Publications

(past and current students & lab members highlighted)

2020

60. Rispe C, Legeai F, Nabity P, Fernández R, (...), Delmotte F, Tagu D. 2020. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation and invasion routes of an iconic pest. BMC Biology 18:90.

59. Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V, Pegueroles C, Gabaldón T, Tagu D. 2020. Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum. Molecular Biology and Evolution, https://doi.org/10.1093/molbev/msaa110

58. Fernández R, Gabaldón T, Dessimoz C. 2020. Orthology inference: definitions, prediction and impact on species phylogeny inference. Book chapter in: Scornavacca C, Délsuc F, Gaultier N. 2020. Phylogenetics in the genomics era. Free online book: https://hal.inria.fr/PGE/

57. Fernández R, Gabaldón T. 2020. Gene gain and loss across the Metazoa Tree of Life. Nature Ecology and Evolution, https://doi.org/10.1038/s41559-019-1069-x

56. Marchán DF, Marta Novo, Nuria Sánchez, Jorge Domínguez, Darío Díaz Cosín, Fernández R. 2020. Local adaptation fuels cryptic speciation in terrestrial annelids. Molecular Phylogenetics and Evolution, https://doi.org/10.1016/j.ympev.2020.106767

 

55. Marchán DF, Fernández R, Domínguez J, Díaz Cosín D, Novo M. 2020. Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae). Systematics and Biodiversity, https://doi.org/10.1080/14772000.2020.1730474

2019

54. Phillips H. (...) Fernández R (author no. 51)(...), Eisenhauer N. 2019. Global distribution of earthworm biodiversity. Science 366 (6464), 480-485.

53. Walker NS, Fernández R, Sneed JM, Paul VJ, Giribet G, Combosch DJ. 2019. Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides. Molecular Ecology 28 (22), 4899-4913.

52. Miller S, Movsesyam A, Zhang S, Fernández R, Posakony J. 2019. Evolutionary emergence of Hairless as a novel component of the Notch signaling pathway. eLife 8: e48115.

51. Laumer, Fernández R, Lemer S, Combosch D, Kocot K, Riesgo R, Andrade S, Sterrer W, Sorensen M, Giribet G. 2019. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proceedings of the Royal Society B: Biological Sciences 286, https://doi.org/10.1098/rspb.2019.0831.

50. Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V, Pegueroles C, Gabaldón T, Tagu D. 2019. Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum. bioRxiv, https://doi.org/10.1101/643544.

49. Fernández R, Gabaldón T, Dessimoz C. 2019. Orthology: definitions, inference, and impact on species phylogeny inference. arXiv: 1903.04530.

2018

48. Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, Hormiga G. 2018. Phylogenomics, diversification dynamics, and comparative transcriptomics across the spider tree of life. Current Biology 28 (9), 1489-1497. e5.

47. Álvarez-Campos P, Kenny NJ, Verdes A, Fernández R, Novo M, Giribet G, Riesgo A. 2018. Delegating sex: differential gene expression in stolonizing syllids uncovers the hormonal control of reproduction. Genome Biology and Evolution 11 (1), 295-318.

46. Kallal RJ, Fernández R, Giribet G, Hormiga G. 2018. A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. Molecular Phylogenetics and Evolution 126, 129-140.

45. Scherbaum S, Hellmann N, Fernández R, Pick C, Burmester T. 2018. Diversity, evolution, and function of myriapod hemocyanins. BMC Evolutionary Biology 18 (1), 107.

44. Marchán DF, Fernández R, Sánchez N, de Sosa I, CosÍn DJD, Novo M. 2018. Insights into the diversity of Hormogastridae (Annelida, Oligochaeta) with descriptions of six new species. Zootaxa 4496 (1), 65-95.

43. Marchán DF, Fernández R, de Sosa I, Sánchez N, Cosín DJD, Novo M. 2018. Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta). Invertebrate systematics 32 (3), 652-671.

42. Fernández R, Edgecombe GE, Giribet G. 2018. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Scientific Reports 8 (1), 83.

2017

41. Fernández R, Sharma PP, Tourinho AL, Giribet G. 2017. The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics. Proceedings of the Royal Society B: Biological Sciences 284 (1849), 20162340.

40. de Sosa I, Marchán DF, Novo M, Cosín DJD, Giribet G, Fernández R. 2017. Insights into the origin of parthenogenesis in oligochaetes: Strong genetic structure in a cosmopolitan earthworm is not related to reproductive mode. European Journal of Soil Biology 81, 31-38.

39. Marchán DF, Fernández R, de Sosa I, Cosín DJD, Novo M. 2017. Pinpointing cryptic borders: fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae). Molecular Phylogenetics and Evolution 112, 185-193.

2016

38. Fernández R, Edgecombe GE, Giribet G. 2016. Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction. Systematic Biology 65 (5), 871-889.

37. Novo M, Fernández R, Andrade SCS, Marchán DF, Cunha L, Díaz Cosín DJ. 2016. Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Molecular Phylogenetics and Evolution 94, 473-478.

36. Giribet G, Boyer SL, Baker CM, Fernández R, Sharma PP, Bivort BL, Daniels SR, Harvey MS, Griswold CE. 2016. A molecular phylogeny of the temperate Gondwanan family Pettalidae (Arachnida, Opiliones, Cyphophthalmi) and the limits of taxonomic sampling. Zoological Journal of the Linnean Society 178 (3), 523-545.

35. Marchán DF, Sánchez N, Novo M, Fernández R, Pardos F, Díaz Cosín DJ. 2016. Zoologischer Anzeiger-A Journal of Comparative Zoology 264, 17-28.

34. Marchán DF, Novo M, Fernández R, de Sosa I, Trigo D, Díaz Cosín DJ. 2016. Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study-the number of typhlosole lamellae in Hormogastridae (Annelida, Oligochaeta). Zoological Journal of the Linnean Society 178 (1), 4-14.

33. Marchán DF, Refoyo P, Fernández R, Novo M, de Sosa I, Díaz Cosín DJ. 2016. Macroecological inferences on soil fauna through comparative niche modeling: the case of Hormogastridae (Annelida, Oligochaeta). European Journal of Soil Biology 75, 115-122.

32. Fernández R, Novo M, Marchán DF, Díaz Cosín DJ. 2016. Diversification patterns in cosmopolitan earthworms: similar mode but different tempo. Molecular Phylogenetics and Evolution 94, 701-708.

2015

31. Fernández R, Giribet G. 2015. Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida). Royal Society open science 2 (6), 150065.

30. Sharma PP, Fernández R, Esposito LA, González-Santillán E, Monod L. Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proceedings of the Royal Society B: Biological Sciences 282 (1804), 20142953.

29. Fernández R, Lemer S, McIntyre E, Giribet G. 2015. Comparative phylogeography and population genetic structure of three widespread mollusc species in the Mediterranean and near Atlantic. Marine Ecology 36 (3), 701-715.

28. Novo M, Fernández R, Marchán DF, Trigo D, Díaz Cosín DJ, Giribet G. 2015. Unearthing the historical biogeography of Mediterranean earthworms (Annelida: Hormogastridae). Journal of Biogeography 42 (4), 751-762.

27. Sharma PP, Fernández R, Santillán GR, Monod L. 2015. Phylogenomic resolution of scorpions reveals discordance with morphological phylogenetic signal. Integrative and Comparative Biology 55, E165-E165.

26. Marchán DF, Refoyo P, Novo M, Fernández R, Trigo D, Díaz Cosín DJ. 2015. Predicting soil micro-variables and the distribution of an endogeic earthworm species through a model based on large-scale variables. Soil Biology and Biochemistry 81, 124-127.

2014

25. Fernández R, Hormiga G, Giribet G. 2014. Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers. Current Biology 24 (15), 1772-1777.

24. Fernández R, Laumer CE, Vahtera V, Libro S, Kaluziak S, Sharma PP, Edgecombe GE, Giribet G. 2014. Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular Biology and Evolution 31 (6), 1500-1513.

23. Vélez S, Fernández R, Giribet R. 2014. A molecular phylogenetic approach to the New Zealand species of Enantiobuninae (Opiliones: Eupnoi: Neopilionidae). Invertebrate Systematics 28 (6), 565-589.

22. Fernández R, Vélez S, Giribet G. 2014. Linking genetic diversity and morphological disparity: biodiversity assessment of a highly unexplored family of harvestmen (Arachnida: Opiliones: Neopilionidae) in New Zealand. Invertebrate Systematics 28 (6), 590-604.

21. Lenihan J, Kvist S, Fernández R, Giribet G, Ziegler A. 2014. A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens. GigaScience 3 (1): 6.

20. Fernández R, Kvist S, Lenihan J, Giribet G, Ziegler A. 2014. Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography. PloS One 9 (5), e96617.

19. Giribet G, Fernández R, Boyer SL. 2014. On four poorly known harvestmen from New Zealand (Arachnida: Opiliones: Cyphophthalmi: Eupnoi: Dyspnoi: Laniatores). New Zealand Journal of Zoology 41 (4), 223-233.

18. Fernández R, Giribet G. 2014. Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi). Invertebrate Systematics 28 (4), 401-414.

17. Gutiérrez M, Ranera E, Novo M, Fernández R, Trigo D. 2014. Does the invasion of the exotic tree Ailanthus altissima affect the soil arthropod community? The case of a riparian forest of the Henares River (Madrid). European journal of Soil Biology 62, 39-48.

16. Díaz Cosín DJ, Novo M, Fernández R, Marchán DF, Gutiérrez M. 2014. A new earthworm species within a controversial genus: Eiseniona gerardoi sp. n.(Annelida, Lumbricidae)-description based on morphological and molecular data. ZooKeys 399: 71.

15. Marchán DF, Fernández R, Novo M, Díaz Cosín DJ. 2014. New light into the hormogastrid riddle: morphological and molecular description of Hormogaster joseantonioi sp. n. (Annelida, Clitellata, Hormogastridae). ZooKeys 414: 1.

2013

14. Novo M, Fernández R, Granado-Yela C, Gutiérrez M, Díaz Cosín DJ. 2013. Does the order of copulation matter? Experimental paternity analyses in the earthworm Hormogaster elisae (Annelida: Hormogastridae). Pedobiologia 56 (2), 97-104.

13. Fernández R, Almodóvar A, Novo M, Gutiérrez M, Díaz Cosín DJ. 2013. Earthworms, good indicators for palaeogeographical studies? Testing the genetic structure and demographic history in the peregrine earthworm Aporrectodea trapezoides (Dugès, 1828) in southern Europe. Soil Biology and Biochemistry 58, 127-135.

2012

12. Fernández R, Almodóvar A, Novo M, Simancas B, Díaz Cosín DJ. 2012. Adding complexity to the complex: New insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae). Molecular Phylogenetics and Evolution 64 (2), 368-379.

11. Novo M, Almodóvar A, Fernández R, Trigo D, Díaz Cosín DJ, Giribet G. 2012. Appearances can be deceptive: different diversification patterns within a group of Mediterranean earthworms (Oligochaeta, Hormogastridae). Molecular Ecology 21 (15), 3776-3793.

10. Novo M, Fernández R, Marchán DF, Gutiérrez M, Díaz Cosín DJ. 2012. Compilation of morphological and molecular data, a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida, Clitellata, Hormogastridae). ZooKeys 242, 1-17.

2011

9. Fernández R, Bergmann P, Almodóvar A, Díaz Cosín DJ, Heethoff M. 2011. Ultrastructural and molecular insights into three populations of Aporrectodea trapezoides (Dugés, 1828)(Oligochaeta, Lumbricidae) with different reproductive modes. Pedobiologia 54 (5-6), 281-290.

8. Novo M, Almodóvar A, Fernández R, Giribet G, Díaz Cosín DJ. 2011. Understanding the biogeography of a group of earthworms in the Mediterranean basin—The phylogenetic puzzle of Hormogastridae (Clitellata: Oligochaeta). Molecular Phylogenetics and Evolution 61 (1), 125-135.

7. Fernández R, Almodóvar A, Novo M, Gutiérrez M, Díaz Cosín DJ. 2011. A vagrant clone in a peregrine species: phylogeography, high clonal diversity and geographical distribution in the earthworm Aporrectodea trapezoides (Dugès, 1828). Soil Biology and Biochemistry 43 (10), 2085-2093.

6. Díaz Cosín DJ, Novo M, Fernández R. 2011. Reproduction of earthworms: sexual selection and parthenogenesis. In: Karaca A. (eds) Biology of Earthworms. Soil Biology, vol 24. Springer, Berlin, Heidelberg. pp 69-86.

2010

5. Gutiérrez M, Jesús JB, Trigo D, Fernández R, Novo M, Díaz Cosín DJ. 2010. Relationships among spatial distribution of soil microarthropods, earthworm species and soil properties. Pedobiologia 53 (6), 381-389.

4. Novo M, Almodóvar A, Fernández R, Díaz Cosín DJ. 2010. Mate choice of an endogeic earthworm revealed by microsatellite markers. Pedobiologia 53 (6), 375-379.

3. Fernández R, Novo M, Gutiérrez M, Almodóvar A, Díaz Cosín DJ. 2010. Life cycle and reproductive traits of the earthworm Aporrectodea trapezoides (Dugès, 1828) in laboratory cultures. Pedobiologia 53 (5), 295-299.

2. Novo M, Almodóvar A, Fernández R, Trigo D, Díaz Cosín DJ. 2010. Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data. Molecular Phylogenetics and Evolution 56 (1), 507-512.

2009

1. Díaz Cosín DJ, Hernández P, Trigo D, Fernández R, Novo M. 2009. Relationships among spatial distribution of soil microarthropods, earthworm species and soil properties. Boletin de la Real Sociedad Espanola de Historia Natural Seccion Biologica 103: 49-57.

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