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Supplementary material for: Long branch attraction biases in phylogenetics
<p>Long branch attraction is a prevalent form of bias in phylogenetic estimation but the reasons for it are only partially understood. We argue here that it is largely due to differences in the sizes of the model spaces corresponding to different trees. Trees with long branches together allow much more flexible internal branch-length parameter estimation. Consequently, although each tree has the same number of parameters, trees with long branches together have larger effective model spaces. The problem of long branch attraction becomes particularly pronounced with partitioned data. Formulation of tree estimation as model selection leads us to propose bootstrap bias corrections as cross-checks on estimation when long branches end up being estimated together. </p>
Supplementary material 3 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S3
Supplementary material 2 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S2
Supplementary material 2 from: Lang A, Dolek M, Lee MS, Freese-Hager A, Otto M (2020) Selection of non-target Lepidoptera species to test Bt maize effects in the laboratory: which species and how to breed them? BioRisk 15: 45-65. https://doi.org/10.3897/biorisk.15.59823
Review breeding information
Supplementary material 1 from: Palmas P, Gouyet R, Oedin M, Millon A, Cassan J-J, Kowi J, Bonnaud E, Vidal E (2020) Rapid recolonisation of feral cats following intensive culling in a semi-isolated context. NeoBiota 63: 177-200. https://doi.org/10.3897/neobiota.63.58005
Figure S1>
Supplementary material 1 from: Lang A, Dolek M, Lee MS, Freese-Hager A, Otto M (2020) Selection of non-target Lepidoptera species to test Bt maize effects in the laboratory: which species and how to breed them? BioRisk 15: 45-65. https://doi.org/10.3897/biorisk.15.59823
Reference list: breeding and rearing Lepidoptera
Supplementary material 4 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S1
Supplementary material 16 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S13
Supplementary material 5 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S2
Supplementary material 8 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S5
Supplementary material 9 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S6
Supplementary material 3 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Table S2
Supplementary material 11 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S8
Supplementary material 15 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S12
Supplementary material 7 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S4
Supplementary material 10 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S7
Supplementary material 12 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S9
Supplementary material 1 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Key to the 26 species of the genus Bombus
Supplementary material 2 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Table S1
Supplementary material 6 from: Robertson DR, Estapé CJ, Estapé AM, Peña E, Tornabene L, Baldwin CC (2020) The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog. ZooKeys 1007: 145-180. https://doi.org/10.3897/zookeys.1007.58515
Plate S3
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.