Hybridisation has shaped a recent radiation of grass-feeding aphids

Background: Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called “super clones” have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals—the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids.   Results: Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression.   Conclusions: Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born “frozen hybrids” via asexual reproduction, increasing the likelihood of hybrid lineage formation

Relaxation of natural selection in the evolution of the giant lungfish genomes

Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when the process of purifying selection becomes weak. Accordingly, species with huge genomes, such as lungfish, are expected to show a genome-wide relaxation signature of selection compared with other organisms. However, few studies have empirically tested this prediction using genomic data in a comparative framework. Here, we show that 1) the newly assembled transcriptome of the Australian lungfish, Neoceratodus forsteri, is characterized by an excess of pervasive transcription, or transcriptional leakage, possibly due to suboptimal transcriptional control, and 2) a significant relaxation signature in coding genes in lungfish species compared with other vertebrates. Based on these observations, we propose that the largest known animal genomes evolved in a nearly neutral scenario where genome expansion is less efficiently constraine

Modelling sustainability performance to achieve absolute reductions in socio-ecological systems

As the world’s natural resources dwindle and critical levels of environmental pollution are approached, sustainability becomes a key issue for governments, organisations and individuals. With the consequences of such an issue in mind, this paper introduces a unifying approach to measure the sustainability performance of socio-economic systems based on the interplay between two key variables: essentiality of consumption and environmental impact. This measure attributes to every system a ‘fitness’ value i.e. a quantity that reflects its ability to remain resilient/healthy by avoiding ecological, social and economic collapse as it consumes the available resources. This new measure is tested on a system where there is a limited supply of resources and four basic consumption types. The analysis has theoretical implications as well as practical importance as it can help countries, organisations or even individuals, in finding better ways to measure sustainability performance

Fertility specialists’ views, behavior, and attitudes towards the use of endometrial scratching in Italy

Background: Endometrial scratching (ES) or injury is intentional damage to the endometrium performed to improve reproductive outcomes for infertile women desiring pregnancy. Moreover, recent systematic reviews with meta-analyses and randomized controlled trials demonstrated that ES is not effective, data on the safety are limited, and it should not be recommended in clinical practice. The aim of the current study was to assess the view and behavior towards ES among fertility specialists throughout infertility centers in Italy, and the relationship between these views and the attitudes towards the use of ES as an add-on in their commercial setting. Methods: Online survey among infertility centers, affiliated to Italian Society of Human Reproduction (SIRU), was performed using a detailed questionnaire including 45 questions with the possibility to give "closed" multi-choice answers for 41 items and "open" answers for 4 items. Online data from the websites of the infertility centers resulting in affiliation with the specialists were also recorded and analyzed. The quality of information about ES given on infertility centers websites was assessed using a scoring matrix including 10 specific questions (scored from 0 to 2 points), and the possible scores ranged from 0 to 13 points ('excellent' if the score was 9 points or more, 'moderate' if the score was between 5 and 8, and 'poor' if it was 4 points or less). Results: The response rate was of 60.6% (43 questionnaires / 71 infertility SIRU-affiliated centers). All included questionnaires were completed in their entirety. Most physicians (~ 70%) reported to offer ES to less than 10% of their patients. The procedure is mainly performed in the secretory phase (69.2%) using pipelle (61.5%), and usually in medical ambulatory (56.4%) before IVF cycles to improve implantation (71.8%) without drugs administration (e.g., pain drugs, antibiotics, anti-hemorrhagics, or others) before (76.8%) or after (64.1%) the procedure. Only a little proportion of infertility centers included in the analysis proposes formally the ES as an add-on procedure (9.3%), even if, when proposed, the full description of the indications, efficacy, safety, and costs is never addressed. However, the overall information quality of the websites was generally "poor" ranging from 3 to 8 and having a low total score (4.7 ± 1.6; mean ± standard deviation). Conclusions: In Italy, ES is a procedure still performed among fertility specialists for improving the implantation rate in IVF patients. Moreover, they have a poor attitude in proposing ES as an add-on in the commercial setting

How the First Year of the COVID-19 Pandemic Impacted Patients’ Hospital Admission and Care in the Vascular Surgery Divisions of the Southern Regions of the Italian Peninsula

Background: To investigate the effects of the COVID-19 lockdowns on the vasculopathic population. Methods: The Divisions of Vascular Surgery of the southern Italian peninsula joined this multicenter retrospective study. Each received a 13-point questionnaire investigating the hospitalization rate of vascular patients in the first 11 months of the COVID-19 pandemic and in the preceding 11 months. Results: 27 out of 29 Centers were enrolled. April-December 2020 (7092 patients) vs. 2019 (9161 patients): post-EVAR surveillance, hospitalization for Rutherford category 3 peripheral arterial disease, and asymptomatic carotid stenosis revascularization significantly decreased (1484 (16.2%) vs. 1014 (14.3%), p = 0.0009; 1401 (15.29%) vs. 959 (13.52%), p = 0.0006; and 1558 (17.01%) vs. 934 (13.17%), p < 0.0001, respectively), while admissions for revascularization or major amputations for chronic limb-threatening ischemia and urgent revascularization for symptomatic carotid stenosis significantly increased (1204 (16.98%) vs. 1245 (13.59%), p < 0.0001; 355 (5.01%) vs. 358 (3.91%), p = 0.0007; and 153 (2.16%) vs. 140 (1.53%), p = 0.0009, respectively). Conclusions: The suspension of elective procedures during the COVID-19 pandemic caused a significant reduction in post-EVAR surveillance, and in the hospitalization of asymptomatic carotid stenosis revascularization and Rutherford 3 peripheral arterial disease. Consequentially, we observed a significant increase in admissions for urgent revascularization for symptomatic carotid stenosis, as well as for revascularization or major amputations for chronic limb-threatening ischemia

APOLLO 11 Project, Consortium in Advanced Lung Cancer Patients Treated With Innovative Therapies: Integration of Real-World Data and Translational Research

Introduction: Despite several therapeutic efforts, lung cancer remains a highly lethal disease. Novel therapeutic approaches encompass immune-checkpoint inhibitors, targeted therapeutics and antibody-drug conjugates, with different results. Several studies have been aimed at identifying biomarkers able to predict benefit from these therapies and create a prediction model of response, despite this there is a lack of information to help clinicians in the choice of therapy for lung cancer patients with advanced disease. This is primarily due to the complexity of lung cancer biology, where a single or few biomarkers are not sufficient to provide enough predictive capability to explain biologic differences; other reasons include the paucity of data collected by single studies performed in heterogeneous unmatched cohorts and the methodology of analysis. In fact, classical statistical methods are unable to analyze and integrate the magnitude of information from multiple biological and clinical sources (eg, genomics, transcriptomics, and radiomics). Methods and objectives: APOLLO11 is an Italian multicentre, observational study involving patients with a diagnosis of advanced lung cancer (NSCLC and SCLC) treated with innovative therapies. Retrospective and prospective collection of multiomic data, such as tissue- (eg, for genomic, transcriptomic analysis) and blood-based biologic material (eg, ctDNA, PBMC), in addition to clinical and radiological data (eg, for radiomic analysis) will be collected. The overall aim of the project is to build a consortium integrating different datasets and a virtual biobank from participating Italian lung cancer centers. To face with the large amount of data provided, AI and ML techniques will be applied will be applied to manage this large dataset in an effort to build an R-Model, integrating retrospective and prospective population-based data. The ultimate goal is to create a tool able to help physicians and patients to make treatment decisions. Conclusion: APOLLO11 aims to propose a breakthrough approach in lung cancer research, replacing the old, monocentric viewpoint towards a multicomprehensive, multiomic, multicenter model. Multicenter cancer datasets incorporating common virtual biobank and new methodologic approaches including artificial intelligence, machine learning up to deep learning is the road to the future in oncology launched by this project

Testudo hermanni: aspetti di genetica e genomica di conservazione

Nell'ultimo secolo e mezzo, il tasso di estinzione delle specie è cresciuto costantemente e molte specie sono in pericolo imminente di estinzione. In questo contesto, la genetica fornisce un supporto essenziale alla biologia della conservazione perché aiuta a comprendere il background evolutivo delle specie minacciate e consente lo sviluppo di migliori strategie di gestione. La testuggine di Hermann (Testudo hermanni), uno dei rettili più a rischio in Europa, è distribuita in popolazioni disgiunte attraverso l'Europa mediterranea. La riduzione degli habitat, insieme alle pratiche agricole intensive e agli incendi boschivi, sono le principali cause di riduzione delle dimensioni delle popolazioni in molte aree del Mediterraneo. La raccolta intensiva per il commercio a scopo domestico, specialmente prima degli anni '80, e il rilascio di individui non nativi nelle popolazioni locali, rappresentano ulteriori minacce. T. hermanni è inclusa nella lista delle specie faunistiche rigorosamente protette dalla Convenzione di Berna e la sottospecie occidentale T. h. hermanni è classificata come "in pericolo" nella Lista Rossa IUCN. Qui abbiamo (i) migliorato la comprensione della struttura genetica delle popolazioni selvatiche, con nuovi dati provenienti da marcatori microsatelliti, da aree geografiche precedentemente non campionate; (ii) testato un pannello di loci microsatelliti (STR) per indagare su possibili traslocazioni illegali in un campione di individui provenienti da centri di recupero in Italia; (iii) analizzato le relazioni genetiche di campioni della sottospecie ipotetica T. h. hercigovinensis (o specie T. hercigovinensis) con le due sottospecie comunemente accettate T. h. hermanni e T. h. boettgeri, utilizzando diversi marcatori genetici (mtDNA e microsatellite); (iv) esaminato la struttura genetica in popolazioni selvatiche con nuovi marcatori (SNP) provenienti dal sequenziamento ddRAD; (v) identificato un piccolo numero di SNP diagnostici e informativi per ridurre i costi delle assegnazioni geografiche di individui di origine sconosciuta; (vi) revisionato gli aspetti delle traslocazioni a fini conservativi al fine di pianificare un progetto pilota di reintroduzione in Italia. Con un piccolo pannello di loci STR, siamo stati in grado di assegnare il 70% delle tartarughe (su un totale di 458 individui) tenuti in cattività alle loro potenziali aree di origine. Abbiamo trovato la presenza di individui della sottospecie orientale nelle popolazioni selvatiche della penisola italiana e della Sicilia probabilmente dovuto all'ampio commercio di animali domestici che ha colpito questa specie, con migliaia di tartarughe esportate nell'Europa occidentale dalla penisola balcanica. Abbiamo osservato che gli individui considerati morfologicamente T. hercegovinensis (o T. t. hercegovinesis), provenienti dalla costa adriatica della penisola balcanica, dovrebbero essere classificati come T. h. boettgeri perché non esiste alcuna divergenza genetica che possa giustificare l'appartenenza di questi esemplari a una sottospecie o a una specie distinta. Migliaia di nuovi marcatori provenienti da un sequenziamento ddRAD hanno rivelato ulteriori approfondimenti sulla sottostruttura delle popolazioni occidentali, specialmente in Calabria (Sud Italia), dove abbiamo rilevato tre gruppi genetici distinti. Inoltre, abbiamo sviluppato un piccolo pannello di SNP diagnostici al fine di ridurre i costi di genotipizzazione (stimati in circa 10-12 euro per individuo). Questo piccolo pannello potrà essere utilizzato per selezionare centinaia di testuggini tenute in cattività e potenzialmente adatte reintroduzioni in natura. Considerando le preoccupazioni sulla conservazione di T. hermanni crediamo che questo lavoro permetta una migliore comprensione della variazione genetica in questa specie e fornisca nuovi strumenti pratici utili per la conservazione e la gestione di individui selvatici e in cattività.For the past half century, it has been broadly perceived that the rate of species extinction is increasing and many species are in imminent extinction danger. In this context, genetics provides essential support to conservation biology because it helps to understand the evolutionary background of endangered species and enables the development of better management strategies. The Hermann’s tortoise (Testudo hermanni), one of the most endangered reptiles in Europe, is distributed in disjoint populations across Mediterranean Europe. Habitat reduction, together with intensive agricultural practices and forest fires, are major causes of reduction in population size in many Mediterranean areas. Intensive harvesting for pet trade, especially before the 1980s when it was banned, and releases of non-native individuals into local populations, represent additional threats. T. hermanni is included in the list of strictly protected fauna species by the Bern Convention on the Conservation of European Wildlife and Natural Habitat, and the western subspecies T. h. hermanni is classified as “Endangered” by the IUCN Red List. Here we (i) increased the understanding of the population genetic structure in wild populations with new microsatellite data from previously unsampled geographic areas; (ii) tested a panel of microsatellite loci (STR) to investigate possible patterns of illegal translocations in a sample of individuals from recovery centers and seizures in Italy; (iii) investigated the genetic relationships of samples from the hypotetical subspecies T. h. hercigovinensis (or species T. hercigovinensis) with the two commonly accepted subspecies T. h. hermanni and T. h. boettgeri, using different genetic markers (mtDNA and microsatellite); (iv) studied the genetic structure in wild populations with new markers (SNPs) coming from ddRAD sequencing; (v) identified a small number of diagnostic and informative SNPs to reduce the costs of geographical assignments of individuals of unknown origin; (vi) reviewed the conservation translocation aspects in order to plan a pilot reintroduction project in Italy. With a small panel of STR loci, we were able to assign 70% of tortoises (out of a total of 458 individuals) kept in captivity to their potential areas of origin. We found the presence of eastern subspecies individuals in the Italian peninsula and Sicily wild populations probably due to the wide pet trade that affected this species, with thousands tortoises exported to Western Europe from the Balkan Peninsula. We argued that individuals considered morphologically T. hercegovinensis (or T. h. hercegovinesis), coming from the Adriatic coast of the Balkan Peninsula, should be classified as T. h. boettgeri because there is no genetic divergence that could justify the belonging of these specimens to a subspecies or distinct species. Thousands of new markers coming from a ddRAD sequencing revealed further insights into the substructure in Western populations, especially in Calabria (South Italy) where we detected three distinct genetic groups. Therefore, we developed a small panel of diagnostic SNPs in order to reduce genotyping costs (estimated to about 10-12 euros per individual). This small panel should be used for the cost-effective selection of hundreds of tortoises kept in captivity and suitable for reintroductions. Considering the concerns about the conservation of T. hermanni we believe that this thesis allows a better understanding of the genetic variation patterns in this species and provides a new practical tools useful for the conservation and management of wild and captive individuals

From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe

Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems

Caratterizzazione della popolazione di testuggine di Hermann (Testudo hermanni) all'interno della Riserva Naturale Dune Fossili di Massenzatica

Testudo hermanni (ord. Testudines, fam. Testudinae), with T. graeca and T. marginata, is one of the three species of Testudinae endemic of the European peninsula. It’s widespread along Mediterrean European’s coasts, in different islands and in the Balkans from south-west Danube to Turkey. Two subspecies are recognized at genetic level: T.h. boettgeri, who’s widespread in the eastern regions, from Balkans to italic North-east and T.h. hermanni, widespread in the western regions, from mainland Italy to the major islands. Near the river’s delta, between Goro’s Po and Volano’s Po, there is the Fossil Dunes of Massenzatica Natural Reserve, an ideal area to study the two subspecies, considered its location. This work is part of a more extensive project designed to characterize and evaluate the wild population of T. hermanni in the Fossil Dunes of Massenzatica Natural Reserve with four major objectives: I) census; II) morphological identification; III) genotyping and IV) helath assesment. Samplings and observations have been carried out from 2019 to 2022, in the period of major activity (from the end of April to the end of August). In total 38 days of captures were carried out, with 125 animals sampled (20 animals with 28 recaptures). Animals were grouped by sex and age and analyzed. Here, we present results from the analysis of morphological data and we show how morphology can be used to characterize sexual dimorphism and to identify subspecies

The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances

The negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species