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29 results for “museomics”
Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield
<h2><strong>Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield</strong></h2> <p>Mathilde Barthe*, Loïs Rancilhac, Maria C. Arteaga, Anderson Feijó, Marie-Ka Tilak, Fabienne Justy, W. J. Loughry, Colleen M. McDonough, Benoit de Thoisy, François Catzeflis, Guillaume Billet, Lionel Hautier, Benoit Nabholz, and Frédéric Delsuc*</p> <p>*Corresponding authors: mathilde.barthe.pro@gmail.com; frederic.delsuc@umontpellier.fr</p> <p> </p> <h2><strong>Description of available files. </strong></h2> <p><strong>01_Figures_&_tables_of_the_main_text.zip </strong><br>- Figure 1: Phylogenetic relationships reconstructed by maximum likelihood and maps representing the distribution of individuals according to their lineage.<br>- Figure 2: Assignment of individuals to lineages according to phylogenetic analyses, admixture analysis and phylogenetic delimitation.<br>- Figure 3: Principal Component Analysis of genetic variance.<br>- Figure 4: Distribution map and genetic composition of individuals of the four recognized species.</p> <p><strong>02_Supplementary_tables_&_figures.zip </strong><br>- Figure S1: Distribution of targeted nuclear loci along a chromosome scale assembly.<br>- Figure S2: Mitochondrial genome depth of coverage.<br>- Figure S3: Calculation of mitochondrial lineage support for detecting contamination.<br>- Figure S4: Mitochondrial lineage support for each individual. <br>- Figure S5: a) Inbreeding coefficient and b) heterozygosity estimate for individuals according to cleaning steps.<br>- Figure S6: Percentage of missing data per captured locus. <br>- Figure S7: Summary information of the 837 cleaned nuclear loci (number of sequences, the proportion of variable sites and the percentage of missing data). <br>- Figure S8: Phylogenetic relationships of the 62 Dasypus individuals obtained using Astral on the 832 ML gene trees from the captured nuclear loci reconstructed with IQ-Tree and ModelFinder.<br>- Figure S9: Results of analyses to detect introgression.<br>- Figure S10: Cross validation errors according to the number of clusters (K) investigated.<br>- Figure S11: Detailed analysis of the substructure within the newly recognized D. novemcinctus (Southern lineage).<br>- Figure S12: Species delimitation estimated by bPTP-h. <br>- Figure S13: Comparison of the three best models from the model selection estimated with PHRAPL.<br>- Figure S14: Species delimitation estimated using GMYC.<br>- Figure S15: Heatmaps of pairwise genetic indexes between lineages. <br>- Figure S16: Effect of filters on admixture results. <br>- Figure S17: Updated map from Arteaga et al. (2020). <br>- Figure S18: Maximum likelihood phylogenetic tree of 212 pb of the 16s ribosomal RNA of five individuals analyzed in Abba et al., (2018) and three from this study.<br>- Table S1: List of biological samples with detailed information.<br>- Table S2a: Quality statistics by locus after filtering steps.<br>- Table S2b: Quality statistics by individuals after filtering steps.<br>- Table S3: Species delimitation estimated using PHRAPL for the four combinations.<br>- Table S4: Comparison of the lineage of the nineteen individuals in common with Arteaga et al. (2020) and our study. <br>- Table S5: Adult cranial measurements (in millimeters) of the four Dasypus species recognized in this study following Feijó & Cordeiro-Estrela (2016). <br>- Table S6: Adult external measurements (in millimeters) of the four Dasypus species recognized in this study. </p> <p><br><strong>03_Mitogenomes.zip</strong><br>- Mitogenome_reference_Dasypus_novemcinctus.fasta: Mitogenome reference used to mapped reads and extract mitochondrial DNA.<br>- Concatenated_mitochondrial_genes.fasta: Concatenated nucleotide sequences of 15 mitochondrial genes (13 protein-coding + 2 rRNAs). Sites with more than 50% missing data were excluded resulting in a total of 13,924 sites. <br>- Concatenated_mitochondrial_genes_partition.txt: Partition file of concatenated sequences of the 15 mitochondrial genes (13 protein-coding + 2 rRNAs). <br>- Concatenated_mitochondrial_genes_TESTNEW.treefile : Maximum likelihood phylogenetic tree inferred from the concatenated sequences of the 15 mitochondrial genes using IQ-TREE under a partitioned model applying ModelFinder on each partition.<br>- Depth_coverage_mitogenomes.csv: Table of mean depth of coverage and proportion of missing data (Ns) of the 72 reconstructed mitochondrial genomes sequenced for this study. </p> <p><br><strong>04_Reanalyses.zip</strong><br>- Dloop_alignment.fasta: Alignment of the D-loop sequences obtained in this study with those from Arteaga et al. (2020). <br>- Dloop_alignment.treefile: Maximum likelihood phylogenetic tree inferred from the D-loop alignment using IQ-TREE (GTR+G model).<br>- Abba_shotgun.fasta: Alignment of the 16S rRNA of individuals from this study and those from Abba et al. (2018).<br>- Abba_shotgun.fasta.treefile: Maximum likelihood phylogenetic tree inferred from the 16S rRNA alignment using IQ-TREE (GTR+G model).</p> <p><br><strong>05_Contamination_exploration.zip</strong><br>- Mitochondrial_diagnostic_positions.csv: Table of the 350 diagnostic mitochondrial positions used to estimate proportion of reads supporting each lineage. Position number refers to the Complete_mitogenome_alignment.fasta file.<br>- Read_support_to_diagnostic_positions.csv: For each individual, this table reports the Diagnostic Rate (proportion of diagnostic positions per lineage supported by at least 3 reads), the Read Proportion (mean read proportion supporting diagnostic positions per lineage), Index (proportion of synapomorphies per lineage normalized by average frequency of reads supporting these synapomorphies) and the type of tissue (museum or fresh tissue).<br>- Contamination_exploration.R: R script used to plot read support to lineages and the effect of tissue type (fresh or museum).</p> <p> </p> <p><strong>06_Nuclear_dataset.zip</strong><br>- TATU_1000exons4baits.fasta: Reference sequences of 1,000 exons and flanking regions used to define the probes for exon capture extracted from the Dasypus novemcinctus genome.<br>- Dasypus_capture_Final_Baits_Set.fas: Sequences of the 16,146 probes used to capture the 997 nuclear loci (exons and flanking regions).<br>- Diploid_837_nuclear_loci.fasta: Diploid sequences of the 837 nuclear loci for the 62 individuals in PopPhyl format (Locus|lineage|individual|Allele).<br>- Mean_coverage_by_individuals.csv: Table of mean depth of coverage, horizontal coverage, and number of loci per individual after filtering. <br>- Mean_coverage_by_loci.csv: Table of mean depth of coverage, horizontal coverage and number of loci per loci after filtering.<br>- Location_loci_targeted.bed : list of the loci targeted by exon capture, with their genomic locations on the chromosome scale assembly of <em>Dasypus novemcinctus</em> (mDasNov1.hap2)</p> <p> </p> <p><strong>07_Disentangling_genotyping_errors.zip</strong><br>- Table_of_heterozygosity_and_inbreeging_coefficient.csv: Table of heterozygosity (He) and inbreeding coefficient (F) estimated for each cleaning steps: initial data, after correction of heterozygous positions (must be supported by a proportion of reads between 0.3 and 0.7), and after exclusion of 159 potentially paralogous loci.<br>- Plot_effect_of_cleaning_on_He&F.R: R script used to plot the effect of cleaning steps on heterozygosity (He) and inbreeding coefficient (F).</p> <p> </p> <p><strong>08_Distribution_maps.zip </strong><br>- Coordinates_according_mito_nuclear_lineages.csv: Table of GPS coordinates of individuals according to their mitochondrial and nuclear lineages.<br>- Plot_mito_nuclear_distribution.R: R script used to plot individuals on the Neotropical map according to their mitochondrial and nuclear lineages in Figure 1.<br>- Mitochondrial_distribution.pdf: Geographical distribution of the 75 individuals according to their mitochondrial lineage.<br>- Nuclear_distribution.pdf: Geographical distribution of the 58 individuals according to their nuclear lineage.</p> <p> </p> <p><strong>09_Phylogenetic_inference.zip</strong><br>● Phylogram_Tree <br>- Concatenated_nuclear_loci.fasta: Concatenated sequences of the 837 nuclear loci representing a total of 506,355 sites. <br>- Concatenated_nuclear_loci_partition.txt: Partition file for the 837 nuclear loci concatenation.<br>- Concatenated_nuclear_loci_TESTNEW.treefile: Maximum likelihood phylogenetic tree inferred from the 837 nuclear loci concatenation using IQ-TREE under a partitioned model applying ModelFinder on each partition.</p> <p>● Ultrametric_Tree<br>- Ultrametric_tree_concatenated_nuclear_loci.treefile: Ultrametric tree inferred from the 837 nuclear loci concatenation (Concatenated_nuclear_loci.fasta in Phylogram_Tree folder) using a partitioned model applying ModelFinder on each partition (Concatenated_nuclear_loci_partition.txt in Phylogram_Tree folder). The ML phylogram (Concatenated_nuclear_loci_TESTNEW.treefile in Phylogram_Tree folder) was used as a guide tree. The root was dated at 6 Mya.</p> <p>● Gene_Tree <br>- Concatenate_gene_tree.treefile: File containing all gene trees reconstructed using IQ-TREE applying ModelFinder to each gene.<br>- Astral_consensus_tree.txt: Summary species tree reconstructed with Astral using Concatenate_gene_tree_TESTNEW.treefile</p> <p>● Introgression analyses:<br>- Concordance_factors_Dasypus.csv <br>- Topology_Weighting_Dasypus_plots.R<br>- SnaQ_results_hmax0.out <br>- SnaQ_results_hmax1.out <br>- SnaQ_results_hmax2.out <br>- SnaQ_results_hmax3.out <br>- twisst_guianensis_spmap.txt <br>- twisst_guianensis_Weights<br>- twisst_mexico_spmap.txt<br>- twisst_mexico_Weights</p> <p> </p> <p><strong>10_Species_delimitation.zip</strong><br>● BPP <br>- input_for_bpp.phy: Sequence alignments of the 837 nuclear loci in phylip format.<br>- lineage_for_BPP: Correspondence file between individuals and lineages.<br>- r1 and r2: folders containing config files (bpp.ctl) and outputs of the BPP analysis. </p> <p>● bPTP <br>- PTPh_Support_Partition.txt: Details of the most supported species partition. <br>- PTPh_tree_partition.png: Tree illustrating the most supported species partition. </p> <p>● GMYC <br>- Script_GMYC.R: R script used to run the GMYC delimitation method on the ultrametric tree (11_Phylogenetic_inference/Ultrametric_Tree/Ultrametric_tree_concatenated_nuclear_loci.treefile).<br>- Figure_GMYC.png: Figure illustrating the results of the GMYC species delimitation analysis.</p> <p>● PHRAPL<br>- Script_PHRAPL.R: R script used to run the PHRAPL delimitation method on the 09_Phylogenetic_inference.zip/Gene_Tree /Concatenate_gene_tree.treefile</p> <p> </p> <p><strong>11_Population_genetic_analyses.zip</strong><br>● PCA<br>- Input_for_PCA.fasta: Diploid sequences of the 57 individuals (DNO-MC21 and DPI-L29 excluded) in PopPhyl format (Locus|species|individual|allele).<br>- PCA_Output: Output of the PopPhyl2PCA analysis using the Input_for_PCA.fasta file.<br>- Script_to_plot_PCA.R: R script used to plot PCA according to the mitochondrial lineage and nuclear composition (Admixture results).</p> <p>● ADMIXTURE<br>- lineage_for_Admixture.list: Correspondence between individuals and lineages file.<br>- Input_Admixture.*: 19,872 SNPs from nuclear data across the Dasypus complex.<br>- Output_Admixture.k.*: Output from the Admixture analysis according to K values (from 1 to 7).<br>- Output_Admixture.cv.error: Summary of the error value according to K. <br>- Plot_Admixture.R: R script used to plot Admixture results reordered by phylogeny. <br>- Plot_map_distribution_admixture.R: R script used to plot Admixture results on the Neotropical map.</p> <p>● Stats_Da_Dxy_GDI<br>- Pairwise_genetic_statistics.csv: Summary statistics computed using ABCstat_global.txt from the DILSmcsnp program for all pairwise combinations of individuals from the different lineages. <br>- Pairwise_GDI.csv: Genetic Differentiation Index estimates for all pairwise combinations of individuals from the different lineages. <br>- Plot_genetic_statistics.R: R script used to plot mean genetic statistics between lineages.</p> <p>● Sublineage_structure <br>○ ADMIXTURE<br>- Plot_map_distribution_sublineage_admixture.R: R script used to plot Admixture results on the Neotropical map.<br>○ PCA<br>- Input_for_PCA_southern_lineage.fasta: Diploid sequences of the 24 individuals of the Southern lineage in PopPhyl format (Locus|species|individual|allele).<br>- PCA_Output_southern_lineage: Output of the PopPhyl2PCA analysis using the Input_for_PCA_southern_lineage.fasta file.<br>- Script_to_plot_PCA_sublineage.R: R script to plot PCA according to the mitochondrial lineage and nuclear composition (Admixture results) focussing on individuals from the Southern lineage.</p> <p><br><strong>12_Morpho_molecular_distribution.zip</strong><br>- Coordinates_according_morphogroup_lineages.csv: GPS coordinates of individuals used in Hautier et al. (2017) according to their morphogroup.<br>- Plot_map_distribution_morpho_admixture.R: R script used to plot Admixture results and the individuals from Hautier et al. (2017) on the Neotropical map in Figure 5.<br>- Skull_lateral_*.png: Illustration of the lateral view of the skull of four individuals representing each species.<br>- Skull_sinuses_*.png: Illustration of the skull and paranasal sinuses of four individuals representing each species.</p> <p> </p>
Data from: Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield
<p>The nine-banded armadillo (<em>Dasypus novemcinctus</em>) is the most widespread xenarthran species across the Americas. Recent studies have suggested it is composed of four morphologically and genetically distinct lineages of uncertain taxonomic status. To address this issue, we used a museomic approach to sequence 80 complete mitogenomes and capture 997 nuclear loci for 71 <em>Dasypus</em> individuals sampled across the entire distribution. We carefully cleaned up potential genotyping errors and cross contaminations that could blur species boundaries by mimicking gene flow. Our results unambiguously support four distinct lineages within the <em>D. novemcinctus</em> complex. We found cases of mito-nuclear phylogenetic discordance but only limited contemporary gene flow confined to the margins of the lineage distributions. All available evidence including the restricted gene flow, phylogenetic reconstructions based on both mitogenomes and nuclear loci, and phylogenetic delimitation methods consistently supported the four lineages within <em>D. novemcinctus</em> as four distinct species. Comparable genetic differentiation values to other recognized <em>Dasypus</em> species further reinforced their status as valid species. Considering congruent morphological results from previous studies, we provide an integrative taxonomic view to recognise four species within the <em>D. novemcinctus </em>complex: <em>D. novemcinctus</em>, <em>D. fenestratus</em>, <em>D. mexicanus</em>, and <em>D. guianensis </em>sp. nov.<em>, </em>a new species endemic of the Guiana Shield that we describe here. The two available individuals of <em>D. mazzai</em> and <em>D. sabanicola</em> were consistently nested within <em>D. novemcinctus </em>lineage and their status remains to be assessed. The present work offers a case study illustrating the power of museomics to reveal cryptic species diversity within a widely distributed and emblematic species of mammals.</p>
Data from: Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity
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Data from: Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield
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Artifactual orthologs and the need for diligent data exploration in complex phylogenomic datasets: A museomic case study from the Andean flora
<p>The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap to our understanding of the World's richest flora, we present the first phylogeny of <em>Freziera</em> (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in <em>Freziera</em>, including a significant proportion of paralogous loci and a high degree of gene tree discordance. Via gene tree filtering, by-eye observation of gene trees, and detailed examination of warnings from recently improved assembly pipelines, we identified that cryptic paralogs (i.e., the presence of only one copy of a multi-copy gene due to assembly errors) were a major source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These cryptic paralogs likely result from limitations in data collection that are common in museomics, combined with a history of genome duplication; they may be common in plant phylogenomic datasets. After accounting for cryptic paralogs as source of gene tree error, we identified a significant, but non-specific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve <em>Freziera</em> into nine well-supported subclades whose histories have been shaped by myriad evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, and point to the need to test for multiple sources of gene tree discordance via careful examination of empirical datasets.</p>
Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)
<p>Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, <em>Pyrgilauda theresae</em>. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using from ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (<em>Montifringilla nivalis</em>).</p>
Museomics unveil systematics, diversity and evolution of Australian cycad-pollinating weevils
<p><span>Weevils have been shown to play significant roles in the obligate pollination of Australian cycads. In this study we apply museomics to produce a first molecular phylogeny estimate of the Australian cycad weevils, allowing an assessment of their monophyly, placement and relationships. Divergence dating suggests that the Australian cycad weevils originated from the late Oligocene to the middle Miocene and that the main radiation of the cycad-pollinating groups occurred from the middle to the late Miocene, which is congruent with the diversification of the Australian cycads, thus refuting any notion of an ancient ciophilous system in Australia. Taxonomic studies reveal the existence of nineteen Australian cycad weevil species and that their associations with their hosts are mostly non-species-specific. Co-speciation analysis shows no extensive co-speciation events having occurred in the ciophilous system of Australian cycads. The distribution pattern suggests that geographic factors, rather than diversifying co-evolution, constitute the overriding process shaping the Australian cycad weevil diversity. The synchronous radiation of cycads and weevil pollinators is suggested to be a result of the post-Oligocene diversification common in Australian organisms.</span></p>
Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)
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Museomics unveil systematics, diversity and evolution of Australian cycad-pollinating weevils
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Artifactual orthologs and the need for diligent data exploration in complex phylogenomic datasets: A museomic case study from the Andean flora
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Code from: Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds
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Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.
Data from: Next-generation museomics disentangles one of the largest primate radiations
Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA dataset from museum specimens, we document how NGS technologies can 'unlock' museum collections, thereby helping to unravel the tree-of-life.
HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution
<p>Abstract Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax (Waterhouse, 1841) nested within the genus Calosoma (Weber, 1801) demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.</p>
Fig. 2 in Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment
Fig. 2. Number of raw loci recovered for each sample per year of collection. The dashed line is for reference and represents the trend. Plot made on R.
Fig. 1 in Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment
Fig. 1. Simplified representation of Epicopeiidae phylogenetic relationships according to Minet (2002) (left) and Wei and Yen (2017) (right). Each genus has a specific color. Minet's alternative hypothesis about the position of Amana is represented by gray lines.
FIGURE 1 in Keratose sponge MuseOMICS: setting reference points in dictyoceratid demosponge phylogeny
FIGURE 1. Maximum Likelihood phylogram of concatenated ITS and 28S sequences from type material of type species for dictyoceratid genera. Numbers at branches are bootstrap values> 50%. Taxon names in bold depict sequences yielded in the course of the target capturing approach as described here. Species names are followed by museum voucher number and type status. The tree is rooted with Candidaspongia flabellata Bergquist, Sorokin & Karuso, a dysideid Dictyoceratida. Scale bar represents substitutions / site.
Figure 3 in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification
Figure 3. Evolutionary and biogeographic history of Petrodromus. Top: Summary of secondary dating using StarBEAST2 with different numbers of lineages. For details for each run see Supporting Information, Fig. S1. Major biogeographic events are annotated to the respective nodes/branches. Boưom: Synoptic hypothesis of Petrodromus' biogeographic history through time. Moist broadleaf forest in neon green, more arid savannas, bushlands and woodlands in olive green.
Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification
Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A, Bayesian phylogenetic tree from mitochondrial (less) and nuclear DNA (right) with major genetic lineages highlighted. Numbers indicate posterior probability of deeper nodes. B, Collecting locations of samples assigned to lineages, with squares representing the P.t.s.s. lineages and dots all other lineages. C, Haplotype network of the nuclear gene IRBP (top) and mitochondrial gene 16S rRNA (boưom).
Figure 1 in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification
Figure 1. Geographic distribution of Petrodromus tetradactylus. Topographic map of Sub-Saharan Africa with the red area showing the species' currently accepted distribution (IUCN Red List 2024, Rathbun 2015). Blue lines and areas represent major rivers and lakes. Black doưed lines indicate the East African Riss Valley, with the easternmost line representing the course of Kingdon's Line (red dots). Yellow circles mark the origin of samples analysed in this study.
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