Biological Journal of the Linnean Society, 2003, 80, 699–715. With 6 figures © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 699–715 699 Blackwell Science, LtdOxford, UKBIJBiological Journal of the Linnean Society0024-4066The Linnean Society of London, 2003? 2003 80? 699715 Original Article DIVERSIFICATION OF PHILIPPINE RODENTS S. J. STEPPAN ET AL . *Corresponding author. E-mail: steppan@bio.fsu.edu Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago SCOTT J. STEPPAN 1 *, CHRISTOPHER ZAWADZKI 1 and LAWRENCE R. HEANEY 2 1 Department of Biological Science, Florida State University, Tallahassee, FL 32306–1100, USA 2 Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA Received 21 January 2003; accepted for publication 22 May 2003 We analysed the phylogenetic relationships of ten of the 13 known species of the genus Apomys using DNA sequences from cytochrome b. Apomys, endemic to oceanic portions of the Philippine archipelago, diversified during the Pliocene as these oceanic islands arose de novo. Several of the speciation events probably took place on Luzon or Mindanao, the two largest, oldest, and most topographically complex islands. Only one speciation event is associated with vicar- iance due to Pleistocene sea-level fluctuation, and a Pleistocene diversification model in which isolation is driven by sea-level changes is inconsistent with the data. Tectonic vicariance is nearly absent from the Philippines, in which tectonic coalescence plays a significant role. Most speciation events (about two-thirds) are associated with dispersal to newly developed oceanic islands. The data imply that the species have persisted for long periods, measured in mil- lions of years after their origins; further implications therefore are that faunal turnover is very slow, and persistence over geological time spans is more prominent than repeated colonization and extinction. Neither the equilibrium nor the vicariance model of biogeography adequately encompasses these results; a model incorporating colonization, extinction, and speciation is necessary and must incorporate long-term persistence to accommodate our observations. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 699–715. ADDITIONAL KEYWORDS: biogeographical models – cytochrome b – dispersal – island biogeography – Pleistocene – speciation – vicariance. INTRODUCTION The process of diversification - the increase in number of species within a given lineage over time - lies at the root of biology, and has a long history of investigation (Heaney & Vermeij, in press). Nevertheless, the num- ber of case studies in which the history and processes of diversification is well documented is small, even among vertebrates (e.g. Otte & Endler, 1989; Ricklefs & Schluter, 1993; Grant, 1998; Magurran & May, 1999). Further, such studies have not usually figured in analysis of the dynamics of species-richness pat- terns under either of the current dominant models, the equilibrium model of island biogeography and vicariance biogeography (Whittaker, 1998; Heaney, 2000; Lomolino, 2000). Much recent progress on some issues involving diversification has been made under the rubric of phylogeography (e.g. Riddle, 1995, 1996; Avise, 2000; Arbogast & Kenagy, 2001), but most such studies deal with single species, not extensive radia- tions, and we know of only two that have been placed in the context of long-term dynamics of patterns of insular species richness (Moritz et al., 2000; Ricklefs & Bermingham, 2001). Here we test hypotheses of speciation and explore patterns of diversification in the Philippine islands using a molecular phylogeny of an endemic rodent clade. The Philippine Islands, comprising c. 7000 islands ranging up to 100 000 km 2 , represent a natural the- atre in which to investigate such issues. With the exception of one small set (the Palawan group), all of the islands are oceanic in origin, having emerged because of a complex but now well-documented set of tectonic events (Hall, 1996, 1998, 2002). Periods of lowered sea level during the many Pleistocene ‘ice ages’ caused some sets of current islands to coalesce Downloaded from https://academic.oup.com/biolinnean/article/80/4/699/2636499 by guest on 01 November 2022