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Data from: Pay up or die: Tradeoffs between costly telomere maintenance, somatic growth, and body condition in embryonic and adult sand lizards
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DATA for manuscript entitled "Integrating Transcriptomes and Somatic Mutations to Identify RNA Methylation Regulators as a Prognostic Marker in Hepatocellular Carcinomas"
<p><strong>Raw data of TCGA dataset and 7-meta data.</strong></p>
Data from: A test of somatic mosaicism in the androgen receptor gene of Canada lynx (Lynx canadensis)
Background: The androgen receptor, an X-linked gene, has been widely studied in human populations because it contains highly polymorphic trinucleotide repeat motifs that have been associated with a number of adverse human health and behavioral effects. A previous study on the androgen receptor gene in carnivores reported somatic mosaicism in the tissues of a number of species including Eurasian lynx (Lynx lynx). We investigated this claim in a closely related species, Canada lynx (Lynx canadensis). The presence of somatic mosaicism in lynx tissues could have implications for the future study of exonic trinucleotide repeats in landscape genomic studies, in which the accurate reporting of genotypes would be highly problematic. Methods: To determine whether mosaicism occurs in Canada lynx, two lynx individuals were sampled for a variety of tissue types (lynx 1) and tissue locations (lynx 1 and 2), and 1,672 individuals of known sex were genotyped to further rule out mosaicism. Results: We found no evidence of mosaicism in tissues from the two necropsied individuals, or any of our genotyped samples. Conclusions: Our results indicate that mosaicism does not manifest in Canada lynx. Therefore, the use of hide samples for further work involving trinucleotide repeat polymorphisms in Canada lynx is warranted.
Data from: Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing
Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long‐lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single‐base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.
FIGURES 10A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 10A–E. Leiobunum hiraiwai, penis, ventral view (left) and tip of penis, lateral view (right), Kinki race. Localities: A. Mt Hoko (14). B. Kisokomakôgen (15). C. Mt Ontake (17). D. Narai (18). E. Mt Kokuzô (19). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 1A–L in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 1A–L. Leiobunum hiraiwai (Sato & Suzuki). A–B. Eye tubercle of male, lateral view. C–F. Genital operculum (C–D male, E–F female). G–H. Labrum of female, lateral view. IK. Chelicera of male, mesal view. L. Body of female, dorsal view. Localities (numerals in parentheses denote code numbers given in Fig. 7): A. Mt Bunagatake (10 — Kinki race). B, J. Mt Utsukushigahara (42 — Utsukushigahara race). C. Mt Hyônosen (8 — Kinki race). D, K. Mt Amagi (40 — Izu race). E, G, L. Kisokomakôgen (15 — Kinki race). F, H. Togakushi (50 — Western Kantô race). I. Mt Hiko (2 — KyushuHiroshima race).
FIGURE 18 in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURE 18. Diagrams illustrating the possible evolution of the races in Leiobunum hiraiwai. Details in the text.
FIGURES 5A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 5A–E. Male karyotypes of Leiobunum hiraiwai. Races: A. KyushuHiroshima race. B–C. Kinki race. D–E. Intermediate populations. Localities: A. Mt Hikosan (2n = 18). B. Mt Bunagatake (2n = 20). C. Tsuetsukitôge Pass (2n = 20). D. Todai (2n = 20). E. Mt Nyûgasa (2n = 20).
FIGURES 6A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 6A–E. Male karyotypes of Leiobunum hiraiwai. Races: A. Kamikôchi race. B–C. Utsukushigaraha race. D. Western Kantô race. E. Izu race. Localities: A. Ariake Spa (2n = 20). B. Mt Utsukushigahara (2n = 20). C. Kowashimizu, 1630 m alt., Mt Kirigamine (2n = 20). D. Mt BushûMitake (2n = 22). E. Mt Amagi (2n = 22).
FIGURES 14A–F in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 14A–F. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right), Utsukushigahara race. Localities: A. Yashajintôge Pass (46). B–D. Mt Kirigamine, Kowashimizu, 1660 m alt. (45). E. Tobira Pass (43). F. Mt Utsukushigahara (42). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 9A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 9A–E. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right), Kinki race. Localities: A. Mt Hyônosen (8). B. Mt Bunagatake (10). C. Mt Ibuki (11). D. Mt Gozaisho (12). E. Mt Hakusan (13). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 8A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 8A–E. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right). Races: A. Tsushima race. B–E. KyushuHiroshima race. Localities: A. Mt Ariake, Is. Tsushima (1). B. Mt Hikosan (2). C. Yoshiwamura (4). D. Sandankyô (5). E. Mt Azuma (7). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 3A–I in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 3A–I. Leiobunum hiraiwai (Sato & Suzuki), palp of male, mesal view. Races: A. KyushuHiroshima race. B–C. Kinki race. D. Kamikôchi race. E. Fuji race. F. Utsukushigahara race. G–H. Western Kantô race. I. Izu race. Localities: A. Mt Hikosan (2). B. Mt Bunagatake (10). C. Tsuetsukitôge (22). D. Kamikôchi (26). E. Lake Kawaguchi (31). F. Mt Utsukushigahara (42). G. Kurumasakatôge (51). H. Mt BushûMitake (57). I. Mt Amagi (40). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 13A–G in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 13A–G. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right). Races: A–C. Izu race. D–G. Utsukushigahara race. Localities: A. Mt Takanosu (36). B. Mt Amagi (40). C. Amagitôge Pass (41). D–E. Umegashima Spa (49). F. Mt Nôtori to Mt Ainodake (48). G. Mt Kitadake, Hirogawara (47). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURE 7 in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURE 7. Distribution and chromosome numbers of eight races of Leiobunum hiraiwai. Localities: 1. Mt Ariake, Is. Tsushima. 2. Mt Hikosan. 3. Is. Miyajima. 4. Yoshiwamura. 5. Sandankyô. 6. Mt Shiraki. 7. Mt Azuma. 8. Mt Hyônosen. 9. Mt Hieizan. 10. Mt Bunagatake. 11. Mt Ibuki. 12. Mt Gozaisho. 13. Mt Hakusan. 14. Mt Hoko. 15. Kisokomakôgen. 16. Kôzenji, Kisofukushima. 17. Mt Ontake. 18. Narai. 19. Mt Kokuzô. 20. Kôzenji, Komagane. 21. InaTakatô. 22. Tsuetsukitôge Pass. 23. Mt Kirigamine, Ikenokurumi. 24. Sakaitôge Pass. 25. Suzuran, Mt Norikura. 26–28. Kamikôchi (26 Konashidaira, 27 Myôjin, 28 Yokoo Hütte). 29. Ariake Spa. 30. Nakabusa Spa. 31. Lake Kawaguchi. 32. Lake Yamanaka. 33. FujiYoshida. 34. Mt Kintoki, Hakone. 35. Yabitsutôge Pass. 36. Mt Takanosu, Hakone. 37. Lake Ashinoko, Hakone. 38. Mt Yahazu. 39. Mt Tôgasa. 40. Mt Amagi. 41. Amagitôge Pass. 42. Mt Utsukushigahara. 43. Tobiratôge Pass. 44–45. Mt Kirigamine, Kowashimizu, populations at 1630–1660 m. 46. Yashajintôge Pass. 47. Hirogawara, Mt Kitadake. 48. Mt Nôtori to Mt Ainodake. 49. Umegashima Spa. 50. Togakushikôgen. 51. Kurumasakatôge Pass. 52. Mt Haruna, Haruna Shrine. 53. Mt Hiuchigatake. 54. Yumoto Spa, Nikko. 55. Daibosatsutôge Pass. 56. Nippara, Okutama. 57. Mt BushûMitake. Dotted line indicates distribution areas of cool temperate broadleaved forest (mainly beech).
FIGURE 16 in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURE 16. Summary of geographic variation in penis morphology of Leiobunum hiraiwai. Localities: 1. Mt Ariake, Is. Tsushima. 2. Mt Hiko. 3. Mt Azuma. 4. Mt Bunagadake. 5. Mt Hakusan. 6. Kôzenji Temple, Komagane. 7. Kamikôchi. 8. Lake Kawaguchi. 9. Mt Amagi, Izu. 10. Umegashima Spa. 11. Kowashimizu, Mt Kirigamine (Kowashimizu population). 12. Mt Bushû Mitake, Tokyo. 13. Yumoto Spa, Nikko. Populations circumscribed by the same enclosure represents a race. Arrow head denotes barbs on the alate part of the penis.
FIGURES 15A–G in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 15A–G. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right), Western Kantô race. Localities: A. TogakushiChûsha (50). B. Kurumasaka Pass (51). C. Mt Haruna (52). D. Mt Hiuchi (53). E. Yumoto Spa (54). F. Nippara (56). G. Mt BushuMitake (57). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 12A–F in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 12A–F. Leiobunum hiraiwai, penis, ventral (left) and lateral view (right). Races: A–D. Kamikôchi race. E–F. Fuji race. Localities: A. Sakaitôge Pass (24). B. Suzuran (25). C. Kamikôchi (26). D. Ariake Spa (29). E. Lake Kawaguchi (31). F. Tanzawa (35). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 11A–F in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 11A–F. Leiobunum hiraiwai, penis, ventral (left) and tip of penis, lateral view (right). Races: A–D. Kinki race. E–F. Intermediate populations. Localities: A. KomaganeKôzenji (20). B. Takatô (21). C. Tsuetsukitôge Pass (22). D. Ikenokurumi (23). E. Todai (59). F. Mt Nyûgasa (58). Numerals in parentheses denote code numbers of localities given in Fig. 7.
FIGURES 2A–Q in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)
FIGURES 2A–Q. Leiobunum hiraiwai (Sato & Suzuki). Labrum of male, lateral (above) and ventral (below) views. Races: A. Tsushima race. B–D. KyushuHiroshima race. E–G. Kinki race. H–I. Kamikôchi race. J–K. Fuji race. L–M. Izu race. N–O. Utsukushigahara race. P–Q. Western Kantô race. Localities: A. Mt Ariake (1). B. Mt Hiko (2). C. Yoshiwamura (4). D. Sandankyô (5). E. Mt Hyônosen (8). F. Mt Bunagatake (10). G. Tsuetsukitôge (22). H. Suzuran (25). I. Kamikôchi (26). J. Lake Kawaguchi (31). K. Tanzawa (35). L. Mt Takanosu (36). M. Mt Amagi (40). N. Mt Utsukushigahara (42). O. Mt Nôtori to Mt Ainodake (48). P. Kurumasakatôge Pass (51). Q. Mt BushûMitake (57). Numerals in parentheses denote code numbers of localities given in Fig. 7.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.