More stories

  • in

    Elevated extinction risk of cacti under climate change

    Boyle, T. H. & Anderson, E. in Cacti: Biology and Uses (ed. Nobel, P. S.) 125–141 (Univ. California Press, 2002).Gibson, A. C. & Nobel, P. S. The Cactus Primer (Harvard Univ. Press, 1986).Bravo Hollis, H. & Sánchez Mejorada, H. Las Cactáceas de México (Univ. Nacional Autónoma de México, 1978).Goettsch, B. et al. High proportion of cactus species threatened with extinction. Nat. Plants 1, 15142 (2015).CAS 
    PubMed 

    Google Scholar 
    Benavides, E., Breceda, A. & Anadón, J. D. Winners and losers in the predicted impact of climate change on cacti species in Baja California. Plant Ecol. 222, 29–44 (2021).
    Google Scholar 
    Nobel, P. S. Responses of some North American CAM plants to freezing temperatures and doubled CO2 concentrations: implications of global climate change for extending cultivation. J. Arid. Environ. 34, 187–196 (1996).
    Google Scholar 
    Reyes-García, C. & Andrade, J. L. Crassulacean acid metabolism under global climate change. N. Phytol. 181, 754–757 (2009).
    Google Scholar 
    Smith, S. D., Didden-Zopfy, B. & Nobel, P. S. High-temperature responses of North American cacti. Ecology 65, 643–651 (1984).
    Google Scholar 
    Larios, E., González, E. J., Rosen, P. C., Pate, A. & Holm, P. Population projections of an endangered cactus suggest little impact of climate change. Oecologia 192, 439–448 (2020).PubMed 

    Google Scholar 
    Esparza-Olguı́n, L., Valverde, T. & Vilchis-Anaya, E. Demographic analysis of a rare columnar cactus (Neobuxbaumia macrocephala) in the Tehuacan Valley, Mexico. Biol. Conserv. 103, 349–359 (2002).
    Google Scholar 
    Seal, C. E. et al. Thermal buffering capacity of the germination phenotype across the environmental envelope of the Cactaceae. Glob. Change Biol. 23, 5309–5317 (2017).
    Google Scholar 
    Huang, J., Yu, H., Guan, X., Wang, G. & Guo, R. Accelerated dryland expansion under climate change. Nat. Clim. Change 6, 166–171 (2016).
    Google Scholar 
    Gurvich, D. E. et al. Combined effect of water potential and temperature on seed germination and seedling development of cacti from a mesic Argentine ecosystem. Flora 227, 18–24 (2017).
    Google Scholar 
    Nuzhyna, N., Baglay, K., Golubenko, A. & Lushchak, O. Anatomically distinct representatives of Cactaceae Juss. family have different response to acute heat shock stress. Flora 242, 137–145 (2018).
    Google Scholar 
    Andrade, J. L. & Nobel, P. S. Microhabitats and water relations of epiphytic cacti and ferns in a lowland neotropical forest. Biotropica 29, 261–270 (1997).
    Google Scholar 
    Williams, D. G., Hultine, K. R. & Dettman, D. L. Functional trade-offs in succulent stems predict responses to climate change in columnar cacti. J. Exp. Bot. 65, 3405–3413 (2014).PubMed 

    Google Scholar 
    Aragón-Gastélum, J. L. et al. Induced climate change impairs photosynthetic performance in Echinocactus platyacanthus, an especially protected Mexican cactus species. Flora Morphol. Distrib. Funct. Ecol. Plants 209, 499–503 (2014).
    Google Scholar 
    Martorell, C., Montañana, D. M., Ureta, C. & Mandujano, M. C. Assessing the importance of multiple threats to an endangered globose cactus in Mexico: cattle grazing, looting and climate change. Biol. Conserv. 181, 73–81 (2015).
    Google Scholar 
    Dávila, P., Téllez, O. & Lira, R. Impact of climate change on the distribution of populations of an endemic Mexican columnar cactus in the Tehuacán-Cuicatlán Valley, Mexico. Plant Biosyst. 147, 376–386 (2013).
    Google Scholar 
    Conver, J. L., Foley, T., Winkler, D. E. & Swann, D. E. Demographic changes over >70 yr in a population of saguaro cacti (Carnegiea gigantea) in the northern Sonoran Desert. J. Arid. Environ. 139, 41–48 (2017).
    Google Scholar 
    Carrillo-Angeles, I. G., Suzán-Azpiri, H., Mandujano, M. C., Golubov, J. & Martínez-Ávalos, J. G. Niche breadth and the implications of climate change in the conservation of the genus Astrophytum (Cactaceae). J. Arid. Environ. 124, 310–317 (2016).
    Google Scholar 
    de Cavalcante, A. M. B. & de Duarte, A. S. Modeling the distribution of three cactus species of the Caatinga biome in future climate scenarios. Int. J. Ecol. Environ. Sci. 45, 191–203 (2019).
    Google Scholar 
    de Cavalcante, A. M. B., de Duarte, A. S. & Ometto, J. P. H. B. Modeling the potential distribution of Epiphyllum phyllanthus (L.) Haw. under future climate scenarios in the Caatinga biome. An. Acad. Bras. Cienc. 92, 351–358 (2020).
    Google Scholar 
    Tellez-Valdes, O. & DiVila-Aranda, P. Protected areas and climate change: a case study of the cacti in the Tehuacan-Cuicatlan biosphere reserve, Mexico. Conserv. Biol. 17, 846–853 (2003).
    Google Scholar 
    dos Santos Simões, S., Zappi, D., da Costa, G. M., de Oliveira, G. & Aona, L. Y. S. Spatial niche modelling of five endemic cacti from the Brazilian Caatinga: past, present and future. Austral Ecol. 45, 1–13 (2019).
    Google Scholar 
    Gorostiague, P., Sajama, J. & Ortega-Baes, P. Will climate change cause spatial mismatch between plants and their pollinators? A test using Andean cactus species. Biol. Conserv. 226, 247–255 (2018).
    Google Scholar 
    Butler, C. J., Wheeler, E. A. & Stabler, L. B. Distribution of the threatened lace hedgehog cactus (Echinocereus reichenbachii) under various climate change scenarios. J. Torre. Bot. Soc. 139, 46–55 (2012).
    Google Scholar 
    Johnson, C. N. Species extinction and the relationship between distribution and abundance. Nature 394, 272–274 (1998).CAS 

    Google Scholar 
    Thuiller, W., Lavorel, S. & Araújo, M. B. Niche properties and geographical extent as predictors of species sensitivity to climate change. Glob. Ecol. Biogeogr. 14, 347–357 (2005).
    Google Scholar 
    Enquist, B. J. Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. Preprint at PeerJ https://doi.org/10.7287/peerj.preprints.2615v2 (2016).Buisson, L., Thuiller, W., Casajus, N., Lek, S. & Grenouillet, G. Uncertainty in ensemble forecasting of species distribution. Glob. Change Biol. 16, 1145–1157 (2010).
    Google Scholar 
    Thuiller, W., Guéguen, M., Renaud, J., Karger, D. N. & Zimmermann, N. E. Uncertainty in ensembles of global biodiversity scenarios. Nat. Commun. 10, 1446 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    Goettsch, B., Durán, A. P. & Gaston, K. J. Global gap analysis of cactus species and priority sites for their conservation. Conserv. Biol. 33, 369–376 (2018).PubMed 

    Google Scholar 
    Maitner, B. S. et al. The bien R package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods Ecol. Evol. 9, 373–379 (2018).
    Google Scholar 
    Karger, D. N. et al. Climatologies at high resolution for the Earth’s land surface areas. Sci. Data 4, 170122 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    Sanderson, B. M., Knutti, R. & Caldwell, P. A representative democracy to reduce interdependency in a multimodel ensemble. J. Clim. 28, 5171–5194 (2015).
    Google Scholar 
    Brodzik, M. J., Billingsley, B., Haran, T., Raup, B. & Savoie, M. H. EASE-Grid 2.0: Incremental but significant improvements for Earth-gridded data sets. ISPRS Int. J. Geo-Inf. 1, 32–45 (2012).
    Google Scholar 
    Venter, O. et al. Global terrestrial human footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Phillips, S. maxnet: Fitting ‘maxent’ species distribution models with ‘glmnet’. R package version 0.1.4. https://CRAN.R-project.org/package=maxnet (2017).Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010).PubMed 
    PubMed Central 

    Google Scholar 
    Dormann, C. F. et al. Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46 (2013).
    Google Scholar 
    Franklin, S. B., Gibson, D. J., Robertson, P. A., Pohlmann, J. T. & Fralish, J. S. Parallel analysis: a method for determining significant principal components. J. Veg. Sci. 6, 99–106 (1995).
    Google Scholar 
    Roberts, D. R. et al. Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography 40, 913–929 (2017).
    Google Scholar 
    Merow, C., Smith, M. J. & Silander, J. A. A practical guide to MaxEnt for modeling species’ distributions: what it does, and why inputs and settings matter. Ecography 36, 1058–1069 (2013).
    Google Scholar 
    Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).
    Google Scholar 
    Calabrese, J. M., Certain, G., Kraan, C. & Dormann, C. F. Stacking species distribution models and adjusting bias by linking them to macroecological models. Glob. Ecol. Biogeogr. 23, 99–112 (2014).
    Google Scholar 
    R Core Team R: A Language and Environment for Statistical Computing Version 3.6.0 (R Foundation for Statistical Computing, 2019). https://www.R-project.org/ More

  • in

    A Mississippian (early Carboniferous) tetrapod showing early diversification of the hindlimbs

    Systematic palaeontology
    Tetrapoda Jaekel, 1909 fide Sues20
    Family undesignated
    Termonerpeton makrydactylus gen. et sp. nov. (Fig. 1)Fig. 1: Termonerpeton makrydactylus gen. et sp. nov. holotype UMZC 2019.1.a Specimen photograph. b Interpretive drawing. Scale bars 10 mm. Abbreviations: acet acetabulum, fem femur, fib fibula, ha haemal arch, ic intercentrum, l left, na neural arch, phal phalanx, piliac p post-iliac process, plc pleurocentrum, r right, sac rib sacral rib, tib tibia.Full size image

    EtymologyGenus: from τέρμωυ (térmon) meaning boundary and ερπετό (erpetó) meaning ‘crawler’, referring to the field boundary walls near the East Kirkton quarry where the late Stan Wood initially discovered fossils from the East Kirkton Limestone and from where the type specimen may have been collected; species: from μακρύς (makrýs) meaning ‘elongate’ and δάχτυλο (dáchtylo; more precisely, δάχτυλο ποδιού, dáchtylo podioú) meaning ‘toe’, referring to the very long pedal digit IV.HolotypeUniversity of Cambridge Museum of Zoology (UMZC) 2019.1. A partial tetrapod postcranium, preserving both pelves, a femur, fibula, tibia, and an almost complete but disarticulated pes. Closely associated with the appendicular elements are dorsally open hoop-shaped centra, a few neural and haemal arches, curved ribs, and a section of articulated gastralia.Locality and horizonEast Kirkton quarry, near Bathgate, Scotland, UK. East Kirkton Limestone, Bathgate Hills Volcanic Formation. Exact horizon is unknown. Brigantian, Viséan, early Carboniferous (=Mississippian)21.Differential diagnosisPossible autapomorphies: ilium with drawn-out, flat, blade-like dorsal process; very large, stout, and elongate metatarsal IV, greatly exceeding the length of metatarsals III and V (~30% or more). Possible tetrapod synapomorphies among post-Devonian taxa: distinct interepipodial space between tibia and fibula; well-ossified tarsus comprising tibiale, fibulare, intermedium, four centralia, and five distal tarsals. Possible amniote synapomorphies, but often showing reversed polarity in several stem- and crown amniote taxa: presumed pedal phalangeal formula 23454; robust and long pedal digit IV; enlarged intermedium and fibulare, together occupying more than half of proximal moiety of tarsus; curved ribs. Characters of uncertain polarity (also present in Caerorhachis): elongate, slender, and posterodorsally oblique post-iliac process; short puboischiadic plate with almost vertical anterior margin; stout femur with poorly pronounced waisting along the shaft, longer than puboischiadic plate; hoop-shaped centra.Attributed specimenNational Museums Scotland (NMS) G.1992.22.1. An articulated, partially complete, large tetrapod pes, preserving a nearly complete array of tarsals, all metatarsals, and the proximal phalanges of digits I–III. Unit 82, East Kirkton Limestone, East Kirkton quarry, near Bathgate, Scotland, UK.
    Specimen description
    Appendicular skeletonMost of the description is based upon the holotype. Both pelves are preserved, one mainly as a natural mould. The puboichiadic plates are short and deep, with an almost vertical anterior margin to the pubis (Fig. 1). In one, the surface of the puboischiadic plate is strongly convex, in the other it is strongly concave. The concave plate may belong to the left pelvis, with the concavity indicating the acetabulum. Both iliac processes of the presumed right ilium are overlain by a neural arch and part of the femur and cannot be seen. The presumed left ilium shows a long, posteriorly pointing post-iliac process that extends as far backward as the posterior edge of the ischium. It retains the proximal, stump-like portion of a dorsal iliac process, continued distally in natural mould as a mediolaterally flattened and blade-like structure. Both processes sit above a short iliac neck. The dorsal iliac process is proportionally longer than in other tetrapods and its knife-like appearance is unique. The angle between the two processes is much more acute than in most other tetrapods, and the nearest comparison is with the divided iliac process of the microsaurs Tuditanus and Ricnodon22 which, however, could merely represent a bifid post-iliac process. Two gaps in ossification are taken as evidence of an ilio-ischiadic suture half-way down the posterior margin on the left pelvis and an ilio-pubic suture halfway down the anterior margin of the right pelvis (Fig. 1). There is no evidence of a puboischiadic suture, although a shallow depression along the ventral margin of the left puboischiadic plate probably marks the junction between pubis and ischium. The complete left puboischiadic plate is 20 mm deep behind the ilium and 30 mm long, with the pubis contributing about one-third of its length and the ischium the remaining two thirds. The anterior margin of the pubis is almost vertical. The dorsal margin of the ischium is shallowly convex for half its length before extending posteroventrally to meet the upturned posterior extremity of the ischium’s ventral margin. There is no evidence as to the angle at which the two pelvic plates met at the symphysis, which would affect the position of the acetabulum relative to the substrate, and thus the effective resting posture of the hindlimb.The left femur is at least 39 mm in length, and longer than the puboischiadic plate. The entire bone is crushed, and its distal end lies partly beneath one of the pelvic halves and a neural arch so that its features cannot easily be made out. A possible intercondylar groove may be present distally, and the extensor surface of its proximal extremity appears to show a subcentral depression. The femur itself is robust with little waisting at mid-shaft. A small internal trochanter lies near its proximal end. The left fibula is approximately 26 mm long along its lateral margin. Its proximal end is narrow and grooved. Its broad and strongly flared distal end suggests a broad contact with the tarsus. The medial turn of the distal end indicates a large interepipodial space. The left tibia is about 20 mm long, slender, and shallowly waisted at mid-shaft. It is not clear which end is proximal and which distal, although probably the proximal is the broader. The tibia is probably more than half the length of the femur. Based upon the femur and tibia lengths, and omitting the ankle and pes, the above figures indicate a total stylopod-zeugopod length of about 65 mm, assuming a fully extended limb.Most of the morphology of the left pes is preserved, showing many well-ossified tarsal bones (Fig. 2). Several of these, including possible distal tarsals II and III lie more or less in anatomical continuity relative to metatarsals II and III, respectively. Other tarsal elements, including possible fibulare, tibiale, centralia, and distal tarsals, are illustrated in Fig. 2. Metatarsal IV lies in anatomical position relative to metatarsals II and III and, at 7 mm in length, it is significantly larger than the latter. The presumed first phalanx of pedal digit IV lies close to metatarsal IV, at an angle of nearly 90° to the latter. It is long and slender, indicating an unusually elongate fourth pedal digit.Fig. 2: Termonerpeton makrydactylus gen. et sp. nov. left hindlimb of UMZC 2019.1.a Specimen photograph, showing close-up view of hindlimb skeleton, b Interpretive drawing, with centralia, distal tarsals, and metatarsals indicated by red, blue, and black Roman numerals, respectively, c Interpretive drawing with dashed lines connecting elements of individual digits, d Reconstruction of left tibia, fibula and pes. Scale bars 10 mm. Abbreviations: interm intermedium, tib tibialia.Full size imageAn array of about 12 phalanges is preserved. They are all disrupted but occur in proximity to one another and, like the first phalanx of pedal digit IV, also mainly lie at right angles to metatarsals III and IV. An additional, acutely angled pointed ungual phalanx, possibly associated with digit II, is also visible. A further two phalanges have been displaced and rest along the anterior edge of the left pelvis. In total, we were, therefore, able to identify 15 elements. The preservation of the pes suggests it was strongly flexed either at death or from tissue shrinkage thereafter. An isolated metatarsal, presumably from the other, missing foot, lies some distance away near the edge of the block. Together, the pedal elements suggest a relatively large foot.A second specimen, NMS G.1992.22.1 (Fig. 3), is represented by an isolated pes. It may belong to Termonerpeton, although it is from a much larger individual. It shows five metatarsals of which the fourth is much longer and more robust than the other four and about twice as long as that of the holotype, while metatarsal V is the smallest. There are three phalanges, plus five distal tarsals. A D-shaped element closely associated with three centralia could be either a fibulare, a displaced intermedium, or centrale IV.Fig. 3: Termonerpeton makrydactylus gen. et sp. nov partial pes, attributed specimen NMS G.1992.22.1.a Specimen photograph, b with centralia, distal tarsals, and metatarsals indicated by red, blue, and black Roman numerals, respectively. Scale bars 10 mm.Full size imageAxial skeletonWhere visible, neural arches have short neural spines and prominent zygapophyses, but their shape is hard to assess as none is well preserved. The element overlying part of the right pelvis and the femur is 7 mm high in total. Numerous dorsally open, hoop-shaped centra about 5 mm in diameter are visible, as well as a few small, oval, shallowly curved elements (Fig. 1). Without further evidence, it is uncertain which of these elements are intercentra and which pleurocentra, though we assume that the larger elements are pleurocentra. The preserved ribs are slender and curved, and include trunk ribs, a possible presacral rib, a possible sacral rib, and a possible postsacral rib. This is long but more or less straight. A bone situated among a cluster of centra, somewhat distant from the other tarsal bones, was originally interpreted by us as a possible fibulare, similar to the fibulare in Proterogyrinus23. However, it might also be interpreted as a sacral rib. If so, its morphology is unique. It is short and widens distally into a fan-shaped structure but does not appear to have a bifid proximal end, unlike the sacral rib in Proterogyrinus23. Three haemal arches are present, one still attached to its half-hoop centrum, a second slightly longer, and a third very short and presumably from a more posterior region of the tail.ComparisonsThe exceptional preservation of tetrapods from the East Kirkton Limestone provides a unique opportunity to study portions of the skeletal anatomy that are otherwise poorly preserved or absent among Mississippian tetrapods. In particular, hindlimbs with a complete or near-complete array of tarsal elements and digits are notably rare. The unusual construction of the pes of Termonerpeton prompted us to examine the hindlimb morphology of six other East Kirkton tetrapods (Fig. 4a–g) alongside a selection of additional, mostly Carboniferous taxa (Fig. 4h–n). We focus on epipodials, tarsi, phalangeal formulae and digit length and proportions. To facilitate visual inspection of these elements, all hindlimbs are drawn to a common tibial length, except for the stem diapsid Petrolacosaurus, in which the epipodials are greatly elongate.Fig. 4: Comparison of the left tibia, fibula, tarsus, and digits of early tetrapods.a Balanerpeton after 2, b Eucritta after 12, c Eldeceeon after 6, d Silvanerpeton after 4, e Westlothiana after 7, f Kirktonecta original, see 15 (the grey area marks the estimated position and extent of the tarsus), g Termonerpeton, h Pederpes after 24, i, Greererpeton after 27, j Caerorhachis after 31, k Archeria after 30, l Hylonomus after 28, m Tuditanus after 22, n Petrolacosaurus after 29. Drawn to the same tibial length apart from n. Scale bars 10 mm.Full size imageIn terms of pes size relative to the tibia, the East Kirkton taxa Balanerpeton, Eucritta, and Silvanerpeton (Fig. 4a, b, d) are similarly proportioned. In contrast, Eldeceeon and Westlothiana (Fig. 4c, e) exhibit somewhat larger pedes. Kirktonecta has proportionally the largest pedes of all (Fig. 4f). Termonerpeton (Fig. 4g) has a pes of similar size to the first three taxa except that digit IV is relatively much longer than in any of the others, with an exceptionally large metatarsal IV. In all those taxa in which digit IV is fully preserved, it is the longest, especially in Eldeceeon and Kirktonecta, but in none does it approach in size and proportions that of Termonerpeton. The illustrated limbs also differ from one another in the degree of ossification of the tarsal bones. Most taxa except Eucritta have some indication of ossified tarsal elements, and some of them, including Balanerpeton and Silvanerpeton, show a complete or almost complete tarsal set. Kirktonecta does have an ossified tarsus, but specimen preservation does not allow us to identify individual elements. The phalangeal count, where known, also varies: 22343 in Balanerpeton2; 223?? in Eucritta12; 23455 in Silvanerpeton4; 23454 in Eldeceeon6, Kirktonecta15, Termonerpeton, and Westlothiana7.In addition, we compared the pedes of East Kirkton tetrapods with those of seven other taxa (Fig. 4h–n): one earlier, Pederpes24; one almost contemporary, Caerorhachis25; four later Carboniferous, Greererpeton26, Hylonomus27, Tuditanus22, and Petrolacosaurus28; and one early Permian, Archeria29. Of these, Greererpeton has relatively the smallest pes. In most, digit IV is the longest, though in Pederpes and Caerorhachis it is incomplete. The pes of Caerorhachis was originally restored with only three phalanges in digit IV30. This is probably incorrect and would be unusual in Carboniferous tetrapods. The pes of the anthracosaur Archeria was originally reconstructed with digit V as the longest29, but again this is unusual among later Carboniferous and early Permian tetrapods and we suspect that digits IV and V have been transposed, and Romer himself expressed doubt about this reconstruction29. In either case, the phalangeal formula of Archeria is similar to that of the East Kirkton anthracosaur Silvanerpeton, as 23455.Among Carboniferous tetrapods, temnospondyls such as Balanerpeton and colosteids such as Greererpeton show a digit IV that is somewhat longer than the others, but metatarsal IV is very similar in length and breadth to the adjacent metatarsals. In anthracosaurs, digit IV is the longest, but again metatarsal IV is not significantly broader than adjacent metatarsals. This is also the case in the early amniote Hylonomus and the microsaur Tuditanus. Among the taxa illustrated here, Termonerpeton shows a strikingly similar pes to that of the Late Pennsylvanian araeoscelidian diapsid Petrolacosaurus (Fig. 4n). In both, metatarsal IV is significantly longer and stouter than others and forms part of a similarly long digit IV. In early amniotes, an elongate digit IV coupled with an elongate metatarsal IV is a common occurrence in other taxa, such as protothyridids (e.g. Anthracodromeus31), basal araeoscelidians (e.g. Spinoaequalis32), younginids (e.g. Youngina33), saurians33, and basal synapsids (e.g. Heleosaurus34,35,36), among others.Based upon available evidence, an elongate digit IV is likely to be the plesiomorphic condition for crown amniotes, being present in Hylonomus, Paleothyris, and Petrolacosaurus (Fig. 4l, n), and shortening of this digit certainly represents a derived feature. In later crown amniotes, the conditions vary, with larger, heavier-bodied tetrapods such as dicynodonts and diadectids having generally shorter toes and adopting a more clearly plantigrade posture. An elongate metatarsal IV and associated digit, however, are not universal among Palaeozoic amniotes, and modifications of these conditions occur repeatedly across clades. For instance, in the eureptile captorhinid Eocaptorhinus, digit IV is also the longest, but the length of metatarsal IV does not greatly exceed that of other metatarsals37. The same is true of some early Permian clades, including seymouriamorphs (e.g. Seymouria38; Discosauriscus39), and diadectids (e.g. Diadectes40), although in the diadectomorph Orobates digit III is a little longer than digit IV41. Among synapsids, dicynodonts such as Diictodon42 and caseids43, to name a few, have five pedal digits of approximately uniform length.We further point out that, while digit IV attains a certain degree of elongation in other early tetrapod groups, such as temnospondyls, in none of them do the relative proportions of this digit (where known) compare to those of several stem and crown amniotes (Fig. 4).Phylogenetic relationshipsThe results of various phylogenetic analyses lend some support to the interpretation of Termonerpeton as a stem amniote, despite its uncertain placement in the unweighted character parsimony analysis (Fig. 5a). In the latter analysis, Termonerpeton appears in a polytomous node alongside baphetids (Eucritta; Baphetes; Megalocephalus), temnospondyls (Balanerpeton; Dendrysekos), the anthracosauroids Eldeceeon and Silvanerpeton, and the problematic Caerorhachis. In all other analyses—implied weights, reweighted characters, and Bayesian—Termonerpeton is placed on the amniote stem group, albeit in different positions, among a diverse array of ‘reptiliomorph’ clades and grades. In the implied weights analysis (Fig. 5b), Termonerpeton, Silvanerpeton, and Eldeceeon form a monophyletic group branching crownward of chroniosaurs plus anthracosaurs and anti-crownward of paraphyletic gephyrostegids. In the reweighted analysis (Fig. 5c), Termonerpeton and Caerorhachis appear as successive sister taxa, in that order, to monophyletic anthracosaurs. In the Bayesian analysis (Fig. 5d), the amniote total group receives moderate support with a credibility value (c.v.) of 76 with Caerorhachis as the most plesiomorphic stem amniote. Crownward of Caerorhachis is a polytomy with low support (c.v. = 59) that subtends Termonerpeton, a clade consisting of Eldeceeon plus Silvanerpeton, a clade of anthracosaurs, and a clade that includes all remaining taxa. In crownward succession, these taxa include chroniosaurs, gephyrostegids, seymouriamorphs, Solenodonsaurus, and Westlothiana as successive sister groups to a strongly supported (c.v. = 100) clade containing diadectomorphs, synapsids, and eureptiles. Although eureptile monophyly is not retrieved, strong support (c.v. = 100) is given to the branch subtending diadectomorphs plus synapsids44.Fig. 5: Results of phylogenetic analyses.a Strict consensus of 120 shortest trees from unweighted analysis (tree length = 1286 steps, ensemble consistency index C.I. = 0.2738 without uninformative characters, ensemble retention index R.I. = 0.5768), b Single tree from implied weights analysis (tree length = 1298 steps, Goloboff fit = −202.59266, C.I. = 0.2712, R.I. = 0.5713), c Single tree from reweighted analysis (tree length = 212,68965 steps, C.I. = 0.4755, R.I. = 0.774), d Bayesian topology with branches reporting credibility values.Full size image More

  • in

    Experimental evidence for snails dispersing tardigrades based on Milnesium inceptum and Cepaea nemoralis species

    Species used in the experimentsMilnesium inceptum32 (Fig. 1A, a picture taken using Olympus BX41 Phase Contrast light Microscope associated with Olympus SC50 digital camera) is an obligatory predatory species with the body length ranging from 326 to 848 μm. It feeds on rotifers, nematodes and other tardigrades and lays smooth eggs in exuviae. To stay active, M. inceptum needs a thin water film around its body14. The species inhabits places exposed to shorter and longer periods of drying i.e. frequently drying mosses growing on cement walls32. Till now it was reported in Poland, Germany, Japan, Switzerland and Bulgaria32. At the same time, it is a perfect organism for our research because (1) it is large and easy to observe, (2) it tolerates frequent periods of entering and leaving anhydrobiosis, (3) it easily creates a tun stage. Milnesium inceptum for experimental purposes were acquired from a moss sample from a cement wall in Poznań, Poland (52°24′15″N, 16°53′18″E). The extraction of tardigrades was conducted under stereomicroscope (Olympus SZ51) using standard methods33. Then specimens, further used in our experiments, have been cultured based on protocol proposed by Roszkowska et al.34. Only fully active, adult specimens were selected for the experiments.Figure 1Model animals used in experiments: (A) Milnesium inceptum; insert shows tardigrade in the tun state; (B) Cepaea nemoralis in its natural environment; (C) a tardigrade that appeared on moss surface during in vivo observation of rehydrated moss cushion (red arrow). Figures were assembled in Corel Photo-Paint 2017 (http://www.corel.com).Full size imageCepaea nemoralis35 (Fig. 1B, a picture taken using Motorola g(9), Camera version 7.3.63.53-whitney) is a stylommatophoran European land snail species, which is widespread and common throughout the continent36. The average maximum shell diameter is 20 to 22 mm37. It feeds on plant materials available, yet has a strong preference for dead and senescent herbs38. C. nemoralis occurs in variable habitats (frequently in synanthropic ones) such as forests, meadows, gardens, near shrubs or dunes36.The period of its activity falls on the growing season; it usually comes out of the shell and crawls when the air humidity reaches 70% or more, independently from solar radiation and air temperature28. The species is a good model for our study due to its: (1) large size compared to tardigrades, and (2) co-occurrence with M. inceptum in natural environments. Individuals of C. nemoralis were harvested from anthropogenic environment: gardens adjacent to detached houses (52°25′28″N, 16°46′52″E). Snails were collected from plants, cement walls and ground surfaces. After collection, all C. nemoralis specimens were washed-up and placed in 30 L (480 × 360 × 252 mm) transparent plastic box with mesh covering for ventilation. Soil and rocks were placed in the box allowing to maintain a moist shelter for snails, and a sepia was used as a source of a calcium. Animals were fed with lettuce, cabbage and nettle twice a week and sprinkled with water to stimulate their activity. Box containing snails was kept in a rearing room, at 17 °C in 12:12 photoperiod. Snails were kept in the box for 1.5 months prior to the experiments. For the experiments we used only adult animals. The snails were checked under Olympus SZX7 stereomicroscope prior to the experiment to ensure they were free of tardigrades.Pilot studiesDoes the tardigrades’ distribution within a moss cushion enable tardigrade-snail contact?To check whether tardigrades may come into a close encounter with the snail in the natural environment (which would be impossible if the tardigrades were only present in the lower layers of the moss), we investigated the distribution of water bears within moss cushions. The observations were performed for 6 samples of dried moss cushions (ca. 1 cm high and 3 cm in diameter). The moss containing M. inceptum specimens, was collected from a concrete wall in Poznań, Poland (52°24′15″N, 16°53′18″E), the same from which tardigrades were initially collected for the culturing purposes. Three moss cushions were rehydrated, and left for 3 h followed by further observation to check whether tardigrades may actively move across the moss cushion. On the remaining three moss samples, a horizontal cut was made through the center of the moss cushion to check in which layer tardigrade tuns are present while the moss remains dry. The extraction of tardigrades from separated layers was conducted under stereomicroscope (Olympus SZ51) using standard methods33.Within the dry moss cushions tardigrades were present in both the upper and lower moss layers. We did not observe any difference in the number of individuals of M. inceptum that would be dependent on the moss layer. A total of 353 tardigrades were extracted from one moss cushion (dry weight of moss = 0.332 g), what gives the density of tardigrades per 1 g of dry moss sample equal to 1063 specimens. The observation of rehydrated moss cushions conducted in vivo using Olympus SZX16 stereomicroscope associated with Olympus DP74 digital camera and cellSens software revealed that single active tardigrades may also appear on the moss surface (Fig. 1C, red arrow). Therefore, observed in the pilot studies tardigrades distribution within the moss cushion enables tardigrade-snail contact.Is it possible for a tardigrade to take a snail ride?The initial observations were carried out for snails and tardigrades to check whenever a tardigrade may be transferred by a snail. In total, 10 snails and 20 active tardigrades were used. Two variants of Petri dishes (ø 90 mm) were prepared: (1) with smooth and (2) scratched bottom, to avoid and allow tardigrade attachment to the bottom of the dish, respectively. We repeated the observation five times per option. For each single observation we used one snail and two tardigrades.Snails and tardigrades were split equally between the pilot’s experimental options (in total 5 snails and 10 tardigrades per option). We checked whether tardigrades may be transferred by snails by putting tardigrades in the drop of water in the center of a Petri dish and releasing an active snail to crawl through the drop. In total, in the case of the smooth-bottom option, three tardigrades glued to the snail’s body within which two were moved to a distance up to a few centimeters. The third one fixed to a snail’s leg and had a potential to be transferred to a greater distance. In the case of the dishes with the scratched bottom, we did not notice any transfer. Tardigrades were attached tightly to the dishes’ bottom and remained unmoved after the snail had passed through them. Therefore, the observation in the pilot study confirmed that tardigrades may stick to snails’ body and be transferred by a gastropod at least when the substratum (bottom of the dish) is smooth.Experimental design
    Experiment 1. Do snails have a significant effect on tardigrade dispersion that depends on the substrate type?As the laboratory environment offers limited possibilities to reflect natural conditions, we aimed to create an environment similar to the natural one by eliminating as many artificial elements as possible and, at the same time, enabling observation and data collection. To imitate a natural microhabitat of water bears we used a piece of moss as a substrate. Moss is a natural shelter and a hunting space for these animals, and a gripping surface that prevents them from being easily carried away by a stream of water or wind. The moss Vesicularia dubyana39 used in the experiment was purchased in an aquarium shop and was derived from an in vitro culture. It was checked under Olympus SZX7 stereomicroscope prior to the experiment to ensure it was free of tardigrades. For experimental purposes we used plastic ventilated boxes with dimensions 950 mm × 950 mm × 600 mm, tightly closed with a plastic lid. The bottom of each box was scratched with sandpaper in order to (1) imitate a rough surface of a concrete wall to which mosses are attached in the natural environment; (2) allow tardigrade locomotion. At the same time, moss and (unfortunately) plastic elements are quite common surroundings of C. nemoralis frequently found in anthropogenic habitats36.Using transparent, non-toxic aquarium silicone, a square with a side length of 3 cm and a height of 0.5 cm was mounted on the bottom of the box. Before starting the experiment, the tightness of the square silicone barrier was checked by pouring 2.5 ml of water inside and leaving the boxes for observation for 24 h. After this time, all silicone squares turned out to be impermeable to water.Boxes for each of the experimental option, namely: (A) control (further in the text referred as C), (B) tardigrades + snail (referred as TS), and (C) tardigrades + snail + moss (referred as TSM, see Fig. 2), were prepared in a following way: 2.5 ml of water was added to the scratched bottom of the box inside the silicone square and 7.5 ml to the area outside of the silicone square to enable survival and active locomotion of tardigrades on both sides of the silicone barrier. Then, 10 active individuals of M. inceptum taken from the culture were transferred to the center of the silicone square. It was repeated for 90 boxes (30 boxes per each C, TS and TSM option). Therefore we used 300 tardigrades per each experimental option which gives 900 tardigrades in total for all experimental options. In case of 30 boxes with TSM option, a piece of moss (ca. 2.5 cm in diameter) was added. It was situated in the center of the silicone square, just after the tardigrades were placed at the boxes in order to isolate tardigrades from the snail during the experiment.Figure 2Graphical representation of three designed experimental options of the experiment 1. (A) 10 tardigrades in the silicone square (control (C)); (B) 10 tardigrades in the silicone square and one snail placed in the box (tardigrades + snail (TS)); (C) 10 tardigrades in the silicone square, one snail placed in the box and additional piece of the moss added as a barrier between tardigrades and snail (tardigrades + snail + moss (TSM)). Figures were assembled in Corel Photo-Paint 2017 (http://www.corel.com).Full size imageFinally, in the boxes targeted for TS and TSM experimental options, one adult and active individual of C. nemoralis snail was placed in each box outside the silicone square. In total, 60 snails were used (30 individuals per experimental option).The boxes were then placed in the rearing room (17 °C, 80% of humidity, photoperiod 12:12) for 72 h. After this time, the number of tardigrades inside and outside the silicone square was counted (both: live and dead) separately for each box, using Olympus SZX7 stereomicroscope.Experiment 2. Effect of the snail’s mucus on tardigrade recovery to active life after anhydrobiosis
    Milnesium inceptum anhydrobiosis protocolOnly fully active, adult specimens of medium body length were selected for the experiment. The animals were transferred to ø 3.5 cm vented Petri-dishes with bottom scratched by sandpaper to allow tardigrade locomotion. Five tardigrade individuals were placed to each Petri dish together with 450 µl of water and then dehydrated. In total, 16 Petri dishes with 5 tardigrades on each were prepared. Dehydration process lasted 72 h and was performed in the Q-Cell incubator (40–50% RH, 20 °C, darkness). After that time tardigrade tuns were kept under the abovementioned conditions for 7 days.Impact of the snail’s mucus on tardigrade tunsAfter 7 days of anhydrobiosis, one individual of C. nemoralis was transferred to each dish with tardigrade tuns and was left there for 1 min allowing the snail to actively crawl over the tuns. 30 min after the snail was removed from the dish, tardigrade tuns were observed under the Olympus SZX7 stereomicroscope for any animal movements. Then, all covered and vented dishes were left in the Q-Cell incubator overnight. After 24 h, the dried tuns were rehydrated by adding 3 ml of water to each Petri dish to check whether snail’s mucus affected mortality rates of tardigrades. After 3 and 24 h following rehydration tardigrade tuns were observed for any animal movements. Pictures of tuns were taken using Olympus SZ61 stereomicroscope associated with Olympus UC30 camera (Fig. 3). As reference data on the rehydration of the M. inceptum tuns free of the snail’s mucus, we used the data from Roszkowska et al.20 who tested anhydrobiosis survivability of above-mentioned species. Individuals used for the tuns preparation in the control option were collected from the same laboratory breeding stock, and prepared at the same laboratory conditions as those used in our experiments20.Figure 3Milnesium inceptum tuns: (A,B) before contact with snail mucus; (C,D) coated with wet snail mucus; (E,F) coated with dry snail mucus. Figures were assembled in Corel Photo-Paint 2017 (http://www.corel.com).Full size imageStatistical analysesThe number of tardigrades relocated in each experimental option (C, TS and TSM) was compared with a one-way ANOVA randomized version using RundomPro 3.14 software40. We used non-parametric methods because of the lack of normality. Differences were considered significant at p  More

  • in

    Genomic evidence for homoploid hybrid speciation between ancestors of two different genera

    Lotsy, J. P. Evolution by Means of Hybridization (Martinus Nijhoff, 1916).Abbott, R. J. et al. Hybridization and speciation. J. Evol. Biol. 26, 229–246 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Schumer, M., Rosenthal, G. G. & Andolfatto, P. How common is homoploid hybrid speciation? Evolution 68, 1553–1560 (2014).PubMed 
    Article 

    Google Scholar 
    Payseur, B. A. & Rieseberg, L. H. A genomic perspective on hybridization and speciation. Mol. Ecol. 25, 2337–2360 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, Z. F. et al. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. Mol. Plant 14, 208–222 (2021).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Müntzing, A. Outlines to a genetic monograph for the genus Galeopsis: with special reference to the nature and inheritance of partial sterility. Hereditas 13, 185–341 (1930).Article 

    Google Scholar 
    Schumer, M., Cui, R., Rosenthal, G. G. & Andolfatto, P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. Plos. Genet. 11, e1005041 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Taylor, S. A. & Larson, E. L. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170–177 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Kong, S. & Kubatko, L. S. Comparative performance of popular methods for hybrid detection using genomic data. Syst. Biol. 70, 891–907 (2021).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Goulet, B. E., Roda, F. & Hopkins, R. Hybridization in plants: old ideas, new techniques. Plant Physiol. 173, 65–78 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Jiang, Y. F. et al. Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. N. Phytol. 228, 409–414 (2020).Article 

    Google Scholar 
    Rokas, A. & Holland, P. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454–459 (2000).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Bapteste, E. & Philippe, H. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol. Biol. Evol. 19, 972–977 (2002).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Mavárez, J. et al. Speciation by hybridization in Heliconius butterflies. Nature 441, 868–871 (2006).ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    Lamichhaney, S. et al. Rapid hybrid speciation in Darwin’s finches. Science 359, 224–228 (2018).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Zhang, B. W. et al. Phylogenomics reveals an ancient hybrid origin of the Persian walnut. Mol. Biol. Evol. 36, 2451–2461 (2019).CAS 
    Article 

    Google Scholar 
    Guo, X., Thomas, D. C. & Saunders, R. M. K. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae). Mol. Phylogenet. Evol. 127, 14–29 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Winkler, H. Betulaceae. In: Pflanzenreich IV (Verlag von Wilhelm Engelmann, 1904).Li, P. Q. & Skvortsov, A. K. Betulaceae. In: Flora of China (Science Press & Missouri Botanical Garden Press, 1999).Crane, P. R. Betulaceous leaves and fruits from the British Upper Palaeocene. Bot. J. Linn. Soc. 83, 103–136 (1981).Article 

    Google Scholar 
    Li, P. Q. & Cheng, S. X. Betulaceae. In: Flora Reipublicae Popularis Sinicae (Science Press, 1979).Yoo, K. O. & Wen, J. Phylogeny and biogeography of Carpinus and subfamily Coryloideae (Betulaceae). Int. J. Plant Sci. 163, 641–650 (2002).Article 

    Google Scholar 
    Li, J. H. Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae). J. Sys. Evol. 46, 333–340 (2008).
    Google Scholar 
    Yang, X. Y. et al. Plastomes of Betulaceae and phylogenetic implications. J. Sys. Evol. 57, 508–518 (2019).Article 

    Google Scholar 
    Yang, Y. Z. et al. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat. Commun. 9, 5449 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Yang, X. Y. et al. A chromosome-level reference genome of the hornbeam, Carpinus fangiana. Sci. Data 7, 24 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li, Y. et al. The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding. Hortic. Res. 8, 54 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Salojärvi, J. et al. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat. Genet. 49, 904–912 (2017).PubMed 
    Article 
    CAS 

    Google Scholar 
    Tajima, F. Evolutionary relationship of DNA-sequences in finite populations. Genetics 105, 437–460 (1983).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Blischak, P. D., Chifman, J., Wolfe, A. D. & Kubatko, L. S. HyDe: a Python package for genome-scale hybridization detection. Syst. Biol. 67, 821–829 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kubatko, L. S. & Chifman, J. An invariants-based method for efficient identification of hybrid species from large-scale genomic data. BMC Evol. Biol. 19, 112 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Baack, E., Melo, M. C., Rieseberg, L. H. & Ortiz-Barrientos, D. The origins of reproductive isolation in plants. N. Phytol. 207, 968–984 (2015).Article 

    Google Scholar 
    Sobel, J. M. & Chen, G. F. Unification of methods for estimating the strength of reproductive isolation. Evolution 68, 1511–1522 (2014).PubMed 
    Article 

    Google Scholar 
    Imura, Y. et al. CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis. Plant Cell Physiol. 53, 287–303 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kim, S.-J. & Bassham, D. C. TNO1 is involved in salt tolerance and vacuolar trafficking in Arabidopsis. Plant Physiol. 156, 514–526 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, F. et al. Control of leaf blade outgrowth and floral organ development by LEUNIG, ANGUSTIFOLIA3 and WOX transcriptional regulators. N. Phytol. 223, 2024–2038 (2019).CAS 
    Article 

    Google Scholar 
    Liu, Z. C., Franks, R. G. & Klink, V. P. Regulation of gynoecium marginal tissue formation by LEUNIG and AINTEGUMENTA. Plant Cell 12, 1879–1891 (2000).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sitaraman, J., Bui, M. & Liu, Z. LEUNIG_HOMOLOG and LEUNIG perform partially redundant functions during Arabidopsis embryo and floral development. Plant Physiol. 147, 672–681 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen, C. L. et al. Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae). J. Sys. Evol. 59, 1198–1208 (2021).Article 

    Google Scholar 
    Morales-Briones, D. F. et al. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70, 219–235 (2021).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Yang, Y. Z. et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants 6, 215–222 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Stull, G. W. et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nat. Plants 7, 1015–1025 (2021).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Luo, X. et al. Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor. Mol. Ecol. 26, 3037–3049 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Grover, C. E. et al. Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol. Phylogenet. Evol. 92, 45–52 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Edger, P. P., McKain, M. R., Bird, K. A. & VanBuren, R. Subgenome assignment in allopolyploids: challenges and future directions. Curr. Opin. Plant Biol. 42, 76–80 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
    Google Scholar 
    Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. Plos ONE 9, e112963 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

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

    Google Scholar 
    Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinf. 5, 4.10.1–4.10.14 (2004).Article 

    Google Scholar 
    Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Marchler-Bauer, A. et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39, D225–D229 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).CAS 
    Article 

    Google Scholar 
    Conesa, A. & Götz, S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832 (2008).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ye, G. et al. De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. Plant J. 97, 779–794 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Marrano, A. et al. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. GigaScience 9, giaa050 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Löytynoja, A. Phylogeny-aware alignment with PRANK. In: Multiple Sequence Alignment Methods, Methods in Molecular Biology (Humana Press, 2014).Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, Y. P. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kielbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 153 (2018).Article 

    Google Scholar 
    Sukumaran, J. & Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569–1571 (2010).CAS 
    PubMed 
    Article 

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

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

    Google Scholar 
    Malinsky, M., Matschiner, M. & Svardal, H. Dsuite—Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).PubMed 
    Article 

    Google Scholar 
    Hudson, R. R., Kreitman, M. & Aguadé, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Selective feeding of three bivalve species on the phytoplankton community in a marine pond revealed by high-throughput sequencing

    Mao, Y. et al. Bivalve production in China (eds. Smaal, A., Ferreira, J., Grant, J., Petersen, J, & Strand, Ø.) 51–72 (Springer, New York, 2019).CFSY. China fishery statistical yearbook. (China Agriculture Publishing House, Beijing, 2021).Muller-Feuga, A. Microalgae for aquaculture: the current global situation and future trends (ed. Richmond, A.) 352–364 (Blackwell Science, Hoboken, 2004).Lindahl, O. Mussel farming as a tool for re‐eutrophication of coastal waters: experiences from Sweden (ed. Shumway, S. E.) 217–237 (Wiley-Blackwell, Hoboken, 2011).Petersen, J. K., Hasler, B., Timmermann, K., Nielsen, P. & Holmer, M. Mussels as a tool for mitigation of nutrients in the marine environment. Mar. Pollut. Bull. 82, 137–143 (2014).CAS 

    Google Scholar 
    Petersen, J. K., Saurel, C., Nielsen, P. & Timmermann, K. The use of shellfish for eutrophication control. Aquacult. Int. 24, 857–878 (2016).
    Google Scholar 
    Hily, C., Grall, J., Chauvaud, L., Lejart, M. & Clavier, J. CO2 generation by calcified invertebrates along rocky shores of Brittany, France. Mar. Freshwater. Res. 64, 91–101 (2013).CAS 

    Google Scholar 
    Filgueira, R. Strohmeier, T. & Strand, Ø. Regulating services of bivalve molluscs in the context of the carbon cycle and implications for ecosystem valuation (eds. Smaal, A., Ferreira, J., Grant, J., Petersen, J. & Strand, Ø.) 231–251 (Springer, New York, 2019).Newell, R. I. Ecosystem influences of natural and cultivated populations of suspension-feeding bivalve molluscs: a review. J. Shellfish. Res. 23, 51–62 (2004).
    Google Scholar 
    Benemann, J. R. Microalgae aquaculture feeds. J. Appl. Phycol. 4, 233–245 (1992).
    Google Scholar 
    Brown, M. R. & Blackburn, I. Live microalgae as feeds in aquaculture hatcheries (eds. Allan, G. & Burnell, G.) 117–156 (Woodhead Publishing Series in Food Science, Technology and Nutrition, 2013).Thajuddin, N. & Subramanian, G. Cyanobacterial biodiversity and potential applications in biotechnology. Curr. Sci. 89, 47–57 (2005).CAS 

    Google Scholar 
    Caers, M., Coutteau, P. & Sorgeloos, P. Dietary impact of algal and artificial diets, fed at different feeding rations, on the growth and fatty acid composition of Tapes philippinarum (L.) spat. Aquaculture 170, 307–322 (1999).CAS 

    Google Scholar 
    Chen, S. M., Tseng, K. Y. & Huang, C. H. Fatty acid composition, sarcoplasmic reticular lipid oxidation, and immunity of hard clam (Meretrix lusoria) fed different dietary microalgae. Fish. Shellfish. Immunol. 45, 141–145 (2015).CAS 

    Google Scholar 
    Rosa, M., Ward, J. E. & Shumway, S. E. Selective capture and ingestion of particles by suspension-feeding bivalve molluscs: a review. J. Shellfish. Res. 37, 727–746 (2018).
    Google Scholar 
    Ward, J. E. & Shumway, S. E. Separating the grain from the chaff: particle selection in suspension-and deposit-feeding bivalves. J. Exp. Mar. Biol. Ecol. 300, 83–130 (2004).
    Google Scholar 
    Tang, B., Liu, B., Wang, G., Tao, Z. & Xiang, J. Effects of various algal diets and starvation on larval growth and survival of Meretrix meretrix. Aquaculture 254, 526–533 (2006).
    Google Scholar 
    Espinosa, E. P., Cerrato, R. M., Wikfors, G. H. & Allam, B. Modeling food choice in the two suspension-feeding bivalves, Crassostrea virginica and Mytilus edulis. Mar. Biol. 163, 1–13 (2016).
    Google Scholar 
    Jones, J., Allam, B. & Espinosa, E. P. Particle selection in suspension-feeding bivalves: does one model fit all?. Biol. Bull. 238, 41–53 (2020).CAS 

    Google Scholar 
    Pales Espinosa, E., Cerrato, R. M., Wikfors, G. H. & Allam, B. Modeling food choice in the two suspension-feeding bivalves, Crassostrea virginica and Mytilus edulis. Mar. Biol. 163, 1–13 (2016).CAS 

    Google Scholar 
    Barillé, L., Prou, J., Héral, M. & Bourgrier, S. No influence of food quality, but ration-dependent retention efficiencies in the Japanese oyster Crassostrea gigas. J. Exp. Mar. Biol. Ecol. 171, 91–106 (1993).
    Google Scholar 
    Petersen, J. K. et al. Intercalibration of mussel Mytilus edulis clearance rate measurements. Mar. Ecol. Prog. Ser. 267, 187–194 (2004).ADS 

    Google Scholar 
    Zhang, T. et al. Effects of environmental factors on the survival and growth of juvenile hard clam Mercenaria mercenaria (Linnaeus,1758). Oceanol. Limnol. Sin. 34, 142–149 (2003).
    Google Scholar 
    Matias, D. et al. The influence of different microalgal diets on European clam (Ruditapes decussatus, Linnaeus, 1758) larvae culture performances. Aquacult. Res. 46, 2527–2543 (2015).
    Google Scholar 
    Liao, K. et al. qPCR analysis of bivalve larvae feeding preferences when grazing on mixed microalgal diets. PLoS ONE 12, e0180730 (2017).
    Google Scholar 
    Sautour, B., Artigas, L. F., Delmas, D., Herbland, A. & Laborde, P. Grazing impact of micro- and mesozooplankton during a spring situation in coastal waters off the Gironde estuary. J. Plankton. Res. 22, 531–552 (2000).
    Google Scholar 
    Manoylov, K. M. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment. J. Phycol. 50, 409–424 (2014).
    Google Scholar 
    Shokralla, S. et al. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol. Ecol. Resour. 14, 892–901 (2014).CAS 

    Google Scholar 
    Hirai, J., Hidaka, K., Nagai, S. & Ichikawa, T. Molecular-based diet analysis of the early post-larvae of Japanese sardine Sardinops melanostictus and Pacific round herring Etrumeus teres. Mar. Ecol. Prog. Ser. 564, 99–113 (2017).ADS 
    CAS 

    Google Scholar 
    Su, M., Liu, H., Liang, X., Gui, L. & Zhang, J. Dietary analysis of marine fish species: enhancing the detection of prey-specific dna sequences via high-throughput sequencing using blocking primers. Estuar. Coast. 41, 560–571 (2018).
    Google Scholar 
    Talwar, C., Nagar, S., Lal, R. & Negi, R. K. Fish gut microbiome: current approaches and future perspectives. Indian J. Microbiol. 58, 397–414 (2018).CAS 

    Google Scholar 
    Yi, X. et al. In situ diet of the copepod Calanus sinicus in coastal waters of the South Yellow Sea and the Bohai Sea. Acta. Oceanol. Sin. 36, 68–79 (2017).CAS 

    Google Scholar 
    Reis, A. D., Jeffs, A. G. & Lavery, S. D. From feeding habits to food webs: exploring the diet of an opportunistic benthic generalist. Mar. Ecol. Prog. Ser. 655, 107–121 (2020).ADS 

    Google Scholar 
    Yeh, H. D., Questel, J. M., Maas, K. R. & Bucklin, A. Metabarcoding analysis of regional variation in gut contents of the copepod Calanus finmarchicus in the North Atlantic Ocean. Deep Sea Res. II 180, 104738 (2020).
    Google Scholar 
    Zeale, M. R., Howeverlin, R. K., Barker, G. L., Lees, D. C. & Jones, G. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol. Ecol. Resour. 11, 236–244 (2011).CAS 

    Google Scholar 
    Sherwood, A. R. & Presting, G. G. Universal primers amplify a 23s rDNA plastid marker in eukaryotic algae and cyanobacteria. J. Phycol. 43, 605–608 (2007).
    Google Scholar 
    Qiao, L., Chang, Z., Li, J. & Chen, Z. Phytoplankton community succession in relation to water quality changes in the indoor industrial aquaculture system for Litopenaeus vannamei. Aquaculture 527, 735441 (2020).CAS 

    Google Scholar 
    Vahl, O. Efficiency of particle retention in Mytilus edulis L. Ophelia 10, 17–25 (1972).
    Google Scholar 
    Riisgård, H. U. Efficiency of particle retention and filtration rate in 6 species of northeast American bivalves. Mar. Ecol. Prog. Ser. 45, 217–223 (1988).ADS 

    Google Scholar 
    Rosa, M. et al. Examining the physiological plasticity of particle capture by the blue mussel, Mytilus edulis (L.): confounding factors and potential artifacts with studies utilizing natural seston. J. Exp. Mar. Biol. Ecol. 473, 207–217 (2015).
    Google Scholar 
    Shumway, S. E. et al. Flow cytometry: a new method for characterization of differential ingestion, digestion and egestion by suspension feeders. Mar. Ecol. Prog. Ser. 24, 201–204 (1985).ADS 

    Google Scholar 
    Dupuy, C. et al. Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the mediterranean thau lagoon. Mar. Ecol. Prog. Ser. 205, 171–184 (2000).ADS 

    Google Scholar 
    Strøhmeier, T., Strand, Ø., Alunno-Bruscia, M., Duinker, A. & Cranford, P. J. Variability in particle retention efficiency by the mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 412, 96–102 (2012).
    Google Scholar 
    Yahel, G., Marie, D., Beninger, P. G., Eckstein, S. & Genin, A. In situ evidence for pre-capture qualitative selection in the tropical bivalve Lithophaga simplex. Aquat. Biol. 6, 235–246 (2009).
    Google Scholar 
    Bass, A. E., Malouf, R. E. & Shumway, S. E. Growth of northern quahogs, Mercenaria mercenaria (Linnaeus, 1758) fed on picophytoplankton. J. Shellfish. Res. 9, 299–307 (1990).
    Google Scholar 
    Leblanc, A. et al. Determination of isotopic labeling of proteins by precursor ion scanning liquid chromatography/tandem mass spectrometry of derivatized amino acids applied to nuclear magnetic resonance studies. Rapid Commun. Mass. Spectrom. 26, 1165–1174 (2012).ADS 
    CAS 

    Google Scholar 
    Sonier, R. et al. Picoplankton contribution to Mytilus edulis growth in an intense culture environment. Mar. Biol. 163, 73–85 (2016).
    Google Scholar 
    Herdman, M., Castenholz, R. W., Waterbury, J. B. & Rippka, R. Form-genus XIII. Synechococcus (eds. Boone, D. R. & Castenholz, R. W.) 508–512 (Springer, New York, 2001).Hibberd, D. J. Notes on the taxonomy and nomenclature of the algal classes Eustigmatophyceae and Tribophyceae (synonym Xanthophyceae). Bot. J. Linn. Soc. 82, 93–119 (1981).
    Google Scholar 
    Wei, Y. Chrysochromulina parva Lackey Prymnesiophyceae new record in China and its seasonal fluctuation in Lake Donghu, Wuhan. Acta Hydrobiol. Sin. 20, 317–321 (1996).
    Google Scholar 
    Stockner, J. G. & Antia, N. J. Algal picoplankton from marine and freshwater ecosystems: a multidisciplinary perspective. Can. J. Fish. Aquat. Sci. 43, 2472–2503 (1986).
    Google Scholar 
    Gallager, S., Waterbury, J. & Stoecker, D. Efficient grazing and utilization of the marine cyanobacterium Synechococcus sp. by larvae of the bivalve Mercenaria mercenaria. Mar. Biol. 119, 251–259 (1994).
    Google Scholar 
    Seychelles, L. H., Audet, C., Tremblay, R., Fournier, R. & Pernet, F. Essential fatty acid enrichment of cultured rotifers (Brachionus plicatilis, Müller) using frozen-concentrated microalgae. Aqua. Nut. 15, 431–439 (2009).CAS 

    Google Scholar 
    Hughes, T. G. The sorting of food particles by Abra sp. (bivalvia: tellinacea). J. Exp. Mar. Biol. Ecol. 20, 137–156 (1975).
    Google Scholar 
    Hernroth, B., Larsson, A. & Edebo, L. Influence on uptake, distribution and elimination of Salmonella typhimurium in the blue mussel, Mytilus edulis, by the cell surface properties of the bacteria. J. Shellfish. Res. 19, 167–174 (2000).
    Google Scholar 
    Rosa, M. et al. Effects of particle surface properties on feeding selectivity in the eastern oyster Crassostrea virginica and the blue mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 446, 320–327 (2013).
    Google Scholar 
    Rosa, M., Ward, J. E., Holohan, B. A., Shumway, S. E. & Wikfors, G. H. Physicochemical surface properties of microalgae and their combined effects on particle selection by suspension-feeding bivalve molluscs. J. Exp. Mar. Biol. Ecol. 486, 59–68 (2017).CAS 

    Google Scholar 
    Grasland, B., Mitalane, J., Briandet, R., Quemener, E. & Haras, D. Bacterial biofilm in seawater: cell surface properties of early-attached marine bacteria. Biofouling 19, 307–313 (2003).CAS 

    Google Scholar 
    Ozkan, A. & Berberoglu, H. Physico-chemical surface properties of microalgae. Colloids. Surf. B. 112, 287–293 (2013).CAS 

    Google Scholar 
    Dadon-Pilosof, A. et al. Surface properties of SAR 11 bacteria facilitate grazing avoidance. Nat. Microbiol. 2, 1608–1615 (2017).
    Google Scholar 
    Xiao, G., Zhang, J., Cai, X., Lu, R. & Fang, J. Studies on the filtration feeding, respiration ration and excretion of Ruditapes philippinarum juvenile. J. Oceanogr. Taiwan Strait 25, 30–35 (2006).
    Google Scholar 
    Atkins, D. On the ciliary mechanisms and interrelationships of lamellibranchs. VII: latero-frontal cilia of the gill filaments and their phylogenetic value. Q. J. Microsc. Sci. 80, 345–433 (1938).
    Google Scholar 
    Owen, G. & Mccrae, J. M. Further studies on the latero-frontal tracts of bivalves. Proc. R. Soc. London. 194, 527–544 (1976).ADS 

    Google Scholar 
    Owen, G. Classification and the bivalve gill. Phil. Trans. R. Soc. Lond. 284, 377–385 (1978).
    Google Scholar 
    Ward, J. E., Sanford, L. P. & Newell, R. A new explanation of particle capture in suspension- feeding bivalve molluscs. Limnol. Oceanogr. 43, 741–752 (1998).ADS 

    Google Scholar 
    Winter, J. E. A review on the knowledge of suspension-feeding in lamellibranchiate bivalves, with special reference to artificial aquaculture systems. Aquaculture 13, 1–33 (1978).
    Google Scholar 
    Newell, C. R., Wildish, D. J. & Macdonald, B. A. The effects of velocity and seston concentration on the exhalant siphon area, valve gape and filtration rate of the mussel Mytilus edulis. J. Exp. Mar. Biol. Ecol. 262, 91–111 (2001).
    Google Scholar 
    Jacobs, P., Troost, K., Riegman, R., Van der, M. & J.,. Length- and weight-dependent clearance rates of juvenile mussels (Mytilus edulis) on various planktonic prey items. Helgol. Mar. Res. 69, 101–112 (2015).ADS 

    Google Scholar 
    Ivlev, V. S. Experimental ecology of the feeding of fish. (Yale University Press New Haven, Connecticut, 1961) p 302.Strauss, R. E. Reliability estimates for Ivlevs electivity index the forage ratio and a proposed linear index of food selection. Trans. Am. Fish. Soc. 108, 344–352 (1979).
    Google Scholar 
    Puig, S., Videla, F., Cona, M. I. & Monge, A. S. Use of food availability by guanacos (Lama guanicoe) and livestock in Northern Patagonia (Mendoza, Argentina). J. Arid. Environ. 47, 291–308 (2001).ADS 

    Google Scholar  More

  • in

    Variation in the ratio of compounds in a plant volatile blend during transmission by wind

    Beyaert, I. & Hilker, M. Plant odour plumes as mediators of plant–insect interactions. Biol. Rev. 89, 68–81 (2014).
    Google Scholar 
    Simpraga, M., Takabayashi, J. & Holopainen, J. K. Language of plants: Where is the word?. J. Integr. Plant Biol. 58, 343–349 (2016).CAS 

    Google Scholar 
    Bruce, T. J. A., Wadhams, L. J. & Woodcock, C. M. Insect host location: A volatile situation. Trends Plant Sci. 10, 269–274 (2005).CAS 

    Google Scholar 
    Bruce, T. J. A. & Pickett, J. A. Perception of plant volatile blends by herbivorous insects—Finding the right mix. Phytochemistry 72, 1605–1611 (2011).CAS 

    Google Scholar 
    Raguso, R. A. Wake up and smell the roses: The ecology and evolution of floral scent. Annu. Rev. Ecol. Evol. S. 39, 549–569 (2008).
    Google Scholar 
    Schiestl, F. P. The evolution of floral scent and insect chemical communication. Ecol. Lett. 13, 643–656 (2010).
    Google Scholar 
    Arimura, G., Kost, C. & Boland, W. Herbivore-induced, indirect plant defences. Biochim. Biophys. Acta. 1734, 91–111 (2005).CAS 

    Google Scholar 
    Hare, J. D. Ecological role of volatiles produced by plants in response to damage by herbivorous insects. Annu. Rev. Entomol. 56, 161–180 (2011).CAS 

    Google Scholar 
    Laothawornkitkul, J., Taylor, J. E., Paul, N. D. & Hewitt, C. N. Biogenic volatile organic compounds in the earth system. New Phytol. 183, 27–51 (2009).CAS 

    Google Scholar 
    Dicke, M., van Loon, J. J. A. & Soler, R. Chemical complexity of volatiles from plant induced by multiple attack. Nature Chem. Biol. 5, 317–324 (2009).CAS 

    Google Scholar 
    Loreto, F. & Schnitzler, J. P. Abiotic stresses and induced BVOCs. Trends Plant Sci. 15, 154–166 (2010).CAS 

    Google Scholar 
    Tasin, M. et al. Synergism and redundancy in a plant volatile blend attracting grapevine moth females. Phytochemistry 68, 203–209 (2007).CAS 

    Google Scholar 
    Riffell, J. A., Lei, H., Christensen, T. A. & Hildebrand, J. G. Characterization and coding of behaviorally significant odor mixtures. Curr. Biol. 19, 335–340 (2009).CAS 

    Google Scholar 
    Riffell, J. A., Lei, H. & Hildebrand, J. G. Neural correlates of behavior in the moth Manduca sexta in response to complex odors. Proc. Natl. Acad. Sci. USA 106, 19219–19226 (2009).ADS 
    CAS 

    Google Scholar 
    Atema, J. Eddy chemotaxis and odor landscapes: Exploration of nature with animal sensors. Biol. Bull. 191, 129–138 (1996).CAS 

    Google Scholar 
    Conchou, L. et al. Insect odorscapes: From plant volatiles to natural olfactory scenes. Front. Physiol. 10, 972 (2019).
    Google Scholar 
    Riffell, J. A., Abrell, L. & Hildebrand, J. G. Physical processes and real-time chemical measurement of the insect olfactory environment. J. Chem. Ecol. 34, 837–853 (2008).CAS 

    Google Scholar 
    Mylne, K. R., Davidson, M. J. & Thomson, D. J. Concentration fluctuation measurements in tracer plumes using high and low frequency response detectors. Bound-Lay. Meteorol. 79, 225–242 (1996).ADS 

    Google Scholar 
    Finelli, C. M., Pentcheff, N. D., Zimmer-Faust, R. K. & Wethey, D. S. Odor transport in turbulent flows: Constraints on animal navigation. Limnol. Oceanogr. 44, 1056–1071 (1999).ADS 
    CAS 

    Google Scholar 
    Murlis, J., Elkinton, J. S. & Cardé, R. T. Odor plumes and how insects use them. Annu. Rev. Entomol. 37, 505–532 (1992).
    Google Scholar 
    Murlis, J., Willis, M. A. & Cardé, R. T. Spatial and temporal structures of pheromone plumes in fields and forests. Physiol. Entomol. 25, 211–222 (2000).CAS 

    Google Scholar 
    Kennedy, J. S. The visual response of flying mosquitoes. Proc. Zool. Soc. London Ser. A 109, 221–242 (1940).
    Google Scholar 
    Bursell, E. Observations on the orientation of tsetse flies (Glossina pallidipes) to wind-borne odours. Physio. Entomol. 9, 133–137 (1984).
    Google Scholar 
    Murlis, J., Elkinton, J. S. & Cardé, R. T. Odor plumes and how insects use them. Annu. Rev. Entomol. 37, 505–532 (1992).
    Google Scholar 
    Kennedy, J. S., Ludlow, A. R. & Sanders, C. J. Guidance of flying male moths by wind-borne sex-pheromone. Physiol. Entomol. 6, 395–412 (1981).
    Google Scholar 
    Koehl, M. A. R. The fluid mechanics of arthropod sniffing in turbulent odor plumes. Chem. Senses 31, 93–105 (2006).CAS 

    Google Scholar 
    Baker, T. C., Willis, M. A., Haynes, K. F. & Phelan, P. L. A pulsed cloud of sex pheromone elicits upwind flight in male moths. Physiol. Entomol. 10, 257–265 (1985).
    Google Scholar 
    Willis, M. A. & Baker, T. C. Effects of intermittent and continuous pheromone stimulation on the flight behavior of the oriental fruit moth, Grapholita molesta. Physiol. Entomol. 9, 341–358 (1984).
    Google Scholar 
    Mafraneto, A. & Cardé, R. T. Fine-scale structure of pheromone plumes modulates upwind orientation of flying moths. Nature 369, 142–144 (1994).ADS 
    CAS 

    Google Scholar 
    Mafraneto, A. & Cardé, R. T. Dissection of the pheromone-modulated flight of moths using single-pulse response as a template. Experientia 52, 373–379 (1996).CAS 

    Google Scholar 
    Vickers, N. J. & Baker, T. C. Reiterative responses to single strands of odor promote sustained upwind flight and odor source location by moths. Proc. Natl. Acad. Sci. USA 91, 5756–5760 (1994).ADS 
    CAS 

    Google Scholar 
    Lei, H., Riffell, J. A., Gage, S. L. & Hildebrand, J. G. Contrast enhancement of stimulus intermittency in a primary olfactory network and its behavioral significance. J. Biol. 8, 21 (2009).
    Google Scholar 
    Kuenen, L. & Carde, R. T. Strategies for recontacting a lost pheromone plume: Casting and upwind flight in the male gypsy moth. Physiol. Entomol. 19, 15–29 (1994).
    Google Scholar 
    Vickers, N. J. & Baker, T. C. Latencies of behavioral response to interception of filaments of sex pheromone and clean air influence flight track shape in Heliothis virescens (F.) males. J. Comp. Physiol. A. 178, 831–847 (1996).
    Google Scholar 
    Vickers, N. J. Mechanisms of animal navigation in odor plumes. Biol. Bull. 198, 203–212 (2000).CAS 

    Google Scholar 
    Cardé, R. T. & Willis, M. A. Navigational strategies used by insects to find distant, wind-borne sources of odor. J. Chem. Ecol. 34, 854–866 (2008).
    Google Scholar 
    Willis, M. A. & Baker, T. C. Effects of varying sex pheromone component ratios on the zigzagging flight movements of the oriental fruit moth, Grapholita molesta. J. Insect. Behav. 1, 357–371 (1988).
    Google Scholar 
    Voskamp, K. E., Den Otter, C. J. & Noorman, N. Electroantennogram responses of tsetse flies (Glossina pallidipes) to host odours in an open field and riverine woodland. Physiol. Entomol. 23, 176–183 (1998).
    Google Scholar 
    Cai, X. M., Xu, X. X., Bian, L., Luo, Z. X. & Chen, Z. M. Measurement of volatile plant compounds in field ambient air by thermal desorption–gas chromatography–mass spectrometry. Anal. Bioanal. Chem. 407, 9105–9114 (2015).CAS 

    Google Scholar 
    Zollner, G. E., Torr, S. J., Ammann, C. & Meixner, F. X. Dispersion of carbon dioxide plumes in African woodland: implications for host-finding by tsetse flies. Physiol. Entomol. 29, 381–394 (2004).
    Google Scholar 
    McFrederick, Q. S., Kathilankal, J. C. & Fuentes, J. D. Air pollution modifies floral scent trails. Atmos. Environ. 42, 2336–2348 (2008).ADS 
    CAS 

    Google Scholar 
    Yuan, J. S., Himanen, S. J., Holopainen, J. K., Chen, F. & NealStewart, C. Jr. Smelling global climate change: mitigation of function for plant volatile organic compounds. Trends Ecol. Evol. 24, 323–331 (2009).
    Google Scholar 
    Weissburg, M. J. The fluid dynamical context of chemosensory behavior. Biol. Bull. 198, 188–202 (2000).CAS 

    Google Scholar 
    Atkinson, R. & Arey, J. Gas-phase tropospheric chemistry of biogenic volatile organic compounds: A review. Atmos. Environ. 37, 197–219 (2003).ADS 

    Google Scholar 
    Helmig, D., Bocquet, F., Pollmann, J. & Revermann, T. Analytical techniques for sesquiterpene emission rate studies in vegetation enclosure experiments. Atmos. Environ. 38, 557–572 (2004).ADS 
    CAS 

    Google Scholar 
    Riffell, J. A, Shlizerman, E., Sanders, E., Abrell, L., Medina, B., Hinterwirth, A. J. & NathanKutz, J. Flower discrimination by pollinators in a dynamic chemical environment. Science 344, 1515–1518 (2014).Shorey, H. H. Animal communication by pheromones (Academic Press, 1976).Cardé, R. T. & Charlton, R. E. Olfactory sexual communication in Lepidoptera: Strategy, sensitivity and selectivity In Insect communication (ed. Lewis, T.) 241–265 (Academic Press, 1984).Elkinton, J. S., Schal, C., Ono, T. & Carde, R. T. Pheromone puff trajectory and upwind flight of male gypsy moths in a forest. Physiol. Entomol. 12, 399–406 (1987).
    Google Scholar 
    Baker, T. C., Fadamiro, H. Y. & Cosse, A. A. Moth uses fine tuning for odour resolution. Nature 393, 530 (1998).ADS 
    CAS 

    Google Scholar 
    Szyszka, P., Stierle, J. S., Biergans, S. & Galizia, C. G. The speed of smell: Odor-object segregation within milliseconds. PLoS One 7, e36096 (2012).ADS 
    CAS 

    Google Scholar 
    Hildebrand, J. G. Analysis of chemical signals by nervous systems. Proc. Natl. Acad. Sci. USA 92, 67–74 (1995).ADS 
    CAS 

    Google Scholar 
    Cai, X. M. et al. Field background odour should be taken into account when formulating a pest attractant based on plant volatiles. Sci. Rep. 7, 41818 (2017).ADS 
    CAS 

    Google Scholar 
    Xu, X. X. et al. Does background odor in tea gardens mask attractants? Screening and application of attractants for Empoasca onukii Matsuda. J. Econ. Entomol. 110, 2357–2363 (2017).CAS 

    Google Scholar 
    Hare, J. D. & Sun, J. J. Production of induced volatiles by Datura wrightii in response to damage by insects: Effect of herbivore species and time. J. Chem. Ecol. 37, 751–764 (2011).CAS 

    Google Scholar 
    Mumm, R., Tiemann, T., Schulz, S. & Hilker, M. Analysis of volatiles from black pine (Pinus nigra): Significance of wounding and egg deposition by a herbivorous sawfly. Phytochemistry 65, 3221–3230 (2004).CAS 

    Google Scholar  More

  • in

    Mutualism promotes insect fitness by fungal nutrient compensation and facilitates fungus propagation by mediating insect oviposition preference

    Franco FP, Túler AC, Gallan DZ, Gonçalves FG, Favaris AP, Peñaflor MFGV, et al. Fungal phytopathogen modulates plant and insect responses to promote its dissemination. ISME J. 2021;15:3522–33.CAS 

    Google Scholar 
    Huang H, Ren L, Li H, Schmidt A, Gershenzon J, Lu Y, et al. The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil. PLoS Pathog. 2020;16:e1008800.CAS 

    Google Scholar 
    Angleró-Rodríguez YI, Blumberg BJ, Dong Y, Sandiford SL, Pike A, Clayton AM, et al. A natural Anopheles-associated Penicillium chrysogenum enhances mosquito susceptibility to Plasmodium infection. Sci Rep. 2016;6:34084.
    Google Scholar 
    Davis TS, Landolt PJ. A survey of insect assemblages responding to volatiles from a ubiquitous fungus in an agricultural landscape. J Chem Ecol. 2013;39:860–8.CAS 

    Google Scholar 
    Flury P, Vesga P, Dominguez-Ferreras A, Tinguely C, Ullrich CI, Kleespies RG, et al. Persistence of root-colonizing Pseudomonas protegens in herbivorous insects throughout different developmental stages and dispersal to new host plants. ISME J. 2018;13:860–72.
    Google Scholar 
    Kandasamy D, Gershenzon J, Andersson MN, Hammerbacher A. Volatile organic compounds influence the interaction of the Eurasian spruce bark beetle (Ips typographus) with its fungal symbionts. ISME J. 2019;13:1788–800.CAS 

    Google Scholar 
    Keesey IW, Koerte S, Khallaf MA, Retzke T, Guillou A, Grosse-Wilde E, et al. Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication. Nat Commun. 2017;8:265.
    Google Scholar 
    Paul GB, Gerhard F, Elżbieta R, Alexandra S, Arne H, Sébastien L, et al. Yeast, not fruit volatiles mediate Drosophila melanogaster attraction, oviposition and development. Funct Ecol. 2012;26:1365–2435.
    Google Scholar 
    Ganter PF. Yeast and invertebrate associations. In: Gábor P, Carlos R, editors. Biodiversity and ecophysiology of yeasts. Berlin, Heidelberg: Springer; 2006. pp 303–70.Anagnostou C, Legrand EA, Rohlfs M. Friendly food for fitter flies?—Influence of dietary microbial species on food choice and parasitoid resistance in Drosophila. Oikos. 2010;119:533–41.
    Google Scholar 
    Günther CS, Knight SJ, Jones R, Goddard MR. Are Drosophila preferences for yeasts stable or contextual? Ecol Evol. 2019;9:8075–86.
    Google Scholar 
    Luo Y, Johnson JC, Chakraborty TS, Piontkowski A, Gendron CM, Pletcher SD. Yeast volatiles double starvation survival in Drosophila. Sci Adv. 2021;7:eabf8896.CAS 

    Google Scholar 
    Fogleman S. Coadaptation of Drosophila and yeasts in their natural habitat. J Chem Ecol. 1986;12:1037–55.
    Google Scholar 
    Droby S, Eick A, Macarisin D, Cohen L, Rafael G, Stange R, et al. Role of citrus volatiles in host recognition, germination and growth of Penicillium digitatum and Penicillium italicum. Postharvest Biol Tec. 2008;49:386–96.CAS 

    Google Scholar 
    Stensmyr MC, Dweck HK, Farhan A, Ibba I, Strutz A, Mukunda L, et al. A conserved dedicated olfactory circuit for detecting harmful microbes in Drosophila. Cell. 2012;151:1345–57.CAS 

    Google Scholar 
    Melo N, Wolff GH, Costa-da-Silva AL, Arribas R, Triana MF, Gugger M, et al. Geosmin attracts Aedes aegypti mosquitoes to oviposition sites. Curr Biol. 2020;30:127–34.CAS 

    Google Scholar 
    Wei DD, He W, Lang N, Miao ZQ, Xiao LF, Dou W, et al. Recent research status of Bactrocera dorsalis: Insights from resistance mechanisms and population structure. Arch Insect Biochem. 2019;102:e21601.CAS 

    Google Scholar 
    Han P, Wang X, Niu CY, Dong YC, Zhu JQ, Desneux N. Population dynamics, phenology, and overwintering of Bactrocera dorsalis (Diptera: Tephritidae) in Hubei Province, China. J Pest Sci. 2011;84:289–95.
    Google Scholar 
    Duyck PF, David P, Quilici S. A review of relationships between interspecific competition and invasions in fruit flies (Diptera: Tephritidae). Ecol Entomol. 2004;29:511–20.
    Google Scholar 
    Wen T, Zheng L, Dong S, Gong Z, Sang M, Long X, et al. Rapid detection and classification of citrus fruits infestation by Bactrocera dorsalis (Hendel) based on electronic nose. Postharvest Biol Tec. 2019;147:156–65.
    Google Scholar 
    Li X, Yang H, Wang T, Wang J, Wei H. Life history and adult dynamics of Bactrocera dorsalis in the citrus orchard of Nanchang, a subtropical area from China: implications for a control timeline. ScienceAsia. 2019;45:212–20.
    Google Scholar 
    Chalupowicz D, Veltman B, Droby S, Eltzov E. Evaluating the use of biosensors for monitoring of Penicillium digitatum infection in citrus fruit. Sens Actuat B-Chem. 2020;311:127896.CAS 

    Google Scholar 
    Turlings TC, Lengwiler UB, Bernasconi ML, Wechsler D. Timing of induced volatile emissions in maize seedlings. Planta. 1998;207:146–52.CAS 

    Google Scholar 
    Wang B, Dong W, Li H, D’Onofrio C, Bai P, Chen R, et al. Molecular basis of (E)-β-farnesene-mediated aphid location in the predator Eupeodes corollae. Curr Biol. 2022;32:951–62.CAS 

    Google Scholar 
    Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods. 2001;25:402–8.CAS 

    Google Scholar 
    Cellar NA, De Nison JE, Seipelt CT, Twohig M, Burgess JA. Title of subordinate document. In: Dramatic improvements in assay reproducibility for water-soluble vitamins using ACQUITY UPLC and the Ultra-Sensitive Xevo TQ-S Mass Spectrometer. 2013. https://www.waters.com/webassets/cms/library/docs/720004690en.pdf.Ren FR, Sun X, Wang TY, Yan JY, Yao YL, Li CQ, et al. Pantothenate mediates the coordination of whitefly and symbiont fitness. ISME J. 2021;15:1655–67.CAS 

    Google Scholar 
    Batta YA. Quantitative postharvest contamination and transmission of Penicillium expansum (Link) conidia to nectarine and pear fruit by Drosophila melanogaster (Meig.) adults. Postharvest Biol Tec. 2006;40:190–6.
    Google Scholar 
    Rohlfs M. Clash of kingdoms or why Drosophila larvae positively respond to fungal competitors. Front Zool. 2005;2:2.
    Google Scholar 
    Becher PG, Bengtsson M, Hansson BS, Witzgall P. Flying the fly: long-range flight behavior of Drosophila melanogaster to attractive odors. J Chem Ecol. 2010;36:599–607.CAS 

    Google Scholar 
    Dionigi C, Ahten T, Wartelle L. Effects of several metals on spore, biomass, and geosmin production by Streptomyces tendae and Penicillium expansum. J Ind Microbiol Biot. 1996;17:84–88.CAS 

    Google Scholar 
    Jin S, Zhou X, Gu F, Zhong G, Yi X. Olfactory plasticity: variation in the expression of chemosensory receptors in Bactrocera dorsalis in different physiological states. Front Physiol. 2017;8:672.
    Google Scholar 
    Li H, Ren L, Xie M, Gao Y, He M, Hassan B, et al. Egg-surface bacteria are indirectly associated with oviposition aversion in Bactrocera dorsalis. Curr Biol. 2020;30:4432–40.CAS 

    Google Scholar 
    Liu Y, Cui Z, Si P, Liu Y, Zhou Q, Wang G. Characterization of a specific odorant receptor for linalool in the Chinese citrus fly Bactrocera minax (Diptera: Tephritidae). Insect Biochem Molec. 2020;122:103389.CAS 

    Google Scholar 
    Ju JF, Bing XL, Zhao DS, Guo Y, Hong XY. Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers. ISME J. 2019;14:1–12.
    Google Scholar 
    Liu F, Wickham JD, Cao Q, Lu M, Sun J. An invasive beetle–fungus complex is maintained by fungal nutritional-compensation mediated by bacterial volatiles. ISME J. 2020;14:2829–42.CAS 

    Google Scholar 
    Douglas AE. The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes. Curr Opin Insect Sci. 2017;23:65–69.
    Google Scholar 
    Honda K, Ômura H, Hayashi N, Abe F, Yamauchi T. Conduritols as oviposition stimulants for the danaid butterfly, Parantica sita, identified from a host plant, Marsdenia tomentosa. J Chem Ecol. 2004;30:2285–96.CAS 

    Google Scholar 
    Soldano A, Alpizar YA, Boonen B, Franco L, Lopez-Requena A, Liu G, et al. Gustatory-mediated avoidance of bacterial lipopolysaccharides via TRPA1 activation in Drosophila. Elife. 2016;5:e13133.
    Google Scholar 
    Hussain A, Üçpunar HK, Zhang M, Loschek LF, Grunwald Kadow IC. Neuropeptides modulate female chemosensory processing upon mating in Drosophila. PLoS Biol. 2016;14:e1002455.
    Google Scholar 
    Stötefeld L, Holighaus G, Schütz S, Rohlfs M. Volatile-mediated location of mutualist host and toxic non-host microfungi by Drosophila larvae. Chemoecology. 2015;5:271–83.
    Google Scholar 
    Gou B, Liu Y, Guntur A, Stern U, Yang HC. Mechanosensitive neurons on the internal reproductive tract contribute to egg-laying-induced acetic acid attraction in Drosophila. Cell Rep. 2014;9:522–30.CAS 

    Google Scholar 
    Mezzera C, Brotas M, Gaspar M, Pavlou HJ, Goodwin SF, Vasconcelos ML. Ovipositor extrusion promotes the transition from courtship to copulation and signals female acceptance in Drosophila melanogaster. Curr Biol. 2020;30:3736–48.CAS 

    Google Scholar 
    Teimoori-Boghsani Y, Ganjeali A, Cernava T, Müller H, Asili J, Berg G. Endophytic fungi of native Salvia abrotanoides plants reveal high taxonomic diversity and unique profiles of secondary metabolites. Front Microbiol. 2020;10:3013–20.
    Google Scholar 
    Holden JT, Furman C, Snell EE. D-alanine and the vitamin B6 content of microorganisms. J Biol Chem. 1949;178:789–97.CAS 

    Google Scholar 
    Michalkova V, Benoit JB, Weiss BL, Attardo GM, Aksoy S. Vitamin B6 generated by obligate symbionts is critical for maintaining proline homeostasis and fecundity in tsetse flies. Appl Environ Micro. 2014;80:5844–53.
    Google Scholar 
    Ren FR, Sun X, Wang TY, Yao YL, Huang YZ, Zhang X, et al. Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits. ISME J. 2020;14:2542–53.CAS 

    Google Scholar 
    Salem H, Bauer E, Strauss AS, Vogel H, Marz M, Kaltenpoth M. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. Proc Biol Sci. 2014;281:20141838.
    Google Scholar  More

  • in

    Metabarcoding the Antarctic Peninsula biodiversity using a multi-gene approach

    Meredith M, Sommerkorn M, Cassotta S, Derksen C, Ekaykin A, Hollowed A. IPCC special report on the ocean and cryosphere in a changing climate In: Pörtner H-O, Roberts D, Masson-Delmotte V, Zhai P, Tignor M, Poloczanska Eea, editors. 2022; chapter 3: https://doi.org/10.1017/9781009157964 (in press).Rozema PD, Venables HJ, van de Poll WH, Clarke A, Meredith MP, Buma AGJ. Interannual variability in phytoplankton biomass and species composition in northern Marguerite Bay (West Antarctic Peninsula) is governed by both winter sea ice cover and summer stratification. Limnol Oceanogr. 2017;62:235–52.Article 

    Google Scholar 
    Venables HJ, Clarke A, Meredith MP. Wintertime controls on summer stratification and productivity at the western Antarctic Peninsula. Limnol Oceanogr. 2013;58:1035–47.Article 

    Google Scholar 
    Barnes DKA, Souster T. Reduced survival of Antarctic benthos linked to climate-induced iceberg scouring. Nat Clim Change. 2011;1:365–8.Article 

    Google Scholar 
    Grange L, Tyler P, Peck L, Cornelius N. Long-term interannual cycles of the gametogenic ecology of the Antarctic brittle star Ophionotus victoriae. Mar Ecol Prog Ser. 2004;278:141–55.Article 

    Google Scholar 
    Schratzberger M, Ingels J. Meiofauna matters: The roles of meiofauna in benthic ecosystems. J Exp Mar Biol Ecol. 2018;502:12–25.Article 

    Google Scholar 
    Mayor D, Thornton B, Jenkins H, Felgate S. Microbiota: the living foundation. In: Beninger P, editor. Mudflat ecology. Switzerland AG: Springer Nature 2018. p. 43–61.Fonseca VG, Sinniger F, Gaspar JM, Quince C, Creer S, Power DM, et al. Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Sci Rep. 2017;7:6094.CAS 
    Article 

    Google Scholar 
    Vause BJ, Morley SA, Fonseca VG, Jazdzewska A, Ashton GV, Barnes DKA, et al. Spatial and temporal dynamics of Antarctic shallow soft-bottom benthic communities: ecological drivers under climate change. BMC Ecol. 2019;19:27.Article 

    Google Scholar 
    Danovaro R, Scopa M, Gambi C, Fraschetti S. Trophic importance of subtidal metazoan meiofauna: evidence from in situ exclusion experiments on soft and rocky substrates. Mar Biol. 2007;152:339–50.Article 

    Google Scholar 
    Watzin MC. The effects of meiofauna on settling macrofauna: meiofauna may structure macrofaunal communities. Oecologia. 1983;59:163–6.Article 

    Google Scholar 
    Schmidt JL, Deming JW, Jumars PA, Keil RG. Constancy of bacterial abundance in surficial marine sediments. Limnol Oceanogr. 1998;43:976–82.Article 

    Google Scholar 
    Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–83.CAS 
    Article 

    Google Scholar 
    Burdige DJ. Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev. 2007;107:467–85.CAS 
    Article 

    Google Scholar 
    Zou K, Thébault E, Lacroix G, Barot S. Interactions between the green and brown food web determine ecosystem functioning. Funct Ecol. 2016;30:1454–65.Article 

    Google Scholar 
    Anderson TR, Pond DW, Mayor DJ. The role of microbes in the nutrition of detritivorous invertebrates: a stoichiometric analysis. Front Microbiol. 2016;7:2113.
    Google Scholar 
    Lacoste E, Piot A, Archambault P, McKindsey CW, Nozais C. Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities. Mar Environ Res. 2018;136:62–70.CAS 
    Article 

    Google Scholar 
    Bonaglia S, Nascimento FJ, Bartoli M, Klawonn I, Bruchert V. Meiofauna increases bacterial denitrification in marine sediments. Nat Commun. 2014;5:5133.CAS 
    Article 

    Google Scholar 
    Riemann F, Helmke E. Symbiotic relations of sediment-agglutinating nematodes and bacteria in detrital habitats: the enzyme-sharing concept. Mar Ecol. 2002;23:93–113.CAS 
    Article 

    Google Scholar 
    dos Santos GAP, Derycke S, Fonseca-Genevois VG, Coelho LCBB, Correia MTS, Moens T. Differential effects of food availability on population growth and fitness of three species of estuarine, bacterial-feeding nematodes. J Exp Mar Biol Ecol. 2008;355:27–40.Article 

    Google Scholar 
    Zeppilli D, Sarrazin J, Leduc D, Arbizu PM, Fontaneto D, Fontanier C, et al. Is the meiofauna a good indicator for climate change and anthropogenic impacts? Mar Biodivers. 2015;45:505–35.Article 

    Google Scholar 
    Moens T, Beninger PG. Meiofauna: an inconspicuous but important player in Mudflat ecology. In: Beninger P, editor. Mudflat ecology aquatic ecology series. 7. Switzerland: Springer; 2018.Webb AL, Hughes KA, Grand MM, Lohan MC, Peck LS. Sources of elevated heavy metal concentrations in sediments and benthic marine invertebrates of the western Antarctic Peninsula. Sci Total Environ. 2020;698:134268.CAS 
    Article 

    Google Scholar 
    Brown KM, Fraser KP, Barnes DK, Peck LS. Links between the structure of an Antarctic shallow-water community and ice-scour frequency. Oecologia. 2004;141:121–9.Article 

    Google Scholar 
    Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.CAS 
    Article 

    Google Scholar 
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.CAS 
    Article 

    Google Scholar 
    Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool. 2013;10:34.Article 

    Google Scholar 
    Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.Article 

    Google Scholar 
    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
    Article 

    Google Scholar 
    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.Article 

    Google Scholar 
    McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.CAS 
    Article 

    Google Scholar 
    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.CAS 
    Article 

    Google Scholar 
    Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2005;33:D34–8.CAS 
    Article 

    Google Scholar 
    Wentworth CK. A scale of grade and class terms for clastic sediments. J Geol. 1922;30:377–92.Article 

    Google Scholar 
    Dean WE. Determination of carbonate and organic matter in calcareous sediments and sedimentary rocks by loss on ignition; comparison with other methods. J Sediment Res. 1974;44:242–8.CAS 

    Google Scholar 
    Tatzber M, Stemmer M, Spiegel H, Katzlberger C, Haberhauer G, Gerzabek MH. An alternative method to measure carbonate in soils by FT-IR spectroscopy. Environ Chem Lett. 2007;5:9–12.CAS 
    Article 

    Google Scholar 
    Hsieh CH, Reiss CS, Hunter JR, Beddington JR, May RM, Sugihara G. Fishing elevates variability in the abundance of exploited species. Nature. 2006;443:859–62.CAS 
    Article 

    Google Scholar 
    Elbrecht V, Braukmann TWA, Ivanova NV, Prosser SWJ, Hajibabaei M, Wright M, et al. Validation of COI metabarcoding primers for terrestrial arthropods. Peer J. 2019;7:e7745–e.Article 

    Google Scholar 
    Kirse A, Bourlat SJ, Langen K, Fonseca VG. Unearthing the potential of Soil eDNA metabarcoding—towards best practice advice for invertebrate biodiversity assessment. Front. Ecol. Evol. 2021;9:630560.Article 

    Google Scholar 
    Zhang GK, Chain FJJ, Abbott CL, Cristescu ME. Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities. Evolut Appl. 2018;11:1901–14.CAS 
    Article 

    Google Scholar 
    Marquina D, Andersson AF, Ronquist F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour. 2019;19:90–104.CAS 
    Article 

    Google Scholar 
    Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, et al. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol. 2018;1:112.Article 

    Google Scholar 
    Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, et al. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour. 2020;20:1333–45.CAS 
    Article 

    Google Scholar 
    Vanhove S, Lee HJ, Beghyn M, Gansbeke DV, Brockington S, Vincx M. The Metazoan Meiofauna in its biogeochemical environment: the case of an Antarctic coastal sediment. J Mar Biol Assoc UK. 1998;78:411–34.Article 

    Google Scholar 
    Pasotti F, Saravia LA, De Troch M, Tarantelli MS, Sahade R, Vanreusel A. Benthic Trophic Interactions in an Antarctic Shallow Water Ecosystem Affected by Recent Glacier Retreat. PLoS ONE. 2015;10:e0141742.Article 

    Google Scholar 
    Griffiths JR, Kadin M, Nascimento FJA, Tamelander T, Tornroos A, Bonaglia S, et al. The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world. Global Change Biology. 2017;23:2179–96.Article 

    Google Scholar 
    Virta L, Gammal J, Järnström M, Bernard G, Soininen J, Norkko J, et al. The diversity of benthic diatoms affects ecosystem productivity in heterogeneous coastal environments. Ecology. 2019;100:e02765.Article 

    Google Scholar 
    Malviya S, Scalco E, Audic S, Vincent F, Veluchamy A, Poulain J, et al. Insights into global diatom distribution and diversity in the world’s ocean. Proc Natl Acad Sci USA. 2016;113:E1516–25.CAS 
    Article 

    Google Scholar 
    Forster D, Dunthorn M, Mahe F, Dolan JR, Audic S, Bass D, et al. Benthic protists: the under-charted majority. Fems Microbiol Ecol. 2016;92:fiw120.Article 

    Google Scholar 
    Fonseca VG, Carvalho GR, Nichols B, Quince C, Johnson HF, Neill SP, et al. Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob Ecol Biogeogr. 2014;23:1293–302.Article 

    Google Scholar 
    O’Malley MA. The nineteenth century roots of ‘everything is everywhere’. Nat Rev Microbiol. 2007;5:647–51.Article 

    Google Scholar 
    Pasotti F, Manini E, Giovannelli D, Wölfl A-C, Monien D, Verleyen E, et al. Antarctic shallow water benthos in an area of recent rapid glacier retreat. Mar Ecol. 2015;36:716–33.Article 

    Google Scholar 
    Molari M, Janssen F, Vonnahme TR, Wenzhöfer F, Boetius A. The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth). Biogeosciences. 2020;17:3203–22.CAS 
    Article 

    Google Scholar 
    Signori CN, Thomas F, Enrich-Prast A, Pollery RCG, Sievert SM. Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula. Front Microbiol. 2014;5:647.Article 

    Google Scholar 
    Ozturk RC, Feyzioglu AM, Altinok I. Prokaryotic community and diversity in coastal surface waters along the Western Antarctic Peninsula. Pol Sci. 2021;31:100764.Article 

    Google Scholar 
    Ghiglione JF, Murray AE. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environ Microbiol. 2012;14:617–29.CAS 
    Article 

    Google Scholar 
    Luria CM, Ducklow HW, Amaral-Zettler LA. Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula. Aquat Microbial Ecol. 2014;73:107–21.Article 

    Google Scholar 
    Cao S, He J, Zhang F, Lin L, Gao Y, Zhou Q. Diversity and community structure of bacterioplankton in surface waters off the northern tip of the Antarctic Peninsula. Pol Res. 2019;38:3491.Article 

    Google Scholar 
    Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D’Hondt S. Bacterial diversity and community composition from seasurface to subseafloor. ISME J. 2016;10:979–89.Article 

    Google Scholar 
    Kiko R, Werner I, Wittmann A. Osmotic and ionic regulation in response to salinity variations and cold resistance in the Arctic under-ice amphipod Apherusa glacialis. Pol Biol. 2009;32:393–8.Article 

    Google Scholar 
    Zeppilli D, Leduc D, Fontanier C, Fontaneto D, Fuchs S, Gooday AJ, et al. Characteristics of meiofauna in extreme marine ecosystems: a review. Mar Biodivers. 2018;48:35–71.Article 

    Google Scholar 
    Arnosti C, Joergensen BB, Sagemann J, Thamdrup B. Temperature dependence of microbial degradation of organic matter in marine sediments: polysaccharide hydrolysis, oxygen consumption, and sulfate reduction. Mar Ecol Prog Ser. 1998;165:59–70.CAS 
    Article 

    Google Scholar 
    Fabiano M, Danovaro R. Enzymatic activity, bacterial distribution, and organic matter composition in sediments of the ross sea (Antarctica). Appl Environ Microbiol. 1998;64:3838–45.CAS 
    Article 

    Google Scholar 
    Kujawinski EB, Longnecker K, Barott KL, Weber RJM, Kido Soule, MC. Microbial community structure affects marine dissolved organic matter composition. Front Mar Sci. 2016;3:45.Article 

    Google Scholar 
    Barrett JE, Virginia RA, Hopkins DW, Aislabie J, Bargagli R, Bockheim JG, et al. Terrestrial ecosystem processes of Victoria Land, Antarctica. Soil Biol Biochem. 2006;38:3019–34.CAS 
    Article 

    Google Scholar 
    Ganzert L, Lipski A, Hubberten H-W, Wagner D. The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. Fems Microbiol Ecol. 2011;76:476–91.CAS 
    Article 

    Google Scholar 
    Rusch A, Huettel M, Reimers CE, Taghon GL, Fuller CM. Activity and distribution of bacterial populations in Middle Atlantic Bight shelf sands. Fems Microbiol Ecol. 2003;44:89–100.CAS 
    Article 

    Google Scholar 
    Hemkemeyer M, Dohrmann AB, Christensen BT, Tebbe CC. Bacterial preferences for specific soil particle size fractions revealed by community analyses. Front Microbiol. 2018;9:149.Article 

    Google Scholar 
    Giere O. Meiobenthology: the microscopic motile fauna of aquatic sediments. 2nd ed: Springer-Verlag Berlin Heidelberg; 2009. 527 p.Fonseca VG, Carvalho GR, Sung W, Johnson HF, Power DM, Neill SP, et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun. 2010;1:98.Article 

    Google Scholar 
    Pitcher RC, Lawton P, Ellis N, Smith SJ, Incze LS, Wei C-L, et al. Exploring the role of environmental variables in shaping patterns of seabed biodiversity composition in regional-scale ecosystems. J Appl Ecol. 2012;49:670–9.Article 

    Google Scholar 
    Rose A, Ingels J, Raes M, Vanreusel A, Arbizu PM. Long-term iceshelf-covered meiobenthic communities of the Antarctic continental shelf resemble those of the deep sea. Heidelberg: Springer; 2014. 743–62 p.Gonçalves-Araujo R, de Souza MS, Tavano VM, Garcia CAE. Influence of oceanographic features on spatial and interannual variability of phytoplankton in the Bransfield Strait, Antarctica. J Mar Syst. 2015;142:1–15.Article 

    Google Scholar 
    Learman DR, Henson MW, Thrash JC, Temperton B, Brannock PM, Santos SR, et al. Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Front Microbiol. 2016;7:284.Article 

    Google Scholar 
    Ghiglione JF, Galand PE, Pommier T, Pedros-Alio C, Maas EW, Bakker K, et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc Natl Acad Sci USA. 2012;109:17633–8.CAS 
    Article 

    Google Scholar 
    Rosli N, Leduc D, Rowden A, Probert P. Review of recent trends in ecological studies of deep-sea meiofauna, with focus on patterns and processes at small to regional spatial scales. Mar Biodivers. 2017;48:13–34.Article 

    Google Scholar 
    Ruff SE, Probandt D, Zinkann A-C, Iversen M, Klaas C, Schwabe L, et al. Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic Polar Front. Deep Sea Res Part II: Top Stud Oceanogr. 2014;108:6–16.Article 

    Google Scholar 
    El-Serehy HA, Al-Rasheid KA, Al-Misned FA, Al-Talasat AA, Gewik MM. Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea. Saudi J Biol Sci. 2016;23:327–34.CAS 
    Article 

    Google Scholar 
    Danovaro R, Company JB, Corinaldesi C, D’Onghia G, Galil B, Gambi C, et al. Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS ONE. 2010;5:e11832.Article 

    Google Scholar 
    Mussmann M, Pjevac P, Kruger K, Dyksma S. Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. ISME J. 2017;11:1276–81.CAS 
    Article 

    Google Scholar 
    Hinger I, Pelikan C, Mußmann M. Role of the ubiquitous bacterial family Woeseiaceae for N2O production in marine sediments. Geophys Res Abstracts. 2019;21:17441.
    Google Scholar 
    Hoffmann K, Bienhold C, Buttigieg PL, Knittel K, Laso-Pérez R, Rapp JZ, et al. Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. ISME J. 2020;14:1042–56.CAS 
    Article 

    Google Scholar 
    Mare MF. A study of a marine benthic community with special reference to the microorganisms. J Mar Biol Assoc UK. 1942;25:517–54.Article 

    Google Scholar 
    Bott TL, Borchardt MA. Grazing of protozoa, bacteria, and diatoms by Meiofauna in lotic epibenthic communities. J North Am Bentholog Soc. 1999;18:499–513.Article 

    Google Scholar 
    Griffiths HJ. Antarctic marine biodiversity-what do we know about the distribution of life in the Southern Ocean? PLoS ONE. 2010;5:e11683.Article 

    Google Scholar 
    Convey P, Chown SL, Clarke A, Barnes DKA, Bokhorst S, Cummings V, et al. The spatial structure of Antarctic biodiversity. Ecol Monogr. 2014;84:203–44.Article 

    Google Scholar 
    Li L, Ma ZS. Species sorting and neutral theory analyses reveal archaeal and bacterial communities are assembled differently in hot springs. Front Bioeng Biotechnol. 2020;8:464.Article 

    Google Scholar 
    Lee JE, Buckley HL, Etienne RS, Lear G. Both species sorting and neutral processes drive assembly of bacterial communities in aquatic microcosms. Fems Microbiol Ecol. 2013;86:288–302.CAS 
    Article 

    Google Scholar 
    Gansfort B, Fontaneto D, Zhai M. Meiofauna as a model to test paradigms of ecological metacommunity theory. Hydrobiologia. 2020;847:2645–63.Article 

    Google Scholar 
    Convey P, Peck LS. Antarctic environmental change and biological responses. Sci Adv. 2019;5:eaaz0888.CAS 
    Article 

    Google Scholar  More