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2,185 results for “Integrative taxonomy”
Lineage and role in integrative taxonomy of a heterotrophic orchid complex
<p>Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological ‘role’ shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the <em>Corallorhiza striata</em> complex, analyzing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data–ISSRseq–demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the ‘extended’ data, albeit with weaker signal. However, none of the ‘extended’ datasets fully satisfy the condition of a significant ‘role’ shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of ‘lineage+role’ to date and illustrates the advantages of such an approach.</p>
Taxonomy, distribution and classification of ecosystem-types, integrating the recent IUCN function-based typology and local conceptualizations
<p>1. Introduction:</p> <p>This dataset is a work in progress. It compiles data gathered on ecosystem-types and their distribution based on a series of field studies led by the author, in Seychelles and West and Central Africa (Senterre 2014, Senterre & Wagner 2014, Senterre 2016, Senterre et al. 2017, 2019, 2020, 2021a, 2022). The aims of this dataset are:</p> <p>a. To share in an explicit and transparent way data on proposed taxonomies of ecosystems, i.e. conceptualizations of ecosystem-types, including explicit ecosystem names and management of synonymies.</p> <p>b. To develop ecosystem red listing based on transparent and falsifiable distribution raw data, combining distribution modeling (maps) and in situ observation of individual stand occurrences.</p> <p>c. To illustrate in detail how to deal with ecosystem data following the approach described in Senterre et al. (2021b) (i.e. "ecosystemology" approach).</p> <p>d. To integrate the above approach with the newly developed function-based typology of ecosystems (Keith et al. 2022), therefore contributing to bridging the persistent gap between the global and the local scales in ecosystem descriptions and classifications.</p> <p> </p> <p>2. Context and versions:</p> <p>This dataset was initially planned for publication on GBIF (Global Biodiversity Information Facility), as part of a project developed for the review of Key Biodiversity Areas in Seychelles: "Mainstreaming recent species and ecosystem distribution data into Key Biodiversity Areas assessments in Seychelles" (<a href="https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf">https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf</a>).</p> <p>In the first version of the GBIF dataset (<a href="https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf">https://www.gbif.org/dataset/f513fe98-b1c3-45ee-8e14-7f2a5b7890bf</a>), we proposed an analysis of the potential 'core' and 'extension' files available in GBIF for a publication of ecosystem-type names (and synonymies) and their corresponding occurrences recorded from field observations. This is an original analysis of taxonomic principles managed entirely at the scale of local observable objects, and their history of identifications or interpretations.</p> <p>Toward the end of the above-mentioned GBIF project, considering the limitations and gaps currently present in GBIF, it was decided to restrict the GBIF dataset to a simple 'metadata' entry and to publish the complete version of this dataset in Zenodo. This allows to include all tables needed, as well as all required fields without having to accommodate them within the limited GBIF structure (see metadata description on GBIF for more details). The fields of the tables published here are described in the GBIF metadata entry and in the ecosystemology paper (Senterre et al. 2021b).</p> <p> </p> <p>3. New development on typology aspects:</p> <p>In addition, considering that the new IUCN global typology of ecosystems is now published (Keith et al. 2022), we have reviewed in detail the possibility of integration of ecosystems conceptualized using our ecosystemology approach within the new IUCN typology. The result of this analysis is being considered for a publication, and this Zenodo dataset would then be published in full (i.e. including all typology aspects) as supplementary materials. In the meantime, I would be happy to discuss any of these aspects with whoever is interested.</p> <p> </p> <p>4. Access to ecosystem data for conservation actors:</p> <p>Finally, the actual data (published here) on ecosystem-types, their names, synonymies, classification, distribution, and red list status are compiled into a format that we designed to be useful to conservation actors in the form of interactive webpages (produced with R as shiny apps). This development is based on very limited resources, and the author is still quite new to R, so any help or feedback on ways to improve the scripts would be very much welcomed.</p> <p>The interactive page is available here (currently filtered to Seychelles' data only, although the dataset contains data beyond the Seychelles): https://shiny.bio.gov.sc/bioeco/</p> <p>The R scripts are available on Github: https://github.com/bsenterre/ecosystemology</p> <p> </p> <p>5. Tables contained in this dataset:</p> <p>a. Ecosystem taxonomy tables:</p> <p>ecoSpecies: Contains the list of all ecosystem-type names with their unique identifier.</p> <p>ecoOccurrences: Contains the list of individual stand occurrences, including ecosystem characters as standardized in Senterre et al. (2021b; i.e. virtual ecosystem specimen).</p> <p>ecoSpeciesProfiles: Contains basic metadata on ecosystem-types, such as their Red List evaluations.</p> <p>ecoIdentifications: Contains all the different interpretations/identifications (referring to the table ecoSpecies or to higher levels of classification, see below) made on the stands observed in the ecoOccurrences table.</p> <p> </p> <p>b. Ecosystem typology tables (TO BE ADDED LATER):</p> <p>IUCNL3: This is just a transcription, as is, of the IUCN global typology version 2.1.</p> <p>IUCNL3BIOCrossover: This table defines and comments correspondences between BIOL2 (the level 2 of the typology used by us) and the IUCN typology L3 (level 3).</p> <p>BIOL2: This is a variation based on the IUCN typology, here our level 2.</p> <p>BIOL3: This is a variation based on the IUCN typology, here our level 3.</p> <p>BIOL4: This is a variation based on the IUCN typology, here our level 4.</p> <p>ecoGenus: This is a general type of stand (thus excluding any regional ecosystem connotation), defined at a local scale and never combined with any geographic connotation (see ecosystemology paper: Senterre et al. 2021b).</p> <p>ecoFamily: This is a generalized version of the ecoGenus (i.e. still excluding any regional, sub-regional or geographic aspect).</p> <p>ecoOrder: This is a further generalized version of the ecoGenus (see also Senterre et al. 2020).</p> <p>lifeZone: This is a basic and incomplete list of life zones as defined following the Holdridge (1967) approach, with some additional elements proposed in Senterre et al. (2021b).</p> <p> </p> <p>6. Literature cited:</p> <p>Holdridge, L. R. 1967. Life zone ecology. Tropical Science Center, San Jose, Costa Rica.</p> <p>Keith, D. A., J. R. Ferrer-Paris, E. Nicholson, M. J. Bishop, B. A. Polidoro, E. Ramirez-Llodra, M. G. Tozer, J. L. Nel, R. Mac Nally, E. J. Gregr, K. E. Watermeyer, F. Essl, D. Faber-Langendoen, J. Franklin, C. E. R. Lehmann, A. Etter, D. J. Roux, J. S. Stark, J. A. Rowland, N. A. Brummitt, U. C. Fernandez-Arcaya, I. M. Suthers, S. K. Wiser, I. Donohue, L. J. Jackson, R. T. Pennington, T. M. Iliffe, V. Gerovasileiou, P. Giller, B. J. Robson, N. Pettorelli, A. Andrade, A. Lindgaard, T. Tahvanainen, A. Terauds, M. A. Chadwick, N. J. Murray, J. Moat, P. Pliscoff, I. Zager, and R. T. Kingsford. 2022. A function-based typology for Earth’s ecosystems. . Nature 610:513–518. doi:10.1038/s41586-022-05318-4.</p> <p>Senterre, B. 2014. Mapping habitat-types within the Hummingbird site at Dugbe (Liberia, West Africa). Consultancy Report, Missouri Botanical Garden. P. 56. https://doi.org/10.13140/RG.2.2.32628.48003.</p> <p>Senterre, B. 2016. Habitat-type ground-truthing and assessment of ecosystem conservation value in the Bel Air Alufer mining site (Guinea, West Africa), with recommendations for improving the draft map of land cover types. Consultancy Report, Missouri Botanical Garden, A study conducted for Alufer Mining Limited. P. 54.</p> <p>Senterre, B., E. Bidault, and T. Stévart. 2019. Identification et évaluation des écosystèmes menacés du Mont Nimba. Rapport de consultance, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 106. https://doi.org/10.13140/RG.2.2.13242.93129.</p> <p>Senterre, B., E. Bidault, T. Stévart, and P. P. Lowry II. 2020. Assessment of Key Biodiversity Areas in the Lofa-Gola-Mano & Nimba complexes (West Africa) using ecosystem criteria. Final Report, Missouri Botanical Garden. P. 146. 10.13140/RG.2.2.17934.89924.</p> <p>Senterre, B., E. Bidault, T. Stévart, M. Wagner, and P. Lowry. 2017. Mapping habitat-types in south-east Kouilou (Republic of Congo). Consultancy Report, Missouri Botanical Garden (MBG), Africa and Madagascar Department, St. Louis, Missouri, USA. P. 163.</p> <p>Senterre, B., R. M. Bristol, G. Gendron, and E. Henriette. 2021a. Fine-tuning conservation priorities in Seychelles at the landscape scale, using global KBA guidelines with both species and ecosystem criteria. Consultancy Report, United Nations Development Programme, GOS/UNDP/GEF Programme Coordination Unit, Victoria, Seychelles.</p> <p>Senterre, B., P. P. Lowry II, E. Bidault, and T. Stévart. 2021b. Ecosystemology: a new approach toward a taxonomy of ecosystems. . Ecological Complexity 47:100945. doi:https://doi.org/10.1016/j.ecocom.2021.100945.</p> <p>Senterre, B., A.-H. Paradis, E. Bidault, T. Stévart, and P. P. Lowry II. 2022. Qualité et distribution des savanes montagnardes du Nimba. Rapport de consultance, Missouri Botanical Garden (MBG), Africa and Madagascar Department. P. 73. http://dx.doi.org/10.13140/RG.2.2.13433.34401.</p> <p>Senterre, B., and M. Wagner. 2014. Mapping Seychelles habitat-types on Mahé, Praslin, Silhouette, La Digue and Curieuse. Consultancy Report, Government of Seychelles, United Nations Development Programme, Victoria, Seychelles. P. 119. https://doi.org/10.13140/RG.2.1.4558.6009.</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.
Figs 54–55. Dyscolus spp., habitus. 54. D in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 54–55. Dyscolus spp., habitus. 54. D. verecundior Moret sp. nov., male holotype (MNHN, COI voucher PM136-04). 55. D. verecundissimus Moret sp. nov., male holotype (MNHN).
Figs 29–31. 29 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 29–31. 29. Dyscolus crespoae Moret sp. nov., habitus of the female holotype (QACZ). 30– 31. D. ravidus Moret sp. nov. 30. Habitus of the male holotype (QACZ). 31. Aedeagus, median lobe in lateral view.
Figs 45–50 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 45–50. Dyscolus spp., habitus (45–47) and aedeagus, median lobe in lateral view (48–50). 45. D. denigratus (Bates, 1891), male specimen from Guamaní. 46. D. denigratus, male specimen from Guagua Pichincha (type locality). 47. D. palatus Moret, 1998, male paratype from Atacazo. 48– 50. D. denigratus. 48. From Guamaní. 49. From Cotacachi. 50. From Guagua Pichincha.
Figs 36–41 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 36–41. Dyscolus spp., habitus (36–38) and aedeagus, median lobe in lateral view (39–40) and apex of the median lobe (41). 36. Dyscolus arauzae Moret sp. nov., male holotype (QCAZ). 37. D. piscator Moret sp. nov., male holotype (QACZ). 38. D. placitus Moret sp. nov., male holotype (MNHN). 39. D. arauzae Moret sp. nov. 40. D. piscator Moret sp. nov. 41. D. placitus Moret sp. nov. (above) and D. piscator Moret sp. nov. (below).
Figs 52–53 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 52–53. Dyscolus silvestris Moret sp. nov., male holotype (QCAZ). 52. Habitus. 53. Male aedeagus, median lobe in lateral view.
Figs 13–14 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 13–14. Dyscolus globoculus Moret sp. nov. 13. Habitus of the male holotype (MNHN, COI voucher CR064). 14. Aedeagus, median lobe in lateral view.
Figs 7–12. 7–8 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 7–12. 7–8. Dyscolus aquator Moret sp. nov. 7. Habitus of the male holotype (QCAZ). 8. Aedeagus, median lobe in lateral view. 9–10. D. incommunis Moret sp. nov. 9. Aedeagus, median lobe in lateral view. 10. Habitus of the male holotype (QCAZ). 11–12. D. rivinus Moret sp. nov. 11. Apex of the elytra. 12. Aedeagus, median lobe in lateral view.
Figs 3–6. 3–4 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes
Figs 3–6. 3–4. Dyscolus eleonorae Moret sp. nov. 3. Habitus of the male holotype (QCAZ). 4. Aedeagus, median lobe in lateral view. 5–6. D. giselae Moret sp. nov. 5. Habitus of the male holotype (QCAZ). 6. Aedeagus, median lobe in lateral view.
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