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opencc-by-4.0Jul 2017View details →

Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene content, gene synteny and inverted repeat length for a set of 15 plastid genomes of early-diverging angiosperms. Seven plastid genomes of the Nymphaeales were newly sequenced for this investigation. We compare gene order and inverted repeat (IR) length across all genomes, review the gene annotations of previously published genomes, generate a multi-gene alignment of 77 plastid-encoded genes and reconstruct the phylogenetic relationships of the taxa under study. Our results show that gene content and synteny are highly conserved across early-diverging angiosperms: All species analyzed display complete gene synteny when accounting for expansions and contractions of the IRs. This conservation was initially obscured by ambiguous and potentially incorrect gene annotations in previously published genomes. We also report the presence of intact open reading frames across all taxa analyzed. The multi-gene phylogeny displays maximum support for the families Cabombaceae and Hydatellaceae, but no support for a clade of all Nymphaeaceae. It further indicates that the genus Victoria is embedded within Nymphaea. Plastid genomes of Trithuria were found to deviate by numerous substitutions and length changes in the IRs. Phylogenetic analyses further indicate that a previously published plastome named Nymphaea mexicana falls into a clade of N. odorata and should be re-evaluated.

opennotspecifiedJan 2022View details →

Fig. 11 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 11. Holotype of Cryptopone gilvatumida (unique specimen identifier CASENT0631951).

opennotspecifiedJan 2022View details →

Fig. 10 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 10. Holotype of Cryptopone gilvagrande (unique specimen identifier CASENT0614525).

opencc-zeroJan 2024View details →

Supplementary material 3 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Syntypes of Populus gonggaensis N. Chao & J.R. He

Figure 4 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Figure 4 Morphological comparison of Populus gonggaensis with P. cathayana and P. lasiocarpaA male flower of P. cathayana (floral disc entire) B female flower of P. cathayana (floral disc entire, ovary glabrous) C male flower of P. lasiocarpa (floral disc parted) D female flower of P. lasiocarpa (floral disc parted, ovary pannose) E capsule of P. cathayana (floral disc persistent, pericarp glabrous) F capsule of P. lasiocarpa (floral disc deciduous, pericarp tomentose) G female flower of P. gonggaensis (floral disc parted, ovary partly pannose) H fruiting branch of P. cathayana (leaf abaxially glabrous, base rounded or subcordate) I leaf of P. lasiocarpa (base deeply cordate) J young leaf of P. lasiocarpa (abaxially tomentose) K young leaf of P. gonggaensis (abaxially glabrous, base subcordate).

opencc-zeroJan 2024View details →

Supplementary material 1 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Information of taxa that were not used for phylogenetic analysis in Populus subg. Tacamahaca

Figure 1 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Figure 1 A ML tree of 57 samples of the genus Populus reconstructed by IQ-TREE, based on 4,790,248 high-quality SNPs with an outgroup of P. euphraticaBML tree of 56 samples (P. gonggaensis is deleted) of the genus Populus reconstructed by IQ-TREE, based on 4,790,248 high-quality SNPs with an outgroup of P. euphratica.

Figure 3 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Figure 3 Hybrid introgression analysis using SNP matrix of Populus species A the results of ABBA-BABA statistics which measured gene flow amongst 12 species when P3 = P. gonggaensis. When D > 0 and the D value is further away from 0, it indicates that a gene swap or hybridisation event is more likely to have occurred, which means the genes of P3 is more likely to swap with those of P1 or P2 B population structure analysis for 12 species of Populus (K = 9). Each coloured bar represents one individual and coloured segments represent proportions of ancestral components. The number of individuals and species names for each lineage are shown at the bottom.

Figure 2 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Figure 2 Principal Component Analysis (PCA), based on genetic distance using SNPs data A all 57 samples representing 22 species B 37 samples representing 12 species, including Populus gonggaensis and its most closely-related species C plotted by adding PC3 (Z-axis) to B. Points inside red circle represents P. lasiocarpa, while those inside blue circle represent P. cathayana and P. koreana.

opencc-by-4.0Mar 2024View details →

Phylogenomics and the rise of the angiosperms

Data repository of Zuntini, Carruthers et al. 2024 - Phylogenomics and the rise of the angiosperms

opencc-zeroNov 2021View details →

Dataset of Phylogenomics of the olive family Oleaceae

Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization and incomplete lineage sorting. Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of incomplete lineage sorting and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the tribes. Furthermore, our results supported that post-speciation introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes. The tribe Oleeae is especially prone to ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage", and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. This study showcases that using diverse phylogenomic methods can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization and ILS.

opencc-zeroNov 2021View details →

Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization

• Background and Aims Abelia (Caprifoliaceae) is a small genus with five species, including one man-made hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, the Taiwan Island, and the Ryukyu Islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. • Methods In this study, we reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the diversification history of Abelia. • Key Results We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times, and morphology, we propose to merge A. macrotera var. zabelioides into A. uniflora. Network analyses suggested that there have been widespread and multiple hybridization events among Abelia species. These hybridization events may have contributed to the speciation mechanism and resulted in a high observed morphological diversity. The diversification of Abelia began in the early Eocene, followed by A. chinensis var. ionandra colonizing the Taiwan Island in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region (HHM) and the Taiwan Island is most likely the consequence of topographic isolation and postglacial contraction. • Conclusions We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. In addition, our results support shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction of the Mainland China-Taiwan Island. This study provides important new insights into the speciation process and taxonomy of Abelia.

opencc-zeroNov 2021View details →

Nuclear and plastid phylogenomic analyses provide insights into the reticulate evolution, species delimitation and biogeography of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights in the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.

opencc-zeroDec 2021View details →

Data from: Taxonomy in the phylogenomic era: Species boundaries and phylogenetic relationships among North American ants of the Crematogaster scutellaris group

We investigate the species-level taxonomy and evolutionary history of Nearctic ants in the Crematogaster scutellaris group (Hymenoptera: Formicidae), drawing on evidence from morphology and UCE (ultraconserved element) phylogenomics. The New World species in this group form a well supported clade that originated in the late Miocene (~7.3 Ma) and subsequently diverged into three major lineages: the coarctata clade (southwest Nearctic), the opaca clade (southwest Nearctic and northern Neotropics), and the lineolata clade (eastern Nearctic and Caribbean, with four isolated Southwest endemics). We hypothesize trans-Beringian dispersal into the New World, west-to-east movement within North America, and restriction of mesophilic species to the east with increasing aridification of the west. The ancestral nesting behavior of these ants is inferred to be ground-dwelling, and this is still the predominant condition in the arid west, whereas most species in eastern United States are arboreal. We resurrect from synonymy nine species, and describe three new species: C. detecta sp. nov. (from Nevada), C. parapilosa sp. nov. (Florida), and C. vetusta sp. nov. (Arizona). We provide a worker-based key to the thirty-four species of Crematogaster occurring in America north of Mexico, but emphasize that there are still ongoing taxonomic issues that need to be resolved.

opencc-zeroDec 2019View details →

Integrating UCE phylogenomics with traditional taxonomy reveals a trove of New World Syscia species (Formicidae, Dorylinae)

The ant genus Syscia is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.

opencc-zeroFeb 2022View details →

Supplementary material 2 from: Ciaccio E, Debray A, Hedin M (2022) Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. ZooKeys 1086: 163-204. https://doi.org/10.3897/zookeys.1086.77190

Appendix II

Figure 8 from: Ciaccio E, Debray A, Hedin M (2022) Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. ZooKeys 1086: 163-204. https://doi.org/10.3897/zookeys.1086.77190

Figure 8 H. pococki male palp comparison, retrolateral views. NE lineageA Green Mtn (MCH 01_162) B Boone Fork (MCH 01_159); ELK lineageC Elk River (MCH 01_155) D Linville Gorge (MCH 01_165); VA lineageE Cliff Mtn (MCH 04_028) F Guest River (MCH 04_027); CENT lineageG Hickory (MCH 01_144) H Wagon Road Gap (MCH 01_181); WEST lineageI Alarka (MCH 02_168) J Starr Mtn (MCH 02_156) K Backbone Rock (MCH 04_025) L Chunky Gal Mtn (MCH 02_142). Detailed specimen information provided in Suppl. material 2.

Figure 9 from: Ciaccio E, Debray A, Hedin M (2022) Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. ZooKeys 1086: 163-204. https://doi.org/10.3897/zookeys.1086.77190

Figure 9 Southern Sierra Nevada topography map with genetic and morphological sample locations (see Suppl. material 1 and Suppl. material 2). Geographic gaps and other notable geographic features mentioned in the text are highlighted.

Figure 7 from: Ciaccio E, Debray A, Hedin M (2022) Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. ZooKeys 1086: 163-204. https://doi.org/10.3897/zookeys.1086.77190

Figure 7 H. pococki male palp comparison, prolateral views. NE lineageA Green Mtn (MCH 01_162) B Boone Fork (MCH 01_159); ELK lineageC Elk River (MCH 01_155) D Linville Gorge (MCH 01_165); VA lineageE Cliff Mtn (MCH 04_028) F Guest River (MCH 04_027); CENT lineageG Hickory (MCH 01_144) H Wagon Road Gap (MCH 01_181); WEST lineageI Alarka (MCH 02_168) J Starr Mtn (MCH 02_156) K Backbone Rock (MCH 04_025) L Chunky Gal Mtn (MCH 02_142). Detailed specimen information provided in Suppl. material 2.

Figure 5 from: Ciaccio E, Debray A, Hedin M (2022) Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. ZooKeys 1086: 163-204. https://doi.org/10.3897/zookeys.1086.77190

Figure 5 Maximum likelihood mitochondrial tree. Black circles designate clusters of sequences collapsed as the same species in multi-threshold GMYC analyses; all other branches supported as separate species (e.g., n = 13 for multi-threshold model). Inset – K2P distances within and among primary mitochondrial lineages.