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96 results for “whitefish”
Data from: Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish
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Data from: Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence
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Data from: Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)
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Data from: Maternal and paternal contributions to pathogen resistance dependent on development stage in a whitefish (Salmonidae)
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De novo profiling of long non-coding RNAs involved in MC-LR–induced liver injury in whitefish: discovery and perspectives
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Figure 11 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 11 Types of the Lake Constance species, Switzerland ACoregonus gutturosus, non-type, NMBE-1076232 (Eawag-248–1), 250 mm, sex unknown, preserved specimen BCoregonus arenicolus, holotype, 296 mm, NMBE-1076223 (Eawag-239–1), sex unknown, preserved specimen CCoregonus macrophthalmus, syntype, MHNG-716.052, 215 mm, sex unknown, preserved specimen DCoregonus wartmanni, non-type, NMBE-1076206, 301 mm, female, preserved specimen. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Supplementary material 1 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Tables S1-S8, Figures S1-S11
Figure 12 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 12 Illustrations of specimens of each species from Lake Thun. From top to bottom: Coregonus alpinus: non-type, NMBE-1077244, 343 mm, male; Coregonus steinmanni: paratype, NMBE-1077218, 289.5 mm, male; Coregonus acrinasus: paratype, NMBE-1077270, 270 mm, male; Coregonus fatioi: nontype, NMBE-1077138, 267 mm, male; Coregonus albellus: non-type, NMBE-1077188, 215 mm, male; Coregonus profundus: non-type, Eawag-123850, 195 mm, male. The black scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Figure 1 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 1 Principal Component Analysis showing that the types of the previously described species C. alpinus, C. albellus and C. fatioi (type locality: Lake Thun) lie within or adjacent to the ranges of the contemporary species of Lake Thun A, B shape PCA of the first vs. the second or third PC-axes explain together 70.05% of the variation in shape and are based on a subset (Suppl. material 1: Table S1) of 30 out of a total of 48 measured linear morphological characters (Table 1), since the type material lacked certain characters. Name-bearing types of the formerly described species are highlighted with enlarged symbols in the plots. The proportion of variance explained by each shape PC is given in brackets in the axis legend. PC-loadings and amount of shape variation explained by size are reported in Suppl. material 1: Table S1.
Figure 10 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 10 Coregonus acrinasus, Lake Thun, Switzerland A holotype, NMBE-1077271, Lake Thun, 239.5 mm SL, male, freshly caught specimen B, C holotype, NMBE-1077271, preserved specimen D paratype, NMBE-1077270, Lake Thun, 270 mm SL, male, freshly caught specimen E paratype, NMBE-1077279, Lake Thun, 234 mm SL, male, freshly caught specimen. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.
Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation
The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes. Motivated by this observation, we test the hypothesis that chromosome organization differs between Lake Whitefish species pairs using cytogenetics. While chromosome and fundamental numbers are conserved between the species (2n = 80, NF = 98), we observe extensive polymorphism of subtle karyotype traits. We describe intrachromosomal differences associated with heterochromatin and repetitive DNA, and test for parallelism among three sympatric species pairs. Multivariate analyses support the hypothesis that differentiation at the level of subchromosomal markers mostly appeared during allopatry. Yet we find no evidence for parallelism between species pairs among lakes, consistent with colonization effect or postcolonization differentiation. The reported intrachromosomal polymorphisms do not appear to play a central role in driving adaptive divergence between normal and dwarf Lake Whitefish. We discuss how chromosomal differentiation in the Lake Whitefish system may contribute to the destabilization of mitotic and meiotic chromosome segregation in hybrids, as documented previously. The chromosome structures detected here are still difficult to sequence and assemble, demonstrating the value of cytogenetics as a complementary approach to understand the genomic bases of speciation.
Figure 6 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 6 Coregonus fatioi, lakes Thun and Brienz, Switzerland A, B lectotype, MHNG-809.059, Lake Thun, 154.5 mm SL, sex unknown, left and right side of the specimen C non-type, NMBE-1077139, Lake Thun, 240 mm SL, male, freshly caught specimen D non-type, NMBE-1077317, Lake Brienz, 202 mm SL, male, frozen and defrosted specimen. The white scale (1 cm) below each fish acts as a reference for the actual size of the specimen.
Figure 2 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 2 Principal Component Analysis showing the morphospace of the contemporary whitefish species C. acrinasus, C. alpinus, C. steinmanni, C. albellus, C. profundus and C. fatioi from Lake Thun A, B shape PCA of the first vs. the second or third PC-axes explain together 56.5% of the variation in shape and are based on all 48 measured linear morphological characters (Table 1). The proportion of variance explained by each shape PC is given in brackets and the PC-loadings and amount of shape variation explained by size in Suppl. material 1: Table S2.
Figure 4 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 4 Coregonus albellus, lakes Thun and Brienz, Switzerland A lectotype, MHNG-816.022, Lake Thun, 165 mm SL, sex unknown B non-type, Eawag-123825, Lake Thun, 221 mm SL, male C non- type, NMBE-1077320, Lake Brienz, 115.5 mm SL, male. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Figure 3 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 3 Principal Component Analysis showing the morphospace of the contemporary whitefish species C. alpinus, C. brienzii, C. albellus and C. fatioi from Lake Brienz (A–D) A, B shape PCA of the first vs. the second or third PC-axes explain together 53–60.7% of the variation in shape and are based on all 48 measured linear morphological characters (Table 1), with a dataset containing specimens once smaller (A, B) and once larger (C, D) than 163.5 mm standard length (SL) to avoid allometry issues. The proportion of variance explained by each shape PC is given in brackets and the PC-loadings and amount of shape variation explained by size in Suppl. material 1: Table S3 (< 163.5 mm) and Suppl. material 1: Table S4 (> 163.5 mm).
Figure 8 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 8 Coregonus brienzii, Switzerland, Lake Brienz A holotype, NMBE-1077126, 223 mm SL, female, freshly caught specimen B, C holotype, NMBE-1077126, preserved specimen D paratype, NMBE-1077116, 210.5 mm SL, female.
Figure 5 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 5 Coregonus alpinus, lakes Thun and Brienz, Switzerland A lectotype, MHNG-717.045, Lake Thun, 283 mm SL, sex unknown B close-up of head of lectotype MHNG-717.045 C non-type, NMBE-1077246, Lake Thun, 251.5 mm SL, male, freshly caught specimen D non-type, NMBE-1077115, Lake Brienz, 253 mm SL, female, frozen and defrosted specimen. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Figure 7 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 7 Coregonus steinmanni, Lake Thun, Switzerland A holotype, NMBE-1077219, Lake Thun, 301 mm SL, female, freshly caught specimen B, C NMBE-1077219, holotype, preserved specimen D paratype, NMBE-1077214, Lake Thun, 234 mm SL, female, freshly caught specimen. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
Figure 9 from: Selz OM, Dönz CJ, Vonlanthen P, Seehausen O (2020) A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). ZooKeys 989: 79-162. https://doi.org/10.3897/zookeys.989.32822
Figure 9 Coregonus profundus, Lake Thun, Switzerland A holotype, NMBE-1077208, Lake Thun, 194 mm SL, male, freshly caught specimen B, C holotype, NMBE-1077208, preserved specimen D paratype, NMBE-1077203, Lake Thun, 315.5 mm SL, male E paratype, NMBE-1077166, Lake Thun, 253.5 mm SL, female. The white scale (1cm) below each fish acts as a reference for the actual size of the specimen.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.