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6. Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Author

Näpflin, Kathrin, O’Connor, Emily A., Becks, Lutz, Bensch, Staffan, Ellis, Vincenzo A., Hafer-Hahmann, Nina, Harding, Karin C., Lindén, Sara K., Olsen, Morten T., Roved, Jacob, Sackton, Timothy B., Shultz, Allison J., Venkatakrishnan, Vignesh, Videvall, Elin, Westerdahl, Helena, Winternitz, Jamie C., Edwards, Scott V., Näpflin, Kathrin, O’Connor, Emily A., Becks, Lutz, Bensch, Staffan, Ellis, Vincenzo A., Hafer-Hahmann, Nina, Harding, Karin C., Lindén, Sara K., Olsen, Morten T., Roved, Jacob, Sackton, Timothy B., Shultz, Allison J., Venkatakrishnan, Vignesh, Videvall, Elin, Westerdahl, Helena, Winternitz, Jamie C., and Edwards, Scott V.

Published
2019
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7. Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Author

Näpflin, Kathrin, primary, O’Connor, Emily A., additional, Becks, Lutz, additional, Bensch, Staffan, additional, Ellis, Vincenzo A., additional, Hafer-Hahmann, Nina, additional, Harding, Karin C., additional, Lindén, Sara K., additional, Olsen, Morten T., additional, Roved, Jacob, additional, Sackton, Timothy B., additional, Shultz, Allison J., additional, Venkatakrishnan, Vignesh, additional, Videvall, Elin, additional, Westerdahl, Helena, additional, Winternitz, Jamie C., additional, and Edwards, Scott V., additional

Published
2019
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8. Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

Author

Lamichhaney, Sangeet, primary, Card, Daren C., additional, Grayson, Phil, additional, Tonini, João F.R., additional, Bravo, Gustavo A., additional, Näpflin, Kathrin, additional, Termignoni-Garcia, Flavia, additional, Torres, Christopher, additional, Burbrink, Frank, additional, Clarke, Julia A., additional, Sackton, Timothy B., additional, and Edwards, Scott V., additional

Published
2019
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9. Infection, microbiota and evolutionary parasitology

Author

Näpflin, Kathrin, Schmid-Hempel, Paul, and Ebert, Dieter

Subjects
GASTROINTESTINAL FLORA (ANIMAL PHYSIOLOGY), TRYPANOSOMATIDEN (PARASITOLOGIE), BOMBUS (ZOOLOGIE), KOLONIEN UND GEMEINSCHAFTEN VON MIKROORGANISMEN (MIKROBIOLOGIE), WIRT-PARASIT BEZIEHUNG (PARASITOLOGIE), HOST-PARASITE INTERACTION (PARASITOLOGY), Life sciences, Zoological sciences, TRYPANOSOMATIDAE (PARASITOLOGY), ddc:590, ddc:570, MAGENFLORA + DARMFLORA (TIERPHYSIOLOGIE), BOMBUS (ZOOLOGY), MICROBIAL COLONIES + MICROBIAL COMMUNITIES (MICROBIOLOGY)
Published
2016
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11. The genomes of two key bumbleblee species with primitive eusocial organization

Author

Sadd, Ben M., Barribeau, Seth M., Buechel, Severine D., Marxer, Monika, Näpflin, Kathrin, Schmid-Hempel, Regula, Schmid-Hempel, Paul, and du Plessis, Louis

Subjects
Odorant Receptor, Transposable Element, Bumblebee Species, Synteny Block, Long Terminal Repeat
Abstract

Background The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation., Genome Biology, 16, ISSN:1474-760X

Published
2015

12. A depauperate immune repertoire precedes evolution of sociality in bees

Author

Barribeau, Seth M., Sadd, Ben M., du Plessis, Louis, Brown, Mark J.F., Buechel, Severine D., Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Colgan, Thomas J., Erler, Silvio, Evans, Jay, Helbing, Sophie, Karaus, Elke, Lattorff, H. Michael G., Marxer, Monika, Meeus, Ivan, Näpflin, Kathrin, Niu, Jinzhi, Schmid-Hempel, Regula, Smagghe, Guy, Waterhouse, Robert M., Yu, Na, Zdobnov, Evgeny M., and Schmid-Hempel, Paul

Subjects
Animals, Bees/classification, Bees/genetics, Behavior, Animal, Evolution, Molecular, Female, Gene Expression Regulation, Genes, Insect, Genetic Variation, Male, Selection, Genetic, Social Behavior, POSITIVE SELECTION, Immune Gene, Social Insect, Biology and Life Sciences, AMINO-ACID SITES, BUMBLEBEE BOMBUS-TERRESTRIS, MULTIPLE SEQUENCE ALIGNMENT, HONEYBEE COLONIES, Bumblebee Species, DISEASE RESISTANCE, GENETIC DIVERSITY, ddc:576.5, HIERARCHICAL CATALOG, CODON-SUBSTITUTION MODELS, Orthologous Group, Toll Pathway, MAXIMUM-LIKELIHOOD
Abstract

Background Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire of two ecologically and commercially important bumblebee species that diverged approximately 18 million years ago, the North American Bombus impatiens and European Bombus terrestris. Results We find that the immune systems of these bumblebees, two species of honeybee, and a solitary leafcutting bee, are strikingly similar. Transcriptional assays confirm the expression of many of these genes in an immunological context and more strongly in young queens than males, affirming Bateman’s principle of greater investment in female immunity. We find evidence of positive selection in genes encoding antiviral responses, components of the Toll and JAK/STAT pathways, and serine protease inhibitors in both social and solitary bees. Finally, we detect many genes across pathways that differ in selection between bumblebees and honeybees, or between the social and solitary clades. Conclusions The similarity in immune complement across a gradient of sociality suggests that a reduced immune repertoire predates the evolution of sociality in bees. The differences in selection on immune genes likely reflect divergent pressures exerted by parasites across social contexts., Genome Biology, 16, ISSN:1474-760X

Published
2015

13. A depauperate immune repertoire precedes evolution of sociality in bees

Author

Barribeau, Seth M, primary, Sadd, Ben M, additional, du Plessis, Louis, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Colgan, Thomas J, additional, Erler, Silvio, additional, Evans, Jay, additional, Helbing, Sophie, additional, Karaus, Elke, additional, Lattorff, H Michael G, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Näpflin, Kathrin, additional, Niu, Jinzhi, additional, Schmid-Hempel, Regula, additional, Smagghe, Guy, additional, Waterhouse, Robert M, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, and Schmid-Hempel, Paul, additional

Published
2015
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14. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M, primary, Barribeau, Seth M, additional, Bloch, Guy, additional, de Graaf, Dirk C, additional, Dearden, Peter, additional, Elsik, Christine G, additional, Gadau, Jürgen, additional, Grimmelikhuijzen, Cornelis JP, additional, Hasselmann, Martin, additional, Lozier, Jeffrey D, additional, Robertson, Hugh M, additional, Smagghe, Guy, additional, Stolle, Eckart, additional, Van Vaerenbergh, Matthias, additional, Waterhouse, Robert M, additional, Bornberg-Bauer, Erich, additional, Klasberg, Steffen, additional, Bennett, Anna K, additional, Câmara, Francisco, additional, Guigó, Roderic, additional, Hoff, Katharina, additional, Mariotti, Marco, additional, Munoz-Torres, Monica, additional, Murphy, Terence, additional, Santesmasses, Didac, additional, Amdam, Gro V, additional, Beckers, Matthew, additional, Beye, Martin, additional, Biewer, Matthias, additional, Bitondi, Márcia MG, additional, Blaxter, Mark L, additional, Bourke, Andrew FG, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cameron, Rossanah, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Ciborowski, Kate L, additional, Clarke, David F, additional, Colgan, Thomas J, additional, Collins, David H, additional, Cridge, Andrew G, additional, Dalmay, Tamas, additional, Dreier, Stephanie, additional, du Plessis, Louis, additional, Duncan, Elizabeth, additional, Erler, Silvio, additional, Evans, Jay, additional, Falcon, Tiago, additional, Flores, Kevin, additional, Freitas, Flávia CP, additional, Fuchikawa, Taro, additional, Gempe, Tanja, additional, Hartfelder, Klaus, additional, Hauser, Frank, additional, Helbing, Sophie, additional, Humann, Fernanda C, additional, Irvine, Frano, additional, Jermiin, Lars S, additional, Johnson, Claire E, additional, Johnson, Reed M, additional, Jones, Andrew K, additional, Kadowaki, Tatsuhiko, additional, Kidner, Jonathan H, additional, Koch, Vasco, additional, Köhler, Arian, additional, Kraus, F Bernhard, additional, Lattorff, H Michael G, additional, Leask, Megan, additional, Lockett, Gabrielle A, additional, Mallon, Eamonn B, additional, Antonio, David S Marco, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Moritz, Robin FA, additional, Nair, Ajay, additional, Näpflin, Kathrin, additional, Nissen, Inga, additional, Niu, Jinzhi, additional, Nunes, Francis MF, additional, Oakeshott, John G, additional, Osborne, Amy, additional, Otte, Marianne, additional, Pinheiro, Daniel G, additional, Rossié, Nina, additional, Rueppell, Olav, additional, Santos, Carolina G, additional, Schmid-Hempel, Regula, additional, Schmitt, Björn D, additional, Schulte, Christina, additional, Simões, Zilá LP, additional, Soares, Michelle PM, additional, Swevers, Luc, additional, Winnebeck, Eva C, additional, Wolschin, Florian, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, Aqrawi, Peshtewani K, additional, Blankenburg, Kerstin P, additional, Coyle, Marcus, additional, Francisco, Liezl, additional, Hernandez, Alvaro G, additional, Holder, Michael, additional, Hudson, Matthew E, additional, Jackson, LaRonda, additional, Jayaseelan, Joy, additional, Joshi, Vandita, additional, Kovar, Christie, additional, Lee, Sandra L, additional, Mata, Robert, additional, Mathew, Tittu, additional, Newsham, Irene F, additional, Ngo, Robin, additional, Okwuonu, Geoffrey, additional, Pham, Christopher, additional, Pu, Ling-Ling, additional, Saada, Nehad, additional, Santibanez, Jireh, additional, Simmons, DeNard, additional, Thornton, Rebecca, additional, Venkat, Aarti, additional, Walden, Kimberly KO, additional, Wu, Yuan-Qing, additional, Debyser, Griet, additional, Devreese, Bart, additional, Asher, Claire, additional, Blommaert, Julie, additional, Chipman, Ariel D, additional, Chittka, Lars, additional, Fouks, Bertrand, additional, Liu, Jisheng, additional, O’Neill, Meaghan P, additional, Sumner, Seirian, additional, Puiu, Daniela, additional, Qu, Jiaxin, additional, Salzberg, Steven L, additional, Scherer, Steven E, additional, Muzny, Donna M, additional, Richards, Stephen, additional, Robinson, Gene E, additional, Gibbs, Richard A, additional, Schmid-Hempel, Paul, additional, and Worley, Kim C, additional

Published
2015
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15. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.

Author

Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, and Edwards SV

Subjects
Animals, Genome, Genomics, Invertebrates classification, Phylogeny, Selection, Genetic, Vertebrates classification, Evolution, Molecular, Invertebrates genetics, Vertebrates genetics
Abstract

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Published
2019
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