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opencc-by-4.0Nov 2020View details →

Fig. 4 in First records and a new genus of comb-tailed spiders (Araneae: Hahniidae) from Thailand with comments on the six-eyed species of this family

Fig. 4. Hahnia ngai sp. nov., holotype, ♀ (RMNH.ARA.18415). a–c. Habitus. a. Ventral view. b. Lateral view. c. Dorsal view. d. Prosoma, anterior view. e. Chelicerae, posterior view. f–g. Epigynum. f. Dorsal view, cleared. g. Ventral view. Scale bars: a–c = 1.0 mm; d–e, g = 0.25 mm; f = 0.1 mm.

FIG. 11 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 11. — Stridulatory apparatus:A, Discoplax longipes A. Milne-Edwards, 1867, ♀ 32.6 × 37 mm, Loyalty Islands, Lifou, Inegoj Cave, MNHN-IU-2008-11402 (= MNHN-B24815): plectrum as a ridge on cheliped merus (see arrow); B, C, Thalassograpsus harpax (Hilgendorf, 1892), ♂ 5.3 × 5.7 mm, Scattered Islands,MNHN-IU-2013-16120; B, pars stridens consisting of elongated tubercles on suborbital ridge (see arrows); C, plectrum as a thickening (see arrow) on inner edge of cheliped merus. Scale bars: A, 5 mm; B, C, 2 mm.

FIG. 9 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 9. — Pleon, thoracic sternum and genital region of Varunidae: A-C, Cyclograpsinae: Cyclograpsus punctatus H. Milne Edwards, 1837, ♂ 24.9 × 30.8.0 mm, South Australia, Kangaroo Island, MNHN-IU-2013-14994 (= MNHN-B12561); D-F, Gaeticinae: Gaetice depressus (De Haan, 1835), ♂ 15.7 × 18.0 mm, China, Amoy, MNHN-IU-2013-14990 (= MNHN-B12089); G-I, Heliceinae Sakai, Türkay & Yang, 2006: Helice tridens (De Haan, 1835), ♂ 28.7 × 34.2 mm, Japan, MNHN- IU-2016-10762 (= MNHN-B12098); J-L,Thalassograpsinae: Thalassograpsus harpax (Hilgendorf, 1892), ♂ 8.1 × 9.3 mm, Scattered Islands, MNHN-IU-2013-16120; M-O, Varuninae: Varuna litterata (Fabricius, 1798), ♂ 49.5 × 57.0 mm, Madagascar, MNHN-IU-2013-14987. Scale bars: A-K, M-O, 10 mm; L, 5 mm.

FIG. 8 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 8. — Pleon, thoracic sternum and genital region of Grapsoidea: A, D, G, J, M, thoracic sternum (brushed) with pleon; B, E, H, K, N, thoracic sternum (brushed) without pleon; C, F, I, L, O, genital region with gonopore and penis: A-C, Grapsidae: Grapsus grapsus Lamarck, 1801, ♂ 23.8 × 26.9 mm, Antilles, MNHN-IU-2013-10764 (= MNHN-B24641);D-F, Glyptograpsidae: Glyptograpsus jamaicensis (Benedict, 1892), ♂ 32.8 × 37.4 mm, Jamaica, MNHN-IU-2017-8401 (= MNHN-B127715); G-I, Percnidae: Percnon planissimum (Herbst, 1804), ♂ 29.7 × 27.7 mm, Réunion Island, MNHN-IU-2010-19798 (= MNHN-B24534); J-L, Plagusiidae: Plagusia squamosa (Herbst, 1790), ♂ 43.6 × 46.3 mm, Marquesas Islands, MNHN-IU-2011-8947; M-O, Xenograpsidae: Xenograpsus testudinatus N. K. Ng, Huang & Ho, 2000, ♂ 21.8 × 23.8 mm, NE Coast of Taiwan, MNHN-IU-2013-14995 (= MNHN-B30314). Scale bars: 10 mm.

FIG. 6 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 6. — Ventral view of Gecarcinidae to show front, proepistome, cephalic appendages, orbit and mxp3: A, Discoplax longipes A. Milne-Edwards, 1867, ♂ 32.4 × 37.2 mm, Loyalty Islands, Lifou, Inegoj Cave, MNHN-IU-2008-11402 (= MNHN-B24815); B, Cardisoma guanhumi Latreille in Latreille, Le Peletier,Serville & Guérin, 1828, ♂ 56.5 × 68.0 mm, Antilles,MNHN-IU-2013-14983 (=MNHN- B12270); C, Tuerkayana aff. hirtipes (Dana, 1851) n. comb., ♂ 61.0 × 79.0 mm, Loyalty Islands, Lifou Island, We cave, MNHN-IU-2017-8397 (= MNHN-B24811); D, T. celeste (Ng & Davie, 2012) n. comb., ♂ 44.4 × 52.2 mm, Australia, Christmas Island, ZRC 2012.0171; E, T. magnum (Ng & Shih, 2014) n. comb., ♂ 49.0 × 58.7 mm, Indonesia, Java, ZRC 2017.0252. Scale bars: 10 mm.

FIG. 7 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 7. —Thoracic sternum and frontal view: A-D, Gecarcinus ruricola (Linnaeus, 1758), ♂ 55.0 × 76.0 mm, Cuba, MNHN-IU-2017-8392 (= MNHN-B13155); E-H, Gecarcoidea lalandii H. Milne Edwards, 1837, ♂ 52.0 × 73.3 mm, Papua New Guinea, MNHN-IU-2013-13254: A, E: thoracic sternum (brushed) with pleon; B, F, thoracic sternum (brushed) without pleon; C, G: genital region with gonopore and penis, D, H, front, proepistome, cephalic appendages, orbit and mxp3. Scale bars: 10 mm.

FIG. 5 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 5. — Pleon, thoracic sternum and genital region of Gecarcinidae. A, D, G, J, M, thoracic sternum (brushed) with pleon; B, E, H, K, N, thoracic sternum (brushed) without pleon; C, F, I, L, O, genital region with gonopore and penis: A-C, Discoplax longipes A. Milne-Edwards, 1867, ♂ 32.4 × 37.2 mm, Loyalty Islands, Lifou, Inegoj Cave, MNHN-IU-2008-11402 (= MNHN-B24815); D-F, Cardisoma guanhumi Latreille in Latreille, Le Peletier, Serville & Guérin, 1828, ♂ 56.5 × 68.0 mm, Antilles, MNHN-IU-2013-14983 (= MNHN-B12270); G-I, Tuerkayana aff. hirtipes (Dana, 1851) n. comb., ♂ 61.0 × 79.0 mm, Loyalty Islands, Lifou Island, We cave, MNHN-IU-2017-8397 (= MNHN-B24811); J-L, Tuerkayana celeste (Ng & Davie, 2012) n. comb., ♂ 44.4 × 52.2 mm, Australia, Christmas Island, ZRC 2012.0171; M-O, T. magnum (Ng & Shih, 2014) n. comb., ♂ 49.0 × 58.7 mm, Indonesia, Java, ZRC 2017.0252. Scale bars: 10 mm.

FIG. 2 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 2. — Leptograpsodes octodentatus (H. Milne Edwards, 1837): A-D, neotype, ♂ 17.3 × 20.6 mm, Australia, Tasmania, King Island, TMAG G1033: A, dorsal view; B, ventral view; C, frontal view, with suborbital ridge as pars stridens; D, close-up view of plectrum as whitish ridge on P1 merus (see arrow); E, syntype of L. webhaysi Montgomery, 1931, ovigerous ♀ 27.0 × 34.0 mm, Abrolhos, WAM C71736. Scale bars: 10 mm.

FIG. 3 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 3. — Leptograpsodes octodentatus (H. Milne Edwards, 1837), ♂ 51.8 × 68.3 mm, South Australia, MNHN-IU-2013-14993 (ex NMV J55301-1): A, thoracic sternum (note sternite 8 not developed medially, only exposed laterally); B, genital area with male gonopore and penis; C, posterior part of thoracic sternum with pleon; D, front and orbit. Abbreviations: b, bridge; b.p., press-button; c, coxo-sternal condyle; cx1-5, P1-P5 coxae; e.p., exposed proximal portion of penis; e.t., extraorbital tooth; e4-e7, episternites 4-7; i.b., suborbital border; i.s., incomplete sulcus; i.t., suborbital tooth; m.l., median line; mxp3; third maxilliped; P1, P2, P3, pleonal somites 1-3; p, penis; p.e., posterior emargination; p.p., proximal portion of penis; p.r., pleonal rim; s.c., stridulating crest; s.p., sterno-pleonal cavity; 1-8, thoracic sternites 1-8; 1/2-7/8, thoracic sternal sutures 1/2-7/8. Scale bars: 10 mm.

FIG. 1 in Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838)

FIG. 1. — Leptograpsodes octodentatus (H. Milne Edwards, 1837), ♂ 51.8 × 68.3 mm, South Australia, MNHN-IU-2013-14993 (ex NMV J55301-1): A, carapace, dorsal surface; B, chelipeds; C, thoracic sternum with pleon (setal tufts visible); D, thoracic sternum without pleon; E, genital area with male gonopore and penis; F, G1, two views; G, front, orbit, antenna (with articles 1-4 and flagellum) and suborbital ridge as pars stridens. Scale bars: 10 mm.

opencc-by-nd-3.0Dec 2020View details →

Worldwide Fraxinus Genome Assemblies, Annotations, and Gene Families v0.2

The worldwide Fraxinus genome project was conducted to assess the pathogenic resistance of 34 Ash tree species to Ash Dieback and Emerald Ash Borer. The project is led by Dr. Richard Buggs. v0.1 genomes are available at ashgenome.org and on ENA. As part of Josiah Seaman's PhD thesis, he improved the assembly of 13 genomes included here as v0.2. New de novo annotations, gene families, and all associated files are included for future studies and reproducibility.  Annotations are done with GeMoMa using F. excelsior as a reference (Keilwagen et al. 2016). Gene families are defined as genes originating from a single copy at the last common ancestor with Solanum. Orthofinder outputs reconciled gene trees, aligned CDS, and gene families (Emms and Kelly 2015; Tekaia 2016). Species tree was calibrated based on fossil evidence using r8s, RAxML across 25,182,399 sites (SpeciesTreeAlignment.fa). More methods details can be found in the full Chapter two of Josiah Seaman's PhD thesis (2021). I'd be happy to talk with you if you'd like any additional information or help visualizing your genomic data. You can find the tools used to browse this data at https://fluentdna.com/ and http://graphgenome.org/ Contact me at josiah@newline.us

New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples fromCapurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

Fig. 14 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 14. Female genitalia of Obtusopyrgus farri sp. nov. µCT scans. Abbreviations: ag = albumen gland; bc = bursa copulatrix; cg = capsule gland; od = oviduct; ov = ovary; rs = receptaculum seminis; vc = ventral channel. Scale bar = 100 µm.

Fig. 12 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 12. Female genitalia of Opacuincola gretathunbergae sp. nov. µCT scans. Abbreviations: ag = albumen gland; bc = bursa copulatrix; cg = capsule gland; od = oviduct; ov = ovary; rs = receptaculum seminis; vc = ventral channel. Scale bar = 50 µm.

Fig. 10 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 10. Genitalia of Opacuincola lisannea sp. nov. µCT scans. A. ♀. B. ³. Abbreviations: ag = albumen gland; bc = bursa copulatrix; cg = capsule gland; od = oviduct; ov = ovary; pe = penis; pl = penial lobe; pr = prostate; pt = penial tip; pv = pallial vas deferens; rs = receptaculum seminis; vc = ventral channel; vd = vas deferens. Scale bars = 50 µm.

Fig. 8. Radula. SEM photographs. A in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 8. Radula. SEM photographs. A. Catapyrgus jami sp. nov. B. Opacuincola lisannea sp. nov. (from type locality). C. Op. gretathunbergae sp. nov. D. Obtusopyrgus farri sp. nov.

Fig. 11. Penis. SEM photographs. A in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 11. Penis. SEM photographs. A. Opacuincola lisannea sp. nov. (from type locality). B. Op. gretathunbergae sp. nov.C. Op. mete kahurangi subsp. nov.D. Obtusopyrgus farri sp. nov. Abbreviations: e = eye; l = penial lobe; s = snout; t = tentacle.

Fig. 6 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 6. Protoconch. SEM photographs of paratypes. A. Catapyrgus jami sp. nov. B–C. Opacuincola lisannea sp. nov. (B, topotype; C, northern locality). D. Op. gretathunbergae sp. nov. E. Op. mete kahurangi subsp. nov. F. Obtusopyrgus farri sp. nov.

Fig. 5 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 5. Shells. SEM photographs of paratypes. A. Catapyrgus jami sp. nov. B–C. Opacuincola lisannea sp. nov. (B, topotype; C, northern locality). D –E. Op. gretathunbergae sp. nov. F –G. Op. mete kahurangi subsp. nov. H–I. Obtusopyrgus farri sp. nov.

Fig. 9 in All-inclusive descriptions of new freshwater snail taxa of the hyperdiverse family Tateidae (Gastropoda, Caenogastropoda) from the South Island of New Zealand

Fig. 9. Genitalia of Catapyrgus jami sp. nov. µCT scans. A. ♀. B. ³. Abbreviations: ac = anterior capsule gland; ag = albumen gland; bc = bursa copulatrix; od = oviduct; ov = ovary; pc = posterior capsule gland; pr = prostate; pv = pallial vas deferens; rs = receptaculum seminis; te = testis; vc = ventral channel; vd = vas deferens; vs = vesicula seminalis. Scale bars = 50 µm.