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Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</p>
Figure 1 in A taxonomic revision of the members of the Camponotus lateralis species group (Hymenoptera: Formicidae) from Europe, Asia Minor and Caucasia
Figure 1. Principal component analysis (PCA) of worker size dimorphism in 285 worker individuals of the long-headed species Camponotus atricolor, C. candiotes, C. heidrunvogtae n.sp. and C. piceus. The PCA is in fully in line with the classification by a two-step cluster analysis separating majors (dark squares) and minors (white rhombs).
Figure 22 in A taxonomic revision of the members of the Camponotus lateralis species group (Hymenoptera: Formicidae) from Europe, Asia Minor and Caucasia
Figure 22. Dorsal aspect of major worker of Camponotus heidrunvogtae n.sp. from Corfou: Klimatia, 2013.06.06.
Figure 12 in A taxonomic revision of the members of the Camponotus lateralis species group (Hymenoptera: Formicidae) from Europe, Asia Minor and Caucasia
Figure 12. Classification of Camponotus atricolor (black bars) against the cryptic species pair C. piceus + C. candiotes (red bars) in three different exploratory data analyses using body size and the full (unselected) set of RAV-corrected shape and setae characters. The error relative to the final species hypothesis is 0% in NC-Ward, 0% in NC-part.hclust and 2.4% in NC-part.kmeans.
Figs. 111 in A taxonomic revision of the Palaearctic members of the subgenus Lasius s.str. (Hymenoptera, Formicidae)
Figs. 111: NC-clustering of 51 nest samples of Lasius precursor sp. nov. (black bars) and 77 nest samples of L. turcicus (grey bars) from the East Aegean and Asia Minor. The hierarchical algorithms, NC-Ward (tree shown) and NC-part.hclust, showed a classification error of 4.7% whereas the non-hierarchical algorythms, NC-part.kmeans and NC-NMDS-k.means (not shown), misclassified only 0.8% of the samples giving an overall mean error of 2.8%. Outliers in NC-part.hclust are indicated by white bars (gaps).
Figs. 112 in A taxonomic revision of the Palaearctic members of the subgenus Lasius s.str. (Hymenoptera, Formicidae)
Figs. 112: NC-clustering of 49 nest samples of Lasius paralienus (light grey bars), 20 nest samples of L. bombycina (black bars) and 15 samples of L. casevitzi (dark grey bars).
Figure 8 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 8 – Telchinia serena (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 40 mm. Madikwe Nature Reserve, North West Province, South Africa. June 1998. M.C. Williams.
Figure 2 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 2 – Acraea horta (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 52 mm. Golden Gate Highlands National Park, Free State Province, South Africa. 9 January 2001. M.C. Williams.
Figure 3 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 3 – Rubraea egina (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 62 mm. Mabira Forest, Uganda. 14 June 2009. J.C.H. Dobson.
Figure 7 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 7 – Actinote parapheles (male upper side), a typical member of the genus. Wingspan: 55 mm. Credit: Wikipedia images.
Figure 5 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 5 – Tildia zetes (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 65 mm. Kakum Forest, Ghana. 20 November 2011. J.C.H. Dobson.
Figure 1 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 1 – Cethosia biblis perakana (male), a typical member of the genus. Left – upper side. Right – underside. Wingspan: 67 mm. Chaweng Beach, Ko Samui, Thailand. 19 March 2019. J.C.H. Dobson.
Figure 4 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 4 – Stephenia caecilia (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 48 mm. Zamaye, Cameroon. July 1993. Ex Henning Collection.
Figure 6 in Taxonomic revision of the tribe Acraeini Boisduval, 1833 (Papilionoidea: Nymphalidae: Heliconiinae)
Figure 6 – Bematistes epaea (male), the type species of the genus. Left – upper side. Right – underside. Wingspan: 60 mm. Biakpa Mountain Paradise, Ghana. 24 November 2011. J.C.H. Dobson.
Figure 5 – C in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part III: An integrative taxonomic revision
Figure 5 – C. chrysantas (Garies). Final instar (top), C. chrysantas distal four larval segments (bottom). Not to scale.
Figure 4 – C. zonarius 2 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part III: An integrative taxonomic revision
Figure 4 – C. zonarius 2nd (top) and 4th (middle) instars (Churchhaven) and 6th/final instar (bottom; Platrug Farm). Not to scale. An egg of C. zonarius is shown in Fig. 7A in HEA23.
Figure 2 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part III: An integrative taxonomic revision
Figure 2 – Male genitalia. (A) C. phosphor lateral view with aedeagus removed (illustration by A. Heath); see also Fig. 1h in HEA23. (B) C. oreas lateral view with aedeagus removed. (C) C. oreas genitalic components; see also Fig. 1c in HEA23. Parts (B) and (C) reproduced from Stempffer (1967) by courtesy of The Natural History Museum, London. Not to scale.
Figure 13 – C in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part III: An integrative taxonomic revision
Figure 13 – C. rileyi (Brand Vlei) 4th instar (top) and final instar (bottom). Not to scale. An egg of C. rileyi is shown in Fig. 7B in HEA23.
Fig. 7 in Taxonomic revision of the antlion tribe Myrmeleontini (Neuroptera: Myrmeleontidae) of Taiwan
Fig. 7. Baliga brunneipennis (Esben-Petersen, 1913), male genitalia (NTU). A. Lateral view. B. Ventral view. C. Caudal view. Abbreviations: gon = gonarcus; med = mediuncus; par = parameres. Scale bar = 0.5 mm.
Fig. 31 in Taxonomic revision of the antlion tribe Myrmeleontini (Neuroptera: Myrmeleontidae) of Taiwan
Fig. 31. Distribution of Myrmeleontini Latreille, 1802 from Taiwan and adjacent islands. A. Baliga asakurae (Okamoto, 1910). B. B. brunneipennis (Esben-Petersen, 1913). C. Myrmeleon tenuipennis Rambur, 1999. D. M. littoralis Miller & Stange, 1999. E. M. wangi Miller & Stange, 1999. F. M. heppneri Miller & Stange, 1999. G. M. persimilis Miller & Stange, 1999. H. M. punctinervis Banks, 1937. I. M. taiwanensis Miller & Stange, 1999.
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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)
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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.