Aim. The Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae–Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes.

Location. South Africa, with emphasis on the south-west.

Methods. The radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes.

Results. Our analyses date Metalasia to approximately 6.9 Ma, after the Miocene–Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4 Ma, whereas Clade A, with a main distribution in the all-year rainfall area, is considerably younger, with a crown group age estimated to 3.3 Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods.

Main conclusions. The diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.

Aim Islands and archipelagos have played an important role in the development of ecological and evolutionary theories. Using a newly compiled molecular phylogeny we infer the biogeographical history of a monarch flycatcher genus, Myiagra, which is distributed across the Indo-Pacific. We subsequently integrate biogeographical and ecomorphological data to examine the role of dispersal and trait evolution in the build-up of avian assemblages. Location Australia, the Moluccas, New Guinea and Pacific islands. Methods We generated a taxonomically densely sampled mitochondrial DNA dataset that included almost all species and subspecies of the reciprocally monophyletic genera Myiagra and Arses. We then used maximum likelihoood and Bayesian inference to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the tree topology and then used Lagrange to infer ancestral geographical areas. Finally, we combined ancestral area reconstructions with information on ecomorphological traits to infer mechanisms underlying community assembly. Results We provide the first comprehensive molecular phylogenetic reconstruction for Myiagra and Arses monarch flycatchers. Our phylogenetic reconstruction reveals a relatively recent diversification from the Miocene associated with several major dispersal events. Ancestral area reconstruction reveals several independent colonizations of the Moluccas, Melanesia, Fiji and the Micronesian islands. Ancestral state reconstruction of ecological traits suggests that the diversity of traits in co-occurring species of monarch flycatchers results from independent colonization events and ecological niche conservatism rather than in situ diversification. Main conclusions Three waves of colonization, non-overlapping in time, led to independent speciation events in the Bismarcks, Fiji and the Moluccas, in addition to in situ speciation events on remote islands of Micronesia, the Solomons, Vanuatu and Samoa. Few of these colonizations have led to the co-occurrence of congenerics or species with similar ecomorphological profiles on the same island. Thus, we suggest that priority effects might prevent new colonizers from establishing themselves if they share high levels of ecological similarity with resident species. We conclude that historical dispersal to and colonization of new islands, combined with ecologically deterministic priority effects, drove the assembly of insular monarch flycatcher communities across the Indo-Pacific.

Aim. The Western Indian Ocean region (WIOR) is home to a very diverse and largely unique flora that has mainly originated via long-distance dispersals. The aim of this study is to gain insight into the origins of the WIOR biodiversity and to understand the dynamics of colonization events between the islands. We investigate spatial and temporal hypotheses of the routes of dispersal, and compare the dispersal patterns of plants of the Coffeeae alliance (Rubiaceae) and their dispersers. Rubiaceae is the second most species-rich plant family in Madagascar, and includes many endemic genera. The neighbouring archipelagos of the Comoros, Mascarenes and Seychelles also harbour several endemic Rubiaceae.

Location. The islands of the Western Indian Ocean.

Methods. Phylogenetic relationships and divergence times were reconstructed from plastid DNA data of an ingroup sample of 340 species, using Bayesian inference. Ancestral areas and range evolution history were inferred by a maximum likelihood method that takes topological uncertainty into account.

Results. At least 15 arrivals to Madagascar were inferred, the majority of which have taken place within the last 10 Myr. Most dispersal events were supported as being from mainland Africa, but Catunaregam may have dispersed from Asia. Although most Coffeeae alliance lineages are zoochorous, the general pattern of dispersals from Africa is incongruent with the biogeographic origins of the extant Malagasy volant frugivores. Several out-of-Madagascar dispersals were inferred to the neighbouring islands, as well as back-colonizations of Africa.

Main conclusions. The African flora has been of foremost importance as source of dispersal to the islands of the Western Indian Ocean. Following the colonization of Madagascar, rapid radiations appear to have taken place in some clades, and Madagascar has also been an important source area for subsequent dispersal to the Comoros, Mascarenes and Seychelles.

Nautilus and Allonautilus, last members of the once widespread nautiloid cephalopods, are today restricted to the deep central Indo-West Pacific Ocean, for reasons that remain unclear. Cephalopod evolution is generally considered as being driven by vertebrate predation; therefore, we investigated the role of whales and seals in the decline of nautiloids through the Cenozoic.

Aim The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of ‘supertramps’, ‘great speciators’ and relictualization. Location The Indo-Pacific, Australia, Asia and Africa. Taxon Corvoid passerine birds. Methods We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckooshrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence. Results The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, Southeast Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated (’supertramps’) or show strong differentiation of local populations (’great speciators’), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in ‘great speciators’ with intermediate levels of dispersal abilities (as per hand-wing index). Main conclusions Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of ‘supertramps’, ‘great speciators’ and relictual palaeoendemics within the temporal stages of the taxon cycle.

We investigated the historical biogeography of the Inuleae–Plucheinae (Asteraceae), a group of arid-adapted plants with partly unresolved generic circumscriptions, in order to understand its origin and spatiotemporal evolutionary history in relation to the Cenozoic climate shifts. Location Global, with highest species diversity in the Southern Hemisphere. The spatiotemporal biogeography of the Plucheinae was estimated by both a discrete method using a set of general distribution areas, and a relaxed random walk based on extant species distributions. The topology was time calibrated using a combination of secondary node ages and secondary derived rates for included loci. Our results indicate the median age of the Plucheinae to be approximately 15.4 Ma. The biogeographical analyses infer an ancestral origin in southern Africa, with the relaxed random walk analysis narrowing the uncertainty down to an area reaching from coastal Namibia to the western Kalahari. Africa was colonized in a (south)western–(north)eastern direction following the spread of arid habitats. Ancestral representatives of the Plucheinae colonized South America on at least three separate occasions (13.0–4.0, 4.3–3.1 and 4.1–3.7 Ma), with one subsequent spread to North America. Australia was colonized three times between 3.6 and 0.4 Ma. Madagascar and the Mascarenes were colonized at least seven times. The origin of the Plucheinae is estimated to the Namib region, with early speciations and radiations concurring with the timing of aridification of southern Africa, following the increase in strength of the Antarctic Circumpolar Current and subsequent formation of the Benguela Upwelling at c. 11.8 Ma. The current biogeographical distribution of the Plucheinae is best explained by several Neogene long-distance dispersal events from tropical Africa.

Aim: East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps).

Location: East Asia.

Methods: We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits.

Results: The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages.

Main conclusions: Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations,allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China, thus obscuring the genetic endemism of the Taiwanese populations.

Aim: The Pleistocene glacial cycles play a prominent role in shaping phylogeographicalpatterns of organisms, while few studies have focused on the regional difference ofglacial effects. By acquiring comprehensive knowledge of the origin, diversification andhistorical demography of an intensively studied passerine species complex, Great Tit,we aim to test the regional variation of the Late Pleistocene glaciation impacts on thiswidely distributed bird lineage.

Location: Eurasia and associated peninsulas and archipelagos.

Taxa: Parus major species complex.

Methods: Phylogeny, divergence times and demographic dynamics were estimatedwith Bayesian methods. Population structure, genetic diversity and correlation betweengenetic and physical distances were estimated based on mtDNA variation.Glacial-to-present distributional changes were assessed via ecological niche modelling(ENM).

Results: Five major clades (Central Asia, Eastern Asia, Eastern Himalaya, Northern and Western Eurasia and Southern Asia) were detected, with divergence timesranging 1.57–0.50 million years ago. Genetic diversity values and Bayesian skylineplots suggest that the three eastern clades had a deeper population history. A morecomplex geographic structure was observed in East Asia. Demographic expansionduring the last glacial cycle was indicated for all five clades. ENM results showed broad conservatism of traits related to climate tolerances, and generally broader andmore continuous distributional patterns under glacial conditions.

Main Conclusions: The Great Tit complex probably originated in Southeast Asia.Geographic barriers, such as the deserts of Central Asia and the Qinghai–TibetPlateau appear to be related to the lineage divergence. Late Pleistocene climate cyclesinfluenced both demographic dynamics and divergence, especially in terms ofeast–west differences in relation to geographic complexity.

Aim.The location of zoogeographical boundaries in eastern China has longbeen the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China.Location. Eastern China.Methods.Two mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny,tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods.Results. A congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c.40°N in easternChina. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene.Main conclusions. Our results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.

Aim Panbiogeographers suggest that the biome in New Caledonia is of vicariant origin, dating from the Cretaceous – rather than being the result of repeated dispersal since c. 37 Ma, when the area is postulated to have re-emerged after c. 15 Ma of submergence. Distributions of the plant family Sapotaceae were used as a model system to test this, and to elucidate the probabilities of ancestral areas, all phrased in six hypotheses.

Location Australasia and the Pacific.

Methods We used a recently published dataset with extensive sampling (168 terminals) from the subfamily Chrysophylloideae and three nuclear ribosomal DNA markers. Phylogenetic divergence times and ancestral areas were estimated in a Bayesian framework using beast, a relaxed clock method, and with fossil calibration points. Area transition probabilities were modelled using a reversible rate matrix, assigning equal prior probability to each transition between two areas.

Results Our analyses suggest that Sapotaceae arrived and diversified in New Caledonia nine times during the period 4.2–33.1 Ma. All crown-node radiations occurred in the Miocene or Pliocene, with stem splits reaching back into the Oligocene. Australia and New Guinea are the most likely source areas for Sapotaceae in New Caledonia, but this archipelago has never acted as a stepping stone for Sapotaceae to disperse into the Pacific.

Main conclusions Repeated dispersal is the only mechanism able to explain the range expansion of Sapotaceae into New Caledonia. The family has successfully colonized the main island nine times since its re-emergence in the Eocene. We reject the panbiogeographical hypotheses that representatives of Sapotaceae in New Caledonia originated in the Cretaceous, differentiated due to vicariance, and were of Pacific origin. We therefore argue that New Caledonia is an old Darwinian island. The Pacific has been colonized repeatedly and terminal lineages are never older than the islands they inhabit (except for Hawaii). Chrysophylloideae extended across Wallace’s Line into Southeast Asia around 20 Ma, when the Australian continent came into juxtaposition with Eurasia.