Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa

The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5–3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.     

Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

Aim To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub‐Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species. Location Sahel and Sudan savannas, Africa. Methods We sequenced the whole cytochrome b gene in 211 individuals from 59 localities distributed from Senegal to Ethiopia. Sequence data were analysed using both phylogenetic (several rooted tree‐construction methods, median‐joining networks) and population genetic methods (spatial analyses of molecular variance, mismatch distributions). Results Haplotypes were distributed into four major monophyletic groups corresponding to distinct geographical regions across a west–east axis. Diversification events were estimated to have occurred between 1.16 and 0.18 Ma. Main conclusions Vicariance events related to the fragmentation of savanna habitats during the Pleistocene era may explain the phylogeographical patterns observed. Genetic structure was consistent with a role of major Sahelian rivers as significant barriers to west–east dispersal. Recent demographic expansions probably occurred during arid phases of the Holocene with the southward expansion of savannas.     

Functional Traits and Water Transport Strategies in Lowland Tropical Rainforest Trees

Understanding how tropical rainforest trees may respond to the precipitation extremes predicted in future climate change scenarios is paramount for their conservation and management. Tree species clearly differ in drought susceptibility, suggesting that variable water transport strategies exist. Using a multi-disciplinary approach, we examined the hydraulic variability in trees in a lowland tropical rainforest in north-eastern Australia. We studied eight tree species representing broad plant functional groups (one palm and seven eudicot mature-phase, and early-successional trees). We characterised the species’ hydraulic system through maximum rates of volumetric sap flow and velocities using the heat ratio method, and measured rates of tree growth and several stem, vessel, and leaf traits. Sap flow measures exhibited limited variability across species, although early-successional species and palms had high mean sap velocities relative to most mature-phase species. Stem, vessel, and leaf traits were poor predictors of sap flow measures. However, these traits exhibited different associations in multivariate analysis, revealing gradients in some traits across species and alternative hydraulic strategies in others. Trait differences across and within tree functional groups reflect variation in water transport and drought resistance strategies. These varying strategies will help in our understanding of changing species distributions under predicted drought scenarios.     

Periodicity of Wood Formation in Some Trees of Lowland Rainforest in Nigeria

Freshly prepared chlor-zinc-iodide was used to determine theperiodicity of wood formation at breast height (144 cm fromthe ground) in the trunks of some trees growing in the LowlandRainforest around Ibadan, Nigeria. Wood formation shows seasonal periodicity in the plants studied.The cambial derivates on the xylem side differentiate into woodcells, which at a certain stage of differentiation have abundantcellulose in their secondary walls. The cellulose stains deepblue in chlor-zinc-iodide. This has been used as a criterionfor deciding that wood formation has started. When no cellswith deep blue staining secondary walls are found the cambiumis known to be dormant or quiscent. The resumption of cambial activity is correlated positivelywith bud break and unfolding of new leaves. In Bombax buonopozenseP. Beauv. the relationship may be obscured by local cambialactivity induced by injury. Wood formation stops in the trunks either towards the end ofthe rainy season or at the early part of the dry season. Itstarts either during the dry season or at the beginning of therainy season; but the bulk of the wood is formed during therainy season. Cambial activity stops in most cases before leaffall. At the cessation of wood formation the fully lignifiedxylem elements abut on the xylem mother cells or on xylem cellswith incompletely thickened cell walls. Presence or absence of a starch-free-zone and the noding ofthe vascular rays also give indications of seasonal periodicityin wood formation. Growth rings are periodic and one growthring is generally formed each year.     

Maclaudia felixii, a new genus and species in the Periplocaceae from Guinea, West Africa

Maclaudiafelixii, a new genus and species from Guinea, West Africa is described. Maclaudia resembles the genera Stomatostemma N.E. Br., Mangenotia Pichon and Ectadium E. Meyer in the structure of the flower. This new taxon is distinguished by the campanulate corolla tube, corniculate corona lobes arising from the corolla mouth, interstaminate lobular discs, and stamens arising from the base of the corolla tube.     

Phylogeography of colour polymorphism in the coral reef fish Pseudochromis fuscus, from Papua New Guinea and the Great Barrier Reef

Body colour has played a significant role in the evolution of coral reef fishes, but the phylogenetic level at which colour variation is expressed and the evolutionary processes driving the development and persistence of different colour patterns are often poorly understood. The aim of this study was to examine the genetic relationships between multiple colour morphs of Pseudochromis fuscus (family Pseudochromidae), both within and among geographic locations. Pseudochromis fuscus is currently described as a single species, but exhibits at least six discrete colour morphs throughout its range. In this study, P. fuscus from Papua New Guinea (PNG) and the Great Barrier Reef (GBR), Australia, formed three genetically distinct clades based on mitochondrial DNA (control region) sequence data: (1) yellow and brown morphs from the GBR and southern PNG, as well as an orange morph from southern PNG; (2) a pink morph from southern PNG; and (3) all three morphs (pink, orange and grey) found in Kimbe Bay, northern PNG. The three groups showed deep levels of divergence (d=14.6–25.4%), suggesting that P. fuscus is a complex of polychromatic species, rather than a single widespread species with many different colour morphs. Population genetic analyses indicate that the three clades have experienced unique evolutionary histories, possibly from differential effects of sea level fluctuations, barriers to gene flow and historical biogeography.     

Phylogeography of West Nile virus: from the cradle of evolution in Africa to Eurasia, Australia, and the Americas

West Nile virus (WNV) is the most widely distributed of the encephalitic flaviviruses and is a major cause of encephalitis, with isolates obtained from all continents, apart from Antarctica. Subsequent to its divergence from the other members of the Japanese encephalitis virus complex, presumably in Africa, WNV has diverged into individual lineages that mostly correspond with geographic distribution. Here we elucidate the phylogeography and evolutionary history of isolates from lineage 1 of WNV. Interestingly, there are many examples of the same amino acid having evolved independently on multiple occasions. In Africa, WNV exists in an endemic cycle, whereas it is epidemic in Europe, being reintroduced regularly from Africa either directly (in western Europe) or via the Middle East (in eastern Europe). Significantly, introduction into other geographic areas has occurred on one occasion only in each region, leading to subsequent establishment and expansion of the virus in these areas. Only one endemic genotype each is present in India and Australia, suggesting that WNV was successfully introduced into these locations once only. Each introduction occurred many centuries ago, probably due to trade and exploration during the 19th century. Likewise, in the Americas, WNV was successfully introduced in 1999 and subsequently became endemic across most temperate regions of North America (NA). In contrast to previous suggestions, an isolate from the epidemic in Israel in 1998 was not the direct progenitor of the NA epidemic; rather, both epidemics originated from the same (unknown) location.     

Phylogeography, risk factors and genetic history of hepatitis C virus in Gabon, central Africa

Background

The epidemiological and molecular characteristics of hepatitis C virus (HCV) infection in the general population have been poorly investigated in Africa. The aim of this study was to determine the prevalence, genotype distribution and epidemic history of HCV in the Gabonese general population.

Methods/Principal Findings

A total of 4042 sera collected from adults in 220 villages in all nine administrative areas of the country were screened for antibodies to HCV. HCV NS5B region sequencing was performed for molecular characterization and population genetic analyses. Of 4042 tested sera, 455 (11.2%) were positive. The seroprevalence of HCV varied significantly by administrative area, with the highest rate in Ogooué-Lolo province (20.4%) and the lowest in Ogooué-Maritine province (3.7%). History of parenteral injections, past hospital admission and age over 55 years were independent risk factors for HCV infection (p<0.0001). Phylogenetic analyses showed that 91.9% of the strains were genotype 4 (HCV-4), 5.7% genotype 1 and 2.2% genotype 2. HCV-4 strains were highly heterogeneous, with more than eight subtypes; subtype 4e predominated (57.3%). Coalescence analyses indicated that subtype 4e was the oldest, with an estimated most recent common ancestor of 1702 [95% CI, 1418–1884]. The epidemic profile indicated that it spread exponentially during the first part of the 20th century, probably by iatrogenic transmission.

Conclusions/Significance

These results confirm the endemicity of HCV subtype 4e in Gabon and show that its spread is due to a cohort effect, with previous, possibly iatrogenic events. More extensive epidemiological studies are needed to better characterize the route of transmission and the dissemination of HCV in Gabon.     

Two new genera of Caenidae (Insecta: Ephemeroptera) from Guinea,West Africa

Larvae of two new genera of Caenidae are described from the River Niandan, Guinea. Their position in the phylogenetic system of Caenidae is discussed. Niandancus alienus gen. n., sp. n. is the first known representative of the Brachycercinae in the Ethiopic region. Aenigmocaenis morgensterni gen. n., sp. n. could represent the sister group to all other Caenidae, as the most important larval synapomorphy of the family, a band or row of microtrichia on the ventral side of the operculate gill, is lacking.     

A systematic revision of the five-spotted Hemichromis complex (Cichliformes: Cichlidae) from West Africa and Lower Guinea,with the description of a new species from Cameroon

Hydrobiologia - The group of large five-spotted Hemichromis species from West Africa and Lower Guinea was&nbsp;revised using an integrative approach combining morphometry (measurements,...     

Malaria vector composition and insecticide susceptibility status in Guinea Conakry,West Africa

This study provides data on malaria vector species composition and insecticide susceptibility status from three localities in Guinea Conakry. A total of 497 mosquitoes were collected resting indoors and morphologically identified as belonging to the Anopheles gambiae complex. The majority of these were An. gambiae s.s. (99.6%), but a small percentage (0.4%) were identified as Anopheles arabiensis. Thirty‐four Anopheles funestus s.s. were also collected. The molecular S form of An. gambiae s.s. was predominant over the M form in Siguiri (95%) and Boffa (97.4%), whereas at Mt Nimba the M form was more abundant (61.4%) than the S form (38.1%). One hybrid M/S specimen was recorded from Mt Nimba. Siguiri populations showed high levels of resistance to DDT, dieldrin and bendiocarb. Anopheles gambiae from Boffa were largely susceptible to the insecticides tested. At Mt Nimba, resistance to DDT and bendicocarb was detected. Biochemical enzyme analysis showed that an altered acetylcholinesterase is operating in the field at low levels. The frequency of the 1014F kdr allele in the An. gambiae S form was 0.24 at Siguiri and 0.14 at Mt Nimba. A single RR specimen was found in the M form. The heterogeneity in species composition and resistance profiles between sites requires vector control interventions to be tailored to each site based on the data collected from ongoing monitoring and surveillance.     

The Role of Isolated Trees in Facilitating Tree Seedling Recruitment at a Degraded Sub-Tropical Rainforest Site

Successional development at abandoned farmlands in southern Queensland, formerly occupied by sub-tropical rain forest is centred around scattered, isolated trees. Soil seed banks contain few woody plants and most tree species appear to be recruited from seed dispersed into the site by birds or bats. Scattered, low-growing trees <3 m in height act as the initial focus for the activities of seed-dispersing birds, but this process is accelerated by the development of taller trees> 6 m in height that act as bird perches. The identity of these trees and whether or not they offer a fruit reward appears to matter less than their structure and suitability as a bird perch. The process of seedling recruitment may be accelerated when two or more trees form a cluster. The proportion of seedlings that survive and grow beyond 150 cm in height appears to be very small. Most of those that do can be classed as secondary rather than primary forest species, even though many primary forest species initially colonize the site. These observations were used to develop guidelines to accelerate the recovery of rainforest at degraded sites. The guidelines promote the early establishment of species that are usually poorly dispersed (e.g., large-fruited species), planted in scattered clumps. The guidelines should be suitable for situations where relatively large areas are in need of rehabilitation.     

Phylogeography of the Walnut Twig Beetle,Pityophthorus juglandis,the Vector of Thousand Cankers Disease in North American Walnut Trees

Thousand cankers disease (TCD) of walnut trees (Juglans spp.) results from aggressive feeding in the phloem by the walnut twig beetle (WTB), Pityophthorus juglandis, accompanied by inoculation of its galleries with a pathogenic fungus, Geosmithia morbida. In 1960, WTB was only known from four U.S. counties (in Arizona, California, and New Mexico), but the species has now (2014) invaded over 115 counties, representing much of the western USA, and at least six states in the eastern USA. The eastern expansion places TCD in direct proximity to highly valuable (> $500 billion) native timber stands of eastern black walnut, Juglans nigra. Using mitochondrial DNA sequences, from nearly 1100 individuals, we examined variation among 77 samples of WTB populations across its extended range in the USA, revealing high levels of polymorphism and evidence of two divergent lineages. The highest level of genetic diversity for the different lineages was found in the neighboring Madrean Sky Island and Western New Mexico regions, respectively. Despite their proximity, there was little evidence of mixing between these regions, with only a single migrant detected among 179 beetles tested. Indeed, geographic overlap of the two lineages was only common in parts of Colorado and Utah. Just two haplotypes, from the same lineage, predominated over the vast majority of the recently expanded range. Tests for Wolbachia proved negative suggesting it plays no role in "driving" the spread of particular haplotypes, or in maintaining deep levels of intraspecific divergence in WTB. Genotyping of ribosomal RNA corroborated the mitochondrial lineages, but also revealed evidence of hybridization between them. Hybridization was particularly prevalent in the sympatric areas, also apparent in all invaded areas, but absent from the most haplotype-rich area of each mitochondrial lineage. Hypotheses about the specific status of WTB, its recent expansion, and potential evolutionary origins of TCD are discussed.     

Valdosaurus, a hypsilophodontid dinosaur from the Lower Cretaceous of Europe and Africa

Material of the hypsilophodontid dinosaur Valdosauruscanaliculatus (Ornithischia: Ornithopoda) is described from the Lower Cretaceous (Barremian) of southern England and a new species is recognized from the Lower Cretaceous (Aptian) of Niger, West Africa. This occurrence of Valdosaurus in Europe and Africa provides evidence of a land connection between these continents across Tethys sometime in the early Cretaceous.     

Phylogeography of Rift Valley Fever virus in Africa reveals multiple introductions in Senegal and Mauritania

Rift Valley Fever (RVF) virus (Family Bunyaviridae) is an arthropod-borne RNA virus that infects primarily domestic ruminants and occasionally humans. RVF epizootics are characterized by numerous abortions and mortality among young animals. In humans, the illness is usually characterized by a mild self-limited febrile illness, which could progress to more serious complications. RVF virus is widespread and endemic in many regions of Africa. In Western Africa, several outbreaks have been reported since 1987 when the first major one occurred at the frontier of Senegal and Mauritania. Aiming to evaluate the spreading and molecular epidemiology in these countries, RVFV isolates from 1944 to 2008 obtained from 18 localities in Senegal and Mauritania and 15 other countries were investigated. Our results suggest that a more intense viral activity possibly took place during the last century compared to the recent past and that at least 5 introductions of RVFV took place in Senegal and Mauritania from distant African regions. Moreover, Barkedji in Senegal was possibly a hub associated with the three distinct entries of RVFV in West Africa.