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From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals
<p>With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus <em>Pocillopora</em>, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus <em>Pocillopora</em>. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em>, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.</p> <p> </p> <p>This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific <em>Pocillopora </em>corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803</p> <p>See 0_README.txt for more content details.</p>
Fig. 19 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 19. Tenuibiotus zandrae sp. nov. Egg chorion morphology seen in SEM. A. Entire egg. B. Magnification of the egg surface. C–F. Details of the egg processes and surface between them. Filled flat arrowheads indicate thickenings/striae on the surface between processes and filled indented arrowheads indicate small tubercles on the process walls. Scale bars in μm.
Fig. 18 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 18. Tenuibiotus zandrae sp. nov. Egg chorion morphology seen in PCM. A. Midsection under 400× magnification. B. Surface under 400× magnification. C–D. Surface between processes under 1000× magnification. E–H. Midsections of processes of four different eggs under 1000× magnification. Filled flat arrowheads indicate thickenings/striae which are visible as dark dots and lines on the surface between processes. Scale bars in μm.
Fig. 14 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 14. Tenuibiotus zandrae sp. nov. Claws (paratypes). A–B. Claws II and IV seen in PCM, respectively. C–D. Claws I and IV seen in SEM, respectively. Filled indented arrowhead indicates horseshoe structure connecting the anterior and the posterior claw. Scale bars in μm.
Fig. 11 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 11. Tenuibiotus zandrae sp. nov. Body granulation seen in PCM (paratypes). A–B. Uniformly distributed granulation on the dorso-cephalic and dorso-caudal part of the body. C–D. Uniformly distributed granulation on the dorso-cephalic and dorso-caudal part of the body with small, random patches of lacking granulation. E–F. Uniformly distributed granulation on the ventral side of the body without and with small random patches lacking granulation, respectively. A–B, E and C–D, F are from two different paratypes. Scale bars in μm.
Fig. 8 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 8. Macrobiotus engbergi sp. nov. Egg chorion morphology seen in SEM. A. Entire egg. B. Magnification of the egg surface. C–D. Details of the terminal discs. Scale bars in μm.
Fig. 4 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 4. Macrobiotus engbergi sp. nov. Claws (paratypes). A–B. Claws III and IV seen in PCM, respectively. C–D. Claws III and IV seen in SEM, respectively. Filled flat arrowheads indicate double muscles attachments under the claws, empty flat arrowhead indicates inverted horseshoe structure under the external and the internal claw, whereas filled indented arrowhead indicates horseshoe structure connecting the anterior and the posterior claw. Scale bars in μm.
Fig. 5 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 5. Macrobiotus engbergi sp. nov. Buccal apparatus and the oral cavity armature seen in PCM (holotype, IZiBB, slide GL.052.22). A. Dorso-ventral projection of the entire buccal apparatus. B–C. Oral cavity armature visible in dorsal (B) and ventral (C) view, respectively. D–E. Placoid morphology visible in dorsal (D) and ventral (E) view, respectively. Filled flat arrowheads indicate the second band of teeth in the oral cavity, empty flat arrowheads indicate the third band of teeth in the oral cavity, empty indented arrowheads indicate central constrictions in the first macroplacoids and subterminal constriction in the second macroplacoids. Scale bars in μm.
Fig. 12 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 12. Tenuibiotus zandrae sp. nov. Patches of dense granulation on legs seen in PCM (paratypes). A. External granulation on leg III (patch of dense granulation encircled). B. Internal granulation on leg III. C. Granulation on leg IV. Scale bars in μm.
Fig. 21 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 21. Tenuibiotus voronkovi (Tumanov, 2007) Egg chorion morphology seen in PCM. A. Midsection under 400× magnification. B. Surface between processes under 1000× magnification. C–J. Details of egg processes under 1000× magnification. Filled flat arrowhead indicates thickenings/striae/sculpture which are visible as dark dots on the surface between processes and indented empty arrowheads indicate broken apices of the egg processes. Scale bars in μm.
Fig. 20 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 20. Tenuibiotus voronkovi (Tumanov, 2007). Body granulation seen in PCM. A. Uniformly distributed granulation of uniform size on the dorso-medial part of the body (cephalic region, paratype). B. Patch of dorso-lateral granulation composed of granules of different size (holotype). Scale bars in μm.
Figures 60–65 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 60–65. Heterolepisma cooloola sp. nov. holotype ♀ (60) presternum, prothoracic sternum and PI; (61) mesothoracic sternum and PII; (62) apex of mesothoracic sternum; (63) metathoracic sternum and PIII; (64) apex of metathoracic sternum; (65) pretarsus of PIII. Scale bars = 0.1 mm.
Figures 24–31 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 24–31. Heterolepisma coorongooba sp. nov. holotype ♀ (24) presternum, prothoracic sternum and PI; (25) mesothoracic sternum; (26) metathoracic sternum and PIII; (27) urotergite III; (28) idem, sublateral comb; (29) idem, submedial comb; (30) urotergite IX, infralateral combs; (31) urotergite X. Scale bars = 0.1 mm.
Figures 15–23 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 15–23. Heterolepisma coorongooba sp. nov. holotype ♀ (15) left lateral, anterior and posterior margins of pronotum; (16) idem, detail of left anterior trichobothrial area; (17) idem, detail of right posterior trichobothrial area; (18) idem, left posterior comb of pronotum; (19) lateral margin of mesonotum; (20) idem, trichobothrial areas of right side; (21) idem, left posterior comb of mesonotum; (22) lateral margin of metanotum; (23) idem, trichobothrial areas of left side. Scale bars = 0.1 mm.
Figures 7–14 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 7–14. Heterolepisma sclerophylla Smith and Heterolepisma coorongooba sp. nov. (7) Heterolepisma sclerophylla Smith, holotype ♀, medial section of pronotal collar. (8–14) Heterolepisma coorongooba sp. nov. holotype ♀ (8) medial section of pronotal collar; (9) lateral bristlecomb of urotergite III and adjacent scale; (10) head; (11) scape, pedicel and basal interval of flagellum, from above; (12) antenna, most distal surviving annuli; (13) maxilla, only larger setae of palp illustrated; (14) labium, setae of palp not strong so not illustrated. Scale bars = 0.1 mm.
Figures 32–36 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 32–36. Heterolepisma coorongooba sp. nov. holotype ♀, unless otherwise indicated by specimen number (32) urosternite III; (33) idem, posterior comb; (34) coxites VIII and IX, ovipositor and styli; (35) coxite IX, paramere and penis (K.260993); (36) paramere (K.260993). Scale bars = 0.1 mm.
Figures 78–85 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 78–85. Heterolepisma cooloola sp. nov. holotype ♀ unless otherwise indicated by specimen number (78) stylet IX (QM 207012); (79) apex of anterior gonapophysis; (80) apex of posterior gonapophysis; (81) bases of terminal filaments; (82) most distal surviving divisions of cerci; (83) most distal surviving divisions of median filament; (84) coxites IX, styli and penis of male (QM 207012); (85) paramere. Scale bars = 0.1 mm.
Figures 49–59 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 49–59. Heterolepisma cooloola sp. nov. holotype ♀ (49) labium, only large setae of palp illustrated; (50) idem, ultimate article of palp; (51) pronotum; (52) idem, right margin; (53) idem, detail of right anterior trichobothrial area; (54) idem, detail of left posterior trichobothrial area; (55) lateral margin of mesonotum; (56) idem, posterior trichobothrial area; (57) idem, anterior trichobothrial area; (58) idem, right posterior comb; (59) lateral margin of metanotum. Scale bars = 0.1 mm.
Figure 4 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 4. BI tree for concatenated COI and 28S genes. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 3 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 3. BI tree for nuclear gene 28S. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
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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.