Differentiation of golden-ringed dragonfly Anotogaster sieboldii (Selys, 1854) (Cordulegastridae: Odonata) in the insular East Asia revealed by the mitochondrial gene genealogy with taxonomic implications

Molecular phylogeographical analyses of Anotogaster sieboldii (Selys, 1854) were conducted to reveal the differentiation process of insular populations. The gene genealogy based on 845 bp of the mitochondrial genes (cytochrome oxidase subunit I and subunit II) indicated that A. sieboldii includes two deeply separated lineages. These two major lineages seem to have differentiated in Miocene before the formation of the insular East Asia. One lineage includes three inner clades that correspond to the populations of northern area (the Japanese main islands, Korean Peninsula, Yakushima), Amamioshima and Okinawajima. Populations of Central Ryukyu, including Amamioshima and Okinawajima, might have been divided from the northern populations in early Pleistocene. The other major lineage includes populations of the Yaeyama Group, Taiwan and East China. The former two populations were reconstructed as a reciprocal monophyletic group. Populations of Taiwan and Yaeyama Groups would have been separated from the continental ones in Pleistocene. These two highly divergent lineages should be recognized as distinct species. Furthermore, the mitochondrial lineages revealed six genetically distinct and geographically isolated assemblages: (1) northern populations, (2) Amamioshima, (3) Okinawajima, (4) Yaeyama Group, (5) Taiwan and (6) East China.     

Phylogeny and phylogeography of the genus Geothelphusa (Crustacea: Decapoda, Brachyura, Potamidae) in southwestern Taiwan based on two mitochondrial genes

Eleven species of Geothelphusa have been reported from southwestern Taiwan (Tainan, Kaohsiung and the northern part of Pingtung counties): G. albogilva Shy, Ng, and Yu, 1994; G. ancylophallus Shy, Ng, and Yu, 1994; G. caesia Shy, Ng, and Yu, 1994; G. lili Chen, Cheng, and Shy, 2005; G. nanhsi Shy, Ng, and Yu, 1994; G. neipu Chen, Cheng, and Shy, 1998; G. olea Shy, Ng, and Yu, 1994; G. pingtung Tan and Liu, 1998; G. shernshan Chen, Cheng, and Shy, 2005; G. tsayae Shy, Ng, and Yu, 1994 and G. wutai Shy, Ng, and Yu, 1994. Comparisons of DNA sequences encoding parts of the mitochondrial large subunit (16S) rRNA and cytochrome oxidase subunit I (COI) genes revealed three major clades, of which one is the species G. ancylophallus, and the other two are species groups here referred to as the G. olea and G. pingtung clades. Geothelphusa ancylophallus is geographically restricted and adapted to an ecologically challenging habitat with an unstable water supply and uneven topology. The G. olea clade (G. olea, G. caesia, G. nanhsi, G. tsayae, and G. wutai) is widely distributed throughout central-western and southwestern Taiwan. The G. pingtung clade (G. pingtung, G. neipu and G. shernshan) is confined to southwestern Taiwan between the previously defined southernmost clades of G. tawu, G. albogilva, and G. ferruginea, and the G. olea clade to the north. It includes an isolated population on distant Chaishan Mountain near Taiwan Strait, which probably dispersed from the peripheral hills of the Central Range during the early Pleistocene. The available genetic evidence indicates that the differential coloration observed in members of the G. olea and G. pingtung clades is not reflected in mtDNA, appears to be dependent on environmental conditions, food, etc., and has little value as a taxonomic character. Possible geological events and climatic factors responsible for the historic isolation of the different freshwater crab clades in southwestern Taiwan are discussed in detail.     

Genetic distance between Nasutitermes takasagoensis (Isoptera: Termitidae) populations in Taiwan and the Yaeyama Islands, analyzed by amplified fragment length polymorphism markers

Dispersal ability and degree of inbreeding in a population can indirectly be assessed using genetic markers. It has been suggested that winged termites are not able to fly distances greater than several hundred meters. Using the amplified fragment length polymorphism (AFLP) technique, we previously analyzed the population substructure of Nasutitermes takasagoensis in the Yaeyama Islands, southern Japan. We found that there is moderate subpopulation structure based on the AFLP data. Moreover, the relatively low G_st and genetic distances among insular populations suggest that there is a possibility that winged termites are able to fly over distances of several kilometers. To learn more about this, in the present study, we compared new samples collected from the Hengchuen Peninsula in southern Taiwan with samples previously collected from the Yaeyama Islands. Using the samples collected in Taiwan, genetic distance was calculated against samples from six of the Yaeyama Islands. Genetic diversity, average heterozygosity, percentage of polymorphic loci, G_st and gene flow (Nm) were calculated. A total of 155 AFLP fragments were obtained for three primer combinations used, with 8 (5%) polymorphic bands. Genetic distance between the populations of Taiwan and the rest of the islands was greater than the genetic distance among the Yaeyama Islands. Although previous studies showed that average Nm among the Yaeyama Islands was 2.47, all of the observed Nm between Taiwan and the Yaeyama Islands were below 1. These findings suggest that the geographic distance between Taiwan and the Yaeyama Islands is large enough to prevent gene flow between them.     

The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (<Emphasis Type="Italic">Haliotis tuberculata</Emphasis>), Revealed by Combined Mitochondrial and Nuclear Marker Analyses

The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea—probably before the separation of the two lineages—and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the geographic distribution of the European abalone. Traces of these events related to maternal inheritance were shown on COI marker.     

Molecular phylogeography of the fruit bat genus Melonycteris in northern Melanesia

Aim To investigate patterns of genetic divergence between populations of the fruit bat genus Melonycteris Dobson 1877 in relation to the possible effects on dispersal of the geological history of water barriers within and between northern Melanesian archipelagos. Location The genus is found only in the Bismarck Archipelago and Solomon Islands of northern Melanesia. Methods Up to 935 aligned bases of cytochrome b and cytochrome c oxidase subunit I DNA sequences were determined for specimens of most species and subspecies of Melonycteris. Measures of genetic distance, analysis of molecular variation and phylogenetic investigations (using maximum parsimony, maximum likelihood and Bayesian approaches) were conducted to assess the evolutionary relationships amongst populations. Results The deepest divergences within Melonycteris separate the genus into two reciprocally monophyletic clades from first, the Bismarck Archipelago, and secondly, the Solomon Islands. Within the Solomon Islands, five major clades received strong support. Listed in a generally north‐western to south‐eastern direction these were: (1) specimens from Choiseul and Santa Isabel; (2) specimens from New Georgia and Kolombangara; (3) specimens from Malaita; (4) specimens from Guadalcanal; and (5) specimens from Makira. Outgroup rooting suggested that the clade from Makira was the most basal within the Solomon Islands, being shown as the sister group to all other Melonycteris from this archipelago. Main conclusions Patterns of genetic variation within Melonycteris were generally consistent, given current knowledge of northern Melanesian geological history, with the hypothesis that the dispersal of these fruit bats is strongly inhibited by water barriers. Within the Solomon Islands the main genetic clades were each restricted to a single island or to a group of islands that are thought to have belonged to larger landmasses (Greater Gatumbangara and Greater Bukida) formed by land bridges during the Pleistocene. The high genetic distance between specimens from the Bismarck Archipelago and from the Solomon Islands reflects the persistently large geographic distance between these archipelagos. The unexpected phylogenetic position of the Makira specimens suggests either that this island was the first colonized by Melonycteris in the Solomon Islands or that this population is the relict of a clade that was previously more widely distributed.     

Rapid allopatric speciation in logperch darters (Percidae: Percina)

Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 +/- 1.06 million years ago (mya) to 0.42 +/- 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches demonstrates that allopatric speciation can occur rapidly.     

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub‐species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree‐building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub‐species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8·89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4·78 mya from the Chinese group. The northern–southern clades of S. nigripinnis began to diverge c. 2·12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0·34 mya.     

Recent vicariant and dispersal events affecting the phylogeny and biogeography of East Asian freshwater crab genus Nanhaipotamon (Decapoda: Potamidae)

The molecular phylogeny and biogeography of the East Asian freshwater crabs of the genus Nanhaipotamon (Decapoda: Brachyura: Potamidae) were studied, using two mitochondrial (16S rRNA and cytochrome oxidase I) and one nuclear (28S rRNA) markers, and correlated with various vicariant and dispersal events which have occurred in this region. The results showed Nanhaipotamon to be a monophyletic taxon with four clades which correspond to the topography of the coastal region of southeastern China and Taiwan Island. Mountains appear to play an important role in the distribution. The genus occurs only from east of the Wuyishan Range (Zhejiang and Fujian) and south of the Nanling Range (Guangdong) in southern China, and is also present west of the Central Range in Taiwan. The molecular and geological data suggest that Nanhaipotamon originated in an area between the Wuyishan and Nanling Ranges. In this area, the main and earliest cladogenesis occurred at ～4.8 million years ago (mya), with speciation probably taking place at around 4mya. The molecular evidence strongly supports the recent invasion of the genus into Taiwan Island from northeastern Fujian, via the paleo-Minjiang River on the landbridge of Taiwan Strait. The presence of the genus in Dongyin Island, however, is through invasion from southeastern Zhejiang, during the Pleistocene glaciation period. Nanhaipotamon reached Taiwan and Dongyin Island at ～1.0 and 0.4 mya, respectively. A small population of Nanhaipotamon formosanum from Penghu Islands (Pescadores) in the central Taiwan Strait has a slightly different genetic constitution and suggests it is a relict of past Pleistocene glaciations.     

Craniid brachiopods: aspects of clade structure and distribution reflect continental drift (Brachiopoda: Craniiformea)

We present maximum likelihood and Bayesian inference relative time‐tree analyses of aligned gene sequences from a worldwide collection of craniiform brachiopods belonging to two genera, Novocrania and Neoancistrocrania. Sequences were obtained from one mitochondrial and three nuclear‐encoded ribosomal RNA genes from varying numbers of specimens. Data‐exploration by network (splits) analyses indicates that each gene identifies the same divergent clades and (with one minor exception) the same inter‐clade relationships. Neoancistrocrania specimens were found only in the Pacific Ocean, near Japan, on the Norfolk and Chesterfield Ridges, and near the Solomon Islands. The Novocrania clades, in approximate order of increasing distance from the root comprise 1. a ‘Northern’ clade of animals collected in the NE. Atlantic, W. Mediterranean and Adriatic; 2. a ‘Tethyan’ clade comprising animals from the E. Mediterranean, Cape Verde islands and the Caribbean (Belize and Jamaica); 3. a ‘NE. Pacific’ clade containing animals from Vancouver Island and from localities near Japan and south of Taiwan; 4. a ‘Southern’ clade that contains two widely separated subclades, one from New Zealand and the other with an extraordinarily wide distribution, ranging from near Japan in the north to the Chesterfield Ridge and Solomon Islands in the West, and in the East to the Galapagos Islands, the coast of South America (Chile) and Richardson seamount (off South Africa) in the South Atlantic. To the South, members of this clade were found in the Weddell, Scotia and Bellinghausen Antarctic Seas. The root of the extant craniid radiation was previously found (by relaxed‐clock analysis) to lie on the branch connecting the two genera so that, in effect, the one clade of Neoancistrocrania serves to polarise evolutionary relationships within the several clades of Novocrania. As previously suggested, all results confirm that Neoancistrocrania is sister to the ‘Northern’ Novocrania clade, and this leads to a proposal that Neoancistrocrania represents one extreme of a wide range of variation in ancestral ventral valve mineralisation, speciation (～90 Ma) resulting from competitive exclusion in rapidly‐growing reef environments. To the extent possible, the identified molecular clades are correlated with named species of Novocrania. The reproductive and population biology of craniid brachiopods is not well known, but from available evidence they are considered to have low‐dispersal potential and, except in enclosed localities such as cold‐water fjords, to have small effective population sizes, features which are consistent with the observed divergent populations in well‐separated localities. Exceptionally slow craniid molecular (rDNA) evolution is suggested by the short branch of Novocrania where it has been used as an outgroup for large‐scale analyses of metazoans. Slow molecular evolution is also indicated by the existence of a distinct Tethyan clade, reflecting restricted dispersal at former times, and by the uniform, short, genetic distances and exceptionally wide geographical distribution of the Southern clade. Thus, the geographical distribution and phylogenetic divergence of craniid brachiopods is an example of phylotectonics, in which relationships revealed by phylogenetic analyses reflect opportunities for dispersal and settlement that were created by tectonic plate movements associated, in this case, with opening and closure of Tethys and the breakup of Gondwana. Molecular dating of craniid divergences and radiochemical dating of tectonic events thus illuminate one another. © 2014 The Linnean Society of London     

Genetic differentiation in the Trinidad endemic Mannophryne trinitatis (Anura: Aromobatidae): Miocene vicariance,in situ diversification and lack of geographical structuring across the island

Trinidad offers a unique study system within the Caribbean to assess the processes and patterns of amphibian speciation. We used mitochondrial DNA sequences to investigate the phylogenetic relationships and patterns of intraspecific genetic variation of Mannophryne trinitatis from Trinidad. Molecular clock estimates point to a genetic split between M. trinitatis and its sister species, M. venezuelensis, dating to the Late Miocene (c. 7–8 Mya), suggesting vicariance as a means of speciation when Trinidad pulled apart from northern Venezuela. M. trinitatis phylogenetic population analyses from ten Northern Range and four Central Range localities recovered three well‐resolved clades: a larger clade formed by haplotypes from Northern Range localities and two additional clades, one formed by haplotypes from the Central Range and another including haplotypes from Northern Range localities and one haplotype from the Central Range. Overall, our results show that the genetic diversity in M. trinitatis is not geographically structured but it is distributed among the various Northern and Central Range localities. In congruence with the vicariance speciation hypothesis, we attribute M. trinitatis present distribution and lack of genetic structure to multiple admixture events caused by climate changes that severely affected the topology of Trinidad throughout the Pliocene/Pleistocene periods.     

Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo‐Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.     

Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan

In order to assess the utility of nested clade analysis, both standard phylogenetic algorithms and nested clade analysis were performed on a geographically widespread survey of mitochondrial DNA haplotypes of the bamboo viper, Trimeresurus stejnegeri, within Taiwan. Gross tree topologies were congruent for all analyses and indicated the presence of two geographically overlapping clades within Taiwan. The smaller lineage was restricted to the north and east coasts, whereas the larger lineage occupied all but the northern range of the species within Taiwan including the Pacific offshore populations of Green and Orchid Islands. The phylogeographical pattern supports the existence of at least one colonization event from the continent since the initial isolation of Taiwan from the mainland in the Pliocene. However, determining the exact number of colonization events was not possible due to the simultaneous vicariant forces of hypothesized continental landbridge connections and the occurrence of dramatic in situ orogenesis throughout the Pleistocene. Nested clade analysis provided multiple temporal and spatial population historical inferences that are not possible with standard analyses and therefore should become widely applied to future phylogeographical studies.     

Molecular phylogeny of the genus Pieris (Ericaceae) with special reference to phylogenetic relationships of insular plants on the Ryukyu Islands

Phylogenetic relationships within the genus Pieris (Ericaceae) were investigated based on the rbcL and matK genes along with five spacer sequences of chloroplast DNA to address questions regarding the phylogeography of the genus in association with insular plants on the Ryukyu Islands. The most parsimonious trees indicated that P. floribunda from eastern North America is a sister taxon to the remaining taxa examined, and suggested that the East Asian taxa examined are monophyletic. A morphologically cohesive group, section Pieris, was revealed to be paraphyletic. Within the East Asian clade, insular endemics from the Ryukyu Islands, Taiwan, and mainland Japan formed a sister group to P. formosa from the Himalayas and southern China. Our data suggest that the insular endemics of the Ryukyu Islands and Taiwan arose via allopatric divergence as a result of a paleogeographical land configuration of a landbridge during the early–middle Pleistocene in the Quaternary Period.     

Origin of Mediterranean insular endemics in the Boraginales: integrative evidence from molecular dating and ancestral area reconstruction

Aim The presence of numerous reliable fossils and the occurrence of many endemic island species make the Boraginales particularly suitable for integrative biogeographical studies. In this paper we aim to elucidate the time frame and events associated with the origin of selected borages endemic to the Mediterranean climate zone. More specifically, we describe and examine the alternative palaeo‐ and neoendemic hypotheses for their origin. Location Corsica and Sardinia (continental fragment islands) and the Canary Islands (an oceanic island archipelago). Methods Eighty‐nine accessions, representing 30 genera from five families ascribed to the Boraginales, were examined for six chloroplast DNA regions. We used an integrative approach including phylogenetic analyses (Mr Bayes ), Bayesian molecular dating (T3 package) with four fossil constraints on nodes, and biogeographical reconstructions (diva ) to elucidate the temporal and spatial origins of the Corso‐Sardinian and Canary Island endemics. Results Species of Echium endemic to the Canary Islands diverged from their continental sister clade during the Miocene (15.3 ± 5.4 Ma), probably after the rise of the oldest islands (c. 20 Ma). Corso‐Sardinian endemics of Borago diverged from their primarily North African sister clade during the late Miocene‐Pliocene (c. 6.9 ± 3.6 Ma), well after the initial fragmentation of the islands (c. 30 Ma). Similarly, Corso‐Sardinian endemics of Anchusa diverged from the South African Anchusa capensis during the Pliocene–Pleistocene (c. 2.7 ± 2.1 Ma). Main conclusions The present study reveals an Anatolian origin for Anchusa, Borago and Echium and underlines the importance of the Eastern Mediterranean region as a possible reservoir for plant evolution in the Mediterranean Basin. For Anchusa and Borago, the divergence from their respective sister clades on the two types of islands post‐dated the formation of the islands, thus supporting the neo‐endemic hypothesis, whereas the dating results for the origin of Echium endemics were less conclusive.     

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura)

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Phylogeography of the pharaoh cuttle Sepia pharaonis based on partial mitochondrial 16S sequence data

The pharaoh cuttle Sepia pharaonis Ehrenberg, 1831 (Mollusca: Cephalopoda: Sepiida) is a broadly distributed species of substantial fisheries importance found from east Africa to southern Japan. Little is known about S. pharaonis phylogeography, but evidence from morphology and reproductive biology suggests that Sepia pharaonis is actually a complex of at least three species. To evaluate this possibility, we collected tissue samples from Sepia pharaonis from throughout its range. Phylogenetic analyses of partial mitochondrial 16S sequences from these samples reveal five distinct clades: a Gulf of Aden/Red Sea clade, a northern Australia clade, a Persian Gulf/Arabian Sea clade, a western Pacific clade (Gulf of Thailand and Taiwan) and an India/Andaman Sea clade. Phylogenetic analyses including several Sepia species show that S. pharaonis sensu lato may not be monophyletic. We suggest that “S. pharaonis” may consist of up to five species, but additional data will be required to fully clarify relationships within the S. pharaonis complex.     

Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern

Aim To study the patterns of genetic variation and the historical events and processes that influenced the distribution and intraspecific diversity in Hyla meridionalis Boettger, 1874. Location Hyla meridionalis is restricted to the western part of the Mediterranean region. In northern Africa it is present in Tunisia, Algeria and Morocco. In south‐western Europe it is found in the south of France, north‐western Italy and north‐eastern and south‐western Iberian Peninsula. There are also insular populations, as in the Canaries and Menorca. Methods Sampling included 112 individuals from 36 populations covering the range of the species. We used sequences of mitochondrial DNA Cytochrome Oxidase I (COI) for the phylogeographical analysis (841 bp) and COI plus a fragment including part of tRNA lysine, ATP synthase subunits 6 and 8 and part of Cytochrome Oxidase III for phylogenetic analyses (2441 bp). Phylogenetic analyses were performed with paup *4.0b10 (maximum likelihood, maximum parsimony) and Mr Bayes 3.0 (Bayesian analysis). Nested clade analysis was performed using tcs 1.18 and Geo Dis 2.2. A dispersal‐vicariant analysis was performed with diva 1.0 to generate hypotheses about the geographical distribution of ancestors. Results We found little genetic diversity within samples from Morocco, south‐western Europe and the Canary Islands, with three well‐differentiated clades. One is distributed in south‐western Iberia and the High Atlas, Anti‐Atlas and Massa River in Morocco. The second is restricted to the Medium Atlas Mountains. The third one is present in northern Morocco, north‐eastern Iberia, southern France and the Canaries. These three groups are also represented in the nested clade analysis. Sequences from Tunisian specimens are highly divergent from sequences of all other populations, suggesting that the split between the two lineages is ancient. diva analysis suggests that the ancestral distribution of the different lineages was restricted to Africa, and that an explanation of current distribution of the species requires three different dispersal events. Main conclusions Our results support the idea of a very recent colonization of south‐western Europe and the Canary Islands from Morocco. South‐western Europe has been colonized at least twice: once from northern Morocco probably to the Mediterranean coast of France and once from the western coast of Morocco to southern Iberia. Human transport is a likely explanation for at least one of these events. Within Morocco, the pattern of diversity is consistent with a model of mountain refugia during hyperarid periods within the Pleistocene. Evaluation of the phylogenetic relationships of Tunisian haplotypes will require an approach involving the other related hylid taxa in the area.     

Repeated range expansion and niche shift in a volcanic hotspot archipelago: Radiation of C4 Hawaiian Euphorbia subgenus Chamaesyce (Euphorbiaceae)

Woody perennial plants on islands have repeatedly evolved from herbaceous mainland ancestors. Although the majority of species in Euphorbia subgenus Chamaesyce section Anisophyllum (Euphorbiaceae) are small and herbaceous, a clade of 16 woody species diversified on the Hawaiian Islands. They are found in a broad range of habitats, including the only known C₄ plants adapted to wet forest understories. We investigate the history of island colonization and habitat shift in this group. We sampled 153 individuals in 15 of the 16 native species of Hawaiian Euphorbia on six major Hawaiian Islands, plus 11 New World close relatives, to elucidate the biogeographic movement of this lineage within the Hawaiian island chain. We used a concatenated chloroplast DNA data set of more than eight kilobases in aligned length and applied maximum likelihood and Bayesian inference for phylogenetic reconstruction. Age and phylogeographic patterns were co‐estimated using BEAST. In addition, we used nuclear ribosomal ITS and the low‐copy genes LEAFY and G3pdhC to investigate the reticulate relationships within this radiation. Hawaiian Euphorbia first arrived on Kaua`i or Ni`ihau ca. 5 million years ago and subsequently diverged into 16 named species with extensive reticulation. During this process Hawaiian Euphorbia dispersed from older to younger islands through open vegetation that is disturbance‐prone. Species that occur under closed vegetation evolved in situ from open vegetation of the same island and are only found on the two oldest islands of Kaua`i and O`ahu. The biogeographic history of Hawaiian Euphorbia supports a progression rule with within‐island shifts from open to closed vegetation.     

Phylogeography of the frog Leptodactylus validus (Amphibia: Anura): Patterns and timing of colonization events in the Lesser Antilles

The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred 1 million years ago (mya) and the colonization of the Lesser Antillean islands occurred 0.4 mya. The coalescent approach supported the scenario where L. validus dispersed from Trinidad to St. Vincent and from there to Grenada, a dispersal event that could have been mediated by human introduction as recent as 1600 years ago.