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

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

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

Bee trypanosomatids: first steps in the analysis of the fenetic variation and population structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae

Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that they were subject to the action of purifying selection on nonsynonymous variants, the levels of within species diversity were similar irrespective of the host, there was evidence of recombination among haplotypes and they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04%) — and a mutation frequency distribution compatible with a population expansion after a bottleneck — that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areasThis study was supported by the Ministerio de Economía y Competitividad (MINECO) (grant number CGL2012-34897), the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) - European Regional Development Fund (ERDF) (grant numbers E-RTA2014-00003-C03-01, 02 and 03), the Eva Crane Trust (grant number ECTA_20210308) and the Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia (grant of Regional Excellence19908/GERM/2015)S

Holistic screening of collapsing honey bee colonies in Spain: A case study

Background: Here we present a holistic screening of collapsing colonies from three professional apiaries in Spain. Colonies with typical honey bee depopulation symptoms were selected for multiple possible factors to reveal the causes of collapse. Results: Omnipresent were Nosema ceranae and Lake Sinai Virus. Moderate prevalences were found for Black Queen Cell Virus and trypanosomatids, whereas Deformed Wing Virus, Aphid Lethal Paralysis Virus strain Brookings and neogregarines were rarely detected. Other viruses, Nosema apis, Acarapis woodi and Varroa destructor were not detected. Palinologic study of pollen demonstrated that all colonies were foraging on wild vegetation. Consequently, the pesticide residue analysis was negative for neonicotinoids. The genetic analysis of trypanosomatids GAPDH gene, showed that there is a large genetic distance between Crithidia mellificae ATCC30254, an authenticated cell strain since 1974, and the rest of the presumed C. mellificae sequences obtained in our study or published. This means that the latter group corresponds to a highly differentiated taxon that should be renamed accordingly. Conclusion: The results of this study demonstrate that the drivers of colony collapse may differ between geographic regions with different environmental conditions, or with different beekeeping and agricultural practices. The role of other pathogens in colony collapse has to bee studied in future, especially trypanosomatids and neogregarines. Beside their pathological effect on honey bees, classification and taxonomy of these protozoan parasites should also be clarified