‘Out‐of‐Africa’ dispersal of tropical floras during the Miocene climatic optimum: evidence from Uvaria (Annonaceae)

Aim African–Asian disjunctions are common in palaeotropical taxa, and are typically explained by reference to three competing hypotheses: (1) ‘rafting’ on the Indian tectonic plate, enabling Africa‐to‐Asia dispersal; (2) migration via Eocene boreotropical forests; and (3) transoceanic long‐distance dispersal. These hypotheses are tested using Uvaria (Annonaceae), which is distributed in tropical regions of Africa, Asia and Australasia. Recent phylogenetic reconstructions of the genus show a clear correlation with geographical provenance, indicating a probable origin in Africa and subsequent dispersal to Asia and then Australasia. Ancestral areas and migration routes are inferred and compared with estimates of divergence times in order to distinguish between the prevailing dispersal hypotheses. Location Palaeotropics. Methods Divergence times in Uvaria are estimated by analysing the sequences of four DNA regions (matK, psbA–trnH spacer, rbcL and trnL–F) from 59 Uvaria species and 77 outgroup species, using a Bayesian uncorrelated lognormal (UCLD) relaxed molecular clock. The ancestral area of Uvaria and subsequent dispersal routes are inferred using statistical dispersal–vicariance analysis (s‐diva ). Results Uvaria is estimated to have originated in continental Africa 31.6 Ma [95% highest posterior density (HPD): 38.4–25.1 Ma] between the Middle Eocene and Late Oligocene. Two main migration events during the Miocene are identified: dispersal into Madagascar around 17.0 Ma (95% HPD: 22.3–12.3 Ma); and dispersal into Asia between 21.4 Ma (95% HPD: 26.7–16.7 Ma) and 16.1 Ma (95% HPD: 20.1–12.1 Ma). Main conclusions Uvaria fruits are widely reported to be consumed by primates, and are therefore unlikely candidates for successful long‐distance transoceanic dispersal. The other biogeographical hypotheses, involving rafting on the Indian tectonic plate, and dispersal via the European boreotropical forests associated with the Eocene thermal maximum, can be discounted due to incongruence with the divergence time estimates. An alternative scenario is suggested, involving dispersal across Arabia and central Asia via the tropical forests that developed during the late Middle Miocene thermal maximum (17–15 Ma), associated with the ‘out‐of‐Africa’ dispersal of primates. The probable route and mechanism of overland dispersal between Africa and Asia for tropical plant groups during the Miocene climatic optimum are clarified based on the Uvaria data.     

An evaluation of new parsimony‐based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony‐based approaches. Here, we compare a parametric method, dispersal–extinction–cladogenesis (DEC), against a parsimony‐based method, dispersal–vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes‐DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World‐wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes‐DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes‐DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events – which in Bayes‐DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes‐DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide‐spanning spatial and temporal model proposed here could prove useful for testing large‐scale biogeographical patterns in plants.     

Taking into account phylogenetic and divergence‐time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae

Aim To examine the biogeographical history of the angiosperm clade Caprifolieae (Caprifoliaceae) using parametric biogeographical reconstruction methods. The existing parametric method was extended to evaluate biogeographical reconstructions over the distribution of dated phylogenies. This method provides a framework for reconstructing large‐scale biogeography with parametric methods, while accounting for uncertainty in the phylogenetic relationships and divergence time. Location Asia, Europe and North America. Methods The biogeographical history of the major lineages of Caprifolieae was reconstructed over the posterior distribution of dated trees generated from Bayesian divergence‐time analyses. Results from a model with no geological constraints were compared with those from one where movement is disallowed across the North Atlantic after the Eocene. The most plausible scenarios were segregated at each node to test whether particular scenarios were reconstructed for particular divergence times. The parametric biogeographical method was also extended to estimate connectivity between areas so that the probability of dispersal between the major areas of the Northern Hemisphere could be explored. Results Phylogenetic results for Caprifolieae agreed with previous estimates using smaller sampling, but uncertainty remained despite efforts to resolve the relationships of the four genera within this clade using multiple markers. In addition to topological uncertainty, there were few fossils available for calibrations, resulting in large confidence intervals for divergence times. Divergence‐time analyses put the diversification of Caprifolieae at between 36 and 51 Ma and showed that Caprifolieae probably originated in Asia, with multiple movements into Europe and western and eastern North America. Main conclusions Newly developed parametric methods for biogeographical reconstruction incorporate more data and better models. Here, the parametric biogeographical reconstruction method has been extended to allow for topological and divergence‐time uncertainty. The analyses of Caprifolieae demonstrated that biogeographical hypotheses can be explored even where there are large confidence intervals on divergence times and uncertainty in topology. These results add to the growing evidence that Asia was an important source of Northern Hemisphere diversity throughout the Cenozoic.     

Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal

Aim Rain forest‐restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location Tropics and boreotropics. Methods Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage‐through‐time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal–extinction–cladogenesis model. Results The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present‐day distribution patterns within the family. Main conclusions Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present‐day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The ‘long‐branch clade’ has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long‐distance dispersal events. In contrast, the ‘short‐branch clade’ dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited.     

Testing for biogeographic mechanisms promoting divergence in Caribbean crickets (genus Amphiacusta)

Aim This work examines whether the history of diversification of Amphiacusta (Orthoptera, Gryllidae) in the Caribbean corresponds to a vicariant or a dispersalist model. Location The Greater Antillean islands of the Caribbean region. Methods The phylogenetic relationships among species were estimated using a procedure that directly estimates the underlying species tree from independent loci (in this case, one mitochondrial and one nuclear locus). This tree was then used to test for topological congruence with a vicariant model, and to estimate divergence times. Results The analyses based on the expected pattern of species divergence (i.e. species‐tree topology) support a vicariant model. With the notable exception of a dispersal event marking the colonization of Jamaica, the timing of the events are generally consistent with a vicariant scenario, given the current taxon sampling and potential errors with dating the divergence events. Main conclusions The tendency of species to co‐segregate by island suggests that intra‐island diversification is common. Despite their flightlessness, species of Amphiacusta are apparently capable of long‐distance dispersal, such as colonization from the Puerto Rican/Virgin Island bank to Jamaica. The topology of the species tree is consistent with a vicariant model of divergence, and the dates of divergence between island groups are generally consistent with an island–island vicariance model. A strict island–island vicariance scenario can, however, be rejected because of inferred dispersal events such as the colonization of Jamaica. Nevertheless, the biogeographic tests suggest that most of the diversity was generated under a combination of intra‐island diversification and island–island vicariance. Additional sampling of taxa will be needed to verify this hypothesized scenario. Our findings indicate that Amphiacusta presents an ideal opportunity for examining the role of sexual selection in promoting diversification, which would complement the large number of studies focused on adaptive divergence of Caribbean taxa.     

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.     

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.     

Evolution of the Madrean–Tethyan disjunctions and the North and South American amphitropical disjunctions in plants

Abstract The present paper reviews advances in the study of two major intercontinental disjunct biogeographic patterns: (i) between Eurasian and western North American deserts with the Mediterranean climate (the Madrean–Tethyan disjunctions); and (ii) between the temperate regions of North and South America (the amphitropical disjunctions). Both disjunct patterns have multiple times of origin. The amphitropical disjunctions have largely resulted from long‐distance dispersal, primarily from the Miocene to the Holocene, with available data indicating that most lineages dispersed from North to South America. Results of recent studies on the Mediterranean disjuncts between the deserts of Eurasia and western North America support the multiple modes of origin and are mostly consistent with hypotheses of long‐distance dispersal and the North Atlantic migration. Axelrod's Madrean–Tethyan hypothesis, which implies vicariance between the two regions in the early Tertiary, has been favored by a few studies. The Beringian migration corridor for semiarid taxa is also supported in some cases.     

Long-distance colonization of the Western Mediterranean by Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms

Aim There are few biogeographical and evolutionary studies that address plant colonization and lineage origins in the Mediterranean. Cistus serves as an excellent model with which to study diaspore dispersal and distribution patterns of plants exhibiting no special long‐distance dispersal mechanisms. Here we analyse the pattern of genetic variation and divergence times to infer whether the African–European disjunction of C. ladanifer L. is the result of long‐distance dispersal or of vicariance events. Location Principally the Western Mediterranean region, with a focus on the Strait of Gibraltar. Methods We used DNA sequence phylogenetic approaches, based on plastid (rbcL/trnK‐matK) and nuclear (ITS) sequence data sets, and the penalized likelihood method, to date the diversification of the 21 species of Cistus. Phylogenetic relationships and phylogeographical patterns in 47 populations of C. ladanifer were also analysed using two plastid DNA regions (trnS‐trnG, trnK‐matK). These sequence data were analysed using maximum parsimony, Bayesian inference and statistical parsimony. Results Dating estimates indicated divergence dates of the C. ladanifer lineage in the Pleistocene. Eight nucleotide‐substitution haplotypes distributed on the European (four haplotypes) and African (five haplotypes) sides of the Strait of Gibraltar were revealed from C. ladanifer sequences. Both the haplotype network and the phylogenetic analyses depicted two main Cistus lineages distributed in both Europe and North Africa. An Iberian haplotype forms part of the North African lineage, and another haplotype distributed on both continents is related to the European lineage. Haplotype relationships with respect to outgroup sequences supported the hypothesis that the centre of genetic diversity is in northern Africa. Main conclusions Based on lineage divergence‐time estimates and disassociation between geographical and lineage haplotype distributions, we inferred at least two intercontinental colonization events of C. ladanifer post‐dating the opening of the Strait of Gibraltar (c. 5 Ma). This result supports a hypothesis of long‐distance dispersal rather than a hypothesis of vicariance. We argue that, despite limited dispersal abilities, preference for disturbed habitats was integral to historical colonization after the advent of the Mediterranean climate (c. 3.2 Ma), when Cistus species diverged and became established as a dominant element in the Mediterranean scrub.     

Modelling the spread of Fagus sylvatica and Picea abies in southern Scandinavia during the late Holocene

Aim To test the hypothesis that dispersal characteristics alone can explain the past migration patterns of Fagus sylvatica and Picea abies observed in southern Scandinavia. Location Scandinavia, Europe. Methods The spreading dynamics of both species were analysed using a quantitative data–model comparison approach. Pollen data recording the arrival of the two species at 24 small forest‐hollow sites distributed across the study area were compared with simulated arrival times. The simulations were based on diffusive spread combined with long‐distance dispersal events. By systematically applying different parameter combinations yielding the desired colonization speeds we could identify values for the long‐distance dispersal component that minimized deviations from the observed arrival times. Results According to the minimization process, the optimal spreading rates were 100 m year^?1 for F. sylvatica and 250 m year^?1 for P. abies. Simulated dispersal alone could adequately explain the wave‐like spread of P. abies but failed to explain the scattered establishment pattern observed for F. sylvatica in Scandinavia. At the fine scale of stand establishment, local microclimatic conditions or site disturbance might be more important. The estimated spreading rates are high because the species colonized Scandinavia from different geographic directions and the rates slowed when their ranges overlapped. We present new estimates for the distance and frequency of long‐distance dispersal events for our modelled species. Main conclusions Our analyses suggest that the late Holocene spread of P. abies in Scandinavia was fairly rapid and was limited only by biological processes of dispersal, while that of F. sylvatica was limited by other factors probably controlled by site properties. Picea abies has maintained a rapid and constant rate of spread throughout at least the last 4000 years, despite significant changes in climate. There is uncertainty about the precise relationship between P. abies and climate in Scandinavia, so future distributions are not easy to forecast. For F. sylvatica in Scandinavia, site quality appears to have been a limiting factor, so future land use is likely to dictate its future distribution dynamics in combination with climatic factors.     

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.     

Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands,the Ryukyu Archipelago,Japan

Aim Phylogeographical patterns in the Ryukyu Archipelago have been explained primarily by landbridge formation and the opening of two straits in the Pliocene, namely the Tokara and Kerama gaps. These old straits have been considered to be the barriers most likely to determine genetic boundaries. To test this, we conducted a molecular analysis of the herb Ophiorrhiza japonica. We discuss the causes of and processes involved in its phylogeographical structure and explore aspects of island separation other than the duration of the straits to explain genetic boundaries at the gaps. Location Ryukyu Archipelago, Japan. Methods Plants were collected from 40 localities in the archipelago and vicinity. Non‐coding regions of chloroplast DNA were sequenced. The genealogical relationships among haplotypes were estimated using a statistical parsimony network. To examine the phylogeographical structure, we compared two parameters of population differentiation, namely G_ST and N_ST, and conducted correlation analysis of genetic and geographical distances. Genetic boundaries were identified using Monmonier’s maximum difference algorithm. To test vicariance–dispersal hypotheses, that is, vicariance after migration via the Pliocene landbridge or over‐sea dispersal in the Pleistocene, molecular dating analysis was conducted. Results A statistical parsimony network revealed that the haplotypes from the Ryukyu Archipelago and northwards coalesce to one ancestral haplotype in Taiwan. A clear phylogeographical structure was observed: plants within the same population and populations in geographical proximity were phylogenetically close. A genetic boundary was recognized across the Kerama Gap, but not across the Tokara Gap. Dating analysis suggested that population divergence across the Kerama Gap occurred in the early to late Pleistocene. Main conclusions The statistical parsimony network suggests migration from Taiwan and northward range expansion in the archipelago. Based on the divergence time, over‐sea dispersal in the Pleistocene is likely, although migration via a Pliocene landbridge is not totally rejected. Negligible genetic differentiation across the Tokara Gap suggests recent over‐sea dispersal, possibly facilitated by the small geographical width of the gap. Conversely, the large genetic differentiation across the Kerama Gap is probably explained by the large geographical distance across it. The past splitting of a landbridge would have had a significant influence on population differentiation after a certain geographical distance was reached.     

Molecular evidence for long-distance dispersal in the New Zealand pteridophyte flora

Aim To examine the relative importance of long‐distance dispersal in shaping the New Zealand pteridophyte (ferns and lycophytes) flora and its relationships with other floras, with the null hypothesis that the extant New Zealand pteridophyte flora has been isolated since New Zealand’s separation from Gondwana. Location New Zealand. Methods rbcL DNA sequences were assembled for 31 New Zealand pteridophyte genera, with each genus represented by one New Zealand species and the most closely related non‐New Zealand species for which data were available. Maximum‐likelihood, maximum‐parsimony, and Bayesian analysis phylograms were constructed and used as input for r 8s molecular dating, along with 23 fossil calibrations. Divergence estimates less than conservatively recent ages for New Zealand’s geological isolation, namely H_o > 30 Ma for pairs involving New Caledonian and Norfolk Island species and H_o > 55 Ma for all others, were taken as rejection of the null hypothesis. Results The null hypothesis was rejected for all pairs except, under some parameter conditions, for those involving the New Zealand species Cardiomanes reniforme, Lindsaea trichomanoides, Loxsoma cunninghamii, Lygodium articulatum, Marattia salicina, and Pteris comans. However, the Lindsaea and Pteris results probably reflect the absence in the analyses of closely related non‐New Zealand samples, while the Marattia divergence was highly contingent on which fossil calibrations were used. Main conclusions Rejection of the null hypothesis for the majority of pairs implies that the extant New Zealand lineage has undergone long‐distance dispersal either into or out of New Zealand. The notion of a long isolation since geological separation can, therefore, be dismissed for much of New Zealand’s pteridophyte flora. The analyses do not identify the direction of the long‐distance dispersal, and these New Zealand lineages could have had vicariant origins with subsequent long‐distance emigration. However, the alternative that many extant New Zealand pteridophyte lineages only arrived by long‐distance immigration after geological isolation seems likely.     

Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)

We analysed mitochondrial genomic sequences under maximum likelihood (ML) criteria to explore phylogenetic relationships, and performed historical biogeography analysis with divergence time estimation for fishes of Order Cypriniformes (Actinopterygii: Ostariophysi). We added mitogenomes for eight new cypriniforms and one outgroup to a data set comprising 53 and six outgroup mitogenomes from a previous study to make our taxon sampling geographically representative. The ML tree reconfirmed monophyly of four basal cypriniform clades (cyprinids, catostomids, gyrinocheilids, and loaches including balitorids and cobitids). It also recovered 18 monophyletic groups largely equivalent to the subfamilial rank, and resolved interrelationships among most of these subfamilial clades. However, lower bootstrap support for the ML tree and higher approximately unbiased (au) probabilities for alternative topologies around some branches indicated problems that still need to be resolved. Historical taxon biogeography by dispersal‐vicariance analysis, a parsimonious reconstruction of past ranges, and gain‐loss ratio analysis at the subfamilial level, identified the geographical region of basal cypriniform divergence as southern Asia. Bayesian divergence time analysis dated the basal otophysan split, which gave birth to Order Cypriniformes, to the late Triassic around 219.5 Mya. The basal cypriniform divergence took place during the late Jurassic around 155.9 Mya. These dates coincide with the onset and completion, respectively, of the Pangaean breakup. Taking biogeographical analysis and node dating into account, we consider the most likely candidate for the initial geographical range of Order Cypriniformes to be the south‐eastern area of Mesozoic Laurasia (present‐day southern Asia, excluding the Indian subcontinent). We also briefly discuss ecological implications of the group's divergence. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 633–662.     

Evidence for Gondwanan vicariance in an ancient clade of gecko lizards

Aim Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post‐Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives. Location Africa, Asia, Europe, South America, Atlantic Ocean. Methods We used parsimony and partitioned Bayesian methods to analyse data from five nuclear genes to generate a phylogeny for the New World sphaerodactyl geckos and their close Old World relatives. We used dispersal–vicariance analysis to determine ancestral area relationships among clades, and divergence times were estimated from the phylogeny using nonparametric rate smoothing. Results We recovered a monophyletic group containing the New World sphaerodactyl genera, Coleodactylus, Gonatodes, Lepidoblepharis, Pseudogonatodes and Sphaerodactylus, and the Old World Gekkotan genera Aristelliger, Euleptes, Quedenfeldtia, Pristurus, Saurodactylus and Teratoscincus. The dispersal–vicariance analysis indicated that the ancestral area for this clade was North Africa and surrounding regions. The divergence between the New World spaherodactyl geckos and their closest Old World relative was estimated to have occurred c. 96 Myr bp . Main conclusions Here we provide the first molecular genetic phylogenetic hypothesis of the New World sphaerodactyl geckos and their closest Old World relatives. A combination of divergence date estimates and dispersal–vicariance analysis informed a biogeographical scenario indicating that the split between the sphaerodactyl geckos and their African relatives coincided with the Africa/South America split and the opening of the Atlantic Ocean. We resurrect the family name Sphaerodactylidae to represent the expanded sphaerodactyl clade.     

Northern Hemisphere origin,transoceanic dispersal,and diversification of Ranunculeae DC. (Ranunculaceae) in the Cenozoic

Aim The role of dispersal versus vicariance for plant distribution patterns has long been disputed. We study the temporal and spatial diversification of Ranunculeae, an almost cosmopolitan tribe comprising 19 genera, to understand the processes that have resulted in the present inter‐continental disjunctions. Location All continents (except Antarctica). Methods Based on phylogenetic analyses of nuclear and chloroplast DNA sequences for 18 genera and 89 species, we develop a temporal–spatial framework for the reconstruction of the biogeographical history of Ranunculeae. To estimate divergence dates, Bayesian uncorrelated rates analyses and four calibration points derived from geological, fossil and external molecular information were applied. Parsimony‐based methods for dispersal–vicariance analysis (diva and Mesquite ) and a maximum likelihood‐based method (Lagrange ) were used for reconstructing ancestral areas. Six areas corresponding to continents were delimited. Results The reconstruction of ancestral areas is congruent in the diva and maximum likelihood‐based analyses for most nodes, but Mesquite reveals equivocal results at deep nodes. Our study suggests a Northern Hemisphere origin for the Ranunculeae in the Eocene and a weakly supported vicariance event between North America and Eurasia. The Eurasian clade diversified between the early Oligocene and the late Miocene, with at least three independent migrations to the Southern Hemisphere. The North American clade diversified in the Miocene and dispersed later to Eurasia, South America and Africa. Main conclusions Ranunculeae diversified between the late Eocene and the late Miocene. During this time period, the main oceanic barriers already existed between continents and thus dispersal is the most likely explanation for the current distribution of the tribe. In the Southern Hemisphere, a vicariance model related to the break‐up of Gondwana is clearly rejected. Dispersals between continents could have occurred via migration over land bridges, such as the Bering Land Bridge, or via long‐distance dispersal.     

Recent divergence,intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi‐Atlantic peatmoss populations

Several lines of evidence suggest that recent long‐distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi‐Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (im and migrate ) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F_ST = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long‐range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000–289 000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi‐Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.     

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.     

Around the world in 10 million years: biogeography of the nearly cosmopolitan true toads (Anura: Bufonidae)

Aim The species‐rich family of true toads (Anura: Bufonidae) has been the focus of several earlier studies investigating the biogeography of geographically widespread taxa. Herein, we employ newly developed Bayesian divergence estimate methods to investigate the biogeographical history of this group. Resulting age estimates are used to test several key temporal hypotheses including that the origin of the bufonid clade pre‐dates Gondwanan vicariance (~105 million years ago, Ma). Area cladograms are also invoked to investigate the geographical origin of the family. Location Worldwide, except the Australia–New Guinea plate, Madagascar and the Antarctic. Methods A phylogenetic hypothesis of the relationships among true toads was derived from analysis of 2521 bp of DNA data including fragments from three mitochondrial (12S, tRNA^val, 16S) and two nuclear (RAG‐1, CXCR‐4) genes. Analysis of multiple, unlinked loci with a Bayesian method for estimating divergence times allowed us to address the timing and biogeographical history of Bufonidae. Resulting divergence estimates permitted the investigation of alternative vicariance/dispersal scenarios that have been proposed for true toads. Results Our area cladogram resulting from phylogenetic analysis of DNA data supports a South American origin for Bufonidae. Divergence estimates indicate that the family originated earlier than had been suggested previously (78–99 Ma). The age of the enigmatic Caribbean clade was dated to the late Palaeocene–early Eocene. A return of bufonids to the New World in the Eocene was followed by rapid diversification and secondary expansion into South America by the early Oligocene (Rupelian). Main conclusions The South American origin of Bufonidae in the Upper Cretaceous was followed by relatively rapid expansion and radiation around the globe, ending with a return to the Americas via a Eurasian/North American land bridge in the Eocene. Though the exact route of this dispersal (Beringia or North Atlantic) remains unclear, an argument is made for the less frequently invoked North Atlantic connection. The origin of the enigmatic Caribbean lineage was found to be consistent with colonization following the bolide impact at the K/T boundary. These findings provide the first, firm foundation for understanding true toad divergence times and their truly remarkable and global radiation.     

Phylogenomics,biogeography, and evolution of morphology and ecological niche of the eastern Asian–eastern North American Nyssa (Nyssaceae)

Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian–eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian–eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here, we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographical history, and investigate the evolution of morphology and ecological niches, aiming at a better understanding of the well‐known EA–ENA floristic disjunction. Results showed that the Central American (CAM) Nyssa talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the Neogene dispersals, respectively, as well as the role of Central America as refugia of the Paleogene flora. The total‐evidence‐based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA–ENA disjunct, supporting the ecological selection driving trait evolutions after geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene, but “out of Asia” migrations in the Neogene, to explain the present disjunct distribution of Nyssa in EA and ENA.