--- _id: '9392' abstract: - lang: eng text: 'Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.' acknowledgement: We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet citation: ama: Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060 apa: Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060 chicago: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060. ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021. ista: Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429. mla: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060. short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429. date_created: 2021-05-16T22:01:46Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:34:38Z day: '10' department: - _id: NiBa doi: 10.1016/j.cub.2021.03.060 external_id: isi: - '000654741200004' pmid: - '33974865' intvolume: ' 31' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2021.03.060 month: '05' oa: 1 oa_version: Published Version page: R428-R429 pmid: 1 publication: Current Biology publication_identifier: eissn: - '18790445' issn: - '09609822' publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the use of species concepts type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '9387' abstract: - lang: eng text: We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift. acknowledgement: This work was supported by the Russian Science Foundation grant N 16-14-10173. article_number: '110729' article_processing_charge: No article_type: original author: - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Tatiana Yu. full_name: Neretina, Tatiana Yu. last_name: Neretina - first_name: Alexey S. full_name: Kondrashov, Alexey S. last_name: Kondrashov citation: ama: Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 2021;524. doi:10.1016/j.jtbi.2021.110729 apa: Khudiakova, K., Neretina, T. Y., & Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. Elsevier . https://doi.org/10.1016/j.jtbi.2021.110729 chicago: Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology. Elsevier , 2021. https://doi.org/10.1016/j.jtbi.2021.110729. ieee: K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” Journal of Theoretical Biology, vol. 524. Elsevier , 2021. ista: Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729. mla: Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” Journal of Theoretical Biology, vol. 524, 110729, Elsevier , 2021, doi:10.1016/j.jtbi.2021.110729. short: K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021). date_created: 2021-05-12T05:58:42Z date_published: 2021-04-24T00:00:00Z date_updated: 2023-08-08T13:32:40Z day: '24' department: - _id: GradSch doi: 10.1016/j.jtbi.2021.110729 external_id: isi: - '000659161500002' intvolume: ' 524' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - Modelling and Simulation - Statistics and Probability - General Immunology and Microbiology - Applied Mathematics - General Agricultural and Biological Sciences - General Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/477489v1 month: '04' oa: 1 oa_version: Preprint publication: Journal of Theoretical Biology publication_identifier: issn: - 0022-5193 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Two linked loci under mutation-selection balance and Muller’s ratchet type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 524 year: '2021' ... --- _id: '12987' abstract: - lang: eng text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4' apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4' chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.' mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.' short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9408' abstract: - lang: eng text: We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype. acknowledgement: The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767). article_number: 2881-2895 article_processing_charge: No author: - first_name: Xudong full_name: Feng, Xudong last_name: Feng - first_name: Jiafeng full_name: Liu, Jiafeng last_name: Liu - first_name: Huamin full_name: Wang, Huamin last_name: Wang - first_name: Yin full_name: Yang, Yin last_name: Yang - first_name: Hujun full_name: Bao, Hujun last_name: Bao - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Weiwei full_name: Xu, Weiwei last_name: Xu citation: ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218 apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218 chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218. ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021. ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895. mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218. short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021). date_created: 2021-05-23T22:01:42Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:45:46Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1109/TVCG.2019.2957218 ec_funded: 1 external_id: isi: - '000649620700009' pmid: - '31804937' file: - access_level: open_access checksum: a78e6ac94e33ade4ffaea66943d5f7dc content_type: application/pdf creator: kschuh date_created: 2021-05-25T15:08:49Z date_updated: 2021-05-25T15:08:49Z file_id: '9427' file_name: 2021_TVCG_Feng.pdf file_size: 6183002 relation: main_file success: 1 file_date_updated: 2021-05-25T15:08:49Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '10772626' issn: - '19410506' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Computational design of skinned Quad-Robots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2021' ... --- _id: '9410' abstract: - lang: eng text: Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains. acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support. article_number: '20200913' article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Paul full_name: Neve, Paul last_name: Neve citation: ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913 apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913 chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913. ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021. ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913. mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913. short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021). date_created: 2021-05-23T22:01:43Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:44:35Z day: '12' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsbl.2020.0913 ec_funded: 1 external_id: isi: - '000651501400001' pmid: - ' 33975485' file: - access_level: open_access checksum: 9c13c1f5af7609c97c741f11d293188a content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:09:03Z date_updated: 2021-05-25T14:09:03Z file_id: '9425' file_name: 2021_BiologyLetters_Lagator.pdf file_size: 726759 relation: main_file success: 1 file_date_updated: 2021-05-25T14:09:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology letters publication_identifier: eissn: - 1744957X publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Adaptation at different points along antibiotic concentration gradients tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ...