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Fig. 16 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Fig. 16. BEAST estimate of species' dated phylogeny as an ultrametric tree (outgroup B. festivus Smith, 1861, not shown) from six genes for the subgenus Alpigenobombus Skorikov, 1914. All nodes have support values> 0.98. Numbers at nodes are estimates of the age of a node in Ma before the present, with grey node bars representing the 95% highest posterior density interval of the age estimates.

Figs 1‒9 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Figs 1‒9. Individuals of the subgenus Alpigenobombus Skorikov, 1914 (with photo credits). 1. Bombus mastrucatus Gerstaecker, 1869, worker Norway robbing (P. Haringsma). 2. B. kashmirensis Friese, 1909 s. str., worker China-Sichuan robbing (PW). 3. B. kashmirensis (taxon meinertzhageni Richards, 1928) worker India-Kashmir-Zanskar (PW). 4. B. sikkimi Friese, 1918, worker India-Arunachal (MS). 5. B. nobilis Friese, 1905 s. str., worker China-Yunnan (ZR). 6. B. genalis Friese, 1918, worker India-Arunachal (MS). 7. B. breviceps Smith, 1852 (taxon dentatus Handlirsch, 1888) worker ChinaYunnan (PW). 8. B. breviceps (taxon channicus Gribodo, 1892) worker Thailand (CT). 9. B. grahami (Frison, 1933) worker India-Arunachal (MS). Some images reversed.

Figs 106–115 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Figs 106–115. Morphology of the male genitalia for species of the subgenus Alpigenobombus Skorikov, 1914, from the dorsal aspect, anterior at the bottom of the image, posterior at the top. 106. Bombus wurflenii Radoszkowski, 1860, Turkey. 107. B mastrucatus Gerstaecker, 1869, Austria. 108. B. kashmirensis Friese, 1909, India-Kashmir. 109. B. rainai Williams, 2022, India-Kashmir. 110. B. sikkimi Friese, 1918, Nepal. 111. B. nobilis Friese, 1905, China-Sichuan. 112. B. validus Friese, 1905, China-Gansu. 113. B. genalis Friese, 1918, China-Yunnan. 114. B. breviceps Smith, 1852, ChinaSichuan. 115. B. grahami (Frison, 1933) China-Sichuan (left penis-valve recurved hook missing). Scale bars = 1 mm.

Figs 13–15 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Figs 13–15. Distribution of the barcoded samples (and matching haplotypes) of the subgenus Alpigenobombus Skorikov, 1914, from Fig. 10 with their interpretation as the 11 species from Fig. 12 and from the associated morphology in the keys, shown as differently coloured spots as in the colour keys on the left, to indicate the approximate relative range extent among the species. 13. The wurflenii- group and kashmirensis-group. 14. The nobilis-group. 15. The breviceps-group. Relief map with hill shading, Cartesian orthonormal projection, the international boundaries shown as narrow grey lines. Images created in ArcGIS using World_Shaded_Relief basemap which is Copyright: ©2014 Esri.

Fig. 17. Diagram representing a in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Fig. 17. Diagram representing a corridor-dispersal model, encompassing a set of short-distance dispersal events permitted (in either direction) between the proposed areas of endemism, based on unique taxa, the geographical proximity of these areas, and the likely disposition of corridors with suitable habitat and favourable climates in the past.

Fig. 12 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Fig. 12. Interpretation of filtered MrBayes estimate of phylogeny as a metric tree (outgroup B. festivus Smith, 1861, not shown) for the subgenus Alpigenobombus Skorikov, 1914, from COI-like sequences from the sequences identified in black and orange in Fig. 11 together with Bayesian Poisson-tree-process (PTP) models re-applied for assessing support for species' gene coalescents by maximum likelihood (for the 11 most likely candidate species). The scale bar is calibrated in substitutions per nucleotide site. Sequence labels and branch colours as in Fig. 10. Numbers above nodes are the Bayesian support values that all daughter haplotypes are parts of a single species. Grey spots show likely mitochondrial-to-nuclear transfers of the low-divergence numts accepted for estimating this tree. Asterisks mark sequences used as informal proxies for the type specimens of each of the taxon names in Table 2. To the right in grey are shown the interpretations of the PTP results as candidate species using the oldest available names for the species.

Figs 19–105 in Bumblebees with big teeth: revising the subgenus Alpigenobombus with the good, the bad and the ugly of numts (Hymenoptera: Apidae)

Figs 19–105 (see pages 28–29). Simplified diagrams for the colour patterns of the hair on the dorsum for particular female (f) and male (m) specimens of the species from Fig. 12. The dorsum is divided into regions, each of which shows only the predominant or most apparent colour for that region, using a simplified colour palette, with olive indicating a mixture of black and yellow hair, and grey indicating a mixture of black and white hair.

opencc-by-4.0Feb 2022View details →

zenodo36/100

Arabidopsis thaliana Col-CEN complete Chromosome 2 numt sequences and alignments

Data associated with the assembly of complete chromosome 2 nuclear insertion of mitochondrial DNA (numt) from the Arabidopsis thaliana accession Columbia (Col-CEN). A full report of this project can be obtained in a manuscript titled "Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome".

dryad36/100

Supplementary information for: NUMT PARSER: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo) because mtDNA is often the marker of choice for ancient DNA studies, and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.

opencc-zeroDec 2022View details →

zenodo36/100

Dataset for "Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"

存放"Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"文章中的相关数据。 包括blastn出来的原始output文件;mtDNA-like short segments fastq文件;ATAC-seq的fastq文件; 以及文章中提及的supplementary 表格和bed文件

opencc-by-4.0Dec 2023View details →

dryad36/100

Supplementary information for: NUMT PARSER: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

Open the record for dataset details and reuse information.

publicDec 2022View details →

FIGURE 1 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)

FIGURE 1. Histogram of frequency of the bases A and T at codon position 3 (AT3%) for the COI barcode-like sequences in Fig. 2, with the expected high-bias AT3% sequences (≥98%) interpreted as orthologous COI barcodes (black) and lower AT3% sequences interpreted as likely numts of varying divergence (orange for the more recent numts; red for the older, more divergent numts; see the text for details of the distinguishing criteria).

FIGURE 2 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)

FIGURE 2. Support for apparent species' gene coalescents from unique haplotypes for COI barcode-like sequences including numts (nuclear copies of mitochondrial sequences), obtained from an evolutionary tree estimated with MRBAYES and using maximum likelihood to fit Poisson-Tree-Process (PTP) models. Numbers at each node show the probability that all daughter sequences to the right are parts of a single unique species. Branches change from blue to red at the node with the best fit (maximum local probability) for the change from inter-species to intraspecies branching PTP models (species' coalescent nodes). Sequence labels include: sequence length in number of bases; taxon name; country in capitals (if not shown then MEXICO) and province; sequence identification code (E# = ECOSUR#). Sequence labels are followed by the percentage of the bases A and T at the third codon position, where low scores (≤97.6%) are likely to indicate numts. Labels for sequences interpreted as likely lower-divergence numts are shown in orange and for likely higher-divergence numts are shown in red (see Fig. 1). The scale bar represents branch length on the tree in substitutions per nucleotide.

FIGURE 6 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)

FIGURE 6. Map showing the distributions of samples examined for this study of the weisi-complex: (white spots) taxon nigrodorsalis s. str. (=B. nigrodorsalis stat. rev.); (grey spots) taxon montezumae (=B. weisi stat. rev.); and (black spots) taxon weisi s. str. (=B. weisi stat. rev.). Larger symbols with spots in their centres show locations from which specimens were sequenced for each taxon. Spherical projection with international boundaries as recognized by the UN shown as grey lines. Map projected in ArcGIS using the World_Shaded_Relief basemap © 2014 ESRI.

FIGURE 3 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)

FIGURE 3. Support for species' gene coalescents from unique haplotypes for COI barcode (orthologous) sequences excluding likely numts (orange and red bars and labels in Figs 1‒2), obtained from an evolutionary tree estimated with MRBAYES and using maximum likelihood to fit Poisson-Tree-Process (PTP) models. Numbers at nodes, treebranch colours, sequence labels, and scale bar as in Fig. 2.

FIGURES 4‒5 in A new wave of Mesoamerican bumblebees? Revising the weisi-complex to reject numts and pseudospecies (Apidae: Bombus)

FIGURES 4‒5. Male genitalia of (4) B. nigrodorsalis and (5) B. weisi from the right lateral aspect, with posterior extremities at the top of the images and dorsal parts to the right of the images.

Figure 5 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)

Figure 5. Phylogenetic informativeness of three mtDNA gene fragments (16S, 12S, and COI) in peppermint, cleaner, and semi-terrestrial shrimps. (A) Phylogenetic informativeness (PI) profiles of the three different mtDNA gene fragments studied through relative time in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. The sum of the instantaneous asymptotic informativeness of all sites in each gene is plotted. The arrows and numbers above or below them indicate the relative time (arrow) and magnitude (numbers) at which PI reaches its maximum value. (B) Tree topology resulting from the maximum-likelihood analysis of the sequences studied with a relative time-enforced branch length. This phylogeny was used to calculate the PI profiles in panel (A). Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3.

Figure 7. Neighbour-nets generated using SplitsTree4 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)

Figure 7. Neighbour-nets generated using SplitsTree4 from the three mtDNA gene fragments studied (16S, 12S, and COI) in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3. Abbreviations: LA, Lysmata ankeri; LABP, Lysmata cf. vittata; LAM, Lysmata amboinensis; LARG, Lysmata argentopuctata; LBA, Lysmata bahia; LBO, Lysmata boggessi; LCA, Lysmata californica; LD, Lysmata debelius; LGA, Lysmata galapagensis; LGB, Lysmata grabhami; LGR, Lysmata gracilirostris; LH, Lysmata hochi; LHO, Lysmata holthuisi; LI, Lysmata intermedia; LIM2, Lysmata cf. intermedia; LK, Lysmata kuekenthali; LM, Lysmata moorei; LN, Lysmata nayaritensis; LNI, Lysmata nilita; LO, Lysmata olavoi; LP, Lysmata pederseni; LRA, Lysmata rafa; LSET, Lysmata seticaudata; LT, Lysmata cf. ternatensis; LV, Lysmata vittata; LU, Lysmata udoi; LWEF, Lysmata wurdemanni EFL; LWG, Lysmata wurdemanni TX; LWWF, Lysmata wurdemanni WFL; EXO, Exhippolysmata oplophoroides; EXE, Exhippolysmata ensirostris; MO, Merguia oligodon; MR, Merguia rhizophorae; and NSP, Nikoides sp.

Figure 3 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)

Figure 3. Tree topology resulting from the combined analysis of the three mtDNA gene fragments studied (16S, 12S, and COI) for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML). Numbers above or below the branches represent the bootstrap values obtained from the maximum likelihood (ML) analysis in TREEFINDER and posterior probabilities from the Bayesian inference (BI) analysis in MrBayes (ML/BI). The general topology of the trees obtained from ML and BI analyses was the same.

Figure 1 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)

Figure 1. Amino acid usage analysis (mean amino acid count per sequence) for COI reference sequences (from selected species of crustaceans: Macrobrachium rosenbergii, Exopalaemon caricaudinata, Halocaridina rubra, and Cherax destructor), for COI orthologous sequences obtained from shrimps from the genus Lysmata, and for COI-like cloned sequences from Lysmata seticaudata. The error bars in each graph represent the highest and lowest amino acid counts per sequence in the three data sets. Amino acid determination and naming follows the invertebrate mitochondrial translation code, and was performed in MEGA 5.