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opencc-zeroMay 2024View details →

Linked collectors and determiners for: Revision of Neotropical Scelolabes Philippi (Diptera, Hybotidae, Ocydromiinae): two new species and a proposal of delimitation.

Natural history specimen data linked to collectors and determiners held within, "Revision of Neotropical Scelolabes Philippi (Diptera, Hybotidae, Ocydromiinae): two new species and a proposal of delimitation". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1f706702-b0ac-4a0b-aa50-de9e77c92fdf">https://bionomia.net/dataset/1f706702-b0ac-4a0b-aa50-de9e77c92fdf</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1f706702-b0ac-4a0b-aa50-de9e77c92fdf">https://gbif.org/dataset/1f706702-b0ac-4a0b-aa50-de9e77c92fdf</a>. Formatted as a Frictionless Data package.

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Data from: Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae)

Species delimitation is fundamental to deciphering the mechanisms that generate and maintain biodiversity. Alpha taxonomy historically relied on expert knowledge to describe new species using phenotypic and biogeographic evidence, which has the appearance of investigator subjectivity. In contrast, DNA‐based methods using the multispecies coalescent model (MSC) promise a more objective approach to describing biodiversity. However, recent criticisms suggest that under some conditions the MSC may over‐split lineages, identifying species that do not reflect biological reality. Here, we reconcile these approaches using empirical data for the Greenthroat Darter complex (Etheostoma lepidum), a small freshwater fish species with a disjunct distribution in Texas and New Mexico, USA. We demonstrate that MSC methods recognizes all nine sampled populations as distinct species, sometimes splitting specimens from a single locality into multiple species. However, environmental, phenotypic and biogeographic evidence do not corroborate the nine species supported by the MSC. Instead, collective evidence indicates that E. lepidum is comprised of just three species that are consistent with the molecular phylogeny: Etheostoma lepidum (Greenthroat Darter) in rivers draining the eastern Edwards Plateau, Etheostoma cf. lepidum (Texas Darter) in the Concho and San Saba rivers and Etheostoma cf. lepidum (Pecos Darter) in the Pecos River. The Pecos Darter is likely highly imperiled due to its localized distribution and reliance on vanishing spring‐fed stream habitats. The impending biodiversity crisis makes integrative and swift species delimitation more necessary than ever. Our study exemplifies how classic taxonomic expertise combined with molecular phylogenetics can produce a more robust description of threatened biodiversity.

opencc-zeroJun 2021View details →

opencc-by-4.0Jul 2021View details →

Cryptic Diversity in Cladosporium cladosporioides Resulting from Species Delimitation Analysis

Concatenated loci alignment (.fasta), Maximum-Likelihood, Maximum-Parsimony and Bayesian reconstruction of Cladosporium cladosporioides phylogeny.  Files represent dataset of the study: "Cryptic Diversity in Cladosporium cladosporioides Resulting from Species Delimitation Analysis"   ABSTRACT Establishing a stable taxonomy is particularly important for understanding fungal biodiversity, as well as the evolution of particular traits related to symbiotic interactions. Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic, and is the most represented Cladosporium species in genetic sequence databases, such as Genbank. Although the taxonomy of Cladosporium species is subjected to frequent revisions, which nowadays mostly rely on molecular data, few studies explored cryptic diversity of this genus using the recently developed species delimitation methods. Considering a previous study which reported several hypothetical species within C. cladosporioides, here we try to fill the gap of knowledge about phylogenetic relationships for this species and tested four different methods of species delimitation using the combined DNA barcodes ITS, translation elongation factor 1 and actin. The analyses involved 105 isolates revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we reported the erroneous taxonomical assignment of several isolates that should be ascribed to C. anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches, in order to minimize the risk of considering false positives.

Figure 4 in Four new species of terrestrial earthworms belonging to the genus Amynthas (Megascolecidae: Oligochaeta) from Taiwan with discussion on speculative synonyms and species delimitation in oligochaete taxonomy

Figure 4. Amynthas cruxus sp. nov., holotype, 170 mm. (A) Ventral view of right male pore region (gp, genital papilla; ma, male aperture; md, male disc); (B) spermathecal pore; (C) dorsal view of right spermathecae (amp, ampulla; dv, diverticulum); (D) dorsal view of right prostate gland (pg) (pd, prostatic duct); (E) dorso-lateral view of right testis sacs (ts) and seminal vesicles (sv) of a 122-mm specimen (coll. no. 2000-81-Shen) (dl, dorsal lobe; vd, vas deferens; ve, vas efferens).

Figure 3 in Four new species of terrestrial earthworms belonging to the genus Amynthas (Megascolecidae: Oligochaeta) from Taiwan with discussion on speculative synonyms and species delimitation in oligochaete taxonomy

Figure 3. Amynthas bilineatus sp. nov. (A) Ventral view of preclitellar region (gp, genital papilla) of holotype; (B) ventral view of male pore (mp) region of holotype; (C) ventral view of male pore region of a 113-mm specimen (coll. no. 2000-3-Shen); (D) dorsal view of preclitellar accessory glands (ag) of holotype; (E) dorsal view of right sperm sacs (ss) and seminal vesicles (sv) of holotype (dl, dorsal lobe); (F) dorsal view of right prostate gland of holotype; (G) dorsal view of right prostate gland and accessory gland of a 113-mm specimen (coll. no. 2000-3- Shen); (H) dorsal view of right caecum of holotype.

Figure 2 in Four new species of terrestrial earthworms belonging to the genus Amynthas (Megascolecidae: Oligochaeta) from Taiwan with discussion on speculative synonyms and species delimitation in oligochaete taxonomy

Figure 2. Amynthas chilanensis sp. nov. (A) Ventral view of right male pore region (gp, genital papilla); (B) dorsal view of spermatheca in VI of holotype (amp, ampulla; dv, diverticulum); (C) dorso-lateral view of left testis sacs (ts) and seminal vesicles (sv) of a 133-mm specimen (coll. no. 2002-25-Shen) (dl, dorsal lobe; vd, vas deferens; ve, vas efferens); (D) dorsal view of right prostatic duct (pd) of a 133-mm specimen (coll. no. 2002-25-Shen).

Figure 1 in Four new species of terrestrial earthworms belonging to the genus Amynthas (Megascolecidae: Oligochaeta) from Taiwan with discussion on speculative synonyms and species delimitation in oligochaete taxonomy

Figure 1. Amynthas shinanmontis sp. nov. (A) Ventral view of right male pore region (p, male porophore); (B) dorsal view of spermathecae of a 110-mm specimen (coll. no. 2000-77-Shen) (amp, ampulla; dv, diverticulum); (C) dorso-lateral view of right testis sacs (ts) and seminal vesicles (sv) of a 178-mm specimen (coll. no. 2000-21- Shen) (dl, dorsal lobe; vd, vas deferens; ve, vas efferens); (D) dorso-lateral view of right testis sacs and seminal vesicles of holotype; (E) large prostate gland (pg) of a 106-mm specimen (coll. no. 2000-77-Shen) (pd, prostatic duct); (F) vestigial prostate gland of a 178-mm specimen (coll. no. 2000-21-Shen); (G) nodule-like prostate gland of a 110-mm specimen (coll. no. 2000-77-Shen); (H) prostate gland absent for a 122-mm specimen (coll. no. 2000-21-Shen).

Figure 5 in Four new species of terrestrial earthworms belonging to the genus Amynthas (Megascolecidae: Oligochaeta) from Taiwan with discussion on speculative synonyms and species delimitation in oligochaete taxonomy

Figure 5. Comparison of male pore regions, ventral views. (A) A. hatomajimensis (Ohfuchi 1957, p 246, Figure 20- 1, Ryukyus, Japan); (B) A. toriii (Ohfuchi 1941, p 246, Figure 2-1, Kyusyu, Japan); (C) A. tajiroensis (Ohfuchi 1938, p 48, Figure 12-2, Honshu, Japan); (D, E) A. corticis (5P. diffringens, Taiwan); (F) P. heterochaeta (5A. corticis) (Chen 1933, p 235, Figure 16B, C, China).

Figure S1 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure S1. Bayesian consensus tree of the Mesobuthus caucasicus complex reconstructed from mitochondrial DNA sequences.

Figure 9 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 9. Phylogeny the Mesobuthus caucasicus complex reconstructed using mitochondrial DNA sequences. The Przewalski's scorpion (M. przewalskii) is deeply diverged from other species and the Chinese scorpion (M. martensii) belongs to the species complex. Node supports are shown by bootstrapping probabilities from 1000 replicates and Bayesian posterior probabilities.

Figures 1–8 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figures 1–8. Mesobuthus przewalskii stat. nov., from Qiemo, Xinjiang. 1. Male, dorsal view. 2. Male, ventral view. 3. Female, dorsal view. 4. Female, ventral view. 5. Male, dentition of pedipalp chela movable finger. 6. Male, dentition of pedipalp chela fixed finger. 7. Male, ventral aspect of genital operculum and pectines. 8. Female, ventral aspect of genital operculum and pectines. Scale bars: 1–4 = 5.0 mm; 5–8 = 2.0 mm.

Figure 11 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 11. Ecological niche models of Mesobuthus scorpions. Potential distribution areas for the Przewalski's scorpion M. przewalsii (purple) is shown together with the Chinese scorpion M. martensii (green) and other species of the M. caucasicus complex (yellow). The entire Tarim Basin and adjacent Gobi region are suitable for survival of M. przewalskii. No area to the west of the Tianshan Mountains and the Pamir Plateau is suitable for M. przewalskii, and similarly no area to the east of the Tianshan Mountains and the Pamir Plateau is suitable for other species of the M. caucasicus complex. There are overlaps in predicted suitable distribution areas between M. przewalskii and M. martensii along the northeast edge of the Qinghai-Tibet Plateau. The suitable areas in the Junggar Basin and to the north of the Tianshan Mountains are likely due to over prediction of the model, because M. przewalskii does not occur in these regions. Ecological niche model for M. martensii was adopted from Shi et al. 2007.

Figure 10 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 10. Phylogenetic network for the Mesobuthus caucasicus species complex. Although the interrelationships between species is poorly resolved, no reticulations have occurred in the most recent common ancestors for each species. The Przewalski's scorpion M. przewalskii is clearly diverged from other member of the species complex and warrants a species rank. The divergence of the Chinese scorpion M. martensii is comparable to the divergences among the members of the species complex.

FIG. 22. Central Blackwater Amazon. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 22. Central Blackwater Amazon. A. Yellow area delimits the distribution pattern. B. Biotoecus spp. (data fom Kullander, 1989). C. Dicrossus spp. (data fom Kullander, 2011). D. Hemigrammus analis (blue dots; records from MZUSP), Hemigrammus coeruleus (red dots; records from MZUSP), Hemigrammus stictus (yellow dots; records from MZUSP).

FIG. 8. Amazon and Paraguay Lowlands. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 8. Amazon and Paraguay Lowlands. A. Yellow area delimits the distribution pattern. B. Epapterus dispilurus (data from Vari and Ferraris, 1998). C. Hemigrammus lunatus (data from Ota et al., 2014). D. Mesonauta festivus (data from Kullander and Silvergrip, 1991, and Schindler, 2005).

FIG. 5. Broadly distributed lineages. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 5. Broadly distributed lineages. A. Yellow area delimits the distribution pattern. B. Hoplias malabaricus (red dots; records from MZUSP), Erythrinus erythrinus (green diamonds; records from MZUSP), Hoplerythrinus unitaeniatus (yellow triangles; records from MZUSP). C. Synbranchus marmoratus, records from MZUSP. D. Callichthys callichthys (data from Lehmann and Reis (2004) with additional records from MZUSP).

FIG. 16. Amazonian uplands. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 16. Amazonian uplands. A. Yellow area delimits the distribution pattern. B. Sartor spp. (records from MZUSP). C. Teleocichla spp. (records from MZUSP). D. Tocantinsia piresi (records from MZUSP).

FIG. 19. Brazilian Shield. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 19. Brazilian Shield. A. Yellow area delimits the distribution pattern. B. Caiapobrycon spp. (records from MZUSP). C. Jupiaba apenima (records from MZUSP). D. Moenkhausia gr. pankilopteryx/pirauba (records from MZUSP).

FIG. 9. Amazon-only Lowland. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 9. Amazon-only Lowland. A. Yellow area delimits the distribution pattern. B. Adontosternarchus balaenops (data from Mago-Leccia et al., 1985). C. Cetopsis candiru (data from Vari et al., 2005). D. Curimatella meyeri (data from Vari, 1992a).

FIG. 21. Cis-Andean foothills. A. Yellow area delimits the distribution pattern. B in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species

FIG. 21. Cis-Andean foothills. A. Yellow area delimits the distribution pattern. B. Astyanacinus spp. (data from Dagosta, 2011). C. Leporinus striatus (data from Birindelli and Britski, 2013). D. Steindachnerina dobula (data from Vari, 1991).