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Figure 4 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 4. Light photomicrographs of upper ovipositor valve bases following maceration in KOH (aq.) and light staining with chlorazol black. (A) Labium (Labeninae); (B) Poemenia (Poemeniinae); (C) Echthromorpha (Pimplinae: Pimplini); (D) Pimpla flavicoxis Thomson (Pimplinae: Pimplini); (E) Limerodops (Ichnumoninae); (F) Oedemopsis (Tryphoninae: Oedemopsini).

Figure 2 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 2. Light photomicrograph of eighth metasomal tergite of female Pimpla rufipes (Miller) following KOH (aq.) maceration and staining with chlorazol black showing "Y"-shaped internal ridge.

Figure 10 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 10. Chitinous venom gland and reservoir intimas. (A) Hyperacmus sp. (Orthocentrinae s.l.); (B) Cylloceria sp. (Cylloceriinae); (C) Eusterinx sp., (Orthocentrinae); (D) Aperileptus sp. (Orthocentrinae).

Figure 13 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 13. Chitinous venom gland and reservoir intimas. (A) Orthopelma mediator (Thunberg) (Orthopelmatinae); (B) Westwoodia sp. (Ctenopelmatinae); (C) Xenoschesis sp. (Ctenopelmatinae); (D) Exenterus sp.; (E) Phytodietus (Neuchorus) sp. (Tryphoninae); (F) Phytodietus sp. (Tryphoninae); (G) Lissonota sp. (Banchinae); (H) Pion sp. (Ctenopelmatinae).

Figure 12 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 12. Chitinous venom gland and reservoir intimas. (A) Ateleute sp.; (B) Ichneumon sp.; (C) Alomya sp. (Alomyinae); (D) Osprynchotus sp. (Cryptinae); (E) Colpognathus sp. (Ichneumoninae); (F) Hoplismenus sp. (Ichneumoninae); (G) Eusterinx sp. (Orthocentrinae).

Figure 9 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 9. Chitinous venom gland and reservoir intimas. (A) Ganodes sp. (Poemeniinae); (B) Labena sp. (Labeninae); (C) Phaenolobus sp. (Acaenitinae); (D) Coleocentrus sp. (Acaenitinae); (E) Euceros sp. (Eucerotinae); (F) Euceros frigidus Cresson.

Figure 7 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 7. Drawings of transverse sections through mid-part of ovipositor valves. (A) Brachycyrtus, dorsal valve only; (B) Grotea sp. (Labeninae); (C) Pseudorhyssa sternat Merrill (Poemeniinae incertae sedis) [NB. virtually identical to Ganodes sp. (Poemeniinae), not illustrated]; (D) Podoschistus sp. (Poemeniinae); (E) Coelichneumon sp. (Ichneumoninae); (F) Peucobius sp. (Phrudinae); (G) Xenoschesis sp. (Ctenopelmatinae).

Figure 15 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 15. Strict consensus of most parsimonious trees from analysis of morphological data alone (length 1291; RI 0.507; CI 0.166).

Figure 3 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 3. Light photomicrographs of base of ovipositor sheath following maceration in KOH (aq.) and light staining with chlorazol black. (A) Odontocolon (Xoridinae); (B) Phaenolobus (Acaenitinae); (C) Nonnus (Nonninae); (D) Hymenoepimecis (Pimplinae); (E) Coleocentrus (Acaenitinae).

Figure 1 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 1. Plot of log10 number of genera sequenced versus number of currently recognized genera in each subfamily (number of recognized extant genera from Yu and Horstmann 1997; Yu et al. 2005). The point at the origin represents 15 monotypic subfamilies.

Figure 19 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Figure 19. Summary of recovery of selected ophioniformes clades as monophyletic in most parsimonious trees from analysis of combined morphological and CLUSTAL-aligned molecular data showing effects of different gap-opening and gap-extension values and treatment of gaps as informative or uninformative. Groups are coloured if they were recovered in any of the most parsimonious trees obtained from a particular combination of parameters.

opencc-zeroSep 2021View details →

Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a

Five new taxa from Phytophthora ITS Clade 2a are described from Cinnamomum cassia plantations and adjacent waterways in Van Yen, Vietnam, and disturbed rainforest in the Hela Province of Papua New Guinea and from disturbed forest on Christmas Island. Phylogenetic analyses were performed using data from nuclear regions (ITS, β-tubulin; Heat shock protein 90) and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c oxidase subunit2; NADH dehydrogenase subunit 1; ribosomal protein L10). The molecular data supported recognition of three species: Phytophthora insulinativitatica, P. multibullata and P. x vanyenensis and two informal taxa, P. sp. germisporangia and P. sp. awatangi. P. x vanyenensis appears to be a hybrid between P. sp. mekongensis and an unknown species. P. multibullata and P. sp. germisporangia are phylogenetically close to P. citrophthora, but morphologically distinct. P. insulinativitatica is most closely related to P. botryosa but has different morphology. P. sp. germisporangia and P. sp. awatangi were morphologically distinct and separated in the phylogeny based on mitochondrial sequences, but their nuclear sequences were identical. When comparing the sequences of these new species to that available on GenBank, it became evident that some of these species shared similarity with isolates submitted to GenBank under other species names and a re-evaluation of all P. meadii and P. colocasiae ITS sequence data identified an additional 7 putatively new species all isolated from Asia. The results support the view that many more Phytophthora species remain to be discovered in the Asia-Pacific region.

opencc-zeroSep 2021View details →

UCE alignments and phylogenetic trees

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a timeframe for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provide highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in BPP and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of northeastern Mexico, and erected a new genus to better reflect evolutionary history. In sum, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbor substantial unrecognized diversity.

opencc-zeroOct 2021View details →

Halophila johnsonii phylogenetic analysis alignments

Halophila johnsonii is an endangered seagrass species that is restricted to the Florida Bay region of Florida, USA. Its taxonomic status has been called into question, in particular, given the close morphological and genetic similarity of H. johnsonii and the widely distributed and morphologically variable H. ovalis, which is largely restricted to the Indo-Pacific region. While a close relationship to H. ovalis is uncontroversial, it remains uncertain whether H. johnsonii represents a distinct lineage or is a recent introduction to the Florida region. Given the conservation status of H. johnsonii, distinguishing these alternatives has important implications for the management of the species and its habitat. Here, we develop molecular data sets for samples of H. johnsonii and H. ovalis including DNA sequences, genome-wide SNPs and microsatellites with the view to resolving the affinities of H. johnsonii with respect to the wider H. ovalis complex. Phylogenetic hypotheses based upon plastid (~18000 bp) and low copy nuclear DNA (~6500 bp) sequences derived from hybrid capture, along with 990 genome-wide ddRAD SNPs consistently resolved H. johnsonii within H. ovalis. Specifically, we found a close affinity between H. johnsonii and H. ovalis sampled from the east coast of Africa. In addition, Halophila specimens collected in Antigua, which are within the range of morphological variation typical for H. ovalis, are virtually identical to H. johnsonii and the East African H. ovalis samples based upon DNA sequence analyses and these group together using Bayesian clustering analyses of microsatellites and ddRAD SNPs. We conducted population genetic analyses using large number of H. johnsonii samples collected over a 17-year period. Genotypic data generated through microsatellites and ddRAD SNPs revealed genetic uniformity for all 132 H. johnsonii samples across the Indian River Lagoon, Florida, while samples of H. ovalis from Antigua shared the same genotype as H. johnsonii. We conclude that the lack of genetic diversity and the absence of sexual reproduction strongly indicates that the total range of H. johnsonii is actually one clone that is closely related to populations in Africa and Antigua and may be derived from a recent introduction from one of those regions.

opencc-zeroOct 2021View details →

Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development

Background Across the Metazoa, similar genetic programs are found in the development of analogous, independently evolved, morphological features. The functional significance of this reuse and the underlying mechanisms of co-option remain unclear. Cephalopods have evolved a highly acute visual system with a cup shaped retina and a novel refractive lens in the anterior, important for a number of sophisticated behaviors including predation, mating and camouflage. Almost nothing is known about the molecular-genetics of lens development in the cephalopod. Results Here we identify the co-option of the canonical bilaterian limb pattering program during cephalopod lens development, a functionally unrelated structure. We show radial expression of transcription factors SP6-9/sp1, Dlx/dll, Pbx/exd, Meis/hth, and a Prdl homolog in the squid Doryteuthis pealeii, similar to expression required in Drosophila limb development. We assess the role of Wnt signaling in the cephalopod lens, a positive regulator in the developing Drosophila limb, and find the regulatory relationship reversed, with ectopic Wnt signaling leading to lens loss. Conclusion This regulatory divergence suggests that duplication of SP6-9 in cephalopods may mediate the co-option of the limb patterning program. Thus our study suggests that the limb network could perform a more universal developmental function in radial pattering and highlights how canonical genetic programs are repurposed in novel structures.

opencc-by-4.0Jan 2016View details →

WMT'16 Biomedical Translation Task - Scielo parallel datasets - GMA alignment files

Aligment files using the GMA tool (https://nlp.cs.nyu.edu/GMA/) for the parallel data from Scielo for the Biomedical Translation Task in the First Conference on Machine Translation (WMT 16) (http://www.statmt.org/wmt16/biomedical-translation-task.html). The parallel data is available here: https://zenodo.org/record/5588265

opennotspecifiedDec 2011View details →

FIGURE 42. Maximum Likelihood consensus tree inferred from the 16S rDNA sequence alignment representing a in Monographic revision of the endemic Helix mazzullii De Cristofori & Jan, 1832 complex from Sicily and re-introduction of the genus Erctella Monterosato, 1894 (Pulmonata, Stylommatophora, Helicidae)

FIGURE 42. Maximum Likelihood consensus tree inferred from the 16S rDNA sequence alignment representing a possible reconstruction of Helicidae phylogeny. Initial trees for the heuristic search were obtained automatically. A GTR + Γ model (alpha= 0.29) was employed. The analysis involved 58 nucleotide sequences. All positions containing gaps and missing data were eliminated.

opencc-by-4.0Oct 2022View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "Molecular and Morphological Assessment of Rain Frogs in the Pristimantis orestes Species Group (Amphibia: Anura: Strabomantidae) with the Description of Three New Cryptic Species from Southern Ecuador"

The aligned matrix is in fasta format. Genes are arranged as follows: 12S = 1–901 16S = 902–2094 RAG-1 = 2095–2733

opencc-by-4.0Nov 2022View details →

Aligned Latin-Myanmar Transliteration Dataset

Aligned Latin-Myanmar Transliteration Dataset                     Chenchen Ding                     Tue Nov 22 00:00:00 JST 2022 * Introduction This data set is a further refined and annotated version of the data at https://www2.nict.go.jp/astrec-att/member/mutiyama/ALT/western-myanmar-transliteration.zip The data set is developed by Chenchen Ding from NICT. The license is Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License https://creativecommons.org/licenses/by-nc-sa/4.0/ * Contents - data.txt : 42,736 segmented and aligned instances. * Format Each line contains a segmented transliteration pair in a format of [Latin segment 1] | [Latin segment 2] ... ||| [Myanmar segment 1] | [Myamar segment 2] | ... where the Latin-Myanmar pair has identical number of segments. * Annotation Guidelines - There is no insertion but only segmentation on the Latin side. - A placeholder @ is inserted in the Myanmar side for unaligned Latin segments. - The consonant clusters at syllable onset are generally segmented and aligned to Myanmar basic letters - The consonants at coda are generally aligned to the placeholder, unless they are absorbed by a rhyme with nasalization or glottal stop, or by an extra explicit killed-letter. - Doubled consonant letters are generally segmented and treated as coda and onset of two neighboring syllables. - Myanmar rhymes are generally not segmented. - The Myanmar letter A (0x1021) is unsegmented in the case of vowel-beginning words as no insertion on Latin side. The data can be directly used to train a sequence-labeling model for Myanmar Romanization. * Disclaimer [1] NICT bears no responsibility for the contents of the corpus and the lexicon and assumes no liability for any direct or indirect damage or loss whatsoever that may be incurred as a result of using the corpus or the lexicon. [2] If any copyright infringement or other problems are found in the corpus or the lexicon, please contact us at alt-info [at] khn [dot] nict [dot] go [dot] jp. We will review the issue and undertake appropriate measures when needed.