The complete mitogenome of the European mantis, Mantis religiosa, from Italy: implications for the origin of North American mantis population

3openInternationalItalian coauthor/editorThe European mantis, Mantis religiosa L. (Mantodea Mantidae), is distributed all over Southern Europe, Africa and Asia, and has been reported as alien species in North America. Here we present the mitogenome sequence of an Italian individual and compare it with previously sequenced Chinese and Canadian samples. The assembled mitogenome has a length of 15,530 nucleotides and includes 13 protein coding genes, two ribosomal RNA genes, 23 tRNA genes (including the additional Arginine tRNA already observed in other M. religiosa mitogenomes), and the control region. Based on the inferred phylogenetic relationships, the Canadian sample is more closely related to the Italian than to the Chinese one, in line with the putative European origin of the North American invasive population. Time-calibrated phylogeny dated the divergence among extant European Mantis lineages at 2.33 million years ago, consistent with the first appearance of M. religiosa fossils. Our results support a European origin of the North American M. religiosa population and suggest that selective processes acting on mitogenome may have contributed to its adaptation in the new area.openLuchetti, A; Ometto, L; Rota Stabelli, O.Luchetti, A.; Ometto, L.; Rota Stabelli, O

Chronological incongruences between mitochondrial and nuclear phylogenies of Aedes mosquitoes

3openInternationalOne-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoesopenZadra, Nicola; Rizzoli, Annapaola; Rota-Stabelli, OmarZadra, N.; Rizzoli, A.; Rota-Stabelli, O

The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes

Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups

Evolutionary scenarios for the origin of an Antarctic tardigrade species based on molecular clock analyses and biogeographic data

The origin of the Antarctic continental extant fauna is a highly debated topic, complicated by the paucity of organisms for which we have clear biogeographic distributions and understanding of their evolutionary timescale. To shed new light on this topic, we coupled molecular clock analyses with biogeographic studies on the heterotardigrade genus Mopsechiniscus. This taxon includes species with endemic distributions in Antarctica and other regions of the southern hemisphere. Molecular dating using different models and calibration priors retrieved similar divergence time for the split between the Antarctic and South American Mopsechiniscus lineages (32\u201348 Mya) and the estimated age of the Drake Passage opening that led to the separation of Antarctica and South America. Our divergence estimates are congruent with other independent studies in dating Gondwanan geological events. Although different analyses retrieved similar results for the internal relationships within the Heterotardigrada, our results indicated that the molecular dating of tardigrades using genes coding for ribosomal RNA (18S and 28S rDNA) is a complex task, revealed by a very wide range of posterior density and a relative difficulty in discriminating between competing models. Overall, our study indicates that Mopsechiniscus is an ancient genus with a clear Gondwanan distribution, in which speciation was probably directed by a cooccurrence of vicariance and glacial events

Evolutionary scenarios for the origin of an Antarctic tardigrade species based on molecular clock analyses and biogeographic data

The origin of the Antarctic continental extant fauna is a highly debated topic, complicated by the paucity of organisms for which we have clear biogeographic distributions and understanding of their evolutionary timescale. To shed new light on this topic, we coupled molecular clock analyses with biogeographic studies on the heterotardigrade genus Mopsechiniscus. This taxon includes species with endemic distributions in Antarctica and other regions of the southern hemisphere. Molecular dating using different models and calibration priors retrieved similar divergence time for the split between the Antarctic and South American Mopsechiniscus lineages (32–48 Mya) and the estimated age of the Drake Passage opening that led to the separation of Antarctica and South America. Our divergence estimates are congruent with other independent studies in dating Gondwanan geological events. Although different analyses retrieved similar results for the internal relationships within the Heterotardigrada, our results indicated that the molecular dating of tardigrades using genes coding for ribosomal RNA (18S and 28S rDNA) is a complex task, revealed by a very wide range of posterior density and a relative difficulty in discriminating between competing models. Overall, our study indicates that Mopsechiniscus is an ancient genus with a clear Gondwanan distribution, in which speciation was probably directed by a co-occurrence of vicariance and glacial events

Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region

Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae)

Polyploidization is a frequent phenomenon in plants, which entails the increase from one generation to the next by multiples of the haploid number of chromosomes. While tetraploidization is arguably the most common and stable outcome of polyploidization, over evolutionary time triploids often constitute only a transient phase, or a “triploid bridge”, between diploid and tetraploid levels. In this study, we reconstructed in a robust phylogenomic and statistical framework the evolutionary history of polyploidization in Arundo, a small genus from the Poaceae family with promising biomass, bioenergy and phytoremediation species. Through the obtainment of 10 novel leaf transcriptomes for Arundo and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor genus. Molecular dating further demonstrates that the species originating by demiduplication stalled in the “triploid bridge” for evolutionary times in the order of millions of years without undergoing tetratploidization. Nevertheless, we found signatures of molecular evolution highlighting some of the processes that accompanied the genus radiation. Our results clarify the complex nature of Arundo evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the Arundo genus and other Arundinoideae

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets

In their letter, Halanych et al. (1) criticize our recent assertion (2) that the phylogenetic placement of ctenophores as the sister group to all other animals (the Ctenophora-sister hypothesis) in three previous studies (3–5) was an artifact caused by undetected systematic error. Halanych et al. (1) claim we used no “objective approaches” to identify sources of systematic error. In fact, we used an objective comparison of Bayesian cross-validation scores to select the best-fitting substitution model, because poorly fitting models are a frequent source of systematic error. Halanych et al. point out that this comparison did not include partitioned site-homogeneous models. However, they do not mention that only one of the studies we address (3) used this approach, and that multiple site-homogeneous partitions still do not account for within-partition site-heterogeneous biochemical constraints, which our results show had a major impact on model fit and the tree topology

Genomic data do not support comb jellies as the sister group to all other animals

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the “Ctenophora-sister” hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae)

Polyploidization is a frequent phenomenon in plants, which entails the increase from one generation to the next by multiples of the haploid number of chromosomes. While tetraploidization is arguably the most common and stable outcome of polyploidization, over evolutionary time triploids often constitute only a transient phase, or a “triploid bridge”, between diploid and tetraploid levels. In this study, we reconstructed in a robust phylogenomic and statistical framework the evolutionary history of polyploidization in Arundo, a small genus from the Poaceae family with promising biomass, bioenergy and phytoremediation species. Through the obtainment of 10 novel leaf transcriptomes for Arundo and outgroup species, our results prove that recurrent demiduplication has likely been a major driver of evolution in this species-poor genus. Molecular dating further demonstrates that the species originating by demiduplication stalled in the “triploid bridge” for evolutionary times in the order of millions of years without undergoing tetratploidization. Nevertheless, we found signatures of molecular evolution highlighting some of the processes that accompanied the genus radiation. Our results clarify the complex nature of Arundo evolution and are valuable for future gene functional validation as well as reverse and comparative genomics efforts in the Arundo genus and other Arundinoideae