More stories

  • in

    The first record of exceptionally-preserved spiral coprolites from the Tsagan-Tsab formation (lower cretaceous), Tatal, western Mongolia

    SizesAs from the measurements, all collected coprolites vary in sizes (Table 1). The smallest and complete specimen is IVPP V 27,545 (Fig. 2D–G), and while IVPP V 27,550 (2 V-Z) is multiple time larger. The maximum length for specimen IVPP V 27,544, IVPP V 27,546, IVPP V 27,547 and IVPP V 27,549 have not been determined due to their incompleteness.Table 1 Biometrical and morphological features of spiral coprolites from Tsagan-Tsab Formation (Lower Cretaceous), Tatal, western Mongolia. Paul Rummy, Kazim Halaclar & He Chen.Full size tableSurface adhesion and marksAll specimens contained some degree of bone fragments and rhomboidal-shaped ganoid scales adhered to the coprolite surfaces (Fig. 3). Additionally, all specimens have smooth surfaces with little abrasion. The inner coil lines of specimen IVPP V 27,549 adhered with a matrix of red clay with silt (Fig. 2S–U). Only specimen IVPP V 27,550 has been seen with concentric cracks (Fig. 2V–Z). Bite marks have also been found on specimen IVPP V 27,545, in which these traces were short, parallel, shallow and isolated. They have been formed from 3 furrows of roughly 3.8 mm long and 0.3 mm deep (Fig. 4).InclusionsThrough CT scans and surface observation, we noticed that all specimens contained bone fragments and scales of varying degrees (Fig. 5). We were unable to identify the bones in detail for specimen IVPP V 27,544, IVPP V 27,546, IVPP V 27,547, IVPP V 27,548, IVPP V 27,549 and IVPP V 27,550, as they were excessive in amount and extremely fragmentary. On the contrary, for specimen IVPP V 27,545, we noticed a rather complete bone structure, such as the ribs and a segment of an infraorbital (Fig. 5H–N). SEM photograph from one random point of specimen IVPP V 27,545 yielded results of the existents of pollen grain (Fig. 6C).BoringsSurface borings of invertebrate burrowing can be seen in 2 spiral coprolites, namely IVPP V 27,547 (Fig. 2D–G) and IVPP V 27,550 (Fig. 2V–Z). CT scans revealed that the borings of specimen IVPP V 27,550 did not intrude internally, and it was the same for some of IVPP V 27,547 as well (Fig. 7). Specimens IVPP V 27,546, IVPP V 27,547, IVPP V 27,548 and IVPP V 27,549 are shown to have traces of internal borings (Fig. 5C–F).EDS analysesIn this work, in regards to Tatal’s coprolites, the mineral elements were examined by using EDS and the photos were taken with SEM. Analyses was conducted on 2 specimens (IVPP V 27,546 and IVPP V 27,545) with two sample points for each. All 4 samples showed high peaks of calcium and phosphorus. EDS results of specimen IVPP V 27,546 (Fig. 6A–B) and specimen IVPP V 27,545 (Fig. 6C–D) gave similar atomic compositions. They were mainly composed of Ca, P and O and small peaks that belong to Nb, Si, C, K, Fe and Al. We have also described a potential pollen structure under SEM image (Fig. 6C). This possible pollen structure in specimen IVPP V 27,545 (Fig. 6C) showed different atomic elements from the other EDS results, where it contained high peaks of Na and Cl.Taphonomy inferencesNo signs of abrasion were found on all of the coprolites. Coloration of the coprolites varied, thus, indicating they were buried in different sedimentary conditions. Through the shape of the coprolites, we can deduce that they have indeed spent different amounts of time or phases in water bodies before burial (see above description/discussion). Meanwhile, specimen IVPP V 27,550 showed shallow coil deepness, therefore, this indicates that it was buried rapidly after excretion.Discussion and interpretationThere are several pivotal evidences that corroborate to fecal origins of the Tsagan-Tsab Formation material: (1) basic morphology; (2) general shape and size (3) inclusions of the fecal matter; (4) high calcium and phosphorus content; (5) bioerosional scars; (6) borings and cavities; (7) concentric cracks.The fundamental puzzle in the studies of coprolite is the difficulty in identifying the potential producer, which can be due to their nature and preservation. Also, that includes the methods used to deduce them with their producer, which were done by inferring with various forms of relationship based on stratigraphy and geographical relationships, as well as on neoichnology studies7,23,54,55. Such problems similarly arose in our context as well, and the materials were collected from a stratum that were interpreted as lake deposit margins, thus, suggesting an amphibious or aquatic producer. The paleoenvironment correlates with the findings of pterosaur fossils such as the Noripterus44 or argued as ‘Phobetor’56, and the diets of these pterosaurs were dependable on the lake environment57,58,59,60. Above all, and more importantly, that the shape of the coprolite has to be intact in order to represent the shape of the internal intestine of the producer, whereby, anatomically it can lead to a certain biological aspect and digestive system of the organism. Despite these, there are on-going controversies on the origin of the spiral shaped bromalites in regards to whether or not they signify fossilized feces, or they are the cololite that was formed within the colon6,21,23,61,62.Spiral coprolites are producer of an animal with spiral intestine valves to increase the surface area of absorption, to slow down food movement in the bowel to maximise nutrient absorption, which has a significant strategy in surviving uncertain and harsh environment conditions28,63,64. Referring to past literature, it is generally agreed upon that the spiral shape is the only distinctively coprolite morphology, whereby it has been regarded as a true coprolite and can be correctly associated to the source animal, such as a range of fishes in particular6,22,52. Many primitive bony fishes (except those of teleosts), fresh water sharks (elasmobranches), coelacanths, Saurichthys, sturgeons and lungfishes are known to have the spiral valve intestine51,64,65,66. Also, Price67 suggested that the amphipolar form could have been derived from palaeoniscoids. Additionally, Romer & Parsons68 noted that the spiral valves are secondarily lost in teleost and tetrapods, while Chin69 noted a few teleosteans still possessing them.The spiral coprolites collected for this study are mainly amphipolar in shape and one in scroll. As we know, generally heteropolar spiral coprolite are produced by sharks, which have complex spiral valves62. Therefore, we can exclude those in the family of elasmobranches as the potential producers and this can also be supported by the non-marine geological settings of Tsagan-Tsab Formation. But it is also noteworthy to mention that in previous studies, some workers have conducted observations on sharks that were kept in tanks, and were not been able to find any spiral fecal pellets. The reasons given were that the sharks’ eating habits could have changed due to the tank environment, which would have differed from the natural marine environment. Also, modern day sharks are totally unrelated to the ancient Permian pleuracanth sharks6. Despite these, evidence of spiral fecal pellet can still be observed in some of the present-day fishes, such as the African lungfish Protopterus annectans, the Australian lungfish Neoceratodus forsteri, the long-nosed gar Lepisosteus osseus and the spotted gar Lepisosteus oculatus6,70,71,72. As for scroll coprolites, it is generally known to be produced by animal with longitudinal valves (valvular voluta), whereby the valves naturally rolls in upon itself , in a way that it maximises nutrient absorption8,9,17,18. Gilmore17 in his work mentioned that this type of valve must be primitive than the transverse valve (valvular spiralis), which could be a modification of the previous ones. This form is especially known to sharks of carcharhiniforms73, and it is evident that it could have been associated with sarcopterygian53, as well as anaspid and thelodont agnathans17.In this study, we recognised four new ichnotaxa for all the seven coprolite specimens. Assigning four new ichnotaxa does not conclude that the coprofauna are of four different types of animals. Considering there are two distinct morphologies, which are the amphipolar spiral and scroll, we can deduce that at least two animals can produce these coprolites. But we have to carefully consider that diverse diets at different times for the same animal can often be variable, and soft fecal materials can range disparately after defecation, as well as taphonomy influence74,75. Specimen IVPP V 27,550 is remarkably huge and its producer should be a massive animal since large animals could produce small excrement, but small animals would not be able to produce big excrement52,54. Moreover, since there are no relevant fossils fauna found in the locality, we were unable to exactly identify the specific producer, rather, we deduced with relevant sources. However, we do know that both amphipolar spiral and scroll coprolites can be attributed to certain types of fishes. As of these, we can conclude that the coprolites were produced by fishes in different sizes. Specimen IVPP V 27,545 differs from the rest by its shape and size, which makes prediction even harder, because it could be produced by either large or smaller animals.CT scans revealed that bony inclusions are evident in all of the coprolites (Fig. 5). However, except in specimen IVPP V 27,545, the bones in the rest of the coprolites are fragmentary. Specifically, bones in specimen IVPP V 27,545 are rather unaffected by the acidity of the digestive enzyme and these were evident by the presence of clusters of entire bones in the coprolite (Fig. 3A–C), as contrast to the fragmentary bones in the rests of the coprolites. Furthermore, we identified an infraorbital bone of a fish. CT scans revealed that the infraorbital bone has a sensory canal where it branches off at both ends (Fig. 5M–N). With these, we can indicate that the producer of specimen IVPP V 27,545 poorly masticated the prey and also had a rather low gut digestion for food28,55,76,77,78. Through these results, we can infer the digestive strategies of the producers were in correlation with food intake and digestion process, as discussed in Barrios-de Pedro & Buscalioni77. Specimen IVPP V 27,545 might belong to the first type of digestive strategy, whereby the producer has limited food processing in the mouth and the food stays in the digestive system for a short period of time. This strategy is regarded to be efficient in conditions where food sources are abundant and the nourishment levels are sufficient79. The rest of the coprolites possibly belong to the second digestive strategy, as the bone content is fragmentary. This suggest the producer might have limited mastication with improved digestive assimilation and longer gut time to favour better absorptions of nutrients55,80,81,82,83. The third type of digestive strategy does not imply in our study. It is also noteworthy to mention that the quantity of the inclusions is not correlated to the size of the coprolite, rather, it is dependable on the above-mentioned biological variables28,84.Carnivorous coprolites are normally composed of calcium phosphate and other organic matter, but it is important to be aware that the initial compositions are usually altered during fossilization processes33. Meanwhile, the excretion of herbivores is generally lacking in phosphates and their fossilization are mostly dependable of the mineral enrichment85. Through the morphological shape, the density of bone and scale inclusions on the surface from the CT scans, we can directly assume that these coprolites are inevitably produced by carnivorous organisms. Despite that, we still conducted SEM–EDS tests on two specimens, IVPP V 27,546 and specimen IVPP V 27,545 (Fig. 6), in order to determine its mineral content, and to prove them as a valid coprolite material because we were not able to compare these materials to any attached locality matrix at the time the study. The reason for that was because the specimens were collected almost two decades ago and they were very well-kept in the archives throughout these years. As predicted, all 4 samples gave higher content of Ca and P, thus, there is no doubt that they are indeed fossilized fecal materials. Also, in regards to the SEM–EDS on specimen IVPP V 27,545 (Fig. 6C–D), when randomly pointed to a particular structure, it yielded unusual results from the rest, in which the EDS peaks are composed of Na and Cl. At the same time, the SEM image potentially showed a pollen grain like structure. Hollocher and Hollocher86 documented a pollen image by using SEM, which brings our potential pollen image (Fig. 6C) dimensionally compatible with their sample. Although specimen IVPP V 27,545 is produced by an unidentified carnivorous vertebrate, it is common for carnivore coprolites to have plant remains within them. Also, it is known that spores and pollens are exceptionally well preserved within the encasement of calcium phosphate, which inhibits sporopollenin degradation87. Various reasons can be inferred for the presence of the pollen in specimen IVPP V 27,545, to which it could either be by accident or by preying on an herbivorous animal. Furthermore, it could also be through the adhesion on the excrement when the fecal is still fresh88. Pollens are in fact valuable information provider for paleoenvironment reconstruction, as well as for understanding the vegetation state of a particular era87,89,90,91,92. Hence, further palynology analyses are needed for future work.EDS mineral composition and coprolite coloration can be correlated to a certain degree, in which it could also explain depositional origin27. Most of the Tatal’s coprolites are pink-whitish in color, which is highly associated with the presence of calcium through its carnivorous diets93,94,95,96. The dark colors can also be due to the presence of iron or it could also be due to complete phosphatisation23,27. However, a large part of the colorations was influenced by diagenesis27,28.Traces of burrows are evident on the surface of specimen IVPP V 27,547 and IVPP V 27,550, but CT scans revealed internal traces burrowing did occur in specimen IVPP V 27,546, IVPP V 27,547, IVPP V 27,548 and IVPP V 27,549 (Fig. 5). Since not all possible burrows were dug-in, we gave the term ‘pseudo-burrow’ on those burrows that were abandoned in the early stages. For example, on all of the burrow traces in specimen IVPP V 27,547, only one traces showed burrowing holes, while the rest did not form a hole. While those specimens with internals, but without any traces on the outer surface, this can be explained by taphonomy processes, whereby the outer surface is covered with sedimentary and non-differentiable. It was reported in Tapanila et al.97, that marine bivalves are potential makers of the burrows in coprolites by expanding the diameter of the hole as they dig in, although Milàn, Rasmussen & Bonde98, reported a contradictory example, where the holes were indeed constant in diameter. In our study, we couldn’t determine if the holes were constantly in diameter or not. Numerous tiny holes were visible on all of the coprolites surface, as well as within it, and these were most probably caused by gases within the fecal matters. These holes can be called as microvoids or ‘degassing holes’, which contain gases trapped during digestion74,99,100. Microvoids are quickly filled with water when fecal matter is excreted from the animal body, thus making the fecal becoming heavy and sinking to the lake floor74.A series of three parallel furrows or bioerosional scars were evident on the surface of specimen IVPP V 27,545 (Fig. 3). Those lines only occurred once without any repetition on the rest of the surface. The information from these furrows were insufficient to deduce any potential biters, as widely discussed in the work of Godfrey & Palmer101, Godfrey & Smith102, Dentzien-Dias et al.103, and Collareta et al.104. On the other hand, deducing from the dented surface on the bitten marks, we predicted that the marks were most probably made by the biting pressures from the fish mandibles, which may indicate coprophagous behavior. The biting could have happened on the lake floor just before sedimentary deposition. Since the bitten marks are on the surface, this probably suggests unintentional scavenging and was eventually aborted during food search.In general, coprolites can be transported from the original place through various modes25 and this can be evident by the traces of abrasion51,65. However, in Tatal’s coprolites, there were little or almost no marks of abrasion. Yet again, this supports our hypothesis that these coprolites were excrements in shallow waters, such as in the lake banks with little turbulence and current, where the fecal matter was dropped in-situ after excrement. As stated in previous literature105,106, radial and concentric cracks are also evident on the surface of specimen IVPP V 27,550, therefore, these indicate that the coprolite was excreted on a very shallow environment where the water body was vastly evaporated and left for subaerial exposure before embedment. This phenomenon caused the coprolite to dehydrate through the cracking, and shrinking occurred in a low magnitude process while retaining its overall shape27,54,107. Previous authors have also discussed that the cracks could possibly be due to synaeresis under certain conditions27,54,108.It has been frequently reported in records that almost all spiral coprolite fossilization from various Phenerozoic ages have occurred in low-energy shallow marine environments54. Feces that are being excreted in this humid environment have a higher chance of preservation due to the rapid burial, as well as on the acidity level of the water bodies5,7,109,110,111. There are also several crucial factors that are involved in fecal fossilization. Among them, one of the most important criteria includes the content and composition of the fecal matter, and those of carnivorous diets tend to form coprolites than those who consumed an herbivorous diet75. As mentioned in Dentzien-Dias et al.111, there are three main stages involved in a coprolite taphonomy history, which include stages before final burial, after the final burial and after exposure. In accordance to this, we introduced the usage of phases to discuss the spiral coprolites morphologies in this study (see material and methods). The phase concept of spiral coprolites disentanglement has been widely discussed in early days by various workers6,22,70. Coprolite specimen IVPP V 27,544 and IVPP V 27,547 are considered as Phase 1, as the coils are not deep, and this can be explained as during excrement, there’s a mucosal membrane covering the surface of the fecal matter and embedment occurring rapidly, thus retaining most of its surface structure. Although there are signs of disentanglement, we predict that the uncoiling on the surface was not by natural processes, but has been caused by a breakage after on. Both of these two coprolites could have been large in actual size. Similar explanations can be given to specimens IVPP V 27,548 and IVPP V 27,550, whereby the coils are shallow, thus, classifying them as to had occurred in Phase 1. We classify specimen IVPP V 27,546 and IVPP V 27,549 as Phase 2, in which the spaces between the coils of IVPP V 27,546 were slightly separated and in IVPP V 27,549, they were strongly separated. Both of these specimens could have spent more time in water bodies before burial. Specimen IVPP V 27,545 does not provide any external information in regards of phases approach because of its non-spiral morphology. While it is also worthwhile to mention that none of them have spent sufficient time in the water bodies in order to possess the Phase 3 structure. Through these, we can also conclude that smaller coprolites are much complete while bigger coprolites tend to easily break-off. However, having mentioned that, the preservation of specimen IVPP V 27,550 is indeed valuable.Through the above morphological points, we predict that the amphipolar spiral coprolites could have belonged to groups of either prehistoric lungfishes or Acipenseriformes (sturgeon and paddlefish). Another aim of this work is to portray the existence of possible prey-predation relationships from the collected coprolites. In order to narrow down the identity of the potential producer and possibly the prey, we looked into some related fauna list from past literature. Geological settings have indicated that the Lower Cretaceous Tsagan-Tsab formation is not only recorded in the area of Tatal, but also in other regions of Mongolia as well36. There are two possibilities on the deduced prey and predator, they are either of Asipenceriformes—Lycopteriformes relationship or Asipenceriformes—Pholidophoriformes relationship. We suggest Pholidophoriformes as a much potential prey than the Lycopteriformes in the Tsagan-Tsab Formation, and the reasons will be explained thoroughly. As for the producer, we knew that Asipenceriformes are largely known from the Lycoptera-Peipiaosteus (Asipenceriformes) Fauna or the “Jehol Fauna”, as these assemblages of fishes were not only abundant in the Lower Cretaceous Yixian Formation of northeastern China, but also widely distributed over the region of eastern Siberia, Mongolia, northern China and northern Korea112. It is also noteworthy to mention that the Tsagan-Tsab formations and the Yixian formation were similar in geological age. In the same context, Jakolev35 described Stichopterus popovi (Asipenceriformes) and recorded amphipolar spiral coprolites from the Aptian lacustrine of Gurvan-Eren Formation of Mongolia , a locality that is close to Tatal. Although there are differences in the geological period of Tsagan-Tsab and Gurvan-Eren Formation, it is highly possible that Asipenceriformes existed in these areas. Furthermore, Asipenceriformes are shown to have spiral valves113, and this can be further proven with the work of Capasso64 on Peipiaosteus pani, thus, contributing to the morphology of the spiral coprolites. With these, we strongly suggest that the amphipolar spiral coprolites of Tsagan-Tsab Formation and for Gurvan-Eren Formation to belong to Asipenceriformes. As for prey, we know from existing literature that there is a close relationship between Asipenceriformes and Lycoptera, as evident in the name Lycoptera-Peipiaosteus Fauna. Yondon et al.36 reported Lycoptera middendorfii, a form of small freshwater Teleost fish from the Eastern Gobi—Tsagan-Tsab formation. But, it was clearly mentioned that Bon-Tsagan/Bon-Chagan (Fig. 1) is the westernmost locality of Lycoptera in Mongolia114. Another fact that was taken into account for the possible prey is the shape of the scales found in the inclusions, whereby Lycoptera are known for their cycloid shaped scales, while the ones in our specimens are more towards rhomboidal-shaped ganoid scales. These facts crucially eliminate the possibilities of Lycoptera for the Tsagan-Tsab fauna. With this, we further examined Jakolev35′s works and discovered the species that he described, Gurvanichthys mongoliensis (Pholidophoriformes) from the Gurvan-Eren Formation has rhomboidal-shaped ganoid scales. The size, shape of the scale and the nature of this fish fits well as a prey for the Stichopterus popovi (Asipenceriformes). Through these interpretations, we can possibly infer that the spiral coprolites in our study might have belonged to Asipenceriformes and Pholidophoriformes as the prey, which could further affirm the occurrence of prey-predator inter-relationship in the Lower Cretaceous of Tsagan-Tsab Formation.As for the sole scroll coprolite in this study, we do not intend to further deduce any detailed possibilities. Based on other works, chondricthyans origins or a sarcopterygian for scroll coprolites were suggested18,53,but such deduction is difficult to be purported in our studies as there is a lack of such fossil materials in the locality and surrounding localities. The chances of the underived producer to be a sarcopterygian is much higher than to be a chondricthyan, mainly due to its geological settings. The discovery of the single scroll coprolite can be a window opening to many paleontological questions for Tsagan-Tsab Formation. More

  • in

    Angiosperm pollinivory in a Cretaceous beetle

    1.Power, A. G. Ecosystem services and agriculture: tradeoffs and synergies. Phil. Trans. R. Soc. B 365, 2959–2971 (2010).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    2.Huang, D.-Y. et al. New fossil insect order Permopsocida elucidates major radiation and evolution of suction feeding in hemimetabolous insects (Hexapoda: Acercaria). Sci. Rep. 6, 23004 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    3.Grimaldi, D. A., Peñalver, E., Barrón, E., Herhold, H. W. & Engel, M. S. Direct evidence for eudicot pollen-feeding in a Cretaceous stinging wasp (Angiospermae; Hymenoptera, Aculeata) preserved in Burmese amber. Commun. Biol. 2, 408 (2019).4.Bao, T., Wang, B., Li, J. & Dilcher, D. Pollination of Cretaceous flowers. Proc. Natl Acad. Sci. USA 116, 24707–24711 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    5.Peris, D. et al. Generalist pollen-feeding beetles during the mid-Cretaceous. iScience 23, 100913 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Ahrens, D., Schwarzer, J. & Vogler, A. P. The evolution of scarab beetles tracks the sequential rise of angiosperms and mammals. Proc. R. Soc. B 281, 20141470 (2014).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    7.Farrell, B. D. ‘Inordinate fondness’ explained: why are there so many beetles? Science 281, 555–559 (1998).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Faegri, K. & van der Pijl, L. The Principles of Pollination Ecology (Pergamon, 1979).9.Poinar, G., Lambert, J. B. & Wu, Y. Araucarian source of fossiliferous Burmese amber: spectroscopic and anatomical evidence. J. Bot. Res. Inst. Tex. 1, 449–455 (2007).
    Google Scholar 
    10.Davies, E. H. Palynological Analysis and Age Assignments of Two Burmese Amber Sample Sets (Branta Biostratigraphy for Leeward Capital, 2001).11.Barrón, E. et al. Palynology of Aptian and upper Albian (lower Cretaceous) amber-bearing outcrops of the southern margin of the Basque-Cantabrian basin (northern Spain). Cretac. Res. 52, 292–312 (2015).Article 

    Google Scholar 
    12.Azar, D., Dejax, J. & Masure, E. Palynological analysis of amber-bearing clay from the lower Cretaceous of central Lebanon. Acta Geol. Sin. Engl. Ed. 85, 942–949 (2011).Article 

    Google Scholar 
    13.Barrón, E., Comas-Rengifo, M. J. & Elorza, L. Contribuciones al estudio palinológico del Cretácico Inferior de la Cuenca Vasco-Cantábrica: los afloramientos ambarigenos de Peñacerrada (España). Coloq. Paleontol. 52, 135–156 (2001).
    Google Scholar 
    14.Cai, C. et al. Basal polyphagan beetles in mid-Cretaceous amber from Myanmar: biogeographic implications and long-term morphological stasis. Proc. R. Soc. B 286, 20182175 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Mao, Y. Y. et al. Various amberground marine animals on Burmese amber with discussions on its age. Palaeoentomology 1, 91–103 (2018).Article 

    Google Scholar 
    16.Shi, G. et al. Age constraint on Burmese amber based on U–Pb dating of zircons. Cretac. Res. 37, 155–163 (2012).Article 

    Google Scholar 
    17.Yu, T. et al. An ammonite trapped in Burmese amber. Proc. Natl Acad. Sci. USA 116, 11345–11350 (2019).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.Jelínek, J. & Cline, A. R. in Handbook of Zoology, Arthropoda: Insecta, Coleoptera, Beetles Morphology and Systematics (eds Leschen, R. A. B. et al.) Vol. 2 386–390 (Walter De Gruyter, 2010).19.Hisamatsu, S. A review of the Japanese Kateretidae fauna (Coleoptera: Cucujoidea). Acta Entomol. Musei Natl Pragae 36, 551–585 (2011).
    Google Scholar 
    20.Peris, D. & Jelínek, J. Atypical short elytra in Cretaceous short-winged flower beetles (Coleoptera: Kateretidae). Palaeoentomology 2, 505–514 (2019).Article 

    Google Scholar 
    21.Peris, D. & Jelínek, J. Syninclusions of two new species of short-winged flower beetle (Coleoptera: Kateretidae) in mid-Cretaceous Kachin amber (Myanmar). Cretac. Res. 106, 104264 (2020).Article 

    Google Scholar 
    22.Poinar, G. & Brown, A. E. Furcalabratum burmanicum gen. et sp. nov., a short-winged flower beetle (Coleoptera: Kateretidae) in mid-Cretaceous Myanmar amber. Cretac. Res. 84, 240–244 (2018).Article 

    Google Scholar 
    23.Kirejtshuk, A. G. New species of nitidulid beetles (Coleoptera, Nitidulidae) of the Australian region. Entomol. Obozr. 65, 559–573 (1986).
    Google Scholar 
    24.Timerman, D., Greene, D. F., Ackerman, J. D., Kevan, P. G. & Nardone, E. Pollen aggregation in relation to pollination vector. Int. J. Plant Sci. 175, 681–687 (2014).Article 

    Google Scholar 
    25.Thomson, P. W. & Pflug, H. D. Pollen und sporen des mitteleuropäischen Tertiärs. Palaeontogr. Abt. B 94, 1–138 (1953).
    Google Scholar 
    26.Tekleva, M. V. & Maslova, N. P. A diverse pollen assemblage found on Friisicarpus infructescences (Platanaceae) from the Cenomanian–Turonian of Kazakhstan. Cretac. Res. 57, 131–141 (2016).Article 

    Google Scholar 
    27.Takahashi, K. Upper Cretaceous and lower Paleogene microfloras of Japan. Rev. Palaeobot. Palynol. 5, 227–234 (1967).Article 

    Google Scholar 
    28.Nadel, H., Peña, J. E. & Peña, J. E. Identity, behavior, and efficacy of nitidulid beetles (Coleoptera: Nitidulidae) pollinating commercial Annona species in Florida. Environ. Entomol. 23, 878–886 (1994).Article 

    Google Scholar 
    29.Sakai, S. A review of brood-site pollination mutualism: plants providing breeding sites for their pollinators. J. Plant Res. 115, 0161–0168 (2002).Article 

    Google Scholar 
    30.Williams, G. & Adam, P. A review of rainforest pollination and plant–pollinator interactions with particular reference to Australian subtropical rainforests. Aust. Zool. 29, 177–212 (1994).Article 

    Google Scholar 
    31.Klavins, S. D., Kellogg, D. W., Krings, M., Taylor, E. L. & Taylor, T. N. Coprolites in a Middle Triassic cycad pollen cone: evidence for insect pollination in early cycads? Evol. Ecol. Res. 7, 479–488 (2005).
    Google Scholar 
    32.Chadwick, C. E., Stevenson, D. W. & Norstog, K. J. The roles of Tranes lyterioides and T. sparsus Boh. (Col., Curculiodidae) in the pollination of Macrozamia communis (Zamiaceae). In The Biology, Structure, and Systematics of the Cycadales: Proc. CYCAD 90, the 2nd International Conference on Cycad Biology (eds. Stevenson, D. W. & Norstog, K. J.) 77–88 (Palm & Cycad Societies of Australia, 1993).33.Post, D. C., Page, R. E. & Erickson, E. H. Honeybee (Apis mellifera L.) queen feces: source of a pheromone that repels worker bees. J. Chem. Ecol. 13, 583–591 (1987).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    34.Weiss, H. B. & Boyd, W. M. Insect feculæ. J. N. Y. Entomol. Soc. 58, 154–168 (1950).
    Google Scholar 
    35.Lancucka-Srodoniowa, M. Tertiary coprolites imitating fruits of the Araliaceae. Acta Soc. Bot. Pol. 33, 469–473 (1964).Article 

    Google Scholar 
    36.Scott, A. C. Trace fossils of plant–arthropod interactions. Short Courses Paleontol. 5, 197–223 (1992).Article 

    Google Scholar 
    37.Weiss, H. B. & Boyd, W. M. Insect feculæ, II. J. N. Y. Entomol. Soc. 60, 25–30 (1952).
    Google Scholar 
    38.Parker, F. D., Tepedino, V. J. & Bohart, G. E. Notes on the biology of a common sunflower bee, Melissodes (Eumelissodes) agilis Cresson. J. N. Y. Entomol. Soc. 89, 43–52 (1981).
    Google Scholar 
    39.Sarzetti, L. C., Labandeira, C. C. & Genise, J. F. Reply to: Melittosphex (Hymenoptera: Melittosphecidae), a primitive bee and not a wasp. Palaeontology 52, 484 (2008).
    Google Scholar 
    40.Ohl, M. & Engel, M. S. Die Fossilgeschichte der Bienen und ihrer nächsten Verwandten (Hymenoptera: Apoidea). Denisia 20, 687–700 (2007).
    Google Scholar 
    41.Pant, D. D. & Singh, R. Preliminary observations on insect–plant relationships in Allahabad plants of Cycas. Palms Cycads 32, 10–14 (1990).
    Google Scholar 
    42.Labandeira, C. C. The paleobiology of pollination and its precursors. Paleontol. Soc. Pap. 6, 233–270 (2000).Article 

    Google Scholar 
    43.Procheş, Ş. & Johnson, S. D. Beetle pollination of the fruit-scented cones of the South African cycad Stangeria eriopus. Am. J. Bot. 96, 1722–1730 (2009).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    44.Tarno, H. et al. Types of frass produced by the ambrosia beetle Platypus quercivorus during gallery construction, and host suitability of five tree species for the beetle. J. For. Res. 16, 68–75 (2011).Article 

    Google Scholar 
    45.Friis, E. M., Pedersen, K. R. & Crane, P. R. Fossil floral structures of a basal angiosperm with monocolpate, reticulate-acolumellate pollen from the Early Cretaceous of Portugal. Grana 39, 226–239 (2000).Article 

    Google Scholar 
    46.Nambudiri, E. M. V. & Binda, P. L. Dicotyledonous fruits associated with coprolites from the upper Cretaceous (Maastrichtian) Whitemud Formation, southern Saskatchewan, Canada. Rev. Palaeobot. Palynol. 59, 57–66 (1989).Article 

    Google Scholar 
    47.Lupia, R., Herendeen, P. S. & Keller, J. A. A new fossil flower and associated coprolites: evidence for angiosperm–insect interactions in the Santonian (Late Cretaceous) of Georgia, U.S.A. Int. J. Plant Sci. 163, 675–686 (2002).Article 

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

    Google Scholar 
    49.Coiro, M., Doyle, J. A. & Hilton, J. How deep is the conflict between molecular and fossil evidence on the age of angiosperms? New Phytol. 223, 83–99 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    50.Liu, Z.-J., Huang, D., Cai, C. & Wang, X. The core eudicot boom registered in Myanmar amber. Sci. Rep. 8, 16765 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    51.Friis, E. M. & Pedersen, K. R. in Palynology: Principles and Applications (ed. Jansonius, J.) 409–426 (American Association of Stratigraphic Palynologists Foundation, 1996).52.Schönenberger, J. & Friis, E. M. Fossil flowers of ericalean affinity from the Late Cretaceous of southern Sweden. Am. J. Bot. 88, 467–480 (2001).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.The Angiosperm Phylogeny Group et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016).54.Peris, D. et al. False blister beetles and the expansion of gymnosperm–insect pollination modes before angiosperm dominance. Curr. Biol. 27, 897–904 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Cai, C. et al. Beetle pollination of cycads in the Mesozoic. Curr. Biol. 28, 2806–2812 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar  More

  • in

    A theoretical analysis of tumour containment

    1.Norton, L. & Simon, R. Tumor size, sensitivity to therapy, and design of treatment schedules. Cancer Treat. Rep. 61, 1307–1317 (1977).CAS 
    PubMed 

    Google Scholar 
    2.Goldie, J. H. & Coldman, A. J. A mathematic model for relating the drug sensitivity of tumors to their spontaneous mutation rate. Cancer Treat. Rep. 63, 1727–1733 (1979).CAS 
    PubMed 

    Google Scholar 
    3.Gatenby, R. A. A change of strategy in the war on cancer. Nature 459, 508–509 (2009).CAS 
    Article 

    Google Scholar 
    4.Zhang, J., Cunningham, J. J., Brown, J. S. & Gatenby, R. A. Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer. Nat. Commun. 8, 1816 (2017).Article 

    Google Scholar 
    5.Martin, R. B., Fisher, M. E., Minchin, R. F. & Teo, K. L. Optimal control of tumor size used to maximize survival time when cells are resistant to chemotherapy. Math. Biosci. 110, 201–219 (1992).CAS 
    Article 

    Google Scholar 
    6.Gatenby, R. A., Silva, A. S., Gillies, R. J. & Frieden, B. R. Adaptive therapy. Cancer Res. 69, 4894–4903 (2009).CAS 
    Article 

    Google Scholar 
    7.Gatenby, R. & Brown, J. The evolution and ecology of resistance in cancer therapy. Cold Spring Harb. Perspect. Med. 10, a040972 (2020).CAS 
    Article 

    Google Scholar 
    8.Bourguet, D. et al. Heterogeneity of selection and the evolution of resistance. Trends Ecol. Evol. 28, 110–118 (2013).Article 

    Google Scholar 
    9.Tabashnik, B. E., Brévault, T. & Carrière, Y. Insect resistance to Bt crops: lessons from the first billion acres. Nat. Biotechnol. 31, 510–521 (2013).CAS 
    Article 

    Google Scholar 
    10.Cunningham, J. J. A call for integrated metastatic management. Nat. Ecol. Evol. 3, 996–998 (2019).Article 

    Google Scholar 
    11.Bacevic, K. Spatial competition constrains resistance to targeted cancer therapy. Nat. Commun. 8, 1995 (2017).Article 

    Google Scholar 
    12.Silva, A. S. et al. Evolutionary approaches to prolong progression-free survival in breast cancer. Cancer Res. 72, 6362–6370 (2012).CAS 
    Article 

    Google Scholar 
    13.Enriquez-Navas, P. M. et al. Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer. Sci. Transl. Med. 8, 327ra24 (2016).Article 

    Google Scholar 
    14.Monro, H. C. & Gaffney, E. A. Modelling chemotherapy resistance in palliation and failed cure. J. Theor. Biol. 257, 292–302 (2009).CAS 
    Article 

    Google Scholar 
    15.Carrère, C. Optimization of an in vitro chemotherapy to avoid resistant tumours. J. Theor. Biol. 413, 24–33 (2017).Article 

    Google Scholar 
    16.Gallaher, J. A., Enriquez-Navas, P. M., Luddy, K. A., Gatenby, R. A. & Anderson, A. R. A. Spatial heterogeneity and evolutionary dynamics modulate time to recurrence in continuous and adaptive cancer therapies. Cancer Res. 78, 2127–2139 (2018).CAS 
    Article 

    Google Scholar 
    17.Hansen, E., Woods, R. J. & Read, A. F. How to use a chemotherapeutic agent when resistance to it threatens the patient. PLoS Biol. 15, e2001110 (2017).Article 

    Google Scholar 
    18.Cunningham, J. J., Brown, J. S., Gatenby, R. A. & Staňková, K. Optimal control to develop therapeutic strategies for metastatic castrate resistant prostate cancer. J. Theor. Biol. 459, 67–78 (2018).CAS 
    Article 

    Google Scholar 
    19.West, J., Ma, Y. & Newton, P. K. Capitalizing on competition: an evolutionary model of competitive release in metastatic castration resistant prostate cancer treatment. J. Theor. Biol. 455, 249–260 (2018).Article 

    Google Scholar 
    20.Pouchol, C., Clairambault, J., Lorz, A. & Trélat, E. Asymptotic analysis and optimal control of an integro-differential system modelling healthy and cancer cells exposed to chemotherapy. J. Math. Pures Appl. 116, 268–308 (2018).Article 

    Google Scholar 
    21.Carrère, C. & Zidani, H. Stability and reachability analysis for a controlled heterogeneous population of cells. Optim. Control Appl. Methods 41, 1678–1704 (2020).Article 

    Google Scholar 
    22.Greene, J. M., Sanchez-Tapia, C. & Sontag, E. D. Mathematical details on a cancer resistance model. Front. Bioeng. Biotechnol. 8, 501 (2020).Article 

    Google Scholar 
    23.Martin, R. B., Fisher, M. E., Minchin, R. F. & Teo, K. L. Low-intensity combination chemotherapy maximizes host survival time for tumors containing drug-resistant cells. Math. Biosci. 110, 221–252 (1992).CAS 
    Article 

    Google Scholar 
    24.Gerlee, P. The model muddle: in search of tumor growth laws. Cancer Res. 73, 2407–2411 (2013).CAS 
    Article 

    Google Scholar 
    25.Noble, R., Burri, D., Kather, J. N. & Beerenwinkel, N. Spatial structure governs the mode of tumour evolution. Preprint at bioRxiv https://doi.org/10.1101/586735 (2019).26.Hansen, E. & Read, A. F. Cancer therapy: attempt cure or manage drug resistance? Evol. Appl. 13, 1660–1672 (2020).Article 

    Google Scholar 
    27.Enriquez-Navas, P. M., Wojtkowiak, J. W. & Gatenby, R. A. Application of evolutionary principles to cancer therapy. Cancer Res. 75, 4675–4680 (2015).CAS 
    Article 

    Google Scholar 
    28.Gatenby, R. A. & Brown, J. S. Integrating evolutionary dynamics into cancer therapy. Nat. Rev. Clin. Oncol. 17, 675–686 (2020).Article 

    Google Scholar 
    29.Strobl, M. A. R. et al. Turnover modulates the need for a cost of resistance in adaptive therapy. Cancer Res. https://doi.org/10.1158/0008-5472.CAN-20-0806 (2020).Article 
    PubMed 

    Google Scholar 
    30.Bozic, I. et al. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife 2, e00747 (2013).Article 

    Google Scholar 
    31.Pérez-García, V. M. et al. Universal scaling laws rule explosive growth in human cancers. Nat. Phys. 16, 1232–1237 (2020).Article 

    Google Scholar 
    32.Greene, J. M., Gevertz, J. L. & Sontag, E. S. Mathematical approach to differentiate spontaneous and induced evolution to drug resistance during cancer treatment. JCO Clin. Cancer Inform. 3, CCI.18.00087 (2019).PubMed Central 

    Google Scholar 
    33.Kuosmanen, T. et al. Drug-induced resistance evolution necessitates less aggressive treatment. Preprint at bioRxiv https://doi.org/10.1101/2020.10.07.330134 (2020).34.Fusco, D., Gralka, M., Kayser, J., Anderson, A. & Hallatschek, O. Excess of mutational jackpot events in expanding populations revealed by spatial Luria–Delbrück experiments. Nat. Commun. 7, 12760 (2016).CAS 
    Article 

    Google Scholar 
    35.Mistry, H. B. Evolutionary based adaptive dosing algorithms: beware the cost of cumulative risk. Preprint at bioRxiv https://doi.org/10.1101/2020.06.23.167056 (2020).36.Benzekry, S. et al. Classical mathematical models for description and prediction of experimental tumor growth. PLoS Comput. Biol. 10, e1003800 (2014).Article 

    Google Scholar 
    37.Vaghi, C. et al. Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors. PLoS Comput. Biol. 16, e1007178 (2020).CAS 
    Article 

    Google Scholar 
    38.Hansen, E., Karslake, J., Woods, R. J., Read, A. F. & Wood, K. B. Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations. PLoS Biol. 18, e3000713 (2020).CAS 
    Article 

    Google Scholar 
    39.Soetaert, K. E. R., Petzoldt, T. & Setzer, R. W. Solving differential equations in R : package deSolve. J. Stat. Softw. 33, 9 (2010). More

  • in

    Reproductive performance in houbara bustard is affected by the combined effects of age, inbreeding and number of generations in captivity

    1.Conde, D. A., Flesness, N., Colchero, F., Jones, O. R. & Scheuerlein, A. An emerging role of zoos to conserve biodiversity. Science 331, 1390–1391 (2011).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    2.Ballou, J. D. et al. Demographic and genetic management of captive populations. in Wild Mammals in Captivity: Principles and Techniques for Zoo Management (eds. Kleiman, D. G., Thompson, K. V. & Kirk Baer, C.) 219–252 (The University of Chicago Press, 2010).3.Ralls, K. & Ballou, J. D. Captive breeding and reintroduction. in Encyclopedia of Biodiversity (ed. Levin, S. A.) 662–667 (Elsevier Academic Press, 2013). https://doi.org/10.1016/B978-0-12-384719-5.00268-9.4.IUCN. Guidelines on the Use of Ex Situ Management for Species Conservation (2nd ed.). www.iucn.org/about/work/programmes/species/publications/iucn_guidelines_and__policy__statements/ (2014).5.Lacy, R. C. Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conserv. Biol. 1, 143–158 (1987).Article 

    Google Scholar 
    6.Lockyear, K. M., MacDonald, S. E., Waddell, W. T. & Goodrowe, K. L. Investigation of captive red wolf ejaculate characteristics in relation to age and inbreeding. Theriogenology 86, 1369–1375 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    7.Frankham, R. Genetic adaptation to captivity in species conservation programs. Mol. Ecol. 17, 325–333 (2008).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Keller, L. F. & Waller, D. M. Inbreeding effects in wild populations. Trends Ecol. Evol. 17, 230–241 (2002).Article 

    Google Scholar 
    9.Robert, A., Couvet, D. & Sarrazin, F. Integration of demography and genetics in population restorations. Écoscience 14, 463–471 (2007).Article 

    Google Scholar 
    10.Charlesworth, D. & Charlesworth, B. Inbreeding depression and its evolutionary consequences. Annu. Rev. Ecol. Syst. 18, 237–268 (1987).Article 

    Google Scholar 
    11.McPhee, M. E. & McPhee, N. F. Relaxed selection and environmental change decrease reintroduction success in simulated populations: altered selection in captive populations. Anim. Conserv. 15, 274–282 (2012).Article 

    Google Scholar 
    12.Ford, M. J. Selection in captivity during supportive breeding may reduce fitness in the wild. Conserv. Biol. 16, 815–825 (2002).Article 

    Google Scholar 
    13.Stockwell, C. A., Hendry, A. P. & Kinnison, M. T. Contemporary evolution meets conservation biology. Trends Ecol. Evol. 18, 94–101 (2003).Article 

    Google Scholar 
    14.Robert, A. Captive breeding genetics and reintroduction success. Biol. Conserv. 142, 2915–2922 (2009).Article 

    Google Scholar 
    15.Araki, H., Cooper, B. & Blouin, M. S. Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318, 100–103 (2007).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    16.Christie, M. R., Marine, M. L., French, R. A. & Blouin, M. S. Genetic adaptation to captivity can occur in a single generation. Proc. Natl. Acad. Sci. 109, 238–242 (2012).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    17.West-Eberhard, M. J. Phenotypic plasticity and the origins of diversity. Annu. Rev. Ecol. Syst. 20, 249–278 (1989).Article 

    Google Scholar 
    18.Gordon, S. P., Hendry, A. P. & Reznick, D. N. Predator-induced contemporary evolution, phenotypic plasticity, and the evolution of reaction norms in guppies. Copeia 105, 514–522 (2017).Article 

    Google Scholar 
    19.Forslund, P. & Pärt, T. Age and reproduction in birds—hypotheses and tests. Trends Ecol. Evol. 10, 374–378 (1995).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    20.Smith, J. M. Review lectures on senescence—I. The causes of ageing. Proc. R. Soc. Lond. B Biol. Sci. 157, 115–127 (1962).ADS 
    Article 

    Google Scholar 
    21.Partridge, L. & Barton, N. H. Optimally, mutation and the evolution of ageing. Nature 362, 305–311 (1993).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Jones, O. R. et al. Diversity of ageing across the tree of life. Nature 505, 169–173 (2014).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    23.Langen, K., Bakker, T. C. M., Baldauf, S. A., Shrestha, J. & Thünken, T. Effects of ageing and inbreeding on the reproductive traits in a cichlid fish I: the male perspective. Biol. J. Linn. Soc. 120, 752–761 (2017).Article 

    Google Scholar 
    24.Kirkwood, T. B. L. Evolution of ageing. Nature 270, 301 (1977).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    25.Benton, C. H. et al. Inbreeding intensifies sex- and age-dependent disease in a wild mammal. J. Anim. Ecol. 87, 1500–1511 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.de Boer, R. A., Eens, M. & Müller, W. Sex-specific effects of inbreeding on reproductive senescence. Proc. R. Soc. B Biol. Sci. 285, 20180231 (2018).Article 

    Google Scholar 
    27.Promislow, D. E. L. & Tatar, M. Mutation and senescence: where genetics and demography meet. Genetica 102, 299–314 (1998).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Charlesworth, B. & Hughes, K. A. Age-specific inbreeding depression and components of genetic variance in relation to the evolution of senescence. Proc. Natl. Acad. Sci. 93, 6140–6145 (1996).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Snoke, M. S. & Promislow, D. E. L. Quantitative genetic tests of recent senescence theory: age-specific mortality and male fertility in Drosophila melanogaster. Heredity 91, 546–556 (2003).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Robert, A., Toupance, B., Tremblay, M. & Heyer, E. Impact of inbreeding on fertility in a pre-industrial population. Eur. J. Hum. Genet. 17, 673–681 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Lesobre, L. et al. Conservation genetics of Houbara Bustard (Chlamydotis undulata undulata): population structure and its implications for the reinforcement of wild populations. Conserv. Genet. 11, 1489–1497 (2010).Article 

    Google Scholar 
    32.Rabier, R., Robert, A., Lacroix, F. & Lesobre, L. Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses. Zoo Biol. 39, 365–447 (2020).Article 

    Google Scholar 
    33.Hardouin, L. A., Legagneux, P., Hingrat, Y. & Robert, A. Sex-specific dispersal responses to inbreeding and kinship. Anim. Behav. https://doi.org/10.1016/j.anbehav.2015.04.002 (2015).Article 

    Google Scholar 
    34.Cornec, C., Robert, A., Rybak, F. & Hingrat, Y. Male vocalizations convey information on kinship and inbreeding in a lekking bird. Ecol. Evol. 9, 4421–4430 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Vuarin, P. et al. No evidence for prezygotic postcopulatory avoidance of kin despite high inbreeding depression. Mol. Ecol. 27, 5252–5262 (2018).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    36.Bacon, L., Hingrat, Y. & Robert, A. Evidence of reproductive senescence of released individuals in a reinforced bird population. Biol. Conserv. 215, 288–295 (2017).Article 

    Google Scholar 
    37.Chantepie, S. et al. Quantitative genetics of the aging of reproductive traits in the houbara bustard. PLoS ONE 10, e0133140 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    38.Preston, B. T., Saint Jalme, M., Hingrat, Y., Lacroix, F. & Sorci, G. Sexually extravagant males age more rapidly. Ecol. Lett. 14, 1017–1024 (2011).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Preston, B. T., Saint Jalme, M., Hingrat, Y., Lacroix, F. & Sorci, G. The sperm of aging male bustards retards their offspring’s development. Nat. Commun. 6, 1–9 (2015).Article 
    CAS 

    Google Scholar 
    40.Vuarin, P. et al. Post-copulatory sexual selection allows females to alleviate the fitness costs incurred when mating with senescing males. Proc. R. Soc. B Biol. Sci. 286, 20191675 (2019).Article 

    Google Scholar 
    41.Chargé, R. et al. Quantitative genetics of sexual display, ejaculate quality and size in a lekking species. J. Anim. Ecol. 82, 399–407 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.Chargé, R. et al. Does recognized genetic management in supportive breeding prevent genetic changes in life-history traits?. Evol. Appl. 7, 521–532 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    43.Gaucher, P. et al. Taxonomy of the Houbara Bustard Chlamydotis undulata subspecies considered on the basis of sexual display and genetic divergence. Ibis 138, 273–282 (1996).Article 

    Google Scholar 
    44.Hingrat, Y., Saint Jalme, M., Chalah, T., Orhant, N. & Lacroix, F. Environmental and social constraints on breeding site selection. Does the exploded-lek and hotspot model apply to the Houbara bustard Chlamydotis undulata undulata?. J. Avian Biol. 39, 393–404 (2008).Article 

    Google Scholar 
    45.Duursma, D. E., Gallagher, R. V., Price, J. J. & Griffith, S. C. Variation in avian egg shape and nest structure is explained by climatic conditions. Sci. Rep. 8, 1–10 (2018).
    Google Scholar 
    46.Cucco, M., Grenna, M. & Malacarne, G. Female condition, egg shape and hatchability: a study on the grey partridge. J. Zool. 287, 186–194 (2012).Article 

    Google Scholar 
    47.Adamou, A.-E. et al. Egg size and shape variation in Rufous Bush Chats Cercotrichas galactotes breeding in date palm plantations: hatching success increases with egg elongation. Avian Biol. Res. 11, 100–107 (2018).Article 

    Google Scholar 
    48.Goriup, P. D. The world status of the Houbara Bustard Chlamydotis undulata. Bird Conserv. Int. 7, 373–397 (1997).Article 

    Google Scholar 
    49.BirdLife International. Chlamydotis undulata. The IUCN Red List of Threatened Species 2016: e.T22728245A90341807. (2016) https://doi.org/10.2305/IUCN.UK.2016-3.RLTS.T22728245A90341807.en.50.Lacroix, F., Seabury, J., Al Bowardi, M. & Renaud, J. The Emirates Center for Wildlife Propagation: developing a comprehensive strategy to secure a self-sustaining population of houbara bustard (Chlamydotis undulata undulata) in Eastern Morocco. Houbara News 5, (2003).
    51.Conway, W. Wild and zoo animal interactive management and habitat conservation. Biodivers. Conserv. 4, 573–594 (1995).Article 

    Google Scholar 
    52.Saint Jalme, M., Gaucher, P. & Paillat, P. Artificial insemination in Houbara bustards (Chlamydotis undulata): influence of the number of spermatozoa and insemination frequency on fertility and ability to hatch. Reproduction 100, 93–103 (1994).CAS 
    Article 

    Google Scholar 
    53.Allendorf, F. W. Delay of adaptation to captive breeding by equalizing family size. Conserv. Biol. 7, 416–419 (1993).Article 

    Google Scholar 
    54.Percie du Sert, N. et al. The ARRIVE guidelines 2.0: updated guidelines for reporting animal research. PLOS Biol. 18, e3000410 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Vuarin, P. et al. Sperm competition accentuates selection on ejaculate attributes. Biol. Lett. 15, 20180889 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Chalah, T., Seigneurin, F., Blesbois, E. & Brillard, J. P. In vitro comparison of fowl sperm viability in ejaculates frozen by three different techniques and relationship with subsequent fertility in vivo. Cryobiology 39, 185–191 (1999).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    57.Hoyt, D. F. Practical methods of estimating volume and fresh weight of bird eggs. Auk 96, 73–77 (1979).
    Google Scholar 
    58.Wellmann, R. optiSel: Optimum Contribution Selection and Population Genetics. R package version 2.0.2. https://CRAN.R-project.org/package=optiSel (2018).59.R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org (2019).60.Princée, F. P. G. Exploring Studbooks for Wildlife Management and Conservation (Springer, Berlin, 2016).
    Google Scholar 
    61.Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. The R Journal. 9, 378–400 (2017).Article 

    Google Scholar 
    62.Ludecke, D., Makowski, D. & Waggoner, P. performance: Assessment of Regression Models Performance. R package version 0.3.0. https://CRAN.R-project.org/package=performance (2019).63.Ludecke, D. ggeffects: tidy data frames of marginal effects from regression models. J. Open Source Softw. 3, 772. https://doi.org/10.21105/joss.00772 (2018).ADS 
    Article 

    Google Scholar 
    64.Wickham, H. ggplot2: elegant graphics for data analysis (Springer, Berlin, 2009).
    Google Scholar 
    65.Newton, I. & Rothery, P. Senescence and reproductive value in sparrowhawks. Ecology 78, 1000–1008 (1997).Article 

    Google Scholar 
    66.Bouwhuis, S., Sheldon, B. C., Verhulst, S. & Charmantier, A. Great tits growing old: selective disappearance and the partitioning of senescence to stages within the breeding cycle. Proc. R. Soc. B Biol. Sci. 276, 2769–2777 (2009).CAS 
    Article 

    Google Scholar 
    67.Angelier, F., Shaffer, S. A., Weimerskirch, H. & Chastel, O. Effect of age, breeding experience and senescence on corticosterone and prolactin levels in a long-lived seabird: the wandering albatross. Gen. Comp. Endocrinol. 149, 1–9 (2006).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    68.Angelier, F., Weimerskirch, H., Dano, S. & Chastel, O. Age, experience and reproductive performance in a long-lived bird: a hormonal perspective. Behav. Ecol. Sociobiol. 61, 611–621 (2007).Article 

    Google Scholar 
    69.Ottinger, M. A. et al. The Japanese quail: a model for studying reproductive aging of hypothalamic systems. Exp. Gerontol. 39, 1679–1693 (2004).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    70.Lecomte, V. J. et al. Patterns of aging in the long-lived wandering albatross. Proc. Natl. Acad. Sci. 107, 6370–6375 (2010).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    71.Opatová, P. et al. Inbreeding depression of sperm traits in the zebra finch Taeniopygia guttata. Ecol. Evol. 6, 295–304 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    72.Croquet, C. et al. Linear and curvilinear effects of inbreeding on production traits for Walloon Holstein cows. J. Dairy Sci. 90, 465–471 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    73.Leroy, G. Inbreeding depression in livestock species: review and meta-analysis. Anim. Genet. 45, 618–628 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    74.Ralls, K. et al. Call for a paradigm shift in the genetic management of fragmented populations: genetic management. Conserv. Lett. 11, e12412 (2018).Article 

    Google Scholar 
    75.Huisman, J., Kruuk, L. E. B., Ellis, P. A., Clutton-Brock, T. & Pemberton, J. M. Inbreeding depression across the lifespan in a wild mammal population. Proc. Natl. Acad. Sci. 113, 3585–3590 (2016).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    76.Frankham, R. & Ralls, K. Inbreeding leads to extinction. Nature 392, 441–442 (1998).ADS 
    CAS 
    Article 

    Google Scholar 
    77.Armbruster, P. & Reed, D. H. Inbreeding depression in benign and stressful environments. Heredity 95, 235–242 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    78.Robert, A. Negative environmental perturbations may improve species persistence. Proc. R. Soc. B Biol. Sci. 273, 2501–2506 (2006).Article 

    Google Scholar 
    79.Crnokrak, P. & Roff, D. A. Inbreeding depression in the wild. Heredity 83, 260–270 (1999).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    80.Araki, H., Berejikian, B. A., Ford, M. J. & Blouin, M. S. Fitness of hatchery-reared salmonids in the wild. Evol. Appl. 1, 342–355 (2008).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    81.Lynch, M. & O’Hely, M. Captive breeding and genetic fitness of natural populations. Conserv. Genet. 2, 363–378 (2001).Article 

    Google Scholar 
    82.Robert, A., Sarrazin, F., Couvet, D. & Legendre, S. Releasing adults versus young in reintroductions: interactions between demography and genetics. Conserv. Biol. 18, 1078–1087 (2004).Article 

    Google Scholar 
    83.Roche, E. A., Cuthbert, F. J. & Arnold, T. W. Relative fitness of wild and captive-reared piping plovers: does egg salvage contribute to recovery of the endangered Great Lakes population?. Biol. Conserv. 141, 3079–3088 (2008).Article 

    Google Scholar 
    84.Ford, N. B. & Seigel, R. A. Phenotypic plasticity in reproductive traits: evidence from a viviparous snake. Ecology 70, 1768–1774 (1989).Article 

    Google Scholar 
    85.Bacon, L. Etude des paramètres de reproduction et de la dynamique d’une population renforcée d’outardes Houbara nord-africaines (Chlamydotis undulata undulata) au Maroc. (Museum National d’Histoire Naturelle, 2017).86.Robert, A. et al. Defining reintroduction success using IUCN criteria for threatened species: a demographic assessment. Anim. Conserv. 18, 397–406 (2015).Article 

    Google Scholar 
    87.Bacon, L., Robert, A. & Hingrat, Y. Long lasting breeding performance differences between wild-born and released females in a reinforced North African Houbara bustard (Chlamydotis undulata undulata) population: a matter of release strategy. Biodivers. Conserv. 28, 553–570 (2019).Article 

    Google Scholar 
    88.Vuarin, P. et al. Paternal age negatively affects sperm production of the progeny. Ecol. Lett. https://doi.org/10.1111/ele.13696 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    89.Keller, L. F., Reid, J. M. & Arcese, P. Testing evolutionary models of senescence in a natural population: age and inbreeding effects on fitness components in song sparrows. Proc. R. Soc. B Biol. Sci. 275, 597–604 (2008).CAS 
    Article 

    Google Scholar 
    90.Reynolds, R. M. et al. Age specificity of inbreeding load in Drosophila melanogaster and implications for the evolution of late-life mortality plateaus. Genetics 177, 587–595 (2007).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    91.Tan, C. K. W., Pizzari, T. & Wigby, S. Parental age, gametic age, and inbreeding interact to modulate offspring viability in Drosophila melanogaster. Evolution 67, 3043–3051 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    92.Deubel, W., Bassukas, I. D., Schlereth, W., Lorenz, R. & Hempel, K. Age dependent selection against HPRT deficient T lymphocytes in the HPRT± heterozygous mouse. Mutat. Res. Mol. Mech. Mutagen. 351, 67–77 (1996).CAS 
    Article 

    Google Scholar 
    93.Réale, D. & Festa-Bianchet, M. Predator-induced natural selection on temperament in bighorn ewes. Anim. Behav. 65, 463–470 (2003).Article 

    Google Scholar 
    94.Coltman, D. W., Pilkington, J. G., Smith, J. A. & Pemberton, J. M. Parasite-mediated selection against Inbred Soay Sheep in a free-living, island population. Evolution 53, 1259 (1999).PubMed 
    PubMed Central 

    Google Scholar 
    95.Wang, J., Hill, W. G., Charlesworth, D. & Charlesworth, B. Dynamics of inbreeding depression due to deleterious mutations in small populations: mutation parameters and inbreeding rate. Genet. Res. 74, 165–178 (1999).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar  More

  • in

    A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation

    Combined culture-dependent and culture-independent approach identifies the prevalent and viable bacterial community members of the human lung post-transplantTo characterize the bacterial community composition of the lung microbiota post-transplant, we performed 16S rRNA gene amplicon sequencing of 234 longitudinal BALF samples from 64 lung transplant recipients collected over a 49-month period (Fig. 1a, Supplementary Table 1). A total of 7164 operational taxonomic units (OTUs) were identified, excluding OTUs contributing to reads in 11 negative control samples32 (see “Methods”, Supplementary Fig. 1a, Supplementary Data 1 and 2). In accordance with previous studies on BALF samples from healthy non-transplant individuals4,5,6,26, we found that Bacteroidetes and Firmicutes followed by Proteobacteria and Actinobacteria are the most abundant phyla in the post-transplant lung (Fig. 1b). Prevalence analysis across all BALF samples showed that the community composition is highly variable with only 22 OTUs shared by ≥50% of the samples (Supplementary Fig. 1b, Supplementary Data 3). However, these 22 OTUs constituted 42% of the total number of rarefied reads, indicating that they are predominant members of the post-transplant lung microbiota (Fig. 1c, Supplementary Fig. 1c, Supplementary Table 2, Supplementary Data 3). They belonged to the genera Prevotella 7, Streptococcus, Veillonella, Neisseria, Alloprevotella, Pseudomonas, Gemella, Granulicatella, Campylobacter, Porphyromonas and Rothia, the majority of which are also prevailing community members in the healthy human lung3,5,7,26, suggesting a considerable overlap in the overall composition of the lung microbiota between the healthy and the transplanted lung.Fig. 1: Combining BALF amplicon sequencing and bacterial culturing to deduce the microbial ecology of deep lung microbiota.a Schematic of the sampling of Bronchoalveolar lavage fluid (BALF) from lung transplant recipients over time (months post-transplant). b Relative abundances (%) of most abundant phyla across BALF samples. Box plots show median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers) as well as outliers (single points). c Prevalence (% samples) vs contribution to total reads across samples for most abundant phyla. Dot color shows different genera and size show total rarefied reads. Gray dashed horizontal line shows prevalence ≥50%. d Scatter plot shows correlation between number of observed OTUs and bacterial counts per BALF sample obtained by quantifying 16S rRNA gene copies with qPCR. Linear regression is shown by the blue line with gray shaded area showing 95% confidence interval (n = 234, two-sided, F(1, 232) = 91.04, P = 2.2 × 10−16), Coefficient of correlation; R2 = 0.28. e Bar chart shows lung taxa (genera; OTU IDs) that contributed ≥75% of total bacterial biomass across samples (n = 234). Venn diagram inset shows overlap (yellow) between the most prevalent (≥50% incidence, light blue) and the most abundant (≥75% total count, red) taxa in the transplanted lung. Bar colors also show the same.Full size imageDifferences in bacterial loads between samples can skew community analyses when based on relative abundance profiling alone. Therefore, we used qPCR to determine the total copies of the 16S rRNA gene as an estimate for bacterial counts, and normalized the abundances of each OTU across the 234 samples (absolute abundance). We found that the bacterial counts vastly differed between samples, ranging between 101 and 106 gene copies per ml of BALF (Supplementary Fig. 1d). The number of observed OTUs increased with decreasing counts (Fig. 1d) suggesting that a large fraction of the OTUs were detected in samples of low bacterial biomass and hence represent either transient or extremely low-abundant community members, or sequencing artefacts and contaminations. In turn, 19 of the 7164 OTUs constituted >75% of the total bacterial biomass detected across the 234 BALF samples (Fig. 1e). This included 11 of the 22 most prevalent OTUs (see above) plus eight OTUs that were detected in only a few samples but at very high abundance (Staphylococcus; OTU_2, Corynebacterium 1; OTU_16 and OTU_24, Anaerococcus; OTU_49 and OTU_234, Haemophilus; OTU_78, Streptococcus; OTU_6768, Peptoniphilus; OTU_63, Supplementary Table 2). It is important to differentiate these opportunistic colonizers from other community members with low incidence, as they reached very high bacterial counts in some samples with potential implications for lung health.To demonstrate the viability of prevalent lung microbiota members and to establish a reference catalogue of bacterial isolates from the human lung for experimental studies, we complemented the amplicon sequencing with a bacterial culturing approach (Supplementary Fig. 2). We cultivated 21 random BALF samples from 18 individuals, on 15 different semi-solid media (both general and selective) in combination with 3 oxygen concentrations; aerobic, 5% CO2, and anaerobic (See “Methods” and Supplementary Table 3), representing 26 different conditions. We cultured fresh BALF immediately upon extraction (within 2 h), as we observed loss in bacterial diversity upon cultivating frozen samples. This resulted in a total of 300 bacterial isolates, representing 5 phyla, 7 classes, 13 orders, and 17 families from which we built an open-access biobank called the Lung Microbiota culture Collection (LuMiCol, Supplementary Data 4, https://github.com/sudu87/Microbial-ecology-of-the-transplanted-human-lung).To examine the extent of overlap between bacteria in LuMiCol and the diversity obtained by amplicon sequencing, we included 16S rRNA gene sequences from 215 isolates that passed our quality filter into the community analysis, which allowed for the retrieval of OTU-isolate matching pairs32 (Methods). We found that 213 isolates matched to 47 OTUs (Fig. 2a, c, Supplementary Data 5), including 17 of the most prevalent and abundant bacteria (Fig. 1e, Supplementary Table 2). As expected, bacteria with high abundance in the amplicon sequencing-based community analysis were isolated more frequently, with Firmicutes revealing the highest isolate diversity (Fig. 2a–c, Supplementary Data 4, 5) and being recovered under the most diverse culturing conditions.Fig. 2: A lung microbiota culture collection (LuMiCol) reveals extended diversity and phenotypic characteristics of the lower airway bacterial community.a Phylogenetic tree of the 47 OTU-isolate matching pairs inferred with FastTree. Branch bootstrap support values (size of dark gray circles) ≥80% are displayed. b Growth characteristics of each OTU-isolate matching pair in three different oxygen conditions (Anaerobic – light brown, 5% CO2-yellow, aerobic-light blue, n = 3). Column with pie charts shows growth on semi-solid agar. Heatmap shows median change in Optical Density (OD) at 600 nm growth in three different liquid media (THY, RPMI, RPMI without glucose) over 3 days. c Cumulative counts of each OTU-isolate matching pair across all BALF samples (gray). d Number of isolates in Lumicol (black) per OTU-isolate matching pair. Taxa are labeled as genus; OTU ID, with an indication of whether they are prevalent (gray rectangle) or opportunistic (magenta rectangle) in the lower airway community. The names of the closest hit in databases: eHOMD and SILVA are used as species descriptor.Full size imageIn summary, our results from the combined culture-dependent and culture-independent approach show that the lung microbiota post-transplant is highly variable in terms of both bacterial load and community composition with many transient and low-abundant bacterial taxa. However, a few community members display relatively high prevalence and/or abundance suggesting that they represent important colonizers of the human lung.LuMiCol informs on the diversity and metabolic preferences of culturable human lung bacteriaWe characterized the culturable community members of the lower respiratory tract contained in LuMiCol by testing a wide range of growth conditions and phenotypic properties (see “Methods”). The majority of the cultured isolates could taxonomically be assigned at the species level based on genotyping of the 16S rRNA gene V1-V5 region. However, the limited taxonomic resolution offered by this method does not allow to discriminate between closely related strains, which can include both pathogenic and non-pathogenic bacteria. Hence for Streptococcus, we additionally tested for type of hemolysis (alpha, beta, or gamma) and resistance to optochin, which differentiates the pathogenic pneumococcus and the non-pathogenic viridans groups (Fig. 2a, Supplementary Fig. 2b, c). This demonstrated that the 16 Streptococcus OTU-isolate pairs belong to the viridans group of streptococci (VS)33. Interestingly, these isolates exhibited the highest genotypic and phenotypic diversity throughout our collection and belonged to five OTUs among the 22 most prevalent community members, with Streptococcus mitis (OTU_11) present in 93.6% of all samples.BALF from healthy individuals contains amino acids, citrate, urate, fatty acids, and antioxidants such as glutathione but no detectable glucose34, which is associated with increased bacterial load and infection35,36,37. To get insights into basic bacterial metabolism, we assessed the growth of all 47 isolates matching an OTU under different oxygen concentrations. We used undefined rich media (Todd-Hewitt Yeast extract) and defined low-complexity liquid media (RPMI 1640), including a glucose-free version to mimic the deep lung environment (see “Methods”). Despite the presence of oxygen in the human lung, the majority of the isolates were either obligate or facultative anaerobes (Fig. 2a), including some of the most prevalent members (Prevotella melaninogenica (OTU_3), Streptococcus mitis (OTU_11), Veillonella atypica (OTU_6) and Granulicatella adiacens (OTU_17). A similar trend was also observed in liquid media under anaerobic conditions, with the exception of the genera Prevotella, Veillonella and Granulicatella. Most streptococci from the human lung grew best in complex liquid media containing glucose under anaerobic conditions, including the most prevalent species in our cohort, S. mitis (OTU_11) (Fig. 2b). However, noticeable exceptions were S. vestibularis (OTU_34), S. oralis (OTU_3427 and OTU_1567), and S. gordonii (OTU_10031), which grew equally well in the presence of oxygen and in low-complexity liquid medium (Fig. 2b). Most Actinobacteria grew best on rich medium in the presence of 5% CO2, with an exception of Actinomyces odontolyticus (OTU_39), which required anaerobic conditions. Some Actinobacteria grew equally well in anaerobic conditions as in the presence of 5% CO2, i.e., Corynebacterium durum (OTU_501), Actinobacteria sp. oral taxon (OTU_328 and OTU_228).The two most predominant opportunistic pathogens in our lung cohort, P. aeruginosa (OTU_1) and S. aureus (OTU_2), grew best in rich liquid medium in the presence of oxygen (Fig. 2c), although these also grew to lower degree under anaerobic conditions. These results indicate that changes in the physicochemical conditions in the lung may favor the growth of these two opportunistic pathogens. In summary, our observations from the bacterial culture collection provide first insights into the phenotypic properties of human lung bacteria and will serve as a basis for future experimental work.Identification of four compositionally distinct pneumotypes post-transplant using machine learning based on ecological metricsTo detect and characterize differences in bacterial community composition between BALF samples from transplant patients, we clustered the samples using an unsupervised machine learning algorithm based on pairwise Bray–Curtis dissimilarity32 (beta diversity, See “Methods”, Supplementary Data 6). This segregated the samples into four partitions around medoids (PAMs) at both phylum and OTU level (Fig. 3a, b, Supplementary Fig. 3a, b). We refer to these clusters as “pneumotypes” PAM1, PAM2, PAM3, and PAM4 (Supplementary Table 4). PAM1 formed the largest cluster consisting of the majority of samples (n = 115) followed by PAM3 (n = 76), PAM2 (n = 19), and PAM4 (n = 24) (Supplementary Data 7). Examination of various diversity measures (Species occurrence, OTU diversity, OTU richness, Fig. 3c–e), distribution of the dominant community members (Fig. 3f), and bacterial counts (16S rRNA gene copies, Fig. 3g) revealed distinctive characteristics between the four pneumotypes.Fig. 3: Bacterial communities of the lung post-transplant fall into four ‘pneumotypes’ with distinct community characteristics.a, b Principal component analysis shows Partition around medoids (PAMs) at phylum and OTU level respectively generated by k-medoid-based unsupervised machine learning using Bray–Curtis dissimilarity (occurrence and abundance). Pneumotypes are color coded: Balanced (red, n = 115), Staphylococcus (green, n = 19), Microbiota-depleted (MD, blue, n = 76), and Pseudomonas (orange, n = 24). c–g Violin plots show distributions of pairwise species occurrence (Sorenson’s index, PERMANOVA, two-sided, F(3, 229) = 8.49, P = 9.9 × 10−5), OTU diversity (Kruskal–Wallis test, χ2 = 89.2, df = 3, two-sided, P = 2.2 × 10−16), OTU richness (ANOVA, F(3, 229) = 43.9, two-sided, P = 2.2 × 10−16), proportion of most dominant OTUs (Kruskal–Wallis test, χ2 = 94.45, df = 3, two-sided, P = 2.2 × 10−16), and total bacterial counts (ANOVA, F(3, 229) = 43.9, two-sided, P = 2.2 × 10−16), respectively, across the four pneumotypes. h, i Enrichment analysis of prevalence (green dotted line ≥50%) and absolute abundance across all samples of the 30 most dominant taxa (i.e., OTUs) in PneumotypeBalanced and PneumotypeMD respectively, when each was compared to the other three combined pneumotypes (gray boxes). Differential abundances after enrichment analysis was calculated between each PAM and the other three PAMs combined, using ART-ANOVA. j Heatmap shows relative percentage of taxa (right colored panel) cultured from paired samples of Bronchial aspiration (BA) and Bronchoalveolar lavage fluid (BALF) from each pneumotype (left colored panel). Oropharyngeal flora mainly corresponds to PneumotypeBalanced (i.e., Streptococcus, Prevotella, Veillonella). All box plots including insets show median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers) as well as outliers (single points). Multiple comparison of beta diversity indices was done by pairwise PERMANOVA (adonis) with False Discovery rate (FDR). Post hoc analyses (95% Confidence Interval) were done by using Tukey’s test (ANOVA) or Dunn’s test (Kruskal test) with False Discovery Rate (FDR) or least-squares means (ART-ANOVA) with False Discovery Rate (FDR). * P  More

  • in

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • in

    Understanding drivers of wild oyster population persistence

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • in

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

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