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opencc-by-4.0Dec 2023View details →

Mapping the Literature on Biodiversity and Taxonomy

Talk at the <a href="https://www.digital-philosophy.org/" target="_blank" rel="noopener">Philosophy [in:of:for:and] Digital Knowledge Infrastructures</a> online workshop 2023 (28/09/2023).

FIGURE 8 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 8 Digital reconstructions of Heteropsammia specimens based on Micro CT scans. A–E: H. moretonensis (HmKTa). A–C) a series of three transverse slices, from calice margin and base of fossa (A, B) and finally base of corallite with sipunculan chamber visible (C–D) lateral slice with yellow dashed lines denoting the position of slices in A–C, E) reconstructed view within coral, with sipunculan chamber and efferent pore channels projecting laterally. F–J: H. cochlea (KTa). F–H) a series of three transverse slices, from calice margin and base of fossa (F, G) and finally base of corallite with sipunculan chamber visible (C); I, J: lateral and top down (I and Downloaded from Brill.com 06/21/2024 06:29:01PM J, respectively) view into coralliteviawith Openvariable Access. This opacityisand an open sipunculanaccesschamber article distributed under the terms visible. Scale bars: 2.5 mm. of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 1 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 1 Map of survey sites in the Gulf of Thailand; A) Koh Samaesan; B) Hin Chalam; C) Koh Mun Nai; D) Koh Mun Klang; E) Site HYE21; F) Koh Mun Nok; G) Sai Nuan; H) Tao Tong; I) Taa Chaa; J) Leuk Bay; K) Tanote Bay.

FIGURE 2 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 2 Digital images of specimens based on micro-CT scans. A– D) Tubastraea stimpsonii comb. nov. (EKTa) A) Series of nine transverse slices from calice margin (i) towards base (ix); B, C) lateral view with varying opacities, yellow dashed lines denote the position of slices in A; D) top down view into corallite showing calicular features. E, G, I) Cladopsammia gracilis (RKTa). E) lateral view of small colony specimen including holdfast; G) close-up of theca with striae visible; I) wide slice of upper portion of a single corallite showing calicular features. F, H) Tubastraea diaphana (TmKT19b). F) lateral view of typical colony specimen including holdfast; H) wide slice of upper portion of a single corallite showing calicularDownloaded features.from ScaleBrill bars.: com 06/21/2024 06:29:01PM 5 mm. via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 7 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 7 Heteropsammia spp. (scale bars: 5 mm). A–C) living specimen of H. moretonensis, showing dorsal, lateral and ventral views respectively; D–F) living specimen of small H. cochlea, showing dorsal, lateral and ventral views respectively; G, H) in situ photos of H. moretonensis (specimens HmKS20, HmKMN21; I–K) H. cochlea specimen KT-1m (one mouth, normal phase), specimen KT-2m (two mouths) and specimen KT-4m (four mouths, amorphous phase); L–N) H. eupsammides specimens Ko1, Ko4, and Ko5 respectively (scale bars: 5 mm). RMNH.COEL.39394. Locality: Teluk Slawi, SE Pulau Lassa, East Komodo (08°36'08"N, 119°29'47"E), 13 November 2002.

FIGURE 4 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 4 Partial phylogeny reconstruction of Dendrophylliidae including the Heteropsammia clade, based on Bayesian Inference and the concatenated dataset (COI + IGR + rDNA). Posterior probability values greater than 0.7 shown, specimens in bold and coloured based on sequences provided in the present study.

FIGURE 6 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 6 Dendrophyllia cf. minima. (B, C specimen HC 20f, D, E specimen HC20g) A) living specimen in situ (scale bar: 5 mm); B) digitial reconstruction of a single corallite with varying opacities highlighting external surface beneath calcified layer of coralline algae (scale bar: 2 mm); C) digital top-down view into corallite with calicular features visible (scale bar: 1 mm); D) top down view of skeleton of different specimen (scale bar: 1 mm); E) dorso-lateral skeletal view of calice (scale: bar 1 mm). Downloaded from Brill.com 06/21/2024 06:29:01PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 5 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 5 Living corals with their specimen numbers (scale bars: 10 mm). A, B) Tubastraea stimpsonii (EKT19, EKT20); C) Tubastaea cf. chloromura (YKT19c) left and Tubastraea diaphana (TmKT19a) right; D) Tubastraea diaphana (TmKT19b); E, F) Cladopsammia gracilis (RKT19, RKS20).

FIGURE 10 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 10 Mean population densities of dendrophylliids from soft substrate habitats at surveyed sites across the Gulf of Thailand. Vertical lines represent S.E. Location of the sites displayed in fig. 1.

FIGURE 3 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 3 Partial phylogeny reconstruction of Dendrophylliidae including the Tubastraea clade, based on Bayesian Inference and the concatenated dataset (COI + IGR + rDNA). Posterior probability values greater than 0.7 shown, specimens in bold and coloured based on sequences provided in the present study. Downloaded from Brill.com 06/21/2024 06:29:01PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 9 in Biodiversity, ecology, and taxonomy of sediment-dwelling Dendrophylliidae (Anthozoa, Scleractinia) in the Gulf of Thailand

FIGURE 9 Variation in morphology and ecology of solitary soft-susbstrate associated Dendrophylliidae in the Gulf of Thailand. A, B) in situ observations of variable polystomatism in Heteropsammia cochlea (scale bars 5 mm); C) a bleached specimen of H. cochlea in situ (scale bar 10 mm); D) simultaneous ingestion of large salps by two mouths in a single H. cochlea colony, individual salps indicated by brackets (scale bar 10 mm); E,F) rare cases of division in H. moretonensis (scale bars 5 mm); G) ecto-parasitism on H. cochlea by an unidentified epitoniid snail (white arrow) with clusters of eggs (red arrow) attached to the corallite (scale bar 10 mm); H) ingestion of an oral disk of ceriantharian (white bracket) by H. moretonensis (scale bar 10 mm); I) ingestion of an anemone tentacle (white bracket) by H. moretonensis (scale bar 10 mm); J) ingestion of a medusa of Pelagia sp. (white bracket) by H. cochlea (scale bar 10 mm); K) proto-cooperative ingestion of a sea pen by Downloadedtwo from Brill.com 06/21/2024 06:29:01PM mouths in a single colony of via TubastraeaOpen Access stimpsonii. This(scale is an baropen 10 mm access). article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

opencc-by-4.0Dec 2015View details →

zenodo36/100

Supplementary Video: An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss

Supplementary video for the article "An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss".

zenodo36/100

Figure:1 Fish classification and taxonomy in Artificial Intelligence Applications in Fish Classification and Taxonomy: Advancing Our Understanding of Aquatic Biodiversity

Figure:1 Fish classification and taxonomy

opencc-by-4.0Dec 2023View details →

dryad36/100

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10+ species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.

opencc-zeroJun 2021View details →

dryad36/100

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

Open the record for dataset details and reuse information.

publicJun 2021View details →

FIGURE 30 in Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

FIGURE 30. Distribution of Cradoscrupocellaria species. Colours: green, Eastern Pacific species; black, Atlantic species; blue, North Sea specimens; red, Mediterranean species; pink, Red Sea and Indian species; orange, Indo-Pacific species; blue, southern Australian species.

FIGURE 28 in Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

FIGURE 28. Cradoscrupocellaria hirsuta (Jullien & Calvet, 1903) n. comb. A–B, MOM 420323, lectotype, Azores. C–F, NHMUK 2012.7.1.1, Azores. A, Frontal surface of branch; note the presence of a dimorphic frontal avicularium and absence of scutum. B, Abfrontal surface of branch. C, Frontal surface of branch bifurcation; note the dimorphic frontal avicularia and three ovicelled zooids proximally in the colony. D, Frontal surface of branch; note the presence of seven long oral spines in each zooid and the absence of a scutum. E, Close-up of four ovicelled zooids and dimorphic frontal avicularia. F, Abfrontal surface of branch.

FIGURE 27. Cradoscrupocellaria odonoghuei n in Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

FIGURE 27. Cradoscrupocellaria odonoghuei n. sp. A–F, NHMUK 2010.12.6.21, holotype, Scotland. A, Frontal surface of colony. B, Frontal surface of branch bifurcation; note the joints passing across gymnocyst of outer zooids at the bifurcation. C, Close-up of a branch bifurcation. D, Close-up of gigantic frontal avicularium. E, Abfrontal surface of colony; note the smooth rhizoids arising from proximal end of some vibracular chambers. F, Abfrontal surface of branch bifurcation.

FIGURE 26. Cradoscrupocellaria macrorhynchoides n in Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

FIGURE 26. Cradoscrupocellaria macrorhynchoides n. sp. A–F, NHMUK 2010.12.6.19, holotype, Queensland, Australia. A, Frontal surface of colony. B, Frontal surface of branch bifurcation; note the gigantic frontal avicularium on axial zooid. C, Close-up of a branch bifurcation; note the ovicelled zooids and the gigantic frontal avicularium. D, Close-up of gigantic frontal avicularium. E, Abfrontal surface of colony. F, Abfrontal surface of branch bifurcation.

FIGURE 21 in Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

FIGURE 21. Cradoscrupocellaria macrorhyncha (Gautier, 1962) n. comb. A–F, NHMUK 1965.9.2.4, lectotype, Mediterranean. A, Frontal surface of branch; note the ovicelled zooid at upper right. B, Frontal surface of branch bifurcation. C, Close-up of a zooid and gigantic frontal avicularium. D, Lateral view of gigantic frontal avicularium; note the fringed rostrum of the avicularium. E, Abfrontal surface of colony. F, Abfrontal surface of branch bifurcation.