber uptake, ingestion, and egestion rates in the blue mussel (Mytilus edulis). Mar. Pollut. Bull. 137, 638–645 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Scott, N. et al. Particle characteristics of microplastics contaminating the mussel Mytilus edulis and their surrounding environments. Mar. Pollut. Bull. 146, 125–133 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Van Cauwenberghe, L., Claessens, M., Vandegehuchte, M. B. & Janssen, C. R. Microplastics are taken up by mussels (Mytilus edulis) and lugworms (Arenicola marina) living in natural habitats. Environ. Pollut. 199, 10e17 (2015).
    Google Scholar 
    Waite, H. R., Donnelly, M. J. & Walters, L. J. Quantity and types of microplastics in the organic tissues of the eastern oyster Crassostrea virginica and Atlantic mud crab Panopeus herbstii from a Florida estuary. Mar. Pollut. Bull. 129(1), 179–185 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Quanbin, L. et al. Uptake and elimination of microplastics by Tigriopus japonicus and its impact on feeding behavior. Asian J. Ecotoxicol. 4, 184–191. https://doi.org/10.7524/AJE.1673-5897.20191216002 (2020).Article 

    Google Scholar 
    Galloway, T. S. & Lewis, C. N. Marine microplastics spell big problems for future generations. Proc. Natl. Acad. Sci. U.S.A. 113(9), 2331e2333 (2016).Article 
    CAS 

    Google Scholar 
    Galloway, T. S., Cole, M. & Lewis, C. Interactions of microplastic debris throughout the marine ecosystem. Nat. Ecol. Evol. 1, 0116. https://doi.org/10.1038/s41559-017-0116 (2017).Article 

    Google Scholar 
    Carlos de Sá, L., Luís, L. G. & Guilhermino, L. Effects of microplastics on juveniles of the common goby (Pomatoschistus microps): Confusion with prey, reduction of the predatory performance and efficiency, and possible influence of developmental conditions. Environ. Pollut. 196, 359–362 (2015).PubMed 
    Article 
    CAS 

    Google Scholar 
    Cole, M., Lindeque, P., Halsband, C. & Galloway, T. S. Microplastics as contaminants in the marine environment: A review. Mar. Pollut. Bull. 62(12), 2588–2597 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Key, P. B., Chung, K. W., West, J. B., Pennington, P. L. & DeLorenzo, M. E. Developmental and reproductive effects in grass shrimp (Palaemon pugio) following acute larval exposure to a thin oil sheen and ultraviolet light. Aquat. Toxicol. 228, 105651 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Allen, D. M., Harding, J. M., Stroud, K. B. & Yozzo, K. L. Movements and site fidelity of grass shrimp (Palaemonetes pugio and P. vulgaris) in salt marsh intertidal creeks. Mar. Biol. 162(6), 1275–1285 (2015).Article 

    Google Scholar 
    Kunz, A. K., Ford, M. & Pung, O. J. Behavior of the grass shrimp Palaemonetes pugio and its response to the presence of the predatory fish Fundulus heteroclitus. Am. Midl. Nat. 155, 286–294. https://doi.org/10.1674/0003-0031 (2006).Article 

    Google Scholar 
    Barbier, E. B. et al. The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193 (2011).Article 

    Google Scholar 
    Cozar, A. et al. Plastic debris in the open ocean. PNAS 111, 10239e10244. https://doi.org/10.1073/pnas.1314705111 (2014).CAS 
    Article 

    Google Scholar 
    Leads, R. R., Burnett, K. G. & Weinstein, J. E. The effect of microplastic ingestion on survival of the grass shrimp Palaemonetes pugio (Holthuis, 1949) challenged with Vibrio campbellii. Environ. Toxicol. Chem. 38(10), 2233–2242 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Beiras, R., Duran, I., Bellas, J. & Sanchez-Marín, P. Biological effects of contaminants: Paracentrotus lividus sea urchin embryo test with marine sediment elutriates. Int. Counc. Explor. Sea. Technol. Environ. Mar. Sci. 51, 113 (2012).
    Google Scholar 
    Kögel, T., Bjorøy, Ø., Toto, B., Bienfait, A. M. & Sanden, M. Micro-and nanoplastic toxicity on aquatic life: Determining factors. Sci. Total Environ. 709, 136050 (2020).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Lindeque, P. K. et al. Are we underestimating microplastic abundance in the marine environment? A comparison of microplastic capture with nets of different mesh-size. Environ Pollut. 265(Pt A), 114721. https://doi.org/10.1016/j.envpol.2020.114721 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Andrady, A. L. Microplastics in the marine environment. Mar. Pollut. Bull. 62(8), 1596e1605 (2011).Article 
    CAS 

    Google Scholar 
    Leight, A. K., Scott, G. I., Fulton, M. H. & Daugomah, J. W. Long term monitoring of grass shrimp Palaemonetes spp. Population metrics at sites with agricultural runoff influences 1, 2. Integr. Comp. Biol. 45(1), 143–150 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Weinstein, J. E. & Garner, T. R. Piperonyl butoxide enhances the bioconcentration and photoinduced toxicity of fluoranthene and benzo [a] pyrene to larvae of the grass shrimp (Palaemonetes pugio). Aquat. Toxicol. 87(1), 28–36 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Key, P. B., Chung, K. W., Hoguet, J., Sapozhnikova, Y. & DeLorenzo, M. E. Toxicity of the mosquito control insecticide phenothrin to three life stages of the grass shrimp (Palaemonetes pugio). J. Environ. Sci. Health B 46(5), 426–431 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Broad, A. C. Larval development of Palaemonetes pugio Holthuis. Biol. Bull. 112, 144–161 (1957).Article 

    Google Scholar 
    Broad, A. C. The relationship between diet and larval development of Palaemonetes. Biol. Bull. 112, 162–170 (1957).Article 

    Google Scholar 
    Sandifer, P. A. Effects of temperature and salinity on larval development of grass shrimp, Palaemonetes vulgaris (Decapoda, Caridea). Fish. Bull. 71(1), 115 (1973).
    Google Scholar 
    Boston, M. A. & Provenzano, A. J. Attempted hybridization of the grass shrimp Palaemonetes (Caridea, palaemonidae) with an evaluation of taxonomic characters of juveniles. Estuaries 5(3), 165–174 (1982).Article 

    Google Scholar 
    Anderson, G. S. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (Gulf of Mexico): Grass shrimp (No. 4). The Service. (1985).Vikas, P. A. et al. Unraveling the effects of live microalgal enrichment on Artemia nauplii. Indian J. Fish. 59(4), 111–121 (2012).
    Google Scholar 
    Provenzano, A. J., Schmitz, K. B. & Boston, M. A. Survival, duration of larval stages, and size of postlarvae of grass shrimp, Palaemonetes pugio, reared from Kepone® contaminated and uncontaminated populations in Chesapeake Bay. Estuaries 1(4), 239–244 (1978).Article 

    Google Scholar 
    Johnson, W. S., & Allen, D. M. Zooplankton of the Atlantic and Gulf Coasts: A Guide to Their Identification and Ecology. (JHU Press, 2012).Hubschman, J. H. The development and function of neurosecretory sites in the eyestalks of larval Palaemonetes (Decapoda: Natantia) (Doctoral dissertation, The Ohio State University, 1962).Wheeler, M. W., Park, R. M. & Bailer, A. J. Comparing median lethal concentration values using confidence interval overlap or ratio tests. Environ. Toxicol. Chem. Int. J. 25(5), 1441–1444 (2006).CAS 
    Article 

    Google Scholar 
    Isobe, A., Kubo, K., Tamura, Y., Nakashima, E. & Fujii, N. Selective transport of microplastics and mesoplastics by drifting in coastal waters. Mar. Pollut. Bull. 89(1–2), 324–330 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Syakti, A. D. et al. Beach macro-litter monitoring and floating microplastic in a coastal area of Indonesia. Mar. Pollut. Bull. 122(1–2), 217–225. https://doi.org/10.1016/j.marpolbul.2017.06.046 (2017) (Epub 2017 Jun 20 PMID: 28645761).CAS 
    Article 
    PubMed 

    Google Scholar 
    Reisser, J. et al. Marine plastic pollution in waters around Australia: Characteristics, concentrations, and pathways. PLoS One 8(11), e80466 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Järlskog, I. et al. Occurrence of tire and bitumen wear microplastics on urban streets and in sweepsand and washwater. Sci. Total Environ. 729, 138950. https://doi.org/10.1016/j.scitotenv.2020.138950 (2020) (Epub 2020 Apr 26. PMID: 32371211).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Key, P. B., Fulton, M. H., Scott, G. I., Layman, S. L. & Wirth, E. F. Lethal and sublethal effects of malathion on three life stages of the grass shrimp, Palaemonetes pugio. Aquat. Toxicol. 40(4), 311–322 (1998).CAS 
    Article 

    Google Scholar 
    DeLorenzo, M. E., Serrano, L., Chung, K. W., Hoguet, J. & Key, P. B. Effects of the insecticide permethrin on three life stages of the grass shrimp, Palaemonetes pugio. Ecotoxicol. Environ. Saf. 64(2), 122–127 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Key, P. B., Meyer, S. L. & Chung, K. W. Lethal and sub-lethal effects of the fungicide chlorothalonil on three life stages of the grass shrimp, Palaemonetes pugio. J. Environ. Sci. Health B 38(5), 539–549 (2003).PubMed 
    Article 
    CAS 

    Google Scholar 
    Key, P. B., Chung, K. W., Hoguet, J., Shaddrix, B. & Fulton, M. H. Toxicity and physiological effects of brominated flame retardant PBDE-47 on two life stages of grass shrimp, Palaemonetes pugio. Sci. Total Environ. 399(1–3), 28–32 (2008).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Ziajahromi, S., Kumar, A., Neale, P. A. & Leusch, F. D. Environmentally relevant concentrations of polyethylene microplastics negatively impact the survival, growth and emergence of sediment-dwelling invertebrates. Environ. Pollut. 236, 425–431 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Redondo-Hasselerharm, P. E., Falahudin, D., Peeters, E. T. & Koelmans, A. A. Microplastic effect thresholds for freshwater benthic macroinvertebrates. Environ. Sci. Technol. 52(4), 2278–2286 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lehtiniemi, M. et al. Exposure to leachates from post-consumer plastic and recycled rubber causes stress responses and mortality in a copepod Limnocalanus macrurus. Mar. Pollut. Bull. 173, 113103 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Martínez-Gómez, C., León, V. M., Calles, S., Gomáriz-Olcina, M. & Vethaak, A. D. The adverse effects of virgin microplastics on the fertilization and larval development of sea urchins. Mar. Environ. Res. 130, 69–76 (2017).PubMed 
    Article 
    CAS 

    Google Scholar 
    Khosrovyan, A., Gabrielyan, B. & Kahru, A. Ingestion and effects of virgin polyamide microplastics on Chironomus riparius adult larvae and adult zebrafish Danio rerio. Chemosphere 259, 127456 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Le Bihanic, F. et al. Organic contaminants sorbed to microplastics affect marine medaka fish early life stages development. Mar Pollut Bull. 154, 111059. https://doi.org/10.1016/j.marpolbul.2020.111059 (2020) (Epub 2020 Mar 31 PMID: 32319895).CAS 
    Article 
    PubMed 

    Google Scholar 
    LeMoine, C. M. et al. Transcriptional effects of polyethylene microplastics ingestion in developing zebrafish (Danio rerio). Environ. Pollut. 243, 591–600 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Freeman, J. A. Regulation of tissue growth in crustacean larvae by feeding regime. Biol. Bull. 178(3), 217–221 (1990).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ma, H. et al. Microplastics in aquatic environments: Toxicity to trigger ecological consequences. Environ. Pollut. 261, 114089 (2020).CAS 
    PubMed 
    Article 

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    Recovery at sea of abandoned, lost or discarded drifting fish aggregating devices

    Relevance for design of dFAD recovery programmesOur results provide guidance for implementing effective dFAD recovery programmes. More than 40% of dFAD trajectories in the Indian and Atlantic oceans drifted away from fishing grounds never to return, potentially later stranding in coastal areas (Imzilen et al.5 estimated that 10–20% of all French dFADs eventually strand, whereas 16.0% of our trajectories that definitively leave fishing zones strand). This loss represents at least 529 tonnes yr−1 of marine litter for the French fleet5,14 and probably 2–3 times that weight including all purse seiners in the two oceans28. More than 20% of dFAD trajectories that drifted away from fishing grounds passed within 50 km of a port (ranging from 3.3% to 31.6% for cut-off distances from 10 to 100 km; potentially underestimated due to remote deactivation of GPS buoys by purse seiners). This result suggests that coastal dFAD recovery programmes could be complementary to other mitigation measures, such as dFAD buoy limits already implemented by tRFMOs and spatio-temporal dFAD deployment closures proposed by Imzilen et al.5. Indeed, Imzilen et al.5 showed that prohibiting dFAD deployments in areas that would probably lead to strandings would principally protect coastal areas of the southwestern Indian Ocean and the eastern Gulf of Guinea, whereas we found that dFADs exiting fishing grounds from other areas, such as the northwestern Indian Ocean and the northern Gulf of Guinea, passed close to regional ports and could potentially be recovered at sea. Although our results are specific to the French and associated purse-seine fleet (representing ~1/3–1/2 of catch and dFAD deployments of all fleets28), available data indicate that other purse-seine fleets have similar spatio-temporal patterns of deployments28, suggesting that our results are applicable to the entire tropical tuna purse-seine fishery in the Indian and Atlantic oceans.These results contrast somewhat with existing analyses from the western and central Pacific Ocean, where it was estimated that 36% of dFADs ended up outside fishing grounds, but that the final recorded position of these abandoned dFADs were typically far from ports (502–952 km)29. Although these differences may be related to the larger spatial scales of the Pacific Ocean, additional analyses based on examinations of entire trajectories are needed to assess viability of recovery programmes based on ports.Consequences of spatial and temporal variation of dFAD lossHigh seas recovery could also be structured around our results on where important percentages of buoys exit fishing grounds towards the high seas. In the Indian Ocean, dFADs definitively leaving from the eastern border (70° E) end up stranded in or transiting through the Maldives and the eastern Indian Ocean. This happens relatively less frequently in the period from June to August and becomes much more frequent from October to December. Low loss rates during June to August are consistent with known seasonal patterns in dFAD deployment and fishing during this period4,25. At that time of the year, dFADs are deployed by fishers with the intent that they drift along the eastern African coast until they reach the main dFAD fishing grounds off Somalia, avoiding strong monsoon-driven currents favourable to eastward export of dFADs from July to December27. This is followed by a more intense dFAD fishing season during August–October. Finally, starting in October/November, a period of transition towards fishing further south in the Indian Ocean occurs, with relatively more focus on free-swimming school sets25,30, probably contributing to abandonment of dFADs in the northern Indian Ocean in the last quarter of the year.In the Atlantic Ocean, dFADs lost to the high seas exit fishing grounds mostly from the northwestern border (between 10° and 20° N) and southwestern border (2°–5° S), which is consistent with transport by the North Equatorial and South Equatorial Currents26. Although the seasonality of loss is less marked in the Atlantic Ocean than in the Indian Ocean, the peak months of July and December are associated with transitions in the spatio-temporal distribution of deployments from principally deploying just north of the equator off of West Africa to focusing on the Gulf of Guinea further east30. These transitions could lead to increased dFAD abandonment in areas highly susceptible to export of dFADs, although seasonality in currents may also play a role.Challenges facing recovery programmesWhile the information provided in this paper on spatio-temporal patterns of dFAD loss provides an essential foundation for implementing dFAD recovery strategies, there are several important practical challenges to the success of such efforts. Most efforts towards reducing or removing marine debris after it has been created have so far focused on beach clean-ups31,32. Such operations are costly, time-consuming and only capture a fraction of the overall debris18,33. Recovery at sea is a promising alternative solution34, but this requires consolidating systems to observe these debris35 and understanding their drift36, as well as putting in place appropriate incentives and socio-economic and political frameworks37. Broadly, data availability (for example, access to near-real-time location data from all fleets), equipment availability (for example, appropriately sized and equipped vessels for collecting large debris such as dFADs)32, recovery programme structure (for example, collaboration with local fishers, NGOs and/or nation-states; use of support vessels, and/or chartering of dFAD recovery vessels) and funding sources (for example, reuse of recovered tracking buoys or dFAD plastic floats, and/or polluter-payer systems collected at dFAD deployment or manufacturing) need to be optimized to recover a maximum number of dFADs while minimizing costs and fishing impacts. These considerations highlight the importance of identifying areas leading to losses and multiple ports of different sizes from which operations could potentially be conducted, as we have done above, as well as careful analysis of the possible impediments to implementation of recovery programmes.Some possible impediments to dFAD recovery programmes are environmental, strategic or geopolitical. For instance, although the Somali coast is identified as a dFADs stranding hotspot in winter5 and has potential for a port-based recovery programme as we show here, recovering dFADs along this coast is unlikely to be a priority due to the area’s relatively limited number of sensitive habitats, such as coral reefs, and because of the difficult and dangerous socio-political situation in the country and its adjacent waters. On the other hand, the Maldives archipelago is likely to be a priority given that it is an area with high dFAD stranding rates on coral reefs5 and also has many dFADs that leave fishing grounds and never return. Implementing a recovery programme in this area could be particularly valuable, especially given that the Maldives is well integrated into regional maritime transport and tuna fisheries. However, implementing such a programme for a large island chain composed of >1,000 individual islands will probably be complex. Extensive collaboration with regional stakeholders, such as research institutes, fisher associations and NGOs, as well as buoy manufacturers, would be essential to operationalize a recovery programme in the Maldives and elsewhere.Another major challenge for at-sea dFAD recovery is availability of appropriate vessels to remove dFADs from the water. The vertical subsurface structure of dFADs generally stretches from 50 to 80 m below the surface. The weight of the materials used to build dFADs and the numerous sessile organisms that attach to the ‘dFAD tail’ eventually make dFADs very heavy (up to hundreds of kilograms) and therefore difficult to remove from the water. Complete removal is probably only possible for medium to large vessels with an appropriate crane or winch for hauling heavy material. Purse-seine vessels themselves could participate in dFAD recovery efforts, but this would be costly and disruptive to fishing. For smaller vessels, it may only be possible to remove some parts of the dFAD, potentially aided by natural breakdown of the object or acoustic release systems, such as the GPS buoy, plastic flotation devices and/or surface raft metallic or plastic structural elements. However, this could still be extremely useful as the remaining material will normally sink before reaching coastal environments, thereby potentially avoiding the most important environmental impacts. This strategy would be particularly valuable if the subsurface structure can be made of biodegradable materials9,23,38. Imzilen et al.5 suggested that the removal of GPS buoys by artisanal fishers is already occurring in coastal areas. Therefore, if dFAD tracking information can be made accessible and appropriate incentive mechanisms are put in place to encourage recovery of dFAD elements, this strategy could substantially reduce marine debris from dFADs. Other practical considerations should be taken into account once at port, such as the availability of infrastructure for shipping, disposing of, recycling and/or reusing tracking buoys and other dFAD components. All of these potential impediments can be addressed, but they will require active engagement from fishers, tRFMOs, NGOs and coastal nations.Complementary measuresIn addition to such recovery programmes, existing complementary measures controlling the numbers of dFADs present at sea (for example, limits on the number of operational GPS-tracking buoys and limits on the use of support vessels) may need to be strengthened, as a higher number of dFADs obviously contributes to higher risks of marine debris and stranding. Lowering limits on the number of dFADs may also encourage vessels to increase sharing of buoy information, thereby maximizing use of dFADs and potentially reducing dFAD loss. However, oddly enough, such measures may aggravate problems of ALD dFADs if their consequences are not accurately anticipated. For example, limits on the number of tracked dFADs implemented by tRFMOs have modified the strategy of some components of the purse-seine fishery, encouraging them to remotely deactivate satellite-transmitting GPS-tracking buoys when dFADs leave fishing grounds to maintain the number of operational buoys below authorized limits. The loss of position information prevents the tracking of dFADs outside fishing grounds and may result in under-estimation and spatial bias in estimates of the risks of stranding and loss5,39. A potential solution would be to consider ALD dFADs as part of a stock of ‘recoverable dFADs’ that are not counted as part of the individual vessel’s quota of operational buoys, but for which position information is transmitted and made available to partners involved in recovery programmes39. Other useful options to facilitate the recovery of buoys include limiting the per vessel number of deployments instead of limiting the number of tracked dFADs and/or making new deployments contingent on recovery of an equivalent number of already deployed dFADs. The current tRFMO-implemented reduction in the number of support vessels in the Indian Ocean is also likely to increase the loss of dFADs because these vessels may be used to recover dFADs before they leave fishing grounds, highlighting the urgent need for complementary dFAD management and recovery approaches.Financial considerationsA final question about dFAD recovery programmes is how they could be financed. The logistical challenges described above, such as chartering appropriate recovery vessels, involve substantial costs that cannot be ignored. The most simple and logical financing scheme would be a polluter-payer programme whereby vessels, dFAD manufacturers and/or fishing nations pay some monetary amount per ALD dFAD, potentially in proportion to its expected negative impacts, into an independently run and verified clean-up fund. The basic elements for identifying which vessels, fishing companies and/or nations are deploying dFADs are largely in place via tRFMO reporting requirements, dFAD vessel logbooks and purse-seine observer programmes. The detailed spatio-temporal maps provided here and in Imzilen et al.5 identify where the losses and impacts are occurring, thereby providing a blueprint for apportioning such funds geographically.Missing elementsThe missing elements for reducing dFAD loss are mostly political: facilitating access to tracking and activation-deactivation information for all ALD dFADs (for example, the EU recently objected at the 2nd Indian Ocean Tuna Commission (IOTC) ad hoc working group on dFADs to making dFAD data publicly available for scientific purposes); implementing requirements for appropriate disposal of ALD dFADs; and improving collaboration between industry and regional stakeholders concerned with clean-up programmes. Although these missing elements may seem formidable, there are very promising precedents for rapidly addressing these types of issues. Throughout the 2010s, various initiatives of purse-seine fleets, national scientists, tRFMOs and organizations such as the International Sustainable Seafood Foundation (ISSF) have allowed the rapid adoption of mitigation measures. This was the case for non-entangling dFADs40, best practices guidelines for the release of sensitive species41,42,43, exhaustive observer coverage44,45 and dFAD management plans46, which are all required for ISSF-participating fishing companies if they wish tuna from their fishing vessels to be accepted by ISSF member canneries. A similar approach could be used to address dFAD loss, using the fulcrums of the ISSF, Marine Stewardship Council certification and European Union (EU) environmental regulations to extend the commitments already made by some of the fleets (for example regarding data availability and tests of recovery mechanisms) to other fleets and other areas, and therefore rapidly transform industry behaviour for the benefit of all. More

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    Forest degradation drives widespread avian habitat and population declines

    The Acadian Forest of eastern Canada has shown a pervasive signal of forest degradation since 1985 (Fig. 1). Since 1985, >3 million ha have been clear-cut (Fig. 1d), with most of this area now occupied by either tree plantations and thinnings (Fig. 1c–e), which are dominated by single tree species20, or a mix of early successional tree species (Fig. 1a,d,e). Despite some ingrowth due to succession, old forest has declined by 39% during the period observed (Extended Data Fig. 1a,b; Supplementary Methods). The pattern of extensive harvest of old forest, followed by rapid regeneration of young forest appears to be common across many forest regions of North America (for example, central Canada, southeastern United States, western United States; Fig. 1b) (ref. 10) and can be considered ‘forest degradation’ in that these practices simplify forest structure, reduce tree species diversity and truncate old-forest age classes6. During the same 35-year time period, forest cover remained relatively stable, increasing by a net 6.5% (Fig. 3a, red line)21.Fig. 3: Forest degradation rather than loss drives habitat declines in old forest-associated bird species.a, Habitat trends (1985–2020) for the seven bird species exhibiting the greatest population declines according to SDMs; all of these species are old forest associated. During the same time interval, total forest cover did not decline (red line, right axis), indicating that habitat loss is a function of forest degradation rather than loss. b,c, Predicted habitat loss (pink) and gain (blue) between 1985 and 2020 for two example species: Blackburnian warbler (33% habitat loss; b) and golden-crowned kinglet (38% habitat loss; c). Habitat loss was quantified using SDMs with Landsat data as independent variables strongly predicted population trends for forest bird species.Full size imageOverall, SDMs using Landsat reflectance bands as predictors performed well for most forest bird species when tested on 50% spatially discrete hold-out data (Extended Data Fig. 2; (bar x) area under the curve (AUC) = 0.73 [range: 0.60–0.90]). SDMs therefore provided reliable estimates of habitat suitability and distribution for most of the 54 species. Species with lower model-prediction success tended to be associated with fine-scale forest structure (for example, individual tall trees, standing and fallen dead wood) which are poorly captured by satellite imagery.We back cast SDMs to quantify habitat change for all 54 forest bird species from 1985 to 2020. Habitat declines occurred for 66% of species during 1985–2020; 93% of species exhibited habitat reductions over the past decade (Fig. 3 and Extended Data Fig. 3). Species showing the greatest decreases in habitat were golden-crowned kinglet (Regulus satrapa; −38%) and Blackburnian warbler (Setophaga fusca; −33%; Supplementary Video 1) with seven species showing habitat declines >25% (Fig. 3). Most species with strongly declining habitat are associated with old forests22 (Fig. 4a,b), which is consistent with forest degradation due to harvesting of old forest. Indeed, clear-cut harvest alone was strongly associated with habitat declines for all old forest-associated species (Fig. 4c and Extended Data Figs. 4 and 5). Forest succession into old age classes was apparently insufficient to compensate for this rate of loss. Fifteen species exhibited habitat increases, but most (14 out of 15) of these tend to be associated with young or immature forests (Fig. 4a,b).Fig. 4: Evidence for the effect of forest degradation on mature-forest bird species.a, The relationship between habitat change, estimated from SDMs and independently derived population change estimates from the BBS for the Acadian forest. Bird species of mature (old) forests (M; dark green dots) exhibit the greatest habitat loss; this is generally reflected in strongly negative population trends. Bird species associated with regenerating forest (R; red dots) tend to have stable or increasing habitat but still show BBS population declines. b, The relationship between quantitatively derived estimates of mature-forest association and habitat change from 1985 to 2020. Mature forest-associated species tend to be losing the most habitat in relation to immature- (I; light-green dots) and regeneration-associated species. Successional stage categorizations (R, I, M) are from Birds of the World (BOW). The regression line was fit using a hierarchical Bayesian model (Supplementary Methods) and grey shading in b shows 95% credible intervals. Only a subset of species is shown in b (those with quantitative data for mature-forest associations; Supplementary Methods). c, The relationship between area clear-cut occurring from 1985 to 2020 in each species’ habitat within a 200 m-diameter buffer surrounding BBS routes (N = 90) and habitat loss (1985–2020) at the same scale for six mature forest-associated species. Black lines are regression lines and grey bands are 95% confidence intervals (regression estimates in Supplementary Table 3). As expected, clear-cutting is strongly associated with habitat loss, which indicates that ingrowth of new habitat is rarely compensated for by habitat loss (a signature of forest degradation via old age–class truncation).Full size imageSeveral lines of evidence support forest management as the primary driver of forest degradation rather than alternative mechanisms (for example, climate-mediated forest decline, natural disturbance, permanent deforestation). First, our SDMs did not include climate data so the reflectance changes from satellite imagery used in our SDMs were predominantly due to forest compositional changes. Although climate (for example, inter-annual differences in precipitation) can cause subtle differences in reflectance (leaf colour) over time, most changes in the magnitude of reflectance are due to changes in forest composition or cover rather than effects of climate23 (Supplementary Figs. 1 and 2). Indeed, if the observed habitat declines were due to climate effects or natural disturbance, we would expect to see parallel habitat declines in protected areas, which we did not (Extended Data Figs. 6 and 7). Second, species exhibiting the greatest declines in habitat are those most strongly associated with old forest (Fig. 4a,b), which is the primary target of timber harvest. Indeed, the amount of area clear-cut was strongly associated with habitat loss for old forest-associated bird species (Fig. 4c and Extended Data Figs. 4 and 5). Third, deforestation (defined as permanent conversion to another land-cover type)24 was not a primary driver of habitat loss in our region; deforestation contributed 0.95, and 20 species had posterior probabilities >0.8. Importantly, most of the species showing an effect of habitat loss along routes on changes in population decline have lost substantial habitat over the time period and are associated with old forest (for example, Blackburnian warbler, northern parula [Setophaga americana], red-breasted nuthatch [Sitta canadensis], boreal chickadee [Poecile hudsonicus], dark-eyed junco [Junco hyemalis]; Extended Data Fig. 8), which would be expected with the harvest of old forest—a component of forest degradation. It is important to note that this test is highly challenging because many factors can drive annual fluctuations in bird abundance (for example, weather, phenology, conditions during migration or on the wintering grounds). Also, in any given year, habitat change along BBS routes can be quite small for some species; this low inter-annual variation in a predictor variable can preclude high statistical power to detect effects.We estimated the net number of breeding individuals that have probably disappeared due to habitat loss from 1985 to 2020 using published accounts of territory sizes for each species22 (Supplementary Table 5). This calculation assumes that available habitat is consistently occupied, which is supported by strong associations between habitat amount along BBS routes and bird abundance over the long term. Across all species, back-cast SDMs indicate that a net 28,215,247 ha (282,153 km2) of habitat has been lost, equating to a loss of between 16,779,704 and 52,243,938 breeding pairs (33,559,408–104,487,876 individuals; Supplementary Methods and Supplementary Table 5). One might expect that forest degradation, rather than resulting in broad-scale declines across species, is simply causing species turnover from old forest-associated bird species to young-forest associates. However, it is important to note that we quantified net bird decline from an unbiased list of the 54 most common forest bird species in eastern Canada. This list included both early and late successional species. Such net bird declines could be due to the fact that (1) even some early seral species are losing habitat (probably due to conversion from diverse early successional forest to species-poor plantations and thinnings)26 and (2) in this region, more species occupy older forests than regenerating forests27.We also quantified overall population trends for 54 species of forest birds using data from the BBS (Fig. 6). These estimates give the total magnitude of population changes which include, but are not limited to, habitat loss or gain effects. Thirty-nine of the 54 species examined (72%) are in population decline (defined as having 95% credible intervals that do not bound zero). The magnitude of the declines for 15 forest bird species is severe ( >5% per year). It is notable that most species exhibiting both habitat loss and population declines are old-forest associates (Fig. 4a; bottom left quadrant, dark green dots), with old-forest species exhibiting the greatest habitat losses (Fig. 4b and Supplementary Methods; hierarchical regression, (hat beta) = −16.66 [6.32 SE]).Fig. 6: Population trends for forest-associated birds in eastern Canada.a, Population trend parameter estimates and posterior distributions for 54 species of forest birds derived from Bayesian models. Seventy-two percent of species that are sufficiently common to model experienced population declines from 1985 to 2019. Colour key is provided in Fig. 5. The vertical green line indicates a population trend of zero. Dashed vertical lines coincide with trends of −15% (−0.15), −10% (−0.10) and −5% (−0.05) annual population trends. b, Predicted linear population trends for 1985–2019 (regression lines are mean trends derived from Bayesian Poisson models, Supplementary Methods) including annual variation estimated from BBS data. Shaded purple areas reflect 95% credible intervals and reflect the magnitude of species population declines shown in a. Populations of these eight old forest-associated species have declined 60–90% over the period observed.Full size imageBBS declines are not restricted to old-forest species; several species in rapid population decline are early seral species (for example, Lincoln’s sparrow [Melospiza lincolnii], mourning warbler [Geothlypis philadelphia]; Fig. 4a, bottom right quadrant). Despite the fact that these species have gained habitat over 35 years, their populations continue to decline. Only three species (black-capped chickadee [Poecile atricapillus], hairy woodpecker [Leuconotopicus villosus] and ruby-throated hummingbird [Archilochus colubris]) are increasing in abundance. Populations of these species increased despite evidence of habitat decline (Fig. 4a, top left quadrant)—perhaps because each benefit from anthropogenic habitats and supplemental food. Importantly, habitat changes from 1985 to 2019 along BBS routes were representative of changes at the scale of the entire region for most species (Extended Data Fig. 9), so BBS population trends are highly likely to reflect population trends at the regional scale. This contrasts to the 1965–1985 period when mature-forest loss along routes was slower than in the broader region28.We also modelled BBS population trends over the past ten years, as this is the period of importance for informing listing decisions under the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). Nine species have exhibited population declines >30% over ten years (Supplementary Fig. 3), which meets the criterion for consideration as ‘threatened’ under COSEWIC Criterion A (ref. 29). More