More stories

  • in

    Reply to: “Results from a biodiversity experiment fail to represent economic performance of semi-natural grasslands”

    1.Schaub, S. et al. Plant diversity effects on forage quality, yield and revenues of semi-natural grasslands. Nat. Commun. 11, 1–11 (2020).Article 

    Google Scholar 
    2.Tonn, B., Komainda, M. & Isselstein, J. Results from a biodiversity experiment fail to represent economic performance of semi-natural grasslands. Nat. Commun. https://doi.org/10.1038/s41467-021-22309-7 (2021).3.Roscher, C. et al. The role of biodiversity for element cycling and trophic interactions: an experimental approach in a grassland community. Basic Appl. Ecol. 5, 107–121 (2004).Article 

    Google Scholar 
    4.Jochum, M. et al. The results of biodiversity–ecosystem functioning experiments are realistic. Nat. Ecol. Evol. 4, 1485–1494 (2020).Article 

    Google Scholar 
    5.Roscher, C., Schumacher, J., Weisser, W. W., Schmid, B. & Schulze, E. D. Detecting the role of individual species for overyielding in experimental grassland communities composed of potentially dominant species. Oecologia 154, 535–549 (2007).ADS 
    Article 

    Google Scholar 
    6.Deak, A., Hall, M., Sanderson, M. & Archibald, D. Production and nutritive value of grazed simple and complex forage mixtures. Agron. J. 99, 814–821 (2007).Article 

    Google Scholar 
    7.Sturludóttir, E. et al. Benefits of mixing grasses and legumes for herbage yield and nutritive value in Northern Europe and Canada. Grass Forage Sci. 69, 229–240 (2014).Article 

    Google Scholar 
    8.Oelmann, Y., Vogel, A., Wegener, F., Weigelt, A. & Scherer-Lorenzen, M. Management intensity modifies plant diversity effects on N yield and mineral N in soil. Soil Sci. Soc. Am. J. 79, 559–568 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    9.Schaub, S., Buchmann, N., Lüscher, A. & Finger, R. Economic benefits from plant species diversity in intensively managed grasslands. Ecol. Econ. 168, 106488 (2020b).Article 

    Google Scholar 
    10.Trenbath, B. R. Biomass productivity of mixtures. Adv. Agron. 26, 177–210 (1974).Article 

    Google Scholar 
    11.Binder, S., Isbell, F., Polasky, S., Catford, J. A. & Tilman, D. Grassland biodiversity can pay. Proc. Natl Acad. Sci. USA 115, 3876–3881 (2018).CAS 
    Article 

    Google Scholar 
    12.Weigelt, A., Weisser, W., Buchmann, N. & Scherer‐Lorenzen, M. Biodiversity for multifunctional grasslands: equal productivity in high‐diversity low‐input and low‐diversity high‐input systems. Biogeosciences 6, 1695–1706 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    13.Vogel, A., Scherer-Lorenzen, M. & Weigelt, A. Grassland resistance and resilience after drought depends on management intensity and species richness. PLoS ONE 7, e36992 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    14.Finn, J. A. et al. Ecosystem function enhanced by combining four functional types of plant species in intensively managed grassland mixtures: a 3‐year continental‐scale field experiment. J. Appl. Ecol. 50, 365–375 (2013).Article 

    Google Scholar 
    15.Jans, F., Kessler, J., Münger, A. & Schlegel, P. in Fütterungsempfehlungen für Wiederkäuer (Grünes Buch) Ch. 7 (Agroscope, 2015).16.FAO (Food and Agriculture Organization of the United Nations), IDF (International Dairy Federation), and IFCN (IFCN Dairy Research Network). World Mapping of Animal Feeding Systems in the Dairy Sector. (FAO, 2014).17.Delaby, L., Peyraud, J. L., Foucher, N. & Michel, G. The effect of two contrasting grazing managements and level of concentrate supplementation on the performance of grazing dairy cows. Anim. Res. 52, 437–460 (2003).Article 

    Google Scholar 
    18.Leiber, F., Wettstein, H. R. & Kreuzer, M. Is the intrinsic potassium content of forages an important factor in intake regulation of dairy cows? J. Anim. Physiol. Anim. Nutr. 93, 391–399 (2009).CAS 
    Article 

    Google Scholar 
    19.Schaub, S. et al. Data: forage quality and biomass yield of the Management Experiment set up within the Jena Experiment. ETH Zur. Res. Collect. https://doi.org/10.3929/ethz-b-000374100 (2019). More

  • in

    Understanding drivers of wild oyster population persistence

    1.Bayne, B. et al. The proposed dropping of the genus Crassostrea for all Pacific cupped oysters and its replacement by a new genus Magallana: a dissenting view. J. Shellfish Res. 36, 545–547 (2017).Article 

    Google Scholar 
    2.Mann, R. Some biochemical and physiological aspects of growth and gametogenesis in Crassostrea gigas and Ostrea edulis grown at sustained elevated temperatures. J. Mar. Biol. Assoc. UK 59, 95–110 (1979).CAS 
    Article 

    Google Scholar 
    3.Humphreys, J., Herbert, R. J., Roberts, C. & Fletcher, S. A reappraisal of the history and economics of the Pacific oyster in Britain. Aquaculture 428, 117–124 (2014).Article 

    Google Scholar 
    4.Ellis, T., Gardiner, R., Gubbins, M., Reese, A. & Smith, D. Aquaculture statistics for the UK, with a focus on England and Wales 2012. Centre for Environment Fisheries & Aquaculture Science (Cefas) Weymouth (2015).5.Herbert, R. J. et al. Ecological impacts of non-native Pacific oysters (Crassostrea gigas) and management measures for protected areas in Europe. Biodivers. Conserv. 25, 2835–2865 (2016).Article 

    Google Scholar 
    6.Reise, K., Buschbaum, C., Büttger, H., Rick, J. & Wegner, K. M. Invasion trajectory of Pacific oysters in the northern Wadden Sea. Mar. Biol. 164, 68 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    7.Geburzi, J. C. & McCarthy, M. L. How do they do it? Understanding the success of marine invasive species. In YOUMARES 8—Oceans Across Boundaries: Learning from each other, 109–124 (Springer, 2018).8.Herbert, R., Roberts, C., Humphreys, J. & Fletcher, S. The Pacific oyster (Crassostrea gigas) in the UK: Economic, legal and environmental issues associated with its cultivation, wild establishment and exploitation. Report for the Shellfish Association of Great Britain (2012).9.Fabioux, C., Huvet, A., Le Souchu, P., Le Pennec, M. & Pouvreau, S. Temperature and photoperiod drive Crassostrea gigas reproductive internal clock. Aquaculture 250, 458–470 (2005).Article 

    Google Scholar 
    10.Diederich, S., Nehls, G., Van Beusekom, J. E. & Reise, K. Introduced Pacific oysters (Crassostrea gigas) in the northern Wadden Sea: Invasion accelerated by warm summers?. Helgol. Mar. Res. 59, 97 (2005).ADS 
    Article 

    Google Scholar 
    11.Mills, S.R.A. Population structure and ecology of wild Crassostrea gigas (Thunberg, 1793) on the south coast of England. Ph.D. thesis, University of Southampton (2016).12.Dutertre, M., Beninger, P. G., Barillé, L., Papin, M. & Haure, J. Rising water temperatures, reproduction and recruitment of an invasive oyster, Crassostrea gigas, on the French Atlantic coast. Mar. Environ. Res. 69, 1–9 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    13.Chávez-Villalba, J. et al. Broodstock conditioning of the oyster Crassostrea gigas: Origin and temperature effect. Aquaculture 214, 115–130 (2002).Article 

    Google Scholar 
    14.Rico-Villa, B., Pouvreau, S. & Robert, R. Influence of food density and temperature on ingestion, growth and settlement of Pacific oyster larvae, Crassostrea gigas. Aquaculture 287, 395–401 (2009).Article 

    Google Scholar 
    15.Li, G. & Hedgecock, D. Genetic heterogeneity, detected by PCR-SSCP, among samples of larval Pacific oysters (Crassostrea gigas) supports the hypothesis of large variance in reproductive success. Can. J. Fish. Aquat. Sci. 55, 1025–1033 (1998).CAS 
    Article 

    Google Scholar 
    16.Hedge, L. H. & Johnston, E. L. Colonisation of the non-indigenous Pacific oyster Crassostrea gigas determined by predation, size and initial settlement densities. PLoS ONE9 (2014).17.Maurer, D. et al. Reproduction de l’huître creuse dans le Bassin d’Arcachon. Année 2015. Ifremer Report (2016).18.Quayle, D.B. Pacific oyster culture in British Columbia (Department of Fisheries and Oceans, 1988).19.Rico-Villa, B. et al. A flow-through rearing system for ecophysiological studies of Pacific oyster Crassostrea gigas larvae. Aquaculture 282, 54–60 (2008).Article 

    Google Scholar 
    20.Kheder, R. B., Moal, J. & Robert, R. Impact of temperature on larval development and evolution of physiological indices in Crassostrea gigas. Aquaculture 309, 286–289 (2010).Article 

    Google Scholar 
    21.Kennedy, V. S. & Breisch, L. L. Maryland’s Oysters: Research and Management Vol. 81 (University of Maryland College Park, Maryland, 1981).
    Google Scholar 
    22.Helm, M. Cultured aquatic species information programme—Crassostrea gigas. Cultured aquatic species fact sheets. FAO Inland Water Resources and Aquaculture Service (2007).23.Child, A. & Laing, I. Comparative low temperature tolerance of small juvenile European, Ostrea edulis L., and Pacific oysters, Crassostrea gigas Thunberg. Aquacul. Res. 29, 103–113 (1998).Article 

    Google Scholar 
    24.Strand, A., Waenerlund, A. & Lindegarth, S. High tolerance of the Pacific oyster (Crassostrea gigas, Thunberg) to low temperatures. J. Shellfish Res. 30, 733–735 (2011).Article 

    Google Scholar 
    25.Rinde, E. et al. Increased spreading potential of the invasive Pacific oyster (Crassostrea gigas) at its northern distribution limit in Europe due to warmer climate. Mar. Freshw. Res. 68, 252–262 (2017).ADS 
    Article 

    Google Scholar 
    26.Wrange, A.-L. et al. Massive settlements of the Pacific oyster, Crassostrea giga, in Scandinavia. Biol. Invasions 12, 1145–1152 (2010).Article 

    Google Scholar 
    27.Spencer, B., Edwards, D., Kaiser, M. & Richardson, C. Spatfalls of the non-native Pacific oyster, Crassostrea gigas, in British waters. Aquat. Conserv. Mar. Freshw. Ecosyst. 4, 203–217 (1994).Article 

    Google Scholar 
    28.England, N. Pacific oyster survey of the North East Kent European marine sites. Natural England Commissioned Report NECR016 (2009).29.Smith, I. P., Guy, C. & Donnan, D. Pacific oysters, Crassostrea gigas, established in Scotland. Aquat. Conserv. Mar. Freshw. Ecosyst. 25, 733–742 (2015).Article 

    Google Scholar 
    30.Cook, E. J. et al. Impacts of climate change on non-native species. Mar. Clim. Change Impact Partnersh. Sci. Rev. 155–166 (2013).31.Cook, E., Beveridge, C., Lamont, P., O’Higgins, T. & Wilding, T. Survey of wild Pacific oyster Crassostrea gigas in Scotland. In Scottish Aquaculture Research Forum Report SARF099 (2014).32.Kochmann, J. Into the wild: documenting and predicting the spread of Pacific oysters (Crassostrea gigas) in Ireland. Ph.D. thesis, University College Dublin (2012).33.Syvret, M., Fitzgerald, A. & Hoare, P. Development of a Pacific oyster aquaculture protocol for the UK: Technical report. Sea Fish Industry Authority, FIFG Project No. 7 (2008).34.d’Auriac, M. B. A. et al. Rapid expansion of the invasive oyster Crassostrea gigas at its northern distribution limit in Europe: Naturally dispersed or introduced? PLoS ONE, 12 (2017).35.Dame, R. F. & Prins, T. C. Bivalve carrying capacity in coastal ecosystems. Aquat. Ecol. 31, 409–421 (1997).Article 

    Google Scholar 
    36.Leguerrier, D., Niquil, N., Petiau, A. & Bodoy, A. Modeling the impact of oyster culture on a mudflat food web in Marennes-Oléron Bay (France). Mar. Ecol. Prog. Ser. 273, 147–162 (2004).ADS 
    Article 

    Google Scholar 
    37.Forrest, B. M., Keeley, N. B., Hopkins, G. A., Webb, S. C. & Clement, D. M. Bivalve aquaculture in estuaries: Review and synthesis of oyster cultivation effects. Aquaculture 298, 1–15 (2009).Article 

    Google Scholar 
    38.Ferreira, J. G. et al. Ecological carrying capacity for shellfish aquaculture: Sustainability of naturally occurring filter-feeders and cultivated bivalves. J. Shellfish Res. 37, 709–726 (2018).Article 

    Google Scholar 
    39.Jordan-Cooley, W. C., Lipcius, R. N., Shaw, L. B., Shen, J. & Shi, J. Bistability in a differential equation model of oyster reef height and sediment accumulation. J. Theor. Biol. 289, 1–11 (2011).MathSciNet 
    PubMed 
    MATH 
    Article 

    Google Scholar 
    40.Lipcius, R. N. et al. Modeling quantitative value of habitats for marine and estuarine populations. Front. Mar. Sci. 6, 280 (2019).Article 

    Google Scholar 
    41.Enríquez-Díaz, M., Pouvreau, S., Chávez-Villalba, J. & Le Pennec, M. Gametogenesis, reproductive investment, and spawning behavior of the Pacific giant oyster Crassostrea gigas: Evidence of an environment-dependent strategy. Aquacult. Int. 17, 491–506 (2009).Article 

    Google Scholar 
    42.Wood, L. E. et al. Unaided dispersal risk of Magallana gigas into and around the UK: Combining particle tracking modelling and environmental suitability scoring. Biological Invasions, 1–20 (2021).43.Hily, C. Prolifération de l’huître creuse du Pacifique Crassotrea gigas sur les côtes manche-atlantique françaises: bilan, dynamique, conséquences écologiques, économiques et ethnologiques, expériences et scénarios de gestion. Rapport LITEAU, 20 (2009).44.McKnight, W. & Chudleigh, I. J. Pacific oyster Crassostrea gigas control within the inter-tidal zone of the North East Kent Marine Protected Areas, UK. Conserv. Evid. 12, 28–32 (2015).
    Google Scholar 
    45.Brown, J. & Hartwick, E. A habitat suitability index model for suspended tray culture of the Pacific oyster, Crassostrea gigas Thunberg.. Aquacult. Res. 19, 109–126 (1988).Article 

    Google Scholar 
    46.Diederich, S. High survival and growth rates of introduced Pacific oysters may cause restrictions on habitat use by native mussels in the Wadden Sea. J. Exp. Mar. Biol. Ecol. 328, 211–227 (2006).Article 

    Google Scholar 
    47.Moran, A. & Manahan, D. Physiological recovery from prolonged ‘starvation’ in larvae of the Pacific oyster Crassostrea gigas. J. Exp. Mar. Biol. Ecol. 306, 17–36 (2004).CAS 
    Article 

    Google Scholar 
    48.Calvo, G. W., Luckenbach, M. W. & Burreson, E. M. A comparative field study of Crassostrea gigas and Crassostrea virginica in relation to salinity in Virginia. Special Report in Applied Marine Science and Ocean Engineering, 349 (1999).49.Petton, B., Boudry, P., Alunno-Bruscia, M. & Pernet, F. Factors influencing disease-induced mortality of Pacific oysters, Crassostrea gigas. Aquacul. Environ. Interact. 6, 205–222 (2015).Article 

    Google Scholar 
    50.Li, L. et al. Divergence and plasticity shape adaptive potential of the Pacific oyster. Nat. Ecol. Evol. 2, 1751–1760 (2018).PubMed 
    Article 

    Google Scholar 
    51.Ferreira, J., Duarte, P. & Ball, B. Trophic capacity of Carlingford Lough for oyster culture-analysis by ecological modelling. Aquat. Ecol. 31, 361–378 (1997).Article 

    Google Scholar 
    52.Cognie, B., Haure, J. & Barillé, L. Spatial distribution in a temperate coastal ecosystem of the wild stock of the farmed oyster Crassostrea gigas (Thunberg). Aquaculture 259, 249–259 (2006).Article 

    Google Scholar 
    53.Enríquez-Díaz, M., Pouvreau, S., Chávez-Villalba, J. & Le Pennec, M. Gametogenesis, reproductive investment, and spawning behavior of the Pacific giant oyster Crassostrea gigas: evidence of an environment-dependent strategy. Aquacult. Int. 17, 491 (2009).Article 

    Google Scholar 
    54.Ben-Horin, T. et al. Intensive oyster aquaculture can reduce disease impacts on sympatric wild oysters. Aquacul. Environ. Interact. 10, 557–567 (2018).Article 

    Google Scholar 
    55.Mailleret, L. & Lemesle, V. A note on semi-discrete modelling in the life sciences. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 367, 4779–4799 (2009).ADS 
    MathSciNet 
    MATH 
    Article 

    Google Scholar 
    56.Powell, E., Klinck, J., Hofmann, E. & Ray, S. Modeling oyster populations. IV: Rates of mortality, population crashes and management. Fish. Bull. 92, 347–373 (1994).
    Google Scholar 
    57.Wilson, R. A stage-structured oyster population model for reef restoration. Undergraduate Honors Theses Paper, 1403 (2019).58.Guo, X., Hedgecock, D., Hershberger, W. K., Cooper, K. & Jr, S. K. A. Genetic determinants of protandric sex in the Pacific oyster, Crassostrea gigas Thunberg. Evolution 52, 394–402 (1998).59.Morris, D. et al. Cefas coastal temperature network (2016).60.Pouvreau, S. et al. Velyger database: The oyster larvae monitoring French project. SEANOE 10, 41888 (2016).
    Google Scholar 
    61.Dhoop, T. & Thompson, C. Directional waverider metadata, supplement for QC data download from Realtime Data page. Channel Coastal Observatory (2019).62.Collins, M. et al. Long-term climate change: projections, commitments and irreversibility. In Climate Change 2013-The Physical Science Basis: Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, 1029–1136 (Cambridge University Press, 2013).63.Pastor, D. Reproductive biology of Crassostrea gigas. Ph.D. thesis, University of Southampton (2010).64.Benton, T. G. & Grant, A. Elasticity analysis as an important tool in evolutionary and population ecology. Trends Ecol. Evol. 14, 467–471 (1999).CAS 
    PubMed 
    Article 

    Google Scholar 
    65.Grant, A. & Benton, T. G. Elasticity analysis for density-dependent populations in stochastic environments. Ecology 81, 680–693 (2000).Article 

    Google Scholar 
    66.Caswell, H. & Gassen, N. S. The sensitivity analysis of population projections. Demogr. Res. 33, 801–840 (2015).Article 

    Google Scholar 
    67.R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2019).68.Soetaert, K., Petzoldt, T. & Setzer, R. W. Solving differential equations in R: Package deSolve. J. Stat. Softw. 33, 1–25 (2010).
    Google Scholar 
    69.Inkscape Project. Inkscape. More

  • in

    Results from a biodiversity experiment fail to represent economic performance of semi-natural grasslands

    The experiment underlying the study provides a diversity gradient of 1–60 plant species, established in assemblages randomly chosen from a pool of species typical of Arrhenatheretum grasslands. Recently sown on fertile arable soil and maintained by weeding, this experiment is a highly artificial system that fails to meet the definition of semi-natural grasslands7. Four years after establishment, a management intensity gradient of one to four annual cuts and three fertilization levels was established in subplots randomly assigned to the 1–60-species plots. Data presented in this study were collected in the following year.Intensive management was thus imposed on plant species typical of Arrhenaterethum meadows, a plant community characterized by two annual cuts8. The potential effect size of increased management intensity is thus underestimated by applying the management to a plant community not adapted to it. More importantly, it is unlikely that the species-richness of high-diversity plots could be maintained under increased management intensity over longer periods. In fact, 22% of these subplots managed at very high intensity had to be excluded for missing or insufficient yield after only two years, indicating that their species did not persist under high defoliation frequency and fertilizer levels, even when competitors were excluded by weeding.While the discussion hardly addresses this crucial trade-off between management intensity and plant diversity, Schaub et al.6 do indicate that repeated resowing is likely to be necessary to maintain high diversity under increased management intensities. In contrast to permanent grasslands, whose species composition is shaped by site conditions and management, species selection in (re-)sown grasslands is a conscious choice. To be advantageous, mixtures have to show larger yields than the most productive monoculture, so-called transgressive overyielding. Transgressive overyielding is one of the reasons why mixtures, especially grass-clover mixtures, are frequently used in sown grasslands. A European-scale experiment demonstrated that four-species mixtures showed transgressive overyielding at a wide range of sites under intensive agricultural management9,10. Although Schaub et al.6 generally quantify the diversity effects in comparison to monocultures, they argue that grasslands with the high-diversity characteristic of semi-natural grasslands have benefits not only over monocultures but over low-diversity grasslands, such as the 1–8 species standard mixtures shown in Fig. 6 of their paper. However, their results fail to demonstrate that their high-diversity plots show any transgressive overyielding even over monocultures, not to speak of low-diversity mixtures. As species assemblages of the experiment are randomly drawn from the species pool, monocultures and low-diversity mixtures cannot be expected to include the most productive species or species combinations and thus cannot be used to assess transgressive overyielding. When transgressive overyielding was quantified for one- to eight-species plots of the same experiment under extensive management in 2003, it decreased with species number. While two-species mixtures showed a mean transgressive overyielding of 5%, eight-species mixtures were only 70% as productive as the corresponding best monoculture, on average11.Accordingly, the experimental design fails to capture the real trade-offs faced by grassland managers, either in permanent or in sown grassland. It cannot answer if high levels of diversity and the associated biodiversity benefits can be maintained under intensive management for a longer period than just a few years. Neither can it show a productivity benefit of high-diversity grassland assemblages compared to species-poor mixtures, or even monocultures, when in practice the sown species are deliberately chosen rather than randomly drawn from a species pool. While the underlying biodiversity experiment has made valuable contributions to our fundamental understanding of plant diversity effects on ecosystem functioning, it thus cannot be used to derive direct management recommendations for managed grassland. More

  • in

    Mature Andean forests as globally important carbon sinks and future carbon refuges

    Study areaThis study was conducted using tree census data collected from 119 forest inventory plots (73 tropical, 46 subtropical) situated across a latitudinal range of 7.1°N (Colombia) to 27.8°S (Argentina), a longitudinal range of 79.5° to −63.8° W, and an elevation range of 500–3511 m asl (Fig. 1). The mean annual temperature (MAT) of plots ranged from 7.3 to 23.8 °C (mean = 16.7 ± 4.1 °C; mean ± SD) and mean annual precipitation (MAP) of the plots ranged from 608 to 4313 mm y−1 (mean = 1405.0 ± 623.9 mm y−1) (External Databases 1). The number of plots sampled in each country was: Argentina = 46, Bolivia = 26, Peru = 16, Ecuador = 21, and Colombia = 10 (Fig. 1). The 119 forest plots ranged in size from 0.32 to 1.28 ha and represent a cumulative sample area of 104.4 ha (horizontal areas corrected for slope) that containe more than 63,000 trees with a diameter at breast height (DBH, 1.3 m) ≥10 cm (External Database 1). Ninety-four of the plots (79.0%) were ≥1 ha in size. Neither secondary forests nor plantations were included. However, only seven of the plots (five in Argentina and two in Bolivia) were located in forests >100 km2 in extent41, which suggests that at least the edges and borders of some plots could have experienced some degree of disturbance or degradation. All plots were censused at least twice between 1991 and 2017 (census intervals ranged between 2 and 9 years).In each plot, we tagged, mapped, measured, and collected vouchers of all trees and palms (DBH ≥ 10 cm). DBH was measured 50 cm above buttresses or aerial roots when present (where the stem was cylindrical). During the second or subsequent set of censuses, DBH growth, recruitment, and mortality were recorded. In cases where the recorded DBH growth of the second census was less than −0.1 cm y−1 or greater than 7.5 cm y−1, the DBH of the second census was augmented/reduced in order to match these minimum/maximum values42. To homogenize and validate species names of palms and trees recorded in each country and plot, we submitted the combined list from all plots to the Taxonomic Name Resolution Service (TNRS; http://tnrs.iplantcollaborative.org/) version 3.0. Any species with an unassigned TNRS accepted name or with a taxonomic status of ‘no opinion’, ‘illegitimate’, or ‘invalid’ was manually reviewed. Families and genera were changed in accordance with the new species names. If a full species name was not provided or could not be found, the genus and/or family name from the original file was retained.Aboveground carbon stocksThe aboveground biomass (AGB) of each tree was estimated using the allometric equation proposed by Chave et al43., defined as: AGB = 0.0673 × (WD × DBH2 × H)0.976 where AGB (kg) is the estimated aboveground biomass, DBH (cm) is the diameter of the tree at breast height, H (m) is the estimated total height, and WD (g cm−3) is the stem wood density. To estimate WD, we assigned the WD values available in the literature44 to each species found in each plot. In cases where we could not assign a WD value at the species level, we used the average value at the genus- or family level. For unidentified individuals, we used the average WD value of all other species in the plot. Tree height (H) was estimated (see below) based on the heights measured on a subset of the individual stems in each plot using digital hypsometers or clinometers. The estimated AGB of each tree was then converted to units of aboveground carbon (AGC) by applying a conversion factor of 1 kg AGB = 0.456 kg C45. The AGC per ha was then determined by converting kg to Mg, summing the values for all trees in a plot, and extrapolating or interpolating to a sample area of 1 ha.Estimates of AGB and AGC are highly dependent on tree height. Unfortunately, tree height was difficult or impossible to measure on all stems due to physical and logistical constraints. Therefore, we estimated the height of each stem based on allometric relationships between DBH and tree height that we developed for each plot based on height and DBH measurements taken on a subset of individuals. Although the AGB/AGC estimates are only for trees with DBH ≥ 10, we used trees with DBH ≥ 5 cm to construct the H:DBH models when possible in order to be as comparable as possible with the existing pantropical H:DBH models46. In total, 44,442 trees had their heights measured in the field and were employed to construct the H:DBH models. The percentage of trees with direct field measurements of H (DBH ≥ 5 cm) in each country was: Argentina = 19%, Bolivia = 98%, Peru = 96%, Ecuador = 97%, and Colombia = 46%. In Argentina, 32 of 46 plots did not have any field measurements of H, while all plots in all other countries had field measurements of H for at least a subset of trees.We tested and compared the expected effects of using H:DBH models constructed using the local (plot), country, or pantropical (regional) level data. To select the best model to estimate H from DBH at the plot and country level, we used the function modelHD available in the BIOMASS package for R47. We chose the best allometric model from four candidate models (two log-log polynomial models, the three-parameter Weibull model, and a two-parameter Michaelis-Menten model (Supplementary Table 7)) by selecting the model with the lowest RSE and bias (Supplementary Table 8). At the regional level, we used a pantropical model46. The use of country and pantropical H:DBH allometries underestimates tree heights in the lowlands and overestimates tree heights in highlands, thereby homogenizing AGB estimates along elevational gradients10,48 (Supplementary Figs. 11, 12, 13). Using plot level allometries eliminates this problem. However, in the 32 plots in Argentina where we had no information about tree height, we used the country-level H:DBH model developed with the data available in the remaining 14 plots to estimate the height of each tree, which could have homogenized the AGC estimates along the Argentinian elevational gradient (Supplementary Figs. 11, 12, 13).Aboveground carbon dynamicsThe AGC dynamics of each plot was estimated from the annualized values of AGC mortality, AGC productivity (AGC change due to recruitment + growth), and AGC net change3. The calculations of the separate AGC dynamic components was performed as follows: (i) AGC mortality (Mg ha−1 y−1) = the sum of the AGC of all individuals that died between censuses divided by the time between measurements. (ii) AGC recruitment (Mg C ha−1 y−1) = the sum of the AGC of individuals that recruited into DBH ≥ 10 cm between censuses divided by the time between measurements. However, for each tree recruited (DBH ≥ 10 cm), we subtracted the corresponding AGC associated with a tree of 9.99 cm (i.e. just below the detection limit) in order to avoid overestimations of the overall increase in AGC due to recruitment49. (iii) AGC growth (Mg ha−1 y−1) = the sum of the increase in AGC of all individuals with DBH ≥ 10 cm that survived between censuses divided by the time between censuses. (iv) AGC net change (Mg ha−1 y−1) = the difference between AGC stock in the last census (AGCfinal) and AGC stock in the first census (AGC1) divided by the elapsed time (t; in years) between measurements [(AGC net change = AGCfinal − AGC1)/t]. We recognize that these methods exclude C stored in soils or in belowground tissues9,48; however, quantifying just aboveground C stocks and fluxes provides valuable information about the overall status of these forests as net C sinks or sources.ClimateClimate variables at each plot location were extracted from the CHELSA28 bioclimatic rasters at a resolution of 30-arcsec (~1 km2 at the equator). The climate variables extracted were: Mean Annual Temperature (MAT), Mean Diurnal Range (MDR), Isothermality (Isoth), Temperature Seasonality (TS), Maximum Temperature of Warmest Month (MaxTWarmM), Minimum Temperature of Coldest Month (MinTCM), Temperature Annual Range (TAR), Mean Temperature of Wettest Quarter (MeanTWarmQ), Mean Temperature of Driest Quarter (MeanTDQ), Mean Temperature of Warmest Quarter (MeanTWetQ), Mean Temperature of Coldest Quarter (MeanTCQ), Mean Annual Precipitation (MAP), Precipitation of Wettest Month (PWetM), Precipitation of Driest Month (PDM), Precipitation Seasonality (PS), Precipitation of Wettest Quarter (PWetQ), Precipitation of Driest Quarter (PDQ), Precipitation of Warmest Quarter (PWarmQ), Precipitation of Coldest Quarter (PCQ). We separated all variables associated with temperature (°C) from those associated with precipitation (mm y−1) and applied a Principal Component Analysis (PCA) to the 11 variables associated with temperature (PCAtemp) and a separate PCA to the eight variables associated with precipitation (PCAprec). The first two principal components of both PCAtemp and PCAprec (four PCA axes in total) were selected for use in subsequent analyses. Plot elevations were estimated based on their coordinates and the SRTM 1 ArcSec Global V3 (https://lta.cr.usgs.gov) 30 m resolution digital elevation model (DEM).PCAtemp1 (Supplementary Fig. 1a) explained 53.0% of the total variance of the temperature variables and had high loading from Isothermality and Maximum Temperature of Warmest Month, which was primarily associated with changes in elevation (r = −0.97, p  More

  • in

    Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

    1.Fushimi, H. Production of juvenile marine finfish for stock enhancement in Japan. Aquaculture 200, 33–53. https://doi.org/10.1016/S0044-8486(01)00693-7 (2001).Article 

    Google Scholar 
    2.Masuda, R. & Tsukamoto, K. Stock enhancement in Japan: review and perspective. Bull. Mar. Sci. 62, 337–358. https://www.ingentaconnect.com/content/umrsmas/bullmar/1998/00000062/00000002/art00005 (1998).3.Sekino, M., Saitoh, K., Yamada, T., Hara, M. & Yamashita, Y. Genetic tagging of released Japanese flounder (Paralichthys olivaceus) based on polymorphic DNA markers. Aquaculture 244, 49–61. https://doi.org/10.1016/j.aquaculture.2004.11.006 (2005).CAS 
    Article 

    Google Scholar 
    4.Arnold, W. S. Bivalve enhancement and restoration strategies in Florida, USA. Hydrobiologia 465, 7–19. https://doi.org/10.1023/A:1014596909319 (2001).Article 

    Google Scholar 
    5.Castell, L. L., Naviti, W. & Nguyen, F. Detectability of cryptic juvenile Trochus niloticus Linnaeus in stock enhancement experiments. Aquaculture 144, 91–101. https://doi.org/10.1016/S0044-8486(96)01320-8 (1996).Article 

    Google Scholar 
    6.McCormick, T. B., Herbinson, K., Mill, T. S. & Altick, J. A review of abalone seeding, possible significance and a new seeding device. Bull. Mar. Sci. 55, 680–693. https://www.ingentaconnect.com/content/umrsmas/bullmar/1994/00000055/f0020002/art00035 (1994).7.Zohar, Y. et al. The Chesapeake Bay blue crab (Callinectes sapidus): A multidisciplinary approach to responsible stock replenishment. Rev. Fish. Sci. 16, 24–34. https://doi.org/10.1080/10641260701681623 (2008).Article 

    Google Scholar 
    8.Funge-Smith, S., Briggs, M. & Miao, W. Regional Overview of Fisheries and Aquaculture in Asia and the Pacific 2012 (RAP Publication (FAO), 2012).
    Google Scholar 
    9.Mao, Y. et al. Chapter 4. Bivalve production in China. In Goods and Services of Marine Bivalves (eds Smaal, A. C. et al.) 51–72 (Springer, 2019).
    Google Scholar 
    10.Ran, Z. et al. Fatty acid and sterol changes in razor clam Sinonovacula constricta (Lamarck 1818) reared at different salinities. Aquaculture 473, 493–500. https://doi.org/10.1016/j.aquaculture.2017.03.017 (2017).CAS 
    Article 

    Google Scholar 
    11.Suzuki, T., Inoue, K. & Ozawa, T. Environmental degradation in Ise and Mikawa Bays after 1960’s as viewed from intertidal molluscan community. Boll. Nagoya Univ. Museum 22, 31–64. https://doi.org/10.18999/bulnum.022.04 (2006).Article 

    Google Scholar 
    12.Nakamura, T. et al. Marine reservoir effect deduced from 14C dates on marine shells and terrestrial remains at archeological sites in Japan. Nucl. Instrum. Methods Phys. Res. B 259, 453–459. https://doi.org/10.1016/j.nimb.2007.01.186 (2007).ADS 
    CAS 
    Article 

    Google Scholar 
    13.Ministry of the Environment, Japan. Ariake Sea and Yatsushiro Sea Comprehensive Survey Evaluation Committee Report. https://www.env.go.jp/council/20ari-yatsu/rep061221/all.pdf (2006).14.Ito, S., Eguchi, T. & Kawahara, I. Rearing experiment on planktonic larvae of the JackKnife clam, Sinonovacula constricta. Boll. Saga Prefect. Ariake Fish. Res. Dev. Cent. 20, 49–53. https://agriknowledge.affrc.go.jp/RN/2010813185.pdf (2001).15.Ohkuma, H., Ymagachi, T., Kawahara, I., Eguchi, T. & Ito, S. A study on the development of techniques for mass production of seeds of jackknife clam, Sinonovacula constricta. Boll. Saga Prefect. Ariake Fish. Res. Dev. Cent. 22, 47–54. https://agriknowledge.affrc.go.jp/RN/2030813210.pdf (2004).16.Tsukuda, M. et al. Variation in the Distribution of the JackKnife Clam, Sinonovacula constricta, on the Muddy Tidal flat of Ariake Sound off Saga Prefecture. Boll. Saga Prefect. Ariake Fish. Res. Dev. Cent. 28, 47–49. https://agriknowledge.affrc.go.jp/RN/2010925685.pdf (2017).17.Holman, L. E., de la Garcia, S. D., Onoufriou, A., Hillestad, B. & Johnston, I. A. A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon. Aquaculture 476, 59–64. https://doi.org/10.1016/j.aquaculture.2017.04.001 (2017).CAS 
    Article 

    Google Scholar 
    18.Li, Y. H. & Wang, H. P. Advances of genotyping-by-sequencing in fisheries and aquaculture. Rev. Fish Biol. Fish. 27, 535–559. https://doi.org/10.1007/s11160-017-9473-2 (2017).Article 

    Google Scholar 
    19.Robledo, D., Palaiokostas, C., Bargelloni, L., Martínez, P. & Houston, R. Applications of genotyping by sequencing in aquaculture breeding and genetics. Rev. Aquac 10, 670–682. https://doi.org/10.1111/raq.12193 (2018).Article 
    PubMed 

    Google Scholar 
    20.You, X., Shan, X. & Shi, Q. Research advances in the genomics and applications for molecular breeding of aquaculture animals. Aquaculture 526, 735357. https://doi.org/10.1016/j.aquaculture.2020.735357 (2020).CAS 
    Article 

    Google Scholar 
    21.Arthington, A. H. Ecological and genetic impacts of introduced and translocated freshwater fishes in Australia. Can. J. Fish. Aquat. Sci. 48, 33–43. https://doi.org/10.1139/f91-302 (1991).Article 

    Google Scholar 
    22.Habtemariam, B. T., Arias, A., García-Vázquez, E. & Borrell, Y. J. Impacts of supplementation aquaculture on the genetic diversity of wild Ruditapes decussatus from northern Spain. Aquacult. Environ. Interact. 6, 241–254. https://doi.org/10.3354/aei00128 (2015).Article 

    Google Scholar 
    23.Williams, S. L. & Orth, R. J. Genetic diversity and structure of natural and transplanted eelgrass populations in the Chesapeake and Chincoteague Bays. Estuaries 21, 118–128. https://doi.org/10.2307/1352551 (1998).Article 

    Google Scholar 
    24.Yamakawa, A. Y. & Imai, H. PCR-RFLP typing reveals a new invasion of Taiwanese Meretrix (Bivalvia: Veneridae) to Japan. Aquat. Invasions 8, 407–415. https://doi.org/10.3391/ai.2013.8.4.04 (2013).Article 

    Google Scholar 
    25.Niu, D. H., Feng, B. B., Liu, D. B., Zhong, Y. M., Shen, H. D. & Li, J. L. Significant genetic differentiation among ten populations of the razor clam Sinonovacula constricta along the coast of china revealed by a microsatellite analysis. Zool. Stud. 51, 406–414. http://zoolstud.sinica.edu.tw/Journals/51.3/406.pdf. (2012).26.DeFaveri, J., Shikano, T., Ghani, N. I. A. & Merilä, J. Contrasting population structures in two sympatric fishes in the Baltic Sea basin. Mar. Biol. 159, 1659–1672. https://doi.org/10.1007/s00227-012-1951-4 (2012).Article 

    Google Scholar 
    27.Jeffery, N. W. et al. RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic. Ecol. Evol. 7, 2513–2524. https://doi.org/10.1002/ece3.2872 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    28.Kato, D. et al. Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis. Sci. Rep. 10, 1533. https://doi.org/10.1038/s41598-020-58324-9 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    29.Yokota, M., Harada, Y. & Iizuka, M. Genetic drift in a hatchery and the maintenance of genetic diversity in hatchery-wild systems. Fish Sci. 69, 101–109. https://doi.org/10.1046/j.1444-2906.2003.00593.x (2003).CAS 
    Article 

    Google Scholar 
    30.Harada, Y., Yokota, M. & Iizuka, M. Genetic risk of domestication in artificial fish stocking and its possible reduction. Popul. Ecol. 40, 311–324. https://doi.org/10.1007/BF02763463 (1998).Article 

    Google Scholar 
    31.Etter, P. D., Bassham, S., Hohenlohe, P. A., Johnson, E. A. & Cresko, W. A. SNP discovery and genotyping for evolutionary genetics using RAD sequencing, in: Molecular methods for evolutionary genetics. Methods Mol. Biol. Humana Press 772, 157–178. https://doi.org/10.1007/978-1-61779-228-1_9 (2011).CAS 
    Article 

    Google Scholar 
    32.Rochette, N. C. & Catchen, J. M. Deriving genotypes from RAD-seq short-read data using stacks. Nat. Protoc. 12, 2640–2659. https://doi.org/10.1038/nprot.2017.123 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    33.Ran, Z. et al. Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818). Mol. Ecol. Resour. 19, 1647–1658. https://doi.org/10.1111/1755-0998.13086 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    34.Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv: 1303.3997. https://arxiv.org/abs/1303.3997 (2013).35.Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328. https://doi.org/10.1093/bioinformatics/bts606 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    37.Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664. https://pubmed.ncbi.nlm.nih.gov/19648217/ (2009).38.Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575. https://doi.org/10.1086/519795 (2007).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Eklund, A. R package beeswarm: the bee swarm plot, an alternative to stripchart. https://cran.r-project.org/web/packages/beeswarm/beeswarm.pdf (2016).40.Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. https://doi.org/10.1093/bioinformatics/btu033 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    41.Chifman, J. & Kubatko, L. Quartet inference from SNP data under the coalescent model. Bioinformatics 30, 3317–3324. https://doi.org/10.1093/bioinformatics/btu530 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Swofford, D. L. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4 (Sinauer Associates, 2002).
    Google Scholar  More

  • in

    A metric for spatially explicit contributions to science-based species targets

    Species threat abatement and restoration (STAR) metricWe developed and analysed a STAR metric that evaluates the potential benefit for threatened species of actions to reduce threats and restore habitat. Like the Red List Index7,8, STAR is derived from existing data in the IUCN Red List and is intended to help address an urgent need. STAR is spatially explicit, enabling identification of specific threat abatement and habitat restoration opportunities in particular places, which, if implemented, could reduce species extinction risk to levels that would exist without ongoing human impact. Abatement of threats to species encompasses reduction in threat intensity and/or action to mitigate the impacts of threats. Positive population and/or distribution changes, along with the resulting reduction of species extinction risk, have been documented in response to threat abatement13. STAR assumes that, for the great majority of species (see Supplementary Discussion), complete alleviation of threats would reduce extinction risk through halting the decline and/or permitting sufficient recovery in population and distribution, such that the species could be downlisted to the IUCN Red List category of Least Concern. We recognize that complete threat reduction is difficult, incremental conservation gains will need to be tracked at the species level14 and species recovery will vary across a species’ range14.For each species, a global STAR threat abatement (START) score is defined. This varies from zero for species of Least Concern to 100 for Near Threatened, 200 for Vulnerable, 300 for Endangered and 400 for Critically Endangered species (using established weighting ratios7,8). The sum of START values across all species represents the global threat abatement effort needed for all species to become Least Concern. START scores can be disaggregated spatially, based on the area of habitat (AOH) currently available for each species in a particular location (as a proxy for population proportion). This shows the potential contribution of conservation actions in that location to reducing the extinction risk for all species globally. The local START score can be further disaggregated by threat, based on the known contribution of each threat to the species’ risk of extinction (see Methods). This quantifies how actions that abate a specific threat at a particular location contribute to the global abatement of extinction risk for all species.The STAR metric also includes a complementary habitat restoration component to reflect the potential benefits to species of restoring lost habitat. During the United Nations Decade on Ecosystem Restoration (2021–2030), restoration efforts are likely to expand. The STAR restoration component applies a similar logic to the STAR threat abatement component, but for habitat that has been lost and is potentially restorable (that is, restorable AOH). The STAR restoration component does not make assumptions about the extent of habitat restoration required for individual species, but instead quantifies the potential contribution that habitat restoration activities could make to reducing species’ extinction risk. For a particular species at a particular location, the STAR restoration (STARR) score reflects the proportion that restorable habitat at the location represents of the global area of remaining habitat for that species. Importantly, a multiplier is applied to STARR scores to reflect the slower and lower success rate in delivering benefits to species from restored habitat compared with conserved existing habitat15. Again, STARR scores can be disaggregated by threat and summed across species within the location.STAR is intended to provide a metric to underpin the establishment of science-based targets as explicit contributions from individual actors towards the post-2020 biodiversity framework, by allowing assessment of actions and locations according to their potential ability to deliver towards international conservation targets. Individual spatially based START and STARR scores, for all species present in a particular location or country, represent a proportion of the global opportunity to reduce species’ extinction risk through threat abatement and restoration, respectively. For each species, the total START score could be achieved by the complete abatement of all threats in remaining habitat, or an equivalent value of the STAR metric can be achieved by a combination of threat abatement in the remaining habitat and restoration of lost habitat (with concomitant threat abatement therein). The metric can support establishment of science-based targets by a range of actors across spatial scales. By enabling governments and non-state actors to quantify their potential contributions, STAR, along with other tools, could facilitate achievement of global policy goals, notably the species component of the Sustainable Development Goals and the expected post-2020 Global Biodiversity Framework.STAR uses existing publicly available datasets: species’ extinction risk categories and threats available from the IUCN Red List6 (or, for country endemics not yet assessed globally, from national red lists); and species’ AOH estimated using species’ ranges, habitat associations, and elevation limits, along with digital elevation models and current and historical land cover maps (here, we used backcast land cover maps of the distribution of habitat pre-human impact, as in ref. 16). To demonstrate the utility of STAR, we calculated global STAR scores for the groups of terrestrial vertebrate species that are comprehensively assessed on the IUCN Red List (that is, threatened and Near Threatened species of amphibians, birds and mammals globally; n = 5,359).Potential to reduce species extinction riskGlobally, the greatest contribution that could be made to reduce the extinction risk of these groups is tackling threats from annual and perennial non-timber crop production, which account for 24.5% of the global START score (Fig. 1). A further 16.4% is contributed by logging and wood harvesting. There are likely to be specific targets for reducing agriculture and forestry threats in the post-2020 framework3, and applying STAR quantifies the large potential contribution that mitigating these threats could make to the goal for species conservation. Appropriate activities to deliver on such targets range along a continuum from land sharing through to land sparing17.Fig. 1: Contribution to the global START score of different threats and the potential contribution of habitat restoration.The total global START score represents the global threat abatement effort needed for all Near Threatened and threatened (Vulnerable, Endangered and Critically Endangered, according to the IUCN Red List) amphibian, bird and mammal species to be reclassified as Least Concern. This score can be disaggregated by threat type, based on the known contribution of each threat to species’ risk of extinction. The STARR score quantifies the potential contribution that habitat restoration activities could make to reducing overall species’ extinction risk. The total START score could thus be achieved by the complete abatement of all threats in existing natural habitat, or through a combination of threat abatement in existing habitat and restoration of lost habitat (with concomitant threat abatement therein).Full size imageSTAR can be used in combination with existing policy and planning tools to quantify the potential contribution of action targets towards species conservation outcomes. The proposed post-2020 framework includes an action target for the protection of sites of particular importance to biodiversity3. Key Biodiversity Areas11, which include Important Bird and Biodiversity Areas18 and Alliance for Zero Extinction sites19, correspond to such sites. Key Biodiversity Areas so far cover 8.8% of the terrestrial surface (www.keybiodiversityareas.org; identification is ongoing), but already capture 47% of the global START score for the vertebrate groups analysed. They represent large proportions of some national START scores: >70% in Mexico and Venezuela and >50% in Madagascar, Ecuador, the Philippines and Tanzania.START scores can also support target setting at national and sub-national scales to help meet international policy goals. The control and eradication of invasive species forms one of the CBD’s proposed post-2020 action targets3. New Zealand has already set a Predator Free 2050 goal that aims to eradicate three invasive mammal species by 2050. New Zealand contributes 0.8% to the global START score for the three vertebrate groups included in this study. Achieving the Predator Free 2050 goal would contribute 30% of the total START score for New Zealand, amounting to 0.2% of the global START score.All countries contribute towards the global START score, but scores are highly skewed, with a few countries having high START scores and most having low scores for the vertebrate groups analysed (Fig. 2a and Extended Data Fig. 1). The highest-scoring countries are located in biodiverse regions with many threatened endemic species20: Indonesia contributes 7.1% of the global START score, Colombia 7.0%, Mexico 6.1%, Madagascar 6.0% and Brazil 5.2%. These top five countries contribute 31.3% of the global START score. In contrast, the lowest-scoring 88 countries together contribute only 1% of the global START score. This does not imply that these low-scoring countries have negligible species conservation responsibilities; the global decline in even common species indicates that all countries must act to reverse the degradation of nature and restore the diversity and abundance of species and integrity of ecosystems21, as well as preventing extinctions at a national scale. Moreover, most countries have a Red List Index22, or an equivalent, quantifying their progress or failure in reducing the global extinction risk of assessed species relative to their national responsibility for global species conservation. STAR provides a means to guide the reduction of extinction risk and so assist all countries in meeting national species conservation targets.Fig. 2: Global distribution of START and STARR scores.a,b, Global STAR scores for amphibians, birds and mammals at a 50-km grid cell resolution for START scores (a) and STARR scores (b). Each species has a global START score, weighted relative to their extinction risk. This global START score can be disaggregated spatially, based on the AOH currently available for each species in a particular location. The total START score per grid cell (a) is thus the sum of the individual species’ START scores per grid cell across all Near Threatened and threatened species of amphibians, birds and mammals included in this study. The global STARR score per species reflects the potential contribution that habitat restoration activities could make to reducing species’ extinction risk, and is spatially disaggregated based on the availability of restorable habitat. Thus, the total STARR score per grid cell (b) is the sum of the individual species’ STARR scores per grid cell across all species included in this study. For the legends in a and b, each range excludes the lower bound and includes the upper bound.Full size imageAt the global level, we estimated that an equivalent to 55.9% of the global START score for vertebrates could, theoretically, be achieved by restoring lost habitat within the current range (Fig. 1). Ecosystem restoration objectives have been identified in many national biodiversity strategies for the CBD, as well as in many countries’ commitments under the Bonn Challenge, and as part of Nationally Determined Contributions under the United Nations Framework Convention on Climate Change. The STAR metric has the potential to support restoration initiatives alongside species conservation targets by quantifying the potential benefit to particular species of restoring habitat in specific places23 (Fig. 2b). Restoration may be particularly important for some species, including those assessed under Red List sub-criteria D/D1 (with a very small population) or Bac (with a small range with severe fragmentation, plus extreme fluctuations). For species uniquely assessed under these criteria (2.8% of those included in this study), threat abatement alone is unlikely to eliminate extinction risk, so this might need to be complemented by restoration in order to achieve Least Concern status (see Supplementary Discussion). Moreover, depending on habitat loss and threat type, restoration of habitat may be beneficial for a larger proportion of threatened species.Application of STAR at the landscape scaleWe tested the landscape-scale application of the STAR metric in the southern part of Bukit Tigapuluh landscape, in central Sumatra, Indonesia (Fig. 3a). The Bukit Tigapuluh Sustainable Landscape and Livelihoods Project is a sustainable commercial rubber initiative. The study area (approximately 88,000 ha) includes a 5-km buffer (which is set aside to support local livelihoods, wildlife conservation areas and forest protection and restoration) and two ecosystem restoration areas (which form a conservation management zone that protects the Bukit Tigapuluh National Park from encroachment).Fig. 3: STAR results for the Bukit Tigapuluh Sustainable Landscape and Livelihoods Project.The Bukit Tigapuluh Sustainable Landscape and Livelihoods Project is a sustainable commercial rubber initiative. The study area (approximately 88,000 ha) includes a 5-km buffer, which is set aside to support local livelihoods, wildlife conservation areas and forest protection and restoration, and two ecosystem restoration areas, which form a conservation management zone that protects the Bukit Tigapuluh National Park from encroachment. a, Mapped START scores in areas with remaining forest (green) and STARR scores in areas where forest has been lost (purple) at the 30-m grid cell resolution. b, START scores per threat for the top five highest-scoring threats across the study area (the concession, 5-km buffer and ecosystem restoration areas combined).Full size imageThe total START score for the study area represents 0.2% of the START score for Sumatra, 0.04% of the START score for Indonesia and 0.003% of the global START. The major threats are from annual and perennial non-timber crops, logging and wood harvesting, and the collection of terrestrial animals (Fig. 3b). The proximate causes of these pressures in the project area are rubber cultivation, oil palm cultivation, industrial logging, subsistence wood cutting and hunting. STAR analysis shows that areas with the greatest potential to contribute to species conservation through threat mitigation are in remaining natural habitat close to the national park, with a small area of high potential also to the west, where the relatively small distribution of the orbiculus leaf-nosed bat (Hipposideros orbiculus) overlaps the site (Fig. 3a). Additionally, due to recent forest loss, 47% of the START score for the study area could be achieved through habitat restoration (that is, STARR). Investment in these management actions has the potential to deliver these quantified contributions to national and global biodiversity targets.Operationalization and future developmentThe STAR metric makes use of the best available data, producing results that are relevant to policy and practice. However, there is scope for future refinement as the underlying data improve. Here, the STAR metric covers amphibians, birds and mammals globally, constituting a well-studied but small proportion of taxonomic diversity (see Extended Data Figs. 2 and 3 for variation among taxa). STAR can be expanded to other taxonomic groups, including freshwater and marine species, as data become available (reptiles, cacti, cycads, conifers, freshwater fish and reef-building corals are among the groups imminently available for incorporation). Global application of STAR will require comprehensive assessment of taxonomic groups, testing of the transferability of the STAR metric assumptions among taxa as Red List coverage expands, and further development of methods to calculate AOH. AOH calculation does not currently capture spatial variation in species’ population density, which will be important for many species14; such data have not been gathered on a global scale yet and could be incorporated as available.The completeness of threat data in the IUCN Red List is uneven but is continually improving. The STAR metric does not currently reflect spatial variation in threat magnitude within species’ ranges; more broadly, there is a lack of information on the spatial distribution of threats24. Most species included in this study have relatively small ranges; the total current AOH is More

  • in

    Horizontally acquired cysteine synthase genes undergo functional divergence in lepidopteran herbivores

    Acuna R, Padilla BE, Florez-Ramos CP, Rubio JD, Herrera JC, Benavides P et al. (2012) Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci USA 109(11):4197–4202CAS 
    PubMed 
    Article 

    Google Scholar 
    Aoyama K, Watabe M, Nakaki T (2008) Regulation of neuronal glutathione synthesis. J Pharm Sci 108(3):227–238CAS 
    Article 

    Google Scholar 
    Arias M, Meichanetzoglou A, Elias M, Rosser N, de-Silva DL, Nay B et al. (2016) Variation in cyanogenic compounds concentration within a Heliconius butterfly community: does mimicry explain everything? BMC Evol Biol 16(1):272PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Baloch MN, Fan JY, Haseeb M, Zhang RZ (2020) Mapping potential distribution of Spodoptera frugiperda (Lepidoptera: Noctuidae) in central Asia. Insects 11(3):172PubMed Central 
    Article 
    PubMed 

    Google Scholar 
    Barbehenn RV, Kochmanski J, Menachem B, Poirier LM (2013a) Allocation of cysteine for glutathione production in caterpillars with different antioxidant defense strategies: a comparison of Lymantria dispar and Malacosoma disstria. Arch Insect Biochem 84(2):90–103CAS 

    Google Scholar 
    Barbehenn RV, Niewiadomski J, Kochmanski J (2013b) Importance of protein quality versus quantity in alternative host plants for a leaf-feeding insect. Oecologia 173(1):1–12PubMed 
    Article 

    Google Scholar 
    Bogicevic B, Berthoud H, Portmann R, Meile L, Irmler S (2012) CysK from Lactobacillus casei encodes a protein with O-acetylserine sulfhydrylase and cysteine desulfurization activity. Appl Microbiol Biot 94(5):1209–1220CAS 
    Article 

    Google Scholar 
    Bonner ER, Cahoon RE, Knapke SM, Jez JM (2005) Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana. J Biol Chem 280(46):38803–38813CAS 
    PubMed 
    Article 

    Google Scholar 
    Boto L (2014) Horizontal gene transfer in the acquisition of novel traits by metazoans. Proc Biol Sci 281(1777):20131834
    Google Scholar 
    Brown ES, Dewhurst CF (2009) The genus Spodoptera (Lepidoptera, Noctuidae) in Africa and the Near East. Bull Entomological Res 65(2):221–262Article 

    Google Scholar 
    Budde MW, Roth MB (2011) The response of Caenorhabditis elegans to hydrogen sulfide and hydrogen cyanide. Genetics 189(2):521–532CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Burkhard P, Rao GS, Hohenester E, Schnackerz KD, Cook PF, Jansonius JN (1998) Three-dimensional structure of O-acetylserine sulfhydrylase from Salmonella typhimurium. J Mol Biol 283(1):121–133CAS 
    PubMed 
    Article 

    Google Scholar 
    Dai X, Li R, Li X, Liang Y, Gao Y, Xu Y et al. (2019) Gene duplication and subsequent functional diversification of sucrose hydrolase in Papilio xuthus. Insect Mol Biol 28(6):862–872CAS 
    PubMed 
    Article 

    Google Scholar 
    Daimon T, Katsuma S, Iwanaga M, Kang WK, Shimada T (2005) The BmChi-h gene, a bacterial-type chitinase gene of Bombyx mori, encodes a functional exochitinase that plays a role in the chitin degradation during the molting process. Insect Biochem Mol Biol 35(10):1112–1123CAS 
    PubMed 
    Article 

    Google Scholar 
    Daimon T, Taguchi T, Meng Y, Katsuma S, Mita K, Shimada T (2008) Beta-fructofuranosidase genes of the silkworm, Bombyx mori – Insights into enzymatic adaptation of B. mori to toxic alkaloids in mulberry latex. J Biol Chem 283(22):15271–15279CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Danchin EG, Rosso MN, Vieira P, de Almeida-Engler J, Coutinho PM, Henrissat B et al. (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci USA 107(41):17651–17656CAS 
    PubMed 
    Article 

    Google Scholar 
    Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27(8):1164–1165CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Doxey AC, Yaish MWF, Moffatt BA, Griffith M, McConkey BJ (2007) Functional divergence in the Arabidopsis beta-1,3-glucanase gene family inferred by phylogenetic reconstruction of expression states. Mol Biol Evol 24(4):1045–1055CAS 
    PubMed 
    Article 

    Google Scholar 
    Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7(10):e1002195CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Bmc Bioinforma 5:1–19Article 
    CAS 

    Google Scholar 
    Fan X, Qiu H, Han W, Wang Y, Xu D, Zhang X et al. (2020) Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions. Sci Adv 6(18):eaba0111CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Farre D, Alba MM (2010) Heterogeneous patterns of gene-expression diversification in mammalian gene duplicates. Mol Biol Evol 27(2):325–335CAS 
    PubMed 
    Article 

    Google Scholar 
    Feldman-Salit A, Wirtz M, Hell R, Wade RC (2009) A mechanistic model of the cysteine synthase complex. J Mol Biol 386(1):37–59CAS 
    PubMed 
    Article 

    Google Scholar 
    Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151(4):1531–1545CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gaitonde MK (1967) A spectrophotometric method for direct determination of cysteine in presence of other naturally occurring amino acids. Biochem J 104(2):627–633CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gan Q, Zhang XW, Zhang DB, Shi L, Zhou Y, Sun TT et al. (2018) BmSUC1 is essential for glycometabolism modulation in the silkworm, Bombyx mori. BBA-Gene Regul Mech 1861(6):543–553CAS 

    Google Scholar 
    Ganko EW, Meyers BC, Vision TJ (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 24(10):2298–2309CAS 
    PubMed 
    Article 

    Google Scholar 
    Gao Y, Liu YC, Jia SZ, Liang YT, Tang Y, Xu YS et al. (2020) Imaginal disc growth factor maintains cuticle structure and controls melanization in the spot pattern formation of Bombyx mori. PLoS Genet 16(9):e1008980CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Goldsmith MR, Shimada T, Abe H (2005) The genetics and genomics of the silkworm, Bombyx mori. Annu Rev Entomol 50:71–100CAS 
    PubMed 
    Article 

    Google Scholar 
    Gu X, Zhang ZQ, Huang W (2005) Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci USA 102(3):707–712CAS 
    PubMed 
    Article 

    Google Scholar 
    Gu ZL, Nicolae D, Lu HHS, Li WH (2002) Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 18(12):609–613CAS 
    PubMed 
    Article 

    Google Scholar 
    Helmkampf M, Cash E, Gadau J (2015) Evolution of the insect desaturase gene family with an emphasis on social Hymenoptera. Mol Biol Evol 32(2):456–471PubMed 
    Article 

    Google Scholar 
    Hendrickson HR, Conn EE (1969) Cyanide metabolism in higher plants. IV. Purification and properties of the beta-cyanolanine synthase of blue lupine. J Biol Chem 244(10):2632–2640CAS 
    PubMed 
    Article 

    Google Scholar 
    Herfurth AM, van Ohlen M, Wittstock U (2017) Beta-cyanoalanine synthases and their possible role in Pierid host plant adaptation. Insects 8(2):62PubMed Central 
    Article 
    PubMed 

    Google Scholar 
    Husnik F, McCutcheon JP (2018) Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol 16(2):67–79CAS 
    PubMed 
    Article 

    Google Scholar 
    Jeschke V, Gershenzon J, Vassao DG (2016) A mode of action of glucosinolate-derived isothiocyanates: detoxification depletes glutathione and cysteine levels with ramifications on protein metabolism in Spodoptera littoralis. Insect Biochem Molec 71:37–48CAS 
    Article 

    Google Scholar 
    Jiggins FM, Hurst GD (2011) Microbiology. Rapid insect evolution by symbiont transfer. Science 332(6026):185–186CAS 
    PubMed 
    Article 

    Google Scholar 
    Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874CAS 
    Article 

    Google Scholar 
    Lai KW, Yau CP, Tse YC, Jiang LW, Yip WK (2009) Heterologous expression analyses of rice OsCAS in Arabidopsis and in yeast provide evidence for its roles in cyanide detoxification rather than in cysteine synthesis in vivo. J Exp Bot 60(3):993–1008CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lee BS, Huang JS, Jayathilaka LP, Lee J, Gupta S (2016) Antibody production with synthetic peptides. Methods Mol Biol 1474:25–47CAS 
    PubMed 
    Article 

    Google Scholar 
    Lee HL, Irish VF (2011) Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol 28(12):3367–3380CAS 
    PubMed 
    Article 

    Google Scholar 
    Leite DJ, Baudouin-Gonzalez L, Iwasaki-Yokozawa S, Lozano-Fernandez J, Turetzek N, Akiyama-Oda Y et al. (2018) Homeobox gene duplication and divergence in arachnids. Mol Biol Evol 35(9):2240–2253CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li ZW, Shen YH, Xiang ZH, Zhang Z (2011) Pathogen-origin horizontally transferred genes contribute to the evolution of lepidopteran insects. Bmc Evolut Biol 11(1):356CAS 
    Article 

    Google Scholar 
    Liu HJ, Tang ZX, Han XM, Yang ZL, Zhang FM, Yang HL et al. (2015) Divergence in enzymatic activities in the soybean GST supergene family provides new insight into the evolutionary dynamics of whole-genome duplicates. Mol Biol Evol 32(11):2844–2859CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lunn JE, Droux M, Martin J, Douce R (1990) Localization of atp sulfurylase and O-acetylserine(Thiol)lyase in spinach leaves. Plant Physiol 94(3):1345–1352CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154(1):459–473CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Nikoh N, McCutcheon JP, Kudo T, Miyagishima S, Moran NA, Nakabachi A (2010) Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host. Plos Genet 6(2):e1000827PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Novakova E, Moran NA (2012) Diversification of genes for carotenoid biosynthesis in aphids following an ancient transfer from a fungus. Mol Biol Evol 29(1):313–323CAS 
    PubMed 
    Article 

    Google Scholar 
    Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299–304CAS 
    PubMed 
    Article 

    Google Scholar 
    Pallen MJ, Wren BW (2007) Bacterial pathogenomics. Nature 449(7164):835–842CAS 
    PubMed 
    Article 

    Google Scholar 
    Polz MF, Alm EJ, Hanage WP (2013) Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29(3):170–175CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S et al. (2016) Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Curr Opin Insect Sci 13:70–76PubMed 
    Article 

    Google Scholar 
    Schramm K, Vassao DG, Reichelt M, Gershenzon J, Wittstock U (2012) Metabolism of glucosinolate-derived isothiocyanates to glutathione conjugates in generalist lepidopteran herbivores. Insect Biochem Molec 42(3):174–182CAS 
    Article 

    Google Scholar 
    Stauber EJ, Kuczka P, van Ohlen M, Vogt B, Janowitz T, Piotrowski M et al. (2012) Turning the ‘mustard oil bomb’ into a ‘cyanide bomb’: aromatic glucosinolate metabolism in a specialist insect herbivore. Plos One 7(4):e35545CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sun BF, Xiao JH, He SM, Liu L, Murphy RW, Huang DW (2013) Multiple ancient horizontal gene transfers and duplications in lepidopteran species. Insect Mol Biol 22(1):72–87CAS 
    PubMed 
    Article 

    Google Scholar 
    Suzuki K, Moriguchi K, Yamamoto S (2015) Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers. Res Microbiol 166(10):753–763CAS 
    PubMed 
    Article 

    Google Scholar 
    Van Ohlen M, Herfurth AM, Kerbstadt H, Wittstock U (2016) Cyanide detoxification in an insect herbivore: molecular identification of beta-cyanoalanine synthases from Pieris rapae. Insect Biochem Molec 70:99–110CAS 
    Article 

    Google Scholar 
    Wada M, Awano N, Yamazawa H, Takagi H, Nakamori S (2004) Purification and characterization of O-acetylserine sulfhydrylase of Corynebacterium glutamicum. Biosci Biotech Bioch 68(7):1581–1583CAS 
    Article 

    Google Scholar 
    Wadleigh RW, Yu SJ (1988) Detoxification of isothiocyanate allelochemicals by glutathione transferase in three lepidopterous species. J Chem Ecol 14(4):1279–1288CAS 
    PubMed 
    Article 

    Google Scholar 
    Wagner A (2002) Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 19(10):1760–1768CAS 
    PubMed 
    Article 

    Google Scholar 
    Wybouw N, Dermauw W, Tirry L, Stevens C, Grbic M, Feyereisen R et al. (2014) A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning. Elife 3:e02365PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wybouw N, Pauchet Y, Heckel DG, Van Leeuwen T (2016) Horizontal gene transfer contributes to the evolution of arthropod herbivory. Genome Biol Evol 8(6):1785–1801CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yamaguchi Y, Nakamura T, Kusano T, Sano H (2000) Three arabidopsis genes encoding proteins with differential activities for cysteine synthase and beta-cyanoalanine synthase. Plant Cell Physiol 41(4):465–476CAS 
    PubMed 
    Article 

    Google Scholar 
    Yi H, Juergens M, Jez JM (2012) Structure of soybean beta-cyanoalanine synthase and the molecular basis for cyanide detoxification in plants. Plant Cell 24(6):2696–2706CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhou YY, Li XT, Katsuma S, Xu YS, Shi LG, Shimada T et al. (2019) Duplication and diversification of trehalase confers evolutionary advantages on lepidopteran insects. Mol Ecol 28(24):5282–5298CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhu B, Lou MM, Xie GL, Zhang GQ, Zhou XP, Li B et al. (2011) Horizontal gene transfer in silkworm, Bombyx mori. Bmc Genomics 12:248PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Genetic homogeneity of the critically endangered fan mussel, Pinna nobilis, throughout lagoons of the Gulf of Lion (North-Western Mediterranean Sea)

    1.Ceballos, G. et al. Accelerated modern human–induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Baillie, J. E. ., Hilton-Taylor, C. & Stuart, S. N. 2004 IUCN Red List of Threatened Species. A Global Species Assessment. (2004).3.Hughes, A. R. & Stachowicz, J. J. Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance. Proc. Natl. Acad. Sci. 101, 8998–9002 (2004).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    4.Cowen, R. K. Scaling of connectivity in marine populations. Science 311, 522–527 (2006).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    5.Ronce, O. How does it feel to be like a rolling stone? Ten questions about dispersal evolution. Annu. Rev. Ecol. Evol. Syst. 38, 231–253 (2007).Article 

    Google Scholar 
    6.Cowen, R. K. & Sponaugle, S. Larval dispersal and marine population connectivity. Ann. Rev. Mar. Sci. 1, 443–466 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    7.White, J. W. et al. Connectivity, dispersal, and recruitment. Oceanography 32, 50–59 (2019).Article 

    Google Scholar 
    8.Munday, P. L. et al. Climate change and coral reef connectivity. Coral Reefs 28, 379–395 (2009).ADS 
    Article 

    Google Scholar 
    9.Saunders, M. I. et al. Human impacts on connectivity in marine and freshwater ecosystems assessed using graph theory: A review. Mar. Freshw. Res. 67, 277 (2016).Article 

    Google Scholar 
    10.Peyran, C., Morage, T., Nebot-Colomer, E., Iwankow, G. & Planes, S. Unexpected residual habitats raise hope for the survival of the over the edge of extinction fan mussel, Pinna nobilis, along the Occitan coast (north-western Mediterranean Sea) (2020).11.De Gaulejac, B. Mise en évidence de l’hermaphrodisme successif à maturation asynchrone de Pinna nobilis. Biol. Pathol. Anim. 1, 99–103 (1995).
    Google Scholar 
    12.Butler, A., Vicente, N. & de Gaulejac, B. Ecology of the pterioid bivalves Pinna bicolor Gmelin and Pinna nobilis L. Mar. Life 3, 37–45 (1993).
    Google Scholar 
    13.Trigos, S., Vicente, N., Prado, P. & Espinós, F. J. Adult spawning and early larval development of the endangered bivalve Pinna nobilis. Aquaculture 483, 102–110 (2018).Article 

    Google Scholar 
    14.Öndes, F., Kaiser, M. J. & Güçlüsoy, H. Human impacts on the endangered fan mussel, Pinna nobilis. Aquat. Conserv. Mar. Freshw. Ecosyst. 30, 31–41 (2020).Article 

    Google Scholar 
    15.IOPR. Premier séminaire international sur la grande nacre de Méditerranée : Pinna nobilis. Mém. Inst. Océanogr. Paul Ricard 134 (2003).16.Katsares, V., Tsiora, A., Galinou-Mitsoudi, S. & Imsiridou, A. Genetic structure of the endangered species Pinna nobilis (Mollusca: Bivalvia) inferred from mtDNA sequences. Biologia 63, 412–417 (2008).CAS 
    Article 

    Google Scholar 
    17.Rabaoui, L. et al. Genetic variation among populations of the endangered fan mussel Pinna nobilis (Mollusca: Bivalvia) along the Tunisian coastline. Hydrobiologia 678, 99–111 (2011).CAS 
    Article 

    Google Scholar 
    18.Sanna, D. et al. Mitochondrial DNA reveals genetic structuring of Pinna nobilis across the mediterranean sea. PLoS ONE 8, e67372 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.González-Wangüemert, M. et al. Gene pool and connectivity patterns of Pinna nobilis in the Balearic Islands (Spain, Western Mediterranean Sea): Implications for its conservation through restocking. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 175–188 (2019).Article 

    Google Scholar 
    20.Wesselmann, M. et al. Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis. Sci. Rep. 8, 4770 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    21.Sanna, D. et al. New mitochondrial and nuclear primers for the Mediterranean marine bivalve Pinna nobilis. Mediterr. Mar. Sci. 15, 416 (2014).Article 

    Google Scholar 
    22.Catanese, G. et al. Haplosporidium pinnae sp. nov., a haplosporidan parasite associated with mass mortalities of the fan mussel, Pinna nobilis, in the Western Mediterranean Sea. J. Invertebr. Pathol. 157, 9–24 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    23.Scarpa, F. et al. Multiple non-species-specific pathogens possibly triggered the mass mortality in Pinna nobilis. Life 10, 238 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    24.Grau, A. et al. Wide-geographic and long-term analysis of the role of pathogens in the decline of Pinna nobilis to critically endangered species. (2021).25.Vázquez-Luis, M. et al. Pinna nobilis: A mass mortality event in Western Mediterranean Sea. Front. Mar. Sci. 4, 1–6 (2017).Article 

    Google Scholar 
    26.Cabanellas-Reboredo, M. et al. Tracking a mass mortality outbreak of pen shell Pinna nobilis populations: A collaborative effort of scientists and citizens. Sci. Rep. 9, 13355 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    27.García-March, J. R. et al. Can we save a marine species affected by a highly infective, highly lethal, waterborne disease from extinction?. Biol. Conserv. 243, 108498 (2020).Article 

    Google Scholar 
    28.Kersting, D. et al. Pinna nobilis. The IUCN Red List of Threatened Species 2019. (2019). https://doi.org/10.2305/IUCN.UK.2019-3.RLTS.T160075998A160081499.en29.Ifremer. Réseau de Suivi Lagunaire du Languedoc-Roussillon. (2014).30.García-March, J. R., García-Carrascosa, A. M. & Pena, Á. L. In situ measurement of Pinna nobilis shells for age and growth studies: A new device. Mar. Ecol. 23, 207–217 (2002).ADS 
    Article 

    Google Scholar 
    31.De Gaulejac, B. Etude écophysiologique du mollusque bivalve méditerranéen Pinna nobilis L. reproduction; croissance; respiration. (1993).32.Peyran, C., Planes, S., Tolou, N., Iwankow, G. & Boissin, E. Development of 26 highly polymorphic microsatellite markers for the highly endangered fan mussel Pinna nobilis and cross-species amplification. Mol. Biol. Rep. https://doi.org/10.1007/s11033-020-05338-1 (2020).Article 
    PubMed 

    Google Scholar 
    33.González-Wangüemert, M. et al. Highly polymorphic microsatellite markers for the Mediterranean endemic fan mussel Pinna nobilis. Mediterr. Mar. Sci. 16, 31 (2014).Article 

    Google Scholar 
    34.Van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. & Shipley, P. micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4, 535–538 (2004).Article 
    CAS 

    Google Scholar 
    35.Peakall, R. & Smouse, P. E. GenAlEx 65: Genetic analysis in Excel. Population genetic software for teaching and research: An update. Bioinformatics 28, 2537–2539 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Szpiech, Z. A., Jakobsson, M. & Rosenberg, N. A. ADZE: A rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24, 2498–2504 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).PubMed 
    Article 

    Google Scholar 
    38.Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358 (1984).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N. & Bonhomme, F. GENETIX 4.05, Population genetics software for Windows TM. Université de Montpellier II (2004).40.Robertson, A. & Hill, W. G. Deviations from Hardy–Weinberg proportions: Sampling variances and use in estimation of inbreeding coefficients. Genetics 107, 703–718 (1984).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    41.Raufaste, N. & Bonhomme, F. Properties of bias and variance of two multiallelic estimators of FST. Theor. Popul. Biol. 57, 285–296 (2000).CAS 
    PubMed 
    MATH 
    Article 
    PubMed Central 

    Google Scholar 
    42.Rice, W. R. Analyzing tables of statistical tests. Evolution 43, 223–225 (1989).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    43.R Core Team. R: A Language and Environment for Statistical Computing. (2018).44.Excoffier, L. & Lischer, H. E. L. Arlequin suite ver 35: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    45.Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of Population Structure Using Multilocus Genotype Data. (2000).46.Earl, D. A. & VonHoldt, B. M. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).Article 

    Google Scholar 
    47.Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Puechmaille, S. J. The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: Subsampling and new estimators alleviate the problem. Mol. Ecol. Resour. 16, 608–627 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    49.Li, Y.-L. & Liu, J.-X. StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Mol. Ecol. Resour. 18, 176–177 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    50.Paradis, E. & Schliep, K. ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Queller, D. C. & Goodnight, K. F. Estimating relatedness using genetic markers. Evolution 43, 258 (1989).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    52.Kraemer, P. & Gerlach, G. Demerelate: Calculating interindividual relatedness for kinship analysis based on codominant diploid genetic markers using R. Mol. Ecol. Resour. 17, 1371–1377 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.Hare, M. P., Karl, S. A. & Avise, J. C. Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves. Mol. Biol. Evol. 13, 334–345 (1996).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    54.Giantsis, I. A., Mucci, N., Randi, E., Abatzopoulos, T. J. & Apostolidis, A. P. Microsatellite variation of mussels (Mytilus galloprovincialis) in central and eastern Mediterranean: Genetic panmixia in the Aegean and the Ionian Seas. J. Mar. Biol. Assoc. UK 94, 797–809 (2014).Article 

    Google Scholar 
    55.Tarnowska, K., Chenuil, A., Nikula, R., Féral, J. & Wolowicz, M. Complex genetic population structure of the bivalve Cerastoderma glaucum in a highly fragmented lagoon habitat. Mar. Ecol. Prog. Ser. 406, 173–184 (2010).ADS 
    Article 

    Google Scholar 
    56.Šegvić-Bubić, T. et al. Translocation and aquaculture impact on genetic diversity and composition of wild self-sustainable Ostrea edulis populations in the Adriatic sea. Front. Mar. Sci. 7, 1–13 (2020).Article 

    Google Scholar 
    57.Dupont, L., Ellien, C. & Viard, F. Limits to gene flow in the slipper limpet Crepidula fornicata as revealed by microsatellite data and a larval dispersal model. Mar. Ecol. Prog. Ser. 349, 125–138 (2007).ADS 
    Article 

    Google Scholar 
    58.Ellegren, H. & Ellegren, N. Determinants of genetic diversity. Nat. Publ. Gr. 17, 422–433 (2016).CAS 

    Google Scholar 
    59.Mendo, T., Moltschaniwskyj, N., Lyle, J. M., Tracey, S. R. & Semmens, J. M. Role of density in aggregation patterns and synchronization of spawning in the hermaphroditic scallop Pecten fumatus. Mar. Biol. 161, 2857–2868 (2014).Article 

    Google Scholar 
    60.Žuljević, A., Despalatović, M., Cvitković, I., Morton, B. & Antolić, B. Mass spawning by the date mussel Lithophaga lithophaga. Sci. Rep. 8, 10781 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    61.Lamare, M. D. & Stewart, B. G. Mass spawning by the sea urchin Evechinus chloroticus (Echinodermata: Echinoidea) in a New Zealand fiord. Mar. Biol. 132, 135–140 (1998).Article 

    Google Scholar 
    62.Soong, K., Chang, D. & Chao, S. Presence of spawn-inducing pheromones in two brittle stars (Echinodermata: Ophiuroidea). Mar. Ecol. Prog. Ser. 292, 195–201 (2005).ADS 
    Article 

    Google Scholar 
    63.Watson, G., Bentley, M., Gaudron, S. & Hardege, J. The role of chemical signals in the spawning induction of polychaete worms and other marine invertebrates. J. Exp. Mar. Biol. Ecol. 294, 169–187 (2003).CAS 
    Article 

    Google Scholar 
    64.Gaulejac, B. D., Henry, M. & Vicente, N. An ultrastructural study of gametogenesis of the marine bivalve Pinna nobilis (Linnaeus 1758) II, Spermatogenesis. J. Molluscan Stud. 61, 393–403 (1995).Article 

    Google Scholar 
    65.Cabanellas-Reboredo, M. et al. Recruitment of Pinna nobilis (Mollusca: Bivalvia) on artificial structures. Mar. Biodivers. Rec. 2, e126 (2009).Article 

    Google Scholar 
    66.Prado, P. et al. Breeding, planktonic and settlement factors shape recruitment patterns of one of the last remaining major population of Pinna nobilis within Spanish waters. Hydrobiologia 847, 771–786 (2020).Article 

    Google Scholar 
    67.Deudero, S. et al. Reproductive investment of the pen shell Pinna nobilis Linnaeus, 1758 in Cabrera National Park (Spain). Mediterr. Mar. Sci. 18, 271 (2017).Article 

    Google Scholar 
    68.Costantini, F., Rugiu, L., Cerrano, C. & Abbiati, M. Living upside down: Patterns of red coral settlement in a cave. Mediterr. Mar. Sci. https://doi.org/10.7717/peerj.4649 (2018).Article 

    Google Scholar 
    69.Cárdenas, L., Castilla, J. C. & Viard, F. Hierarchical analysis of the population genetic structure in Concholepas concholepas, a marine mollusk with a long-lived dispersive larva. Mar. Ecol. 37, 359–369 (2016).ADS 
    Article 

    Google Scholar 
    70.Morvezen, R. et al. Genetic structure of a commercially exploited bivalve, the great scallop Pecten maximus, along the European coasts. Conserv. Genet. 17, 57–67 (2016).Article 

    Google Scholar 
    71.Borsa, P., Jarne, P., Belkhir, K. & Bonhomme, F. Genetic structure of the palourde 103. Genet. Evol. Aquat. Org. 103, 1–12 (1994).
    Google Scholar 
    72.Skalamera, J., Renaud, F., Raymond, M. & de Meeûs, T. No evidence for genetic differentiation of the mussel Mytilus galloprovincialis between lagoons and the seaside. Mar. Ecol. Prog. Ser. 178, 251–258 (1999).ADS 
    Article 

    Google Scholar 
    73.Boissin, E., Hoareau, T. B. & Berrebi, P. Effects of current and historic habitat fragmentation on the genetic structure of the sand goby Pomatoschistus minutus (Osteichthys, Gobiidae). Biol. J. Linn. Soc. 102, 175–198 (2011).Article 

    Google Scholar 
    74.Pérez-Ruzafa, A. et al. Connectivity between coastal lagoons and sea: Asymmetrical effects on assemblages’ and populations’ structure. Estuar. Coast. Shelf Sci. 216, 171–186 (2019).ADS 
    Article 

    Google Scholar 
    75.Frankham, R. Quantitative genetics in conservation biology. Genet. Res. 74, 237–244 (1999).CAS 
    PubMed 
    Article 

    Google Scholar  More