An official website of the United States government
Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.
more »
« less
A New Family of Stoneflies (Insecta: Plecoptera), Kathroperlidae, fam. n., with a Phylogenomic Analysis of the Paraperlinae (Plecoptera: Chloroperlidae)
Abstract Recent molecular analyses of transcriptome data from 94 species across 92 genera of North American Plecoptera identified the genus Kathroperla Banks, 1920 as sister group to Chloroperlidae + Perlodidae. Given that the genus Kathroperla has historically been included as a member of the family Chloroperlidae, this discovery indicated further investigation of the genus and the subfamily Paraperlinae was needed. Both transcriptome and genome sequencing datasets were generated from 32 species of the infraorder Systellognatha, including all described species of the Paraperlinae, to test the phylogenetic placement of these taxa. From these datasets, a large phylogenomic data matrix of 800 orthologous genes was produced, and multiple analyses were conducted, including both concatenated and coalescent analyses. Morphological comparisons were made among all Paraperlinae using light microscopy. All molecular results support a monophyletic Kathroperla, which is supported as sister taxon to the remaining Perloidea by five of six molecular analyses. Postocular head length is determined to be a distinct morphological character of this genus. Combined molecular and morphological evidence support the designation of Kathroperlidae, fam. n., as the seventeenth family of extant Plecoptera.
more »
« less
- Award ID(s):
- 1639014
- PAR ID:
- 10301261
- Editor(s):
- Ware, Jessica
- Date Published:
- Journal Name:
- Insect Systematics and Diversity
- Volume:
- 5
- Issue:
- 4
- ISSN:
- 2399-3421
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The octocoral genusPseudothelogorgiavan Ofwegen, 1994 has presented taxonomic challenges since its original description, with its higher-level placement uncertain and obscured by morphological convergence and lack of molecular data. Here, we integrate detailed morphological examination with phylogenomic analyses of newly collected shallow-water specimens from the Gulf of Oman, alongside a redescription of the type material. Our results recoverPseudothelogorgiaas a deeply divergent lineage within Malacalcyonacea, sister to Plexauridae but unrelated to Keroeididae, the family in which it was formerly placed. Distinct morphological characters, together with strong phylogenomic support, warrant the establishment of Pseudothelogorgiidaefam. nov.The shallow-water occurrences documented here extend the known depth range of the genus from mesophotic to shallow reef habitats, indicating ecological plasticity and highlighting the need for targeted exploration of under-surveyed Indian Ocean coral assemblages.more » « less
-
The Opiliones family Neopilionidae is restricted to the terranes of the former temperate Gondwana: South America, Africa, Australia, New Caledonia and New Zealand. Despite decades of morphological study of this unique fauna, it has been difficult reconciling the classic species of the group (some described over a century ago) with recent cladistic morphological work and previous molecular work. Here we attempted to investigate the pattern and timing of diversification of Neopilionidae by sampling across the distribution range of the family and sequencing three markers commonly used in Sanger-based approaches (18S rRNA, 28S rRNA and cytochrome-c oxidase subunit I). We recovered a well-supported and stable clade including Ballarra (an Australian ballarrine) and the Enantiobuninae from South America, Australia, New Caledonia and New Zealand, but excluding Vibone (a ballarrine from South Africa). We further found a division between West and East Gondwana, with the South American Thrasychirus/Thrasychiroides always being sister group to an Australian–Zealandian (i.e. Australia + New Zealand + New Caledonia) clade. Resolution of the Australian–Zealandian taxa was analysis-dependent, but some analyses found Martensopsalis, from New Caledonia, as the sister group to an Australian–New Zealand clade. Likewise, the species from New Zealand formed a clade in some analyses, but Mangatangi often came out as a separate lineage from the remaining species. However, the Australian taxa never constituted a monophyletic group, with Ballarra always segregating from the remaining Australian species, which in turn constituted 1–3 clades, depending on the analysis. Our results identify several generic inconsistencies, including the possibility of Thrasychiroides nested within Thrasychirus, Forsteropsalis being paraphyletic with respect to Pantopsalis, and multiple lineages of Megalopsalis in Australia. In addition, the New Zealand Megalopsalis need generic reassignment: Megalopsalis triascuta will require its own genus and M. turneri is here transferred to Forsteropsalis, as Forsteropsalis turneri (Marples, 1944), comb. nov.more » « less
-
Abstract—Podostemaceae are a clade of aquatic flowering plants that form important components of tropical river ecosystems. Species in the family exhibit highly derived growth forms and high vegetative phenotypic plasticity, both of which contribute to taxonomic confusion. The backbone phylogeny of the family remains poorly resolved, many species remain to be included in a molecular phylogenetic analysis, and the monophyly of many taxa remains to be tested. To address these issues, we assembled sequence data for 73 protein-coding plastid genes from 132 samples representing 68 species (∼23% of described species) that span the breadth of most major taxonomic, morphological, and biogeographic groups of Podostemaceae. With these data, we conducted the first plastid phylogenomic analysis of the family with broad taxon sampling. These analyses resolved most nodes with high support, including relationships not recovered in previous analyses. No evidence of widespread, well-supported conflict among individual plastid genes and the concatenated phylogeny was observed. We present new evidence that four genera (Apinagia,Marathrum,Oserya, andPodostemum), as well as four species, are not monophyletic. In particular, we show thatPodostemum flagelliformeshould not be included inPodostemumand is better recognized asDevillea flagelliformis,and thatMarathrum capillaceumis embedded withinLophogynes.l. and should be recognized asLophogyne capillacea. We also place a previously unsampled and undescribed species that likely represents a new genus. In contrast to previous studies, the neotropical generaDiamantina,Ceratolacis,Cipoia,andPodostemumare resolved as successive sister groups to a clade of all paleotropical Podostemoideae taxa sampled, suggesting a single dispersal event from the neotropics to the paleotropics in the history of the subfamily. These results provide a strong basis for improving the classification of Podostemaceae and a framework for future phylogenomic studies of the clade employing data from the nuclear genome.more » « less
-
null (Ed.)Abstract The first molecular phylogeny of the tribe Sepidiini is inferred from analyses of DNA sequence data from the following five loci (CAD, wg, COI, COII, 28S rRNA). Bayesian and maximum likelihood analyses were performed on a dataset containing 41 taxa, of which a majority represent Molurina (27) and Phanerotomeina (6). The resulting topologies were used to discuss phylogenetic placement and diagnostic characters of all of the genera representing Molurina. Within the subtribe, the results revealed paraphyly of the genus Psammodes. The P. vialis species-group, currently classified within Psammodes, was recovered as sister to all other Molurina genera. Based on this topology and morphological investigations, a new genus named Toktokkus gen. nov. is established. Within Phanerotomeina, Ocnodes is paraphyletic with regard to Tarsocnodes. In order to restore the monophyly of Ocnodes, the subgenus Chiliarchum stat. nov. is elevated to generic level. Finally, as the homology of female terminalia structures has never been fully assessed for Sepidiini, a comparative study of ovipositor morphology was conducted. As a result, this paper presents the first fully annotated ovipositors for tok-tokkie beetles.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/isd/ixab014
