Coccoliths

@inproceedings{gartner1971phylogenetic1,
    author = "Gartner, S. and Jr",
    title = "Phylogenetic lineages in the Lower Tertiary coccolith genus Chiasmolithus",
    year = "1971",
    booktitle = "North American Paleontological Convention, Proceedings, p. 930-957; Part G",
    note = "talkorigins\_source = {true}; raw\_reference = {Gartner, S., Jr., 1971, Phylogenetic lineages in the Lower Tertiary coccolith genus Chiasmolithus: North American Paleontological Convention, Proceedings, p. 930-957; Part G.}"
}

@article{black1972british,
    author = "Black, Maurice",
    title = "British Lower Cretaceous Coccoliths. I. Gault Clay",
    year = "1972",
    journal = "Monographs of the Palaeontographical Society",
    url = "https://doi.org/10.1080/25761900.2022.12131720",
    doi = "10.1080/25761900.2022.12131720",
    number = "534",
    openalex = "W4296160015",
    pages = "1-50",
    volume = "126"
}

Comment: In open-ocean warm-water assemblages, Nephrolithus frequens and Lithraphidites quadratus are not commonly observed.The original zonal interval was indicated between the first occurrence of these species.Micula mura and Tetralithus trifidus are more consistent stratigraphic indicators for the same general interval in low-latitude oceanic assemblages.

@incollection{doi102973dsdpproc151161973,
    author = "Bukry, David",
    title = "Low-Latitude Coccolith Biostratigraphic Zonation",
    year = "1973",
    booktitle = "U.S. Government Printing Office eBooks",
    abstract = "Comment: In open-ocean warm-water assemblages, Nephrolithus frequens and Lithraphidites quadratus are not commonly observed.The original zonal interval was indicated between the first occurrence of these species.Micula mura and Tetralithus trifidus are more consistent stratigraphic indicators for the same general interval in low-latitude oceanic assemblages.",
    url = "https://doi.org/10.2973/dsdp.proc.15.116.1973",
    doi = "10.2973/dsdp.proc.15.116.1973",
    openalex = "W2499395972",
    references = "doi101038225289a0, doi101111j216409471970tb02746x, doi102110pec74200094, doi1023071484276, doi1023071484577, doi102973dsdpproc141141972, doi102973dsdpproc431171979, doi103929ethza000086603, openalexw1505582348, openalexw2270089487, openalexw2722196962, openalexw2725455224"
}

@article{doi1010160377839876900050,
    author = "Honjo, Susumu",
    title = "Coccoliths: Production, transportation and sedimentation",
    year = "1976",
    journal = "Marine Micropaleontology",
    url = "https://doi.org/10.1016/0377-8398(76)90005-0",
    doi = "10.1016/0377-8398(76)90005-0",
    openalex = "W2036323089",
    references = "doi1010160011747167900654, doi1010160011747173900594, doi101016001282527290102x, doi101111j216409471970tb02746x, doi101126science15437561542, doi102307201400, doi104319lo19731840534, doi104319lo19741960881, openalexw100537358, openalexw2913708518"
}

In this preliminary biometric study of the calcareous nannofossil species Chiasmolithus expansus, Chiasmolithus oamaruensis, and Chiasmolithus altus from the upper middle Eocene to lower Oligocene of Sites 647 and 748, we document a complete gradation of forms among all three species. Chiasmolithus oamaruensis has significantly higher morphologic variance than the other species. The Chiasmolithus population at each site changes from C. expansus to C. oamaruensis and then to C. altus. This may not reflect a true evolutionary sequence because a major reversal in shape change of the central cross-bar structure accompanies this sequence, and because C. altus is morphologically closer to C. expansus than it is to C. oamaruensis. The change in the width of the cross-bar structure is primarily a result of changes in the alignment of the central connecting bar, rather than of changes in the cross-bar angle. At Site 748, two fluctuations in morphology produce sample populations intermediate between all three species. In addition, reported stratigraphic and paleogeographic occurrences of C. oamaruensis and C. altus show different latitudinal distributions. These morphological and distributional patterns may be explained by a continuous morphologic gradient between C. oamaruensis and C. altus, with C. oamaruensis occurring more commonly in cool-water paleoenvironments, and C. altus occurring more commonly in cold-water paleoenvironments. Thus, paleoenvironmental fluctuations at Site 748 may be the cause of the morphologic fluctuations in Chiasmolithus. This hypothesis can be tested against previously proposed evolutionary models by more detailed sampling of sections along a latitudinal transect.

@article{doi102973odpprocsr1201571992,
    author = "Firth, John V. and Wise, S.W. Jr.",
    title = "A Preliminary Study of the Evolution of Chiasmolithus in the Middle Eocene to Oligocene of Sites 647 and 748",
    year = "1992",
    abstract = "In this preliminary biometric study of the calcareous nannofossil species Chiasmolithus expansus, Chiasmolithus oamaruensis, and Chiasmolithus altus from the upper middle Eocene to lower Oligocene of Sites 647 and 748, we document a complete gradation of forms among all three species. Chiasmolithus oamaruensis has significantly higher morphologic variance than the other species. The Chiasmolithus population at each site changes from C. expansus to C. oamaruensis and then to C. altus. This may not reflect a true evolutionary sequence because a major reversal in shape change of the central cross-bar structure accompanies this sequence, and because C. altus is morphologically closer to C. expansus than it is to C. oamaruensis. The change in the width of the cross-bar structure is primarily a result of changes in the alignment of the central connecting bar, rather than of changes in the cross-bar angle. At Site 748, two fluctuations in morphology produce sample populations intermediate between all three species. In addition, reported stratigraphic and paleogeographic occurrences of C. oamaruensis and C. altus show different latitudinal distributions. These morphological and distributional patterns may be explained by a continuous morphologic gradient between C. oamaruensis and C. altus, with C. oamaruensis occurring more commonly in cool-water paleoenvironments, and C. altus occurring more commonly in cold-water paleoenvironments. Thus, paleoenvironmental fluctuations at Site 748 may be the cause of the morphologic fluctuations in Chiasmolithus. This hypothesis can be tested against previously proposed evolutionary models by more detailed sampling of sections along a latitudinal transect.",
    url = "https://doi.org/10.2973/odp.proc.sr.120.157.1992",
    doi = "10.2973/odp.proc.sr.120.157.1992",
    openalex = "W2186724448",
    references = "doi101016003101828690009x, doi1010160377839889900340, doi101144gslmem19850100115, doi1023071484276, doi102973dsdpproc431171979, doi102973dsdpproc801171985, doi102973odpprocsr1051471989, doi102973odpprocsr1191651991, openalexw1523529762, openalexw2725455224"
}

@article{bralower1996morphometrics,
    author = "Bralower, Timothy J. and Parrow, Matthew",
    title = "Morphometrics of the Paleocene Coccolith Genera Cruciplacolithus, Chiasmolithus and Sullivania: a Complex Evolutionary History",
    year = "1996",
    journal = "The Paleontological Society Special Publications",
    url = "https://doi.org/10.1017/s2475262200000459",
    doi = "10.1017/s2475262200000459",
    openalex = "W4251350497",
    pages = "43-43",
    volume = "8"
}

@article{doi101016s037783989600028x,
    author = "Bollmann, Jörg",
    title = "Morphology and biogeography of Gephyrocapsa coccoliths in Holocene sediments",
    year = "1997",
    journal = "Marine Micropaleontology",
    url = "https://doi.org/10.1016/s0377-8398(96)00028-x",
    doi = "10.1016/s0377-8398(96)00028-x",
    openalex = "W1990111902",
    references = "doi1010160011747167900654, doi1010160011747173900594, doi1010160012825272900384, doi101016001282529190035e, doi101029eo064i049p0096202, doi101111j216409471970tb02746x, doi101126science19142321131, doi1011300091761319775400gsolqc20co2, openalexw1505582348, openalexw1532540194, openalexw1593551441, openalexw653466241"
}

coccoliths, biomineralization, calcite, AFM, SPM, crystal morphology, function

@article{doi1021130540189,
    author = "Young, J. R.",
    title = "Biomineralization Within Vesicles: The Calcite of Coccoliths",
    year = "2003",
    journal = "Reviews in Mineralogy and Geochemistry",
    abstract = "coccoliths, biomineralization, calcite, AFM, SPM, crystal morphology, function",
    url = "https://doi.org/10.2113/0540189",
    doi = "10.2113/0540189",
    openalex = "W2057382012",
    references = "doi101006jsbi19994132, doi1010079783662062784, doi1010079789401149020, doi101016092181819390061r, doi101016s0016703799002392, doi101038365499a0, doi101073pnas1132069100, doi101093oxfordjournalsmolbeva026092, doi102216i003188844065031, doi105860choice330923"
}

Botryosphaeria is a species-rich genus with a cosmopolitan distribution, commonly associated with dieback and cankers of woody plants. As many as 18 anamorph genera have been associated with Botryosphaeria, most of which have been reduced to synonymy under Diplodia (conidia mostly ovoid, pigmented, thick-walled), or Fusicoccum (conidia mostly fusoid, hyaline, thin-walled). However, there are numerous conidial anamorphs having morphological characteristics intermediate between Diplodia and Fusicoccum, and there are several records of species outside the Botryosphaeriaceae that have anamorphs apparently typical of Botryosphaeria s.str. Recent studies have also linked Botryosphaeria to species with pigmented, septate ascospores, and Dothiorella anamorphs, or Fusicoccum anamorphs with Dichomera synanamorphs. The aim of this study was to employ DNA sequence data of the 28S rDNA to resolve apparent lineages within the Botryosphaeriaceae. From these data, 12 clades are recognised. Two of these lineages clustered outside the Botryosphaeriaceae, namely Diplodia-like anamorphs occurring on maize, which are best accommodated in Stenocarpella (Diaporthales), as well as an unresolved clade including species of Camarosporium/Microdiplodia. We recognise 10 lineages within the Botryosphaeriaceae, including an unresolved clade (Diplodia/Lasiodiplodia/Tiarosporella), Botryosphaeria s.str. (Fusicoccum anamorphs), Macrophomina, Neoscytalidium gen. nov., Dothidotthia (Dothiorella anamorphs), Neofusicoccum gen. nov. (Botryosphaeria-like teleomorphs, Dichomera-like synanamorphs), Pseudofusicoccum gen. nov., Saccharata (Fusicoccum- and Diplodia-like synanamorphs), "Botryosphaeria" quercuum (Diplodia-like anamorph), and Guignardia (Phyllosticta anamorphs). Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known. The taxonomy of some clades and isolates (e.g. B. mamane) remains unresolved due to the absence of ex-type cultures.

@article{doi103114sim551235,
    author = "Crous, P.W. and Slippers, Bernard and Wingfield, Michael J. and Rheeder, John P. and Marasas, Walter F. O. and Philips, Alan J L and Alves, Artur and Burgess, Treena I. and Barber, P.A. and Groenewald, J.Z.",
    title = "Phylogenetic lineages in the Botryosphaeriaceae",
    year = "2006",
    journal = "Studies in Mycology",
    abstract = {Botryosphaeria is a species-rich genus with a cosmopolitan distribution, commonly associated with dieback and cankers of woody plants. As many as 18 anamorph genera have been associated with Botryosphaeria, most of which have been reduced to synonymy under Diplodia (conidia mostly ovoid, pigmented, thick-walled), or Fusicoccum (conidia mostly fusoid, hyaline, thin-walled). However, there are numerous conidial anamorphs having morphological characteristics intermediate between Diplodia and Fusicoccum, and there are several records of species outside the Botryosphaeriaceae that have anamorphs apparently typical of Botryosphaeria s.str. Recent studies have also linked Botryosphaeria to species with pigmented, septate ascospores, and Dothiorella anamorphs, or Fusicoccum anamorphs with Dichomera synanamorphs. The aim of this study was to employ DNA sequence data of the 28S rDNA to resolve apparent lineages within the Botryosphaeriaceae. From these data, 12 clades are recognised. Two of these lineages clustered outside the Botryosphaeriaceae, namely Diplodia-like anamorphs occurring on maize, which are best accommodated in Stenocarpella (Diaporthales), as well as an unresolved clade including species of Camarosporium/Microdiplodia. We recognise 10 lineages within the Botryosphaeriaceae, including an unresolved clade (Diplodia/Lasiodiplodia/Tiarosporella), Botryosphaeria s.str. (Fusicoccum anamorphs), Macrophomina, Neoscytalidium gen. nov., Dothidotthia (Dothiorella anamorphs), Neofusicoccum gen. nov. (Botryosphaeria-like teleomorphs, Dichomera-like synanamorphs), Pseudofusicoccum gen. nov., Saccharata (Fusicoccum- and Diplodia-like synanamorphs), "Botryosphaeria" quercuum (Diplodia-like anamorph), and Guignardia (Phyllosticta anamorphs). Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known. The taxonomy of some clades and isolates (e.g. B. mamane) remains unresolved due to the absence of ex-type cultures.},
    url = "https://doi.org/10.3114/sim.55.1.235",
    doi = "10.3114/sim.55.1.235",
    openalex = "W2156957853",
    references = "doi101128jb1728423842461990, openalexw2733548038"
}

@article{crous2013phylogenetic,
    author = "Crous, P.W. and Braun, U. and Hunter, G.C. and Wingfield, M.J. and Verkley, G.J.M. and Shin, H.-D. and Nakashima, C. and Groenewald, J.Z.",
    title = "Phylogenetic lineages in Pseudocercospora",
    year = "2013",
    journal = "Studies in Mycology",
    url = "https://doi.org/10.3114/sim0005",
    doi = "10.3114/sim0005",
    openalex = "W2093219539",
    pages = "37-114",
    volume = "75",
    references = "doi1010160968000490902527, doi101016b9780123721808500421, doi101073pnas1117018109, doi101093bioinformaticsbtg180, doi101093molbevmsm092, doi101093nargki198, doi101093sysbio422182, doi101128jb1728423842461990, doi1023072992540, doi105860choice392183"
}

The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1- α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including Diaporthe alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are designated for D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA- lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.

@article{doi101007s1322501402972,
    author = "Udayanga, Dhanushka and Castlebury, Lisa A. and Rossman, Amy Y. and Chukeatirote, Ekachai and Hyde, Kevin D.",
    title = "Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex",
    year = "2014",
    journal = "Fungal Diversity",
    abstract = "The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1- α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including Diaporthe alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are designated for D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA- lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.",
    url = "https://doi.org/10.1007/s13225-014-0297-2",
    doi = "10.1007/s13225-014-0297-2",
    openalex = "W2001517763",
    references = "doi103114sim0012"
}

@misc{crossref2018review,
    title = {Review of: A refinement of coccolith separation methods: Measuring the sinking characters of coccoliths"},
    year = "2018",
    url = "https://doi.org/10.5194/bg-2018-82-rc2",
    doi = "10.5194/bg-2018-82-rc2",
    openalex = "W4234196604"
}

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

@article{doi101007s13225019004292,
    author = "Hyde, Kevin D. and Tennakoon, Danushka S. and Jeewon, Rajesh and Bhat, D. Jayarama and Maharachchikumbura, Sajeewa S. N. and Rossi, Walter and Leonardi, Marco and Lee, Hyang Burm and Mun, Hye Yeon and Houbraken, Jos and Nguyen, Thuong T. T. and Jeon, Sun Jeong and Frisvad, Jens C. and Wanasinghe, Dhanushka N. and Lücking, Robert and Aptroot, André and Cáceres, Marcela E. S. and Karunarathna, Samantha C. and Hongsanan, Sinang and Phookamsak, Rungtiwa and de Silva, Nimali I. and Thambugala, Kasun M. and Jayawardena, Ruvishika S. and Senanayake, Indunil C. and Boonmee, Saranyaphat and Chen, Jie and Luo, Zong-Long and Phukhamsakda, Chayanard and Pereira, Olinto Liparini and de Abreu, Vanessa Pereira and Rosado, André Wilson Campos and Bart, Buyck and Randrianjohany, Émile and Hofstetter, Valérie and Gibertoni, Tatiana Baptista and Soares, A.M. and Plautz, Helio Longoni and Sotão, Helen Maria Pontes and Xavier, William Kalhy Silva and Bezerra, Jadson Diogo Pereira and de Oliveira, Thays Gabrielle Lins and de Souza‐Motta, Cristina Maria and Magalhães, Oliane Maria Correia and Bundhun, Digvijayini and Harishchandra, Dulanjalee and Manawasinghe, Ishara S. and Dong, Wei and Zhang, Shengnan and Bao, Dan-Feng and Samarakoon, Milan C. and Pem, Dhandevi and Karunarathna, Anuruddha and Lin, Chuan-Gen and Yang, Jing and Perera, Rekhani H. and Kumar, Vinit and Huang, Shi-Ke and Dayarathne, Monika C. and Ekanayaka, Anusha H. and Jayasiri, Subashini C. and Xiao, Yuan-Pin and Konta, Sirinapa and Niskanen, Tuula and Liimatainen, Kare and Dai, Yu-Cheng and Ji, Xiao-Hong and Tian, Xue-Mei and Mešić, Armin and Singh, Sanjay K. and Phutthacharoen, Kunthida and Cai, Lei and Sorvongxay, Touny and Thiyagaraja, Vinodhini and Norphanphoun, Chada and Chaiwan, Napalai and Lu, Yong‐Zhong and Jiang, Hong-Bo and Zhang, Jin-Feng and Abeywickrama, Pranami D. and Aluthmuhandiram, Janith V. S. and Brahmanage, Rashika S. and Zeng, Ming and Chethana, K. W. Thilini and Wei, De-Ping and Réblová, Martina and Fournier, Jacques and Nekvindová, Jana and do Nascimento Barbosa, Renan and dos Santos, José Ewerton Felinto and de Oliveira, Neiva Tinti and Li, Guojie and Ertz, Damien and Shang, Qiu-Ju and Phillips, Alan J. L. and KUO, CHANG-HSIN and Camporesi, Erio and Bulgakov, Timur S. and Lumyong, Saisamorn and Jones, E. B. Gareth and Chomnunti, Putarak",
    title = "Fungal diversity notes 1036–1150: taxonomic and phylogenetic contributions on genera and species of fungal taxa",
    year = "2019",
    journal = "Fungal Diversity",
    abstract = "This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.",
    url = "https://doi.org/10.1007/s13225-019-00429-2",
    doi = "10.1007/s13225-019-00429-2",
    openalex = "W2953029298",
    references = "doi101007s1322501703860"
}

Marine phytoplankton form functional biominerals with intricate morphologies and architectures. Coccolithophores occupy a special position among these organisms because of their production of intricate calcite scales, called coccoliths. Although coccolith morphologies differ across different species, crystals are organized around an organic matrix systematically to form an arrangement of astounding symmetry. We demonstrate the opportunities emerging from four-dimensional scanning transmission electron microscopy (4D-STEM), to spatially solve the crystallography of such biominerals. Through the development of a computational pipeline, which automatically solves the orientation at image pixels corresponding to crystals, we can map the orientation of the entangled and overlapping crystalline building blocks composing the coccolith. The present work exemplifies how parallel real space and diffraction space recordings can facilitate and improve the throughput of deciphering the complex network of biomineral superstructures.

@article{doi101093mamozaf087,
    author = "Leghziel, Rebecca C and Addadi, Lia and Gal, Assaf and Houben, Lothar",
    title = "Solving the Crystal Architecture of Coccoliths Using 4D-STEM.",
    year = "2025",
    journal = "Microscopy and microanalysis: the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada",
    abstract = "Marine phytoplankton form functional biominerals with intricate morphologies and architectures. Coccolithophores occupy a special position among these organisms because of their production of intricate calcite scales, called coccoliths. Although coccolith morphologies differ across different species, crystals are organized around an organic matrix systematically to form an arrangement of astounding symmetry. We demonstrate the opportunities emerging from four-dimensional scanning transmission electron microscopy (4D-STEM), to spatially solve the crystallography of such biominerals. Through the development of a computational pipeline, which automatically solves the orientation at image pixels corresponding to crystals, we can map the orientation of the entangled and overlapping crystalline building blocks composing the coccolith. The present work exemplifies how parallel real space and diffraction space recordings can facilitate and improve the throughput of deciphering the complex network of biomineral superstructures.",
    url = "https://pubmed.ncbi.nlm.nih.gov/41056096/",
    doi = "10.1093/mam/ozaf087",
    openalex = "W4414912265",
    pmid = "41056096",
    references = "doi101006jcis19960217, doi101006jsbi19994132, doi101016jactbio201405024, doi101017s1431927619000497, doi101017s1431927621000477, doi101038356516a0, doi101093icb244893, doi101093oso97801950497700010001, doi1021130540189, openalexw92296177"
}

Coccoliths are multicrystalline calcite structures formed by microalgae within an intracellular vesicle. The morphology of each crystal is complex, and recent studies postulate that coccolith morphogenesis is regulated by the bounding membrane of its vesicle. However, the limited information about the native-state organization within the cell makes it difficult to understand which structural aspects of the membrane are responsible for morphogenesis. Here, we examined the vesicular environment during the formation of Calcidiscus leptoporus coccoliths, using advanced cryo-electron microscopy and X-ray fluorescence tomography. Our findings show two distinct types of crystal surfaces that persist during coccolith development: flat and curved, which differ also in roughness. Interestingly, even though both types of surfaces have variable degrees of membrane confinement, they are separated by distinct "bands" of intimate contact between the crystals and the membrane. We propose that these "bands" serve as boundaries, creating subcompartments within the coccolith vesicle that regulate crystal growth and its cessation. These results suggest that the coccolith vesicle membrane maintains distinct and functional chemical environments on the nanometer scale.

@article{doi101021jacs6c02151,
    author = "Avrahami, Emanuel M and Karpov, Dmitry and Aram, Lior and Elad, Nadav and Safadi, Razi and Rosenhek-Goldian, Irit and Sui, Xiao-Meng and de Haan, Diede and Varsano, Neta and Cohen, Sidney R and Zlotnikov, Igor and Gal, Assaf",
    title = "Spatial Relations between Coccoliths and Their Confining Membrane During Crystal Morphogenesis.",
    year = "2026",
    journal = "Journal of the American Chemical Society",
    abstract = {Coccoliths are multicrystalline calcite structures formed by microalgae within an intracellular vesicle. The morphology of each crystal is complex, and recent studies postulate that coccolith morphogenesis is regulated by the bounding membrane of its vesicle. However, the limited information about the native-state organization within the cell makes it difficult to understand which structural aspects of the membrane are responsible for morphogenesis. Here, we examined the vesicular environment during the formation of Calcidiscus leptoporus coccoliths, using advanced cryo-electron microscopy and X-ray fluorescence tomography. Our findings show two distinct types of crystal surfaces that persist during coccolith development: flat and curved, which differ also in roughness. Interestingly, even though both types of surfaces have variable degrees of membrane confinement, they are separated by distinct "bands" of intimate contact between the crystals and the membrane. We propose that these "bands" serve as boundaries, creating subcompartments within the coccolith vesicle that regulate crystal growth and its cessation. These results suggest that the coccolith vesicle membrane maintains distinct and functional chemical environments on the nanometer scale.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC13067266/",
    doi = "10.1021/jacs.6c02151",
    openalex = "W7140159870",
    pmcid = "PMC13067266",
    pmid = "41875313",
    references = "doi101006jsbi19994132, doi101021ie800900f, doi101038356516a0, doi101038nature04382, doi101038nature14365, doi101073pnas1118120109, doi10108800344885684r03, doi101146annurevmarine122414034032, doi1021130540189, doi102216i003188844065031"
}

UNLABELLED: Coccoliths are individual plates of calcium carbonate that comprise the shells of marine calcifying haptophyte algae. Their remains provide an excellent sedimentary archive for the reconstruction of past environmental parameters. Using nano-scale secondary ion mass spectrometry (NanoSIMS), we measured the Mg, Sr, Na and K contents in individual coccoliths of Emiliania huxleyi, now named Gephyrocapsa huxleyi, to explore their potential as a paleoproxy. For recent environmental samples from the Mediterranean and Black Sea as well as cultured specimens, all elements appeared to be homogeneously distributed within, but highly variable among, the individual coccoliths. Mg/Ca and Sr/Ca ratios covered a range of 0.06–83 mmol mol−1 and 1.9–3.8 mmol mol−1, respectively, and were in line with the previously determined values. Na/Ca ranged between 1.6–186 mmol mol−1. K/Ca could not be calibrated, but the measured 39K+/44Ca+ ion count ratios varied between 0.03–2.7. Although the Na/Ca ratios significantly decreased with increasing total alkalinity and salinity in the Mediterranean samples, these trends were not observed in samples collected from cultures where the alkalinity and salinity varied separately. Similarly, K/Ca ratios showed no clear trends with total alkalinity or salinity of the culture medium. Calcification in coccolithophores is biologically controlled and this may mask the impact of environmental factors on the observed variation in the Na and K content of individual coccoliths of E. huxleyi. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40623-2.

@article{doi101038s41598026406232,
    author = "Roepert, Anne and Middelburg, Jack J and Weiss, Gabriella M and van der Meer, Marcel T J and Polerecky, Lubos",
    title = "Sodium and potassium analysis of individual coccoliths by secondary ion mass spectrometry.",
    year = "2026",
    journal = "Scientific reports",
    abstract = "UNLABELLED: Coccoliths are individual plates of calcium carbonate that comprise the shells of marine calcifying haptophyte algae. Their remains provide an excellent sedimentary archive for the reconstruction of past environmental parameters. Using nano-scale secondary ion mass spectrometry (NanoSIMS), we measured the Mg, Sr, Na and K contents in individual coccoliths of Emiliania huxleyi, now named Gephyrocapsa huxleyi, to explore their potential as a paleoproxy. For recent environmental samples from the Mediterranean and Black Sea as well as cultured specimens, all elements appeared to be homogeneously distributed within, but highly variable among, the individual coccoliths. Mg/Ca and Sr/Ca ratios covered a range of 0.06–83 mmol mol−1 and 1.9–3.8 mmol mol−1, respectively, and were in line with the previously determined values. Na/Ca ranged between 1.6–186 mmol mol−1. K/Ca could not be calibrated, but the measured 39K+/44Ca+ ion count ratios varied between 0.03–2.7. Although the Na/Ca ratios significantly decreased with increasing total alkalinity and salinity in the Mediterranean samples, these trends were not observed in samples collected from cultures where the alkalinity and salinity varied separately. Similarly, K/Ca ratios showed no clear trends with total alkalinity or salinity of the culture medium. Calcification in coccolithophores is biologically controlled and this may mask the impact of environmental factors on the observed variation in the Na and K content of individual coccoliths of E. huxleyi. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40623-2.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC13048990/",
    doi = "10.1038/s41598-026-40623-2",
    openalex = "W7132837306",
    pmcid = "PMC13048990",
    pmid = "41764317",
    references = "doi10100797836620627845, doi101016007919467990106x, doi101016s0016703798000970, doi101038320129a0, doi101038330367a0, doi101038347462a0, doi101038nature10295, doi101111j152988171987tb04217x, doi101126sciadv1501822, doi101126science1110063"
}

@misc{crossrefNonetable,
    title = "Table 6: Spotted hyena densities recorded in the literature.",
    year = "None",
    url = "https://doi.org/10.7717/peerj.12307/table-6",
    doi = "10.7717/peerj.12307/table-6"
}