Professor Davide Pisani

BSC(Parma), PhD(Bristol)

  • BS8 1TQ

20022020

Research output per year

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Research Output

  • 77 Article (Academic Journal)
  • 4 Chapter in a book
  • 3 Comment/debate (Academic Journal)
2020

A Cambrian–Ordovician terrestrialization of arachnids

Lozano-Fernandez, J., Tanner, A., Puttick, M. N., Vinther, J., Edgecombe, GD. & Pisani, D., 11 Mar 2020, In : Frontiers in Genetics.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
39 Downloads (Pure)

A draft genome sequence of the elusive giant squid, Architeuthis dux

da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R. & Gilbert, M. T. P., 16 Jan 2020, In : GigaScience. 9, 1, 12 p., giz152.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
48 Downloads (Pure)
Open Access
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50 Downloads (Pure)
1 Downloads (Pure)

Performance of a priori and a posteriori calibration strategies in divergence time estimation

Beavan, A. J. S., Donoghue, P. C. J., Beaumont, M. A. & Pisani, D., 18 May 2020, (Accepted/In press) In : Genome Biology and Evolution. evaa105.

Research output: Contribution to journalArticle (Academic Journal)

Spectral Diversification and Trans-Species Allelic Polymorphism during the Land-to-Sea Transition in Snakes

Simões, B. F., Gower, D. J., Rasmussen, A., Sarker, M., Fry, G. C., Casewell, N. R., Harrison, R., Hart, N., Partridge, J. C., Hunt, D., Chang, B., Pisani, D. & Sanders, K., 28 May 2020, In : Current Biology. 30, p. 1-8 13 p.

Research output: Contribution to journalArticle (Academic Journal)

2019

Author Correction: Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida (Nature Communications, (2019), 10, 1, (2295), 10.1038/s41467-019-10244-7)

Lozano-Fernandez, J., Tanner, A. R., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G. D. & Pisani, D., 1 Dec 2019, In : Nature Communications. 10, 1, 1 p., 4534 (2019).

Research output: Contribution to journalComment/debate (Academic Journal)

Open Access
File
59 Downloads (Pure)

Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan

Zhao, Y., Vinther, J., Parry, L., Wei, F., Green, E., Pisani, D., Hou, X., Edgecombe, G. D. & Cong, P., 1 Apr 2019, In : Current Biology. 29, 7, p. 1112-1125.e2 14 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
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10 Citations (Scopus)
30 Downloads (Pure)

Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks

Howard, R., Edgecombe, G. D., Legg, D., Pisani, D. & Lozano-Fernandez, J., 1 Mar 2019, In : Organisms Diversity and Evolution. 19, 1, p. 71-86 16 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
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6 Citations (Scopus)
176 Downloads (Pure)

Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics

Siu-Ting, K., Torres-Sánchez, M., San Mauro, D., Wilcockson, D., Wilkinson, M., Pisani, D., O'Connell, M. J. & Creevey, C. J., Jun 2019, In : Molecular Biology and Evolution. 36, 6, p. 1344-1356 13 p., msz067.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
3 Citations (Scopus)
104 Downloads (Pure)

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Lozano-Fernandez, J., Tanner, A., Giacomelli, M., Carton, R., Vinther, J., Edgecombe, G. D. & Pisani, D., 24 May 2019, In : Nature Communications. 10, 1, 2295.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
11 Citations (Scopus)
196 Downloads (Pure)

Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling

Lozano-Fernandez, J., Giacomelli, M., Fleming, J. F., Chen, A., Vinther, J., Thomsen, P. F., Glenner, H., Palero, F., Legg, D. A., Iliffe, T. M., Pisani, D. & Olesen, J., 4 Jul 2019, In : Genome Biology and Evolution. 11, 8, p. 2055-2070 16 p., evz097.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
9 Citations (Scopus)
93 Downloads (Pure)

Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

Puttick, M. N., O'Reilly, J. E., Pisani, D. & Donoghue, P. C. J., Jan 2019, In : Palaeontology. 62, 1, p. 1-17 17 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
165 Downloads (Pure)

The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates

Püschel, H., O'Reilly, J., Pisani, D. & Donoghue, P., 21 Aug 2019, In : Palaeontology. 17 p.

Research output: Contribution to journalArticle (Academic Journal)

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

Pett, W., Adamski, M., Adamska, M., Warren, F., Eitel, M., Pisani, D. & Wörheide, G., Apr 2019, In : Molecular Biology and Evolution. 36, 4, p. 643-649 7 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
12 Citations (Scopus)
95 Downloads (Pure)
2018

Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al.

O'Reilly, J. E., Puttick, M. N., Pisani, D. & Donoghue, P. C. J., 1 Jul 2018, In : Palaeontology. 61, 4, p. 631-635 5 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
9 Citations (Scopus)
205 Downloads (Pure)

Homeobox Gene Duplication and Divergence in Arachnids

Lozano-Fernandez, J., Leite, D., Baudouin-Gonzalez, L., Iwasaki-Yokozawa, S., Turetzek, N., Akiyama-Oda, Y., Prpic, N-M., Pisani, D., Hiroki, O., Sharma, P. & McGregor, A., Sep 2018, In : Molecular Biology and Evolution. 35, 9, p. 2240-2253 14 p., msy125.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
16 Citations (Scopus)
156 Downloads (Pure)

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

Betts, H. C., Puttick, M. N., Clark, J. W., Williams, T. A., Donoghue, P. C. J. & Pisani, D., Oct 2018, In : Nature Ecology and Evolution. 2, 10, p. 1556-1562 7 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
58 Citations (Scopus)
311 Downloads (Pure)

Molecular palaeontology illuminates the evolution of ecdysozoan vision

Fleming, J. F., Kristensen, R. M., Sørensen, M. V., Park, T. Y. S., Arakawa, K., Blaxter, M., Rebecchi, L., Guidetti, R., Williams, T. A., Roberts, N. W., Vinther, J. & Pisani, D., 5 Dec 2018, In : Proceedings of the Royal Society B: Biological Sciences. 285, 1892, 9 p., 20182180.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
237 Downloads (Pure)

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

Puttick, M., Morris, J. L., Williams, T., Cox, C. J., Edwards, D., Kenrick, P., Pressel, S., Wellman, C. H., Harald, S., Pisani, D. & Donoghue, P., 5 Mar 2018, In : Current Biology. 28, 5, p. 733-745.e2 16 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
107 Citations (Scopus)
281 Downloads (Pure)

Well-annotated microRNAomes do not evidence pervasive miRNA loss

Tarver, J., Taylor, R., Puttick, M., Lloyd, G., Pett, W., Fromm, B., Schirrmeister, B., Pisani, D., Peterson, K. J. & Donoghue, P., 18 May 2018, In : Genome Biology and Evolution. 10, 6, p. 1457-1470

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
8 Citations (Scopus)
163 Downloads (Pure)
2017

Early photosynthetic eukaryotes inhabited low salinity habitats

Sanchez-Baracaldo, P., Raven, J., Pisani, D. & Knoll, A., 12 Sep 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 37, p. E7737-E7745 9 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
74 Citations (Scopus)
415 Downloads (Pure)

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G. & Pisani, D., 18 Dec 2017, In : Current Biology. 27, 24, p. 3864-3870.e4 11 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
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84 Citations (Scopus)
335 Downloads (Pure)

Model choice requires biological insight when studying the ancestral habitat of photosynthetic eukaryotes

Sánchez-Baracaldo, P., Bianchini, G., Huelsenbeck, J. P., Raven, J. A., Pisani, D. & Knoll, A. H., 12 Dec 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 50, p. E10608-E106099

Research output: Contribution to journalComment/debate (Academic Journal)

3 Citations (Scopus)

Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution

Tanner, A., Fuchs, D., winkelmann, I. E., Gilbert, M. T. P., Pankey, S., Ribeiro, A. M., Kocot, K., Halanych, K., Oakley, T. H., Fonseca, R. R. D., Pisani, D. & Vinther, J., Mar 2017, In : Proceedings of the Royal Society B: Biological Sciences. 284, 1850, 7 p., 20162818.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
257 Downloads (Pure)

Parsimony and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: A response to Brown et al.

Puttick, M. N., O’Reilly, J. E., Oakley, D., Tanner, A. R., Fleming, J. F., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L. A., Tarver, J. E., Pisani, D. & Donoghue, P. C. J., 11 Oct 2017, In : Proceedings of the Royal Society B: Biological Sciences. 284, 1864, 3 p., 20171636.

Research output: Contribution to journalComment/debate (Academic Journal)

Open Access
File
11 Citations (Scopus)
220 Downloads (Pure)

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

O'Reilly, J., Puttick, M., Pisani, D. & Donoghue, P., 31 Oct 2017, In : Palaeontology. 14 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
25 Citations (Scopus)
250 Downloads (Pure)

RelTime rates collapse to a strict clock when estimating the timeline of animal diversification

Lozano-Fernandez, J., dos Reis, M., Donoghue, P. & Pisani, D., 1 May 2017, In : Genome Biology and Evolution. 9, 5, p. 1320-1328 9 p., evx079.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
14 Citations (Scopus)
201 Downloads (Pure)

Uncertain-tree: Discriminating among competing approaches to the phylogenetic analysis of phenotype data

Puttick, M., O'Reilly, J., Tanner, A., Fleming, J., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L., Tarver, J., Pisani, D. & Donoghue, P., 11 Jan 2017, In : Proceedings of the Royal Society B: Biological Sciences. 284, 1846, 9 p., 20162290.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
58 Citations (Scopus)
220 Downloads (Pure)
2016

A molecular palaeobiological exploration of arthropod terrestrialisation

Lozano-Fernandez, J., Carton, R., Tanner, A., Puttick, M. N., Blaxter, M., Vinther, J., Olesen, J., Giribet, G., Edgecombe, G. D. & Pisani, D., 19 Jul 2016, In : Philosophical Transactions B: Biological Sciences. 371, 1699, 12 p., 20150133.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
51 Citations (Scopus)
245 Downloads (Pure)

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

O'Reilly, J., Puttick, M. N., Parry, L. A., Tanner, A., Tarver, J. E., Fleming, J., Pisani, D. & Donoghue, P. C. J., Apr 2016, In : Biology Letters. 12, 4, 5 p., 20160081.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
89 Citations (Scopus)
260 Downloads (Pure)

Reply to Halanych et al. Ctenophore misplacement is corroborated by independent datasets

Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N. & Wörheide, G., 23 Feb 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 8, p. E948-949 2 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
9 Citations (Scopus)
219 Downloads (Pure)

The Cambrian Explosion: A Molecular Paleobiological Overview

Parry, L. & Pisani, D., 21 Apr 2016, Encyclopedia of Evolutionary Biology. Kliman, R. (ed.). Oxford: Amsterdam:Elsevier, p. 246-253 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter in a book

The evolution of olfactory gene families in Drosophila and the genomic basis of chemical-ecological adaptation in Drosophila suzukii

Ramasamy, S., Ometto, L., Crava, C. M., Revadi, S., Kaur, R., Horner, D., Pisani, D., Dekker, T., Anfora, G. & Rota-Stabelli, O., Aug 2016, In : Genome Biology and Evolution. 8, 8, p. 2297-2311 15 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
24 Citations (Scopus)
201 Downloads (Pure)

The interrelationships of placental mammals and the limits of phylogenetic inference

Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R., Parker, S., O'Reilly, J., King, B. L., O'Connell, M. J., Asher, R. J., Warnow, T., Peterson, K. J., Donoghue, P. C. J. & Pisani, D., Feb 2016, In : Genome Biology and Evolution. 8, 2, p. 330-344 15 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
84 Citations (Scopus)
366 Downloads (Pure)
2015

Anhydrobiosis and freezing-tolerance: adaptations that facilitate the establishment of Panagrolaimus nematodes in polar habitats

McGill, L. M., Shannon, A. J., Pisani, D., Félix, M-A., Ramløv, H., Dix, I., Wharton, D. A. & Burnell, A. M., 2015, In : PLoS ONE. 10, 3, p. e0116084

Research output: Contribution to journalArticle (Academic Journal)

16 Citations (Scopus)

Animal Evolution: Only Rocks Can Set the Clock

Pisani, D. & Liu, A. G. S. C., 16 Nov 2015, In : Current Biology. 25, 22, p. R1079-R1081 3 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
5 Citations (Scopus)
211 Downloads (Pure)

Biogeography of worm lizards (Amphisbaenia) driven by end-Cretaceous mass extinction

Longrich, N. R., Vinther, J., Alexander Pyron, R., Pisani, D. & Gauthier, J. A., 7 May 2015, In : Proceedings of the Royal Society B: Biological Sciences. 282, 1806

Research output: Contribution to journalArticle (Academic Journal)

33 Citations (Scopus)

Concatabominations: identifying unstable taxa in morphological phylogenetics using a heuristic extension to safe taxonomic reduction

Siu-Ting, K., Pisani, D., Creevey, C. J. & Wilkinson, M., Jan 2015, In : Systematic Biology. 64, 1, p. 137-43 7 p.

Research output: Contribution to journalArticle (Academic Journal)

8 Citations (Scopus)

Genomic data do not support comb jellies as the sister group to all other animals

Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N. & Wörheide, G., Dec 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 50, p. 15402-15407 6 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
149 Citations (Scopus)
295 Downloads (Pure)

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Akanni, W. A., Siu-Ting, K., Creevey, C. J., McInerney, J. O., Wilkinson, M., Foster, P. G. & Pisani, D., 26 Sep 2015, In : Philosophical Transactions B: Biological Sciences. 370, 1678

Research output: Contribution to journalArticle (Academic Journal)

14 Citations (Scopus)

Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics

Akanni, W. A., Wilkinson, M., Creevey, C. J., Foster, P. G. & Pisani, D., Aug 2015, In : Royal Society Open Science. 2, 9 p., 140436.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
14 Citations (Scopus)
409 Downloads (Pure)

The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data

McInerney, J., Pisani, D. & O'Connell, M. J., 26 Sep 2015, In : Philosophical Transactions B: Biological Sciences. 370, 1678

Research output: Contribution to journalArticle (Academic Journal)

6 Citations (Scopus)
2014

A pluralistic account of homology: adapting the models to the data

Haggerty, L. S., Jachiet, P-A., Hanage, W. P., Fitzpatrick, D. A., Lopez, P., O'Connell, M. J., Pisani, D., Wilkinson, M., Bapteste, E. & McInerney, J. O., Mar 2014, In : Molecular Biology and Evolution. 31, 3, p. 501-16 16 p.

Research output: Contribution to journalArticle (Academic Journal)

27 Citations (Scopus)

Evolutionary relationships of the critically endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses

Siu-Ting, K., Gower, D. J., Pisani, D., Kassahun, R., Gebresenbet, F., Menegon, M., Mengistu, A. A., Saber, S. A., de Sá, R., Wilkinson, M. & Loader, S. P., 2014, In : BMC Evolutionary Biology. 14, 1, p. 44

Research output: Contribution to journalArticle (Academic Journal)

7 Citations (Scopus)

L.U.St: a tool for approximated maximum likelihood supertree reconstruction

Akanni, W. A., Creevey, C. J., Wilkinson, M. & Pisani, D., 2014, In : BMC Bioinformatics. 15, p. 183

Research output: Contribution to journalArticle (Academic Journal)

9 Citations (Scopus)

The comb jelly opsins and the origins of animal phototransduction

Feuda, R., Rota-Stabelli, O., Oakley, T. H. & Pisani, D., Aug 2014, In : Genome Biology and Evolution. 6, 8, p. 1964-71 8 p.

Research output: Contribution to journalArticle (Academic Journal)

34 Citations (Scopus)

The hybrid nature of the Eukaryota and a consilient view of life on Earth

McInerney, J. O., O'Connell, M. J. & Pisani, D., Jun 2014, In : Nature Reviews Microbiology. 12, 6, p. 449-455 7 p.

Research output: Contribution to journalArticle (Academic Journal)

76 Citations (Scopus)

The shape of modern tree reconstruction methods

Holton, T. A., Wilkinson, M. & Pisani, D., May 2014, In : Systematic Biology. 63, 3, p. 436-41 6 p.

Research output: Contribution to journalArticle (Academic Journal)

8 Citations (Scopus)

Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Field, D. J., Gauthier, J. A., King, B. L., Pisani, D., Lyson, T. R. & Peterson, K. J., 7 May 2014, In : Evolution and Development. 16, 4, p. 189-96 8 p.

Research output: Contribution to journalArticle (Academic Journal)

59 Citations (Scopus)