Scientific contributions



As a researcher and teacher in evolutionary biology, my work focuses on different aspects of the diversity of life, through the three following main axes:

I. Origin, evolution and structure of the biodiversity : Herpetological systematics

Through an integrative approach mainly combining molecular phylogenetics, population genetics and comparative morpho-anatomy, my work addresses several issues related to the origins and the diversification of reptiles and amphibians. The core of my expertise is the systematics of tropical squamates, mainly from South America and Madagascar. How many species remain to be discovered (alpha-taxonomy), what historical processes have shaped their current distribution on Earth (bio- and phylogeography) or how to explain their remarkable ecological and morphological diversification are among the various questions I am exploring at the light of evolutionary biology. This work also contributes to various conservation initiatives, either related to specific or global assessment of extinction risks (IUCN skink specialist group) or to the definition of priority conservation units for groups that fall under my expertise.

Examples. On the fossorial origin of snakes... (Miralles et al 2018, J. Evol. Biol.).
Defining priority conservation units for Galapagos marine Iguanas (Miralles et al 2017, Biol. J. Lin. Soc.).
Risk assessment for skink conservation around the globe (Chapple et al 2021, Biol. Conserv.).
My last contribution to the inventory of life on Earth (Miralles et al 2021, Vert. Zool.).


II. Inventorying biodiversity in the digital age : Concept and methods

Over the past two centuries, we may have discovered and described less than 10% of the world's biodiversity. Given the urgency of the current biodiversity crisis, taxonomy must take better advantage of new technologies to accelerate the rate of species inventory and provide more rigorous and stable species hypotheses over time. The hindsight I gained on my integrative practice of taxonomy has led me to work on these broader research themes addressed to the whole community of systematists. They are mostly dealing with methodological and theoretical issues related to the species delimitation (i.e. the work of determining whether divergent populations represent a single species or distinct biological species), and contribute to equipping the taxonomy community with new tools fully adapted to its daily practices (eg. favouring interoperability, specimen-based architectures, or user-friendliness), and also to revise and strengthen the secular epistemological foundation on which the discipline is based.

Examples. Repositories for Taxonomic Data: Where We Are and What is Missing (Miralles et al 2020, Syst. Biol.).
LIMES, a tool for comparing species partitions (Ducasse et al 2020, Bioinformatics).
iTaxoTools, a user-friendly toolbox for cybertaxonomists (Vences et al 2021, Megataxa).
SPART, a standardized data-exchange format for species delimitation (Miralles et al 2022, Mol. Ecol. Ress.).

III. The biodiversity and us : A matter of perceptions ?

As environmentalist and animalist concerns (whose object are the preservation of biodiversity and animal welfare, respectively) are constantly gaining ground in social debates, the question of our relationships with others species has never been so topical. How can we explain that the fate of some species (eg. Orangutan) affects us far more than many others? To what extent can these powerful anthropomorphic biases impact societal debates about the living world ? And more fundamentally, what can they tell us about how the ape species to which we belong perceives and cognitively processes other living beings, including our fellows? For several years, I have been developing an innovative and transdisciplinary research activity, located at the border of cognitive sciences, biodiversity sciences and anthropology. This program aims more specifically at studying our empathic and emotional perceptions toward the different organisms living on Earth, through an evolutionary analytical framework.

Examples. A cartography of the living world through our empathic and compassionate responsiveness (Miralles et al 2019, Sci. Reports)
Exploring Neurodiversity through Biodiversity (Miralles et al. Sci. Reports 2022) .

Full list of my publications

60. Miralles A, Grandgeorge M, Raymond M (2022). Self-perceived empathic abilities of people with autism towards living beings mostly differs for humans. Scientific Reports, 6300,
59. Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre (2022). SPART, a versatile and standardized data exchange format for species partition information. Molecular Ecology Resources, 22(1):430-438
58. Herrel A, Lowie A, Miralles A, Gaucher P, Kley NJ, Measey J, Tolley KA (2021). Burrowing in blindsnakes: A preliminary analysis of burrowing forces and consequences for the evolution of morphology. The Anatomical Records, 2292-2302.
57. Chapple DG, Roll U, Böhm M, Aguilar R, Amey AP, Austin CC, Baling M, Barley AJ, Bates MF, Bauer AM, Blackburn DG, Bowles P, Brown RM, Chandramouli SR, Chirio L, Cogger H, Colli GR, Conradie W, Couper PJ, Cowan MA, Craig MD, Das I, Datta-Roy A, Dickman CR, Ellis RJ, Fenner AL, Ford S, Ganesh SR, Gardner MG, Geissler P, Gillespie GR, Glaw F, Greenlees MJ, Griffith OW, Grismer LL, Haines ML, Harris DJ, Hedges SB, Hitchmough RA, Hoskin CJ, Hutchinson MN, Ineich I, Janssen J, Johnston GR, Karin BR, Keogh JS, Kraus F, LeBreton M, Lymberakis P, Masroor R, McDonald PJ, Mecke S, Melville J, Melzer S, Michael DR, Miralles A, Mitchell NJ, Nelson NJ, Nguyen TQ, de Campos Nogueira C, Ota H, Pafilis P, Pauwels OSG, Perera A, Pincheira-Donoso D, Reed RN, Ribeiro-Júnior MA, Riley JL, Rocha S, Rutherford PL, Sadlier RA, Shacham B, Shea GM, Shine R, Slavenko A, Stow A, Sumner J, Tallowin OJS, Teale R, Torres-Carvajal O, Trape JF, Uetz P, Ukuwela KDB, Valentine L, Van Dyke JU, van Winkel D, Vasconcelos R, Vences M, Wagner P, Wapstra E, While GM, Whiting MJ, Whittington CM, Wilson S, Ziegler T, Tingley R, Meiri S (2021). Conservation status of the world's skinks (Scincidae): Taxonomic and geographic patterns in extinction risk. Biological Conservation, 257:109101
56. Vences M, Miralles A, Brouillet S, Ducasse J, Fedosov A, Kharchev V, Kostadinov I, Kumari S, Patmanidis S, Scherz MD, Puillandre N, Renner SS (2021). iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa, 006(2): 77-92.
55. Miralles A, Bruy T, Crottini A., Rakotoarison A, Ratsoavina FM, Scherz MD, Schmidt R, Köhler J, Glaw F, Vences M (2021). Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae). Vertebrate Zoology, 71: 27-48.
54. Scherz MD, Schmidt L, Crottini A, Miralles A, Rakotoarison A, Raselimanana AP, Köhler J, Glaw F, Vences M (2021). Into the Chamber of Horrors: A proposal for the resolution of nomenclatural chaos in the Scaphiophryne calcarata complex (Anura: Microhylidae) with a new species-level phylogenetic hypothesis for Scaphiophryninae. Zootaxa, 4938(1): 392-420.
53. Porcel X, Dubos N, Rosa GM, Miralles A, Nöel J, Lava H, Velo JH, Rendrirendry G, Andreone F, Crottini A (2021). The kiwi of all skinks: an unusual egg size in a species of Madascincus (Scincidae: Scincinae) from eastern Madagascar. Herpetology notes, 14: 365–369
52. Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner S, Vences M (2020). Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic Biology, 69(6): 1231–1253
51. Le Guilloux M, Miralles A, Measey J, Vanhooydonck B, O’Reilly JC, Lowie A, Herrel A (2020). Trade-offs between burrowing and biting force in fossorial scincid lizards? Biological Journal of the Linnean Society, 130(2): 310-319.
50. Gemeinholzer B, Vences M, Beszteri B, Bruy T, Felden J, Kostadinov I, Miralles A, Nattkemper TW, Printzen C, Renz J, Rybalka N, Schuster T, Weibulat T, Wilke T, Renner SS (2020). Data storage and data re-use in taxonomy - the need for improved storage and accessibility of heterogeneous data. Organisms Diversity and Evolution, 20(1): 1-8.
49. Miralles A , Geniez P., Beddek M., Mendez Aranda D., Brito JC, Leblois R., Crochet P-A (2020). Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas. Zootaxa, 4747(2). doi: http://dx.doi.org/10.11646/zootaxa.4747.2.4
48. Ducasse J, Ung V, Lecointre G, Miralles A (2020). LIMES, a tool for comparing species partition. Bioinformatics, 2282-2283.
47. Miralles A , Raymond M, Lecointre G (2019). Empathy and compassion toward other species decrease with evolutionary divergence time. Scientific Reports, 9: 19555.
46. Miralles A , Marin J, Markus D, Herrel A, Hedges SB, Vidal N (2018). Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications. Journal of Evolutionary Biology, 31(12): 1782-1793.
45. Quah ESH, Grismer LL, Jetten T, Wood PL, Miralles A, SAM Sah, Guek KHP, Brady ML (2018). The rediscovery of Schaefer’s Spine-jawed Snake (Xenophidion schaeferi Günther & Manthey, 1995) (Serpentes, Xenophidiidae) from Peninsular Malaysia with notes on its variation and the first record of the genus from Sumatra, Indonesia. Zootaxa, 4441(2): 366-378.
44. Cornelis G, Funk M, Vernochet C, Leal F, Tarazona OA, Meurice G, Heidmann O, Dupressoir A, Miralles A, Ramirez-Pinilla MP, Heidmann T (2017). An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. Proceedings of the National Academy of Sciences, 114: E10991-E11000.
43. Miralles A, Gomes R, Angin B, Ibéné B (2017). Étude systématique des scinques Mabuya de l'archipel guadeloupéen (Squamata, Scincidae). Bulletin de la SHF,163: 67-84.
42. Miralles A, Macleod A, Rodriguez A, Ibanez A, Glaw F, Jimenez G, Quezada G, Vences M, Steinfartz S (2017). Shedding light on the Imps of Darkness: An integrative taxonomic revision of the Galápagos marine iguanas (genus Amblyrhynchus). Zoological Journal of the Linnean Society,181: 678-710.
41. Erens J, Miralles A, Glaw F, Chatrou L, Vences M (2016). Extended molecular phylogenetics and revised systematics of Malagasy scincine lizards. Molecular Phylogenetics and Evolution, 107: 466-472.
40. Miralles A, Kölhler J, Glaw F, Vences M (2016). Species delimitation methods put into taxonomic practice: Two new Madascincus species formerly allocated to historical species names (Squamata: Scincidae). Zoosystematics and Evolution, 92(2): 257-275.
39. Ceriaco LMP, Gutierrez EE, Dubois A, + 493 signatories (2016). Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa, 4196(3): 435-445.
38. Miralles A, Jono T, Mori A, Gandola R, Erens J, Kölhler J, Glaw F, Vences M (2016). A new perspective on the reduction of cephalic scales in fossorial legless skinks (Squamata, Scincidae). Zoologica Scripta, 45(4): 380-393.
37. Nagy ZT, Marion AB, Glaw F, Miralles A, Nopper J, Vences M, Hedges SB (2015). Molecular systematics and cryptic diversity of Madagascan scolecophidian snakes (Squamata: Serpentes). Zootaxa, 4040 : 31-47.
36. Pinto-Sancheza NR, Calderón-Espinosa ML, Miralles A, Crawford AJ, Ramirez-Pinilla MP (2015). Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya (Squamata: Scincidae) Fitzinger (1826) with emphasis on Colombian populations. Molecular Phylogenetic and Evolution, 93 : 188-211.
35. Ratsoavina FM, Ranjanaharisoa FA, Glaw F, Raselimanana AP, Miralles A, Vences M (2015). A new leaf-tailed gecko of the Uroplatus ebenaui group (Squamata: Gekkonidae) from Madagascar's central eastern rainforests. Zootaxa, 4006 : 143-160.
34. Miralles A, Hipsley CA, Erens J, Gehara M, Rakotoarison A, Glaw F, Müller J, Vences M (2015). Distinct Patterns of Desynchronized Limb Regression in Malagasy Scincine Lizards (Squamata, Scincidae). PlosONE, 10 (6): e0126074.
33. Miralles A, Glaw F, Ratsoavina FM, Vences M (2015). A likely microendemic new species of terrestrial iguana, genus Chalarodon, from Madagascar. Zootaxa, 3946 (2) : 201-220.
32. Crottini A, Harris DJ, Miralles A, Glaw F, Jenkins RKB, Randrianantoandro JC, Bauer AM, Vences M (2015). Morphology and molecules reveal two new species of the poorly studied gecko genus Paragehyra (Squamata: Gekkonidae) from Madagascar. Organisms Diversity & Evolution, 15 (1) : 175-198.
31. Siegel DS, Trauth SE, Rheubert JL, Rabe B, Ruopp B, Miralles A, Murray CM, Aldridge RD (2014).
Novel Cloacal Glands in Snakes: The Phylogenetic Distribution of Ventral Urodaeal Glands in Thamnophiini. Herpetologica, 70 (3): 279-289.
30. Vences M, Lima A, Miralles A, Glaw F (2014). DNA barcoding assessment of genetic variation in two widespread skinks from Madagascar, Trachylepis elegans and T. gravenhorstii (Squamata: Scincidae). Zootaxa, 3755 (5): 477–484.
29. Lima A, Miralles A, Glaw F, Ahlburg J, Börner M, Hoven JF, Kruse B, Küssner F, Ludwig M, Molde F, Michel A-M, Müller K, Panpeng S, Schneider C, Worm J, Vences M (2014). A preliminary assessment of morphological differentiation between two common Malagasy skink species, Trachylepis elegans and T. gravenhorstii. Herpetology Notes, 7:247-260.
28. Ineich I, Miralles A (2014). Amblyrhynchus cristatus (marine iguana) polydactyly. Herpetological Review. 45 (2): 322-323.
27. Miralles A, Vences M (2013). New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards. PlosONE, 8 (7): e68242.
26. Lima A, Harris DJ, Rocha S, Miralles A, Glaw F, Vences M. (2013). Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Scincidae: Lygosominae). Molecular Phylogenetic and Evolution, 67(3): 615-620.
25. Siegel DS, Miralles A, Rheubert JL, Aldridge RD. (2013). Heloderma suspectum (Gila Monster). Female reproductive anatomy. Herpetological Review, 44:142-143
24. Vences M, Guayasamin JM, Miralles A, De la Riva, I. (2013). To name or not to name: Criteria to promote economy of change in supraspecific Linnaean classification schemes. Zootaxa, 3636(2): 201-244.
23. Miralles A, Anjeriniana, M., Hipsley, C.A., Mueller, J., Glaw, F. & Vences, M. (2012). Variations on a bodyplan: description of a new Malagasy “mermaid skink” with flipper-like forelimbs only (Scincidae: Sirenoscincus). Zoosystema, 34(4): 701-710.
22. Crottini, A., Miralles A., Glaw, F., Harris, D.J., Lima, A.& Vences, M. (2012). Description of a new pygmy chameleon (Chamaeleonidae: Brookesia) from central Madagascar. Zootaxa, 3090: 63-74.
21. Siegel, D, Miralles A., Trauth, S.E., Aldridge, R. (2012). The phylogenetic distribution and morphological variation of the "pouch" in female snakes. Acta Zoologica, 93(4): 400-408.
20. Miralles A, A.P. Raselimanana, D. Rakotomalala, M. Vences & D.R. Vieites (2011). A new large and colorful skink of the genus Amphiglossus from Madagascar revealed by morphology and multilocus molecular study. Zootaxa, 2918:47-67.
19. Miralles A, Kölhler J, Glaw F, Vences M (2011). A molecular phylogeny of the Madascincus polleni species complex, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar. Zootaxa, 2876:1-16.
18. Miralles A, Kölhler J, Vieites DR, Glaw F, Vences M (2011). Developing hypotheses on rostral shield evolution in head-first digging squamates from a molecular phylogeny and new species of the genus Paracontias (Scincidae). Organisms Diversity and Evolution, 11: 135-150.
17. Siegel, D, Miralles A, Aldridge, R. (2011). Controversial snake relationships supported by reproductive anatomy. Journal of Anatomy, 218(3): 342-348.
16. Miralles A, Vasconcelos R, Perera A, Harris DJ, Carranza S (2011). An integrative taxonomic revision of the Cape Verdean skinks (Squamata, Scincidae). Zoologica Scripta, 40(1): 16-44.
15. Miralles A, David P (2010). First record of Ahaetulla mycterizans (Linnaeus, 1758) from Sumatra, Indonesia (Squamata, Colubridae), with an expanded definition of this poorly known species. Zoosystema, 32(3): 449-456.
14. Padial JM, Miralles A, De la Riva I, Vences M (2010). The integrative future of taxonomy. Frontiers in Zoology, 7:16 doi:10.1186/1742-9994-7-16.
13. Miralles A, Carranza S (2010). Systematics and biogeography of the neotropical genus Mabuya, with special emphasis on the Amazonian skink Mabuya nigropunctata (Reptilia, Scincidae). Molecular Phylogenetics & Evolution, 54(3): 857-869.
12. Miralles A, Rivas Fuenmayor G, Bonillo C, Schargel WE, Barros T, Garcia-Pérez JE & Barrio-Amoros CL (2009). Molecular systematics of Carribean skinks of the genus Mabuya (Reptilia, Scincidae), with descriptions of two new species from Venezuela. Zoological Journal of the Linnean Society, 156: 598-616.
11. Miralles A, Chaparro JC & Harvey MB (2009). Three rare and enigmatic South American Skinks. Zootaxa, 2012: 47-68.
10. Harvey MB, Aguayo R & Miralles A (2008). Description and Distribution of Mabuya cochabambae Dunn with Comments on Bolivian Congeners (Lacertilia: Scincidae). Zootaxa, 1828: 43-56.
9. Ziegler T, David P, Miralles A, Doan Van Kien & Nguyen Quang Truong (2008). A new species of the snake genus Fimbrios from Phong Nha - Ke Bang National Park, Truong Son, central Vietnam (Squamata: Xenodermatidae). Zootaxa, 1729: 37-48.
8. Miralles A, Barrio-Amoros CL, Rivas G & Chaparro-Auza JC (2006). Speciation in the "Várzéa" flooded forest: a new Mabuya (Squamata: Scincidae) from Western Amazonia. Zootaxa, 1188: 1-22.
7. Miralles A & Ineich I (2006). Presence of gular and parietal pits by Atretium schistosum (Serpentes, Colubridae). A characteristic not only associated to psammophine snakes. Comptes Rendus Biologies 329: 180-184.
6. Miralles A (2006). A New Species of Mabuya (Reptilia, Squamata, Scincidae) from the Caribbean Island of San Andrés, with a new interpretation of nuchal scales: character of taxonomic importance. The Herpetological Journal, 16(1): 1-7
5. Miralles A, Rivas G. & Barrio-Amoros CL. (2005). Taxonomy of the genus Mabuya (Reptilia, Squamata, Scincidae) in Venezuela. Zoosystema, 27(4): 825-837.
4. Miralles A, Rivas G & Schargel WS (2005). A new species of Mabuya (Squamata, Scincidae) from the Venezuelan Andes. Zootaxa 895: 1-11.
3. Miralles A (2005). Description of a neotype for Lacertus mabouya Lacepède, 1788 (Squamata: Scincidae), with comment on the validity of this binomen. Herpetologica 61: 46-53.
2. Rivas Fuenmayor G, Ugueto G, Rivero R & Miralles A (2005). The Herpetofauna of Isla de Margarita, Venezuela: New Records and Comments. Carribean Journal of Science 41 (2): 346-351.
1. Miralles A (2004). Lepidophyma flavimaculatum (yellow-spotted night lizard). Placentophagia. Herpetological Review 35(2): 170.

Book chapters:

2. Siegel DS, Miralles A, Rheubert JL, Sever DM. (2014).
Female reproductive anatomy: Cloaca, Oviduct and sperm storage, In: Reproductive biology and phylogeny of Lizards and Tuatara, (Eds. J.L. Rheubert, D.S. Siegel DS and S.E. Strauth). Volume 10. Reproductive Biology and Phylogeny. CRC Press, Boca Raton.
1. Siegel D, Miralles A, Chabarria R, Aldridge R (2011).
Pp. 347-409. Female Reproductive Anatomy: Oviducts and Cloaca, In: Reproductive Biology and Phylogeny of Snakes, (Eds. R. D. Aldridge and D. M. Sever). Volume 9. Reproductive Biology and Phylogeny. Science Publishers, Inc., Enfield, NH.




Copyright A. Miralles - Last update : Feb 2022.