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opencc-zeroNov 2021View details →

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.

opencc-zeroJan 2022View details →

A global phylogenomic study of the Thelypteridaceae

The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing more than 1000 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships have been gained from recent phylogenetic studies, especially for the Neotropics; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. In the present study, we sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. Our phylogenomic results, coupled with morphological study, provide a foundation for a new generic classification. Our recently recognized monophyletic genera demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile, and are thus inadequate for defining genera.

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).

opencc-by-4.0Dec 2021View details →

Molecular data from "Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)"

Phylogenetic_dataset.csv: Unfiltered DArTseq data used in phylogenetic analyses. Readable by 'dartR' (Gruber et al. 2018). Population_dataset.csv: Unfiltered DArTseq data used in population-level analyses. Readable by 'dartR' (Gruber et al. 2018). Reference.csv: Spreadsheet listing individuals included in molecular analyses. Includes vouchers, species, name of each sample in DArTseq data sets, and GenBank accession numbers (GB) for mitochondrial data. ABTC stands for Australian Biological Tissue Collection; AA and CCM for field numbers of uncatalogued specimens. Other collection acronyms follow Sabaj (2019). We refrain from assigning individuals that were not included in the molecular analyses to any given species.

opencc-zeroApr 2022View details →

Data from: Phylogenomics of elongate-bodied Springtails reveals independent transitions from aboveground to belowground habitats in deep time

Soil has become a major hotspot of biodiversity studies, yet the pattern and timing of the evolution of soil organisms are poorly known because of the scarcity of palaeontological data. To overcome this limitation, we conducted a genome-based macroevolutionary study of an ancient, diversified, and widespread lineage of soil fauna, the elongate-bodied springtails (class Collembola, order Entomobryomorpha). To build the first robust backbone phylogeny of this previously refractory group, we sampled representatives of major higher taxa (6 out of 8 families, 11 out of 16 subfamilies) of the order with an emphasis on the most problematic superfamily Tomoceroidea, applied whole-genome sequencing (WGS) methods, and compared the performance of different combinations of datasets (universal single-copy orthologues/USCO versus ultraconserved elements/UCE) and modelling schemes. The fossil-calibrated timetree was used to reconstruct the evolution of body size, sensory organs, and pigmentation to establish a time frame of the ecomorphological divergences. The resultant trees based on different analyses were congruent in most nodes. Several discordant nodes were carefully evaluated by considering method fitness, morphological information, and topology test. The evaluation favoured the well-resolved topology from analyses using USCO amino acid matrices and complex site-heterogeneous models (CAT+GTR and LG+PMSF (C60)). The preferred topology supports the monophyletic superfamily Tomoceroidea as an early-diverging lineage and a sister relationship between Entomobryoidea and Isotomoidea. The family Tomoceridae was recovered as monophyletic, while Oncopoduridae was recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae and hence deserving a separate family status as Harlomillsiidae Yu and Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as surface-living, supporting independent origins of soil-living groups across the Palaeozoic–Mesozoic, and highlighting the ancient evolutionary interaction between aboveground and belowground fauna.

opencc-zeroApr 2022View details →

Saguaro cactus within-species phylogenomics

Reconstructing accurate historical relationships between populations within a species poses numerous challenges, not least in many plant groups in which gene flow can extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we infer a population tree and evaluate its significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, population trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects post-glacial expansion from the far south following retreat to refugia there. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.

opencc-zeroApr 2022View details →

Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus Torreya. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of Torreya that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern Torreya from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on T. jackii, suggesting differential lineage sorting of plastid genomes among Torreya species or plastid genome capture in T. jackii.

opencc-zeroJun 2022View details →

Supplementary data for: McFadden et al., Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics

The anthozoan sub-class Octocorallia includes over 3500 nominal species of soft corals and gorgonian sea fans, many of which serve as critical foundation species in benthic marine ecosystems in shallow waters to the deep sea. Despite their familarity and ecological importance, the diversity and taxonomy of octocorals remain poorly known. All of the orders, subordinal groups and a majority of families have been recognized to be poly- or paraphyletic, but poor resolution of the deeper nodes in mitochondrial or single-locus nuclear gene trees have hindered formal revision of the higher level taxonomy of the group. We used sequence data from target-capture of 739 ultraconserved and exon loci to reconstruct a fully resolved phylogeny for 185 octocoral taxa representing 55 of 63 currently recognized families. We use this phylogeny, supplemented with a gene tree for mitochondrial mtMutS for an additional 107 taxa, to guide a revision of the families and orders of Octocorallia. We: (1) elevate the anthozoan sub-classes Octocorallia and Hexacorallia to the rank of Class; (2) replace the three currently recognized orders of Octocorallia (Alcyonacea, Pennatulacea, Helioporacea) with two new orders reflecting reciprocally monophyletic major clades; and (3) revise all families with the exception of the 15 recognized families of sea pens, which we accommodate within a new superfamily. The revised classification of Octocorallia thus comprises 79 families, including 18 that are newly described and three that have been reinstated or elevated in rank. In addition, two new genera are described and another three reinstated. We leave the family assignment of 46 of 411 genera as incertae sedis until further molecular or morphological data can be obtained to confirm their phylogenetic affinities.

opencc-by-4.0Jun 2022View details →

A higher-level nuclear phylogenomic study of the carrot family (Apiaceae)

Premise The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. Methods Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. Results We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysaceresolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. Conclusions We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.