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Supplementary material 3 from: Trujano-Ortega M, García-Vázquez UO, Callaghan CJ, Ávalos-Hernández O, Luis-Martínez MA, Llorente-Bousquets JE (2018) Two new genera of metalmark butterflies of North and Central America (Lepidoptera, Riodinidae). ZooKeys 729: 61-85. https://doi.org/10.3897/zookeys.729.20179

Maximum likelihood tree of the relationships among Apodemia and selected species in the Riodinidae inferred with Cytochrome Oxidase I (COI). Numbers near branch nodes are bootstrap branch support : Explanation note: Tree infered with Cytochrome Oxidase I gene.

Supplementary material 1 from: Doorenweerd C, Leblanc L, Norrbom AL, Jose MS, Rubinoff D (2018) A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera, Tephritidae). ZooKeys 730: 19-56. https://doi.org/10.3897/zookeys.730.21786

A global checklist of the 932 fruit fly species in the tribe Dacini (Diptera: Tephritidae), spreadsheet table. :

Supplementary material 3 from: Brix S, Lorz A-N, Jazdzewska AM, Hughes L, Tandberg AHS, Pabis K, Stransky B, Krapp-Schickel T, Sorbe JC, Hendrycks E, Vader W, Frutos I, Horton T, Jazdzewski K, Peart R, Beermann J, Coleman CO, Buhl-Mortensen L, Corbari L, Havermans C, Tato R, Campean AJ (2018) Amphipod family distributions around Iceland. In: Brix S, Lorz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 1-53. https://doi.org/10.3897/zookeys.731.19854

Supplementary material 3 from: Brix S, Lorz A-N, Jazdzewska AM, Hughes L, Tandberg AHS, Pabis K, Stransky B, Krapp-Schickel T, Sorbe JC, Hendrycks E, Vader W, Frutos I, Horton T, Jazdzewski K, Peart R, Beermann J, Coleman CO, Buhl-Mortensen L, Corbari L, Havermans C, Tato R, Campean AJ (2018) Amphipod family distributions around Iceland. In: Brix S, Lorz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 1-53. https://doi.org/10.3897/zookeys.731.19854

Supplementary material 1 from: Brix S, Lorz A-N, Jazdzewska AM, Hughes L, Tandberg AHS, Pabis K, Stransky B, Krapp-Schickel T, Sorbe JC, Hendrycks E, Vader W, Frutos I, Horton T, Jazdzewski K, Peart R, Beermann J, Coleman CO, Buhl-Mortensen L, Corbari L, Havermans C, Tato R, Campean AJ (2018) Amphipod family distributions around Iceland. In: Brix S, Lorz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 1-53. https://doi.org/10.3897/zookeys.731.19854

Table 1. Samples used for present study. : Explanation note: Stations are organised according to the percentage of amphipods identified to the family level. Only the stations marked in green were used for primer analysis, while all were the basis for map preparation. Amphipod taxa are presented from the most to the least abundant in all samples.

Supplementary material 2 from: Trujano-Ortega M, García-Vázquez UO, Callaghan CJ, Ávalos-Hernández O, Luis-Martínez MA, Llorente-Bousquets JE (2018) Two new genera of metalmark butterflies of North and Central America (Lepidoptera, Riodinidae). ZooKeys 729: 61-85. https://doi.org/10.3897/zookeys.729.20179

Collection and voucher data for Riodinids genetic samples used in this study : Explanation note: Voucher data and GenBank accession numbers of samples used in the molecular analyses. The table is arranged alphabetically by species name and voucher number.

Supplementary material 2 from: van Nieukerken EJ, Lees DC, Doorenweerd C, Koster S(JC), Bryner R, Schreurs A, Timmermans MJTN, Sattler K (2018) Two European Cornus L. feeding leafmining moths, Antispila petryi Martini, 1899, sp. rev. and A. treitschkiella (Fischer von Röslerstamm, 1843) (Lepidoptera, Heliozelidae): an unjustified synonymy and overlooked range expansion. Nota Lepidopterologica 41(1): 39-86. https://doi.org/10.3897/nl.41.22264

Figure S1. Cornus species, details of leaf underside. a C. sanguinea subsp. sanguinea, fresh leaf, Netherlands, Leiden, 26.ix.2017. b C. sanguinea subsp. australis, dried leaf, Greece, RMNH.INS.41827. c C. mas, fresh leaf, Netherlands, Leiden, 26.ix.2017. d C. sericea, dried leaf, Netherlands, RMNH.INS.41493. e C. officinalis, dried leaf, UK, Wisley 1996, Wisley herbarium. Figure S2. NJ tree of barcodes, from BOLD. : Explanation note: Tree topology for the phylogenetic hypothesis adopted, to be used as input in applications reading nexus (requires some slight previous edition).

Supplementary material 1 from: Lörz A-N, Tandberg AHS, Willassen E, Driskell A (2018) Rhachotropis (Eusiroidea, Amphipoda) from the North East Atlantic. In: Brix S, Lörz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 75–101. https://doi.org/10.3897/zookeys.731.19814

Table S1. Extended overview of all samples used in analyses with geographical and environmental details : Explanation note: Depths indicated in red have been found using the latitude and longitude information with the datapoint and the bathymetry-layer on Google Earth Pro. Depths indicated in blue are inferred from the general depths in the named (no latitude or longitude given) geographical location, given bathymetry-layer on Google Earth Pro.

Supplementary material 4 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

OTU ID, taxonomy of identified species, BOLD Bin, sequence abundancies per site an time and OTU sequences

Supplementary material 3 from: Theissinger K, Kästel A, Elbrecht V, Makkonen J, Michiels S, Schmidt S, Allgeier S, Leese F, Brühl C (2018) Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. Metabarcoding and Metagenomics 2: e21060. https://doi.org/10.3897/mbmg.2.21060

We pooled the library according to the number of specimens per sample and could show that our read abundance highly correlates with specimen abundance. Thus, we could use the read abundancies as surrogates for relative species abundancies.

Supplementary material 1 from: Studer A, Cardoso de Sousa M, Barcena Goyena B (2018) Breeding biology and nest success of Short-tailed Antthrush Chamaeza campanisona (Aves: Formicariidae) in the Atlantic rainforest of northeastern Brazil. Zoologia 35: 1-8. https://doi.org/10.3897/zoologia.35.e12906

Nests of Chamaeza campanisona found during the study period (1986–2016) with their respective characteristics : Data type: species data

Supplementary material 1 from: Jażdżewska AM, Corbari L, Driskell A, Frutos I, Havermans C, Hendrycks E, Hughes L, Lörz A-N, Stransky B, Tandberg AHS, Vader W, Brix S (2018) A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies. In: Brix S, Lörz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 55–73. https://doi.org/10.3897/zookeys.731.19931

Table S1 : Explanation note: Amphipod and outgroup accession numbers in BOLD, GenBank and station data.

Supplementary material 4 from: Lörz A-N, Tandberg AHS, Willassen E, Driskell A (2018) Rhachotropis (Eusiroidea, Amphipoda) from the North East Atlantic. In: Brix S, Lörz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 75–101. https://doi.org/10.3897/zookeys.731.19814

Figure S2. Bayesian consensus tree from COI sequences. Numbers on branches are posterior probabilities. See text for further information. :

Supplementary material 1 from: Unterweger PA, Klammer J, Unger M, Betz O (2018) Insect hibernation on urban green land: a winter-adapted mowing regime as a management tool for insect conservation. BioRisk 13: 1-29. https://doi.org/10.3897/biorisk.13.22316

Table with all captured species / morphotypes sorted by order, family and species / morphotype. : Explanation note: Collection: University of Tübingen, Evolutionary Biology of Invertebrates, Auf der Morgenstelle 28, 72076 Tübingen, Germany. Individuals with scientific species name that were checked by a taxonomic expert were counted as taxonomic species (s); all the other determinations were counted as morphotypes (m). Morphotypes are defined by the lowest practical taxonomic level (e.g. Hanula et al. 2009; Kutschbach-Brohl et al. 2010). In some cases, the family or the morphometric body length (in mm, numbers in column C, Mini: smaller than 1 mm) was counted as a morphotype (Daly 1985). In cases for which the determination was not validated by a taxonomic expert, our species determination was checked for plausibility in terms of its geographical occurrence via the Entomofauna Germanica (http://www.colkat.de, 2017.11.06). Alternatively (if no taxonomic name could be found), a classification letter / number was assigned for a morphotype. The provided author name refers to the lowest practical taxonomic level (e.g. Hanula et al. 2009; Kutschbach-Brohl et al. 2010). Validation: name of scientific expert who checked the taxonomic determination. Management type of meadow in autumn: mown /unmown. Plant compartment: flower head, stem, tuft, leaves. All numbers represent total sums of all sample sites over the entire study period. Brown-labelled species names are thought to have hibernated in the soil. Green-labelled species names could only be found in flower heads and stems. Black-labelled species occurred in all plant compartments without any preference for a specific plant compartment.

Supplementary material 1 from: Guimarães EC, Brito PS De, Ferreira BRA, Ottoni FFE (2018) A new species of Charax (Ostariophysi, Characiformes, Characidae) from northeastern Brazil. Zoosystematics and Evolution 94(1): 83-93. https://doi.org/10.3897/zse.94.22106

Distribution of Charax awa sp.n., C. leticiae, C. pauciradiatus, and C. niger : Explanation note: Information of this map was based on our examined material and data provided by Menezes and Lucena (2014).

FIGURE 4 in Identification of type materials of the species of Protypotherium Ameghino, 1885 and Patriarchus Ameghino, 1889 (Notoungulata: Interatheriidae) erected by Florentino Ameghino

FIGURE 4. Patriarchus leptocephalus, holotype MACN-A 3989, incomplete skull, in ventral (A) and dorsal (B) views. Patriarchus altus, holotype MACN-A 4001, incomplete skull, in ventral (C) and dorsal (D) views. Patriarchus icochiloides, holotype MACN-A 4021, right maxillary fragment with alveolus of P1 and P2–M3, in occlusal view (E); holotype MACN-A 4022, right mandibular fragment with alveoli of p2–3 and p4–m3, in occlusal view (F). Scale bar = 10 mm.

FIGURE 3 in Identification of type materials of the species of Protypotherium Ameghino, 1885 and Patriarchus Ameghino, 1889 (Notoungulata: Interatheriidae) erected by Florentino Ameghino

FIGURE 3. Patriarchus palmidens, holotype MACN-A 9651a, mandibular symphysis with right i1–p1 and left i1–2 and the alveolus of i3, in labial (A), occlusal (B) and antero-labial (C) views; reproductions of figures 2 (D), 2a (E) and 2b (F) from Ameghino (1889, plate 15). Patriarchus furculosus, syntype MACN-A 3970, left maxillary fragment with P2–M3, in occlusal view (G); syntype MACN-A 3972, right mandibular fragment with p2–m3, in occlusal view (H); syntype MACN-A 3977, incomplete skull, dorsal view (I). Patriarchus distortus, holotype MACN-A 9634 to MACN-A 9638: MACN-A 9634, skull, ventral (J) and dorsal (K) views; MACN-A 9636, proximal epiphysis of right femur, in anterior view (L); MACN-A 9637 and MACN-A 9638, proximal epiphyses of right tibia and fibula, articulated with the distal epiphysis of right femur, in lateral view (M). Patriarchus rectus, holotype MACN-A 4005, right maxillary fragment (vertically rotated) with alveolus of C and series P1–M3, in occlusal view (N); holotype MACN-A 4006, left maxillary fragment (vertically rotated) with M1–3, in occlusal view (O); holotype MACN-A 4007, mandibular fragment with incomplete symphysis, broken alveoli of left and right i1-2 and complete left i3–m3 series, in occlusal view (P). Patriarchus diastematus, holotype MACN-A 4044, two maxillae with alveoli of C–P1 and right P2–M3 and left P2–M2, in occlusal view (Q). Scale bar = 10 mm.

FIGURE 2 in Identification of type materials of the species of Protypotherium Ameghino, 1885 and Patriarchus Ameghino, 1889 (Notoungulata: Interatheriidae) erected by Florentino Ameghino

FIGURE 2. Protypotherium attenuatum, syntype MACN-A 524, left maxilla with P2–M3 but lacking P1, in occlusal view (A); syntype MACN-A 628, right fragmented mandible with alveoli of i1–3 and c (broken)–m1 but lacking m2–3, in labial (B) and occlusal (C) views; reproductions of figures 21 (D), 20 (E) and 20a (F) from Ameghino (1889, plate 14). Protypotherium obstructum, holotype MACN-A 1677, lower premolar in labial, oclusal and lingual views (G); reproduction of figure 19 (H) from Ameghino (1889, plate 15). Protypotherium claudum, holotype MACN-A 551, right mandibular fragment with alveolus of p2 and p3–m2, in labial (I) and occlusal (J) views; reproductions of figures 22 (K) and 22a (L) from Ameghino (1889, plate 14). Protypotherium globosum, holotype MACN-A 4049, skull, in ventral (M) and dorsal (N) views. Protypotherium convexidens, holotype MACN-A 4054, right maxillary fragment with P3–M2 (broken), in occlusal view (O). Protypotherium diversidens, holotype MACN-A 4052, right maxillary fragment with alveolus of P1 and P2–M3, in occlusal view (P). Protypotherium compressidens, holotype MACN-A 4029, left maxillary fragment with P3–M3, in occlusal view (Q); holotype MACN-A 4030, left mandibular fragment with p4 (talonid)–m3, in occlusal view (R). Protypotherium lineare, holotype MACN-A 4039, right mandibular fragment with alveolus of p1 and p2–m1, in occlusal view (S); holotype MACN-A 4038, left mandibular fragment with p3–m2, in occlusal view (T). Scale bar = 10 mm.

FIGURE 1. Protypotherium antiquum, lectotype ZMK 21 in Identification of type materials of the species of Protypotherium Ameghino, 1885 and Patriarchus Ameghino, 1889 (Notoungulata: Interatheriidae) erected by Florentino Ameghino

FIGURE 1. Protypotherium antiquum, lectotype ZMK 21/1877, right mandibular fragment with p4-m3, in labial (A) and occlusal (B) views; reproductions of figures 1 (C) and 1a (D) from Ameghino (1889, plate 15); and MACN-A 1288, cast of lectotype, in labial (E) and occlusal (F) views. Protypotherium australe, MACN-A 1338, cast of the holotype, in occlusal view (G). Protypotherium praerutilum, holotype MACN-A 1081, incomplete skull, in ventral (H) and dorsal (I) views; holotype MACN-A 1082, incomplete mandible, in lateral (J) and occlusal (K) views; reproductions of figures 6 (L) and 6a (M) from Ameghino (1889, plate 14); reproductions of figures 7 (N) and 7a (O) from Ameghino (1889, plate 14). Scale bar = 10 mm.

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Michael P. Dunne: DPhil Thesis, Supplementary Material

ch2       1-orthogroups    (list of orthogroup members for plants and fungi)     2-passed_hits    (all accepted candidate hits as listed in Table 2.9)     3-og_categories  (all accepted hits belonging to various categories as listed in Table 2.10)   ch3     1-juncScores     (splice junction recall scores for all annotated plant and fungal transcripts)     2-covScores      (coverage scores for all annotated plant and fungal transcripts)     3-aliScore       (alignment score calculator)     4-DOGs           (FASTA alignments for all discrepant orthogroups)     5-subcell        (subcellular localisation predictions and stats for all orthogroups)   ch4     1-newGenes        (GTF and FASTA files for all newly obtained genes)   ch5     1-results         (all changed genes, with GTFs, coverage and junction scores, and AA alignments with entropy scores)