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Fig. 14 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 14. Wadeura species, petiole lateral views. (A) W. guianensis (CASENT0640150). (B) W. pauli (CASENT0637806). (C) W. holmgreni (CASENT0373370). (D) W. holmgrenita (CASENT0637779). Scale bars are 0.2 mm.

Fig. 6 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 6. Biogeography of the Cryptopone gilva complex within Central America. Chronogram inferred using BEAST2, 300 UCE loci, and a fixed topology (all UCE samples and SWSC-EN partitioning). Only results for the C. gilva complex are shown (see Supp Fig. 6 [online only] for the full results). Numbers on nodes are mean ages in millions of years ago and node bars are 95% Highest Posterior Densities (HPD).The map inset shows the distribution of C. gilva-clade samples within Central America. Colored dots match tip labels of the chronogram. Sites where specimens were identified by morphology alone (no sequencing) are shown as x for C. gilvagrande and a small black dot for C. guatemalensis. Samples of true C. gilva from the United States are not shown in the map.

Fig. 7 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 7. Shape of third abdominal sternite, Cryptopone vs.Wadeura. Cryptopone gilvagrande (CASENT064143), lateral view (A), oblique ventral view (B). Wadeura guianensis (CASENT0640149), lateral view (C), oblique ventral view (D). Scale bars are 0.2 mm.

Fig. 1 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 1. Relationships among Cryptopone lineages based on analysis of 2,232 UCE loci and the SWSC-EN partitioning scheme. Among lineages, the South American clade is separate from the North/Central American clade of Cryptopone and they are not closely related.The constituent species of the South American clade are transferred to the resurrected genus Wadeura. All node support values are at maximum (UFB/SH-aLRT values of 100/100).The photo insets are of Wadeura holmgreni (CASENT0373370, Credit: Michelle Esposito) and C. gilva (CASENT0003325, Credit: April Nobile). The same tree with support values is available in Supp Fig. 1 (online only).

Fig. 5 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 5. Species tree and species delimitation in the Cryptopone gilva complex.The species tree was inferred using SNP data and the Bayesian program SNAPP, with the resulting tree set displayed using DensiTree.The SNAPP densitree shows at least four clearly differentiated species-level lineages. Species delimitation using the programs BPP, SODA, and bPTP, recovered between 4 and 17 species.The results for the UCE samples only are mapped onto the SNAPP densitree result. The connected red bars represent single species that were not monophyletic in the SNAPP phylogeny. The colored boxes and blue species names represent the final species delimitation and taxonomy.

Fig. 3. Relationships among samples within the C in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 3. Relationships among samples within the C. gilva complex based on analysis of 2,199 UCE loci and the SWSC-EN partitioning scheme. Four main clades were recovered and these were delimited as species using an integrative approach. Support values are UFB/SH-aLRT with maximum supports (100/100) not shown.The photo inset is of C. guatemalensis (CASENT0646802; Credit: John Longino).The same tree with support values is available in Supp Fig. 2 (online only).

opennotspecifiedJul 2024View details →

FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P in A new species of Plumarella (Octocorallia: Calcaxonia: Primnoidae) from the Northeast Pacific, and the redescription of Plumarella longispina Kinoshita, 1908

FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P. williamsi (in bold), the redescribed species P. longispina (in red), the related taxa and rooted to outgroup genera. ML bootstrap support values>70% are shown above branches.

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Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

opencc-zeroDec 2015View details →

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UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders

The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.

opencc-zeroJul 2021View details →

opencc-by-4.0Jun 2021View details →

Quality Control, Assembly and Phylogenomics results using UCEasy from the UCEs

UCEasy was used to reproduce the results of the analysis of UCEs of 115 individuals representing 53 species of birds of the genus Turdus, present in the work of Batista et al. (2020), available at https://doi.org/10.1098/rspb.2019.2400. The methodology adopted by UCEasy can be seen at https://github.com/uceasy/uceasy, and we obtained results for different constructions of phylogenetic matrices. Based on the amount of UCE loci, these matrices vary in the degree of missing data allowed, where 75% represents a matrix that allows a greater amount of missing data compared to the 85% matrix, since these percentages represent how complete the matrices of data are.

Fig. 11 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 11. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia madrensis (holotype worker), S. JTL066 (worker, CASENT0610648), S. benevidesae (holotype worker), S. chiapaneca (holotype worker), S. parietalis (holotype worker), S. setosa (holotype worker), S. JTL073 (worker, MCZ-ENT00511569), S. JTL075 (worker, CASENT0601445), S. disjuncta (holotype worker), and S. augustae (worker, CASENT0644275). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 10 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 10. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia jennierussae (holotype worker), S. persimilis (holotype worker), S. JTL018 (worker, JTLC000013995), S. machaquila (holotype worker), S. murillocruzae (holotype worker), S. truncata (holotype worker), S. JTL084 (worker, FMNHINS0000095760), S. JTL050 (worker, CASENT0249320), S. JTL082 (worker, CASENT0617700), and S. honduriana (lectotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 7 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 7. Phylogenetic relationships among COI barcode sequences for Syscia. Red samples were sequenced for UCEs. Black samples were downloaded from the BOLD database.The tree was inferred using IQ-TREE with the data partitioned by codon position. Black circles on nodes indicate high support, which we define as ≥95% ultrafast bootstrap support and ≥95% SH-like branch support. Clades of named species are shaded as a visual aid, with gray outlines indicating non-monophyly of species.

Fig. 1 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 1. Variation in Syscia occipital carina. (A) Flange weakly developed, less visible in face view. (B) Flange strongly developed, easily visible in face view.

Fig. 6 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 6. Phylogeny of New World Syscia, inferred using the program IQ-TREE and 1,388 UCE loci.Two outgroup taxa (two species of Ooceraea) are not shown. Node support values (ultrafast bootstrap/SH-like) <100/100 are depicted with red dots.The imaged specimen is S. ticomontana (CASENT0644376).

Fig. 3 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 3. Variation in Syscia profiles and pilosity. (A) AIII in dorsal view trapezoidal, with convex sides. (B) AIII in dorsal view weakly trapezoidal, with convex sides. (C) AIII in dorsal view trapezoidal, with flat sides. (D) AIV in dorsal view, with convex sides, anterior margin not truncate. (E) AIV in dorsal view, with convex sides, anterior margin moderately truncate. (F) AIV in dorsal view, with nearly flat sides, anterior margin strongly truncate. (G) AIII dorsal profile strongly convex. (H) AIII dorsal profile weakly convex. (I) AIII dorsal profile flat. (J) AIV dorsal profile convex. (K) AIV dorsal profile weakly convex. (L) AIV dorsal profile flat. (A, B, G, J) Standing pilosity long, coarse. (C, H, K) Standing pilosity of medium length and thickness. (I, L) Standing pilosity short, fine.

Fig. 13 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 13. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia latepunctata (holotype worker), S. borowieci (holotype worker), S. volucris (holotype worker), S. JTL076 (queen, CASENT0614221),S. JTL064 (worker, CASENT0631661), S. JTL033 (worker, CASENT0611831),S. grandis (holotype worker), and S. JTL003 (worker, INB0003213589). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 9 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 9. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia pervagata (holotype worker), S. peten (holotype worker), S. JTL074 (worker, MCZ-ENT00511564), S. brachyptera (holotype worker), S. valenzuelai (holotype worker), S. JTL071 (worker, FMNHINS0000095759), S. quisquillis (holotype worker), S. sumnichti (holotype worker), S. JTL060 (worker, CASENT0644220), and S. JTL085 (worker, CASENT0602939). Scale bars 0.2 mm. Species are in order of mean HW, which is shown in the lower left of the distribution map. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 2 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 2. Variation in Syscia subpetiolar process. (A) Subtriangular with flat to concave posterior margin. (B) Subtriangular with convex posterior margin. (C) Subtriangular with small tooth on posterior margin. (D) Subquadrate. (E) Subtriangular with large acute tooth on posterior margin. F. With fenestra and notch on posterior margin.

Fig. 4 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 4. Illustrations of Syscia measurements. HL: head length, HW: head width, MSL: mesosoma length, AIIIL: abdominal tergite III length, AIIIW: abdominal tergite III width, AIVL: abdominal tergite IV length, AIIVW: abdominal tergite IV width.