Find research datasets worth reusing

opencc-by-4.0May 2020View details →

Fig. 1 in Integrative taxonomy of the genus Dyscolus (Coleoptera, Carabidae, Platynini) in Ecuadorian Andes

Fig. 1. Map of the Ecuadorian Andes with the localisation of the sampled sites.

opencc-by-4.0Mar 2019View details →

Figure 37 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species

Figure 37. Heterolepisma cooloola sp. nov. from leaf litter at Carlo Point.

opencc-by-4.0Mar 2019View details →

Figure 1 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species

Figure 1. Collection localities.

opencc-by-4.0Mar 2019View details →

Figure 6 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species

Figure 6. Heterolepisma coorongooba sp. nov. Glen Davis, NSW.

opencc-zeroJan 2022View details →

Speciation hypotheses from phylogeographic delimitation yield an integrative taxonomy for Seal Salamanders (Desmognathus monticola)

Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases; a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large datasets. Integrative taxonomy can therefore reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover two geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As datasets grow more comprehensive, species delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies.

opencc-zeroMay 2022View details →

Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study,we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses. Our results reveal that the isolated north-central Chinese populations of Tarsiger cyanurus, described as the subspecies albocoeruleus but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic T. indicus formosanus to be distinctive in genetics, song and morphology from T. i. indicus and T. i. yunnanensis of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both albocoeruleus and formosanus merit full species status. We propose their treatment as 'Qilian Bluetail' T. albocoeruleus and 'Taiwan Bush Robin' T. formosanus, respectively.

opencc-zeroJun 2022View details →

Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

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 due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has 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 (SNPs) were first used to resolve Pocillopora 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 previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. 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 Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus.

opencc-zeroAug 2022View details →

Underestimated Neotropical diversity: Integrative taxonomy reveals two unrelated look-alike species in a suboscine bird (Pachyramphus albogriseus)

We applied an integrative taxonomic framework to evaluate the systematics of the Neotropical Black-and-white Becard, Pachyramphus albogriseus Sclater 1857. Combining phylogenomic (ultraconserved elements), morphological, and vocalization data, we confirmed that this species is polyphyletic; some individuals form a clade sister to P. polychopterus and should be afforded species rank as P. salvini Richmond 1899 (Slender-billed Becard), whereas the remaining subspecies of P. albogriseus (Broad-banded Becard) are sister to P. major. We found that P. salvini differs from P. albogriseus in song, color of the lores, wing-bar width, body size, and bill width. Whereas P. albogriseus occurs in montane forest in Costa Rica and Panama (ssp. ornatus) and along the eastern slope of the Andes from to N Venezuela to S Peru (ssp. albogriseus), P. salvini is found in the lowlands from Pacific Colombia south to NW Peru and in the Río Marañón drainage. The latter also occurs, possibly only seasonally, along the eastern slope of the Andes, where the two species' ranges approach closely. We treat P. a. guayaquilensis Zimmer 1936 as a junior synonym of P. salvini Richmond 1899, and P. a. coronatus Phelps and Phelps 1953 as a junior synonym of P. a. albogriseus Sclater 1857. This study provides a striking example of a major problem for comparative biology: underestimated and mischaracterized diversity. We argue that there are likely many more cases like this awaiting discovery.

opencc-by-4.0Oct 2021View details →

Figure 1 in Integrated taxonomy supports the identification of some species of Phytoseiidae (Acari: Mesostigmata) from Georgia

Figure 1 Neighbour joining phylogenetic tree includingAmblyseius eharaifrom Georgia, specimens

opencc-by-4.0Mar 2018View details →

Concatenated SNP data: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data

Concatenated unliked SNP data in phylip format used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.

opencc-by-4.0Mar 2018View details →

Raw genomic RadSeq data from: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data

Raw genomic RadSeq data from individuals used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.

opencc-by-4.0Jul 2019View details →

Fig. 11 in Integrative taxonomy resuscitates two species in the Lasioglossum villosulum complex (Kirby, 1802) (Hymenoptera: Apoidea: Halictidae)

Fig. 11. Geographical distribution of Lasioglossum villosulum trichopse (Strand, 1914).

opencc-by-4.0Jul 2019View details →

Fig. 5. Halictus hirtellus Schenck, 1896 in Integrative taxonomy resuscitates two species in the Lasioglossum villosulum complex (Kirby, 1802) (Hymenoptera: Apoidea: Halictidae)

Fig. 5. Halictus hirtellus Schenck, 1896, lectotype, ♀.

Fig. 6 in Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta)

Fig. 6. Epipterygium biauritum sp. nov. A, Habitus; B, Dorsal leaf; C, Perichaetial leaf apex.

Fig. 9. Epipterygium nagasakense. A in Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta)

Fig. 9. Epipterygium nagasakense. A, Habitus; B, Dorsal leaf; C, Perichaetial leaf apex.

Fig. 5 in Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta)

Fig. 5. Epipterygium atlanticum sp. nov. A, Habitus; B, Dorsal leaf; C, Perichaetial leaf apex.

Fig. 4 in Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta)

Fig. 4. Epipterygium tozeri (Grev.) Lindb. A, Habitus; B, Dorsal leaf; C, Perichaetial leaf apex.

Fig. 7 in Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta)

Fig. 7. Epipterygium oreophilum sp. nov. A, Habitus; B, Dorsal leaf; C, Perichaetial leaf apex.