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    Scientists warn deal to save biodiversity is in jeopardy

    A strawberry poison-dart frog (Oophaga pumilio) in Guatemala. Biodiversity is at risk as talks on a deal to protect it founder.Credit: Yuri Cortez/AFP via Getty

    Some conservation scientists are warning that a global deal to protect the environment is under threat after negotiations stalled during international talks in Nairobi last week. They are calling on global leaders to rescue the talks — and biodiversity — from the brink. Others are more hopeful that, although progress has been slow, a deal will be struck by the end of the year.Negotiators from around 200 countries that have signed up to the United Nations Convention on Biological Diversity (CBD) met in Nairobi from 21 to 26 June to thrash out key details of the deal, known as the post-2020 global biodiversity framework. But the talks made such little progress that many scientists are worried that nations will be unable to finalize the deal at the UN biodiversity summit in Montreal, Canada, in December. A key sticking point is how much funding rich nations will provide to low-income nations. Failure to agree on the framework at this summit — the 15th meeting of the Conference of the Parties (COP15) — will be devastating for the natural world, they say.“This is a huge missed opportunity and puts the framework in jeopardy,” says Brian O’Donnell, director of the Campaign for Nature in Washington DC, a partnership of private charities and conservation organizations advocating a deal to safeguard biodiversity.The framework consists of 4 broad goals, including reining in species extinction, and 21 targets — most of them quantitative — such as protecting at least 30% of the world’s land and seas. Without a deal, estimates say, one million plant and animal species could go extinct in the next few decades because of climate change, disease and human actions, among other triggers.Researchers were relieved when the CBD announced earlier this month that COP15 would take place in Montreal instead of Kunming, China, where lockdowns to quash SARS-CoV-2 infections could have prevented the meeting. The COVID-19 pandemic has already delayed in-person CBD meetings for two years, and threatened to derail the summit.Stalling tacticsSome conservation groups said that a few nations bore most of the responsibility for impeding progress. Marco Lambertini, head of conservation organization WWF International, based in Gland, Switzerland, referred in a statement to “a small number of countries, Brazil first and foremost, that are actively working to undermine the talks”.Others who were at the conference spoke on the condition of anonymity because parts of the negotiations are confidential. They say that Brazil asked for changes to the text simply to slow down the process, and argued against essential elements.Nature contacted representatives of Brazil for a response but did not receive a reply by the time of publication.Francis Ogwal, co-chair of the framework negotiations working group, acknowledged that the talks had not advanced as much as had been hoped. But he is buoyed by some headway gained on targets to improve access to nature in urban areas and to increase scientific and technological capacity in lower-income nations. Ogwal is hopeful that countries will iron out further differences at an extra meeting scheduled for just days before COP15.“There are still some big disagreements. We are not yet at the level we expected. But come December, we shall have a framework in good shape,” Ogwal told reporters at a press briefing on 26 June.Lack of leadershipBut scientists and conservation groups say political leadership is urgently needed to save the deal. In an open letter to UN secretary-general António Guterres and heads of state of CBD member nations, a group of eight organizations that support conservation and Indigenous people’s rights said that a lack of management is stalling the negotiations.“There is a notable absence of the high level political engagement, will and leadership to drive through compromise and to guide and inspire the commitments that are required,” the letter says.Some countries have restated that they back the biodiversity talks. On 26 June, UK Prime Minister Boris Johnson assured Canadian Prime Minister Justin Trudeau of his support for the December summit in Montreal. The two were speaking before the meeting of the G7 group of industrialized nations in Krün, Germany.In addition, some “hero” countries including Costa Rica and Columbia worked particularly hard in Nairobi to drive agreement, says O’Donnell.Speaking on condition of anonymity so as not to offend the CBD, others criticized the structure and organization of the Nairobi meeting, which they say didn’t help negations to move forwards. “The session facilitators were not able to shepherd negotiations towards consensus,” they say. Nature contacted the CBD for a response but did not hear back in time for publication.But despite the setbacks, some scientists are still hopeful that countries can strike a deal. “The negotiations are typically well-spirited. There is even a sense of collaboration arising,” says Juha Siikamäki, chief economist at the International Union for Conservation of Nature in Gland, who attended the Nairobi meeting.Elizabeth Mrema, executive secretary of the CBD, says countries will have to compromise. “Biodiversity is too important to fail,” she says. More

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    Mangrove dispersal disrupted by projected changes in global seawater density

    Mangrove forests thrive along tropical and subtropical shorelines and their distribution extends to warm temperate regions1. They are globally recognized for the valuable ecosystem services they provide2 but are expected to be substantially influenced by climate change-related physical processes in the future3,4. Under warming winter temperatures, poleward expansion is predicted for mangroves5,6, with potential implications for ecosystem structure and functioning, as well as human livelihoods and well-being7,8. The global distribution, abundance and species richness of mangroves is governed by a broad range of biotic and environmental factors, including temperature and precipitation9 and diverse geomorphological and hydrological gradients10. Climate and aspects related to coastal geography (for example, floodplain area) determine the availability of suitable habitat for establishment11,12. However, the potential for mangroves to track changing environmental conditions and expand their distributions ultimately depends on dispersal11,13. The importance of dispersal in controlling mangrove distributions has been demonstrated by mangrove distributional responses to historical climate variability14, past mangrove (re)colonization of oceanic islands15 and from the long-term survival of mangrove seedlings planted beyond natural range limits16. As such, quantifying changes in the factors that influence dispersal is important for understanding climate-driven distributional responses of mangroves under future climate conditions.In mangroves, dispersal is accomplished by buoyant seeds and fruits (hereafter referred to as ‘propagules’). In combination with prevailing currents, the spatial scale of this process, ranging from local retention to transoceanic dispersal over thousands of kilometres13, is determined by propagule buoyancy17, that is, the density difference between that of propagules and the surrounding water. Hence, the course of dispersal trajectories for propagules from these species depends on the interaction between spatiotemporal changes in both propagule density and that of the surrounding water, rendering this process sensitive to climate-driven changes in coastal and open-ocean water properties. The biogeographic implications of such density differences were recognized more than a century ago by Henry Brougham Guppy, who discussed18 ‘the far-reaching influence on plant-distribution and on plant-development that the relation between the specific weight of seeds and fruits and the density of sea-water must possess’.Since the time of Guppy’s early observations, climate change from human activities has driven pronounced changes in ocean temperature and salinity, with further changes predicted throughout the twenty-first century19. Ocean density is a nonlinear function of temperature, salinity and pressure20; therefore, these changes may influence dispersal patterns of mangrove propagules by altering their buoyancy and floating orientation. As Guppy noted18, ‘[for] plants whose seeds or fruits are not much lighter than seawater […] the effect of increased density of the water is to extend the flotation period’ or ‘to increase the number that floated for a given period’. Guppy also reported that the seedlings of the widespread mangrove genera Rhizophora and Bruguiera present exceptional examples of propagules with densities somewhere between seawater and freshwater18. Previous studies of the impacts of climate change on mangroves have focused on factors such as sea level rise, altered precipitation regimes and increasing temperature and storm frequency4,21,22,23 but the potential impact of climate-driven changes in seawater properties on mangroves has not yet been examined. This is somewhat surprising, as the ocean is the primary dispersal medium of this ‘sea-faring’ coastal vegetation and dispersal is a key process that governs a species’ response to climate change by changing its geographical range. This knowledge gap contrasts with recent efforts to expose links between climate change and dispersal in other ecologically important marine taxa such as zooplankton and fish species24,25,26,27.In this study, we investigate predicted changes in sea surface temperature (SST), sea surface salinity (SSS) and sea surface density (SSD) for coastal waters bordering mangrove forests (hereafter referred to as ‘coastal mangrove waters’), over the next century. Using a biogeographic classification system for coastal and shelf areas28, we examine spatiotemporal changes in these surface ocean properties, with a particular focus on the world’s two major mangrove diversity hotspots: (1) the Atlantic East Pacific (AEP) region, including all of the Americas, West and Central Africa and (2) the Indo West Pacific (IWP) region, extending from East Africa eastwards to the islands of the central Pacific1. Finally, we synthesize available data on the density of mangrove propagules for different mangrove species and explore the potential impact of climate-driven changes in SSD on propagule dispersal.To assess changes in SST and SSS throughout the global range of mangrove forests, we used present (2000–2014) and future (2090–2100) surface ocean properties from the Bio-ORACLE database29,30. SSD estimates were derived from these variables using the UNESCO EOS-80 equation of state polynomial for seawater31. Changes in SST, SSS and SSD (Fig. 1) were calculated for four representative concentration pathways (RCPs) and derived for coastal waters closest to the 583,578 polygon centroids from the 2015 Global Mangrove Watch (GMW) database32. After removing duplicates, our dataset contained 10,108 unique mangrove occurrence locations, with corresponding present conditions and predicted future changes in mean SST, SSS and SSD. Under the low-warming scenario RCP 2.6, mean SST of coastal mangrove waters is predicted to change by +0.64 (±0.11) °C and mean SSS by −0.06 (±0.25) practical salinity units (PSU). Combined, this results in an average change in mean SSD of −0.25 (±0.20) kg m−3 in coastal mangrove waters by the late twenty-first century (Supplementary Table 1). These values roughly double under RCP 4.5 (Supplementary Table 2), while under RCP 6.0, a change of +1.69 (±0.14) °C in mean SST, −0.21 (±0.42) PSU in mean SSS and −0.71 (±0.32) kg m−3 in mean SSD is predicted (Supplementary Table 3). Under RCP 8.5, our study predicts a change in SST of +2.84 (±0.21) °C (range 2.11–4.01 °C), a change in SSS of −0.30 (±0.74) PSU (−2.01–1.26 PSU) and a corresponding change in SSD of −1.17 (±0.56) kg m−3 (−2.53–0.03 kg m−3) (Supplementary Table 4).Fig. 1: Global map showing the change in sea surface variables across mangrove bioregions under RCP 8.5.a–c, Change in SST (a), SSS (b) and SSD (c). Changes in SST and SSS are based on present-day (2000–2014) and future (2090–2100) marine fields from the Bio-ORACLE database29,30, from which SSD data were derived. The vertical line (19° E) separates the two major mangrove bioregions: the AEP and IWP.Full size imageSpatial variability in predicted surface ocean property changes was examined by considering the two major mangrove bioregions (AEP and IWP) (Fig. 2) and using the Marine Ecoregions of the World (MEOW) biogeographic classification28 (Fig. 3). Both the range and changes in mean SST were comparable for the AEP and IWP mangrove bioregions, for all respective RCP scenarios (Fig. 2a and Supplementary Tables 1–4). Under RCP 8.5, mean SST in both mangrove bioregions is predicted to warm ~2.8 °C by 2100, which is roughly 4.5 times the predicted increase in mean SST under RCP 2.6 (Supplementary Tables 1 and 4). Predictions for the RCP 8.5 scenario are generally consistent with reported global ocean temperature trends33 and show that the greatest warming occurs in coastal waters near the Galapagos Islands (change in mean SST of 3.92 ± 0.06 °C). Pronounced SST increases are also predicted for Hawaii (change in mean SST of 3.36 ± 0.05 °C), the Southeast Australian Shelf (3.30 ± 0.25 °C), Northern and Southern New Zealand (3.25 ± 0.07 °C and 3.34 ± 0.02 °C, respectively), Warm Temperate Northwest Pacific (3.27 ± 0.16 °C), the Red Sea and Gulf of Aden (3.24 ± 0.08 °C), Somali/Arabian Coast (3.23 ± 0.15 °C), South China Sea (3.07 ± 0.10 °C), the Tropical East Pacific (3.09 ± 0.15 °C) and the Warm Temperate Northwest Atlantic (3.14 ± 0.13 °C) (Fig. 3b and Supplementary Tables 4).Fig. 2: Change in surface ocean properties for coastal waters bordering mangrove forests and in the two major mangrove bioregions, the AEP and IWP, for different RCPs.a–c, Variation in SST (a), SSS (b) and SSD (c) under various RCP scenarios. Grey indicates global distribution (n = 10,108), orange denotes AEP (n = 3,190) and green represents IWP (n = 6,918). Data for SST and SSS consist of present-day (2000–2014) and future (2090–2100) marine fields from the Bio-ORACLE database29,30, from which SSD data were derived. The cat-eye plots50 show the distribution of the data. Median and mean values are indicated with black and white circles, respectively, and the vertical lines represent the interquartile range.Full size imageFig. 3: Global spatial variability in SST, SSS and SSD for coastal waters bordering mangrove forests under RCP 8.5.a, Global map showing the provinces (colour code and numbers) from the MEOW database28 used to investigate spatial patterns in mangrove coastal ocean water changes by 2100. b–d, Longitudinal gradient of the change in SST (b), SSS (c) and SSD (d) under RCP 8.5 in the AEP and the IWP mangrove bioregions; circles are coloured according to the MEOW province in which respective mangrove sites are located.Full size imagePredicted SSS changes exhibit an opposite trend in the AEP and IWP bioregions, with increased salinity in the AEP and reduced salinity in the IWP under global warming (RCP 2.6–RCP 8.5; Fig. 2b); this is reflected in contrasting SSD changes in both mangrove bioregions (Fig. 2c) and associated with predicted global changes in precipitation, with extensions of the rainy season over most of the monsoon domains, except for the American monsoon34. Under RCP 8.5, the spatially averaged change in mean SSS is +0.51 (±0.57) PSU in the AEP and −0.68 (±0.44) PSU in the IWP region. The maximum decrease in mean SSS (−2.01 PSU) is predicted for the Gulf of Guinea in the AEP bioregion (Fig. 3c and Supplementary Table 4). Within the IWP, the Western Indian Ocean region shows little or no changes in SSS, which contrasts with the pronounced freshening trends predicted in the eastern part of this ocean basin and the Tropical West Pacific (Figs. 1b and 3c). Increased freshening is predicted in the Bay of Bengal (SSS change: −1.17 ± 0.43 PSU), the Sunda Shelf (SSS change: −1.21 ± 0.29 PSU) and the Western Coral Triangle province (mean SSS change: −0.80 ± 0.17 PSU) (Fig. 3c and Supplementary Table 4). Within the AEP, salinity increases exceed +0.96 PSU in the Tropical Northwestern Atlantic, +0.80 in the Warm Temperate Northwest Atlantic and +0.68 in the West African Transition (Fig. 3c and Supplementary Table 4). The spatial heterogeneity in SSS across the global range of mangrove forests corresponds with observed changes in SSS35. Trends in SSD (Fig. 3d) strongly track changes in SSS (Fig. 3c) rather than SST. All RCP scenarios predict an overall decrease in SSD for both mangrove bioregions; however, the predicted decrease in SSD in the IWP region was a factor of 2 (RCP 6.0) and 2.5 (RCP 2.6, RCP 4.5 and RCP 8.5) stronger than in the AEP (Figs. 2 and 3d and Supplementary Tables 1–4).Propagule density values from our literature survey range from 1,080 kg m−3 for different mangrove species (Fig. 4 and Supplementary Table 5). The low densities reported for Heritiera littoralis propagules provide a strong contrast with the near-seawater propagule densities reported for Avicennia and members of the Rhizophoraceae (Bruguiera, Rhizophora and Ceriops). Floating characteristics of the latter may be particularly sensitive to changes in SSD. To illustrate the potential influence of changing ocean conditions on mangrove propagule dispersal, we considered threshold water density values (1,020 and 1,022 kg m−3) that are within the range where elongated propagules of important mangrove genera tend to change floating orientation (Fig. 4a). More specifically, we determined the ocean surface area with an SSD below or equal to these thresholds under different climate change scenarios (Fig. 5). Under RCP 8.5, the ocean surface covered by mangrove coastal waters (coastal waters bordering present mangrove forests) with a density ≤1,020 kg m−3 increases ~27% by 2100, notably more so in the IWP (~37%) than in the AEP (~6%) (Supplementary Table 6). A threshold of 1,022 kg m−3 results in increases of roughly +11% (global), +12% (IWP) and +8% (AEP) (Supplementary Table 7). Similar spatial patterns are observed for open-ocean waters within the global latitudinal range of mangroves (Fig. 5 and Supplementary Figs. 1 and 2).Fig. 4: Potential effect of future declines in SSD on mangrove propagule dispersal.a, Range of reported propagule density values for wide-ranging mangrove species and present and future range of SSD for coastal waters along the range of those mangrove species. Mangrove propagule data are extracted from the literature (Supplementary Table 5). H. lit, Heritiera littoralis; X. gra, Xylocarpus granatum; A. ger, Avicennia germinans; A. mar, Avicennia marina; B. gym, Bruguiera gymnorrhiza; C. tag, Ceriops tagal; R. man, Rhizophora mangle; R. muc, Rhizophora mucronata. Bottom part adapted from ref. 51. b, Conceptual figure of the potential effects of ocean warming and freshening on mangrove propagule dispersal. Ocean warming and freshening drive changes in SSD and may reduce the timeframe for opportunistic colonization. For a propagule with a specific density and floating profile under present surface ocean conditions, reduced SSD of coastal and open-ocean waters may reduce floatation time (shaded area) and hence, reduce the proportion of long-distance dispersers. For simplicity, the density of propagules is assumed to increase linearly over time, although the actual increase may be nonlinear.Full size imageFig. 5: Future changes in SSD.a–d, Spatial extent of coastal and open-ocean surface waters with a density ≤1,020 kg m−3 (a,b) and 1,022 kg m−3 (c,d), for present (2000–2014) (a,c) and future (2090–2100; RCP 8.5) (b,d) scenarios. Data are shown for surface ocean waters within the global latitudinal range of mangrove forests (between 32° N and 38° S). The two density thresholds considered are within the range of densities at which mangrove propagule buoyancy and floating orientation of several mangrove genera change, as reported in available literature. Black dots along the coast represent the global mangrove extent from the 2015 GMW dataset32. Magenta-coloured circles represent SSD values More

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    Microbial community structure is stratified at the millimeter-scale across the soil–water interface

    McClain ME, Boyer EW, Dent CL, Gergel SE, Grimm NB, Groffman PM, et al. Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems. 2003;6:301–12.CAS 
    Article 

    Google Scholar 
    Borch T, Kretzschmar R, Kappler A, Van Cappellen P, Ginder-Vogel M, Voegelin A, et al. Biogeochemical redox processes and their impact on contaminant dynamics. Environ Sci Technol. 2010;44:15–23.CAS 
    Article 

    Google Scholar 
    Stegen JC, Lin XJ, Konopka AE, Fredrickson JK. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 2012;6:1653–64.CAS 
    Article 

    Google Scholar 
    Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA. 2015;112:E1326–32.CAS 
    Article 

    Google Scholar 
    Behrendt L, Larkum AWD, Trampe E, Norman A, Sorensen SJ, Kuhl M. Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella. ISME J. 2012;6:1222–37.CAS 
    Article 

    Google Scholar 
    Becker KW, Elling FJ, Schroder JM, Lipp JS, Goldhammer T, Zabel M, et al. Isoprenoid quinones resolve the stratification of redox processes in a biogeochemical continuum from the photic zone to deep anoxic sediments of the Black Sea. Appl Environ Microbiol. 2018;84:e02736–17.CAS 
    Article 

    Google Scholar 
    Locey KJ, Muscarella ME, Larsen ML, Bray SR, Jones SE, Lennon JT. Dormancy dampens the microbial distance-decay relationship. Phil Trans R Soc B. 2020;375:20190243.CAS 
    Article 

    Google Scholar 
    Blagodatskaya E, Kuzyakov Y. Active microorganisms in soil: critical review of estimation criteria and approaches. Soil Biol Biochem. 2013;67:192–211.CAS 
    Article 

    Google Scholar 
    Meyer KM, Memiaghe H, Korte L, Kenfack D, Alonso A, Bohannan BJM. Why do microbes exhibit weak biogeographic patterns? ISME J. 2018;12:1404–13.Article 

    Google Scholar 
    Xue R, Zhao KK, Yu XL, Stirling E, Liu S, Ye SD, et al. Deciphering sample size effect on microbial biogeographic patterns and community assembly processes at centimeter scale. Soil Biol Biochem. 2021;156:108218.CAS 
    Article 

    Google Scholar 
    Morriss A, Meyer K, Bohannan B. Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms. Phil Trans R Soc B. 2020;375:20190244.Article 

    Google Scholar 
    Armitage DW, Jones SE. How sample heterogeneity can obscure the signal of microbial interactions. ISME J. 2019;13:2639–46.Article 

    Google Scholar 
    Dini-Andreote F, Kowalchuk GA, Prosser JI, Raaijmakers JM. Towards meaningful scales in ecosystem microbiome research. Environ Microbiol. 2021;23:1–4.Article 

    Google Scholar 
    Meyerhof MS, Wilson JM, Dawson MN, Beman JM. Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau. Environ Microbiol. 2016;18:4907–19.CAS 
    Article 

    Google Scholar 
    Zhou ZC, Meng H, Liu Y, Gu JD, Li M. Stratified bacterial and archaeal community in mangrove and intertidal wetland mudflats revealed by high throughput 16S rRNA gene sequencing. Front Microbiol. 2017;8:02148.Article 

    Google Scholar 
    Gutierrez-Preciado A, Saghai A, Moreira D, Zivanovic Y, Deschamps P, Lopez-Garcia P. Functional shifts in microbial mats recapitulate early Earth metabolic transitions. Nat Ecol Evol. 2018;2:1700–8.Article 

    Google Scholar 
    Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–7.CAS 
    Article 

    Google Scholar 
    Murase J, Frenzel P. A methane-driven microbial food web in a wetland rice soil. Environ Microbiol. 2007;9:3025–34.CAS 
    Article 

    Google Scholar 
    Reim A, Lüke C, Krause S, Pratscher J, Frenzel P. One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME J. 2012;6:2128–39.CAS 
    Article 

    Google Scholar 
    Peiffer S, Kappler A, Haderlein SB, Schmidt C, Byrne JM, Kleindienst S, et al. A biogeochemical–hydrological framework for the role of redox-active compounds in aquatic systems. Nat Geosci. 2021;14:264–72.CAS 
    Article 

    Google Scholar  More

  • in

    eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages

    Zou, K. et al. eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci. Total Environ. 702, 134704 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Almond, R., Grooten, M. & Peterson, T. Living Planet Report 2020-Bending the Curve of Biodiversity Loss (World Wildlife Fund, 2020).
    Google Scholar 
    Beverton, R. Fish resources; threats and protection. Neth. J. Zool. 42, 139–175 (1991).Article 

    Google Scholar 
    Jackson, S. & Head, L. Australia’s mass fish kills as a crisis of modern water: Understanding hydrosocial change in the Murray-Darling Basin. Geoforum 109, 44–56 (2020).Article 

    Google Scholar 
    Rees, H. C. et al. REVIEW: The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51, 1450–1459 (2014).CAS 
    Article 

    Google Scholar 
    Rees, H. C. et al. The application of eDNA for monitoring of the Great Crested Newt in the UK. Ecol. Evol. 4, 4023–4032 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, C. et al. Research on the biodiversity of Qinhuai River based on environmental DNA metabacroding. Acta Ecol. Sin. 42, 611–624 (2022).Article 

    Google Scholar 
    Deiner, K., Walser, J.-C., Mächler, E. & Altermatt, F. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol. Cons. 183, 53–63 (2015).Article 

    Google Scholar 
    Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Miralles, L., Parrondo, M., Hernandez de Rojas, A., Garcia-Vazquez, E. & Borrell, Y. J. Development and validation of eDNA markers for the detection of Crepidula fornicata in environmental samples. Mar. Pollut. Bull. 146, 827–830 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z. Estimation of fish biomass using environmental DNA. PLoS ONE 7, e35868 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aglieri, G. et al. Environmental DNA effectively captures functional diversity of coastal fish communities. Mol. Ecol. 30, 3127–3139 (2020).PubMed 
    Article 

    Google Scholar 
    Yang, H. et al. Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci. Rep. 11, 24241 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Altermatt, F. et al. Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems. Oikos 129, 607–618 (2020).Article 

    Google Scholar 
    Stat, M. et al. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conserv. Biol. 33, 196–205 (2019).PubMed 
    Article 

    Google Scholar 
    Hallam, J., Clare, E. L., Jones, J. I. & Day, J. J. Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods. Environ. DNA 3, 1247–1266 (2021).Article 

    Google Scholar 
    Gao, W. Beijing Vertebrate Key (Beijing Publishing House, 1994).
    Google Scholar 
    Wang, H. Beijing Fish and Amphibians and Reptiles (Beijing Publishing House, 1994).
    Google Scholar 
    Chen, W., Hu, D. & Fu, B. Research on Biodiversity of Beijing Wetland (Science Press, 2007).
    Google Scholar 
    Zhang, C. et al. Fish species diversity and conservation in Beijing and adjacent areas. Biodivers. Sci. 19, 597–604 (2011).Article 

    Google Scholar 
    Yamamoto, S. et al. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep. 7, 40368 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shaw, J. L. A. et al. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol. Cons. 197, 131–138 (2016).Article 

    Google Scholar 
    Fu, M., Xiao, N., Zhao, Z., Gao, X. & Li, J. Effects of Urbanization on Ecosystem Services in Beijing. Res. Soil Water Conserv. 23, 235–239 (2016).
    Google Scholar 
    Hao, L. & Sun, G. Impacts of urbanization on watershed ecohydrological processes: progresses and perspectives. Acta Ecol. Sin. 41, 13–26 (2021).
    Google Scholar 
    Su, G. et al. Human impacts on global freshwater fish biodiversity. Science 371, 835–838 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Yan, B. et al. Effects of urban development on soil microbial functional diversity in Beijing. Res. Environ. Sci. 29, 1325–1335 (2016).CAS 

    Google Scholar 
    Xiao, N., Gao, X., Li, J. & Bai, J. Evaluation and Conservation Measures of Beijing Biodiversity (China Forestry Publishing House, 2018).
    Google Scholar 
    Xu, S., Wang, Z., Liang, J. & Zhang, S. Use of different sampling tools for comparison of fish-aggregating effects along horizontal transect at two artificial reef sites in Shengsi. J. Fish. China 40, 820–831 (2016).
    Google Scholar 
    Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2, 150088 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (Oxford, England) 30, 614–620 (2014).CAS 
    Article 

    Google Scholar 
    Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, 884–890 (2018).Article 
    CAS 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (Oxford, England) 26, 2460–2461 (2010).CAS 
    Article 

    Google Scholar 
    Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Iwasaki, W. et al. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol. Biol. Evol. 30, 2531–2540 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, H. Beijing Fish Records (Beijing Publishing House, 1984).
    Google Scholar 
    Du, L. et al. Fish community characteristics and spatial pattern in major rivers of Beijing City. Res. Environ. Sci. 32, 447–457 (2019).
    Google Scholar 
    Shen, W. & Ren, H. TaxonKit: A practical and efficient NCBI taxonomy toolkit. J. Genet. Genomics 48, 844–850 (2021).PubMed 
    Article 

    Google Scholar 
    Karr, J. R. Assessment of biotic integrity using fish communities. Fisheries 6, 21–27 (1981).Article 

    Google Scholar 
    Zhang, C. & Zhao, Y. Fishes in Beijing and Adjacent Areas (China. Science Press, 2013).
    Google Scholar 
    Wu, H. & Zhong, J. Fauna Sinica, Osteichthyes, Perciformess(Five),Gobioidei (Science Press, 2008).
    Google Scholar 
    Di, Y. et al. Distribution of fish communities and its influencing factors in the Nansha and Beijing sub-center reaches of the Beiyun River. Acta Sci. Circumst. 41, 156–163 (2020).
    Google Scholar 
    Walters, D. M., Freeman, M. C., Leigh, D. S., Freeman, B. J. & Pringle, C. M. in Effects of Urbanization on Stream Ecosystems Vol. 47 American Fisheries Society Symposium 69–85 (2005).Hu, X., Zuo, D., Liu, B., Huang, Z. & Xu, Z. Quantitative analysis of the correlation between macrobenthos community and water environmental factors and aquatic ecosystem health assessment in the North Canal River Basin of Beijing. Environ. Sci. 43, 247–255 (2022).
    Google Scholar 
    Kadye, W. T., Magadza, C. H. D., Moyo, N. A. G. & Kativu, S. Stream fish assemblages in relation to environmental factors on a montane plateau (Nyika Plateau, Malawi). Environ. Biol. Fishes 83, 417–428 (2008).Article 

    Google Scholar 
    Smith, T. A. & Kraft, C. E. Stream fish assemblages in relation to landscape position and local habitat variables. Trans. Am. Fish. Soc. 134, 430–440 (2005).Article 

    Google Scholar 
    Blabolil, P. et al. Environmental DNA metabarcoding uncovers environmental correlates of fish communities in spatially heterogeneous freshwater habitats. Ecol. Ind. 126, 107698 (2021).CAS 
    Article 

    Google Scholar 
    Xie, R. et al. eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity. Environ. Res. 201, 111602 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Qu, C. et al. Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding. Sci. Rep. 10, 16715 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pont, D. et al. Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Sci. Rep. 8, 10361 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Doble, C. J. et al. Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika. Environ. DNA 2, 24–41 (2020).Article 

    Google Scholar 
    Xu, N. et al. Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA. Sci. Nat. 105, 62 (2018).Article 
    CAS 

    Google Scholar 
    Laramie, M. B., Pilliod, D. S. & Goldberg, C. S. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol. Cons. 183, 29–37 (2015).Article 

    Google Scholar 
    Harper, L. R. et al. Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius). Freshw. Biol. 64, 93–107 (2019).CAS 
    Article 

    Google Scholar 
    Ushio, M. et al. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding Metagenomics 2, e2329 (2018).
    Google Scholar 
    Evans, N. T. et al. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol. Ecol. Resour. 16, 29–41 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: and this is not optional. Front. Microbiol. 8, 2224 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Harrison, J. B., Sunday, J. M. & Rogers, S. M. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc. Biol. Sci. 286, 20191409 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kelly, R. P., Shelton, A. O. & Gallego, R. Understanding PCR processes to draw meaningful conclusions from environmental DNA studies. Sci. Rep. 9, 12133 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Civade, R. et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11, e0157366 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Barnes, M. A. et al. Environmental conditions influence eDNA persistence in aquatic systems. Environ. Sci. Technol. 48, 1819–1827 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Shogren, A. J. et al. Water flow and biofilm cover influence environmental DNA detection in recirculating streams. Environ. Sci. Technol. 52, 8530–8537 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhao, B., van Bodegom, P. M. & Trimbos, K. The particle size distribution of environmental DNA varies with species and degradation. Sci. Total Environ. 797, 149175 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    American dog ticks along their expanding range edge in Ontario, Canada

    Sonenshine, D. E. Insects of Virginia No. 13. Ticks of Virginia (Acari: Metastigmata). Res. Div. Bull. 139, 1–44 (1979).
    Google Scholar 
    Lindquist, E. E. et al. A Handbook to the Ticks of Canada (Ixodida: Ixodidae, Argasidae) (Biological Survey of Canada, 2016).
    Google Scholar 
    Campbell, A. & MacKay, P. R. Distribution of the American dog tick, Dermacentor variabilis (Say), and its small-mammal hosts in relation to vegetation types in a study area in Nova Scotia. Can. J. Zool. 57, 1950–1959 (1979).CAS 
    PubMed 

    Google Scholar 
    Barker, I. K. et al. Distribution of the Lyme disease vector, Ixodes dammini (Acari: Ixodidae) and isolation of Borrelia burgdorferi in Ontario, Canada. J. Med. Entomol. 29, 1011–1022 (1992).CAS 
    PubMed 

    Google Scholar 
    Morshed, M. G., Scott, J. D., Fernando, K., Mann, R. B. & Durden, L. A. Lyme disease spirochete, Borrelia burgdorferi endemic at epicenter in Rondeau Provincial Park, Ontario. J. Med. Entomol. 40, 91–94 (2003).PubMed 

    Google Scholar 
    Nelder, M. P. et al. Population-based passive tick surveillance and detection of expanding foci of blacklegged ticks Ixodes scapularis and the Lyme disease agent Borrelia burgdorferi in Ontario, Canada. PLoS ONE 9, e105358 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Clow, K. M. et al. Distribution of ticks and the risk of Lyme disease and other tick-borne pathogens of public health significance in Ontario, Canada. Vector Borne Zoonotic Dis. 16, 215–222 (2016).PubMed 

    Google Scholar 
    Smith, K. A. et al. Tick infestations of wildlife and companion animals in Ontario, Canada, with detection of human pathogens in Ixodes scapularis ticks. Ticks Tick Borne Dis. 10, 72–76 (2019).PubMed 

    Google Scholar 
    Scott, J. D. et al. Extensive distribution of the Lyme disease bacterium, Borrelia burgdorferi sensu lato, in multiple tick species parasitizing avian and mammalian hosts across Canada. Healthcare 6, 131 (2018).PubMed Central 

    Google Scholar 
    James, A. M., Burdett, C., McCool, M. J., Fox, A. & Riggs, P. The geographic distribution and ecological preferences of the American dog tick, Dermacentor variabilis (Say), in the USA. Med. Vet. Entomol. 29, 178–188 (2015).CAS 
    PubMed 

    Google Scholar 
    Blouin, E. F., Kocan, A. A., Glenn, B. L., Kocan, K. M. & Hair, J. A. Transmission of Cytauxzoon felis Kier, 1979 from bobcats, Felis rufus (Schreber), to domestic cats by Dermacentor variabilis (Say). J. Wildl. Dis. 20, 241–242 (1984).CAS 
    PubMed 

    Google Scholar 
    Yunik, M. E., Galloway, T. D. & Lindsay, L. R. Active surveillance of Anaplasma marginale in populations of arthropod vectors (Acari: Ixodidae; Diptera: Tabanidae) during and after an outbreak of bovine anaplasmosis in southern Manitoba, Canada. Can. J. Vet. Res. 80, 171–174 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Trumpp, K. M., Parsley, A. L., Lewis, M. J., Camp, J. W. Jr. & Taylor, S. D. Presumptive tick paralysis in 2 American miniature horses in the United States. J. Vet. Intern. Med. 33, 1784–1788 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Léger, E., Vourc’h, G., Vial, L., Chevillon, C. & McCoy, K. D. Changing distributions of ticks: Causes and consequences. Exp. Appl. Acarol. 59, 219–244 (2013).PubMed 

    Google Scholar 
    Ogden, N. H., Mechai, S. & Margos, G. Changing geographic ranges of ticks and tick-borne pathogens: Drivers, mechanisms and consequences for pathogen diversity. Front. Cell. Infect. Microbiol. 3, 46 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    Bouchard, C. et al. Increased risk of tick-borne diseases with climate and environmental changes. Can. Commun. Dis. Rep. 45, 83–89 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Artsob, H. et al. Isolation of Francisella tularensis and Powassan virus from ticks (Acari: Ixodidae) in Ontario, Canada. J. Med. Entomol. 21, 165–168 (1984).CAS 
    PubMed 

    Google Scholar 
    Gregson, J. D. The Ixodoidea of Canada. Canadian Department of Agriculture Publication 930 (Canadian Department of Agriculture, 1956).
    Google Scholar 
    Scholten, T. Human tick infestations in Ontario: Findings at the Toronto Public Health Laboratory, 1967–1977. Can. J. Public Health 68, 494–496 (1977).CAS 
    PubMed 

    Google Scholar 
    Jarvis, D. The Acarina, with a host index to the species found in Ontario. 48th Ann. Rept. Ent. Soc. Ontario 1909 36, 82–109 (1910).Dergousoff, S. J., Galloway, T. D., Lindsay, L. R., Curry, P. S. & Chilton, N. B. Range expansion of Dermacentor variabilis and Dermacentor andersoni (Acari: Ixodidae) near their northern distributional limits. J. Med. Entomol. 50, 510–520 (2013).PubMed 

    Google Scholar 
    Ministry of Natural Resources and Forestry. Forest resources of Ontario 2016 (Ministry of Natural Resources and Forestry, 2018).Crins, W. J., Gray, P. A., Uhlig, P. W. C. & Wester, M. C. The ecosystems of Ontario, Part 1: Ecozones and ecoregions. (Ministry of Natural Resources and Forestry, 2009).Nelder, M. P. et al. Human pathogens associated with the blacklegged tick Ixodes scapularis: A systematic review. Parasit. Vectors 9, 265 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    University of Toronto. FSA land area file. https://mdl.library.utoronto.ca/collections/numeric-data/census-canada/2016/geo (2018).Lehane, A. et al. Reported county-level distribution of the American dog tick (Acari: Ixodidae) in the contiguous United States. J. Med. Entomol. 57, 131–155 (2020).PubMed 

    Google Scholar 
    Dennis, D. T., Nekomoto, T. S., Victor, J. C., Paul, W. S. & Piesman, J. Reported distribution of Ixodes scapularis and Ixodes pacificus (Acari: Ixodidae) in the United States. J. Med. Entomol. 35, 629–638 (1998).CAS 
    PubMed 

    Google Scholar 
    Springer, Y. P., Eisen, L., Beati, L., James, A. M. & Eisen, R. J. Spatial distribution of counties in the continental United States with records of occurrence of Amblyomma americanum (Ixodida: Ixodidae). J. Med. Entomol. 51, 342–351 (2014).PubMed 

    Google Scholar 
    Eisen, R. J., Eisen, L. & Beard, C. B. County-scale distribution of Ixodes scapularis and Ixodes pacificus (Acari: Ixodidae) in the continental United States. J. Med. Entomol. 53, 349–386 (2016).PubMed 

    Google Scholar 
    Clow, K. M. et al. Northward range expansion of Ixodes scapularis evident over a short timescale in Ontario, Canada. PLoS ONE 12, e0189393 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Rand, P. W. et al. Passive surveillance in Maine, an area emergent for tick-borne diseases. J. Med. Entomol. 44, 1118–1129 (2007).PubMed 

    Google Scholar 
    Baldwin, D., Desloges, J. & Band, L. Physical geography of Ontario in Ecology of a managed terrestrial landscape: patterns and processes of forest landscapes in Ontario (eds. Perera, A. H., Euler, D. L. & Thompson, I. D.) 12–29 (UBC Press, 2000).Minigan, J. N., Hager, H. A., Peregrine, A. S. & Newman, J. A. Current and potential future distribution of the American dog tick (Dermacentor variabilis, Say) in North America. Ticks Tick Borne Dis. 9, 354–362 (2018).PubMed 

    Google Scholar 
    Wilkinson, P. R. The distribution of Dermacentor ticks in Canada in relation to bioclimatic zones. Can. J. Zool. 45, 517–537 (1967).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Bishopp, F. C. & Trembley, T. H. Distribution and hosts of certain North American ticks. J. Parasitol. 31, 1–54 (1945).
    Google Scholar 
    Walker, E. D. et al. Geographic distribution of ticks (Acari: Ixodidae) in Michigan, with emphasis on Ixodes scapularis and Borrelia burgdorferi. J. Med. Entomol. 35, 872–882 (1998).CAS 
    PubMed 

    Google Scholar 
    Harlan, H. J. Observations of host seeking behaviour in American dog ticks, Dermacentor variabilis (Say) (Acari: Ixodidae) in Ohio. Med. Entomol. 4, 23–33 (2003).
    Google Scholar 
    Dodds, D. G., Martell, A. M. & Yescott, R. E. Ecology of the American dog tick, Dermacentor variabilis (Say) Nova Scotia. Can. J. Zool. 47, 171–181 (1969).
    Google Scholar 
    Judd, W. W. Recent records of ticks, Ixodes cookei Packard and Dermacentor variabilis (Say) (Acarina: Ixodoidea) in southwestern Ontario. Entomol. News 86, 157–159 (1975).CAS 
    PubMed 

    Google Scholar 
    Snetsinger, R., Jacobs, S. B., Kim, K. C. & Tavris, D. Extension of the range of Dermacentor variabilis (Acari: Ixodidae) in Pennsylvania. J. Med. Entomol. 30, 795–798 (1993).CAS 
    PubMed 

    Google Scholar 
    Saura, S., Bodin, Ö. & Fortin, M.-J. Stepping stones are crucial for species’ long-distance dispersal and range expansion through habitat networks. J. Appl. Ecol. 51, 171–182 (2014).
    Google Scholar 
    Sagurova, I. et al. Predicted northward expansion of the geographic range of the tick vector Amblyomma americanum in North America under future climate conditions. Environ. Health Perspect. 127, 107014 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Mierzejewska, E. J., Estrada-Peña, A., Alsarraf, M., Kowalec, M. & Bajer, A. Mapping of Dermacentor reticulatus expansion in Poland in 2012–2014. Ticks Tick Borne Dis. 7, 94–106 (2016).PubMed 

    Google Scholar 
    Gray, J. S., Dautel, H., Estrada-Peña, A., Kahl, O. & Lindgren, E. Effects of climate change on ticks and tick-borne diseases in Europe. Interdiscip. Perspect. Infect. Dis. 2009, 593232 (2009).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gasmi, S. et al. Evidence for increasing densities and geographic ranges of tick species of public health significance other than Ixodes scapularis in Quebec, Canada. PLoS ONE 13, e0201924 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Pak, D., Jacobs, S. B. & Sakamoto, J. M. A 117-year retrospective analysis of Pennsylvania tick community dynamics. Parasit. Vectors 12, 189 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Garvie, M. B., McKiel, J. A., Sonenshine, D. E. & Campbell, A. Seasonal dynamics of American dog tick, Dermacentor variabilis (Say), populations in southwestern Nova Scotia. Can. J. Zool. 56, 28–39 (1978).CAS 
    PubMed 

    Google Scholar 
    Burg, J. G. Seasonal activity and spatial distribution of host-seeking adults of the tick Dermacentor variabilis. Med. Vet. Entomol. 15, 413–421 (2001).CAS 
    PubMed 

    Google Scholar 
    Newhouse, V. F. Variations in population density, movement, and rickettsial infection rates in a local population of Dermacentor variabilis (Acarina: Ixodidae) ticks in the Piedmont of Georgia. Environ. Entomol. 12, 1737–1746 (1983).
    Google Scholar 
    Mackenzie, A. M. R., Rossier, E., Polley, J. R. & Corber, S. J. Rocky Mountain spotted fever—Ontario. Can. Dis. Wkly. Rep. 5, 130–132 (1979).
    Google Scholar 
    Gary, A. T., Webb, J. A., Hegarty, B. C. & Breitschwerdt, E. B. The low seroprevalence of tick-transmitted agents of disease in dogs from southern Ontario and Quebec. Can. Vet. J. 47, 1194–1200 (2006).PubMed 
    PubMed Central 

    Google Scholar 
    Walker, W. J. & Moore, C. A. Tularemia: Experience in the Hamilton area. Can. Med. Assoc. J. 105, 390–396 (1971).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ontario Agency for Health Protection and Promotion (Public Health Ontario). 2019 tularemia data at a glance. https://www.publichealthontario.ca/en/diseases-and-conditions/infectious-diseases/vector-borne-zoonotic-diseases/tularemia (2020).Wood, H. & Artsob, H. Spotted fever group rickettsiae: a brief review and a Canadian perspective. Zoonoses Public Health 59(Suppl 2), 65–79 (2012).PubMed 

    Google Scholar 
    Wood, H., Dillon, L., Patel, S. N. & Ralevski, F. Prevalence of Rickettsia species in Dermacentor variabilis ticks from Ontario, Canada. Ticks Tick Borne Dis. 7, 1044–1046 (2016).PubMed 

    Google Scholar 
    Kaufman, E. L. et al. Range-wide genetic analysis of Dermacentor variabilis and its Francisella-like endosymbionts demonstrates phylogeographic concordance between both taxa. Parasit. Vectors 11, 306 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Statistics Canada. Census profile. 2016 Census. https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/prof/index.cfm?Lang=E (2017).Statistics Canada. Land use, census of agriculture historical data. Table: 32–10–0153–01. https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/prof/index.cfm?Lang=E (2022). More

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    Simulation-based evaluation of two insect trapping grids for delimitation surveys

    Key delimitation trapping survey performance factorsTrap attractivenessThe performance of the current Medfly design was unexpectedly inferior to that of the leek moth even with a more vagile target insect, 2.8 times greater trap density in the core, and a grid size over three times larger. Despite all those factors, p(capture) for the leek moth grid with 1/λ = 20 m was 15 percentage points greater than that for Medfly at 30 days duration. Thus, trap attractiveness was the key determinant for delimiting survey performance, as it was for detection13.One straightforward way to improve p(capture) and the accuracy of boundary setting, while also cutting costs, would be to develop more attractive traps. Poorly attractive traps include food-based attractants48 and traps based solely on visual stimuli36. But developing better traps is difficult. Pheromone-based attractants generally perform best49, but these are unavailable for many insects. For instance, scientists have searched for decades for effective pheromones for Anastrepha suspensa (Loew) and A. ludens (Loew) without success50. Common issues include the complexity of components, costs of synthesis, and chemical stability.Trap densitiesAll else being equal, increasing the trap density will generally improve p(capture) for any survey grid, and intuitively this can help compensate for using less attractive traps. However, the impact of increasing density is limited when attractiveness is low13,47, and large surveys or grids with many traps can become prohibitively expensive51. The Medfly grid designers likely understood that the available trap and lure was not highly attractive, and used higher densities in inner bands to try to reach some desired (non-quantitative) survey performance level. By contrast, the designers of the leek moth grid used a (constant) density three times smaller, likely because the trap and lure were known to be relatively strong. Here, for both species, marginal ROI decreased as densities increased (Tables 2, 3). Hence, increasing densities has limited benefit, but may be useful when better lures are unavailable13.In that context, the use of variable densities in the Medfly grid is understandable. At its standard size, the survey grid would require 8,100 traps if the core trap density were constant (Table 1). The designers likely intuited that lower densities could be used in outer bands because captures there were less likely. However, doing so reduces the likelihood of detection in outer bands and could increase the possibility of undetected egress, especially with longer survey durations. As far as we know, natural egress has not been raised as a concern following the numerous Medfly quarantines that have used this survey grid over the years, in Southern California in particular52.Generally, however, we think the variable Medfly grid densities run counter to delimitation goals. Greater core and Band 2 densities have proportionally more impact on p(capture), but only a few detections in the core are necessary to confirm the presence of the population (Goal 1), and inner area detections probably contribute little to boundary setting (see below). Therefore, lower or intermediate densities (at most) may be optimal for the core when considering ROI. For the outer bands, increasing densities might improve boundary setting (Goal 2) and help mitigate potential egress, but the sizes of those bands already limit cost efficiency (Table 2), making greater densities less advisable. Our simulation results can help elucidate how to balance these interests to achieve delimitation goals while minimizing costs47.Grid size considerationsThe simulation results indicated that the standard survey sizes for these two pests were excessive. We have verified that empirically for Medfly using trapping detections data53. A 14.5-km grid has been widely used for many other insects in the CDFA (2013) guidelines10, such as Mexfly and OFF, and the same analysis indicated that those are also oversized for use in short-term delimitation surveys53. From the same analysis, the predicted survey radius for leek moth, with D = 500 m2 per day, would be 2,382 m, or a diameter of nearly 4.8 km, which matches the results here. Similarly, Dominiak and Fanson45 analyzed trapping data for Qfly and found that the recommended quarantine area distance of 15 km could be reduced to 3 to 4 km.Grids with radii larger than 4.8-km only seem necessary for highly vagile insects, those with D ≥ 50,000 m2 per day47. This should not be surprising. Small insect populations are unlikely to move very far31,54, especially if hosts are available20,39,55. The (proposed) short duration of a delimitation survey would also limit dispersal potential (see below). Many delimiting survey plans may be oversized, because they were developed before much dispersal research had been done37, thus uncertainty was high. Our dispersal distance analysis included species with a wide range of dispersal abilities, so it can be used generally to choose smaller survey grid radii53.Reducing grid sizes down to about 4.8-km diameters may have little impact on p(capture), since detections in bands outside that distance contributed little to overall performance. The cores of both the leek moth and Medfly grids accounted for 86 percent or more of overall p(capture). While core area detections will confirm the presence of the population, they are less useful for defining spatial extent. The furthest detections from the presumed source are usually used to delimit the incursion46,56 (although in our experience formal boundary setting exercises seem rare). Delimiting surveys may often yield few captures anyway, because adventive populations can be very small and subject to high mortality31. Because size reductions eliminate traps in proportionally larger outer areas, the impact on survey costs is substantial. Removing just the outermost bands of each grid would directly reduce costs by $11,200 for leek moth (400 traps) and by $7,488 for Medfly (288 traps; Table 1).Another reason for the large size of the standard Medfly grid may be that it was designed for monitoring and management in addition to delimitation57. Medfly quarantines end after at least three generations without a detection, so the surveys may last for months. The grid size was reportedly originally determined by multiplying the estimated dispersal distance by three (PPQ, personal communication), to account for uncertainty. This implies that the estimated distance was about 2,400 m per 30 days. Thus, the design may not have been built for the 30-d duration used here, but our recommended design is valid if a shorter delimitation activity without further monitoring is appropriate.Although it seemed too large for leek moth, an 8-km grid for delimitation could be appropriate for some other moths. For example, the delimiting survey plans for Spodoptera littoralis (Boisduval) and S. exempta Walker use this size9. S. littoralis is described as dispersing “many miles”, and S. exempta can travel hundreds of miles9, which clearly exceeds the described dispersal ability of leek moth. On the other hand, the survey plan for summer fruit tortrix moth (Adoxophyes orana Fischer von Röeslerstamm) also specifies an 8-km grid for delimitation but contains little information on dispersal, suggesting only that most movement is local8. Like leek moth, a 4.8-km grid for that species seems likely to be more appropriate.Limiting egress potential is probably the main consideration when setting survey size, but uncertainty about the source population location may also be a factor. Survey grids placed over the earliest insect detection may sometimes be off center from the location of the source population54. However, so far as we know for our agency, most adventive populations have been localized, based on post-discovery detections (PPQ, personal communication). Likewise, we have found53 and other researchers have found that dispersal distances for different species in outbreaks and mark-recapture studies are often less than 1 km58,59,60. That may often be the case for detection networks of traps (e.g., for high risk fruit flies), which increase the likelihood of capture before the population has had much time to grow and disperse. Here, we focused explicitly on localized populations, but allowed for uncertainty in the simulations by varying outbreak locations over one mile in the central part of the grid. If the outbreak population is very large and has extensively spread out (e.g., spotted lanternfly, Lycorma delicatula (White) in 201461), delimitation will not be localized, but “area-wide”2. The results here do not apply to area-wide outbreaks, and we are currently studying how to effectively delimit them.Optimizing delimitation surveysMany trapping survey designs in use were based not on “hard” science but on local experience62. Scientists have recognized the need for more cost-effective surveillance strategies63,64. Quantitatively assessing p(capture) in different designs for the same target pest allows us to determine grid sizes and densities that lower costs while maintaining performance. Results here demonstrated that the sizes and densities of these two survey grids could be optimized to save up to $20,244 per survey for the leek moth and $38,168 per survey for the Medfly. In practical terms, that means more than five leek moth surveys could be run for the cost of one standard design survey. Additionally, over seven Medfly delimitation surveys could be funded by the budget of one standard plan. The magnitudes of reduction seen here may be typical, since about 90 percent of the costs in trapping surveys are for transportation and maintenance related to traps65.Quantifying survey performance was not possible until very recently, so it has been little discussed in the literature5,66, and no standard thresholds exist. We think 0.5 may be a reasonable minimum threshold for the choice of p(capture), to try to ensure that population detection is “more likely than not”. Designs that aim to maximize p(capture) could be realistic with high attractiveness traps, but those designs seem very likely to have lower ROIs (e.g., Table 2). Even for the most serious insect pests, we think targeting near-perfect population detection during delimitation is likely not justified. Designs achieving p(capture) from 0.6 to 0.75 could be highly effective in terms of both costs and performance.Another potential area of improvement is grid shape. Circular grids perform as well as square grids but use fewer traps and less service area to achieve equivalent p(capture)47. Moreover, detections in the corners of a square grid are evidence that insects could have traveled beyond the square along the axes, resulting in uncertain boundary setting. Most published survey grids are square10,46, but many field managers tend to use approximately circular trapping grids in the field (PPQ, personal communication). The conversion to a circular grid with a radius of half the square side length reduces the area and number of traps by around 21 percent47. Our findings were consistent with that value.This new quantification ability also indicates that some delimiting survey designs in the U.S.A. may not be performing as well as expected47. For instance, the delimiting survey design for Mexfly uses approximately 31 traps per km2 in the core of a 14.5 km square grid11, but the traps are only weakly attractive (1/λ ≈ 5 m). In this scenario, p(capture) was only around 0.23 with a 30-d survey duration47. A much greater density ( > 80 traps per km2) could be used in the core to achieve p(capture) ≥ 0.5, but this may not be feasible depending on the survey budget.Technical and modeling considerationsExamining diffusion-based movement for these two insects in TrapGrid can give insight into why simulations indicated that smaller grids may be adequate47. The value of σ for Medfly after 30 days is only about 1,550 m. In a normal distribution, σ = 1,550 m gives a 95th percentile distance of 2,550 m, which is similar to the estimated distance above of 2,400 m. Over 90 days, σ = 2,700 m for Medfly, which gives a 95th percentile distance of 4,441 m, still much shorter than the grid radius of 7,250 m. A 95th percentile of 7,250 m requires σ ≈ 4,408 m, which equals t = 253 days. In addition, the maximum total distance (up to 39 days after detection) we observed in trapping detections data for Medfly in Florida was about 4,800 m53.The same calculations for leek moth give σ ≈ 490 m for 30 days, with a 95th percentile distance of only 806 m. That is half the length of the recommended shortened radius above of 2.4 km, and nearly five times shorter than the radius of the standard 8-km grid. A 95th percentile of 4,000 m requires σ = 2,432 m, which implies t = 740 days, which is about two years. Therefore, the leek moth grid is arguably even more oversized than the Medfly grid.The default capture probability calculation in the current version (Ver. 2019-12-11) of TrapGrid is not sensitive to population size32 and does not consider the effects of ambient factors (e.g., wind speed and direction, rainfall, temperature). Many other factors can also impact trapping survey outcomes, such as topography of the environment, availability of host plants, seasonality of pest, and population dynamics. These factors are not considered in the current version of TrapGrid. More

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    Milk microbiomes of three great ape species vary among host species and over time

    Kim, S. Y. & Yi, D. Y. Components of human breast milk: From macronutrient to microbiome and microRNA. Clin. Exp. Pediatr. 63(8), 301 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Power, M. L. & Schulkin, J. Maternal regulation of offspring development in mammals is an ancient adaptation tied to lactation. Appl. Transl. Genomics. 2, 55–63 (2013).CAS 
    Article 

    Google Scholar 
    Pannaraj, P. S. et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 171(7), 647–654 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lyons, K. E., Ryan, C. A., Dempsey, E. M., Ross, R. P. & Stanton, C. Breast milk, a source of beneficial microbes and associated benefits for infant health. Nutrients 12(4), 1039 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Fehr, K. et al. Breastmilk feeding practices are associated with the co-occurrence of bacteria in mothers’ milk and the infant gut: The CHILD cohort study. Cell Host Microbe. 28(2), 285–297 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Moossavi, S. & Azad, M. B. Origins of human milk microbiota: New evidence and arising questions. Gut Microbes. 12(1), 1667722. https://doi.org/10.1080/19490976.2019.1667722 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Groer, M. W., Morgan, K. H., Louis-Jacques, A. & Miller, E. M. A scoping review of research on the human milk microbiome. J. Hum. Lact. 36(4), 628–643 (2020).PubMed 
    Article 

    Google Scholar 
    Gopalakrishna, K. P. & Hand, T. W. Influence of maternal milk on the neonatal intestinal microbiome. Nutrients 12(3), 823 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Ayoub Moubareck, C., Lootah, M., Tahlak, M. & Venema, K. Profiles of human milk oligosaccharides and their relations to the milk microbiota of breastfeeding mothers in Dubai. Nutrients 12(6), 1727 (2020).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Henrick, B. M. et al. Bifidobacteria-mediated immune system imprinting early in life. Cell 184, 3884–3898 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Walker, W. A. & Iyengar, R. S. Breast milk, microbiota, and intestinal immune homeostasis. Pediatr. Res. 77(1), 220–228 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Petrullo, L. et al. The early life microbiota mediates maternal effects on offspring growth in a nonhuman primate. Iscience. 25(3), 103948 (2022).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bowen, W. D., Boness, D. J. & Oftedal, O. T. Mass transfer from mother to pup and subsequent mass loss by the weaned pup in the hooded seal, Cystophora cristata. Can. J. Zool. 65(1), 1–8 (1987).Article 

    Google Scholar 
    Smith, T. M., Austin, C., Hinde, K., Vogel, E. R. & Arora, M. Cyclical nursing patterns in wild orangutans. Sci. Adv. 3(5), e1601517 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Park, Y. W. & Haenlein, G. F. W. Handbook of Milk of Non-Bovine Mammals (Wiley, 2008).
    Google Scholar 
    Oftedal, O. T. Use of maternal reserves as a lactation strategy in large mammals. Proc. Nutr. Soc. 59(1), 99–106 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hinde, K. & Milligan, L. A. Primate milk: Proximate mechanisms and ultimate perspectives. Evol. Anthropol. Issues News Rev. 20(1), 9–23 (2011).Article 

    Google Scholar 
    Osthoff, G., Hugo, A., De Wit, M., Nguyen, T. P. M. & Seier, J. Milk composition of captive vervet monkey (Chlorocebus pygerythrus) and rhesus macaque (Macaca mulatta) with observations on gorilla (Gorilla gorilla gorilla) and white handed gibbon (Hylobates lar). Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 152(4), 332–338 (2009).CAS 
    Article 

    Google Scholar 
    Power, M. L., Oftedal, O. T. & Tardif, S. D. Does the milk of callitrichid monkeys differ from that of larger anthropoids?. Am. J. Primatol. Off. J. Am. Soc. Primatol. 56(2), 117–127 (2002).
    Google Scholar 
    Power, M. L. et al. Patterns of milk macronutrients and bioactive molecules across lactation in a western lowland gorilla (Gorilla gorilla) and a Sumatran orangutan (Pongo abelii). Am. J. Primatol. 79(3), e22609 (2017).Article 
    CAS 

    Google Scholar 
    Garcia, M., Power, M. L. & Moyes, K. M. Immunoglobulin A and nutrients in milk from great apes throughout lactation. Am. J. Primatol. 79(3), e22614 (2017).Article 
    CAS 

    Google Scholar 
    Muletz-Wolz, C. R. et al. Diversity and temporal dynamics of primate milk microbiomes. Am. J. Primatol. 81(10–11), e22994 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Rodríguez, J. M. The origin of human milk bacteria: Is there a bacterial entero-mammary pathway during late pregnancy and lactation?. Adv. Nutr. 5(6), 779–784 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    LaTuga MS, Stuebe A, Seed PC. A review of the source and function of microbiota in breast milk. In Seminars in Reproductive Medicine, Vol 32, 68–73 (Thieme Medical Publishers, 2014).Chen, W. et al. Lactation stage-dependency of the sow milk microbiota. Front. Microbiol. 9, 945 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McInnis, E. A., Kalanetra, K. M., Mills, D. A. & Maga, E. A. Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity. Food Microbiol. 46, 121–131 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gonzalez, E. et al. Distinct changes occur in the human breast milk microbiome between early and established lactation in breastfeeding Guatemalan mothers. Front. Microbiol. 12, 194 (2021).Article 

    Google Scholar 
    Ge, Y. et al. The maternal milk microbiome in mammals of different types and its potential role in the neonatal gut microbiota composition. Animals 11(12), 3349 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kordy, K. et al. Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve. PLoS ONE 15(1), e0219633 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jost, T., Lacroix, C., Braegger, C. & Chassard, C. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health. Nutr. Rev. 73(7), 426–437 (2015).PubMed 
    Article 

    Google Scholar 
    Fernández, L. et al. The human milk microbiota: Origin and potential roles in health and disease. Pharmacol. Res. 69(1), 1–10 (2013).PubMed 
    Article 
    CAS 

    Google Scholar 
    Cabrera-Rubio, R. et al. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am. J. Clin. Nutr. 96(3), 544–551 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gomez-Gallego, C., Garcia-Mantrana, I., Salminen, S. & Collado, M. C. The human milk microbiome and factors influencing its composition and activity. In Seminars in Fetal and Neonatal Medicine. Vol 21, 400–405 (Elsevier, 2016).Khodayar-Pardo, P., Mira-Pascual, L., Collado, M. C. & Martínez-Costa, C. Impact of lactation stage, gestational age and mode of delivery on breast milk microbiota. J. Perinatol. 34(8), 599–605 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wan, Y. et al. Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status. Gut Microbes. 11(5), 1438–1449 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hunt, K. M. et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE 6(6), e21313 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Petrullo, L., Jorgensen, M. J., Snyder-Mackler, N. & Lu, A. Composition and stability of the vervet monkey milk microbiome. Am. J. Primatol. 81(10–11), e22982 (2019).PubMed 

    Google Scholar 
    Mittermeier, R. A. et al. Primates in peril: The world’s 25 most endangered primates 2008–2010. Primate Conserv. 24(1), 1–57 (2009).Article 

    Google Scholar 
    Williams, J. E. et al. Human milk microbial community structure is relatively stable and related to variations in macronutrient and micronutrient intakes in healthy lactating women. J. Nutr. 147(9), 1739–1748 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kumar, H. et al. Distinct patterns in human milk microbiota and fatty acid profiles across specific geographic locations. Front. Microbiol. 7, 1619 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Keady, M. et al. Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants. Anim. Microbiome. 3, 1–19 (2021).Article 
    CAS 

    Google Scholar 
    RStudio Team. RStudio: Integrated Development for R. http://www.rstudio.com/ (2020).Bolyen, E. et al. QIIME 2: Reproducible, Interactive, Scalable, and Extensible Microbiome Data Science. PeerJ Preprints (2018).Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 13(7), 581 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cole, J. R. et al. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42(D1), D633–D642 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 6(1), 1–14 (2018).Article 

    Google Scholar 
    McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4), e61217 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Beule, L. & Karlovsky, P. Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): Application to microbial communities. PeerJ 8, e9593 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: And this is not optional. Front. Microbiol. 8, 2224 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oksanen, J. et al. vegan: Community Ecology Package. https://cran.r-project.org/package=vegan (2020).Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).MathSciNet 
    MATH 

    Google Scholar 
    Kumbhare, S. V., Patangia, D. V., Patil, R. H., Shouche, Y. S. & Patil, N. P. Factors influencing the gut microbiome in children: From infancy to childhood. J. Biosci. 44(2), 1–19 (2019).Article 

    Google Scholar 
    Amato, K. R. et al. Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia 180(3), 717–733 (2016).ADS 
    PubMed 
    Article 

    Google Scholar 
    Mulligan, M. E. et al. Methicillin-resistant Staphylococcus aureus: A consensus review of the microbiology, pathogenesis, and epidemiology with implications for prevention and management. Am. J. Med. 94(3), 313–328 (1993).CAS 
    PubMed 
    Article 

    Google Scholar 
    Ruegg, P. L. A 100-Year Review: Mastitis detection, management, and prevention. J. Dairy Sci. 100(12), 10381–10397 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Clarridge, J. E. III. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17(4), 840–862 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Martín, V., Mediano, P., Del Campo, R., Rodríguez, J. M. & Marín, M. Streptococcal diversity of human milk and comparison of different methods for the taxonomic identification of streptococci. J. Hum. Lact. 32(4), NP84–NP94 (2016).PubMed 
    Article 

    Google Scholar 
    Ghebremedhin, B., Layer, F., Konig, W. & Konig, B. Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences. J. Clin. Microbiol. 46(3), 1019–1025 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen, Q. et al. Quantification of human oral and fecal Streptococcus parasanguinis by use of quantitative real-time PCR targeting the groEL gene. Front. Microbiol. 10, 2910 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Plows, J. F. et al. Longitudinal changes in human milk oligosaccharides (HMOs) over the course of 24 months of lactation. J. Nutr. 151(4), 876–882 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Boehm, G. & Stahl, B. Oligosaccharides from milk. J. Nutr. 137(3), 847S-849S (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    van Leeuwen, S. S. et al. Goat milk oligosaccharides: Their diversity, quantity, and functional properties in comparison to human milk oligosaccharides. J. Agric. Food Chem. 68(47), 13469–13485 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Tao, N. et al. Evolutionary glycomics: Characterization of milk oligosaccharides in primates. J. Proteome Res. 10(4), 1548–1557 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yu, Z.-T., Chen, C. & Newburg, D. S. Utilization of major fucosylated and sialylated human milk oligosaccharides by isolated human gut microbes. Glycobiology 23(11), 1281–1292 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bolotin, A. et al. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat. Biotechnol. 22(12), 1554–1558 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schwab, C. & Gänzle, M. Lactic acid bacteria fermentation of human milk oligosaccharide components, human milk oligosaccharides and galactooligosaccharides. FEMS Microbiol. Lett. 315(2), 141–148 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Marcobal, A. et al. Consumption of human milk oligosaccharides by gut-related microbes. J. Agric. Food Chem. 58(9), 5334–5340 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Uriot, O. et al. Streptococcus thermophilus: From yogurt starter to a new promising probiotic candidate?. J. Funct. Foods. 37, 74–89 (2017).CAS 
    Article 

    Google Scholar 
    Duar, R. M., Henrick, B. M., Casaburi, G. & Frese, S. A. Integrating the ecosystem services framework to define dysbiosis of the breastfed infant gut: The role of B. infantis and human milk oligosaccharides. Front. Nutr. 7, 33 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Singh, R. P., Niharika, J., Kondepudi, K. K., Bishnoi, M. & Tingirikari, J. M. R. Recent understanding of human milk oligosaccharides in establishing infant gut microbiome and roles in immune system. Food Res. Int. 151, 110884. https://doi.org/10.1016/j.foodres.2021.110884 (2022).CAS 
    Article 
    PubMed 

    Google Scholar 
    Ximenez, C. & Torres, J. Development of microbiota in infants and its role in maturation of gut mucosa and immune system. Arch. Med. Res. 48(8), 666–680. https://doi.org/10.1016/j.arcmed.2017.11.007 (2017).Article 
    PubMed 

    Google Scholar 
    Meehan, C. L. et al. Social networks, cooperative breeding, and the human milk microbiome. Am. J. Hum. Biol. 30(4), e23131 (2018).PubMed 
    Article 

    Google Scholar 
    Bornbusch, S. L. et al. Stable and transient structural variation in lemur vaginal, labial and axillary microbiomes: Patterns by species, body site, ovarian hormones and forest access. FEMS Microbiol. Ecol. 96(6), fiaa090 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bornbusch, S. L. & Drea, C. M. Antibiotic resistance genes in lemur gut and soil microbiota along a gradient of anthropogenic disturbance. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2021.704070 (2021).Article 

    Google Scholar 
    Grieneisen, L. E. et al. Genes, geology and germs: Gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc. R. Soc. B. 2019(286), 20190431 (1901).
    Google Scholar 
    Ellison, S. et al. The influence of habitat and phylogeny on the skin microbiome of amphibians in Guatemala and Mexico. Microb. Ecol. 78(1), 257–267 (2019).PubMed 
    Article 

    Google Scholar 
    Phillips, C. D. et al. Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography. Mol. Ecol. 21(11), 2617–2627 (2012).PubMed 
    Article 

    Google Scholar  More

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    Vision and vocal communication guide three-dimensional spatial coordination of zebra finches during wind-tunnel flights

    Dynamic in-flight flock organizationIt is commonly assumed that during flocking, flock members follow three basic interaction rules: Attraction, Repulsion and Alignment, to coordinate spatial positions between each other18. To study the spatial organization of our zebra finch flock during flight, the spatial positions of all birds in the flight section were tracked in every fifth frame (sample rate: 24 Hz (that is, frames per second)) of the synchronized footage recorded by two high-speed digital video cameras (Camera 1: centred upwind view, Fig. 1a,b; Camera 2: upturned vertical view, Fig. 1a,c) for the entire duration (51.7, 58.3, 69.2 and 127 s) of four (session 2, 5, 8 and 13) out of 13 flight sessions. Flight paths were reconstructed from the tracking data for each bird in the flock, with horizontal and vertical coordinates delivered by Camera 1 and coordinates in wind direction delivered by Camera 2. The data show that each bird mainly occupied a particular area in the flight section, and that this spatial preference was stable over different flight sessions. Bird Green, for example, was preferentially flying very low above the flight section’s floor, and bird Lilac preferred to fly at upwind positions in front of the flock (Fig. 1d, Extended Data Figs. 1 and 3 and Supplementary Information).Despite their preference in flight area, all birds constantly changed their spatial positions fast and rhythmically along the horizontal dimension of the flight section (Fig. 1e–g, Extended Data Figs. 2 and 4, Supplementary Video 1 and Supplementary Information). This behaviour is reminiscent of the flight behaviour of wild zebra finches: when being surprised in flight by a predator, zebra finches fly in a rapid zig-zag course low above the ground, heading for nearby vegetation16. Whether the sideways oscillating flight manoeuvres, which are performed by both wild birds in open space and domesticated birds in the wind tunnel’s flight section, are caused by the close proximity to the ground or are part of an escape reaction is yet unknown.From the tracking data, we further calculated the spatial distances in all three dimensions between all pairwise combinations of birds throughout the four flight sessions (sample rate: 24 Hz). When normalized to the maximum distance detected for each bird pairing, each dimension and each flight session, mean distances of bird pairings in all dimensions were narrowly distributed within a range of 27.7–38.0% of maximum distance (Fig. 1h and Supplementary Table 1). This may indicate that during flocking flight, zebra finches actively balance Attraction and Repulsion to maintain a stable 3D distance towards all other members of the flock. Owing to the spatial limitations in the wind tunnel’s flight section, we did not expect the zebra finches to perform large-scale flight manoeuvres with movements aligned between all flock members (Extended Data Fig. 5 and Supplementary Information), as can be observed, for example, in freely flying flocks of homing pigeons (Columba livia domestica)19 and white storks (Ciconia Ciconia)20.Visually guided horizontal repositioningWhen observing the dynamic spatial organization of our zebra finch flock, a question immediately arises: how do the birds prevent collisions during their frequent horizontal position changes? When considering the spatial limitation experienced by the flock of six birds during flight in the flight section and their highly dynamic flight style, collision rates seemed to be astonishingly low (median: 0.02 Hz; interquartile range (IQR): 0–0.03 Hz; n = 13 sessions) during flocking flight (in total 16 collisions in 13 min of analysed flight time). In birds, the visual system represents the main input channel for environmental information. To tackle the above question, we therefore first investigated the role of vision during flocking flight, and tested whether a bird’s viewing direction was correlated with the direction of horizontal position change. As gaze changes are governed by head movements in birds21, we used a bird’s head direction as an indicator for the orientation of its visual axis. We tracked (sample rate: 120 Hz) the position of a bird’s beak tip and neck in each frame of the footage during ten horizontal position changes (Fig. 2a and Supplementary Video 2) per bird, and found a strong interaction between a bird’s head angle relative to the wind direction and its direction of horizontal position change. During horizontal position changes, the birds always turned their heads in the direction of the position change (Fig. 2b). While the population’s median absolute angle of position change was 84.0° (IQR: 78.6–87.2°; n = 60) relative to 0° in wind direction, the population’s median absolute head turning angle was 36.0° (IQR: 26.4–42.5°; n = 60; see Supplementary Information for results on head movements during solo flight). The eyes of zebra finches are positioned laterally on their heads22 and each retina features a small region of highest ganglion cell density (fovea, that is, region of highest visual spatial resolution) at an area that receives visual input from horizontal positions at 60° relative to the midsagittal plane23. By turning their heads by about 36° during horizontal position changes, the zebra finches roughly align the foveal area in the retina of one eye with their direction of position change, and in the retina of the other eye with the wind direction (Fig. 2c,d). Thus, head turns in the direction of position change may indicate that the birds use visual cues while repositioning themselves within the flock. This hypothesis is supported by a study on zebra finch head movements performed during an obstacle avoidance task. In this study, instead of fixating on the obstacle, zebra finches turned their head in the direction of movement while navigating around the obstacle24.Fig. 2: Horizontal position changes are accompanied by head turns.a, Head and body orientation of bird Orange (ventral view) during one example of position changes to the right, tracked (sample rate: 120 Hz) in the footage of Camera 2. Circles: beak tip positions; plus signs: neck positions; upward pointing triangles: tail base positions. Cutouts of freeze frames of the footage taken with Camera 2 show the bird’s head and body posture for 11 time points during the position change. b, In all birds, the median angle of head turn during horizontal position change in flocking flight is positively correlated (linear mixed effects model (LMM), estimates ± s.e.m.: 2.05 ± 0.1, P  More