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FIGURE 4 in Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations

FIGURE 4. Labels of Neotropical Phyllocnistis types found in museums. (A) P. abatiae; (B) P. aurilinea; (C) P. baccharidis; (D) P. bourquini; (E) P. citrella; (F) P. dorcas; (G) P. drimiphaga; (H) P. helios; (I) P. jupiter; (J) P. kawakitai; (K) P. maxberryi; (L) P. meliacella; (M) P. norak; (N) P. ohshimai; (O) P. ourea; (P) P. perseafolia; (Q) P. petronellii; (R) P. phoebus; (S) P. puyehuensis; (T) P. rotans; (U) P. sciophanta; (V) P. selene; (W) P. sexangula; (X) P. tethys; (Y) P. tropaeolicola; (Z) P. wygodzinskyi; (AA) P. xylopiella.

FIGURE 2. A in Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations

FIGURE 2. A Neighbor-Joining tree of the studied taxa, based on COI barcode fragments, generated under the K2P nucleotide substitution model. Each specimen is identified by its Process ID code (see Tab. 3). Branch lengths represent the number of substitutions per site. BIN numbers from BOLD system are given in parentheses for all clusters.

FIGURE 3 in Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations

FIGURE 3. Forewings of Neotropical Phyllocnistis. (A) P. abatiae holotype (left forewing reversed); (B) P. aurilinea lectotype (left, reversed); (C) P. baccharidis holotype (left, reversed); (D) P. bourquini holotype (right); (E) P. citrella lectotype (left, reversed); (F) P. dorcas holotype (right); (G) P. drimiphaga holotype (right); (H) P. helios holotype (right); (I) P. jupiter paratype (left, reversed); (J) P. kawakitai holotype (left, reversed); (K) P. maxberryi holotype (right); (L) P. meliacella holotype (right); (M) P. norak holotype (right); (N) P. ohshimai holotype (right); (O) P. ourea paratype (right); (P) P. perseafolia holotype (left, reversed); (Q) P. petronellii paratype (right); (R) P. phoebus paratype (left, reversed); (S) P. puyehuensis holotype (right); (T) P. rotans lectotype (right); (U) P. sciophanta holotype (left, reversed); (V) P. selene specimen (left, reversed); (W) P. sexangula lectotype (left, reversed); (X) P. tethys specimen (right); (Y) P. tropaeolicola holotype (right); (Z) P. wygodzinskyi holotype (left, reversed); (AA) P. xylopiella holotype (right). Scale bars: 1 (A–H, K, L, O, P, R–Z), 0.5 mm (I, J, M, N, Q, AA).

FIGURE 6 in Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations

FIGURE 6. Genital morphology of the new species of Phyllocnistis. (A) P. helios; (B) P. jupiter; (C) P. ohshimai; (D, E, I) P. xylopiella; (G, J) P. norak; (F, K) P. kawakitai; (H) P. petronellii. (A–D) male genitalia, ventral view; (E–H) female genitalia, lateral; (I–K) detail of female signa. Scale bars: 50 (A–D), 100 (E–H), 50 µm (I–K).

opencc-by-4.0Oct 2023View details →

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

BACKGROUND: The datafiles deposited here are products of the research project "Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study"Authors: Ayşe Demirkan1,2, Jenny van Dongen3,4, Casey T. Finnicum5, Harm-Jan Westra1, Soesma Jankipersadsing1, Gonneke Willemsen3,4, Richard G. Ijzerman6, Dorret I. Boomsma3,4, Erik A. Ehli5, Marc Jan Bonder1, Jingyuan Fu,1,7 Lude Franke1, Cisca Wijmenga1, Eco J.C. de Geus3,4, Alexander Kurilshikov1, Alexandra Zhernakova11 Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands2 Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom3 Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands4 Amsterdam Public Health Research Institute, Amsterdam, the Netherlands5 Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA6 Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands7 Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the NetherlandsCorresponding Authors: Alexandra Zhernakova; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the NetherlandsAyse Demirkan; Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom.FILES: 1-merged_lld16s.Rata: Epigenome-wide association of 16s microbial abundances in LifeLines-Deep (LLD, n = 616, 450k methylation array) 2-lld_mgs.Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived taxa relative abundances (n = 683, 450k methylation array))3-lld_mgs_pathways. Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived bacterial pathway relative abundances (n = 683, 450k methylation array)FUNDING: The Lifelines initiative has been made possible by subsidy from the Dutch Ministry of Health, Welfare and Sport, the Dutch Ministry of Economic Affairs, the University Medical Center Groningen (UMCG), Groningen University and the Provinces in the North of the Netherlands (Drenthe, Friesland, Groningen). The Netherlands Twin Register acknowledges funding from the Netherlands Organization for Scientific Research (NWO): (NWO 911–09–032; NWO 480-04-004; 480-15-001/674, NWO 916-130-82), Biobanking and Biomolecular Research Infrastructure (184.033.111),  and the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), NWO Large Scale infrastructures X-Omics (184.034.019), Genotype/phenotype database for behaviour genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); the Avera Institute, Sioux Falls (USA), the European Research Council (Genetics of Mental Illness 230374), the European Research Council (Genetics of Mental Illness 230374), and INRA-Pfizer. Pfizer provided support for data collection, but did not have any additional role in the study design, data analysis, decision to publish, or preparation of the manuscript.

Supplementary material 3 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Table S1 : Explanation note: List of measurements of teliospore characters of R.evansii. Obtained values were sorted by voucher and by individual teliospores. All measurements are given in μm.

Supplementary material 4 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Table S2 : Explanation note: List of measurements of teliospore characters of R.macowaniana and R.xanthophloeae. Obtained values were sorted by voucher and by individual teliospores. All measurements are given in μm.

Supplementary material 2 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Figure S2 : Explanation note: Boxplot of measurements of the six defined teliospore characteristics of R.macowaniana and R.xanthophloeae. Values were obtained from teliospores derived from three different host species of in total 10 individual trees. The boxplots are based on mean values calculated for all investigated teliospores for each specimen, respectively.

Supplementary material 1 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090

Figure S1 : Explanation note: Boxplot of measurements of the six defined teliospore characters of R.evansii. Values were obtained from teliospores derived from seven different host species of in total 18 individual trees. The boxplots are based on mean values calculated for all investigated teliospores for each specimen, respectively.

FIGURE 13 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 13. Mines of Phyllonorycter spp. from the Russian Far East. (A–B) Ph. ringoniella, host plant Malus mandshurica; (C–D) Ph. sorbicola, Prunus padus and Prunus maackii respectively; (E) Ph. strigulatella, Alnus hirsuta; (F) Phyllonorycter sp. 1, Tilia mandshurica; (G–H) Phyllonorycter sp. 6, Acer pseudosieboldianum. Indications: (m) mine; (t) epidermal tunnel; (b) blotch. Close up: (B–C, F, H) mine. Sampling locations: (A–D, F–H) PK, Gornotaezhnoe, MTS and forest, 22–26.VII.2016; (E) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, 11–20.VII.2017.

FIGURE 15 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 15. Similarity of gracillariid faunas of the Russian regions and Japan. Gracillariid species number is given in the corresponding bar, number of shared species is in the circles. The similarity Sørensen–Dice coefficient is given in red.

FIGURE 12 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 12. Mines of Phyllonorycter spp. from the Russian Far East. (A) Ph. cretata, host plant Quercus mongolica; (B) Ph. ermani, B. platyphylla; (C) Ph. issikii, Tilia mandshurica; (D) Ph. japonica, Corylus mandshurica; (E) sampling location of Ph. junoniella; (F) Ph. nigristella, Quercus dentata; (G) Ph. orientalis, Acer pictum; (H) Ph. pastorella, Salix sp. Indications: (m) mine; (t) epidermal tunnel; (l) larva; (p) pupa. Close up: (B) deformation of the leaf due to mines (the view from the upper side); (C, F–H) mine, (E) the bush from that the specimens were collected. Sampling locations: (A–B, F) SO, Sakhalin Isl., Yuzhno- Sakhalinsk, Gagarin's Park, 11–20.VII.2017; (E) SO, Sakhalin Isl., Susunay mountain range, 14.VII.2017; (C–D, G–H) PK, Gornotaezhnoe, MTS and forest, 22–26.VII.2016.

FIGURE 8 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 8. Male genitalia of Phyllonorycter and Cameraria spp. from the Russian Far East. (A) Ph. reduncata, host plant Lonicera maackii, [23Pr-2016-male]; (B) Ph. ringoniella, Malus mandshurica, [10Prin-2016-male]; (C) Ph. similis, Quercus dentata, [8Psim-2016-male]; (D) Ph. ulmifoliella [15Pu-2016-male]; (E) Cameraria niphonica, Acer pseudosieboldianum, [1Cn-2016-male]. Sampling location: Gornotaezhnoe, Primorskii Krai, 22–26.VII.2016. Scale bars: (A–D) 200, (E) 250 µm.

FIGURE 4 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 4. Forewing pattern of Phyllonorycter spp. from the Russian Far East. (A) Ph. caraganella, host plant Caragana fruticosa, NK- 184-16-9A; (B) Ph. cavella, Betula dahurica, 111.1; (C) Ph. cretata, Quercus mongolica, NK-85-17-4; (D) Ph. issikii, T. mandshurica, NK596; (E) Ph. japonica, Corylus mandshurica, 36.2; (F) Ph. jozanae, Crataegus sp., 44.1; (G) Ph. kisoensis, Alnus hirsuta, 45.1; (H) Ph. pastorella, Salix sp., 49.1; (I) Ph. reduncata, Lonicera maackii, 55.3; (K) Ph. ringoniella, Malus mandshurica, NK-179-16-1A; (L) Ph. similis, Quercus dentata, 42.1; (M) Ph. ulmifoliella, 37.1. Sampling locations: (A) PK, Rakovka, 27.VII.2016; (B, D–M) ibidem, Gornotaezhnoe, 16.VII.2013 (D), 22-25.VII.2016 (B, E–M); (C) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, 12.VII.2017. Scale bars 1 mm.

FIGURE 3 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 3. COI Neighbor-Joining tree of Gracillariidae species sampled in the Russian Far East. Each specimen is accompanied by its sequence number (BOLD "process ID"), species name, sampling location and host plant. Sampling locations are given between two vertical lines, i.e. |Skov.| Skovorodino; |Blag.| Blagoveshchensk; |MTS| Komarov Mountain-Taiga Station FEB RAS and the forest around; |Rakovka|, |Glukhovka| forest around the villages Rakovka and Glukhovka respectively; |Vlad.| Vladivostok; |Sikhote-Alin| Sikhote-Alin Mountains, national park "Zov tigra", |Y-S| Yuzhno-Sakhalinsk and the area around including Susunay mountain range (see Fig. 1 for details). Host plants: A. pseudosieb.—Acer pseudosieboldianum; * sampling done by sweep netting from the bush, whereas all other gracillariids were collected/ reared directly from their mines. Each leafminer species is supplied with its BIN number retrieved from BOLD; blue BINs correspond to known species, red—new BINs.

FIGURE 1 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 1. The area of study in the Russian Far East, June–July 2010–2017. Black circles indicate cities, yellow circles with the numbers 1–12 are the sampling locations: (1) AO, Skovorodino, tree plantation nearby train station; (2) AO, Blagoveshchensk, Friendship park; (3) KK, Komsomolsk-na-Amure, tree lines along the road; (4) PK, Gornotaezhnoe, MTS; (5) ibidem, forest; (6) PK, Glukhovka, forest; (7) PK, Rakovka, forest; (8) PK, Vladivostok, suburb, tree plantation; (9) PK, Sikhote-Alin Mountains, national park "Zov tigra"; (10) SO, Sakhalin Isl., Yuzhno-Sakhalinsk, Botanical garden FEB RAS Sakhalin Branch; (11) ibidem, Gagarin park; (12) SO, Sakhalin Isl., Susunay mountain range, pass "Verblyud". In the left corner, on the map of Russia the sampled area is shaded in gray. Regions: (ChAO) Chukotsky Autonomous Okrug, (KamK) Kamchatskii Krai, (MA) Magadanskaya Oblast, (AO) Amurskaya Oblast, (KK) Khabarovskii Krai, (JAO) Jewish Autonomous Oblast, (AO) Amurskaya Oblast, (PK) Primorskii Krai, (SO) Sakhalinskaya Oblast (includes Sakhalin Island and Kuril Islands).

FIGURE 7 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 7. Male genitalia of Phyllonorycter spp. from the Russian Far East. (A) Phyllonorycter junoniella, genitalia slide [21-male]; (B) Ph. pastorella, host plant Salix sp., [12Pp-2016-male]; (C) Ph. populifoliella, Populus balsamifera, [NK-561- 1-male]; (D) Ph. pseudojezoniella, Acer saccharum, [20Pps-2016-male]; (E) Ph. kisoensis, Alnus hirsuta, [5Pk-2016-male]. Sampling location: (A) SO, Sakhalin Isl., 14.VII.2017; (B, D) PK, Gornotaezhnoe, MTS, 22–26.VII.2016; (C) AO, Blagoveshchensk, 27.VI.2016. Scale bars 200µm.

FIGURE 11 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 11. Mines and leaf shelters of Gracillaria, Callisto, Parornix and Phyllonorycter spp. from the Russian Far East. (A) Gracillaria sp., host plant Syringa amurensis; (B–C) Callisto sp. on Malus sp.; (D) Parornix ermolaevi, Corylus sieboldiana; (E–F) Ph. caraganella, Caragana fruticosa; (G–H) Ph. cavella, Betula platyphylla, (H) "green island" and the mine. Indications: (m) mine; (b) blotch part of the mine; (t) epidermal tunnel; (e) exit hole; (f–f2) folded leaf margin or leaf tip (the indexes 1 and 2 indicate the order of construction appearance); (g.i.) green island region. Close up: (B, E–G) mine. Sampling locations: (A–D, G–H) PK, Gornotaezhnoe, MTS and forest, 22–27.VII.2016; (E–F) ibidem, Glukhovka, forest, 27.VII.2016.

FIGURE 2 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 2. Sampling localities in the Russian Far East. (A–C) PK, Gornotaezhnoe, MTS: (A) European woody plant species zone, (B) Juglans mandshurica plantation, (C) East Asian woody plant species zone; (D) PK, 20 km west of MTS, artificial lake on the way to Glukhovka and Rakovka; (E–H) SO, Sakhalin Isl., Susunay mountain range: (E–G) pass "Verblud", sampling and camping area, (H) foothills of the Susunay mountain range, the Erman's birch groove. Personalities: (C) S. Gorokhova, (F) V. Sheiko, (H) N. Kirichenko (the photographs are published with the permission of SG, VS and NK). (PK) Primorskii Krai, (SO) Sakhalinskaya Oblast (includes Sakhalin Island and Kuril Islands).

FIGURE 9 in Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding

FIGURE 9. Number of gracillariid species found on various plant plants in the Russian Far East in 2010–2017. In some cases, the same gracillariid species were found on more than one plant genus (for example, Gracillaria sp. on Syringa and Fraxinus, Phyllonorycter pastorella on Salix and Populus etc.), therefore the sum of all bars is more than the total number of species identified in the study.