Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K–T boundary in Madagascar Angelica Crottinia,b,1, Ole Madsenc, Celine Pouxd,e,f, Axel Straußa, David R. Vieitesg, and Miguel Vencesa,2 aDivision of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, 38106 Braunschweig, Germany; bSezione di Zoologia e Citologia, Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milan, Italy; cAnimal Breeding and Genomics Centre, Wageningen University, 6700 AH Wageningen, The Netherlands; dUniversité Lille Nord de France, Campus Lille 1-Université des Sciences et Technologies de Lille, Laboratoire de Génétique et Évolution des Populations Végétales, F-59650 Villeneuve d’Ascq, France; eCentre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8198, F-59650 Villeneuve d’Ascq, France; fVertebrate Department, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium; and gMuseo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain Edited by David B. Wake, University of California, Berkeley, CA, and approved January 18, 2012 (received for review August 25, 2011) The geographic and temporal origins of Madagascar’s biota have reconstruction of molecular time-trees have started to resolve long been in the center of debate. We reconstructed a time-tree the biogeography of Madagascar, previously characterized as one including nearly all native nonflying and nonmarine vertebrate of the greatest mysteries of natural history (10, 11). For numerous clades present on the island, from DNA sequences of two single-copy Malagasy clades of amphibians, squamates, and mammals, sister- BDNF RAG1 protein-coding nuclear genes ( and ) and a set of congru- group relationships to African taxa and a Cenozoic age are now ent time constraints. Reconstructions calculated with autocorrelated well established, suggesting a predominance of Out-of-Africa over- or independent substitution rates over clades agreed in placing the – origins of the 31 included clades in Cretaceous to Cenozoic times. The seas dispersal favored by oceanic paleocurrents (11 15). However, two clades with sister groups in South America were the oldest, the exact timing of colonizations, as well as their possible clustering followed by those of a putative Asian ancestry that were significantly in particular periods, remain unstudied for many vertebrate clades older than the prevalent clades of African ancestry. No colonizations and are contentious for others (11), largely because of the use of EVOLUTION from Asia occurred after the Eocene, suggesting that dispersal and different molecular markers and time constraints. In addition, the vicariance of Asian/Indian groups were favored over a comparatively closest relatives of several other taxa are found in South America short period during, and shortly after, the separation of India and or Asia (16, 17). The temporal pattern of vertebrate colonization Madagascar. Species richness of clades correlates with their age but of Madagascar from these different source continents has not been those clades that have a large proportion of species diversity in rain- comprehensively studied to date. fi fi forests are signi cantly more species-rich. This nding suggests an Analyses of molecular data have led to great progress in un- underlying pattern of continuous speciation through time in Mada- derstanding the timing of vertebrate diversification (18, 19). Here, gascar’s vertebrates, with accelerated episodes of adaptive diversifi- cation in those clades that succeeded radiating into the rainforests. we generated a comprehensive dataset that uses the same molec- ular markers and time constraints for nearly all terrestrial and Cretaceous-Tertiary | historical biogeography | lineage diversification | freshwater vertebrate clades occurring on Madagascar and their rainforest adaptation | overseas dispersal sister taxa. The selected genes, BDNF (brain-derived neurotrophic factor) and RAG1 (recombination activating gene 1), are single- adagascar’s unique biodiversity has attracted the interest copy, protein-coding, and universal among gnathostomes. We use Mof evolutionary biologists and biogeographers for a long multiple cross-validated time constraints in a single time-tree to time. This island was part of the Gondwana supercontinent. As a obtain compatible age estimates across clades (20). Those esti- part of Indo-Madagascar, it separated from Africa 160–130 Mya. mates allow us to assess general biogeographic patterns of Mada- The breakup of Indo-Madagascar and northwards drifting of gascar’s colonization by vertebrates, for which we test whether: (i) India and the Seychelles started 88 Mya, leaving Madagascar the majority of extant vertebrate clades colonized Madagascar isolated in the Indian Ocean and without subaerial connection to – – during or after the K T boundary, as suggested by the fossil record any other landmass for the last 65 80 Myr (1). (7); (ii) colonizations followed different temporal patterns The isolation of Madagascar coincided with the end of the depending on the source continent; (iii) species richness of clades Cretaceous, a period of global mass extinction and biotic turnover, fi probably linked to a major meteorite impact marking the Creta- are related to their age in Madagascar; and (iv) clade diversi cation fl ceous–Tertiary (K–T) boundary at 65.5 Mya (2). In Madagascar, was in uenced by habitat type. the different composition of the Late Cretaceous vs. the extant vertebrate fauna led to the hypothesis of a major biotic change in deep time (3). The Cretaceous fauna included lungfishes, gars, Author contributions: D.R.V. and M.V. designed research; A.C., O.M., C.P., and D.R.V. nonranoid giant frogs, dinosaurs, and marsupial and gondwana- performed research; A.C., O.M., C.P., A.S., and M.V. analyzed data; and A.C. and M.V. – wrote the paper. therian mammals (3 8), whereas the extant vertebrate fauna is fl composed of mainly percomorph freshwater fishes, ranoid frogs, The authors declare no con ict of interest. modern squamate reptiles, lemurs, rodents, carnivores, afro- This article is a PNAS Direct Submission. therian mammals, bats, and numerous families of birds (9). Data deposition: The sequences reported in this paper have been deposited in the Gen- bank database (accession nos. JQ073048–JQ073135, JQ073138–JQ073291). The full align- Reconstructing the temporal pattern of this striking biotic ments reported in this paper have been deposited in the Dryad data repository, turnover is hampered by the almost complete lack of post-Cre- datadryad.org (http://dx.doi.org/10.5061/dryad.50r80407). taceous and pre-Pleistocene terrestrial fossil deposits. This fossil 1Present address: Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus gap presents difficulties in understanding how and when the extant Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal. clades of vertebrates colonized the island, and how their sub- 2To whom correspondence should be addressed. E-mail: [email protected]. fi sequent diversi cation took place. In recent times, explicit pa- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. leogeographic and paleoclimatic modeling associated with the 1073/pnas.1112487109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1112487109 PNAS Early Edition | 1of6 Results after the Oligocene (Fig. 2B). The dispersal of the ancestors of day Vertebrate Time-Trees Based on Congruent Time Constraints. Phy- geckos to the Mascarene Islands located east of Madagascar oc- logenetic analyses of the combined 1,747 base pairs of RAG1 curred at 22 Mya, and dispersals to the continental Seychelles, and and BDNF for 188 taxa representing nonflying and nonmarine to Asia and Africa occurred in the Oligocene and Eocene (36–28 Malagasy vertebrate clades, their known non-Malagasy sister- Mya). Dispersals to the Comoro islands west of Madagascar were groups, and a set of other vertebrate taxa, recovered most of the recovered by both analyses post-Oligocene, in agreement with fi generally accepted deep and shallow relationships among verte- favorable surface currents in this period, a pattern con rmed by brates (Fig. 1). Time-tree reconstruction with 43 selected time the cross-validations also for those Comoro-Malagasy splits used constraints was based on two approaches that either allow sub- as age constraints in the main analyses. stitution rates to vary independently over clades (ICR) or in an fl autocorrelated fashion (ACR) (Materials and Methods). The Clade Age and Rainforest Habitat In uence Species Richness. Besides the extraordinary degree of endemism at higher taxonomic levels, extremes of the 95% credibility intervals (CrIs) from the two ’ approaches were merged into a single composite CrI (21). Madagascar s biota is characterized by a high, although in- A high congruence among most of an initial set of 48 time completely known, species richness, and by a high proportion of range-restricted species that are microendemic to particular areas constraints was obtained in three cross-validation approaches of the island (9). This pattern might also be typical for other using ACR, here named CV1–CV3 (see SI Appendix for details). tropical regions, but Madagascar is a particularly well-suited In CV1 we assessed statistically the effect of removing single model region to determine the underlying patterns of biotic di- constraints on the overall