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Figure 6 in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 6. Potamonautes karooensis sp. nov., male holotype (SAM-MB A094477) A, major right cheliped; B, minor left cheliped. Scale bar represents 10 mm.

Figure 5 in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 5. Potamonautes karooensis sp. nov., male holotype (CL = 47.48 mm) (SAM-MB A094477) Erasmuskloof, Eastern Cape Province, South Africa. A, whole animal dorsal aspect; B, whole animal ventral aspect; C, cephalothorax, frontal aspect. Scale bar represents 10 mm.

Figure 4 in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 4. BEAST chronogram of the three concatenated mtDNA loci (16S rRNA, 12S rRNA + COI) dataset for all the described southern African Potamonautes species. Node bars show 95% highest posterior distributions for each divergence date estimate. The terminal labelled P. sp. nov., represents a yet undescribed species from Hogsback. Posterior probability values> 0.95 (PP) together with bootstrap values> 75% are shown above and below branches, respectively.

Figure 3 in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 3. Ultrametric BEAST tree phylogeny of the COI sequence data for the four Afrotropical genera: A, Potamonautes; B, Liberonautes; C, Nesonautes; D,

Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S rRNA + COI sequence data, demonstrating the evolutionary relationships within the P. sidneyi s.l. species complex. Statistical support for nodes is provided as posterior probability values above nodes (> 0.95 PP) and bootstrap values below nodes (> 75%). An * or # denotes nodal relationships that were not supported (<0.95 PP/ <75%). Potamonautes sidneyi s.s. (clade 3) localities are marked with a dark blue triangle, while P. danielsi (clade 5) localities are marked by an orange square. The two new species, P. karooensis, (clade 2) and P. Ʋalles (clade 4), are marked by a light-blue circle and a green diamond, respectively. Specimens of P. barbarai are confined to clade 1.

Figure 1. A in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods

Figure 1. A map of southern Africa (South Africa and Eswatini) showing the sites where freshwater crabs were collected during the present study. The 30 Potamonautes sidneyi s.s. sample localities are represented by solid, black triangles; the eight P. danielsi sample localities are represented by brown squares, while the four sample localities for P. karooensis sp. nov. are represented by a turquoise circle and three sample localities for P. Ʋalles sp. nov., are represented by a green diamond. The Papkuilsfontein locality of P. barbarai was combined with specimens from 13 conspecific populations sequenced by Daniels et al. (2006) and represented by a red triangle. The sample numbers correspond to the 59 localities in Table 1.

opencc-zeroMay 2023View details →

dryad32/100

Species delimitation beyond phylogenomics: integrative approaches reveal gentoo penguin speciation

<p>Isolation and adaptation to new environments are important steps for reproductive isolation and consequently speciation. Seabirds have low phenotypic variation along their ranges in the absence of clear geographic or environmental barriers to dispersal. Despite the lacking visible phenotypic differences, the number of taxa for the gentoo penguin (<em>Pygoscelis papua</em>, Forster 1781) in the Southern Ocean has been under debate for the last decade, ranging from one to six different taxa. Here, we provide several lines of evidence from genomics, ecology, morphological data, and a complete systematic review that supports four distinctive gentoo penguin species, including the description of a new species. We also provide future niche projections for each of these species. Gentoo penguin genomes (n = 64) recover four main lineages: the northern gentoo (from South America), the southern gentoo (Antarctic Peninsula and maritime Antarctica, south of the Antarctic Polar Front, APF), the southeastern gentoo (from Kerguelen Islands), and the eastern gentoo (colonies located at lower latitudes north of the APF). Our analysis of selection across the genome recovered between 42 and 101 genes under selection for each of the four species, demonstrating that the four species are experiencing differing selective pressures that have caused them to diverge adaptively. The function of these genes affects traits that include reproduction, thermoregulation, osmoregulation, feed efficiency, and morphological variation. Morphological data were taken from museum individuals of all lineages, including from South Georgia gentoos, which have previously been considered a distinct taxon. Multivariate morphological comparisons of all pairs of lineages showed that the northern, southern, southeastern, and South Georgia gentoo penguins are morphologically distinct from each other (p < 0.05 for all pairwise comparisons), while the eastern lineage is intermediate in size and overlaps in morphospace with other lineages. This result also suggests that body size across latitudes is in direct contrast to Bergmann's rule. Here, we describe the southeastern gentoo penguin from Kerguelen Island and confirm the taxonomic rank of gentoos from Macquarie Island and South Georgia Island as subspecies. Species distribution modelling suggests that climate change will expand the favourable space for the southern range expansion of the southern gentoo penguin but would result in a net loss of suitable habitats for compensatory niche shift relocation for the northern and southeastern gentoos. Despite this, amongst the three subantarctic species, the northern and southeastern gentoos possess high neutral and adaptive genetic diversity, including genes related to cold and heat response. This may represent a higher potential to evolve under environmental changes compared with the eastern gentoo penguin; therefore, the future resilience of each species remains uncertain. This study reinforces the urgent need for explicit recognition and protection of the four regional gentoo species based on their genetic, morphological, and ecological distinctiveness.</p>

FIGURE. 4 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 4. Plot of first against second canonical variates from CAN for three species. Closed circle: H. akiensis; open triangle: H. sumidai; open square: H. geiyoensis.

FIGURE. 3 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 3. Results of STRUCTURE analysis based on the 403 SNPs. (A) Estimated mean lnL and Delta K values for each number of cluster (K). (B)

FIGURE. 2 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 2. Bayesian tree based on the complete cyt-b gene for the Hynobius akiensis sensu lato and related species. Asterisks above branches indicate nodes with bootstrap supports for ML inference (bs)>70 % and Bayesian posterior probability (bpp)>95 %.

FIGURE. 1 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 1. Map of Chugoku and Shikoku district showing ranges of Hynobius akiensis, H. sumidai, H. geiyoensis, H. utsunomiyaorum, H. setouchi and H. iwami.

opencc-zeroMay 2023View details →

Supplementary material 2 from: Souza CS, Mattox GMT, Vita G, Ochoa LE, Melo BF, Oliveira C (2023) Molecular species delimitation and description of a new species of Phenacogaster (Teleostei, Characidae) from the southern Amazon basin. ZooKeys 1164: 1-21. https://doi.org/10.3897/zookeys.1164.102436

Best-score results of Assemble Species by Automatic Partitioning (ASAP) delimitation of species of Phenacogaster

opencc-zeroJun 2023View details →

Supplementary material 4 from: Monjaraz-Ruedas R, Mendez RW, Hedin M (2023) Species delimitation, biogeography, and natural history of dwarf funnel web spiders (Mygalomorphae, Hexurellidae, Hexurella) from the United States / Mexico borderlands. ZooKeys 1167: 109-157. https://doi.org/10.3897/zookeys.1167.103463

Ingroup + outgroup UCE concatenated ML tree. Specimen numbers correspond to those in Suppl. material 1.

Fig. 2 in Phylogeography and species delimitation of the Asian cavity-nesting honeybees

Fig. 2. Bayes Factor species delimitation tests hypotheses of the number of species in a set of samples based on the multi-locus data. Blue lines show trace coalescence of SNPs, in which simultaneous coalescences to an ancestor node indicate a higher likelihood of speciation event. The best-supported model recognized A. nigrocincta and 6 species among populations currently placed within A. cerana.

Fig. 4 in Phylogeography and species delimitation of the Asian cavity-nesting honeybees

Fig. 4. RASP uses the localities of individuals and RADseq SNP data to reconstruct ancestral ranges for the major nodes. Above: Ultrametric tree; colors of the vertical blocks on the right indicate the single most likely reconstructed ancestral range for each of the major nodes.The 2 most likely ancestral ranges are shown by color-coded pie diagrams at the major nodes on the tree. Additional possible, but less likely, ancestral ranges at each node are indicated in black. Below: Event graph; X-axis shows time along the same scale as the ultrametric tree.Y-axis shows number of estimated events (dispersal, vicariance, extinction, and "standard̎, or corrected number of events considering the probabilities of all vicariance, dispersal, and extinction events).

Fig. 1 in Phylogeography and species delimitation of the Asian cavity-nesting honeybees

Fig. 1. (A) BEAST maximum clade credibility tree with 10 Apis clades indicated by colored bars, including: the dwarf honey bees Apis andreniformis and A. m. florea; the giant honey bees, A. dorsata; and the cavity-nesting species A. mellifera, A. koschevnikovi, A. nigrocincta, and A. cerana in the broad sense. Within A. cerana in the broad sense there are 5 clades associated with their geographic distribution: oceanic Philippine, India-yellow, Sundaland, Mainland, and Indiablack, which is nested within the Mainland clade.Terminals are individual bee samples, black, gray, and white circles indicate strength of support for nodes, and colored bars flanking nodes indicate the maximum credibility interval. Numbered nodes indicate the most recent common ancestors of clades discussed in the text. (B-F) STRUCTURE analyses support the hypothesis that populations currently placed in A. cerana can be divided into 4 lineages: oceanic Philippines, Indiayellow, Sundaland, and Mainland in the narrow sense.

Fig. 3 in Phylogeography and species delimitation of the Asian cavity-nesting honeybees

Fig. 3. Discriminant analysis of principle components (DAPC) indicates the number of isolated clusters among the individuals included in the analyses. Crosses represent the centroid of each group. Discriminant analyses were conducted using the first 20 principal component axes for cumulated variance (inset graphs in A and B show PCA eigenvalues; first 20 principal component axes are shaded black). (A) Apis mellifera and A. koschevnikovi are isolated from other cavitynesting Apis populations. Oceanic Philippine cavity-nesters and A. nigrocincta are shown as distinct groups very near the remaining populations. (B) This analysis shows 3 well-isolated groups among populations currently placed within A. cerana (excluding the Philippine cavity-nesters): Sundaland, India-yellow, and Mainland A. cerana.

opennotspecifiedSep 2023View details →

FIGURE 2 in DNA barcoding of the genus Apaidia Hampson, 1900 for species delimitation from Western Mediterranean fauna (Lepidoptera, Erebidae)

FIGURE 2. Distribution of Apaidia samples studied (red squares: A. mesogona; green triangles: A. rufeola; black circles: A. barbarica) Note that each point may represent more than one specimen. The map was created using www.simplemappr.net.

opennotspecifiedSep 2023View details →

FIGURE 1. A, B in DNA barcoding of the genus Apaidia Hampson, 1900 for species delimitation from Western Mediterranean fauna (Lepidoptera, Erebidae)

FIGURE 1. A, B. Male and female specimens of Apaidia mesogona; C, D. Male and female specimens of Apaidia barbarica; E, F. Male and female specimens of Apaidia rufeola (Photographies by J. Gastón).