Genetic evidence for Rift Valley fever outbreaks in Madagascar resulting from virus introductions from the East African mainland rather than enzootic maintenance

Rift Valley fever virus (RVFV), a mosquito-borne phlebovirus, has been detected in Madagascar since 1979, with occasional outbreaks. In 2008 to 2009, a large RVFV outbreak was detected in Malagasy livestock and humans during two successive rainy seasons. To determine whether cases were due to enzootic maintenance of the virus within Madagascar or to importation from the East African mainland, nine RVFV whole genomic sequences were generated for viruses from the 1991 and 2008 Malagasy outbreaks. Bayesian coalescent analyses of available whole S, M, and L segment sequences were used to estimate the time to the most recent common ancestor for the RVFVs. The 1979 Madagascar isolate shared a common ancestor with strains on the mainland around 1972. The 1991 Madagascar isolates were in a clade distinct from that of the 1979 isolate and shared a common ancestor around 1987. Finally, the 2008 Madagascar viruses were embedded within a large clade of RVFVs from the 2006-2007 outbreak in East Africa and shared a common ancestor around 2003 to 2004. These results suggest that the most recent Madagascar outbreak was caused by a virus likely arriving in the country some time between 2003 and 2008 and that this outbreak may be an extension of the 2006-2007 East African outbreak. Clustering of the Malagasy sequences into subclades indicates that the viruses have continued to evolve during their short-term circulation within the country. These data are consistent with the notion that RVFV outbreaks in Madagascar result not from emergence from enzootic cycles within the country but from recurrent virus introductions from the East African mainland.     

Ectomycorrhizal Associations of the Dipterocarpaceae

Dipterocarps are one of the most important tree families in the lowland forests of Southeast Asia and are somewhat unusual among tropical trees in that they form ectomycorrhizal (EcM) symbiotic root‐inhabiting fungal associations. It has been hypothesized that dipterocarps have been partnered in this mutualistic association prior to the separation of Gondwana. Under many conditions EcMs form rapidly on dipterocarp seedlings through inocula present in the soil, although few studies have been conducted to provide evidence that they improve seedling establishment and performance. There are hundreds of EcM species associated with dipterocarps. Fungal fruit body surveys suggest that the most important families are Amanitaceae, Boletaceae, and Russulaceae, although Thelephoraceae also become numerically important when root tips are examined. EcM communities are affected by various biotic and abiotic factors, as well as anthropogenic perturbations, and the importance of these in structuring EcM communities is examined herein.     

Evolution of gliding in Southeast Asian geckos and other vertebrates is temporally congruent with dipterocarp forest development

Gliding morphologies occur in diverse vertebrate lineages in Southeast Asian rainforests, including three gecko genera, plus frogs, snakes, agamid lizards and squirrels. It has been hypothesized that repeated evolution of gliding is related to the dominance of Asian rainforest tree floras by dipterocarps. For dipterocarps to have influenced the evolution of gliding in Southeast Asian vertebrates, gliding lineages must have Eocene or later origins. However, divergence times are not known for most lineages. To investigate the temporal pattern of Asian gliding vertebrate evolution, we performed phylogenetic and molecular clock analyses. New sequence data for geckos incorporate exemplars of each gliding genus (Cosymbotus, Luperosaurus and Ptychozoon), whereas analyses of other vertebrate lineages use existing sequence data. Stem ages of most gliding vertebrates, including all geckos, cluster in the time period when dipterocarps came to dominate Asian tropical forests. These results demonstrate that a gliding/dipterocarp correlation is temporally viable, and caution against the assumption of early origins for apomorphic taxa.     

Pisolithus indicus, a new species of ectomycorrhizal fungus associated with Dipterocarps [corrected] in India

Pisolithus is cosmopolitan in both tropical and temperate regions and forms ectomycorrhizal associations with a wide range of woody plants. Pisolithus indicus, a new species associated with Vateria indica (Dipterocarpaceae) is reported in this study from a dipterocarp native forest in the Western Ghats in India, using both morphological and molecular tools. The length of ITS1 and ITS2 regions of the present collection differed with other sequences of Pisolithus available in the databases. Phylogenetic analysis indicates that this species did not show significant homology with existing Pisolithus sequences reported previously and formed a separate branch linking with another Pisolithus isolate from dipterocarps. Molecular and morphological evidence showed that P. indicus is a new species associated with dipterocarps in India.     

Phylogeny and biogeography of exacum (gentianaceae): a disjunctive distribution in the Indian ocean basin resulted from long distance dispersal and extensive radiation

Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacum is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacum, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India-Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance dispersals followed by extensive range expansion and subsequent fragmentation. The extant African species E. oldenlandioides is confirmed to be recently dispersed from Madagascar.     

The evolutionary origin of Indian Ocean tortoises (Dipsochelys)

Today, the only surviving wild population of giant tortoises in the Indian Ocean occurs on the island of Aldabra. However, giant tortoises once inhabited islands throughout the western Indian Ocean. Madagascar, Africa, and India have all been suggested as possible sources of colonization for these islands. To address the origin of Indian Ocean tortoises (Dipsochelys, formerly Geochelone gigantea), we sequenced the 12S, 16S, and cyt b genes of the mitochondrial DNA. Our phylogenetic analysis shows Dipsochelys to be embedded within the Malagasy lineage, providing evidence that Indian Ocean giant tortoises are derived from a common Malagasy ancestor. This result points to Madagascar as the source of colonization for western Indian Ocean islands by giant tortoises. Tortoises are known to survive long oceanic voyages by floating with ocean currents, and thus, currents flowing northward towards the Aldabra archipelago from the east coast of Madagascar would have provided means for the colonization of western Indian Ocean islands. Additionally, we found an accelerated rate of sequence evolution in the two Malagasy Pyxis species examined. This finding supports previous theories that shorter generation time and smaller body size are related to an increase in mitochondrial DNA substitution rate in vertebrates.     

Out of Africa? A dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot & Audinet‐Serville

The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four‐gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa. The tribe appears to have diversified during the Cenozoic, beginning c. 50–32 Ma, with most extant African lineages originating in the Miocene or later, well after the breakup of the Gondwanan landmass. Biogeographical analysis suggests an African origin for the tribe and a single dispersal event founding the Asian platypleurines, although additional taxon sampling and genetic data will be needed to confirm this pattern because key nodes in the tree are still weakly supported. Two Platypleurini genera from Madagascar (Pycna Amyot & Audinet‐Serville, Yanga Distant) are found to have originated by late Miocene dispersal of a single lineage from Africa. The genus Platypleura is recovered as polyphyletic, with Platypleura signifera Walker from South Africa and many Asian/Indian species apparently requiring assignment to different genera, and a new Platypleura concept is proposed with the synonymization of Azanicada Villet syn.n. The genera Orapa Distant and Hamza Distant, currently listed within separate tribes but suspected of platypleurine affinity, are nested deeply within the Platypleurini radiation. The tribe Orapini syn.n . is here synonymized while the tribe Hamzini is pending a decision of the ICZN to preserve nomenclatorial stability.     

An ancient African radiation of corvoid birds (Aves: Passeriformes) detected by mitochondrial and nuclear sequence data

The Malaconotidae, Platysteiridae and Vangidae represent an African and Malagasy assemblage of closely related corvoid taxa with distinctive morphology. Their relationships with their putative Asian closest relatives, and thus their biogeographic history, have not hitherto been thoroughly evaluated. We present evidence that the African and Malagasy groups originated through a single African colonization event c. 37.7 ± 4.6 Myr BP. Three main groups that differ in their foraging behaviour diverged c. 35.8 ± 4.5 Myr BP, suggesting that an African radiation occurred around that time. Several disperal events out of Africa to Madagascar (Vangidae) and Indo-Malaya ( Philentoma , Hemipus and Tephrodornis ) took place about 28.9 ± 4.0 Myr BP (Oligocene), a period when faunistic exchanges between Eurasia and Africa seem to have been common. Our estimation of the colonization of Madagascar by the Vangidae is 28.9 ± 4.0 Myr BP, in congruence with the estimated colonization of Madagascar by several African vertebrate groups (carnivorous mammals, snakes, sylvioid passerines, treefrogs, turtles).     

The genetic or mythical ancestry of descent groups: lessons from the Y chromosome

Traditional societies are often organized into descent groups called "lineages," "clans," and "tribes." Each of these descent groups claims to have a common ancestor, and this ancestry distinguishes the group's members from the rest of the population. To test the hypothesis of common ancestry within these groups, we compared ethnological and genetic data from five Central Asian populations. We show that, although people from the same lineage and clan share generally a recent common ancestor, no such common ancestry is observed at the tribal level. Thus, a tribe might be a conglomerate of clans who subsequently invented a mythical ancestor to strengthen group unity.     

Pakaraimaea dipterocarpacea is ectomycorrhizal, indicating an ancient Gondwanaland origin for the ectomycorrhizal habit in Dipterocarpaceae

The consistent association of Paleotropical Dipterocarpaceae with ectomycorrhizal (ECM) fungi suggests that ECM status is an ancestral character in the family. Despite its distinctive morphology, Pakaraimaea dipterocarpacea, a Neotropical Dipterocarpaceae endemic to the Guayana Region, is phylogenetically related to the Paleotropical Dipterocarpaceae. The confirmation of P. dipterocarpacea ECM status would indicate that Paleotropical Dipterocarpaceae and P. dipterocarpacea probably had a common ECM ancestor. Mycorrhizal colonization of P. dipterocarpacea was assessed, and ECMs were recorded using histological and molecular methods. P. dipterocarpacea was highly colonized by typical ECMs, and several ECM fungal taxa belonging to Clavulinaceae, Sebacinaceae, Cortinariaceae and Amanitaceae were identified. This paper provides the first documented evidence of ECM in a neotropical genus of Dipterocarpaceae and indicates that ECMs possibly evolved in Gondwana in ancestors of Dipterocarpaceae before the separation of South America from Africa by the Atlantic, c. 135 million years ago. The observation of Sebacinaceae and Clavulinaceae suggests that broad host range fungi are important components of P. dipterocarpacea ECM communities.     

Why does the biota of the Madagascar region have such a strong Asiatic flavour?

A corollary of island biogeographical theory is that islands are largely colonized from their nearest mainland source. Despite Madagascar’s extreme isolation from India and proximity to Africa, a high proportion of the biota of the Madagascar region has Asian affinities. This pattern has rarely been viewed as surprising, as it is consistent with Gondwanan vicariance. Molecular phylogenetic data provide strong support for such Asian affinities, but often not for their vicariant origin; most divergences between lineages in Asia and the Madagascar region post‐date the separation of India and Madagascar considerably (up to 87 Myr), implying a high frequency of dispersal that mirrors colonization of the Hawaiian archipelago in distance. Indian Ocean bathymetry and the magnitude of recent sea‐level lowstands support the repeated existence of sizeable islands across the western Indian Ocean, greatly reducing the isolation of Madagascar from Asia. We put forward predictions to test the role of this historical factor in the assembly of the regional biota. © The Willi Hennig Society 2009.     

Molecular phylogeny among local populations of weaver ant Oecophylla smaragdina

The molecular phylogeny of 24 Oecophylla smaragdina populations and two O. longinoda populations was studied using 647 bp of the mitochondrial cyt b gene. The phylogenetic analysis suggested that O. smaragdina and O. longinoda were separated from each other first, and after that the first within-species divergence of O. smaragdina occurred in early stage of their history, in which the Asian, Australian, and Sulawesian groups rose. This grouping was almost coincident with the distribution of landmass in glacial periods in Pleistocene. Thereafter, each group seemed to have independently diverged into present populations on each landmass.     

New evidence of ectomycorrhizal fungi in the Hawaiian Islands associated with the endemic host Pisonia sandwicensis (Nyctaginaceae)

Ectomycorrhizal plants and fungi are ubiquitous in mainland forests, but because of dispersal limitations are predicted to be less common on isolated islands. For instance, no native ectomycorrhizal plants or fungi have ever been reported from Hawaii, one of the most remote archipelagos on Earth. Members of the plant tribe Pisonieae are common on many islands, and prior evidence shows that some species associate with ectomycorrhizal fungi. However, until now, the Pisonieae species of Hawaii had yet to be examined for their mycorrhizal status. Here we sampled roots from members of the genus Pisonia growing on the Hawaiian islands of Oahu, Maui and Hawaii. We used molecular and microscopic techniques to categorize trees with respect to their mycorrhizal associations. We report that the Hawaiian endemic Pisonia sandwicensis forms ectomycorrhizas with at least five fungal operational taxonomic units (corresponding closely to species) belonging to four genera. We also report that this tree species is monophyletic with other ectomycorrhizal Pisonia species. We suggest that in light of the newly discovered Hawaiian ectomycorrhizal fungal community and other island ectomycorrhizal communities, dispersal limitations do not prevent the colonization of remote islands by at least some ectomycorrhizal fungi.     

DNA-based fungal diversity in Madagascar and arrival of the ectomycorrhizal fungi to the island

Madagascar is known for its high diversity and endemism of fauna and flora. Fungi, however, have been largely overlooked in diversity and evolution studies on the island, and whether fungi exhibit the same patterns as animals and plants has yet to be further examined. We collected fungal sporocarps and ectomycorrhizal (EcM) roots during three opportunistic surveys in five forests in Madagascar and generated a dataset of fungal Internal Transcribed Spacer (ITS) DNA sequences. We analyzed them together with all publicly available fungal ITS DNA sequences and identified 620 Operational Taxonomic Units (OTUs) from Madagascar, 10% of which contained only sequences from our surveys. Two hundred and ninety-two OTUs belonged to EcM species with /russula-lactarius, /boletus, /tomentella-telephora, /cortinarius, and /amanita being the most abundant EcM lineages. Overall, 60% of all fungi and 81% of the EcM species from Madagascar appear to be endemic. We conducted a phylogenetic analysis using all the OTUs in Amanitaceae, Boletaceae, and Russulaceae families to elucidate their relative timing of arrival in Madagascar. We found that most EcM species from Madagascar in the three families diverged less than 22 million years ago (mya), long after the separation of India and Madagascar (88 mya), which is consistent with a dispersal mediated process of arrival to the island. Our study provides the first comprehensive view of the overall DNA-based fungal diversity in Madagascar and the current state of knowledge of EcM fungi based on DNA sequences, useful for further ecological and evolutionary studies. Abstract in Malagasy is available with online material.     

Agro-Environmental Determinants of Avian Influenza Circulation: A Multisite Study in Thailand,Vietnam and Madagascar

Outbreaks of highly pathogenic avian influenza have occurred and have been studied in a variety of ecological systems. However, differences in the spatial resolution, geographical extent, units of analysis and risk factors examined in these studies prevent their quantitative comparison. This study aimed to develop a high-resolution, comparative study of a common set of agro-environmental determinants of avian influenza viruses (AIV) in domestic poultry in four different environments: (1) lower-Northern Thailand, where H5N1 circulated in 2004–2005, (2) the Red River Delta in Vietnam, where H5N1 is circulating widely, (3) the Vietnam highlands, where sporadic H5N1 outbreaks have occurred, and (4) the Lake Alaotra region in Madagascar, which features remarkable similarities with Asian agro-ecosystems and where low pathogenic avian influenza viruses have been found. We analyzed H5N1 outbreak data in Thailand in parallel with serological data collected on the H5 subtype in Vietnam and on low pathogenic AIV in Madagascar. Several agro-environmental covariates were examined: poultry densities, landscape dominated by rice cultivation, proximity to a water body or major road, and human population density. Relationships between covariates and AIV circulation were explored using spatial generalized linear models. We found that AIV prevalence was negatively associated with distance to the closest water body in the Red River Delta, Vietnam highlands and Madagascar. We also found a positive association between AIV and duck density in the Vietnam highlands and Thailand, and with rice landscapes in Thailand and Madagascar. Our findings confirm the important role of wetlands-rice-ducks ecosystems in the epidemiology of AI in diverse settings. Variables influencing circulation of the H5 subtype in Southeast Asia played a similar role for low pathogenic AIV in Madagascar, indicating that this area may be at risk if a highly virulent strain is introduced.     

On the distributional patterns of Southeast-East Asian freshwater fish and their history

Abstract Aim The extensively published data on Southeast‐East Asian freshwater fish communities and distributions were compiled and expressed into phenograms. Location River basins of Southeast China, the Indochinese Peninsula and Sundaland were studied and compared for possible lineages. Methods The Hennig86 program was employed to cluster the basins of the various subregions on the basis of their similarity in fish assemblages. In this cluster analysis, the outgroup comparison method was used, in which a reference was based on which to make corrections for unequal rates of evolution among the lineages. Results South‐eastern China, the Indochinese Peninsula and Sundaland are groups of landmass that share a common ancestor and that evolved at distinct epochs and through different geological processes, as shown from the association between the distribution of freshwater fish of Southeast‐East Asia and the twenty‐one river basins they inhabit. Main conclusions Southeast‐East Asia comprises an estimated 3500 cyprinid species. The phenograms obtained, based on their compositional and distributional patterns, suggest that the riverine fish communities of the area studied fall into nineteen biogeographical zones defined by the main river systems and their underlying geology.     

Neoendemism in Madagascan scaly tree ferns results from recent, coincident diversification bursts

More than 80% of Madagascar's 12,000 plant species are endemic with the degree of endemism reaching as much as 95% in the scaly tree ferns, an important species rich component of Madagascar's evergreen rainforests. Predominantly African or Asian ancestry and divergence times usually postdating the separation of Madagascar from the Gondwanan landmasses have been demonstrated for several Madagascan animal and angiosperm groups. However, evolutionary studies of rainforest-specific lineages are scarce and the ecological context of radiation events has rarely been investigated. Here, we examine the evolution of Madagascan tree ferns as a rainforest-specific model family, integrate results from bioclimatic niche analysis with a dated phylogenetic framework, and propose an evolutionary scenario casting new light on our knowledge of the evolution of large island endemic clades. We show that Madagascar's extant tree fern diversity springs from three distinct ancestors independently colonizing Madagascar in the Miocene and that these three monophyletic clades diversified in three coincident radiation bursts during the Pliocene, reaching exceptionally high diversification rates and most likely responding to a common climatic trigger. Recent diversification bursts may thus have played a major role in the evolution of the extant Madagascan rainforest biome, which hence contains a significant number of young, neoendemic taxa.     

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice

Understanding how crop species spread and are introduced to new areas provides insights into the nature of species range expansions. The domesticated species Oryza sativa or Asian rice is one of the key domesticated crop species in the world. The island of Madagascar off the coast of East Africa was one of the last major Old World areas of introduction of rice after the domestication of this crop species and before extensive historical global trade in this crop. Asian rice was introduced in Madagascar from India, the Malay Peninsula and Indonesia approximately 800-1400 years ago. Studies of domestication traits characteristic of the two independently domesticated Asian rice subspecies, indica and tropical japonica, suggest two major waves of migrations into Madagascar. A population genetic analysis of rice in Madagascar using sequence data from 53 gene fragments provided insights into the dynamics of island founder events during the expansion of a crop species' geographic range and introduction to novel agro-ecological environments. We observed a significant decrease in genetic diversity in rice from Madagascar when compared to those in Asia, likely the result of a bottleneck on the island. We also found a high frequency of a unique indica type in Madagascar that shows clear population differentiation from most of the sampled Asian landraces, as well as differential exchange of alleles between Asia and Madagascar populations of the tropical japonica subspecies. Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island.