Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

A genome-wide comparison of transposable elements reveals evidence for unexpectedly high rates of horizontal transfer between three species of Drosophil

Genomic degradation of a young Y chromosome in Drosophila miranda

Background: Y chromosomes are derived from ordinary autosomes and degenerate because of a lack of recombination. Well-studied Y chromosomes only have few of their original genes left and contain little information about their evolutionary origin. Here, we take advantage of the recently formed neo-Y chromosome of Drosophila miranda to study the processes involved in Y degeneration on a genomic scale. Results: We obtained sequence information from 14 homologous bacterial artificial chromosome (BAC) clones from the neo-X and neo-Y chromosome of D. miranda, encompassing over 2.5 Mb of neo-sex-linked DNA. A large fraction of neo-Y DNA is composed of repetitive and transposable-element-derived DNA (20% of total DNA) relative to their homologous neo-X linked regions (1%). The overlapping regions of the neo-sex linked BAC clones contain 118 gene pairs, half of which are pseudogenized on the neo-Y. Pseudogenes evolve significantly faster on the neo-Y than functional genes, and both functional and non-functional genes show higher rates of protein evolution on the neo-Y relative to their neo-X homologs. No heterogeneity in levels of degeneration was detected among the regions investigated. Functional genes on the neo-Y are under stronger evolutionary constraint on the neo-X, but genes were found to degenerate randomly on the neo-Y with regards to their function or sex-biased expression patterns. Conclusion: Patterns of genome evolution in D. miranda demonstrate that degeneration of a recently formed Y chromosome can proceed very rapidly, by both an accumulation of repetitive DNA and degeneration of protein-coding genes. Our data support a random model of Y inactivation, with little heterogeneity in degeneration among genomic regions, or between functional classes of genes or genes with sex-biased expression patternsThis research is funded by NIH Grant GM076007 and a Sloan Fellowship to DB. BAC library construction was funded by a Wellcome Trust grant to P Keightley and B Charlesworth. P Andolfatto provided funds for the sequence of two BAC clonesS

Invasion patterns of Vespa velutina nigrithorax in Southern Europe: a genetic perspective

Vespa velutina was seen for the first time in Europe in 2004, in pots imported from China into France. Since then, the population rapidly build up and expanded within France and, in 2010, started spreading across other countries, giving rise to one of the most phenomenal insect invasions ever seen in the European continent. Early studies suggested that the invasion originated from a single multi-mated queen introduced from China. However, little was known, until this study, about the genetics underlying the expansion towards south and east of the introduction point in France. Our aim was to further understand V. velutina invasion in Europe by surveying the Iberian and Italian peninsulas using microsatellites and mitochondrial DNA. Our results show that the French population was the source of the colonies expanding in Spain, Portugal and Italy, therefore leading to rejection of the hypothesis of multiple introductions from the native habitats. While Spain and Italy were invaded by leading-edge expansions from the French core population, in Portugal this invasion started from a long-distance jump. Both types of expansion were accompanied by a significant reduction in the population genetic diversity, with Portugal presenting the highest loss values (Ar = 17.4%; uHe = 42.3%) than Spain (Ar = 9.0%; uHe = 20.6%) or Italy (Ar = 16.3%; uHe = 26.8%). Population structure results and signatures of differentiation show that a secondary contact occurred between the front derived from the primary propagule introduced in France and the front derived from the secondary propagule introduced in Portugal. First-generation migrants were detected in Iberia and Italy, suggesting that a continuous gene flow is bringing in new alleles in the three invaded countries. This effect is more prominent in Portugal, as it is reflected by a 20.3% increase in allelic richness. Overall, this study provides new insights into the invasion genetics of the honey bee predator V. velutina in Europe, which can help developing strategies to manage this major threat to beekeeping.info:eu-repo/semantics/publishedVersio

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

Background: Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. Results: In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Conclusions: Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome

Estudo genético da invasão da vespa asiática (Vespa velutina nigrithorax) no sul da Europa

A Vespa velutina (Vespidae), também conhecida como vespa asiática, partilha com outros himenópteros um conjunto de características biológicas únicas (e.g. vida colonial, sistema de castas, divisão de tarefas), as quais têm contribuído de forma inequívoca para o sucesso das inúmeras invasões biológicas causadas por estes insetos sociais. Nas últimas décadas, mais de 30 espécies da família Vespidae foram acidentalmente introduzidas em todo o mundo (Beggs et al. 2011). A Europa manteve-se livre destes poderosos invasores até 2004, ano em que a vespa asiática foi avistada pela primeira vez em Nérac, Lot-et-Garonne, França (Villemant et al. 2006). Desde então, a vespa asiática tem-se expandido rapidamente pela maior parte da Europa ocidental e já se encontra em pelo menos nove países vizinhos da França. A primeira incursão deste invasor fora de França ocorreu na localidade espanhola de Amaiur (Navarra), que se situa a 180 km a sul de Nérac (López et al. 2011), seis anos após a introdução. Depois de Espanha, a chegada da V. velutina a outros países foi muito rápida. Na Bélgica (Rome et al. 2013) e em Portugal (Grosso-Silva e Maia 2012) os primeiros indivíduos foram avistados em 2011, em Itália em 2012 (Demichelis et al. 2014), na Alemanha em 2014 (Witt 2015), na Grã-Bretanha (Budge et al. 2017) e nos Países Baixos em 2016 (Smit et al. 2018), na Suíça em 2017 (Poidatz et al. 2018) e 2021 na Irlanda. A vespa asiática ocupa assim uma vasta área do território Europeu, a qual continua a crescer.Este trabalho foi financiado pelo programa POSEUR-03-2215-FC-000008, através do projeto “GesVespa: Estratégias de gestão sustentável da Vespa velutina no Norte de Portugal”. Os autores agradecem ainda à Fundação para a Ciência e a Tecnologia (FCT) o apoio financeiro ao CIMO (UIDB/00690/2020), através de fundos nacionais FCT/MCTES. Dora Henriques é financiada pelo projeto “BeeHappy: Bee (Apis mellifera L.) Health in the Azores: comparing ePidemiological Patterns in a unique natural laboratory” (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio

Effectiveness of electric harps in reducing Vespa velutina predation pressure and consequences for honey bee colony development

BACKGROUND: Vespa velutinahas become a species of concern in invaded regions of Europe and Asia, due to its impacts onbiodiversity, apiculture and society. This hornet, a ferocious hunter of pollinating insects, poses a serious threat to biodiversityand pollination services. Despite ongoing efforts, its extermination in continental Europe is hampered by a lack of effective con-trol methods, thus effective mitigation measures are primary concerns. The aims of this work were: (i) to study the effects of V. velutina predating on honey bee colonies, and (ii) to assess the effectiveness of electric harps in reducing hunting pressureand predation. We assessed the predation pressure and compared honey bee colony performance, body weight of workers, andwinter survivorship for protectedversusunprotected colonies in 36 experimental hives across three apiaries. RESULTS: Electric harps protected honey bees by reducing predation pressure and therefore mitigating foraging paralysis. Consequently, foraging activity, pollen income, brood production and worker body weight were higher in protected colonies whichin turn showed greater winter survivorship than those that were unprotected, especially at sites with intermediate to highlevels of predation. CONCLUSION: The predation of V. velutina affects foraging activity, breeding, body weight and colony survivorship of Apis mellifera. Electric harps contribute significantly to mitigate the impact of this invasive hornet on apiaries; however, they should bedeployed in tandem with additional measures to preserve honey bee colony stocks, such as facilitating access to food sourcesfor colonies during the periods of highest predation pressure.Programa Interreg Atlantic Area (Fondo Europeo de Desarrollo Regional, Unión Europea) | Ref. EAPA_800/2018–Atlantic-PositiveUniversidade de Vigo/CISU

Frequent parasitism of Apis mellifera by trypanosomatids in geographically isolated areas with restricted beekeeping movements

Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae had a significantly lower prevalence of the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A High-Throughput Sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.This work was funded by the Consejería de Educación, Cultura y Deportes, of the Junta de Castilla – La Mancha (European Regional development Fund) project No. SBPLY/19/180501/000334 and through the program COMPETE 2020—POCI (Programa Operacional para a Competividade e Internacionalização) and FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio

Population Genetics of Nosema apis and Nosema ceranae: One Host (Apis mellifera) and Two Different Histories

Two microsporidians are known to infect honey bees: Nosema apis and Nosema ceranae. Whereas population genetics data for the latter have been released in the last few years, such information is still missing for N. apis. Here we analyze the patterns of nucleotide polymorphism at three single-copy loci (PTP2, PTP3 and RPB1) in a collection of Apis mellifera isolates from all over the world, naturally infected either with N. apis (N = 22) or N. ceranae (N = 23), to provide new insights into the genetic diversity, demography and evolution of N. apis, as well as to compare them with evidence from N. ceranae. Neutral variation in N. apis and N. ceranae is of the order of 1%. This amount of diversity suggests that there is no substantial differentiation between the genetic content of the two nuclei present in these parasites, and evidence for genetic recombination provides a putative mechanism for the flow of genetic information between chromosomes. The analysis of the frequency spectrum of neutral variants reveals a significant surplus of low frequency variants, particularly in N. ceranae, and suggests that the populations of the two pathogens are not in mutation-drift equilibrium and that they have experienced a population expansion. Most of the variation in both species occurs within honey bee colonies (between 62%-90% of the total genetic variance), although in N. apis there is evidence for differentiation between parasites isolated from distinct A. mellifera lineages (20%-34% of the total variance), specifically between those collected from lineages A and C (or M). This scenario is consistent with a long-term host-parasite relationship and contrasts with the lack of differentiation observed among host-lineages in N. ceranae (< 4% of the variance), which suggests that the spread of this emergent pathogen throughout the A. mellifera worldwide population is a recent event.This study was supported by funds from the Instituto Nacional de Investigación y Tecnología Agraria (INIA; http://www.inia.es/; grant numbers RTA2013-00042-C10-05 and 06), the Regional Government of Murcia (Fundación Séneca; http://fseneca.es/; grant number 19908/GERM/2015) and the Ministerio de Agricultura, Alimentación y Medio Ambiente (MAGRAMA; Plan Apícola Nacional 2014; http://www.magrama.gob.es). PDR is presently a member and receives support from COST Action FA1307, Sustainable pollination in Europe: joint research on bees and other pollinators, SUPER-B (http://www.cost.eu/COST_Actions/fa/Actions/FA1307)S

Survival of honey bees (Apis mellifera) infected with Crithidia mellificae spheroid forms (Langridge and McGhee: ATCC® 30254™) in the presence of Nosema ceranae

Crithidia mellificae, a trypanosomatid parasite of Apis mellifera, has been proposed to be one of the pathogens responsible for the serious honey bee colony losses produced worldwide in the last decade, either alone or in association with Nosema ceranae. Since this pathogenic effect contradicts the results of the experimental infections originally performed by Langridge and McGhee nearly 40 years ago, we investigated the potential linkage of this protozoan with colony decline under laboratory conditions. Nosema-free and trypanosomatid-free honey bees from three different colonies were experimentally infected with fresh C. mellificae spheroid forms (reference strain ATCC30254), with N. ceranae fresh spores and with both parasites at the same time. Replicate cages were kept at 27 °C and used to analyse survival. C. mellificae spheroid forms did not reduce significantly the survival of the worker bees (64.5% at 30 days post-infection vs. 77.8% for the uninfected bees used as controls; differences were non statistically significant) under these experimental conditions. In contrast, the cages infected with N. ceranae exhibited higher rates of mortality from the 20th day post-infection onwards, irrespective of the presence of C. mellificae, suggesting that the spheroid forms of the latter have no pathological effect on A. melliferaINIA-FEDER (RTA2013-00042-C10-06 and E-RTA2014-00003-C03)S