Molecular systematics and biogeography of the fanged frogs of Southeast Asia

Our analysis of parts of the mitochondrial ribosomal 12S and 16S genes from 39 populations of Southeast Asian ranid frogs confirms that the fanged frogs are a monophyletic clade. This group, properly called Limnonectes, appears to have arisen in the early Tertiary at a time when free faunal exchange was possible among Southeast Asia, Borneo, Sumatra, Java, and, probably, Sulawesi. Four species groups are tentatively identified within the clade. Part of group 1 includes species related to L. kuhlii that occur in Borneo. Another part of group 1 includes species from Malay Peninsula and Thailand that are related to L. pileata. Species group 2, L. leporina, occurs only in Borneo. Species group 3 is restricted to species distributed in Sulawesi and the Philippines. Species group 4 includes L. blythii and relatives. There is a lack of compatibility between phylogenetic hypotheses generated from molecular and morphological data sets. These differences are related, in large part, to whether some species of Limnonectes have secondarily lost fangs or whether lack of fangs represents the primitive condition.     

Taxonomic revision of shrews of the genus Crociduras from the Sunda Shelf and Sulawesi with description of two new species (Mammalia: Soricidae)

The skulls of 387 shrews of the genus Crocidura sampled in peninsular Malaysia, Sumatra, Borneo, Java and Sulawesi were submitted to principal component and stepwise discriminant analyses. These analyses helped to delineate morphological taxa in this species-rich genus of mammals. Most morphologic groups could be attributed to described species, except one taxon from Sumatra and one from Sulawesi, which are described and named as new. Most of the 21 species recognized in this paper are endemic to one major island. Although Sulawesi has never been connected to the mainland, it supports at least six species, followed by Sumatra (5–6 species), Java and the Malay Peninsula (4 spp) and Borneo (3 spp). C. monticola is apparently the only widespread species whose distribution range covers the entire Malay Archipelago except the Philippines and Sulawesi. In contrast, the continental C. fuliginosa enters only marginally into the Sunda Shelf: its southernmost record is on the Malay Peninsula. This interpretation is completely different from the classical view that C. fuliginosa is a cosmopolitan species occupying the whole of Southeast Asia. Identification keys, tables of measurements and discriminant functions provided in this work may aid in identification of the various species and subspecies of Crocidura living in the Malaya Archipelago.     

The flea genus Sigmactenus (Siphonaptera: Leptopsyllidae): three new taxa from Sulawesi, updated identification key, and distribution map for all known species and subspecies

One new species and two new subspecies of fleas are described. These are S. sulawesiensis n. sp. from North and Central Sulawesi, S. alticola pilosus n. ssp. from Central Sulawesi, and S. alticola crassinavis n. ssp. from North Sulawesi. All three of these new taxa are ectoparasites of native, endemic murine rodents. Two of the new taxa, S. sulawesiensis and S. alticola crassinavis, coexist on the same mountain, Gunung Moajat, in North Sulawesi. The related S. alticola alticola, which becomes the nominate subspecies, parasitises the murine rodent Maxomys alticola in northern Borneo (Sabah) and it is hypothesized that Sigmactenus first colonized Sulawesi as an ectoparasite of ancestral Maxomys, or perhaps Rattus, as these murines dispersed from southeast Asia to Sulawesi; 15 endemic murine rodent species belonging to these two genera are known to currently inhabit Sulawesi. An identification key and distribution map are included for all known species and subspecies of Sigmactenus. In addition to the three new taxa and S. a. alticola, these include: S. celebensis from South Sulawesi, S. timorensis from Timor, S. toxopeusi from New Guinea, and S. werneri from the Philippines (Mindanao and Negros).     

A molecular test of Huxley's line: Cyrtandra (Gesneriaceae) in Borneo and the Philippines

A biogeographic and phylogenetic study of Cyrtandra (Gesneriaceae) in the Sundaland region (Borneo and Peninsular Malaysia) and the Philippines using nuclear ribosomal (ITS) DNA sequence data reveals a major division between the Cyrtandra floras of Sundaland and the Philippines. Palawan, the most westerly of the Philippine islands, emerges as an area of mixing between these two. The Bornean element in the Cyrtandra flora of Palawan (two species in our sample) appears to result from recent (i.e. Pleistocene) dispersal from Borneo. The remaining seven species sampled from Palawan are most closely related to those from elsewhere in the Philippines. However, the Palawan clade is sister to the other Philippine taxa, suggesting an ancient (possibly Pliocene) vicariance event. Huxley's line–a zoogeographic boundary placing Palawan and Borneo together–receives some support from this study as there is evidence of recent dispersal of Bornean flora into Palawan. However, in terms of more ancient biogeographic patterning of the region, Palawan has stronger links with the other Philippine islands.     

Insular radiation of the genus Hydropsyche (Insecta,Trichoptera: Hydropsychidae) Pictet, 1834 in the Philippines and its implications for the biogeography of Southeast Asia

Aims To record and elucidate the phylogeny and biogeography of a species swarm of the genus Hydropsyche (Insecta, Trichoptera) in the Philippines. All species belong to the hamifera group. Location The Philippines and neighbouring areas. Methods A phylogenetic analysis based on variation of morphological characters of the male phallic apparatus. Results The species swarm is differentiated into three clades of different age. Conclusion Alternative dispersal and vicariance hypotheses are considered in an attempt to explain the colonization of the Philippine archipelago and the subsequent ramification of the group. The vicariance hypothesis based on the late Miocene accretion of continental fragments to the Philippines appears to be the most parsimonious. The evolution of the swarm occurred on the Philippines. Later on species dispersed to Borneo, Sulawesi and the Moluccas. The species swarm has undergone an adaptive radiation which enabled the simultaneous occurrence of species in the same streams.     

猪科的系统发育与系统地理分化

猪科动物是最为昌盛的哺乳动物之一,但它们的分类及系统发育关系却尚待解决。为此,用PCR直接测序法测定了一个红河猪(Potamochoerusporcus)、一个马来西亚野猪(Susbarbatus)以及数头欧亚野猪(Susscorfa)线粒体细胞色素b全序列1140bp。结合从GenBank中获得的其他猪科物种胞色素b序列,用邻接法和最大简约法构建了猪科物种的系统发育关系,其结果显示苏拉威西鹿猪与其他猪科物种为姐妹群的关系。非洲物种疣猪和河猪聚为一枝,而欧亚猪属物种聚为另一支。各物种在系统发育关系中的位置与它们的地理分布对应。猪属物种可以被划分为3个种组:分布于菲律宾群岛、苏拉威西岛及其邻近岛屿的猪属物种形成一个种组,包括苏拉威西岛疣猪、菲律宾疣猪和印度尼西亚疣猪;欧亚野猪种组,包括欧亚野猪和姬猪;须猪和爪哇疣猪形成一个种组。     

Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

We investigated the phylogenetic relationships and estimated the history of species diversification and character evolution in two ichthyophiid genera: Caudacaecilia and Ichthyophis. We estimated the phylogenetic relationships of 67 samples from 33 localities in Southeast Asia from 3840-bp sequences of the mitochondrial 12S rRNA, 16S rRNA, and cyt b genes using Bayesian inference, maximum likelihood, and maximum parsimony methods. The Southeast Asian samples formed a well-supported clade differentiated from a South Asian sample. The Southeast Asian clade was divided into two subclades, one containing samples from South China, Indochina, Malay Peninsula, and Java. The other consisted of samples from Borneo and the Philippines. Neither Caudacaecilia nor Ichthyophis was monophyletic, nor did samples with or without light stripes lateral to the body form clades. We found several distinct sympatric lineages and undescribed species, especially from Sundaland.     

Molecular phylogenetics of babblers (Timaliidae): revaluation of the genera Yuhina and Stachyris

The babblers (Timaliidae) form a large songbird family, which achieves its highest diversity in South-East Asia. As part of an ongoing phylogenetic investigation of this group, we focus here on the systematic position of two Asian genera, Yuhina and Stachyris , using cytochrome b , 16S and 12S sequence data. The analysis suggests that the two genera, as defined by morphological characters, are not monophyletic. The white-bellied yuhina Yuhina zantholeuca , which has been placed among the typical yuhinas by most authors, is not a babbler. The other yuhinas studied, six continental species and a species endemic to Taiwan, form a clade that includes also three species of Stachyris endemic to the Philippines. The other Stachyris are not related to this clade, and can be divided into two groups that correspond to morphological and geographical differences among the species.     

Systematics, molecular genetics and historical zoogeography of the viviparous freshwater gastropod Pseudopotamis (Cerithioidea, Pachychilidae): a relic on the Torres Strait Islands, Australia

Freshwater snails of the genus Pseudopotamis Martens, 1894 exemplify one of the most enigmatic distributional patterns among limnic organisms in Australasia. These viviparous cerithioidean gastropods are endemic to the Torres Strait Islands, located on the Sahul shelf corridor between Australia and New Guinea. The occurrence of the two constituent species is highly restricted: P. supralirata (Smith, 1887) on Prince of Wales Island, and P. semoni Martens, 1894 on Hammond Island. Long recognized erroneously as members of the heterogeneous, polyphyletic and widespread Thiaridae, morphological and molecular data presented here reveal that the taxon has to be placed within Pachychilidae, a family otherwise absent from Australia. Comparison with other South East Asian pachychilids, in particular Brotia H. Adams, 1866, Tylomelania Sarasin & Sarasin, 1897, and Jagora Köhler & Glaubrecht, 2003 suggests that Pseudopotamis is most closely related to taxa endemic to Sulawesi (Celebes), thus occurring disjunctly about 2000 km to the west of the Torres Strait. It is only with the Sulawesi pachychilids that Pseudopotamis shares its peculiar uterine brood pouch. Consequently, all pachychilid taxa east of the much-debated Wallace's line (east of Bali, Borneo and the Philippines) possess this uterine incubatory structure. In this paper the historical background of the discovery, the taxonomic history, and an evaluation of the systematic position of Pseudopotamis is provided, including molecular genetic data (genes of cytochrome c oxidase subunit I and 16S ribosomal DNA). Finally, based on the phylogenetic assignment and the recent distribution, implications for a historical biogeography are discussed utilizing a recently developed model for the palaeogeography in Australasia. According to these available data, we favour early vicariant event(s) over recent dispersal.     

Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the asian and Australian faunal zones

The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.     

A phylogeny of the Australian Sphenomorphus group (Scincidae: Squamata) and the phylogenetic placement of the crocodile skinks (Tribolonotus): Bayesian approaches to assessing congruence and obtaining confidence in maximum likelihood inferred relationships

Australian scincid lizards are a diverse squamate assemblage ( approximately 385 species), divided among three major clades (Egernia, Eugongylus, and Sphenomorphus groups). The Sphenomorphus group is the largest, comprising 61% of the Australian scincid fauna. Phylogenetic relationships within the Australian Sphenomorphus group and the phylogenetic placement of Tribolonotus are inferred using mtDNA (12S and 16S rRNA genes, ND4 protein-coding gene, and associated tRNA genes; 2185bp total). These data were analyzed separately (structural RNA vs protein-coding partitions) and combined using maximum likelihood. Confidence in inferred clades was assessed using non-parametric bootstrapping and Bayesian analysis. Analysis of the combined data strongly supports Sphenomorphus group (as well as the Australian subgroup) monophyly. Notoscincus is strongly placed as the sister taxon of the remaining Australian Sphenomorphus group taxa, with this more exclusive clade being divided into two major groups (one restricted to mesic eastern Australia and the other continent wide). The speciose Australian "Eulamprus" and "Glaphyromorphus" are both polyphyletic. All remaining non-Sphenomorphus group lygosomine skinks strongly form a clade, with Tribolonotus placed as the sister taxon of the Australian Egernia group.     

Biogeographical implications of mitochondrial DNA variation in the Bockadam snake (Cerberus rynchops, Serpentes: Homalopsinae) in Southeast Asia

Aim The biogeography of Southeast Asia has been greatly affected by Pleistocene sea‐level changes and the consequent alteration of coastline and land mass configurations. We investigated the effect of these Pleistocene events on genetic divergence in Cerberus rynchops, the Bockdam, an Asian water snake (Homalopsinae) associated with tidal mudflats and coastal mangrove forests in Southeast Asia. Location Localities for the Cerberus included the Andaman sea coast of Thailand, Sumatra, and Borneo (Sunda Shelf localities), the Philippines and Sulawesi, and from northern Australia (Sahul Shelf). Methods We analysed mtDNA sequences (12 s, 16 s, and cyt b) from seven C. rynchops populations (twenty‐six specimens), from two specimens of Cerberus microlepis (a freshwater species known only from Lake Buhi in the Philippines), and from one Enhydris enhyris (Schneider), another homalopsine used as an outgroup. Results We found a strong correlation between genetic divergence and geographical distance (r = 0.922, P < 0.001) and the biogeographic history of the region. Cerberus rynchops populations from the Sunda Shelf localities, the Philippines, Sulawesi and C. microlepis from the Philippines were genetically similar (mean divergence = 2.1%, range = 0.7–2.8%) compared to the C. rynchops population from northern Australia (mean divergence from all other Cerberus populations = 6.6%, range = 6.0–7.3%). This divergence was comparable to that observed between the E. enhydris outgroup and all Cerberus populations (mean distance = 7.3%, range = 6.8–8.6%). Main conclusions These findings suggest a relatively high degree of movement and gene flow among Sunda Shelf localities, the Philippines, and Sulawesi (biogeographic region west of Weber’s Line) and isolation of the northern Australian (Sunda Shelf) Cerberus. Taxa will be differentially affected by these Pleistocene sea level changes dependent on their physiology and ecology. We discuss how the dispersal of the coastal, saltwater tolerant C. rynchops would have been affected by changing configurations of Pleistocene coastlines and the implications of these results for the systematics of Cerberus.     

Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids

Aim To test the hypothesis that continental drift drives diversification of organisms through vicariance, we selected a group of primitive arachnids which originated before the break‐up of Pangaea and currently inhabits all major landmasses with the exception of Antarctica, but lacks the ability to disperse across oceanic barriers. Location Major continental temperate to tropical landmasses (North America, South America, Eurasia, Africa, Australia) and continental islands (Bioko, Borneo, Japan, Java, New Caledonia, New Guinea, New Zealand, Sri Lanka, Sulawesi, Sumatra). Methods Five kb of sequence data from five gene regions for more than 100 cyphophthalmid exemplars were analysed phylogenetically using different methods, including direct optimization under parsimony and maximum likelihood under a broad set of analytical parameters. We also used geological calibration points to estimate gross phylogenetic time divergences. Results Our analyses show that all families except the Laurasian Sironidae are monophyletic and adhere to clear biogeographical patterns. Pettalidae is restricted to temperate Gondwana, Neogoveidae to tropical Gondwana, Stylocellidae to Southeast Asia, and Troglosironidae to New Caledonia. Relationships between the families inhabiting these landmasses indicate that New Caledonia is related to tropical Gondwana instead of to the Australian portion of temperate Gondwana. The results also concur with a Gondwanan origin of Florida, as supported by modern geological data. Main conclusions By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats, but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted. Our results strongly support the presence of a circum‐Antarctic clade of formerly temperate Gondwanan species, a clade restricted to tropical Gondwana and a Southeast Asian clade that originated from a series of early Gondwanan terranes that rifted off northwards from the Devonian to the Triassic and accreted to tropical Laurasia. The relationships among the Laurasian species remain more obscure.     

Cladistic analysis of the fire ants of the Solenopsis saevissima species-group (Hymenoptera: Formicidae)

Results are presented from a phylogenetic study of the fire ants comprising the Solenopsis saevissima species-group (Hymenoptera: Formicidae). Six most-parsimonious trees were identified following a cladistic analysis utilizing 18 taxa and 36 morphological characters derived from three castes and two developmental stages. A strict consensus tree recovered the following relationships: ( S. daguerrei (( S. electra , S. pusilignis ) ( S. saevissima ( S. pythia ( S. interrupta , S. 'undescribed species' , S. weyrauchi ( S. richteri , S. invicta ( S. megergates ( S. quinquecuspis , S. macdonaghi )))))))). This phylogenetic hypothesis implies trends in fire ant evolution towards both polygyny (multiple egg-laying queens per colony) and large major worker size. The phylogeny also provides a test of Emery's Rule, which is not supported in its strictest sense because the social parasite S. daguerrei is not the sister species to its host species. A modified version of Emery's Rule is supported, because the social parasite is the sister species to a larger clade containing its hosts, as well as nonhosts.     

Morphological and genetic discordance in two species of Bornean Leptobrachium (Amphibia, Anura, Megophryidae)

Recent phylogenetic studies of Southeast Asian megophryid Leptobrachium, while clarifying (1) distinct specific status of three Philippine populations and (2) high genetic diversities within Bornean Leptobrachium montanum, posed two questions, (1) relationships and divergence histories of two Philippine species and Bornean Leptobrachium gunungense, and (2) possible discordance between phylogenetically and morphologically defined lineages. In order to solve these questions, and especially reviewing current taxonomy of Bornean species, we estimated the phylogenetic relationships of endemic Bornean species together with their putative relatives from Philippines and Sumatra, using 2451 bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA genes. With respect to Leptobrachium hasseltii and Leptobrachium chapaense, lineages from Borneo, Philippines, and Sumatra formed a monophyletic group with Leptobrachium lumadorum from Mindanao as the basal clade, while two other Philippine species from Palawan and Mindoro formed a clade and nested in Bornean lineages. Sister species relationship of the two Philippine species and L. gunungense is not supported, rejecting the hypothesis of Philippine origin of L. gunungense. Phylogeny does not conform to morphological variation, and the topotypic L. montanum and one lineage of Leptobrachium abbotti are genetically very close despite their clear difference in ventral color pattern. Furthermore, each of these species forms a paraphyletic group and contains several lineages, each of which is a candidate of good species. These results clearly indicate that current taxonomy of Bornean species based on several morphological characteristics requires complete revision. Detailed studies on adult and larval morphology, as well as acoustic characteristics, are necessary to evaluate the taxonomic status of all lineages recovered.     

Systematics and biogeography of Indo-Pacific ground-doves

Ground-doves represent an insular bird radiation distributed across the Indo-Pacific. The radiation comprises sixteen extant species, two species believed to be extinct and six species known to be extinct. In the present study, we present a molecular phylogeny for all sixteen extant species, based on two mitochondrial markers. We demonstrate that the Gallicolumba as currently circumscribed is not monophyletic and recommend reinstalling the name Alopecoenas for a monophyletic radiation comprising ten extant species, distributed in New Guinea, the Lesser Sundas and Oceania. Gallicolumba remains the name for six species confined to New Guinea the Philippines and Sulawesi. Although our phylogenetic analyses fail to support a single origin for the remaining Gallicolumba species, we suspect that the addition of nuclear sequence data may alter this result. Because a number of ground-dove taxa have gone extinct, it is difficult to assess biogeographical patterns. However, the Alopecoenas clade has clearly colonized many remote oceanic islands rather recently, with several significant water crossings. The Gallicolumba radiation(s), on the other hand, is significantly older and it is possible that diversification within that group may in part have been shaped by plate tectonics and corresponding re-arrangements of land masses within the Philippine and Sulawesi region.     

Origin and diversification of Philippine bulbuls

We examine the origin and diversification of Philippine bulbuls using a phylogenetic framework. Maximum likelihood and Bayesian methods are used to construct trees from DNA sequences of two mitochondrial and two nuclear genes obtained from 11 Philippine bulbul species as well as 32 other Asian and African taxa. The study finds eight independent colonization events of bulbuls to the Philippines, including one clade comprising Philippine members of the genus Ixos that underwent extensive diversification within the archipelago. Each Philippine clade of bulbuls invaded either the Palawan region or the oceanic islands of the Philippines, but not both. Genetic data reveal at least five lineages that warrant recognition as full species. This study underscores how Philippine avian diversity is currently underestimated and highlights the need for further phylogenetic studies in other Philippine bird groups.     

Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis)

We studied the mitochondrial DNA (mtDNA) polymorphism of 304 Macaca fascicularis fascicularis (M. f. fascicularis) individuals, representative of 4 cynomolgus macaque populations (Indochina, Indonesia, Philippines, and Mauritius). By sequencing a 590-bp fragment in the hypervariable II region of the D-loop region, we defined 70 haplotypes. The homologous region was also characterized in 22 Chinese Macaca mulatta and 2 Macaca sylvanus. The phylogenetic analysis confirms the monophyly of M. f. fascicularis and defines 2 haplotype groups inside the M. f. fascicularis clade: one "insular," encompassing 6 Philippines, 2 Mauritius, and 31 Indonesian haplotypes, the other "continental" that contains all Indochinese and 6 Indonesian haplotypes. Continental and insular group divergence time was estimated to be approximately 10(6) years before present (BP). Among Indonesian haplotypes, some have a continental origin. This suggests either direct migration from mainland to Indonesia or that remnant lineages from an ancient population genetically close to the mainland (i.e., in the Sunda Shelf, <550 000 years BP) were subsequently brought southward to Indonesia. The low nucleotide diversity in the Philippines population suggests a bottleneck following colonization by Indonesian individuals, around 110 000 years BP. mtDNA and further observations of nuclear genetic data corroborate the mixed origin (Indonesian/continental) hypothesis of Mauritius individuals and a population bottleneck.     

Repeated evolution of carnivory among Indo‐Australian rodents

Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo‐Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.     

Evolution in a tropical archipelago: comparative phylogeography of Philippine fauna and flora reveals complex patterns of colonization and diversification

An unusual geological setting and a high level of endemism makes the Philippine islands of great interest to biogeography. These islands lie adjacent to the continental (Sunda) shelf, yet the majority of the islands have never been directly attached to the mainland. Existing hypotheses of colonization and diversification processes have been tested across multiple taxa, but only in ahistorical contexts. We present explicit phylogenetic predictions based on these hypotheses, and then test them using new molecular datasets for four Philippine birds. Two proposed colonization routes to the northern Philippines (from mainland Asia and Palawan) are difficult to differentiate from each other, except on the basis of outgroup, as are the two routes from the south (Sulu archipelago and Sulawesi). We find unique colonization and diversification patterns for each taxon. These results contrast with expectations from Pleistocene geography, with Luzon and Mindoro indistinguishable genetically, and Negros and Panay are often nonsister taxa. Combining these data with a literature search for studies addressing these patterns, Philippine organisms shows some evidence for each proposed colonization route but the greatest support is for the two routes from Borneo. Many taxa exhibit multiple colonization events using several of these routes, contrasting with past assumptions of single colonization events. Island‐by‐island differentiation within the Philippines follows, with patterns reflecting colonization patterns rather than Pleistocene geography, particularly for highland species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 620–639.