More stories

  • in

    A 3D taphonomic model of long bone modification by lions in medium-sized ungulate carcasses

    Humerus
    Left humeri display a non-stationary (i.e., spatially variable in intensity) distribution of tooth marks, with inhomogeneous intensity and with a clustering trend, especially on the proximal end. Tooth marks cluster on the proximal epiphyses, both on the tubercles as well as the articular surface area and proximal metadiaphyses. They also occur in the vicinity of the deltoid crest. Shafts present more abundant modifications on the caudal and medial sides. The cranial and lateral distal shafts show very few tooth marks in comparison. This distribution shows a connection between tooth mark occurrence and areas of muscle and ligament insertions. Tooth marks were probably created during defleshing and limb detachment from the trunk. They are most abundant on the neck junction between the articular head and the proximal metadiaphysis (Fig. 2).
    Figure 2

    Examples of three-dimensional tooth mark distribution from the lion-consumed carcass sample on each of the four long bones. Distribution of marks is shown on bilateral representation.

    Full size image

    Both, the K function and the pair-correlation function indicate an overall trend of clustering. This is nuanced by the other functions. The near-neighbour G function shows a slight clustering trend in short distances and a general asymptotic trend of dispersal in longer distances. The empty-space F function suggests a trend towards clustering within an overall CSR pattern (Fig. 3).
    Figure 3

    Three-dimensional plot of the distribution of tooth marks on the left humerus. (A) K-function plot. (B) G near-neighbour function plot. (C) F empty space function. (C) Pair-correlation function. The F function suggests a pattern non-differentiable from CSR. The other three functions suggest a mild clustering trend in short distances. Key to (A,B,D) Dotted red line shows the Poisson Complete Spatial Random (CSR) process and the gray band shows its confidence envelope. Black line shows the point process of the target sample (here, tooth marks on humerus). When above the CSR Poisson process, it indicates a clustering trend. When below, it indicates a regular scattering trend. The interpretation is reverse for (C) (F empty space function). Same interpretation applies to equivalent figures in the Supplementary Information.

    Full size image

    Right humeri show a similar tendency of mark clustering around the neck under the articular surface with both tubercles impacted. Marks on the medial shaft are slightly more abundant than on the lateral shaft, while the latter shows higher concentrations around the deltoid crest. Interestingly, marks on the shaft cluster on the proximal and distal portions and the mid-shaft is mostly devoid of marks, regardless of orientation. The cranial side, especially the shaft, is again the least impacted by lions. All the functions show a moderate tendency to clustering; so much so in the K and pair-correlation functions because the latter is a modified version of the former (by using rings within the distance radius). The G function shows a very slight clustering trend in short distances, which in the F function is barely outside the CSR envelope (Fig. S4).
    In sum, the slight clustering trends in both sides indicate a redundant pattern of tooth mark location. This shows that mark distribution in humeri is not random, since it is repeated across all the carcasses studied.
    Femur
    Left femora do not show a more widespread distribution of tooth marks than documented in both humeri. Most tooth marks also occur on the proximal half of the element. Most distal tooth marks appear concentrated on the epiphyses. They occur mostly on the medial condyle (on its medial facet) and on the medial portion of the trochlea. Marks on the proximal end occur on the trochanters and also on the spiral line of the neck. The lateral sides of the shaft are the least modified, followed by the caudal distal shaft. Tooth marks on the caudal shaft occur on both sides of the line aspera. As was the case with the humerus, a large portion of marks appear at or near muscle insertion areas. All the functions show a slight clustering trend in short distances and a CSR pattern in longer distances (Fig S5).
    Right femora appear substantially more toothmarked than the left ones. Again, the proximal and distal ends exhibit the highest amount of marks. Both trochanters and the proximal metadiaphysis contain large numbers of modifications. Marks on the distal epiphysis occur both on the medial facet of the throclea and on both condyles. Marks on the caudal shaft, along the linea aspera, are more abundant than on the cranial shaft. All functions coincide in finding a moderate clustering trend, which indicates that BSM are not following a CSR pattern (Fig. S6).
    As was the case for humeri, the non-random and moderately clustered pattern shows that there are locations, mostly coinciding with tendon and muscle insertions, that are more prone to be impacted by lions during carcass consumption than others.
    Radius-ulna
    Radii from carcasses consumed by lions are generally left unmodified12,26,27. Most of the damage concentrates on the olecranon of the ulna (Fig. S7). Only a few tooth marks have been documented scattered on the proximal metadiaphysis, some under the articular facet of the lateral epiphysis. The rest occur mostly in the form of isolated marks, without any specific preference for clustering or side. The left radius shows this distribution. Marks outside the ulna are very few and occur on the cranial and lateral sides of the proximal metadiaphysis, in proximity to the articular facet. Scattered marks can be observed on the distal end. In contrast with the stylopodials, the left radius-ulna shows more intense clustering of tooth marks, as denoted by the K,G, F and pair-correlation functions (Fig. S4). This may be the effect of the intense damage on the olecranon.
    The right radius appears also very slightly toothmarked, despite the large number of carcasses involved. Most tooth marks concentrate on the ulnar olecranon, with very few scattered along the ulnar shaft and even less so on the radial shaft. The few tooth marks documented on the shaft appear on the uppermost cranial shaft and a couple on the lower caudal shaft. As was the case with the left radius, the second-order functions indicate a clear clustering of tooth marks in slightly longer distances than documented in the stylopods (Fig. S8).
    In sum, marks in radii are few and mostly clustered on the ulna. Those on the radial shaft are scattered but also seem to be in connection with damage on the proximal end imparted during defleshing by lions.
    Tibia
    The left tibia shows a concentration of tooth marks on the proximal end, more specifically, on the epiphysis and, especially, on the crest. Marks on the shaft are not common and they cluster mostly on the lateral and medial sides and on the lateral portion of the caudal side. Marks in the lower half of the shaft are uncommon regardless of orientation (Fig. S9). This element exhibits the lowest frequency of marks of the whole long bone set. The second-order functions indicate a very minor clustering trend in short distances, probably caused by redundancy in damage in the proximal portion of the element, but most of the shaft, where the few scattered marks occur, seems very similar to a Poisson process. This suggests that damage to the tibia (with the exception of the crest and proximal end) is more stochastic than on the other elements.
    Right tibiae are only slightly more toothmarked than the left tibiae. Given its overall greater length than other long bones, its low toothmarking frequencies renders them the least impacted elements in number of tooth marks. Most marks cluster on the proximal end, more specifically, on the tibial crest. The lateral side is more damaged than the other sides. In the whole collection, only one tooth mark was found in the distal half of the shaft (Fig. 2). Again, most of the damage on the caudal side was concentrated on the proximal lateral side, coinciding with the more intensive damage on the lateral portion of the cranial side. The second-order functions suggest also a very minor clustering trend, slightly more marked than on left tibiae, probably because all tooth marks documented concentrate on the proximal half of the element (Fig. S10).
    In sum, tibiae show some of the least intense point processes resulting from toothmarking by lions on long bones. Marks occurring on the shaft are usually isolated and more random than on other elements, where they are more spatially recurrent.
    Bilateral element comparison
    Left and right humeri display a similar pattern in the location of most damage as the three-dimensional coordinates of the PCA show (Fig. 4). This is reinforced by the bivariate wavelet analysis, which shows that both sides of humeri show a strong correlation ( > 0.8) in the location of most tooth marks in specific locations (Fig. 5). Both humeri display high frequencies of tooth marks (remember, the lower the frequency, the higher the scale) and a clear clustering on the proximal epiphysis and proximal metadiaphysis, as well as on the distal shaft. Most of the mid-shaft shows almost no tooth marks and when they do, they occur in very low frequencies. High frequency marks have only been documented on the proximal epiphyseal portion (Fig. 5). The frequency distribution also shows that the medial and caudal sides bear more marks than the lateral and cranial sides. Most cranial marks are concentrated in the articular surface, tubercles and metadiaphyseal portion of the proximal end.
    Figure 4

    Principal component analysis (PCA) of each of the four long bones (humerus, femur, radius-ulna and tibia) according to side (left–right) showing point distribution according to components generated by compressing the three-dimensional coordinates. A 95% confidence ellipse per side shows variation and similarity of toothmark patterns in each of the bones. Percentages shown are for the first and second component respectively.

    Full size image

    Figure 5

    Bivariate wavelet coherence plot showing the correlation of most tooth mark damage on the proximal and distal sections of left and right humeri in low frequencies. Arrows indicate that in these two high-correlation areas, both humeral sides are in phase (i.e., the covary together in the same direction). In the distal area, the right humerus is leading (arrows pointing to the right-down or left-up) and in the proximal area, the left humerus leads (arrows pointing to the right-up or left-down). Binning of histograms is described in Table 3. (A) frequency of marks from distal end (left) to proximal (right) end; (B) frequency of marks from lateral (left) to medial (right), and, (C) frequency of marks on caudal (left) to cranial (right).

    Full size image

    Table 3 Binning of histograms according to bone length.
    Full size table

    Left and right femora also display a similar toothmarking pattern (Fig. 4). Both 95% confidence PCA ellipses overlap in most of their areas. The wavelet coherence analysis shows that both sides display a high correlation ( > 0.8) in toothmarking on proximal and distal ends as well as on the shaft when the frequency of marks is low or moderate. Most marks occur on the proximal portion of the element, with a higher impact on the cranial side and more medial for the left femur and more lateral for the right one (Fig. 6). Femoral mid-shafts, thus, appear more highly toothmarked than humeral shafts. Interestingly, the wavelet analysis also shows that when modifications are abundant, there is correspondence between left and right sides only at the distal end. This seems to respond to bone and muscle insertions and ways in which lions deflesh carcasses at this part of the limb. A moderate correlation ( > 0.6) between both sides of the element can be found at the level of the proximal articular neck (metadiaphysis) and surrounding the trochanter section (see yellow islands at the level of the 20th-23rd bins in Fig. 6).
    Figure 6

    Bivariate wavelet coherence plot showing the correlation of tooth mark damage on the proximal and distal sections of left and right femora in moderate frequencies. Arrows indicate that in these two high-correlation areas, both femoral sides are in phase (i.e., the covary together in the same direction). The right femur is leading (arrows pointing to the right-down or left-up). Binning of histograms is described in Table 3. (A) frequency of marks from distal end (left) to proximal (right) end; (B) frequency of marks from lateral (left) to medial (right), and, (C) frequency of marks on caudal (left) to cranial (right).

    Full size image

    As was the case of the upper limb bones, radii-ulnae also exhibit a localized tooth mark pattern. The 95% confidence PCA ellipses overlap for both sides is more intense even than with the stylopodials. The only points falling outside the confidence ellipse are those that appear in the form of single marks and are caused stochastically. The wavelet coherence analysis indicates a strong pattern between both sides, with marks clustering in the proximal epiphysis and strong correlation in the exhibition of low-impact modifications (i.e., few isolates marks) in most of the shaft (high scale = low frequency). There is a high frequency of modifications on the proximal end (see black line sloping upwards in Fig. 7), which decreases as we go down the shaft. The low frequency is maintained throughout the length of the shaft. Only because a few more marks have been documented on the distal and proximal ends, do we see a lower scale (i.e., higher frequency) at the beginning and end of the plot. The high correlation spread along the element shaft indicates that both the right and left radii-ulnae display virtually the same modification pattern.
    Figure 7

    Bivariate wavelet coherence plot showing the correlation of tooth mark damage on the proximal and distal sections of left and right radius-ulna in moderate to high frequencies. Arrows indicate that in these two high-correlation areas, both femoral sides are in phase (i.e., the covary together in the same direction). The right radius-ulna is leading (arrows pointing to the right-down or left-up). Binning of histograms is described in Table 3. (A) frequency of marks from distal end (left) to proximal (right) end; (B) frequency of marks from lateral (left) to medial (right), and, (C) frequency of marks on caudal(left) to cranial (right).

    Full size image

    Tibiae also show similar tooth-marking patterns when comparing right and left sides of the skeleton. A PCA shows that a 95% confidence ellipse of samples from both sides overlap in most of their areas (Fig. 4). However, it should be remarked that there is more coordinate variation (i.e., variation in distribution) of tooth marks in tibiae compared to the other long bones. The reason may be double. On the one hand, the tibia exhibits the longest length dimensions of the appendicular skeleton. On the other side, the occurrence of tooth marks outside the area surrounding the tibial crest is commonly in the form of isolated marks that are more prone to occur randomly during defleshing because no muscle insertions occur on the cranial aspect of the element. Only in the proximal caudal side are tooth marks more prone to cluster because of the muscle insertions on that side. A wavelet coherence analysis shows that tibiae show a low density of modifications, similar to radii-ulnae but over a more widespread area. This creates a situation of high correlation between the left and right sides in the location of the few scattered marks (Fig. 8). The correlation is also similar in the proximal and distal ends when modifications are more clustered. Overall, the lack of intensive (i.e., abundant clustering) modifications on the shaft, makes both tibial sides to lack a pattern, with the exception of the lateral and caudal proximal shafts. This moderate clustering there creates the small peninsula between bins 5 and 11 of Fig. 8.
    Figure 8

    Bivariate wavelet coherence plot showing the correlation of tooth mark damage on the proximal and distal sections of left and right tibiae in moderate to high frequencies. Notice different location of proximal and distal ends compared to the other elements. Arrows indicate that in these two high-correlation areas, both tibial sides are in phase (i.e., the covary together in the same direction). Binning of histograms is described in Table 3. (A) frequency of marks from distal end (right) to proximal (left) end; (B) frequency of marks from lateral (right) to medial (left), and, (C) frequency of marks on caudal(left) and cranial (right).

    Full size image

    In summary, the humeri, femora and radii-ulnae exhibit strong patterning on how lions modify them after consumption, as reflected in tooth mark distribution on both sides of the same elements. The tibiae display a more variable pattern, which overall is reflected on fewer modifications, especially along the shaft. Given the commonly isolated nature of most marks created along the shaft, these respond more to stochastic processes and reflect higher variability than in the other elements. Exceptions to this observation are found in BSM observed on the tibial crest and proximal caudal-lateral portions of the shaft.
    Multi-element comparison
    The information contained in the three-dimensional coordinates of the toothmark pattern documented on each of the elements, when approached through the holistic consideration of the mean values of their global interrelation (as documented through the second-order functions), provides identity information (i.e., element-specific identification) for each of the bones analyzed. On a different scale, this could be applied to individual assemblages instead of individual elements as done here. In the comparison among the different elements and their sides, the way marks were distributed in each of their respective point processes (considering their intensity and distances per element) contained sufficient information to differentiate four different clusters corresponding to the four different elements (Table 2, Fig. 9). Within each element set, both sides were contained within the same node. This is of utmost interest, because in the variables used for this analysis, it is the patterns and not the raw coordinates of marks on each element that were used. This enabled the relativization of the actual location of marks on the different long bone elements and only the emergent properties of the mark assemblage in each of them (understood as individual point process) was considered. Thus, multi-element comparison was possible and different bones were successfully differentiated (Fig. 9).
    Figure 9

    Hierarchical clustering of the selected variables from the second-order functions, intensity, and nearest-neighbour distance. A phylogenetic dendrogram was used. Four groups were identified (different colors) corresponding to each of the four elements analyzed. Key: lHum (left humerus); rHum (right humerus); lFem (left femur); rFem (right femur); lRad (left radius-ulna); rRad (right radius-ulna); lTib (left tibia); rTib (right tibia).

    Full size image More

  • in

    Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

    Alcala N, Goudet J, Vuilleumier S (2014) On the transition of genetic differentiation from isolation to panmixia: what we can learn from GST and D. Theor Popul Biol 93:75–84
    PubMed  Article  Google Scholar 

    Barton NH (1996) Natural selection and random genetic drift as causes of evolution on islands. Philos Trans R Soc Lond B Biol Sci 351:785–795
    CAS  PubMed  Article  Google Scholar 

    Bellemain E, Ricklefs RE (2008) Are islands the end of the colonization road? Trends Ecol Evol 23:461–468
    PubMed  Article  Google Scholar 

    Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B-Methodol 57:289–300
    Google Scholar 

    Bolger A, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Bouckaert R (2010) DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 26:1372–1373
    CAS  PubMed  Article  Google Scholar 

    Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D et al. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    Bryant D, Moulton V (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255–265
    CAS  PubMed  Article  Google Scholar 

    Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917–1932
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
    PubMed  PubMed Central  Article  Google Scholar 

    Chapin III FS, Matson PA, Vitousek PM (2002) Principles of terrestrial ecosystem ecology. Springer, New York
    Google Scholar 

    Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B et al. (2009) The last glacial maximum. Science 325:710–714
    CAS  PubMed  Article  Google Scholar 

    DeChaine EG, Martin AP (2005) Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains. Am J Bot 92:477–486
    CAS  PubMed  Article  Google Scholar 

    Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
    PubMed  Article  Google Scholar 

    Foote AD, Morin PA (2016) Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity 117:316–325
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Frankham R (1997) Do island populations have less genetic variation than mainland populations? Heredity 78:311–327
    PubMed  Article  Google Scholar 

    Frichot E, François O (2015) LEA: an R package for landscape and ecological association studies. Methods Ecol Evol 6:925–929
    Article  Google Scholar 

    Frichot E, Mathieu F, Trouillon T, Bouchard G, François O (2014) Fast and efficient estimation of individual ancestry coefficients. Genetics 196:973–983
    PubMed  PubMed Central  Article  Google Scholar 

    Frichot E, Schoville SD, Bouchard G, François O (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30:1687–1699
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Frichot E, Schoville SD, De Villemereuil P, Gaggiotti OE, François O (2015) Detecting adaptive evolution based on association with ecological gradients: orientation matters! Heredity 115:22–28
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Funk WC, Lovich RE, Hohenlohe PA, Hofman CA, Morrison SA, Sillett TS et al. (2016) Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol 25:2176–2194
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Garot E, Joët T, Combes M, Severac D, Lashermes P (2019) Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island. N Phytol 224:974–986
    CAS  Article  Google Scholar 

    Gillespie R (2004) Community assembly through adaptive radiation in Hawaiian spiders. Science 303:356–359
    CAS  PubMed  Article  Google Scholar 

    Hamabata T, Kinoshita G, Kurita K, Cao PL, Ito M, Murata J et al. (2019) Endangered island endemic plants have vulnerable genomes. Commun Biol 2:244
    PubMed  PubMed Central  Article  Google Scholar 

    Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638
    CAS  PubMed  Article  Google Scholar 

    Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267
    CAS  PubMed  Article  Google Scholar 

    Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ et al. (2017) The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae). Mol Ecol 26:1515–1532
    CAS  PubMed  Article  Google Scholar 

    James JE, Lanfear R, Eyre-Walker A (2016) Molecular evolutionary consequences of island colonization. Genome Biol Evol 8:1876–1888
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Juan C, Emerson BC, Oromı́ P, Hewitt GM (2000) Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands. Trends Ecol Evol 15:104–109
    CAS  PubMed  Article  Google Scholar 

    Kamijo T, Hashiba K (2003) Island ecosystem and vegetation dynamics before and after the 2000-year eruption on Miyake-jima Island, Japan, with implications for conservation of the island’s ecosystem. Glob Environ Res 7:69–78
    Google Scholar 

    Kier G, Kreft H, Lee TM, Jetz W, Ibisch PL, Nowicki C et al. (2009) A global assessment of endemism and species richness across island and mainland regions. Proc Natl Acad Sci USA 106:9322–9327
    CAS  PubMed  Article  Google Scholar 

    Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498
    CAS  Article  Google Scholar 

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

    MacArthur RH, Wilson EO (1963) An equilibrium theory of insular zoogeography. Evolution 17:373–387
    Article  Google Scholar 

    Maekawa F (1949) Makinoesia and its bearing to Oriental Asiatic flora. J Jpn Bot 24:91–96. in Japanese
    Google Scholar 

    McGlaughlin ME, Wallace LE, Wheeler GL, Bresowar G, Riley L, Britten NR et al. (2014) Do the island biogeography predictions of MacArthur and Wilson hold when examining genetic diversity on the near mainland California Channel Islands? Examples from endemic Acmispon (Fabaceae). Bot J Linn Soc 174:289–304
    Article  Google Scholar 

    Ministry of the Environment of Japan (2019) Threatened wildlife of Japan – red list 2019. http://www.env.go.jp/press/106383.html

    Murray M, Thompson W (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Nakamura K, Denda T, Kokubugata G, Suwa R, Yang TYA, Peng C-I et al. (2010) Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan. J Biogeogr 37:1907–1918
    Google Scholar 

    Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170
    CAS  PubMed  Article  Google Scholar 

    Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94
    CAS  PubMed  Article  Google Scholar 

    Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    Petit JR, Jouzel J, Raynaud D, Barkov NI, Barnola J-M, Basile I et al. (1999) Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Nature 399:429–436
    CAS  Article  Google Scholar 

    Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    R Development Core Team (2019) R: a language and environment for statistical computing. https://www.R-project.org/

    Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370
    PubMed  Article  Google Scholar 

    Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P et al. (2015) Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – Phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation. Mol Ecol 24:2477–2494
    CAS  PubMed  Article  Google Scholar 

    Stuessy TF, Takayama K, López-Sepúlveda P, Crawford DJ (2014) Interpretation of patterns of genetic variation in endemic plant species of oceanic islands. Bot J Linn Soc 174:276–288
    PubMed  Article  Google Scholar 

    Sundqvist L, Keenan K, Zackrisson M, Prodöhl P, Kleinhans D (2016) Directional genetic differentiation and relative migration. Ecol Evol 6:3461–3475
    PubMed  PubMed Central  Article  Google Scholar 

    Taira A, Saito S, Aoike K, Morita S, Tokuyama H, Suyehiro K et al. (1998) Nature and growth rate of the northern Izu-Bonin (Ogasawara) arc crust and their implications for continental crust formation. Isl Arc 7:395–407
    CAS  Article  Google Scholar 

    Takahashi H (1971) Fossa Magna element plants. Res Reports Kanagawa Prefect Museum. Nat Hist 2:2–59. in Japanese
    Google Scholar 

    Takahashi H, Katsuyama T (1992) Natural hybrids between Rhododendron tsusiophyllum and R. kaempferi var. macrogemma (Ericaceae). Bull Kanagawa Prefect. Museum 21:59–71. in Japanese
    Google Scholar 

    Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752
    CAS  PubMed  Article  Google Scholar 

    Tanaka N (1999) Plant communities in Mt. Tenjo, Koudzu Island, Tokyo. Actinia 12:147–158. in Japanese
    Google Scholar 

    Vaxevanidou Z, González-Martínez SC, Climent J, Gil L (2006) Tree populations bordering on extinction: a case study in the endemic Canary Island pine. Biol Conserv 129:451–460
    Article  Google Scholar 

    Velo-Antón G, Zamudio K, Cordero-Rivera A (2012) Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra). Heredity 108:410–418
    PubMed  Article  Google Scholar 

    Wagner DB, Furnier GR, Saghai-Maroof MA, Williams SM, Dancik BP, Allard RW (1987) Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci USA 84:2097–2100
    CAS  PubMed  Article  Google Scholar 

    Warren BH, Simberloff D, Ricklefs RE, Aguilée R, Condamine FL, Gravel D et al. (2015) Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson. Ecol Lett 18:200–217
    PubMed  Article  Google Scholar 

    Weigelt P, Jetz W, Kreft H (2013) Bioclimatic and physical characterization of the world’s islands. Proc Natl Acad Sci USA 110:15307–15312
    CAS  PubMed  Article  Google Scholar 

    Yamada T, Maki M (2012) Impact of geographical isolation on genetic differentiation in insular and mainland populations of Weigela coraeensis (Caprifoliaceae) on Honshu and the Izu Islands. J Biogeogr 39:901–917
    Article  Google Scholar 

    Yamamoto S, Kikuchi T, Yamagiwa Y, Handa T (2017) Genetic diversity of Lilium auratum var. platyphyllum endemic to the Izu archipelago and its relationship to a nearby population of L. auratum var. auratum by morphological and SSR analysis. Hortic J 86:379–388
    Article  Google Scholar 

    Yoichi W, Minamitani T, Oh S-H, Nagano AJ, Abe H, Yukawa T (2019) New taxa of Rhododendron tschonoskii alliance (Ericaceae) from East Asia. PhytoKeys 134:97–114
    PubMed  PubMed Central  Article  Google Scholar  More

  • in

    The food web in a subterranean ecosystem is driven by intraguild predation

    1.
    Mulec, J. Phototrophs in caves. In Cave Ecology (eds Moldovan, O. T. et al.) 91–106 (Springer, Cham, 2018). https://doi.org/10.1007/978-3-319-98852-8_6
    Google Scholar 
    2.
    Culver, D. C. & Pipan, T. The Biology of Caves and Other Subterranean Habitats (Oxford University Press Inc., New York, 2009).
    Google Scholar 

    3.
    Engel, A. S. Chemoautotrophy. In Encyclopedia of caves 2nd edn (eds White, W. B. & Culver, D. C.) 125–134 (Elsevier, Amsterdam, 2012).
    Google Scholar 

    4.
    Kinkle, B. K. & Kane, T. C. Chemolithotrophic microorganisms and their potential role in subsurface environments. In Ecosystems of the World 30 Subterranean Ecosystems (eds Wilkens, H. et al.) 309–319 (Elsevier, Amsterdam, 2000).
    Google Scholar 

    5.
    Sarbu, S. M. Movile cave: A chemoautotrophically based groundwater ecosystem. In Ecosystems of the World 30 Subterranean Ecosystems (eds Wilkens, H. et al.) 319–343 (Elsevier, Amsterdam, 2001).
    Google Scholar 

    6.
    Simon, K. S., Pipan, T. & Culver, D. C. A conceptual model of the flow and distribution of organic carbon in caves. J. Cave Karst Stud. 69, 279–284 (2007).
    CAS  Google Scholar 

    7.
    Camassa, M. M. Food resources. In Encyclopaedia of Caves and Karst Science (ed. Gunn, J.) 755–760 (Fitzroy Dearborn, London, 2004).
    Google Scholar 

    8.
    Poulson, T. L. & Lavoie, K. H. (The trophic basis of subsurface ecosystems. In Ecosystems of the World 30 Subterranean Ecosystems (eds Wilkens, H. et al.) 323–334 (Elsevier, Amsterdam, 2000).
    Google Scholar 

    9.
    Gibert, J. & Deharveng, L. Subterranean ecosystems: A truncated functional biodiversity. Bioscience 52(6), 473–481. https://doi.org/10.1641/0006-3568(2002)052[0473:SEATFB]2.0 (2002).
    Article  Google Scholar 

    10.
    Chen, B. & Wise, D. H. Bottom-up limitation of predaceous arthropods in a detritus-based terrestrial food web. Ecology 80(3), 761–772. https://doi.org/10.2307/177015 (1999).
    Article  Google Scholar 

    11.
    Venarsky, M. P. & Huntsman, B. M. Food webs in caves. In Cave Ecology (eds Moldovan, O. T. et al.) 309–331 (Springer, Cham, 2018). https://doi.org/10.1007/978-3-319-98852-8_14
    Google Scholar 

    12.
    Gnaspini, P. Guano communities. In Encyclopedia of caves 2nd edn (eds White, W. B. & Culver, D. C.) 357–364 (Elsevier, Amsterdam, 2012).
    Google Scholar 

    13.
    Ipsen, A. The Segeberger Höhle—A phylogenetically young cave ecosystem in northern Germany. In Ecosystems of the World 30. Subterranean Ecosystems (eds Wilkens, H. et al.) 569–579 (Elsevier, Amsterdam, 2000).
    Google Scholar 

    14.
    Stone, F. D., Howarth, F. G., Hoch, H. & Asche, M. Root communities in lava tubes. In Encyclopedia of Caves 2nd edn (eds White, W. B. & Culver, D. C.) 658–664 (Elsevier, Amsterdam, 2012).
    Google Scholar 

    15.
    Mammola, S., Piano, E. & Isaia, M. Step back! Niche dynamics in cave-dwelling predators. Acta Oecol. 75, 35–42. https://doi.org/10.1016/j.actao.2016.06.011 (2016).
    ADS  Article  Google Scholar 

    16.
    Mammola, S. & Isaia, M. Cave communities and species interactions. In Cave Ecology (eds Moldovan, O. T. et al.) 255–269 (Springer, Cham, 2018). https://doi.org/10.1007/978-3-319-98852-8_11
    Google Scholar 

    17.
    Scheu, S. & Setälä, H. Multitrophic interactions in decomposer food webs. In Multitrophic Interactions in Terrestrial Systems (eds Tscharntke, T. & Hawkins, B. A.) 223–264 (Cambridge, Cambridge University Press, 2001).
    Google Scholar 

    18.
    Wood, P. J. Subterranean ecology. In Encyclopaedia of Caves and Karst Science (ed. Gunn, J.) 1514–1519 (Fitzroy Dearborn, London, 2004).
    Google Scholar 

    19.
    Pekár, S., García, L. F. & Viera, C. Trophic niche and trophic adaptations of prey specialised spiders of the Neotropics: A guide. In Behavioural Ecology of Neotropical Spiders (eds Viera, C. & Gonzaga, M. O.) 247–274 (Springer, Cham, 2017).
    Google Scholar 

    20.
    Pohlman, J. W., Iliffe, T. M. & Cifuentes, L. A. A stable isotope study of organic cycling and the ecology of an anchialine cave ecosystem. Mar. Ecol. Prog. Ser. 155, 17–27 (1997).
    ADS  CAS  Article  Google Scholar 

    21.
    Pohlman, J. W., Cifuentes, L. A. & Iliffe, T. M. Food web dynamics and biogeochemistry of anchialine caves: A stable isotope approach. In Ecosystems of the World 30 Subterranean Ecosystems (eds Wilkens, H. et al.) 345–357 (Elsevier, Amsterdam, 2000).
    Google Scholar 

    22.
    Sarbu, S. M., Galdenzi, S., Menichetti, M. & Gentile, G. Geology and biology of the Frasassi caves in Central Italy: An ecological multi-disciplinary study of a hypogenic underground karst system. In Ecosystems of the World 30 Subterranean Ecosystems (eds Wilkens, H. et al.) 359–378 (Elsevier, Amsterdam, 2000).
    Google Scholar 

    23.
    Eitzinger, B., Micic, A., Körner, M., Traugott, M. & Scheu, S. Unveiling soil food web links: New PCR assays for detection of prey DNA in the gut of soil arthropod predators. Soil Biol. Biochem. 57, 943–945. https://doi.org/10.1016/j.soilbio.2012.09.001 (2013).
    CAS  Article  Google Scholar 

    24.
    Juen, A. & Traugott, M. Revealing species-specific trophic links in soil food webs: Molecular identification of scarab predators. Mol. Ecol. 16, 1545–1557. https://doi.org/10.1111/j.1365-294X.2007.03238.x (2007).
    CAS  Article  PubMed  Google Scholar 

    25.
    King, R. A., Read, D. S., Traugott, M. & Symondson, W. O. C. Molecular analysis of predation: A review of best practice for DNA-based approaches. Mol. Ecol. 17, 947–963. https://doi.org/10.1111/j.1365-294X.2007.03613.x (2008).
    CAS  Article  PubMed  Google Scholar 

    26.
    Symondson, W. O. C. Molecular identification of prey in predator diets. Mol. Ecol. 11(4), 627–641. https://doi.org/10.1046/j.1365-294x.2002.01471.x (2002).
    CAS  Article  PubMed  Google Scholar 

    27.
    Traugott, M., Kamenova, S., Ruess, L., Seeber, J. & Plantegenest, M. Empirically characterising trophic networks: What emerging DNA-based methods, stable isotope and fatty acid analyses can offer. Adv. Ecol. Res. 49, 177–224. https://doi.org/10.1016/B978-0-12-420002-9.00003-2 (2013).
    Article  Google Scholar 

    28.
    Kováč, Ľ. et al. Terrestrial arthropods of the Domica Cave system and the Ardovská Cave (Slovak Karst): Principal microhabitats and diversity. In Contributions to Soil Zoology in Central Europe I (eds Tajovský, K. et al.) 61–70 (ISB AS CR, České Budějovice, 2005).
    Google Scholar 

    29.
    Kováč, Ľ. et al. The cave biota of Slovakia. Speleologia Slovaca 5. (Liptovský Mikuláš, State Nature Conservancy SR, Slovak Caves Administration, 2014). https://doi.org/10.13140/2.1.3473.0569

    30.
    Kováč, Ľ, Parimuchová, A. & Miklisová, D. Distributional patterns of cave Collembola (Hexapoda) in association with habitat conditions, geography and subterranean refugia in the Western Carpathians. Biol. J. Linn. Soc. Lond. 119(3), 571–592. https://doi.org/10.1111/bij.12555 (2016).
    Article  Google Scholar 

    31.
    Smrž, J., Kováč, Ľ, Mikeš, J. & Lukešová, A. Microwhip scorpions (Palpigradi) feed on heterotrophic Cyanobacteria in Slovak caves: A curiosity among Arachnida. PLoS ONE 8(10), e75989. https://doi.org/10.1371/journal.pone.0075989 (2013).
    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

    32.
    Pekár, S., Coddington, J. A. & Blackledge, T. Evolution of stenophagy in spiders (Araneae): Evidence based on the comparative analysis of spider diets. Evolution 66(3), 776–806. https://doi.org/10.1111/j.1558-5646.2011.01471.x (2012).
    Article  Google Scholar 

    33.
    Alderweireldt, M. Prey selection and prey capture strategies of linyphiid spiders in highinput agricultural fields. Bull. Br. Arachnol. Soc. 9, 300–308 (1994).
    Google Scholar 

    34.
    Lukić, M., Collembola in caves. Croatian Biospeleological Society, DVD, 10.25 min (2012).

    35.
    Roewer, C. F. Palpigradi. In Klassen und Ordnungen des Tierreichs 5: Arthropoda IV: Arachnoidea (ed. Bronns, H. G.) 640–707 (Akademische Verlagsgesellschaft MBH, Leipzig, 1932).
    Google Scholar 

    36.
    van der Hammen, L. Comparative studies in Chelicerata II. Epimerata (Palpigradi and Actinotrichida). Zool. Verh. 196, 3–70 (1982).
    Google Scholar 

    37.
    Wheeler, W. M. A singular arachnid Koenenia mirabilis (Grassi) occurring in Texas. Am. Nat. 34, 837–850 (1900).
    Article  Google Scholar 

    38.
    Harwood, J. D., Phillips, S. W., Sunderland, K. D. & Symondson, W. O. C. Secondary predation: quantification of food chain errors in an aphid–spider–carabid system using monoclonal antibodies. Mol. Ecol. 10(8), 2049–2057. https://doi.org/10.1046/j.0962-1083.2001.01349.x (2001).
    CAS  Article  PubMed  Google Scholar 

    39.
    Szafranek, P., Lewandowski, M. & Kozak, M. Prey preference and life tables of the predatory mite Parasitus bituberosus (Acari: Parasitidae) when offered various prey combinations. Exp. Appl. Acarol. 61(1), 53–67. https://doi.org/10.1007/s10493-013-9701-y (2013).
    Article  PubMed  PubMed Central  Google Scholar 

    40.
    Al-Amidi, A. H. K. & Downes, M. J. Parasitus bituberosus (Acari: Parasitidae), a possible agent for biological control of Heteropeza pygmaea (Diptera: Cecidomyiidae) in mushroom compost. Exp. Appl. Acarol. 8(1–2), 13–25 (1990).
    Article  Google Scholar 

    41.
    Adams, B. J. & Nguyen, K. B. Nematode parasites of insects. In Encyclopedia of Entomology (ed. Capinera, J. L.) 2577–2584 (Springer, Cham, 2008).
    Google Scholar 

    42.
    Cokendolpher, J. C. Pathogens and parasites of opiliones (arthropoda: arachnida). J. Arachnol. 21(2), 120–146 (1993).
    Google Scholar 

    43.
    Kruse, P. D., Toft, S. & Sunderland, K. D. Temperature and prey capture: Opposite relationships in two predator taxa. Ecol. Entomol. 33(2), 305–312. https://doi.org/10.1111/j.1365-2311.2007.00978.x (2008).
    Article  Google Scholar 

    44.
    Krooss, S. & Schaefer, M. How predacious are predators? A study on Ocypus similis, a rove beetle of cereal fields. Ann. Appl. Biol. 133(1), 1–16. https://doi.org/10.1111/j.1744-7348.1998.tb05797.x (1998).
    Article  Google Scholar 

    45.
    Waldbauer, G. P. & Friedman, S. Self-selection of optimal diets by insects. Annu. Rev. Entomol. 36(1), 43–63. https://doi.org/10.1146/annurev.en.36.010191.000355 (1991).
    Article  Google Scholar 

    46.
    Mayntz, D. & Toft, S. Nutrient composition of the prey’s diet affects growth and survivorship of a generalist predator. Oecologia 127, 207–213. https://doi.org/10.1007/s004420000591 (2001).
    ADS  Article  PubMed  Google Scholar 

    47.
    Finke, D. L. & Denno, R. F. Intraguild predation diminished in complex-structured vegetation: implications for prey suppression. Ecology 83, 643–652. https://doi.org/10.2307/3071870 (2002).
    Article  Google Scholar 

    48.
    Staudacher, K. et al. Habitat heterogeneity induces rapid changes in the feeding behaviour of generalist arthropod predators. Funct. Ecol. 32(3), 809–819. https://doi.org/10.1111/1365-2435.13028 (2018).
    Article  PubMed  PubMed Central  Google Scholar 

    49.
    Finke, D. L. & Denno, R. F. Predator diversity and the functioning of ecosystems: the role of intraguild predation in dampening trophic cascades. Ecol. Lett. 8, 1299–1306. https://doi.org/10.1111/j.1461-0248.2005.00832.x (2005).
    Article  Google Scholar 

    50.
    Schausberger, P. & Croft, B. A. Nutritional benefits of intraguild predation and cannibalism among generalist and specialist phytoseiid mites. Ecol. Entomol. 25(4), 473–480. https://doi.org/10.1046/j.1365-2311.2000.00284.x (2000).
    Article  Google Scholar 

    51.
    Schausberger, P. Cannibalism among phytoseiid mites: a review. Exp. Appl. Acarol. 29(3/4), 173–191. https://doi.org/10.1023/a:1025839206394 (2003).
    Article  PubMed  Google Scholar 

    52.
    Elgar, M. A. & Crespi, B. J. Cannibalism: Ecology and Evolution Among Diverse Taxa (Oxford University Press, Oxford, 1992).
    Google Scholar 

    53.
    Polis, G. A. The evolution and dynamics of intraspecific predation. Annu. Rev. Ecol. Syst. 12(1), 225–251. https://doi.org/10.1146/annurev.es.12.110181.001301 (1981).
    Article  Google Scholar 

    54.
    Fagan, W. F. et al. Nitrogen in insects: Implications for trophic complexity and species diversification. Am. Nat. 160(6), 784–802. https://doi.org/10.1086/343879 (2002).
    Article  Google Scholar 

    55.
    Fagan, W. F. & Denno, R. F. Stoichiometry of actual vs. potential predator–prey interactions: Insights into nitrogen limitation for arthropod predators. Ecol. Lett. 7(9), 876–883. https://doi.org/10.1111/j.1461-0248.2004.00641.x (2004).
    Article  Google Scholar 

    56.
    Denno, R. F. & Fagan, W. F. Might nitrogen limitation promote omnivory among carnivorous arthropods?. Ecology 84(10), 2522–2531. https://doi.org/10.1890/02-0370 (2003).
    Article  Google Scholar 

    57.
    Snyder, W. E., Joseph, S. B., Preziosi, R. F. & Moore, A. J. Nutritional benefits of cannibalism for the lady beetle Harmonia axyridis (Coleoptera: Coccinellidae) when prey quality is poor. Environ. Entomol. 29(6), 1173–1179. https://doi.org/10.1603/0046-225x-29.6.1173 (2000).
    Article  Google Scholar 

    58.
    Nováková, A. et al. Feeding sources of invertebrates in the Ardovská Cave and Domica Cave systems: preliminary results. In Contributions to Soil Zoology in Central Europe I (eds Tajovský, K. et al.) 107–112 (ISB AS CR, České Budějovice, 2005).
    Google Scholar 

    59.
    Crossley, D. & Blair, J. M. A high efficiency, “low-technology” Tullgren-type extractor for soil microarthropods. Agric. Ecosyst. Environ. 34, 187–192 (1991).
    Article  Google Scholar 

    60.
    Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3(5), 294–299 (1994).
    CAS  PubMed  Google Scholar 

    61.
    de Groot, A. G., Laros, I. & Geisen, S. Molecular identification of soil eukaryotes and focused approaches targeting protist and faunal groups using high-throughput meta-barcoding methods in molecular biology. Methods Mol. Biol. 1399, 125–140. https://doi.org/10.1007/978-1-4939-3369-3_7 (2016).
    CAS  Article  Google Scholar 

    62.
    Aronesty, E. Comparison of sequencing utility programs. Open Bioinform. J. 7(1), 1–8. https://doi.org/10.2174/1875036201307010001 (2013).
    MathSciNet  Article  Google Scholar 

    63.
    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12. https://doi.org/10.14806/ej.17.1.200 (2011).
    Article  Google Scholar 

    64.
    Mahé, F., Rognes, T., Quince, C., de Vargas, C. & Dunthorn, M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ. 2, e593 (2014).
    Article  Google Scholar 

    65.
    Belshaw, R., Lopez-Vaamonde, C., Degerli, N. & Quicke, D. L. J. Paraphyletic taxa and taxonomic chaining: Evaluation the classification of braconine wasps (Hymenoptera: Braconidae) using 28S D2–3 rDNA sequences and morphological characters. Biol. J. Linn. Soc. Lond. 73(4), 411–424. https://doi.org/10.1111/j.1095-8312.2001.tb01370.x (2001).
    Article  Google Scholar 

    66.
    Hurlbert, S. H. The measurement of niche overlap and some relatives. Ecology 59(1), 67–77. https://doi.org/10.2307/1936632 (1978).
    Article  Google Scholar 

    67.
    Novakowski, G. C., Hahn, N. S. & Fugi, R. Diet seasonality and food overlap of the fish assemblage in a pantanal pond. Neotrop. Ichthyol. 6(4), 567–576. https://doi.org/10.1590/S1679-62252008000400004 (2008).
    Article  Google Scholar 

    68.
    Pianka, E. R. The structure of lizard communities. Annu. Rev. Ecol. Syst. 4(1), 53–74. https://doi.org/10.1146/annurev.es.04.110173.000413 (1973).
    Article  Google Scholar 

    69.
    Pekár, S. & Brabec, M. Modern Analysis of Biological Data. Generalized Linear Models in R (MUNI Press, Brno, 2016).
    Google Scholar 

    70.
    R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, Vienna). https://www.R-project.org/ (2017).

    71.
    Breheny, P. & Burchett, W. Visualization of regression models using visreg. R J. 9, 56–71 (2017).
    Article  Google Scholar 

    72.
    Kučera, B. Krasová morfologie a vývoj Ardovské jeskyně v Jihoslovenském krasu. Československý Kras. 16, 41–56 (1964) ([in Czech]).
    Google Scholar  More

  • in

    Author Correction: Vertical transmission of sponge microbiota is inconsistent and unfaithful

    Author notes
    These authors jointly supervised this work: Elizabeth A. Archie and José M. Montoya.

    Affiliations

    Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
    Johannes R. Björk & Elizabeth A. Archie

    Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
    Johannes R. Björk & José M. Montoya

    Natural History Museum, London, UK
    Cristina Díez-Vives

    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Carmen Astudillo-García

    Authors
    Johannes R. Björk

    Cristina Díez-Vives

    Carmen Astudillo-García

    Elizabeth A. Archie

    José M. Montoya

    Corresponding authors
    Correspondence to Johannes R. Björk or Elizabeth A. Archie or José M. Montoya. More

  • in

    Preparation and application of a thidiazuron·diuron ultra-low-volume spray suitable for plant protection unmanned aerial vehicles

    Screening of solvent and adjuvant
    The results of solvent screening are shown in Table 1. The original pesticide could not be completely dissolved using a single solvent. However, 5% N-methyl-2-pyrrolidone + 10% cyclohexanone could completely dissolve the original pesticide. There was no solid precipitation at room temperature, so the formulation could be used for the subsequent experiment. According to Table 2, a mixture of sulfonate adjuvants (70b) and fatty alcohol polyoxyethylene ether adjuvants (AEO-4, -5, -7, -9, 992) could stabilize the system in a single, transparent, homogeneous phase. Therefore, sulfonate adjuvant (70b) was selected and mixed with five adjuvants of the AEO series to prepare thidiazuron·diuron ultra-low-volume sprays, numbered 1–5 (as shown in Table 3).
    Table 1 Selection of solvent type and dosage (%: mass fraction).
    Full size table

    Table 2 Selection of adjuvants type and dosage (%: mass fraction).
    Full size table

    Table 3 Ultra-low-volume formulations used in this study.
    Full size table

    Surface tension measurement
    The critical surface tension of cotton leaves is 63.30–71.81 mN/m. Figure 1 shows that the surface tension of each sample was 31.67–33.37 mN/m, which was much lower than the critical surface tension of the leaf, indicating the agent was able to completely wet the leaf and be fully distributed on the leaf surface. The maximum surface tension of the reference product was 38.90 mN/m. Under the same dosage of adjuvant, sample 5 with adjuvant 992 had the smallest surface tension of 31.67 mN/m.
    Figure 1

    Surface tensions of different samples. Different letters (a–d) indicate significant differences between means. Means followed by the same letter are not significant at the 5% significance level by the LSD test (LSD = 0.05). Vertical bars indicate a standard deviation of the mean. The detailed data of the histogram is shown in Supplementary Table S1.

    Full size image

    Contact angle measurement
    According to Young’s equation, the smaller the surface tension, the smaller the contact angle40,41. Figure 2 shows the contact angle of different samples on cotton leaves and the change in contact angle over time. The contact angles of oil agents containing the adjuvant 992, AEO-7 and AEO-9 were smaller than that of the reference product, and the spreading effect was superior to that of the reference product. In the surface tension test, sample 5 had the smallest surface tension of 31.67 mN/m; this sample showed the minimum initial contact angle (39°) and a static contact angle (22°). The surface tension of the reference product was 38.90 mN/m., with the maximum initial contact angle (65.5°). Therefore, the relationship between surface tension and contact angle conformed to Young’s equation.
    Figure 2

    Contact angles of different samples on cotton leaves in 0–10 s. The detailed data of drawing the contact Angle curve is shown in Supplementary Table S2.

    Full size image

    Volatilization rate measurement
    As shown in Fig. 3, the volatilization rate of the oil agent was much lower than that of the reference product. The volatilization rate of the five treatments was 5.80–8.74%, while the volatilization rate of the reference product was 22.97%. The volatilization rate of the oil agent met the quality requirements of an ultra-low-volume spray (≤ 30%). A low volatilization rate helps with spraying defoliants in hot and dry areas such as Xinjiang, effectively preventing evaporation of the droplets and increasing deposition.
    Figure 3

    Volatilization of different samples on filter paper. Different letters (a–e) indicate significant differences between means. Means followed by the same letter are not significant at the 5% significance level by the LSD test (LSD = 0.05). Vertical bars indicate a standard deviation of the mean. The detailed data of the histogram is shown in Supplementary Table S3.

    Full size image

    Viscosity measurement
    Viscosity is an important factor affecting the atomization performance of a formulation42. Figure 4 shows that the viscosity of the five oil agents ranged from 12.9 to 18.3 mPa s, meeting the quality requirements of an ultra-low-volume spray ( 20 V), the droplet size distribution tended to be stable. This coincided with data shown in Fig. 6, where the inflection point appeared when rotation speed was 9600 rpm (voltage = 20 V).
    Figure 6

    Relationship between the rotation speed of the centrifugal spray atomizer and droplet size. D10: 10% cumulative volume diameter, D50: 50% cumulative volume diameter, D90: 90% cumulative volume diameter. The detailed data of drawing the curve is shown in Supplementary Table S6.

    Full size image

    Figure 7

    Relationship between the rotation speed of the centrifugal spray atomizer and the fog droplet spectrum. The detailed data of drawing the curve is shown in Supplementary Table S6.

    Full size image

    Therefore, we determined that the optimal working conditions for the rotary atomizer were achieved by setting the DC voltage stabilized power supply current to 1.00 A and voltage to 20 V, which were used for subsequent experiments.
    Atomization performance
    The relationship between viscosity and droplet spectrum are shown in Table 4 and Fig. 8. The cumulative volume diameter for the five treatments was less than 150 μm meeting the requirements of the ULV spray32. The cumulative volume diameter for the five treatments was larger than that for the reference product, the width of the droplet spectrum was narrower, and the droplet distribution was more uniform. Droplet size affects the drift of droplets43. The D10 of the reference product was 25.62 μm under these working conditions. This droplet size was highly susceptible to drift and deposition on non-target organisms. Water suspension was not suitable for this application at low dosage.
    Table 4 Droplet size and droplet size distribution of different sample sprays.
    Full size table

    Figure 8

    Relationship between formulation viscosity and droplet spectrum. The detailed data of drawing the figure is shown in Supplementary Table S7.

    Full size image

    As presented in Table 4, droplet size increased with increasing viscosity, which influenced the droplet spectrum. The results in Fig. 8 show that the span of droplet size decreased with the increase of viscosity, indicating that droplets with more uniform distribution could be obtained by increasing the viscosity of the formulation41.
    Droplet deposition effect
    We tested the efficacy of the ULV spray formulation by spraying cotton plants using an UAV. The test results in Table 5 indicate that increasing the dosage of application would increase droplet size, coverage, and deposition density. At the same application dosage, the droplet size of the ultra-low-volume spray was slightly larger than that of the reference product, and the coverage and deposition density were greater than those of the reference product. The droplet spectral width (Rs) of the five treatments was less than 1, and the coefficient of variation was less than 7%, indicating that the droplet distribution was relatively uniform. Among treatments, T2 had the narrowest Rs and coefficient of variation (CV), where the droplet size distribution was the most uniform. For the ultra-low-volume spray, at the application dosage of 4.5–9.0 L/ha, the droplet coverage gradually increased from 0.85 to 4.15%; the droplet deposition densities were 15.63, 17.24, 28.45, and 42.57 pcs/cm2, which were larger than requirements suggested in the literature. The droplet coverage of the reference product (T5) was 0.73%, and the deposition density was only 11.32 pcs/cm2.
    Table 5 Droplet size, coverage, deposition density, spectral width and variation coefficient for each treatment.
    Full size table

    Efficacy trials
    The efficacy of cotton defoliant is reflected in the defoliation rate and boll opening rate of cotton after application. Therefore, we surveyed the defoliation rate and boll opening rate of cotton in the test area 3–15 days after application. The results are shown in Figs. 9 and 10.
    Figure 9

    Defoliation rate 3–15 days after treatment. The detailed data of drawing the curve is shown in Supplementary Table S8.

    Full size image

    Figure 10

    Boll opening rate 3–15 days after treatment. The detailed data of drawing the curve is shown in Supplementary Table S9.

    Full size image

    Figure 9 indicates that the defoliation rates of the five treatments 15 days after the pesticide treatment were 59.82%, 63.96%, 71.40%, 77.84%, and 54.58%, respectively. The defoliation rates of T1, T2, and T5 were less than 70%.
    Application of the ultra-low-volume spray at 4.50 L/ha or 6.00 L/ha and the reference product at 6.00 L/ha had a poor defoliation effect. T4 (9.00 L/ha) was superior to the others, and the defoliation rate reached 77.84% 15 days after application. As shown in Fig. 10, the boll opening rates of the five treatments were 58.54%, 67.74%, 95.35%, 100%, and 44.68% 15 days after application. Similarly, the boll opening rates of T1, T2, and T5 were poor, with the boll opening rate of the control T5 only 44.68%. We analyzed significant differences between the defoliation rates and boll opening rates of the five treatments. The results showed that the defoliation rate and boll opening rate associated with the thidiazuron·diuron ultra-low-volume spray on cotton plants were significantly different from those of the reference product.
    Overall, the defoliation rate and boll opening rate produced by the ultra-low-volume spray were superior to those produced by the reference product. This result was consistent with data shown in Table 5. The higher the droplet coverage rate, the higher the droplet deposition density and the higher the defoliation rate and boll opening rate. T1, T2 and T5 had poor deposition effect on cotton plants, and the effective pesticide utilization rate was low, resulting in dissatisfactory defoliation rates and boll opening rates. Both the droplet coverage rate and the droplet deposition density of T3 and T4 were large. Therefore, droplets of pesticide solution could deposit more easily and uniformly on cotton leaves, allowing the plants to defoliate and open their bolls easily. More

  • in

    The UN Environment Programme needs new powers

    Indian prime minister Indira Gandhi meets Maurice Strong, who chaired the 1972 Stockholm Conference on the Human Environment. Gandhi saw UNEP’s potential at a time when other countries doubted its value.Credit: Yutaka Nagata/UN Photo

    The United Nations Environment Programme (UNEP) will be 50 next year. But the globe’s green watchdog, which helped to create the Intergovernmental Panel on Climate Change (IPCC), very nearly didn’t exist.
    During talks hosted by Sweden in 1972, low- and middle-income countries were concerned that such a body would inhibit their industrial development. Some high-income countries also questioned its creation. UK representative Solly Zuckerman, a former chief scientific adviser to prime ministers including Winston Churchill, said the science did not justify warnings that human activities could have irreversible consequences for the planet. The view in London was that, on balance, environmental pollution was for individual nations to solve — not the UN.
    But the idea of UNEP had powerful supporters, too. India’s prime minister, Indira Gandhi, foresaw its potential in enabling industry to become cleaner and more humane. And the host nation made a wise choice in picking Canadian industrialist Maurice Strong to steer the often fractious talks to success. He would become UNEP’s first executive director. Two decades later, Strong re-emerged to chair the 1992 Earth Summit in Rio de Janeiro, Brazil, which created three landmark international agreements: to protect biodiversity, safeguard the climate and combat desertification.
    UNEP has chalked up some impressive achievements in science and legislation. In 1988, working with the World Meteorological Organization, it co-founded the IPCC, whose scientific assessments have been pivotal to global climate action. It also responded to scientists’ warnings about the hole in the ozone layer, leading to the creation of the 1987 Montreal Protocol, an international law to phase out ozone-depleting chemicals.
    Strong’s successors would go on to identify emerging green-policy issues and nudge them into the mainstream. UNEP has pushed the world of finance to think about how to stop funding polluting industries. It has also advocated working with China to green its rapid industrial growth — including the Belt and Road Initiative to develop global infrastructure. It is essential that this work continues.
    UNEP also accelerated the creation of environment ministries around the world. Their ministers sit on the programme’s governing council; at their annual meeting last week, they reflected on what UNEP must do to tackle the environmental crisis. Although the environment is a rising priority for governments, businesses and civil society, progress on the UN’s flagship Sustainable Development Goals — in biodiversity, climate, land degradation, pollution, finance and more — is next to non-existent. Moreover, the degradation of nature is putting hard-won gains at risk, argues a report that UNEP commissioned as part of its half-century commemorations.
    The report, Making Peace with Nature, assesses much of the same literature as would a climate- or land-degradation assessment, but its key strength is in how it brings together researchers from across environmental science. In doing so, UNEP is helping to accelerate a mode of working that should be standard. If, for example, there is to be an assessment of how climate change affects biodiversity, it makes much more sense for this to be carried out by a joint team from the IPCC and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) than by researchers from just one of these organizations.
    The UNEP report’s authors stop short of recommending such changes to the architecture of the UN’s scientific advisory bodies. That is a missed opportunity. Also missing is a discussion and recommendations on how to make countries more accountable for their environmental pledges.
    Both these actions are sorely needed if the world is to take more meaningful steps to battle climate change and biodiversity loss. Countries have become expert in capturing data and reporting them to UN organizations. But there is no mechanism that holds nations to account. For example, there is no system to ensure compliance with targets for the Sustainable Development Goals.
    Last week, the UN produced a report in which countries published their progress towards commitments under the 2015 Paris climate agreement, known as nationally determined contributions. The agreement includes almost 200 countries, but just 75 reported their data. There are few incentives for success and no penalties for failure. Without such measures, it is hard to see how meaningful change could ever happen.
    In the past, researchers have proposed that UNEP’s member states upgrade its powers so it becomes more of a compliance body — a World Environment Organization that, like the World Trade Organization, has the power to censure countries for failing to keep to agreements. But this has been resisted as too radical a step, which would upend the autonomy of the UN biodiversity and climate organizations that UNEP itself helped to bring into being.
    Twenty years ago, there might have been some justification for such a view, but now, with the world on a path to extreme climate change, any action will need to be radical, including considering how to give UNEP more teeth.
    UNEP helped to lay the foundations for a scientific consensus on environmental decline, and it should be proud of the body of law that has been enacted globally. Alas, such measures risk being too little, too late. As it embarks on a year of reflection ahead of its anniversary, member states must consider what more they need to do to empower UNEP to tackle the planetary emergency. More

  • in

    Large-scale spatial patterns of small-mammal communities in the Mediterranean region revealed by Barn owl diet

    1.
    de Lattin, G. Grundriss der Zoogeographie (Gustav Fischer Verlag, 1976).
    2.
    Hewitt, G. M. Post-glacial re-colonization of European biota. Biol. J. Linn. Soc. Lond. 68, 87–112. https://doi.org/10.1006/bijl.1999.0332 (1999).
    Article  Google Scholar 

    3.
    Wallace, A. R. The geographical distribution of animals; with a study of the relations of living and extinct faunas as elucidating the past changes of the Earth’s surface (Harper & Brothers, 1876).

    4.
    Mittermeier, R. A., Myers, N., Mittermeier, C. G. & Robles Gil, P. Hotspots: Earth’s biologically richest and most endangered terrestrial ecoregions (CEMEX, 1999).
    Google Scholar 

    5.
    Médail, F. & Quézel, P. Biodiversity hotspots in the Mediterranean Basin: setting global conservation priorities. Conserv. Biol. 13(6), 1510–1513 (1999).
    Article  Google Scholar 

    6.
    Temple, H. J. & Cuttelod, A. (Compilers). The Status and Distribution of Mediterranean Mammals. Gland, Switzerland and Cambridge (UK: IUCN, vii+32pp, 2009).

    7.
    Blondel, J. The nature and origin of the vertebrate fauna. pp. 139–163 In: Woodward, C. J. (ed.) The Physical Geography of the Mediterranean (Oxford University Press, Oxford, 2009).

    8.
    Aulagnier, S., Hafner, P., Mitchell-Jones, A. J., Moutou, F. & Zima, J. Mammals of Europe, North Africa and the Middle East (A&C Black Publishers, 2009).
    Google Scholar 

    9.
    Horáček, I., Hanák, V. & Gaisler, J. Bats of the Palearctic region: a taxonomic and biogeographic review. In Proceedings of the VIIIth European bat research symposium (Vol. 1, pp. 11–157) (Kraków, CIC ISEZ PAN, 2000).

    10.
    Smith, C. H. A system of world mammal faunal regions. I. Logical and statistical derivation of the regions. J. Biogeogr. 10, 455–466. https://doi.org/10.2307/2844752 (1983).

    11.
    Dobson, M. Mammal distributions in the western Mediterranean: the role of human intervention. Mammal Rev. 28(2), 77–88 (1998).
    Article  Google Scholar 

    12.
    Sans-Fuentes, M. A. & Ventura, J. Distribution patterns of the small mammals (Insectivora and Rodentia) in a transitional zone between the Eurosiberian and the Mediterranean regions. J. Biogeogr. 27(3), 755–764 (2000).
    Article  Google Scholar 

    13.
    Kryštufek, B. & Vohralík, V. Mammals of Turkey and Cyprus: introduction, checklist, Insectivora (Zgodovinsko društvo za južno Primorsko, 2001).

    14.
    Kryštufek, B. A quantitative assessment of Balkan mammal diversity. In Balkan Biodiversity (pp. 79–108) (Springer, Dordrecht, 2004).

    15.
    Kryštufek, B., Vohralík, V. & Janžekovič, F. Mammals of Turkey and Cyprus: Rodentia I: Sciuridae, Dipodidae, Gliridae (Arvicolinae, 2005).
    Google Scholar 

    16.
    Kryštufek, B. & Vohralík, V. Mammals of Turkey and Cyprus, Rodentia II: Cricetinae, Murridae, Spalacidae, Calomyscidae, Capromyidae, Hystricidae Castoridae. J. Mammal. 96, 1–373 (2010).
    Google Scholar 

    17.
    Kryštufek, B., Donev, N. R. & Skok, J. Species richness and distribution of non-volant small mammals along an elevational gradient on a Mediterranean mountain. Mammalia 75(1), 3–11 (2011).
    Article  Google Scholar 

    18.
    Svenning, J. C., Fløjgaard, C. & Baselga, A. Climate, history and neutrality as drivers of mammal beta diversity in Europe: Insights from multiscale deconstruction. J. Anim. Ecol. 80(2), 393–402 (2011).
    Article  Google Scholar 

    19.
    Gaston, K., & Blackburn, T. Pattern and process in macroecology (John Wiley & Sons, 2008).

    20.
    Darwin, C. On the Origin of Species by Means of Natural Selection (J. Murray, 1859).

    21.
    Wallace, A. R. Tropical Nature and Other Essays (Macmillan, 1878).

    22.
    Hawkins, B. A. et al. Energy, water and broad-scale geographic patterns of species richness. Ecology 84, 3105–3117. https://doi.org/10.1890/03-8006 (2002).
    Article  Google Scholar 

    23.
    Hillebrand, H. On the generality of the latitudinal diversity gradient. Am. Nat. 163(2), 192–211 (2004).
    Article  Google Scholar 

    24.
    Kindlmann P, Schödelbauerová I, Dixon AF.G. Inverse latitudinal gradients in species diversity. pp. 246–257 in Storch D. et al. (eds.) Scaling Biodiversity (Cambridge University Press, 2007).

    25.
    Boone, R. B. & Krohn, W. B. Relationship between avian range limits and plant transition zones in Maine. J. Biogeogr. 27, 471–482 (2000).
    Article  Google Scholar 

    26.
    Storch, D., Evans, K. L. & Gaston, K. J. The species-area-energy relationship in orchids. Ecol. Lett. 8, 487–492. https://doi.org/10.15517/lank.v7i1-2.19504 (2005).
    Article  PubMed  Google Scholar 

    27.
    Valladares, F. et al. Global change and Mediterranean forests: current impacts and potential responses in Forests and Global Change (eds. Burslem, D. F. R. & Simonson, W. D.), 47–75 (Cambridge University Press, 2014).

    28.
    MacArthur, R. H. Patterns of Species Diversity. Geographical Ecology: Patterns in the Distributions of Species (Harper & Row, 1972).

    29.
    Whittaker, R. J. & Fernández-Palacios, J. M. Island biogeography: ecology, evolution, and conservation. Oxford University Press (2007).

    30.
    Sólymos, P. & Lele, S. R. Global pattern and local variation in species-area relationships. Glob. Ecol. Biogeogr. 21, 109–120. https://doi.org/10.1111/j.1466-8238.2011.00655.x (2012).
    Article  Google Scholar 

    31.
    Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: patterns, scale, and synthesis. Annu. Rev. Ecol. Evol. Syst. 34, 273–309. https://doi.org/10.1146/annurev.ecolsys.34.012103.144032 (2003).
    Article  Google Scholar 

    32.
    Prevedello, J., Gotelli, N. J. & Metzger, J. A stochastic model for landscape patterns of biodiversity. Ecol. Monogr. 86, 462–479. https://doi.org/10.1002/ecm.1223 (2016).
    Article  Google Scholar 

    33.
    Blondel, J., Aronson, J., Bodiou, J. Y. & Boeuf, G. The Mediteranean region. Biological diversity in space and time (Oxford University Press, 2010).

    34.
    Vigne, J. D. The large “true” Mediterranean islands as a model for the Holocene human impact on the European vertebrate fauna? Recent data and new reflections. The Holocene history of the European vertebrate fauna. Modern aspects of research, 295–322 (1999).

    35.
    Harding, A.F., Palutikof, J. & Holt, T. The climate system. pp. 69–88 In: Woodward, C.J. (ed.) The Physical Geography of the Mediterranean (Oxford University Press, Oxford, 2009).

    36.
    Zdruli, P. Desertification in the Mediterranean Region. Mediterranean year book 2011 (European Institute of the Mediterranean, 2012).

    37.
    Bilton, D. T. et al. Mediterranean Europe as an area of endemism for small mammals rather than a source for northwards postglacial colonization. Proc. Royal Soc. B 265(1402), 1219–1226 (1998).
    CAS  Article  Google Scholar 

    38.
    Hewitt, G. M. Mediterranean peninsulas: The evolution of hotspots. In Biodiversity hotspots (pp. 123–147) (Springer, Berlin, Heidelberg, 2011).

    39.
    Bilgin, R. Back to the suture: the distribution of intraspecific genetic diversity in and around Anatolia. Int. J. Mol. Sci. 12, 4080–4103. https://doi.org/10.3390/ijms12064080 (2011).
    Article  PubMed  PubMed Central  Google Scholar 

    40.
    Vigne, J. D. The origins of mammals on the Mediterranean islands as an indicator of early voyaging. Euras. Prehistory 10(1–2), 45–56 (2014).
    Google Scholar 

    41.
    Masseti, M. Mammals of the Mediterranean islands: Homogenisation and the loss of biodiversity. Mammalia 73, 169–202. https://doi.org/10.1515/MAMM.2009.029 (2009).
    Article  Google Scholar 

    42.
    Angelici, F. M., Laurenti, A. & Nappi, A. A. checklist of the mammals of small Italian islands. Hystrix 20, 3–27. https://doi.org/10.4404/hystrix-20.1-4429 (2009).
    Article  Google Scholar 

    43.
    Cunningham, P. L. & Aspinall, S. The diet of Little Owl Athene noctua in the UAE, with notes on Barn Owl Tyto alba and Desert Eagle Owl Bubo (b.) ascalaphus. Tribulus 11, 13–15 (2001).

    44.
    Taylor, I. R. How owls select their prey: A study of Barn owls Tyto alba and their small mammal prey. Ardea 97, 635–644. https://doi.org/10.5253/078.097.0433 (2009).
    Article  Google Scholar 

    45.
    Yom-Tov, Y. & Wool, D. Do the contents of barn owl pellets accurately represent the proportion of prey species in the field?. Condor 99, 972–976. https://doi.org/10.2307/1370149 (1997).
    Article  Google Scholar 

    46.
    Dodson, P. & Wexlar, D. Taphonomic investigations of owl pellets. Paleobiology 5, 275–284 (1979).
    Article  Google Scholar 

    47.
    Heisler, L., Somers, C. & Poulin, R. Owl pellets: A more effective alternative to conventional trapping for broad-scale studies of small mammal communities. Methods Ecol. Evol. 7, 96–103. https://doi.org/10.1111/2041-210X.12454 (2015).
    Article  Google Scholar 

    48.
    Torre, I., Arrizabalaga, A. & Flaquer, C. Three methods for assessing richness and composition of small mammal communities. J. Mammal. 85, 524–530. https://doi.org/10.1644/BJK-112 (2004).
    Article  Google Scholar 

    49.
    Yalden, D. W. & Morris, P. A. The analysis of owl pellet (Occasional publications)(The Mammal Society, 1990).

    50.
    Williams, D. F. & Braun, S. E. Comparison of pitfall and conventional traps for sampling small mammal populations. J. Wildl. Manage. 47, 841–845 (1983).
    Article  Google Scholar 

    51.
    Glennon, M. J., Porter, W. F. & Demers, C. L. An alternative field technique for estimating diversity of small-mammal populations. J. Mammal. 83, 734–742. https://doi.org/10.1644/1545-1542 (2002).
    Article  Google Scholar 

    52.
    Morris, P. A., Burgis, M. J., Morris, P. A. & Holloway, R. A method for estimating total body weight of avian prey items in the diet of owls. J. Zool. 210, 642–644 (1986).
    Article  Google Scholar 

    53.
    Vukićević Radić, O., Jovanović, T. B., Matić, R. & Katarinovski, D. Age structure of yellow-necked mouse (Apodemus flavicollis Melchior 1834) in two samples obtained from live traps and owl pellets. Arch. Biol. Sci. 57, 53–56 (2005).

    54.
    Coda, J., Gomez, D., Steinmann, A. R. & Priotto, J. Small mammals in farmlands of Argentina: Responses to organic and conventional farming. Agric. Ecosyst. Environ. 211, 17–23 (2015).
    Article  Google Scholar 

    55.
    Andrade, A., de Menezes, J. F. S. & Monjeau, A. Are owl pellets good estimators of prey abundance?. J. King Saud Univ. Sci. 28, 239–244. https://doi.org/10.1016/j.jksus.2015.10.007 (2016).
    Article  Google Scholar 

    56.
    Moysi, M., Christou, M., Goutner, V., Kassinis, N. & Iezekiel, S. Spatial and temporal patterns in the diet of barn owl (Tyto alba) in Cyprus. J. Biol. Res-Thessalon. 25(1), 9 (2018).
    Article  Google Scholar 

    57.
    Romano, A., Séchaud, R. & Roulin, A. Global biogeographical patterns in the diet of a cosmopolitan predator. J. Biogeogr. 47, 1467–1481. https://doi.org/10.1111/jbi.13829 (2020).
    Article  Google Scholar 

    58.
    Baquero, R. A. & Tellería, J. L. Species richness, rarity and endemicity of European mammals: A biogeographical approach. Biodivers. Conserv. 10(1), 29–44 (2001).
    Article  Google Scholar 

    59.
    Mitchell-Jones, A. J. et al. The Atlas of European Mammals (T & AD Poyser, 1999).

    60.
    Kross, S. M., Bourbour, R. P. & Martinico, B. L. Agricultural land use, arn owl diet, and vertebrate pest control implications. Agric. Ecosyst. Environ. 223, 167–174. https://doi.org/10.1016/j.agee.2016.03.002 (2016).
    Article  Google Scholar 

    61.
    Krishnapriya, T. & Ramakrishnan, U. Higher speciation and lower extinction rates influence mammal diversity gradients in Asia. BMC Evol. Biol. 15, 11. https://doi.org/10.1186/s12862-015-0289-1 (2015).
    Article  Google Scholar 

    62.
    Kouki, J., Niemela, P. & Viitasaari, M. Reversed latitudinal gradient in species richness of sawflies (Hymenoptera, Symphyta). Ann. Zool. Fenn. 31, 83–88 (1994).
    Google Scholar 

    63.
    Rabenold, K. N. A reversed latitudinal diversity gradient in avian communities of eastern deciduous forests. Am. Nat. 114, 275–286. https://doi.org/10.1086/283474 (1979).
    Article  Google Scholar 

    64.
    Ruffino, L. & Vidal, E. Early colonization of Mediterranean islands by Rattus rattus: A review of zooarcheological data. Biol. Invasions 12(8), 2389–2394 (2010).
    Article  Google Scholar 

    65.
    Thomes, J. B. Land degradation. pp. 563–581. In: Woodward, C.J. (ed.) The Physical Geography of the Mediterranean (Oxford University Press, Oxford, 2009).

    66.
    Allen, H. D. Vegetation and ecosystem dynamics. pp. 203–227. In: Woodward, C.J. (ed.) The Physical Geography of the Mediterranean (Oxford University Press, Oxford, 2009).

    67.
    Dov Por, F. & Dimentman, C. Mare Nostrum. Neogene and anthropic natural history of the Mediterranean basin, with emphasis on the Levant (Pensoft, Sofia-Moscow, 2006).

    68.
    Zohary, D., Hopi, M. & Weiss, E. Domestication of Plants in the Old World 4th edn. (Oxford University Press, 2012).
    Google Scholar 

    69.
    Roulin, A. Spatial variation in the decline of European birds as shown by the Barn Owl Tyto alba diet. Bird Study 62, 271–275. https://doi.org/10.1080/00063657.2015.1012043 (2015).
    Article  Google Scholar 

    70.
    Pezzo, F. & Morimando, F. Food habits of the barn owl, Tyto alba, in a mediterranean rural area: Comparison with the diet of two sympatric carnivores. Boll. Zool. 62, 369–373. https://doi.org/10.1080/11250009509356091 (1995).
    Article  Google Scholar 

    71.
    Soranzo, N., Alia, R., Provan, J. & Powell, W. Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations. Mol. Ecol. 9, 1205–1211. https://doi.org/10.1046/j.1365-294x.2000.00994.x (2000).
    CAS  Article  PubMed  Google Scholar 

    72.
    van Andel, T. H. The climate and landscape of the middle part of the Weichselian Glaciation in Europe: The stage 3 project. Q. Res. 57, 2–8. https://doi.org/10.1006/qres.2001.2294 (2002).
    ADS  Article  Google Scholar 

    73.
    Johnston, D. W. & Hill, J. M. Prey selection of Common Barn-owls on islands and mainland sites. J. Raptor. Res. 21(1), 3–7 (1987).
    Google Scholar 

    74.
    Sommer, R., Zoller, H., Kock, D., Böhme, W. & Griesau, A. Feeding of the barn owl, Tyto alba with first record of the European free-tailed bat, Tadarida teniotis on the island of Ibiza (Spain, Balearics). Fol. Zool. 54, 364–370 (2005).
    Google Scholar 

    75.
    Kryštufek, B., Reed, J. Pattern and process in Balkan biodiversity – an overview in A quantitative assesment of Balkan mammal diversity (eds. Griffiths, H. I., Kryštufek, B. & Reed, J. M.) 79–108 (Kluwer Academic, 2004).

    76.
    Ricklefs, R. E. & Lovette, I. J. The roles of island area per se and habitat diversity in the species-area relationships of four Lesser Antillean faunal groups. J. Anim. Ecol. 68, 1142–1160 (1999).
    Article  Google Scholar 

    77.
    Heaney, L. R. Mammalian species richness on islands on the Sunda Shelf Southeast Asia. Oecologia 61, 11–17 (1984).
    ADS  Article  Google Scholar 

    78.
    Carvajal, A. & Adler, G. H. Biogeography of mammals on tropical Pacific islands. J. Biogeogr. 32, 1561–1569. https://doi.org/10.1111/j.1365-2699.2005.01302.x (2005).
    Article  Google Scholar 

    79.
    Millien-Parra, V. & Jaeger, J. J. Island biogeography of the Japanese terrestrial mammal assemblages: An example of a relict fauna. J. Biogeogr. 26, 959–972. https://doi.org/10.1046/j.1365-2699.1999.00346.x (1999).
    Article  Google Scholar 

    80.
    Amori, G., Rizzo Pinna, V., Sammuri, G. & Luiselli, L. Diversity of small mammal communities of the tuscan archipelago: Testing the effects of island size, distance from mainland and human density. Fol. Zool. 64, 161–166. https://doi.org/10.25225/fozo.v64.i2.a9.2015 (2015).

    81.
    Audoin-Rouzeau, F. & La Vigne, J. D. colonisation de l’Europe par le rat noir (Rattus rattus). Rev. de Paléobiologie 13, 125–145. https://doi.org/10.1134/S1062359011020130 (1994).
    Article  Google Scholar 

    82.
    Towns, D. R., Atkinson, I. A. E. & Daugherty, Ch. H. Have the harmful effects of introduced rats on islands been exaggerated?. Biol. Invasions 8, 863–891. https://doi.org/10.1007/s10530-005-0421-z (2006).
    Article  Google Scholar 

    83.
    Martin, J. L., Thibault, J. C. & Bretagnolle, V. Black rats, island characteristics, and colonial nesting birds in the Mediterranean: Consequences of an ancient introduction. Conserv. Biol. 14, 1452–1466. https://doi.org/10.1046/j.1523-1739.2000.99190.x (2000).
    Article  Google Scholar 

    84.
    Landová, E., Horáček, I. & Frynta, D. Have black rats evolved a culturally-transmitted technique of pinecone opening independently in Cyprus and Israel?. Isr. J. Ecol. Evol. 52(2), 151–158 (2006).
    Article  Google Scholar 

    85.
    Sarà, M. & Morand, S. Island incidence and mainland population density: Mammals from Mediterranean islands. Divers. Distrib. 8, 1–9 (2002).
    Article  Google Scholar 

    86.
    Libois, M. R., Fons, R., Saint Girons, M. C. Le régime alimentaire de la chouette effraie Tyto alba, dans les Pyrénées-orientales. Etude des variations ecogéographiques. Rev. Ecol.-Terre Vie 37, 187–217 (1983).

    87.
    Di Russo, C. Dati sui micromammiferi da borre di barbacianni, Tyto alba, di un Sito della Sardegna Centro-orientale. Hystrix 2, 57–62. https://doi.org/10.4404/hystrix-2.1-3885 (1987).
    Article  Google Scholar 

    88.
    Guerra, C., García, D. & Alcover, J. A. Unusual foraging patterns of the barn owl, Tyto alba (Strigiformes: Tytonidae), on small islets from the Pityusic archipelago (Western Mediterranean Sea). Fol. Zool. 63, 180–187. https://doi.org/10.25225/fozo.v63.i3.a5.2014 (2014).

    89.
    Patterson, B. D. & Atmar, W. Nested subsets and the structure of insular mammalian faunas and archipelagos. Biol. J. Linn. Soc. Lond. 28, 65–82. https://doi.org/10.1111/j.1095-8312.1986.tb01749.x (1986).
    Article  Google Scholar 

    90.
    Kutiel, P., Peled, Y. & Geffen, E. The effect of removing shrub cover on annual plants and small mammals in a coastal sand dune ecosystem. Biol. Conserv. 94, 235–242. https://doi.org/10.1016/S0006-3207(99)00172-X (2000).
    Article  Google Scholar 

    91.
    Tores, M., Motro, Y., Motro, U. & Yom-Tov, Y. The barn owl-a selective opportunist predator. Israel J. Zool. 51, 349–360. https://doi.org/10.1560/7862-9E5G-RQJJ-15BE (2005).
    Article  Google Scholar 

    92.
    Obuch, J. & Benda, P. Food of the Barn Owl (Tyto alba) in the Eastern Mediterranean. Slovak Raptor J. 3, 41–50. https://doi.org/10.2478/v10262-012-0032-4 (2009).
    Article  Google Scholar 

    93.
    Anděra, M. & Horáček, I. Determining our mammals (Sobotáles, 2005).

    94.
    Dor, M. Observations sur les Micromammiferes trouves dans les Pelotes de la Chouette effraye (Tyto alba) en Palestine. Mammalia 11, 50–54 (1947).
    Article  Google Scholar 

    95.
    De Pablo, F. Alimentación de la Lechuza Común (Tyto alba) en Menorca. Bolleti Soc. Hist. Nat. Balear. 43, 15–26 (2000).
    Google Scholar 

    96.
    Rihane, A. Contribution to the study of the diet of Barn Owl Tyto alba in the semi-arid plains of Atlantic Morocco. Alauda 71, 363–369 (2003).
    Google Scholar 

    97.
    Kennedy, C. M., J. R. Oakleaf, D. M. Theobald, Baruch-Mordo, S. & Kiesecker, J. Managing the middle: A shift in conservation priorities based on the global human modification gradient. Global Change Biol. 25(3), 811–826. https://doi.org/10.1111/gcb.14549 (2019).

    98.
    Kennedy, C. M., Oakleaf, J. R., Theobald, D. M., Baruch-Mordo, S. & Kiesecker, J. Global Human Modification of Terrestrial Systems. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). https://doi.org/10.7927/edbc-3z60. Accessed DAY MONTH YEAR (2020).

    99.
    Shannon, C. & Weaver, W. The Mathematical Theory of Communication (The University of Illinois Press, 1964).

    100.
    R Development Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Found Stat Comp (2011).

    101.
    Anderson, D. R. & Burnham, K. P. Avoiding pitfalls when using information-theoretic methods. J. Wildl. Manag. 66, 912–918 (2002).
    Article  Google Scholar 

    102.
    Whittingham, M. J., Stephens, P. A., Bradbury, R. B. & Freckleton, R. P. Why do we still use stepwise modelling in ecology and behaviour?. J. Anim. Ecol. 75, 1182–1189. https://doi.org/10.1111/j.1365-2656.2006.01141.x (2006).
    Article  PubMed  Google Scholar 

    103.
    Burnham, K. P., Anderson, D. R. & Huyvaert, K. P. AIC model selection and multimodel inference in behavioral ecology: Some background, observations, and comparisons. Behav. Ecol. Sociobiol. 65, 23–35. https://doi.org/10.1007/s00265-010-1039-4 (2011).
    Article  Google Scholar 

    104.
    ter Braak, C. & Šmilauer, P. Canoco reference manual and user’s quide: software for ordination, version 5.0 (Microcomputer Power, 2012).

    105.
    StatSoft Inc. Statistica (data analysis software system), version 12. http://www.statsoft.com (2013). More

  • in

    Experimental identification and in silico prediction of bacterivory in green algae

    1.
    Jost C, Lawrence CA, Campolongo F, Van De Bund W, Hill S, DeAngelis DL. The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model. Theor Popul Biol. 2004;66:37–51.
    PubMed  Article  Google Scholar 
    2.
    Tittel J, Bissinger V, Zippel B, Gaedke U, Bell E, Lorke A, et al. Mixotrophs combine resource use to outcompete specialists: Implications for aquatic food webs. Proc Natl Acad Sci. 2011;100:12776–81.
    Article  CAS  Google Scholar 

    3.
    Ward BA, Follows MJ. Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux. Proc Natl Acad Sci. 2016;113:2958–63.
    CAS  PubMed  Article  Google Scholar 

    4.
    Hansen PJ, Tillmann U. Mixotrophy among dinoflagellates—prey selection, physiology and ecological imporance. In: Subba Rao DV, editor. Dinoflagellates: classification, evolution, physiology and ecological significance. Hauppauge, NY, USA: Nova; 2020;201–60.

    5.
    Unrein F, Gasol JM, Not F, Forn I, Massana R. Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters. ISME J. 2014;8:164–76.
    CAS  PubMed  Article  Google Scholar 

    6.
    Anderson R, Charvet S, Hansen P. Mixotrophy in chlorophytes and haptophytes – effect of irradiance, macronutrient, micronutrient and vitamin limitation. Front Microbiol. 2018;9:1704.
    PubMed  PubMed Central  Article  Google Scholar 

    7.
    Lewitus AJ, Caron DA, Miller KR. Effect of light and glycerol on the organization of the photosynthetic apparatus in the facultative heterotroph Pyrenomonas salina (cryptophyceae). J Phycol. 1991;27:578–87.
    Article  Google Scholar 

    8.
    Du YooY, Seong KA, Jeong HJ, Yih W, Rho J-R, Nam SW, et al. Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters. Harmful Algae. 2017;68:105–17.
    Article  Google Scholar 

    9.
    Caron DA, Porter KG, Sanders RW. Carbon, nitrogen, and phosphorus budgets for the mixotrophic phytoflagellate Poterioochromonas malhamensis (Chrysophyceae) during bacterial ingestion. Limnol Oceanogr. 1990;35:433–43.
    CAS  Article  Google Scholar 

    10.
    Holen DA, Boraas ME. Mixotrophy in chrysophytes. Chrysophyte algae. Cambridge, UK: Cambridge University Press; 1995;119–40.

    11.
    Fenchel T. Ecology of heterotrophic microflagellates. II. Bioenerg growth Mar Ecol Prog Ser. 1982;8:225–31.
    Article  Google Scholar 

    12.
    Rottberger J, Gruber A, Boenigk J, Kroth P. Influence of nutrients and light on autotrophic, mixotrophic and heterotrophic freshwater chrysophytes. Aquat Micro Ecol. 2013;71:179–91.
    Article  Google Scholar 

    13.
    Bell EM, Laybourn-Parry J. Mixotrophy in the antarctic phytoflagellate, Pyramimonas gelidicola (Chlorophyta: Prasinophyceae). J Phycol. 2003;39:644–9.
    Article  Google Scholar 

    14.
    McKie-Krisberg ZM, Sanders RW. Phagotrophy by the picoeukaryotic green alga Micromonas: implications for Arctic Oceans. ISME J. 2014;8:1953–61.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    15.
    McKie-Krisberg ZM, Gast RJ, Sanders RW. Physiological responses of three species of Antarctic mxotrophic phytoflagellates to changes in light and dissolved nutrients. Micro Ecol. 2015;70:21–29.
    CAS  Article  Google Scholar 

    16.
    Paasch A. Physiological and genomic characterization of phagocytosis in green algae. New York, NY, USA: American Museum of Natural History; 2017.

    17.
    Not F, Latasa M, Scharek R, Viprey M, Karleskind P, Balagué V, et al. Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes. Deep Res Part I Oceanogr Res Pap. 2008;55:1456–73.
    Article  Google Scholar 

    18.
    Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE. 2009;4:e7657.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    19.
    Rii YM, Duhamel S, Bidigare RR, Karl DM, Repeta DJ, Church MJ. Diversity and productivity of photosynthetic picoeukaryotes in biogeochemically distinct regions of the South East Pacific Ocean. Limnol Oceanogr. 2016;61:806–24.
    Article  Google Scholar 

    20.
    Maruyama S, Kim E. A modern descendant of early green algal phagotrophs. Curr Biol. 2013;23:1081–4.
    CAS  PubMed  Article  Google Scholar 

    21.
    O’Kelly C. Flagellar apparatus architecture and the phylogeny of ‘green’ algae: Chlorophytes, Euglenoids, Glaucophytes. In: Menzel D, editor. The cytoskeleton of the algae. Boca Raton: CRC Press; 1992. p. 315–41.
    Google Scholar 

    22.
    Burns JA, Pittis AA, Kim E. Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic. Nat Ecol Evol. 2018;2:697–704.
    PubMed  Article  Google Scholar 

    23.
    Wilken S, Yung CCM, Hamilton M, Hoadley K, Nzongo J, Eckmann C, et al. The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments. Philos Trans R Soc B Biol Sci. 2019;374:20190090.
    CAS  Article  Google Scholar 

    24.
    Inouye I, Hori T, Chihara M. Absolute configuration analysis of the flagellar apparatus of Pterosperma Cristatum (Prasinophyceae) and consideration of Its phylogenetic position. J Phycol. 1990;26:329–44.
    Article  Google Scholar 

    25.
    Bhuiyan MAH, Faria DG, Horiguchi T, Sym SD, Suda S. Taxonomy and phylogeny of Pyramimonas vacuolata sp. nov. (Pyramimonadales, Chlorophyta). Phycologia. 2015;54:323–32.
    CAS  Article  Google Scholar 

    26.
    Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol. 2019;66:4–119.
    PubMed  PubMed Central  Article  Google Scholar 

    27.
    Burns JA, Paasch A, Narechania A, Kim E. Comparative genomics of a bacterivorous green alga reveals evolutionary causalities and consequences of phago-mixotrophic mode of nutrition. Genome Biol Evol. 2015;7:3047–61.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    28.
    Guillard R. Culture of phytoplankton for feeding marine invertebrates. In: Smith WL, Chanley WH, editors. Culture of marine invertebrate animals. 1975. New York: Plenum Press; 1975. p. 22–60.

    29.
    Cho J-C, Giovannoni SJ. Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol. 2006;56:855–9.
    CAS  PubMed  Article  Google Scholar 

    30.
    Thrash JC, Cho J-C, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ. Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera. J Bacteriol. 2010;192:5552–3.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    31.
    First MR, Park NY, Berrang ME, Meinersmann RJ, Bernhard JM, Gast RJ, et al. Ciliate ingestion and digestion: Flow cytometric measurements and regrowth of a digestion-resistant Campylobacter jejuni. J Eukaryot Microbiol. 2012;59:12–19.
    PubMed  Article  Google Scholar 

    32.
    Sherr BF, Sherr EB, Fallon RD. Use of monodispersed, fluorescently labeled bacteria to estimate in situ protozoan bacterivory. Appl Environ Microbiol. 1987;53:958–65.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    33.
    Vazquez-Dominguez E, Peters F, Gasol JM, Vaqué D. Measuring the grazing losses of picoplankton: methodological improvements in the use of fluorescently labeled tracers combined with flow cytometry. Aquat Micro Ecol. 1999;20:119–28.
    Article  Google Scholar 

    34.
    Leebens-Mack J, Barker M, Carpenter EJ. One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 2019;574:679–85.
    Article  CAS  Google Scholar 

    35.
    Wincker P. A thousand plants’ phylogeny. Nat Plants. 2019;5:1106–7.
    PubMed  Article  PubMed Central  Google Scholar 

    36.
    Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLOS Biol. 2014;12:e1001889.
    PubMed  PubMed Central  Article  CAS  Google Scholar 

    37.
    Johnson LK, Alexander H, Brown CT. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience. 2019;8:1–12.
    Google Scholar 

    38.
    Besemer J. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607–18.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    39.
    Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
    PubMed  PubMed Central  Google Scholar 

    40.
    Gawryluk RMR, Tikhonenkov DV, Hehenberger E, Husnik F, Mylnikov AP, Keeling PJ. Non-photosynthetic predators are sister to red algae. Nature. 2019;572:240–3.
    CAS  PubMed  Article  Google Scholar 

    41.
    Newcombe RG. Interval estimation for the difference between independent proportions: comparison of eleven methods. Stat Med. 1998;17:873–90.
    CAS  PubMed  Article  Google Scholar 

    42.
    Kursa M, Rudnicki W. Feature selection with the Boruta package. J Stat Softw. 2010;36:1–13.
    Article  Google Scholar 

    43.
    Chasset PO. Probabilistic neural network for the R statistical language. https://github.com/chasset/pnn. Github. 2013.

    44.
    Maia R, Eliason CM, Bitton P-P, Doucet SM, Shawkey MD. pavo: an R package for the analysis, visualization and organization of spectral data. Methods Ecol Evol. 2013;4:906–13.
    Google Scholar 

    45.
    Jimenez V, Burns J, Le Gall F, Not F, Vaulot D. No evidence of phago-mixotropy in Micromonas polaris, the dominant picophytoplankton species in the Arctic. J Phycol. 2021. https://doi.org/10.1111/jpy.13125.

    46.
    R Core Team. R development core team. R A Lang Environ Stat Comput. Vienna: R Foundation for Statistical Computing; 2016.

    47.
    Figueroa-Martinez F, Nedelcu AM, Smith DR, Reyes-Prieto A. When the lights go out: the evolutionary fate of free-living colorless green algae. N. Phytol. 2015;206:972–82.
    Article  Google Scholar 

    48.
    Nakada T, Misawa K, Nozaki H. Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses. Mol Phylogenet Evol. 2008;48:281–91.
    CAS  PubMed  Article  Google Scholar 

    49.
    Johnson I. The molecular probes handbook: a guide to fluorescent probes and labeling technologies. 11th ed. Waltham, MA, USA: Life Technologies Corporation; 2010.

    50.
    Leliaert F, Smith DR, Moreau H, Herron MD, Verbruggen H, Delwiche CF, et al. Phylogeny and molecular evolution of the green algae. CRC Crit Rev Plant Sci. 2012;31:1–46.
    Article  Google Scholar 

    51.
    Leliaert F. Green algae: chlorophyta and streptophyta. Reference module in life sciences. Amsterdam, DK: Elsevier; 2019.

    52.
    Parke M, Adams I. The Pyramimonas-like motile stage of Halosphaera viridis Schmitz. Bull Res Counc Isr. 1961.

    53.
    Thorndsen J. Cymbomonas Schiller (Prasinophyceae) reinvestigated by light and electron microscopy. Arch fur Protistenkd. 1988;136:327–36.
    Article  Google Scholar 

    54.
    González JM, Sherr BF, Sherr EB. Digestive enzyme activity as a quantitative measure of protistan grazing: the acid lysozyme assay for bacterivory. Mar Ecol Prog Ser. 1993;100:197–206.
    Article  Google Scholar 

    55.
    Moestrup Ø, Inouye I, Hori T. Ultrastructural studies on Cymbomonas tetramitiformis (Prasinophyceae). I. General structure, scale microstructure, and ontogeny. Can J Bot. 2003;81:657–71.
    Article  Google Scholar 

    56.
    Turmel M, Lopes dos Santos A, Otis C, Sergerie R, Lemieux C. Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code. Genome Biol Evol. 2019;11:1275–92.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    57.
    Lopes dos Santos A, Gourvil P, Tragin M, Noël M, Decelle J, Romac S, et al. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J. 2017;11:512–28.
    PubMed  Article  Google Scholar 

    58.
    Lemieux C, Turmel M, Otis C, Pombert J-F. A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus. Nat Commun. 2019;10:4061.
    PubMed  PubMed Central  Article  Google Scholar 

    59.
    Zingone A, Borra M, Brunet C, Forlani G. Kooistra WHCF, Procaccini G. Phylogenetic position of Crustomatix stigmatica sp. nov. and Dolichomastix tenuilepis in relation to the mamiellales (Prasinophyceae, Chlorophyta). J Phycol. 2002;38:1024–39.
    CAS  Article  Google Scholar 

    60.
    Liang Z, Geng Y, Ji C, Du H, Wong CE, Zhang Q, et al. Mesostigma viride genome and transcriptome provide insights into the origin and evolution of Streptophyta. Adv Sci. 2020;7:1901850.
    CAS  Article  Google Scholar 

    61.
    Buckley CM, Gopaldass N, Bosmani C, Johnston SA, Soldati T, Insall RH, et al. WASH drives early recycling from macropinosomes and phagosomes to maintain surface phagocytic receptors. Proc Natl Acad Sci. 2016;113:E5906–15.
    CAS  PubMed  Article  Google Scholar 

    62.
    Shpak M, Kugelman JR, Varela-Ramirez A, Aguilera RJ. The phylogeny and evolution of deoxyribonuclease II: An enzyme essential for lysosomal DNA degradation. Mol Phylogenet Evol. 2008;47:841–54.
    CAS  PubMed  Article  Google Scholar 

    63.
    Gast RJ, McKie-Krisberg ZM, Fay SA, Rose JM, Sanders RW. Antarctic mixotrophic protist abundances by microscopy and molecular methods. FEMS Microbiol Ecol. 2014;89:388–401.
    CAS  PubMed  Article  Google Scholar 

    64.
    Mitra A, Flynn KJ, Tillmann U, Raven JA, Caron D, Stoecker DK, et al. Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition: Incorporation of diverse mixotrophic strategies. Protist. 2016;167:106–20.
    CAS  Article  Google Scholar 

    65.
    Kirkham AR, Lepère C, Jardillier LE, Not F, Bouman H, Mead A, et al. A global perspective on marine photosynthetic picoeukaryote community structure. ISME J. 2013;7:922–36.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    66.
    Moon-van Der Staay SY, Wachter R De, Vaulot D. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature. 2001;409:607–10.
    CAS  PubMed  Article  Google Scholar 

    67.
    Worden A. Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquat Micro Ecol. 2006;43:165–75.
    Article  Google Scholar 

    68.
    Van Hannen EJ, Veninga M, Bloem J, Gons HJ, Laanbroek HJ. Genetic changes in the bacterial community structure associated with protistan grazers. Fundam Appl Limnol. 1999;145:25–38.
    Article  Google Scholar 

    69.
    Jürgens K, Güde H. The potential importance of grazing-resistant bacteria in planktonic systems. Mar Ecol Prog Ser. 1994;112:169–88.
    Article  Google Scholar 

    70.
    Jürgens K, Pernthaler J, Schalla S, Amann R. Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl Environ Microbiol. 1999;65:1241–50.
    PubMed  PubMed Central  Article  Google Scholar 

    71.
    Suzuki M. Effect of protistan bacterivory on coastal bacterioplankton diversity. Aquat Micro Ecol. 1999;20:261–72.
    Article  Google Scholar 

    72.
    Sherr EB, Sherr BF. Significance of predation by protists in aquatic microbial food webs. Antonie van Leeuwenhoek2. 2002;81:293–308.
    CAS  Article  Google Scholar 

    73.
    González J, Sherr EB, Sherr BF. Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol. 1990;56:583–9.
    PubMed  PubMed Central  Article  Google Scholar 

    74.
    Sherr BF, Sherr EB, McDaniel J. Effect of protistan grazing on the frequency of dividing cells in bacterioplankton assemblages. Appl Environ Microbiol. 1992;58:2381–5.
    CAS  PubMed  PubMed Central  Article  Google Scholar 

    75.
    González J, Sherr EB, Sherr BF. Differential feeding by marine flagellates on growing vs starving bacteria, and on motile vs non-motile bacteria. Mar Ecol Prog Ser. 1993;102:257–67.
    Article  Google Scholar 

    76.
    del Giorgio PA, Gasol JM, Vaqué D, Mura P, Agustí S, Duarte CM. Bacterioplankton community structure: Protists control net production and the proportion of active bacteria in a coastal marine community. Limnol Oceanogr. 1996;41:1169–79.
    Article  Google Scholar 

    77.
    Andersen OK, Goldman JC, Caron DA, Dennett MR. Nutrient cycling in a microflagellate food chain: III. Phosphorus dynamics. Mar Ecol Prog Ser. 1986;31:47–55.
    CAS  Article  Google Scholar 

    78.
    Fenchel T. Protistan filter feeding. Prog Protistol. 1986;1:65–113.
    Google Scholar 

    79.
    Epstein S, Shiaris M. Size selective grazing of coastal bacterioplankton by natural assemblages of pigmented flagellates, colourless flagellates and ciliates. Micro Ecol. 1992;23:211–25.
    CAS  Article  Google Scholar 

    80.
    Montagnes D, Barbosa A, Boenigk J, Davidson K, Jurgens K, Macek M, et al. Selective feeding behaviour of key free-living protists: avenues for continued study. Aquat Micro Ecol. 2008;53:83–98.
    Article  Google Scholar 

    81.
    Pfister G, Arndt H. Food selectivity and feeding behaviour in omnivorous filter-feeding ciliates: a case study for Stylonychia. Eur J Protistol. 1998;34:446–57.
    Article  Google Scholar 

    82.
    Boenigk J, Arndt H. Bacterivory by heterotrophic flagellates: community structure and feeding strategies. Antonie Van Leeuwenhoek. 2002;81:465–80.
    PubMed  Article  Google Scholar 

    83.
    Pickup ZL, Pickup R, Parry JD. Growth of Acanthamoeba castellanii and Hartmannella vermiformis on live, heat-killed and DTAF-stained bacterial prey. FEMS Microbiol Ecol. 2007;61:264–72.
    CAS  PubMed  Article  Google Scholar 

    84.
    Legrand C, Johansson N, Johnsen G, Borsheim K, Graneli E. Phagotrophy and toxicity variation in mixotrophic Prymnesium patelliferum (Haptophyceae). Limnol Oceanogr. 2001;46:1208–14.
    Article  Google Scholar 

    85.
    Caron DA, Sanders RW, Lim EL, Marrasé C, Amaral LA, Whitney S, et al. Light-depend phagotrophy freshwater mixotrophic chrysophyte Dinobryon cylindricum. Micro. Ecol. 1993;25:93–111.
    CAS  Article  Google Scholar 

    86.
    Fenchel T. The microbial loop – 25 years later. J Exp Mar Bio Ecol. 2008;366:99–103.
    Article  Google Scholar 

    87.
    Tittel J, Bissinger V, Zippel B, Gaedke U, Bell E, Lorke A, et al. Mixotrophs combine resource use to outcompete specialists: Implications for aquatic food webs. Proc Natl Acad Sci. 2003;100:12776–81.
    CAS  PubMed  Article  Google Scholar 

    88.
    Moorthi S, Ptacnik R, Sanders R, Fischer R, Busch M, Hillebrand H. The functional role of planktonic mixotrophs in altering seston stoichiometry. Aquat Micro Ecol. 2017;79:235–45.
    Article  Google Scholar 

    89.
    Katechakis A, Haseneder T, Kling R, Stibor H. Mixotrophic versus photoautotrophic specialist algae as food for zooplankton: The light: nutrient hypothesis might not hold for mixotrophs. Limnol Oceanogr. 2005;50:1290–9.
    CAS  Article  Google Scholar 

    90.
    Weisse T, Anderson R, Arndt H, Calbet A, Hansen PJ, Montagnes D. Functional ecology of aquatic phagotrophic protists – concepts, limitations, and perspectives. Eur J Protistol. 2016;55:50–74.
    PubMed  Article  Google Scholar 

    91.
    Graham LE, Graham JM, Wilcox WL, Cook ME. Algae. 3rd ed. Madison, WI, USA: LJLM Press; 2016.

    92.
    Guillou L, Eikrem W, Chrétiennot-Dinet M-J, Le Gall F, Massana R, Romari K, et al. Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist. 2004;155:193–214.
    CAS  PubMed  Article  Google Scholar 

    93.
    Lemieux C, Otis C, Turmel M. Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species. BMC Genom. 2014;15:857.
    Article  CAS  Google Scholar  More