Multiple Outgroups Can Cause Random Rooting in Phylogenomics

A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data

Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs-which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella-have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.

Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach

Montane landscapes present an array of abiotic challenges that drive adaptive evolution amongst organisms. These adaptations can promote habitat specialisation, which may heighten the risk of extirpation from environmental change. For example, higher metabolic rates in an endothermic species may contribute to heightened cold tolerance, whilst simultaneously limiting heat tolerance. Here, using the climate-sensitive American pika (Ochotona princeps), we test for evidence of intraspecific adaptive variation amongst environmental gradients across the Intermountain West of North America. We leveraged results from previous studies on pika adaptation to generate a custom nuclear target enrichment design to sequence several hundred candidate genes related to cold, hypoxia and dietary detoxification. We also applied a 'genome skimming' approach to sequence mitochondrial DNA. Using genotype-environment association tests, we identified rare genomic variants associated with elevation and temperature variation amongst populations. Amongst mitochondrial genes, we identified intraspecific variation in selective signals and significant changes to the amino acid property equilibrium constant, which may relate to electron transport chain efficiency. These results illustrate a complex dynamic of adaptive variation amongst O. princeps where lineages and populations have adapted to unique regional conditions. Some of the clearest signals of selection were in a genetic lineage that includes pikas of the Great Basin region, which is also where recent localised extirpations have taken place and highlights the risk of losing adaptive alleles during environmental change.

Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida

Acoelomorpha is a broadly accepted clade of bilaterian animals made up of the fast-evolving, morphologically simple, mainly marine flatworm lineages Acoela and Nemertodermatida. Phylogenomic studies support Acoelomorpha's close relationship with the slowly evolving and similarly simplistic Xenoturbella, together forming the phylum Xenacoelomorpha. The phylogenetic placement of Xenacoelomorpha amongst bilaterians is controversial, with some studies supporting Xenacoelomorpha as the sister group to all other bilaterians, implying that their simplicity may be representative of early bilaterians. Others propose that this placement is an error resulting from the fast-evolving Acoelomorpha, and instead suggest that they are the degenerate sister group to Ambulacraria. Perhaps as a result of this debate, internal xenacoelomorph relationships have been somewhat overlooked at a phylogenomic scale. Here, I employ a highly targeted approach to detect and overcome possible phylogenomic error in the relationship between Xenoturbella and the fast-evolving acoelomorph flatworms. The results indicate that the subphylum Acoelomorpha is a long-branch attraction artefact obscuring a previously undiscovered clade comprising Xenoturbella and Acoela, which I name Xenacoela. The findings also suggest that Xenacoelomorpha is not the sister group to all other bilaterians. This study provides a template for future efforts aimed at discovering and correcting unrecognized long-branch attraction artefacts throughout the tree of life.

Complete mitochondrial genomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae)

We describe the complete mitogenomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1790) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). The analysed specimens include the holotype of Alternatipathesmirabilis, collected from Derickson Seamount (North Pacific Ocean; Gulf of Alaska) at 4,685 m depth and a potential topotype of Parantipatheslarix, collected from Secca dei Candelieri (Mediterranean Sea; Tyrrhenian Sea; Salerno Gulf; Italy) at 131 m depth. We also assemble, annotate and make available nine additional black coral mitogenomes that were included in a recent phylogeny (Quattrini et al. 2023b), but not made easily accessible on GenBank. This is the first study to present and compare two mitogenomes from the same species of black coral (Stauropathesarctica (Lütken, 1871)) and, thus, place minimum boundaries on the expected level of intraspecific variation at the mitogenome level. We also compare interspecific variation at the mitogenome-level across five different specimens of Parantipathes Brook, 1889 (representing at least two different species) from the NE Atlantic and Mediterranean Sea.

Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination

Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.