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opennotspecifiedMar 2021View details →

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.

opennotspecifiedMar 2021View details →

Fig. 12 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 12. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia tolteca (lectotype worker), S. atitlana (holotype worker), S. lacandona (holotype worker), S. JTL049 (worker, CASENT0644222), S. JTL065 (worker, CASENT0602939), S. amblyogyna (holotype worker), S. ticomontana (holotype worker), S. JTL017 (worker, INB0003693097), S. JTL079 (worker, CASENT0642985), and S. transisthmica (holotype 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 (not shown for S. tolteca, with type locality 'Guatemala').

opennotspecifiedMar 2021View details →

Fig. 8 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 8. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia minuta (holotype worker), S. parva (holotype worker), S. JTL067 (worker, CASENT0644012), S. pollula (holotype worker), S. JTL069 (worker, CASENT0644008), S. JTL068 (queen, CASENT0613276), S. austrella (holotype worker), S. JTL037 (worker, CASENT0635747), S. quisquillis Arizona form (worker, FMNHINS0000095772), and S. boudinoti (holotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.1 mm for S. minuta to S. JTL037, 0.2 mm for S. quisquillis Arizona form and S. boudinoti. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.

Fig. 5 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia

Fig. 5. Female holotype of Schwarzia gretae sp. nov. (A) Habitus, dorsal view. (B) Habitus, frontal view. (C) Habitus, lateral view. (D) Label information as deposited with the holotype. (E) Details ofT4–T5. Scale bars show 1 mm.

Fig. 4 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia

Fig. 4. Habitat photographs of Schwarzia collecting sites in Kenya.(A) Ukasi Hill, November 2011.Specimens of S. elizabethae and paratypes of S.gretae and S. icipensis were collected in the area during this month. (B) Ukasi Hill, April 2018.The holotype and paratypes of S. gretae were collected near the Hill in April and May. Pictured from left to right are field worker Ken Katinga Ngalu, technical assistant Josephat Bukhebi, technician Joseph Gitau Ndungu, and field worker Richard Maithyia Munyao. (C) Mulu Musingila's farm in Kitui Co. nearTsavo East National Park. Standing next to the trap is farm owner and field worker Mulu Musingila. Schwarzia elizabethae and S. emmae were collected on the farm in a Malaise trap (December 2016). (D) Sosoma area, April 2018. Habitat of S. emma. Pictured from left to right are field worker Richard Maithyia Munyao.Technician Joseph Gitau Ndungu,Technical assistant Josephat Bukhebi and field worker Mung'atu Kimanzi Mwanzau.

Fig. 1 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia

Fig. 1. Fossil-calibrated chronogram of Neolarrini in the new sense (including Biastes, Neolarra, Rhopalolemma, Townsendiella and Schwarzia) based on 773 ultraconserved elements. Pie charts show possible ancestral ranges. Individual slices are scaled according to their probability as calculated through BioGeoBEARS. Bootstrap support (BS) values and posterior probabilities are omitted but correspond to 100 and 1.0 for all nodes, except for the branching of Oreopasites which has a lower BS value.Asterisks (*) indicate newly described species. Stem and crown ages of host taxa along the timeline on the left are taken from Cardinal et al. (2018). Scale bars next to specimen photographs indicate 2 mm length.

Fig. 2 in Phylogenomic and Morphological Reevaluation of the Bee Tribes Biastini, Neolarrini, and Townsendiellini (Hymenoptera: Apidae) With Description of Three New Species of Schwarzia

Fig. 2. Summary of phylogenetic relationships of Neolarrini with all described species, except for Neolarra. Solid lines show relationships estimated with molecular data and placements with dashed lines are derived from morphology or taxonomic information. Mapped diagnostic characters are listed in Table 3. Larval morphological characters are indicated by a gray background. Information on bee and floral hosts is taken from various sources (Michener 1936,Torchio et al. 1967, Krombein et al. 1979, Warncke 1981, Warncke 1982, Janzon and Svensson 1984, Westrich 1990, Rozen and McGinley 1991, Rozen et al. 1997, Bogusch 2003, Proshchalykin and Lelej 2004, Rozen et al. 2009, Orr and Griswold 2015, Scheuchl and Willner 2016, Westrich 2018). The higher classification of plants follows the APG IV system (The Angiosperm Phylogeny group 2016). Warncke (1982) also lists Systropha curvicornis and S. planidens as hosts of Biastes emarginatus but the source for this information is unclear and has been doubted by other authors (Westrich 2018). No host information is available for Schwarzia and species for which boxes are gray. Asterisks (*) indicate newly described species.

opencc-zeroSep 2021View details →

Supplementary material 1 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259

Voucher information, characters of chloroplast (cp) genomes and GenBank BioSample accession of genome skimming raw reads in this study

opencc-zeroSep 2021View details →

Supplementary material 2 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259

Chloroplast protein coding sequences (cpCDSs) and their corresponding substitution models generated from PartitionFinder 2

opencc-zeroSep 2021View details →

Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

<ul> <li>The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved.</li> <li>Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. </li> <li>We find that two recently described species from northeast Brazil's Atlantic forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization including into savannas and rainforests within South America. We identify the closest wild relatives to M. esculenta including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species including M. glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava.</li> <li>Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.</li> </ul>

opencc-zeroOct 2021View details →

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades were detected: the "EA clade" comprised two species (<a name="_Hlk63130225">T. standishii</a> and <a name="_Hlk63130201">T. sutchuenensis</a>) from EA, and the "disjunct clade" comprising T. koraiensis, T. occidentalis, and T. plicata, with the first two comprising an EA–ENA disjunct pattern and T. plicata in western North America. The disjunct clade experienced a rapid radiation in the Mid–Miocene, and furthermore multispecies coalescent analysis revealed that ancient lineages of Thuja had large population sizes. These two factors might have contributed to the significant levels of incomplete lineage sorting (ILS) we detected within Thuja, and especially the disjunct clade. Because of this, EA–ENA disjunct pattern of T. koraiensis and T. occidentalis is exhibited by only 13.98% of genes examined. In addition, we found that ~20% of the T. sutchuenensis nuclear genome is derived from an as–yet–unrecognized ancestral lineage of Thuja, which might explain the close resemblance of cone morphology between T. sutchuenensis and the Paleocene fossil species T. ehrenswaerdii. Overall, our study demonstrates that single genes may produce incomplete or inaccurate phylogenies for disjunct taxa, and that more accurate results will come from using genomic data, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

opencc-zeroNov 2022View details →

Supplementary material 1 from: Liu L, Liu Q, Gao T (2022) Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes). ZooKeys 1129: 55-72. https://doi.org/10.3897/zookeys.1129.91543

K-mer analyses (K = 71) of Chirolophis japonicus, X-axis and Y-axis represent the K-mer depth and frequency for the corresponding depth

opencc-zeroJan 2023View details →

Supplementary alignment, phylogenetic, and biogeographic analysis data for: Phylogenomics of Gars

Reconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes (Actinopterygii), which include more than half of living vertebrates, are no exception. Although many of the most species-rich clades of ray-finned fishes diversified after the Cretaceous-Paleogene mass extinction, a handful of ancient and species-depauperate lineages persist today. One of the most iconic ancient lineages of ray-finned fishes are gars, a clade of seven freshwater species restricted to continental North America and Cuba. Here, we use DNA sequences of more than 1,000 exons collected for all living species of gars and a morphological dataset that includes 16 fossil species to infer their phylogenetic relationships and estimate divergence times using fossil-tip dated relaxed molecular clock analyses. Our analyses show that the two major lineages of living gars, Atractosteus and Lepisosteus, diverged approximately 105 million years ago. Using the time-calibrated phylogeny of the living and fossil gar species and model-based biogeographic reconstructions, we find that many of the inferred vicariant events in the evolutionary history of gars closely track the Mesozoic fragmentation of Laurasia in the Northern Hemisphere and the Cretaceous reorganization of North American river drainage systems. In particular, we tie the initial diversification of living gars to the expansion of the early Atlantic and subsequent loss of shallow marine habitat between the Americas and Africa in the Cretaceous. All living gar species originated after the Cretaceous in eastern North America, implying that this region has both served as the ancestral area of extant gar diversity and a refugium of this iconic ancient vertebrate lineage.

opencc-zeroFeb 2023View details →

Phylogenomic data of Camellia section Paracamellia based on transcriptomes and plastomes

Camellia section Paracamellia of the genus Camellia (Theaceae) includes major woody oil crops in China and relative wild species as valuable genetic resources for breeding. However, the phylogeny and origin of C. oleifera and its relative species are still uncertain. In this study, the transcriptomes of 22 samples and plastomes of 19 samples were sequenced and assembled. Finally, the dataset of phylogenomic matrices was generated, including 982 and 326 single-copy orthologous (SCO) genes generated from transcriptomes data and the plastid matrix used for phylogenetic analysis. Please cite this article as doi: 10.1111/jse.12948.

opencc-zeroFeb 2023View details →

Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.

opencc-zeroFeb 2023View details →

Phylogenomic data of Litsea complex based on genome-wide single-nucleotide variants (SNVs) and plastomes

In this study, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of evergreen broadleaved forests (EBLFs) in East Asia to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) and plastomes. Finally, the dataset of phylogenomic matrices was generated, including five genome-wide SNVs dataset and plastomes matrix used for phylogenetic analysis.

opennotspecifiedFeb 2023View details →

FIGURE 1 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings

FIGURE 1. Phylogram of Neuropterida relationships based on the CAT-GTR+G4 analysis of anchored hybrid enrichment (AHE) amino acid data. All branches have a support value of ≥ 0.93 Bayesian posterior probability (BPP) except those indicated by red dots (BPP <0.9). Abbreviations: Conio., Coniopterygoidea; Dilar., Dilaroidea; Ithon., Ithonoidea; Megal., Megaloptera; Psych., Psychopsoidea; Raphi., Raphidioptera. Superfamilial classification is adapted from Engel et al. (2018).

opennotspecifiedFeb 2023View details →

FIGURE 2 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings

FIGURE 2. Congruent interfamilial relationships of Neuropterida inferred from transcriptomic (left) and AHE (right) amino acid data respectively under the site-heterogeneous CAT-GTR+G4 model. All branches have a strong support (BPP> 0.93), except for the monophyly of Myrmeleontidae (only weakly supported in AHE nucleotide data under the CAT-GTR+G4 model). Note that the transcriptomic dataset has fewer and sparser familial sampling than the AHE data.

opennotspecifiedMar 2023View details →

FIGURE 1 in Plastome phylogenomics of Micromeles (Rosaceae)

FIGURE 1. Gene map of 14 Micromeles plastomes. Genes inside and outside the circle are transcribed clockwise and counter-clockwise, respectively. Genes are color-coded indicates the different functional groups. The dark gray in inner circle indicates the GC contents.