Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

Reticulate, or non-bifurcating, evolution is now recognized as an important phenomenon shaping the histories of many organisms. It appears to be particularly common in plants, especially in ferns, which have relatively few barriers to intra- and interspecific hybridization. Reticulate evolutionary patterns have been recognized in many fern groups, though very few have been studied rigorously using modern molecular phylogenetic techniques in order to determine the causes of the reticulate patterns. In the current study, we examine patterns of branching and reticulate evolution in the genus Dryopteris, the woodferns. The North American members of this group have long been recognized as a classic example of reticulate evolution in plants, and we extend analysis of the genus to all 30 species in the New World, as well as numerous taxa from other regions. We employ sequence data from the plastid and nuclear genomes and use maximum parsimony (MP), maximum likelihood (ML), Bayesian inference (BI), and divergence time analyses to explore the relationships of New World Dryopteris to other regions and to reconstruct the timing and events which may have led to taxa displaying reticulate rather than strictly branching histories. We find evidence for reticulation among both the North and Central/South American groups of species, and our data support a classic hypothesis for reticulate evolution via allopolyploid speciation in the North America taxa, including an extinct diploid progenitor in this group. In the Central and South American species, we find evidence of extensive reticulation involving unknown ancestors from Asia, and we reject deep coalescent processes such as incomplete lineage sorting in favor of more recent intercontinental hybridization and chloroplast capture as an explanation for the origin of the Latin American reticulate taxa.     

Vicariance or long‐distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)

Aim Continental disjunctions in pantropical taxa have been explained by vicariance or long‐distance dispersal. The relative importance of these explanations in shaping current distributions may vary, depending on historical backgrounds or biological characteristics of particular taxa. We aimed to determine the geographical origin of the pantropical subfamily Chrysophylloideae (Sapotaceae) and the roles vicariance and dispersal have played in shaping its modern distribution. Location Tropical areas of Africa, Australasia and South America. Methods We utilized a recently published, comprehensive data set including 66 species and nine molecular markers. Bayesian phylogenetic trees were generated and dated using five fossils and the penalized likelihood approach. Distributional ranges of nodes were estimated using maximum likelihood and parsimony analyses. In both biogeographical and molecular dating analyses, phylogenetic and branch length uncertainty was taken into account by averaging the results over 2000 trees extracted from the Bayesian stationary sample. Results Our results indicate that the earliest diversification of Chrysophylloideae was in the Campanian of Africa c. 73–83 Ma. A narrow time interval for colonization from Africa to the Neotropics (one to three dispersals) and Australasia (a single migration) indicates a relatively rapid radiation of this subfamily in the latest Cretaceous to the earliest Palaeocene (c. 62–72 Ma). A single dispersal event from the Neotropics back to Africa during the Neogene was inferred. Long‐distance dispersal between Australia and New Caledonia occurred at least four times, and between Africa and Madagascar on multiple occasions. Main conclusions Long‐distance dispersal has been the dominant mechanism for range expansion in the subfamily Chrysophylloideae. Vicariance could explain South American–Australian disjunction via Antarctica, but not the exchanges between Africa and South America and between New Caledonia and Australia, or the presence of the subfamily in Madagascar. We find low support for the hypothesis that the North Atlantic land bridge facilitated range expansions at the Palaeocene/Eocene boundary.     

Patterns of long-distance dispersal in Tiquilia subg. Tiquilia (Boraginaceae): implications for the origins of amphitropical disjuncts and Galapagos Islands endemics

Plant biogeographers have long argued whether plant disjunctions result from vicariance or dispersal. One of the classic patterns of plant disjunction involves New World amphitropical disjuncts, as exemplified by Tiquilia subg. Tiquilia (Boraginaceae). Subgenus Tiquilia forms a heterogeneous group of ~20 species that is amphitropically distributed in the deserts of North and South America, with four taxa endemic to the Galápagos Islands. The current study reconstructs the biogeographic history of subg. Tiquilia in order to explore the origins of New World amphitropical disjunction and of Galápagos endemism. A strongly supported phylogeny of the subgenus is estimated using sequence data from matK, ndhF, rps16, ITS, and waxy. Biogeographic analyses using combined and individual marker data sets reveal a complex history of long-distance dispersal in subg. Tiquilia. Biogeographic reconstructions imply a North American origin of the subgenus and its three major lineages and require at least four long-distance dispersal events to explain its current distribution. The South American taxa of subg. Tiquilia result from three independent and nonsimultaneous colonization events, while the monophyly and continental origins of the Galápagos endemics are unresolved. This study contributes to a growing body of evidence that intercontinental dispersal has been more common than previously realized.     

Molecular clocks keep dispersal hypotheses afloat: evidence for trans‐Atlantic rafting by rodents

Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time‐frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence‐date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location The primary centres of distribution are in Africa and South America. Methods We implemented parsimony, maximum‐likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed‐molecular‐clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c. 50 Ma. Main conclusions Our phylogenetic hypothesis and divergence‐date estimates are strongly at odds with Gondwanan‐vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular‐clock analyses imply a trans‐Tethys dispersal event, broadly confined to the Late Cretaceous, and trans‐Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular‐clock inferences.     

Biogeographic mirages? Molecular evidence for dispersal‐driven evolution in Hydrobiusini water scavenger beetles

Water beetles of the tribe Hydrobiusini are globally distributed in the northern hemisphere and all austral continents except Antarctica. A remarkable clade also occurs in the Hawaiian Islands. The phylogenetic relationships among genera were recently investigated using a combination of molecules and morphology. Here, we use this phylogenetic framework to address the biogeographic evolution of this group using Bayesian fossil‐based divergence times, and model‐based maximum likelihood ancestral range estimations. We recover an origin of the tribe in the Cretaceous ca. 100 Ma. Our biogeographic analyses support an origin of the tribe in Laurasia followed by the colonization of Australia. However, a Gondwanan origin of the group cannot be ruled out when considering the fossil record. The timeframe of the tribe's evolution as well as the model‐based approach of ancestral range estimation favour a scenario invoking multiple transoceanic dispersal events over a Gondwana vicariance hypothesis. The Hawaiian radiation originated from long‐distance dispersal to now‐submerged islands, paired with dispersal to new islands as they formed.     

Canary Grasses (Phalaris,Poaceae): biogeography,molecular dating and the role of floret structure in dispersal

Canary grasses (Phalaris, Poaceae) include 21 species, widely spread throughout the temperate and subtropical regions of the world with two centres of diversity: the Mediterranean Basin and western North America. The genus contains annual and perennial, endemic, cosmopolitan, wild, and invasive species with diploid, tetraploid and hexaploid cytotypes. As such, Phalaris presents an ideal platform to study diversification via historic hybridization and polyploidy events, and geographical dispersal in grasses. We present the first empirical phylogeographic study for Phalaris testing current, intuitive hypotheses on the centres of origin, historic dispersal events and diversification within a geological timeframe. Bayesian methods (beast , version 1.6.2) were used to establish divergence dates, and dispersal–vicariance analyses (rasp , version 2.1b) were implemented for ancestral node reconstructions. Our phylogeographic results indicate that the genus emerged during the Miocene epoch [20.6–8.4 Ma (million years ago)] in the Mediterranean basin followed by dispersal and vicariance events to Africa, Asia and the Americas. We propose that a diploid ancestor of P. arundinacea migrated to western North America via the Bering Strait, where further diversification emerged in the New World. It appears that polyploidy played a major role in the evolution of the genus in the Old World, while diversification in the New World followed a primarily diploid pathway. Dispersal to various parts of the Americas followed different routes. Fertile florets with hairy protruding sterile lemmas showed significant correlation with wider geographical distribution.     

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia

The geological history of Australasia, New Caledonia, and Southeast Asia, has been complex, resulting in competing biogeographic hypotheses for taxa found here. Alternative hypotheses-Gondwanan vicariance, rafting terranes, long-distance dispersal-may be distinguished by different predicted divergence times between disjunct sister taxa. Taxa within Rutaceae subfamily Aurantioideae are ideal for testing these hypotheses because of their distributions. Therefore, the ages of Rutaceae and Aurantioideae were estimated using molecular dating. One data set comprised 51 sequences of rbcL and atpB with sampling across rosids and three fossil calibrations: crown Fabales+Fagales+Rosales (>94 Ma), Fabaceae (>51 Ma) and stem Ailanthus, Simaroubaceae (>52 Ma). Another data set comprised 81 Aurantioideae using >8 kb of chloroplast sequence and secondary calibration. Confidence in estimated divergence times was explored by varying the root age, dating method (strict, local, and relaxed clocks), and inclusion of internal calibrations. We conclude that the Rutaceae crown diverged in the Eocene (36.4-56.8 Ma, mean 47.6), whereas the Aurantioideae crown originated in the early Miocene (12.1-28.2 Ma, mean 19.8). This young age suggests that Gondwanan vicariance does not explain the distributions of extant Aurantioideae. Taxa found in New Caledonia may have arrived by separate transoceanic dispersal events.     

From Africa via Europe to South America: migrational route of a species‐rich genus of Neotropical lowland rain forest trees (Guatteria,Annonaceae)

Aim Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than by vicariance. In general, three routes have been documented for the dispersal of taxa onto the South American continent: (1) via the North Atlantic Land Bridge, (2) via the Bering Land Bridge, or (3) from Africa directly onto the continent. Here a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae) is used as a model to investigate these three hypotheses. Location The Neotropics. Methods The phylogenetic relationships within the long‐branch clade of Annonaceae were reconstructed (using maximum parsimony, maximum likelihood and Bayesian inference) in order to gain insight in the phylogenetic position of Guatteria. Furthermore, Bayesian molecular dating and Bayesian dispersal–vicariance (Bayes‐DIVA) analyses were undertaken. Results Most of the relationships within the long‐branch clade of Annonaceae were reconstructed and had high support. However, the relationship between the Duguetia clade, the Xylopia–Artabotrys clade and Guatteria remained unclear. The stem node age estimate of Guatteria ranged between 49.2 and 51.3 Ma, whereas the crown node age estimate ranged between 11.4 and 17.8 Ma. For the ancestral area of Guatteria and its sister group, the area North America–Africa was reconstructed in 99% of 10,000 DIVA analyses, while South America–North America was found just 1% of the time. Main conclusions The estimated stem to crown node ages of Guatteria in combination with the Bayes‐DIVA analyses imply a scenario congruent with an African origin followed by dispersal across the North Atlantic Land Bridge in the early to middle Eocene and further dispersal into North and Central America (and ultimately South America) in the Miocene. The phylogenetically and morphologically isolated position of the genus is probably due to extinction of the North American and European stem lineages in the Tertiary.     

A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.     

Molecular systematics of the trans-Pacific alpine genus Oreomyrrhis (Apiaceae): phylogenetic affinities and biogeographic implications

The alpine ecosystem is the only terrestrial biogeographic unit that is distributed globally. Studying phylogenetics of the plant species in this widespread ecosystem can provide insights into the historical biogeographic processes that have shaped the global biodiversity. The trans-Pacific disjunct alpine genus Oreomyrrhis (Apiaceae) was investigated using nrDNA ITS sequences to test the taxonomic and biogeographic hypotheses. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum sect. Chaerophyllum (subtribe Scandicinae, tribe Scandiceae). The optimal solutions of dispersal-vicariance analysis indicate that the ancestor of Chaerophyllum sect. Chaerophyllum (including Oreomyrrhis) was distributed in Eurasia and subsequently dispersed to North America and southern Pacific Rim. Based on dating using ITS sequence variation, these dispersal events were most likely recent, probably during late Tertiary to Quaternary. The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. Furthermore, evolution toward smaller mericarp size and a transition from outcrossing to selfing during Oreomyrrhis's evolution might have increased the chances for long-distance dispersal, facilitating its range expansion and occupation on alpine environments.     

Phylogeographic analysis of Pimoidae (Arachnida: Araneae) inferred from mitochondrial cytochrome c oxidase subunit I and nuclear 28S rRNA gene regions

Using mitochondrial DNA cytochrome c oxidase subunit I and nuclear DNA 28S rRNA data, we explored the phylogenetic relationships of the family Pimoidae (Arachnida: Araneae) and tested the North America to Asia dispersal hypothesis. Sequence data were analysed using maximum parsimony and Bayesian inference. A phylogenetic analysis suggested that vicariance, instead of dispersal, better explained the present distribution pattern of Pimoidae. Times of divergence events were estimated using penalized likelihood method. The dating analysis suggested that the emergence time of Pimoidae was approximately 140 million years ago (Ma). The divergence time of the North American and Asian species of Pimoa was approximately 110 Ma. Our phylogenetic hypothesis supports the current morphology‐based taxonomy and suggests that the cave dwelling might have played an important role in the speciation of pimoids in arid areas.     

Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration

Data from four DNA regions (rbcL, matK, 26S rDNA, and ITS) as well as extant and fossil morphology were used to reconstruct the phylogeny and biogeographic history of an intercontinentally disjunct plant group, the cornelian cherries of Cornus (dogwoods). The study tests previous hypotheses on the relative roles of two Tertiary land bridges, the North Atlantic land bridge (NALB) and the Bering land bridge (BLB), in plant migration across continents. Three approaches, the Bayesian, nonparametric rate smoothing (NPRS), and penalized likelihood (PL) methods, were employed to estimate the times of geographic isolations of species. Dispersal and vicariance analysis (DIVA) was performed to infer the sequence and directionality of biogeographic pathways. Results of phylogenetic analyses suggest that among the six living species, C. sessilis from western North America represents the oldest lineage, followed by C. volkensii from Africa. The four Eurasian species form a clade consisting of two sister pairs, C. mas-C. officinalis and C. chinensis-C. eydeana. Results of DIVA and data from fossils and molecular dating indicate that the cornelian cherry subgroup arose in Europe as early as the Paleocene. Fossils confirm that the group was present in North America by the late Paleocene, consistent with the DIVA predictions that, by the end of the Eocene, it had diversified into several species and expanded its distribution to North America via the NALB and to Africa via the last direct connection between Eurasia and Africa prior to the Miocene, or via long-distance dispersal. The cornelian cherries in eastern Asia appear to be derived from two independent dispersal events from Europe. These events are inferred to have occurred during the Oligocene and Miocene. This study supports the hypothesis that the NALB served as an important land bridge connecting the North American and European floras, as well as connecting American and African floras via Europe during the early Tertiary.     

Explosive avian radiations and multi-directional dispersal across Wallacea: evidence from the Campephagidae and other Crown Corvida (Aves)

The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35 Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace's line have revealed a particularly complex movement of terranes over the last 20-30 Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace's line are complex and began at least 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographic pattern in the region.     

Inverse dispersal patterns in a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae) and their ant hosts

When postulating evolutionary hypotheses for diverse groups of taxa using molecular data, there is a tradeoff between sampling large numbers of taxa with a few Sanger-sequenced genes or sampling fewer taxa with hundreds to thousands of next-generation-sequenced genes. High taxon sampling enables the testing of evolutionary hypotheses that are sensitive to sampling bias (i.e. dating, biogeography and diversification analyses), whereas high character sampling improves resolution of critical nodes. In a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae), we analyse both of these types of datasets independently (203 taxa with five Sanger loci, 92 taxa with 348 anchored hybrid enrichment loci) and in combination (229 taxa, 353 loci) to explore divergence dating, biogeography, host relationships and differential rates of diversification. Oraseminae specialize as parasitoids of the immature stages of ants in the subfamily Myrmicinae (Hymenoptera: Formicidae), with ants in the genus Pheidole being their most common and presumed ancestral host. A general assumption is that the distribution of the parasite must be limited by any range contraction or expansion of its host. Recent studies support a single New World to Old World dispersal pattern for Pheidole at c. 11–27 Ma. Using multiple phylogenetic inference methods (parsimony, maximum likelihood, dated Bayesian and coalescent analyses), we provide a robust phylogeny showing that Oraseminae dispersed in the opposite direction, from Old World to New World, c. 24–33 Ma, which implies that they existed in the Old World before their presumed ancestral hosts. Their dispersal into the New World appears to have promoted an increased diversification rate. Both the host and parasitoid show single unidirectional dispersals in accordance with the presence of the Beringian Land Bridge during the Oligocene, a time when the changing northern climate probably limited the dispersal ability of such tropically adapted groups.     

Out of Africa: Biogeography and diversification of the pantropical pond skater genus Limnogonus Stål, 1868 (Hemiptera: Gerridae)

Gondwanan vicariance, long‐distance dispersal (LDD), and boreotropical migration have been proposed as alternative hypotheses explaining the pantropical distribution pattern of organisms. In this study, the historical biogeography of the pond skater genus Limnogonus was reconstructed to evaluate the impact of biogeographical scenarios in shaping their modern transoceanic disjunction. We sampled almost 65% of recognized Limnogonus species. Four DNA fragments including 69 sequences were used to reconstruct a phylogram. Divergence time was estimated using a Bayesian relaxed clock method and three fossil calibrations. Diversification dynamics and ancestral area reconstruction were investigated by using maximum likelihood and Bayesian approaches. Our results showed the crown group of Limnogonus originated and diversified in Africa in the early Eocene (49 Ma, HPD: 38–60 Ma), subsequently expanding into other regions via dispersal. The colonization of the New World originated from the Oriental Region probably via the Bering Land Bridge in the late Eocene. Two split events between the Old World and New World were identified: one between Neotropics and Oriental region around the middle Oligocene (30 Ma, HPD: 22–38 Ma), and the other between Neotropics and Africa during the middle Miocene (14 Ma, HPD: 8–21 Ma). The evolutionary history of Limnogonus involved two biogeographical processes. Gondwanan vicariance was not supported in our analyses. The diversification of Limnogonus among Africa, Oriental, and Neotropical regions corresponded with the age of land bridge connection and dispersed as a member associated with the broad boreotropical belt before local cooling (34 Ma). The current transoceanic disjunctions in Limnogonus could be better explained by the disruption of “mixed‐mesophytic” forest belt; however, the direct transoceanic LDD between the Neotropics and Africa could not be ruled out. In addition, the “LDD” model coupled with island hopping could be a reasonable explanation for the diversification of the Oriental and Australian regions during the Oligocene.     

Ancient host shifts followed by host conservatism in a group of ant parasitoids

While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with ant hosts. We present the most comprehensive molecular phylogeny of Eucharitidae to date, including 44 of the 53 genera and fossil-calibrated estimates of divergence dates. Eucharitidae arose approximately 50 Ma after their hosts, during the time when the major ant lineages were already established and diversifying. We incorporate host association data to test for congruence between eucharitid and ant phylogenies and find that their evolutionary histories are more similar than expected at random. After a series of initial host shifts, clades within Eucharitidae maintained their host affinity. Even after multiple dispersal events to the New World and extensive speciation within biogeographic regions, eucharitids remain parasitic on the same ant subfamilies as their Old World relatives, suggesting host conservatism despite access to a diverse novel ant fauna.     

Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes

Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).     

Phylogeny and biogeography of the sandalwoods (Santalum, Santalaceae): repeated dispersals throughout the Pacific

Results of the first genus-wide phylogenetic analysis for Santalum (Santalaceae), using a combination of 18S-26S nuclear ribosomal (ITS, ETS) and chloroplast (3' trnK intron) DNA sequences, provide new perspectives on relationships and biogeographic patterns among the widespread and economically important sandalwoods. Congruent trees based on maximum parsimony, maximum likelihood, and Bayesian methods support an origin of Santalum in Australia and at least five putatively bird-mediated, long-distance dispersal events out of Australia, with two colonizations of Melanesia, two of the Hawaiian Islands, and one of the Juan Fernandez Islands. The phylogenetic data also provide the best available evidence for plant dispersal out of the Hawaiian Islands to the Bonin Islands and eastern Polynesia. Inability to reject rate constancy of Santalum ITS evolution and use of fossil-based calibrations yielded estimates for timing of speciation and colonization events in the Pacific, with dates of 1.0-1.5 million yr ago (Ma) and 0.4-0.6 Ma for onset of diversification of the two Hawaiian lineages. The results indicate that the previously recognized sections Polynesica, Santalum, and Solenantha, the widespread Australian species S. lanceolatum, and the Hawaiian species S. freycinetianum are not monophyletic and need taxonomic revision, which is currently being pursued.     

Support for vicariant origins of the New Zealand Onychophora

Aim The distribution of Onychophora across the southern continents has long been considered the result of vicariance events. However, it has recently been hypothesized that New Zealand was completely inundated during the late Oligocene (25–22 Ma) and therefore that the entire biota is the result of long-distance dispersal. We tested this assumption using phylogenetic and molecular dating of DNA sequence data from Onychophora. Location New Zealand, Australia, South Africa, Chile (South America). Methods We obtained DNA sequence data from the nuclear genes 28S and 18S rRNA to reconstruct relationships among species of Peripatopsidae (Onychophora). We performed molecular dating under a Bayesian relaxed clock model with a range of prior distributions using the rifting of South America and South Africa as a calibration. Results Our phylogenetic trees revealed that the New Zealand genera Ooperipatellus and Peripatoides, together with selected Australian genera (Euperipatoides, Phallocephale and an undescribed genus from Tasmania), form a monophyletic group that is the sister group to genera from Chile (Metaperipatus) and South Africa (Peripatopsis and Opisthopatus). The relaxed clock dating analyses yielded mean divergence times from 71.3 to 78.9 Ma for the split of the New Zealand Peripatoides from their Australian sister taxa. The 0.95 Bayesian posterior intervals were very broad and ranged from 24.5 to 137.6 Ma depending on the prior assumptions. The mean divergence of the New Zealand species of Ooperipatellus from the Australian species Ooperipatellus insignis was estimated at between 39.9 and 46.2 Ma, with posterior intervals ranging from 9.5 to 91.6 Ma. Main conclusions The age of Peripatoides is consistent with long-term survival in New Zealand and implies that New Zealand was not completely submerged during the Oligocene. Ooperipatellus is less informative on the question of continuous land in the New Zealand region because we cannot exclude a post-Oligocene divergence. The great age of Peripatoides is consistent with a vicariant origin of this genus resulting from the rifting of New Zealand from the eastern margin of Gondwana and supports the assumptions of previous authors who considered the Onychophora to be a relict component of the New Zealand biota.     

Missing fossils, molecular clocks, and the origin of the Melastomataceae

In a recent analysis of the historical biogeography of Melastomataceae, Renner, Clausing, and Meyer (2001; American Journal of Botany 88(7): 1290-1300) rejected the hypothesis of a Gondwana origin. Using a fossil-calibrated chloroplast DNA (ndhF) phylogeny, they placed the early diversification of Melastomataceae in Laurasia at the Paleocene/Eocene boundary (ca. 55 Ma) and suggested that long-distance oceanic dispersals in the Oligocene and Miocene (34 to 5 Ma) account for its range expansion into South America, Africa, and Madagascar. Their critical assumption-that oldest northern mid-latitude melastome fossils reflect tribal ages and their geographic origins-may be erroneous, however, because of the sparse fossil record in the tropics. We show that rates of synonymous nucleotide substitutions derived by the Renner et al. (2001) model are up to three times faster than most published rates. Under a Gondwana-origin model advocated here, which includes dispersals from Africa to Southeast Asia via the "Indian ark" and emphasizes filter rather than either sweepstakes dispersal or strict vicariance, rates of nucleotide substitution fall within the range of published rates. We suggest that biogeographic reconstructions need to consider the paucity of Gondwanan fossils and that frequently overlooked interplate dispersal routes provide alternatives to vicariance, boreotropical dispersal, and long-distance oceanic dispersal as explanations for the amphi-oceanic disjunctions of many tropical rain forest plants.