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Research data for UCE phylogenomics of sawflies and woodwasps
<p>Input files, scripts and newick tree files for the ongoing project on reconstructing a comprehensive phylogeny and biogeography for sawflies and woodwasps (Hymenoptera). </p>
Do alignment and trimming methods matter for phylogenomic (UCE) analyses?
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from dozens, hundreds, or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e. removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these datasets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data (~5,000 loci) and subsampled datasets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic datasets (e.g. length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses.
Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of "legacy" phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
Fig. 11 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 11. Lateral view of propodeum, showing: A) Propodeal spiracle separated from declivity margin by a distance longer than its diameter (Typhlomyrmex lavra); B) Propodeal spiracle close to the declivous face of propodeum (Holcoponera relicta—USNMENT00412058). Photos by Gabriela Camacho (A) and Jeffrey Sosa-Calvo; available from www.antweb.org (Antweb 2021).
Fig. 10 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 10. Lateral view of gaster, showing: A) Second gastric segment (IV abdominal) relatively straight (Gnamptogenys acuminata—USNMENT00441095); B) Second gastric segment (IV abdominal) slightly arched ventrally (Poneracantha mecotyle—CASENT0281530). Photos by Jeffrey Sosa-Calvo (A) and Zach Lieberman (B); available from www.antweb.org (Antweb 2021).
Fig. 8 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 8. Lateral view of gaster, showing: A) Second gastral (IV abdominal) sternite not strongly reduced in relation to the tergite; dorsal profile of gaster gently convex, so that the apex of gaster is only discretely directed ventrally (Gnamptogenys acuminata—USNMENT00441095); B) Second gastral (IV abdominal) sternite strongly reduced in relation to the tergite; dorsal profile of gaster extremely convex, so that the gaster is strongly directed ventrally and anterad (Alfaria minuta—CASENT0281213). Photos by Jeffrey Sosa-Calvo (A) and Estella Ortega (B); available from www.antweb.org (Antweb 2021).
Fig. 5 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 5. Lateral view of pronotum, showing: A) Pronotal tubercles present; mesonotum prominent, separated from propodeum by a deep transversal suture (Ectatomma tuberculatum—CASENT0173380); B) Pronotal tubercles or projections absent; mesonotum not prominent, forming a continuous profile with propodeum (Holcoponera striatula—CASENT0173386). Photos by April Nobile; available from www.antweb.org (Antweb 2021).
Fig. 7 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 7. Frontal view of head, showing: A) Expanded frontal lobes (Alfaria falcifera—CASENT0179971); B) Occipital lobes absent (Gnamptogenys continua— CASENT0173383). Photos by Erin Prado (A) and April Nobile (B); available from www.antweb.org (Antweb 2021).
Fig. 1 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 1. In lateral view, workers of the Ectatomminae genera, showing the morphological diversity within the clade. (A) Acanthoponera mucronata (CASENT0173540), (B) Alfaria minuta (CASENT0281213), (C) Ectatomma planidens (CASENT0173379), (D) Gnamptogenys acuminata (USNMENT00441095), (E) Heteroponera panamensis (CASENT0106021), (F) Holcoponera ammophila (CASENT0281512), (G) Poneracantha mecotyle (CASENT0281530), (H) Rhytidoponera metallica (CASENT0172345), (I) Stictoponera biroi (CASENT0172380), (J) Typhlomyrmex rogenhoferi (CASENT0173390). See Fig. 3 for images of Boltonia microps. Images by April Nobile, Estella Ortega, Michael Branstetter, Zach Lieberman, and Jeffrey Sosa-Calvo; available from www.antweb.org (Antweb 2021).
Fig. 3 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 3. Worker of Boltonia microps in A) frontal view; B) dorsal view; and C) lateral view. Images by April Nobile (CASENT0173544); available from www.antweb. org (Antweb 2021).
Fig. 2 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 2. Phylogeny of the subfamily Ectatomminae based on phylogenomic analyses of the UCE 90% complete data set (150 taxa). Figure is based on IQ-Tree besttree searches with ultrafast bootstrap (UFB) frequencies of less than 100% mapped onto the respective nodes. UFB searches consisted of 1000 replicates.The eleven larger ectatommine lineages are indicated. Branch color indicates the biogeographical range of the species.Taxa marked with asterisk (*) were classified in Gnamptogenys prior to this revision and those with double asterisk (**) were included in Heteroponera prior to this revision. See Supplementary material for the 75% complete matrix (Supp Fig. S1 [online only]). Ant photos show heads in frontal view of, from top to bottom:Gnamptogenys acuminata (USNMENT00441095), Typhlomyrmex rogenhoferi (CASENT0004700), Holcoponera striatula (CASENT0106042), Alfaria simulans (CASENT0603729), Poneracantha rastrata (CASENT0281223), Stictoponera biroi (CASENT0281519), Rythidoponera metallica (CASENT0172345), Ectatomma lugens (USNMENT00445341), Heteroponera brounii (CASENT0172105), Acanthoponera mucronata (CASENT0173540), and Boltonia microps (CASENT0173544). Images by April Nobile, Jeffrey Sosa-Calvo, Zach Lieberman,Will Ericson, Michael Branstetter, and Estella Ortega; available from www.antweb.org (Antweb 2021).
Fig. 4 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 4. Dorsal view of head, showing: A) Cephalic median longitudinal carina present, extending from the anterior clypeal margin to the vertex (Acanthoponera minor—CASENT0178699); B) Cephalic median longitudinal carina not extending from the anterior clypeal margin to the vertex (Ectatomma tuberculatum— CASENT0173380); C) Cephalic median longitudinal carina absent (Holcoponera striatula—CASENT0173386). Photos by April Nobile; available from www. antweb.org (Antweb 2021).
Fig. 9 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 9. Dorsal view of mesosoma, showing: A) Promesonotal suture absent (Gnamptogenys acuminata—USNMENT00441095); B) Promesonotal suture feeble, never interrupting dorsal mesosomal sculpture (Poneracantha banksi—INBIOCRI001281007); C) Promesonotal suture well marked, totally interrupting dorsal mesosomal sculpture (Holcoponera moelleri—CASENT0173384). Photos by Jeffrey Sosa-Calvo (A), Estella Ortega (B), and April Nobile (C); available from www. antweb.org (Antweb 2021).
Fig. 6 in UCE Phylogenomics Resolves Major Relationships Among Ectaheteromorph Ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A New Classification For the Subfamilies and the Description of a New Genus
Fig. 6. Dorsal view of pronotum, showing: A) Pronotum and mesonotum separated by a distinct suture (Rhytidoponera abdominalis—CASENT0281333); B) Pronotum and mesonotum continuous with a discrete groove (Gnamptogenys stellae—CASENT0281227). Photos by Cerise Chen (A) and Estella Ortega (B) available from www.antweb.org (Antweb 2021).
Data from: Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants
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Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
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UCE phylogenomics illuminate the evolutionary history and biogeography of Dorymyrmex pyramid ants
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Phylogenomics of bivalvia using ultraconserved elements (UCEs) reveal new topologies for Pteriomorphia and Imparidentia
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Do alignment and trimming methods matter for phylogenomic (UCE) analyses?
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Data from: Ultraconserved yet informative for species delimitation: UCEs resolve long-standing systematic enigma in Central European bees
Accurate and testable species delimitation hypotheses are essential for measuring, surveying and managing biodiversity. Today, taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not necessarily reflect the species history. For instance, what is regarded as one single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to deep within-species mitochondrial divergences with no reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of mitochondrial DNA barcoding can only be addressed with nuclear genomic markers, which are expensive, labour intensive, poorly repeatable, and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved nuclear genetic elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation. This genomic method was assessed using six different bee species complexes suspected to harbour cryptic diversity, mitochondrial introgression, or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1860 homologous nuclear loci and provided explicit species delimitation hypotheses in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, this study provided the first conclusive evidence for both mitochondrial introgression among distinct species, and mitochondrial paraphyly within a single bee species.
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