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Figure 1 from: Cordaux R, Pichon S, Ben Afia Hatira H, Doublet V, Grève P, Marcadé I, Braquart-Varnier C, Souty-Grosset C, Charfi-Cheikhrouha F, Bouchon D (2012) Widespread Wolbachia infection in terrestrial isopods and other crustaceans. ZooKeys 176: 123-131. https://doi.org/10.3897/zookeys.176.2284
Figure 1 - Phylogenetic tree of B-supergroup Wolbachia strains based on wsp sequences, using Minimum Evolution analysis. The tree is rooted with two A-supergroup Wolbachia strains. Bootstrap values inferred from 1000 replicates are shown as percentages. Strains are identified by the host species from which they were isolated. Wolbachia strains from terrestrial isopods and non terrestrial isopod crustaceans are shown in blue and red, respectively. New crustacean Wolbachia infections reported in this study are underlined. Wolbachia strains from insects are shown in black. Names assigned to groups of Wolbachia strains are shown on the right, following Cordaux et al. (2001).
Figure 1 from: Edgecombe GD, Vahtera V, Giribet G, Kaunisto P (2015) Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 65-77. https://doi.org/10.3897/zookeys.510.8573
Figure 1 - Map of Mesoamerica, the Caribbean and northern South America showing geographic distribution of Newportia specimens analyzed herein (see Table 1 for coordinates of samples).
Figure 2 from: Edgecombe GD, Vahtera V, Giribet G, Kaunisto P (2015) Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 65-77. https://doi.org/10.3897/zookeys.510.8573
Figure 2 - Strict consensus of two optimal cladograms for Newportia under parameter set 111 for parsimony (POY) analysis. Abbreviations: BRA, Brazil; COL, Colombia; CR, Costa Rica; DR, Dominican Republic; ECU, Ecuador; FRG, French Guiana; GUA, Guatemala; HON, Honduras; MEX, Mexico.
eDNA from archived leaves reveals no losses of α-diversity, but widespread community turnover and biotic homogenization as drivers of forest insect decline
<p>A major limitation of current reports on insect declines is the lack of standardized, long-term, and taxonomically broad time series. Here, we demonstrate the utility of environmental DNA from archived leaf material to characterize plant-associated arthropod communities. We base our work on several multi-decadal leaf time series from tree canopies in four land use types, which were sampled as part of a long-term environmental monitoring program across Germany. Using these highly standardized and well-preserved samples, we analyze temporal changes of diversity and relative biomass in communities of several thousand arthropod species belonging to 23 orders using multilocus metabarcoding and quantitative PCR. Our data do not support widespread declines of α-diversity or genetic diversity within species. Instead, we find a gradual community turnover, which results in temporal and spatial biotic homogenization. Colonization by novel widespread taxa and loss of range-restricted taxa cause spatial diversity loss. At the same time, increasingly similar species occurrences between consecutive sampling years cause a temporal decline of diversity. These effects are independent of land use and observed for all arthropod orders. Our results suggest that insect decline is more complex than mere α-diversity loss, but can be driven by β-diversity decay across space and time.</p>
Supplementary material 1 from: Kaltenbach T, Kluge NJ, Gattolliat J-L (2022) A widespread new genus of Baetidae (Baetidae, Ephemeroptera) from Southeast Asia. ZooKeys 1135: 1-59. https://doi.org/10.3897/zookeys.1135.93800
ML reconstruction Branchiobaetis gen. nov.
Data for Widespread seasonal speed-up of west Antarctic Peninsula glaciers from 2014-2021
<p>Data made available to support "Widespread seasonal speed-up of west Antarctic Peninsula glaciers from 2014-2021" Wallis et al. 2023 (accepted). For details, see publication.</p> <p>Data included:</p> <p>Calving front positions for 8 glaciers 2015-2021.</p> <p>Ice speed time series for 105 glaciers 2014-2021, raw measurements and smoothed.</p> <p>Glacier drainage basin ice speed measurements for 8 glaciers 2014-2021.</p> <p>RACMO 2.3p2 5.5km Antarctic Peninsula data: snowfall, precipitation, snowmelt, runoff, smb.</p> <p>All geospatial definitions.</p> <p>Version 2 was updated to include a mean ice speed map.</p>
Supplementary material 1 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
List of literature sources with records of red-eared slider in Eurasia
Supplementary material 2 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Eurasian subregions as accepted in the current article
Supplementary material 8 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Comparison of mean values of the Log-transformed predictor variables
Supplementary material 9 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Original list of 68 Eurasian countries colonized by the red-eared slider Trachemys scripta elegans
Supplementary material 6 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Locations of the training areas based on the available occurrence records
Supplementary material 4 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Coding of collected field data
Supplementary material 3 from: Reshetnikov AN, Zibrova MG, Ayaz D, Bhattarai S, Borodin OV, Borzée A, Brejcha J, Çiçek K, Dimaki M, Doronin IV, Drobenkov SM, Gichikhanova UA, Gladkova AY, Gordeev DA, Ioannidis Y, Ilyukh MP, Interesova EA, Jadhav TD, Karabanov DP, Khabibullin VF, Khabilov TK, Khan MMH, Kidov AA, Klimov AS, Kochetkov DN, Kolbintsev VG, Kuzmin SL, Lotiev KY, Louppova NE, Lvov VD, Lyapkov SM, Martynenko IM, Maslova IV, Masroor R, Mazanaeva LF, Milko DA, Milto KD, Mozaffari O, Nguyen TQ, Novitsky RV, Petrovskiy AB, Prelovskiy VA, Serbin VV, Shi H-t, Skalon NV, Struijk RPJH, Taniguchi M, Tarkhnishvili D, Tsurkan VF, Tyutenkov OY, Ushakov MV, Vekhov DA, Xiao F, Yakimov AV, Yakovleva TI, Yang P, Zeleev DF, Petrosyan VG (2023) Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia. NeoBiota 81: 91-127. https://doi.org/10.3897/neobiota.81.90473
Data base of georeferenced records of Trachemys scripta elegans in Eurasia
Morphological, genetic and ecological divergence in cryptic bryophyte species widespread in the Holarctic: The Dicranum acutifolium complex (Dicranales: Dicranaceae) revisited in the Alps
<p>Alignment of the nr ITS region and the cp trnL-trnF locus</p>
FIG. 3 in Hygrophorus roseodiscoideus Bon & Chevassut: epitypification and updated biogeography of a poorly known but widespread thermophilous species
FIG. 3. — ITS phylogeny of Hygrophorus Fr. pro parte. Maximum likelihood phylogenetic tree of 12 ITS sequences of H. roseodiscoideus Bon & Chevassut, including that of the epitype designated in the present work. Thick branches are supported by SH-aLRT> 0.81 and BPP ≥ 95 %, others display support values as SH-aLRT/% BPP. Sequences printed in bold were obtained during this study.
FIG. 5 in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 5. Genotypes corresponding to Admixture plot at K = 9
FIG. 3. Graph indicating the appropriate K in Reconstructing the genomic diversity of a widespread Sub-Saharan bat (Pteropodidae: Eidolon helvum) using archival museum collections
FIG. 3. Graph indicating the appropriate K value where CV error is lowest from Admixture
Supplementary material 3 from: Thanoosing C, Orr MC, Warrit N, Vogler AP, Williams PH (2023) A taxonomic re-assessment of the widespread oriental bumblebee Bombus flavescens (Hymenoptera, Apidae). Journal of Hymenoptera Research 96: 507-541. https://doi.org/10.3897/jhr.96.104715
Primer testing with gradient annealing temperatures
Supplementary material 2 from: Thanoosing C, Orr MC, Warrit N, Vogler AP, Williams PH (2023) A taxonomic re-assessment of the widespread oriental bumblebee Bombus flavescens (Hymenoptera, Apidae). Journal of Hymenoptera Research 96: 507-541. https://doi.org/10.3897/jhr.96.104715
Primer testing
Supplementary material 7 from: Thanoosing C, Orr MC, Warrit N, Vogler AP, Williams PH (2023) A taxonomic re-assessment of the widespread oriental bumblebee Bombus flavescens (Hymenoptera, Apidae). Journal of Hymenoptera Research 96: 507-541. https://doi.org/10.3897/jhr.96.104715
Ancestral area reconstruction model selection, estimated in BioGeoBEARS
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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