Publications by authors named "Davide Pisani"

93 Publications

Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times.

Sci Adv 2021 Jun 11;7(24). Epub 2021 Jun 11.

School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.
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http://dx.doi.org/10.1126/sciadv.abf2257DOI Listing
June 2021

The Role of Quantic Molecular Resonance (QMR) in the Treatment of Inferior Turbinate Hypertrophy (ITH): Our Experience With Long-Term Follow-Up in Allergic and Nonallergic Rhinitis Refractory to Medical Therapy. Preliminary Results.

Ear Nose Throat J 2021 Jun 3:1455613211001599. Epub 2021 Jun 3.

Ear Nose and Throat Unit, Azienda 18617Ospedaliera di Rilievo Nazionale Antonio Cardarelli, vi Antonio Caradelli, Napoli, Italy.

Objective: The aim of this study was to assess the long-term effectiveness of quantic molecular resonance (QMR) in the treatment of inferior turbinate hypertrophy (ITH) in allergic and nonallergic rhinitis refractory to medical therapy.

Methods: This study enrolled 281 patients, 160 males (56.9%) and 121 females (43.1%), mean age 37.8 ± 4.1 years, range 18 to 71. Fifty-four patients have been lost to follow up and have been therefore excluded from the final analysis. Based on skin prick test results, 69 patients were considered allergic (group A) and 158 nonallergic (group B). All subjects underwent before surgery (T0) and 3 (T1), 12 (T2), 24 (T3), and 36 months (T4) after QMR treatment to: 4-phase rhinomanometric examination, nasal endoscopy evaluation, and visual analogue scale to quantify the subjective feelings about nasal obstruction.

Results: Subjective and objective parameters showed statistically significant improvement in both groups. Group B parameters not changed during follow-up, while group A showed significant worsening between T1 and subsequent assessments. T4 outcome indicates a better result in nonallergic patients.

Conclusions: In accordance with the literature, our preliminary data validate QMR treatment as a successful therapeutic option for nasal obstruction due to ITH. Nonallergic patients had a very good T4 outcome. Allergic patients showed a worsening trend after 1 year probably due to other causes.
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http://dx.doi.org/10.1177/01455613211001599DOI Listing
June 2021

Integrated Bimodal Fitting for Unilateral CI Users with Residual Contralateral Hearing.

Audiol Res 2021 May 12;11(2):200-206. Epub 2021 May 12.

Unit of Audiology, Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples "Federico II", via Pansini 5, 80131 Naples, Italy.

Background: The aim of this study was to compare, in users of bimodal cochlear implants, the performance obtained using their own hearing aids (adjusted with the standard NAL-NL1 fitting formula) with the performance using the Phonak Naìda Link Ultra Power hearing aid adjusted with both NAL-NL1 and a new bimodal system (Adaptive Phonak Digital Bimodal (APDB)) developed by Advanced Bionics and Phonak Corporations.

Methods: Eleven bimodal users (Naìda CI Q70 + contralateral hearing aid) were enrolled in our study. The users' own hearing aids were replaced with the Phonak Naìda Link Ultra Power and fitted following the new formula. Speech intelligibility was assessed in quiet and noisy conditions, and comparisons were made with the results obtained with the users' previous hearing aids and with the Naída Link hearing aids fitted with the NAL-NL1 generic prescription formula.

Results: Using Phonak Naìda Link Ultra Power hearing aids with the Adaptive Phonak Digital Bimodal fitting formula, performance was significantly better than that with the users' own rehabilitation systems, especially in challenging hearing situations for all analyzed subjects.

Conclusions: Speech intelligibility tests in quiet settings did not reveal a significant difference in performance between the new fitting formula and NAL-NL1 fittings (using the Naída Link hearing aids), whereas the performance difference between the two fittings was very significant in noisy test conditions.
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http://dx.doi.org/10.3390/audiolres11020018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8161435PMC
May 2021

Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian-Triassic co-origination with insectivores.

R Soc Open Sci 2020 Nov 11;7(11):201689. Epub 2020 Nov 11.

School of Earth Sciences, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.

Stick and leaf insects (Phasmatodea) are a distinctive insect order whose members are characterized by mimicking various plant tissues such as twigs, foliage and bark. Unfortunately, the phylogenetic relationships among phasmatodean subfamilies and the timescale of their evolution remain uncertain. Recent molecular clock analyses have suggested a Cretaceous-Palaeogene origin of crown Phasmatodea and a subsequent Cenozoic radiation, contrasting with fossil evidence. Here, we analysed transcriptomic data from a broad diversity of phasmatodeans and, combined with the assembly of a new suite of fossil calibrations, we elucidate the evolutionary history of stick and leaf insects. Our results differ from recent studies in the position of the leaf insects (Phylliinae), which are recovered as sister to a clade comprising Clitumninae, Lancerocercata, Lonchodinae, Necrosciinae and . We recover a Permian to Triassic origin of crown Phasmatodea coinciding with the radiation of early insectivorous parareptiles, amphibians and synapsids. Aschiphasmatinae and Neophasmatodea diverged in the Jurassic-Early Cretaceous. A second spur in origination occurred in the Late Cretaceous, coinciding with the Cretaceous Terrestrial Revolution, and was probably driven by visual predators such as stem birds (Enantiornithes) and the radiation of angiosperms.
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http://dx.doi.org/10.1098/rsos.201689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7735357PMC
November 2020

Tinnitus and equilibrium disorders in COVID-19 patients: preliminary results.

Eur Arch Otorhinolaryngol 2020 Oct 23. Epub 2020 Oct 23.

Department of Experimental and Clinical Medicine, Unit of Audiology, Regional Centre for Cochlear Implants and ENT Diseases, Magna Graecia University, Catanzaro, Italy.

Purpose: Tinnitus and equilibrium disorders such as dizziness and vertigo have been reported by patients with COVID-19; however, they have been rarely investigated. The aim of this study was to study the prevalence of subjective tinnitus and dizziness in a sample of COVID-19 patients using an online 10-item close-ended questionnaire.

Methods: A multicentric study that included 15 Italian hospitals in different regions was conducted using an online 10-item close-ended questionnaire developed to identify the presence of tinnitus and balance disorders in patients with COVID-19 between May 5 and June 10, 2020. The questionnaire was administered to 185 patients in a period of > 30 - < 60 days after diagnosis of COVID-19; responses were recorded in an online Excel spreadsheet. The questionnaire was composed of three sections: (1) demographic information; (2) presence and characteristics of tinnitus and dizziness after COVID-19 diagnosis; (3) possible association with migraine.

Results: Thirty-four patients (18.4%) reported equilibrium disorders after COVID-19 diagnosis. Of these, 32 patients reported dizziness (94.1%) and 2 (5.9%) reported acute vertigo attacks. Forty-three patients (23.2%) reported tinnitus; 14 (7.6%) reported both tinnitus and equilibrium disorders.

Conclusion: This study suggests that the presence of subjective otoneurological symptoms such as tinnitus and balance disorders can affect COVID-19 patients; further studies are necessary to investigate the prevalence and pathophysiological mechanisms underlying these subjective symptoms in COVID-19 patients.
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http://dx.doi.org/10.1007/s00405-020-06440-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7582442PMC
October 2020

Objective bilateral tinnitus from palatal nystagmus. Audio and video features of a rare case of palatal myoclonus.

Am J Otolaryngol 2020 Nov - Dec;41(6):102739. Epub 2020 Sep 19.

Department of Experimental and Clinical Medicine, Unit of Audiology, Regional Centre for Cochlear Implants and ENT Diseases, Magna Graecia University, Catanzaro, Italy.

Tinnitus is one of the most represented otological symptom, affecting 15% of adults, worldwide. Literature describes subjective tinnitus when it's perceived by the patient only, and objective tinnitus when it's heard both, by patient and examiner. An objective tinnitus can be caused by a large variety of anomalies and diseases; one of them is Palatal Myoclonus, characterized by rhytmic movements of soft palatal muscles and, only occasionally, involving other near districts. Case presentation. We observed a rare case of essential palatal myoclonus in a 54 y.o. female, suffering from chronic objective bilateral tinnitus, since 35 years, who underwent a wide number of clinical evaluations over the years, without receiving any conclusive diagnosis. In this video, we illustrate all the districts involved in clonic movements: soft palate, larynx and nasal wings. At the same time, we report the spectrographic analysis of tinnitus, recorded in esternal ear canal, taken together with the muscle movements. Palatal Myoclonus has to be considered in the etiological diagnosis of each objective tinnitus and should always be investigated properly.
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http://dx.doi.org/10.1016/j.amjoto.2020.102739DOI Listing
December 2020

Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera).

Sci Rep 2020 09 3;10(1):14515. Epub 2020 Sep 3.

School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK.

Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18 A. mellifera subspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin of A. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic. A. mellifera colonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.
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http://dx.doi.org/10.1038/s41598-020-71393-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471700PMC
September 2020

The role of endogenous Antisecretory Factor (AF) in the treatment of Ménière's Disease: A two-year follow-up study. Preliminary results.

Am J Otolaryngol 2020 Nov - Dec;41(6):102673. Epub 2020 Aug 11.

Department of Experimental and Clinical Medicine, Unit of Audiology, Regional Centre for Cochlear Implants and ENT Diseases, Magna Graecia University, Catanzaro, Italy.

Purpose: To evaluate the effects of increased endogenous Antisecretory Factor (AF) synthesis using specially processed cereals (SPC) in a sample of patients with defined unilateral Meniere's disease (MD), compared to the results of a treatment protocol of intravenous glycerol and dexamethasone.

Materials And Methods: Twenty-six patients with unilateral MD were divided in 2 groups and treated with SPC and with intravenous glycerol and dexamethasone for 24 months. Audio-vestibular evaluation was performed before (T0) and every six months. The number of vertigo spells were evaluated before and after therapy and the Efficacy Index (EI) was calculated. Questionnaires for hearing loss, tinnitus and quality of life were administered.

Results: EI decreased in the SPC group after 18 (T18) (p = .0017) and 24 (T24) months of therapy (p = .0111). There was a significant reduction for tinnitus score in the SPC group at T24 (p = .0131). No significant differences were found between the two groups at T0 (p = .4723), while a significant difference was found at T24 (p = .0027). Quality of life showed a significant improvement in daily activities in the SPC group (p = .0033) compared to the infusion therapy group. No statistically significant changes in PTA thresholds were found in both groups between T0 and T24.

Conclusion: The preliminary results of our study show a significant reduction of vertigo spells and a positive effect on tinnitus severity and on quality of life in patients with unilateral MD treated with SPC and when compared to patients treated with intravenous glycerol and dexamethasone. No effects on hearing thresholds were noted in both groups.
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http://dx.doi.org/10.1016/j.amjoto.2020.102673DOI Listing
December 2020

Sudden olfactory loss as an early marker of COVID-19: a nationwide Italian survey.

Eur Arch Otorhinolaryngol 2021 Jan 4;278(1):247-255. Epub 2020 Aug 4.

Unit of Audiology, Department of Experimental and Clinical Medicine, Regional Centre for Cochlear Implants and ENT Diseases, Magna Graecia University, Catanzaro, Italy.

Purpose: The presence of many asymptomatic COVID-19 cases may increase the risks of disease dissemination, mainly for physicians. There are numerous reports on the frequent findings of sudden anosmia or hyposmia, before or at the same time of the typical COVID-19 symptoms onset. The aim of this study was to verify the association of olfactory impairment and COVID-19, providing a basis for subsequent research in the field of COVID-19 clinical heterogeneity.

Methods: We developed a 15-item online questionnaire on "Sudden Olfactory Loss (SOL) and COVID-19" that was administered during March 2020 to Italian general practitioners registered to a social media group.

Results: One hundred and eighty responses were received. SOL was identified as a significant sign of infection in COVID-19 patients, mainly aged between 30 and 40 years, even in the absence of other symptoms. SOL was present as an initial symptom in 46.7% of subjects, and in 16.7%, it was the only symptom. Among the COVID-19 confirmed cases, SOL occurred as the only symptom in 19.2% of patients.

Conclusion: SOL could represent a possible early symptom in otherwise asymptomatic COVID-19 subjects. Subjects affected by SOL should be considered as potential COVID-19 cases.

Level Of Evidence: 4.
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http://dx.doi.org/10.1007/s00405-020-06252-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7399588PMC
January 2021

Sensory Neuroscience: A Taste for Light and the Origin of Animal Vision.

Curr Biol 2020 07;30(13):R773-R775

Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.

Opsins are genes underpinning vision in animals. A new study shows that they are also involved in taste perception in fruit flies, significantly expanding their scope of action. This has important implications for our understanding of the evolution of vision.
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http://dx.doi.org/10.1016/j.cub.2020.05.009DOI Listing
July 2020

Disequilibrium and Risk of Falling in the Elderly is a Priority for Health Services.

Rev Recent Clin Trials 2020 ;15(3):162-163

Unit of Audiology Department of Experimental and Clinical Medicine Regional Centre for Cochlear Implants and ENT Diseases Magna Graecia University, Catanzaro, Italy.

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http://dx.doi.org/10.2174/1574887115666200630105529DOI Listing
January 2020

Prevention of COVID-19 Infection in the Medical Population: Possible Help from Anosmia?

Rev Recent Clin Trials 2020 ;15(3):244-245

Unit of Audiology, Department of Experimental and Clinical Medicine, Regional Centre for Cochlear Implants and ENT Diseases, University "Magna Graecia", Catanzaro, Italy.

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http://dx.doi.org/10.2174/1574887115666200603152637DOI Listing
October 2020

Spectral Diversification and Trans-Species Allelic Polymorphism during the Land-to-Sea Transition in Snakes.

Curr Biol 2020 07 28;30(13):2608-2615.e4. Epub 2020 May 28.

The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, South Australia 5005, Australia; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.

Snakes are descended from highly visual lizards [1] but have limited (probably dichromatic) color vision attributed to a dim-light lifestyle of early snakes [2-4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ∼300 terrestrial species (cobras, taipans, etc.) and ∼60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, and RH1) have evolved under positive selection in elapids, and in sea snakes they have undergone multiple shifts in spectral sensitivity toward the longer wavelengths that dominate below the sea surface. Several relatively distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded "UV-blue" spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates.
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http://dx.doi.org/10.1016/j.cub.2020.04.061DOI Listing
July 2020

Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation.

Genome Biol Evol 2020 07;12(7):1087-1098

School of Biological Sciences, University of Bristol, United Kingdom.

Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales.
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http://dx.doi.org/10.1093/gbe/evaa105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486956PMC
July 2020

A Cambrian-Ordovician Terrestrialization of Arachnids.

Front Genet 2020 11;11:182. Epub 2020 Mar 11.

School of Biological Sciences, University of Bristol, Bristol, United Kingdom.

Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molecular dating on a phylogenomic tree that recovers arachnid monophyly, constrained by 27 rigorously vetted fossil calibrations, estimates that Arachnida originated during the Cambrian or Ordovician. After the common ancestor colonized the land, the main lineages appear to have rapidly radiated in the Cambrian-Ordovician boundary interval, coinciding with high rates of molecular evolution. The highest rates of arachnid diversification are detected between the Permian and Early Cretaceous. A pattern of ancient divergence estimates for terrestrial arthropod groups in the Cambrian while the oldest fossils are Silurian (seen in both myriapods and arachnids) is mirrored in the molecular and fossil records of land plants. We suggest the discrepancy between molecular and fossil evidence for terrestrialization is likely driven by the extreme sparseness of terrestrial sediments in the rock record before the late Silurian.
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http://dx.doi.org/10.3389/fgene.2020.00182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7078165PMC
March 2020

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga).

Mol Phylogenet Evol 2020 06 5;147:106782. Epub 2020 Mar 5.

School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK. Electronic address:

Diving beetles and their allies are an almost ubiquitous group of freshwater predators. Knowledge of the phylogeny of the adephagan superfamily Dytiscoidea has significantly improved since the advent of molecular phylogenetics. However, despite recent comprehensive phylogenomic studies, some phylogenetic relationships among the constituent families remain elusive. In particular, the position of the family Hygrobiidae remains uncertain. We address these issues by re-analyzing recently published phylogenomic datasets for Dytiscoidea, using approaches to reduce compositional heterogeneity and adopting a site-heterogeneous mixture model. We obtained a consistent, well-resolved, and strongly supported tree. Consistent with previous studies, our analyses support Aspidytidae as the monophyletic sister group of Amphizoidae, and more importantly, Hygrobiidae as the sister of the diverse Dytiscidae, in agreement with morphology-based phylogenies. Our analyses provide a backbone phylogeny of Dytiscoidea, which lays the foundation for better understanding the evolution of morphological characters, life habits, and feeding behaviors of dytiscoid beetles.
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http://dx.doi.org/10.1016/j.ympev.2020.106782DOI Listing
June 2020

A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans.

Genome Biol Evol 2020 02;12(2):3906-3916

School of Earth Sciences, University of Bristol, United Kingdom.

Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
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http://dx.doi.org/10.1093/gbe/evaa015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058159PMC
February 2020

A draft genome sequence of the elusive giant squid, Architeuthis dux.

Gigascience 2020 01;9(1)

Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia.

Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
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http://dx.doi.org/10.1093/gigascience/giz152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438PMC
January 2020

Author Correction: Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida.

Nat Commun 2019 Oct 1;10(1):4534. Epub 2019 Oct 1.

University of Bristol School of Biological Sciences, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41467-019-12259-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773737PMC
October 2019

Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling.

Genome Biol Evol 2019 08;11(8):2055-2070

Natural History Museum of Denmark, University of Copenhagen, Denmark.

The relationships of crustaceans and hexapods (Pancrustacea) have been much discussed and partially elucidated following the emergence of phylogenomic data sets. However, major uncertainties still remain regarding the position of iconic taxa such as Branchiopoda, Copepoda, Remipedia, and Cephalocarida, and the sister group relationship of hexapods. We assembled the most taxon-rich phylogenomic pancrustacean data set to date and analyzed it using a variety of methodological approaches. We prioritized low levels of missing data and found that some clades were consistently recovered independently of the analytical approach used. These include, for example, Oligostraca and Altocrustacea. Substantial support was also found for Allotriocarida, with Remipedia as the sister of Hexapoda (i.e., Labiocarida), and Branchiopoda as the sister of Labiocarida, a clade that we name Athalassocarida (="nonmarine shrimps"). Within Allotriocarida, Cephalocarida was found as the sister of Athalassocarida. Finally, moderate support was found for Hexanauplia (Copepoda as sister to Thecostraca) in alliance with Malacostraca. Mapping key crustacean tagmosis patterns and developmental characters across the revised phylogeny suggests that the ancestral pancrustacean was relatively short-bodied, with extreme body elongation and anamorphic development emerging later in pancrustacean evolution.
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http://dx.doi.org/10.1093/gbe/evz097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684935PMC
August 2019

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida.

Nat Commun 2019 05 24;10(1):2295. Epub 2019 May 24.

University of Bristol School of Biological Sciences, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.

Chelicerates are a diverse group of arthropods, represented by such forms as predatory spiders and scorpions, parasitic ticks, humic detritivores, and marine sea spiders (pycnogonids) and horseshoe crabs. Conflicting phylogenetic relationships have been proposed for chelicerates based on both morphological and molecular data, the latter usually not recovering arachnids as a clade and instead finding horseshoe crabs nested inside terrestrial Arachnida. Here, using genomic-scale datasets and analyses optimised for countering systematic error, we find strong support for monophyletic Acari (ticks and mites), which when considered as a single group represent the most biodiverse chelicerate lineage. In addition, our analysis recovers marine forms (sea spiders and horseshoe crabs) as the successive sister groups of a monophyletic lineage of terrestrial arachnids, suggesting a single colonisation of land within Chelicerata and the absence of wholly secondarily marine arachnid orders.
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http://dx.doi.org/10.1038/s41467-019-10244-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534568PMC
May 2019

Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan.

Curr Biol 2019 04 21;29(7):1112-1125.e2. Epub 2019 Mar 21.

Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, China; MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming 650091, China; Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. Electronic address:

The origin of ctenophores (comb jellies) is obscured by their controversial phylogenetic position, with recent phylogenomic analyses resolving either sponges or ctenophores as the sister group of all other animals. Fossil taxa can provide morphological evidence that may elucidate the origins of derived characters and shared ancestries among divergent taxa, providing a means to "break" long branches in phylogenetic trees. Here we describe new fossil material from the early Cambrian Chengjiang Biota, Yunnan Province, China, including the putative cnidarian Xianguangia, the new taxon Daihua sanqiong gen et sp. nov., and Dinomischus venustus, informally referred to as "dinomischids" here. "Dinomischids" possess a basal calyx encircled by 18 tentacles that surround the mouth. The tentacles carry pinnules, each with a row of stiff filamentous structures interpreted as very large compound cilia of a size otherwise only known in ctenophores. Together with the Cambrian tulip animal Siphusauctum and the armored Cambrian scleroctenophores, they exhibit anatomies that trace ctenophores to a sessile, polypoid stem lineage. This body plan resembles the polypoid, tentaculate morphology of cnidarians, including a blind gastric cavity partitioned by mesenteries. We propose that comb rows are derived from tentacles with paired sets of pinnules that each bear a row of compound cilia. The scleroctenophores exhibit paired comb rows, also observed in Siphusauctum, in addition to an organic skeleton, shared as well by Dinomischus, Daihua, and Xianguangia. We formulate a hypothesis in which ctenophores evolved from sessile, polypoid suspension feeders, sharing similarities with cnidarians that suggest either a close relationship between these two phyla, a striking pattern of early convergent evolution, or an ancestral condition for either metazoans or eumetazoans.
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http://dx.doi.org/10.1016/j.cub.2019.02.036DOI Listing
April 2019

Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.

Mol Biol Evol 2019 06;36(6):1344-1356

Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom.

Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa.
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http://dx.doi.org/10.1093/molbev/msz067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526904PMC
June 2019

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content.

Mol Biol Evol 2019 04;36(4):643-649

Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.

Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
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http://dx.doi.org/10.1093/molbev/msz013DOI Listing
April 2019

Molecular palaeontology illuminates the evolution of ecdysozoan vision.

Proc Biol Sci 2018 12 5;285(1892). Epub 2018 Dec 5.

School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK

Colour vision is known to have arisen only twice-once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35-71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.
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http://dx.doi.org/10.1098/rspb.2018.2180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283943PMC
December 2018

Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.

Nat Ecol Evol 2018 10 20;2(10):1556-1562. Epub 2018 Aug 20.

School of Earth Sciences, University of Bristol, Bristol, UK.

Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.
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http://dx.doi.org/10.1038/s41559-018-0644-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152910PMC
October 2018

Homeobox Gene Duplication and Divergence in Arachnids.

Mol Biol Evol 2018 09;35(9):2240-2253

Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom.

Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterized and compared the homeobox repertoires in a range of arachnids. We found that many families and clusters of these genes are duplicated in all studied arachnopulmonates (Parasteatoda tepidariorum, Pholcus phalangioides, Centruroides sculpturatus, and Mesobuthus martensii) compared with nonarachnopulmonate arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp., and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analyzed the expression of P. tepidariorum homeobox genes during embryogenesis and found pervasive changes in the level and timing of their expression. Furthermore, we compared the spatial expression of a subset of P. tepidariorum ohnologs with their single copy orthologs in P. opilio embryos. We found evidence for likely subfunctionlization and neofunctionalization of these genes in the spider. Overall our results show a high level of retention of homeobox genes in spiders and scorpions post-WGD, which is likely to have made a major contribution to their developmental evolution and diversification through pervasive subfunctionlization and neofunctionalization, and paralleling the outcomes of WGD in vertebrates.
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http://dx.doi.org/10.1093/molbev/msy125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107062PMC
September 2018

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.

Genome Biol Evol 2018 06;10(6):1457-1470

School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom.

microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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http://dx.doi.org/10.1093/gbe/evy096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007596PMC
June 2018

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte.

Curr Biol 2018 03 15;28(5):733-745.e2. Epub 2018 Feb 15.

School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK. Electronic address:

The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.
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http://dx.doi.org/10.1016/j.cub.2018.01.063DOI Listing
March 2018

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data.

Palaeontology 2018 01 31;61(1):105-118. Epub 2017 Oct 31.

School of Earth Sciences University of Bristol Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK.

Fossil taxa are critical to inferences of historical diversity and the origins of modern biodiversity, but realizing their evolutionary significance is contingent on restoring fossil species to their correct position within the tree of life. For most fossil species, morphology is the only source of data for phylogenetic inference; this has traditionally been analysed using parsimony, the predominance of which is currently challenged by the development of probabilistic models that achieve greater phylogenetic accuracy. Here, based on simulated and empirical datasets, we explore the relative efficacy of competing phylogenetic methods in terms of clade support. We characterize clade support using bootstrapping for parsimony and Maximum Likelihood, and intrinsic Bayesian posterior probabilities, collapsing branches that exhibit less than 50% support. Ignoring node support, Bayesian inference is the most accurate method in estimating the tree used to simulate the data. After assessing clade support, Bayesian and Maximum Likelihood exhibit comparable levels of accuracy, and parsimony remains the least accurate method. However, Maximum Likelihood is less precise than Bayesian phylogeny estimation, and Bayesian inference recaptures more correct nodes with higher support compared to all other methods, including Maximum Likelihood. We assess the effects of these findings on empirical phylogenies. Our results indicate probabilistic methods should be favoured over parsimony.
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http://dx.doi.org/10.1111/pala.12330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784394PMC
January 2018