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Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.

Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.

Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.

Figure 4 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 4. Stacked barplots showing the number of reads uniquely matching different reference sequences for the three targeted mitochondrial genes with a similarity threshold of 98%. The Rana pigra type was not included because the number of reads was too low.

Figure 8 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 8. Lateral views of the heads of preserved adult males of Mantidactylus (Mantidactylus) radaka sp. nov. in comparison with M. (M.) guttulatus and M. (M.) grandidieri. Note the more distinct and larger tympanum (indicated by yellow arrows) in the latter two species. Not to scale.

Figure 6 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

Figure 6. Photographs of living specimens of Mantidactylus radaka sp. nov. (a, b) Male holotype ZSM 644/2001 (field number FGMV 2001.132) from Manarikoba forest, Tsaratanana Massif. (c–f) Female paratype ZSM 1800/2010 (ZCMV 12345) from Camp 1 (Antevialambazaha), Tsaratanana Massif. (g, h) Female paratype ZSM 97/2016 (MSZC 0080) from Ampotsidy. (i, j) Male paratype MSZC 0120 (uncatalogued in UADBA) from Ampotsidy. (k) Unidentified specimen from Camp 0 (Ankijagna Lagnana), Tsaratanana Massif. (l) Paratype ZSM 582/2014 (DRV 6073) from Camp 0 (Ankijagna Lagnana). (m, n) Unidentified female specimen from Manongarivo (Camp 0), probably preserved in UADBA collection.

opennotspecifiedApr 2021View details →

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.

opennotspecifiedApr 2021View details →

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.

FIG. 3 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 3. Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the anostomoid dataset with family names in color. Parodon hilarii is the outgroup taxon, and bootstrap support is indicated at each node. The numbers in parentheses to the right of each taxon denote the count of loci enriched from that organism. See Data Accessibility for tree file.

FIG. 5 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 5. Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the characiform dataset with family names in color. Ictalurus punctatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.

FIG. 7 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 7. Venn diagram indicating the number of ultraconserved element (UCE) loci detected in four genomeenabled taxa for each of three existing UCE bait sets designed for fishes (Faircloth et al., 2013; Alfaro et al., 2018; this study).

FIG. 2 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 2. Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the gymnotiform dataset with family names in color. Danio rerio is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.

FIG. 6 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 6. Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the otocephalan dataset with family names in color. Lepisosteus oculatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.

FIG. 4 in A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

FIG. 4. Maximum likelihood phylogenetic hypothesis of relationships among taxa comprising the loricarioid dataset with family names in color. Ictalurus punctatus is the outgroup taxon, and bootstrap support is indicated at each node. An asterisk by any taxon name indicates that these data were harvested, in silico, from existing genome assemblies, and the numbers in parentheses to the right of each taxon denote the count of loci enriched/harvested from that organism. See Data Accessibility for tree file.

opencc-zeroDec 2012View details →

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Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci was similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

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Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

opencc-zeroDec 2014View details →

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Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)

The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic

opencc-zeroOct 2021View details →

opencc-by-4.0Jul 2022View details →

Data from: A new genus in the diverse Andean Pedaliodes complex uncovered using target enrichment (Lepidoptera, Nymphalidae)

A new genus of Neotropical Satyrinae butterflies, Viloriodes Pyrcz & Espeland gen. n. is described in the Pedaliodes complex comprising 11-13 genera and more than 400 species. Support for the new genus is provided by a phylogenetic analysis based on target enrichment data (TE) including 618 nuclear loci with a total of 248 940 nucleotides, and the mitochondrial gene COI. Five species, whose DNA sequences were obtained by TE during this study, form a strongly supported clade sister to the large clade comprising Pedaliodes Butler and other four genera. Complementary COI analysis confirms the monophyly of Viloriodes gen. n., with the above five plus eight other species clustering in highly supported clades in both Bayesian Inference (BI) and Maxium Likelihood analyses, and a TE+COI concatenated tree. Based on molecular and morphological data, 30 species are assigned to Viloriodes gen. n. The new genus can be recognized by a set of subtle morphological of colour patterns characters, male and female genitalia. The shape of the valva is diagnostic, with a finger-like tip and, in some species, an ampulla produced into an elongated process. The female genitalia are characterized by the ductus bursae having a strongly sclerotized 'keel' with a bifurcate terminus. An analysis of divergence times indicates that Viloriodes gen. n. and Steromapedaliodes Forster separated around 5.9 Mya. Viloriodes gen. n. has a wider geographic distribution than any other genus of the Pedaliodes complex, being found from central Mexico to northern Argentina and to the Guyana Shield, typically occurring at lower elevations than Pedaliodes.

opencc-by-4.0Mar 2023View details →

Data for: Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Satyrinae, Nymphalidae)

The diverse, largely Neotropical subtribe Euptychiina (Satyrinae, Nymphalidae) is widely regarded as one of the most taxonomically challenging groups among all butterflies. Over the last two decades, morphological and molecular studies have revealed widespread paraphyly and polyphyly among genera, and a comprehensive, robust phylogenetic hypothesis is needed to build a firm generic classification to support ongoing taxonomic revisions at the species level. Here, we generated a dataset which includes sequences for up to nine nuclear genes and the mitochondrial COI 'barcode' for a total of 1280 specimens representing 449 described and undescribed species of Euptychiina and 39 outgroups, resulting in the most complete phylogeny for the subtribe to date. In combination with a recently developed genomic backbone tree this dataset resulted in a topology with strong support for most branches.