Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.     

Energy requirements of migrating Great White Pelicans Pelecanus onocrotalus

The Great White Pelican Pelecanus anocrotalus is the largest migrating bird in Israel and is an endangered species. The Palearctic populations of the Great White Pelican breed in eastern Europe and Asia and most of them pass through the ‘bottleneck’ of Israel to wintering grounds in Africa. Natural feeding sites for pelicans have diminished during recent decades due to human activities, and sites of extensive aquaculture have become the favourite feeding places for wintering and migrating Great White Pelicans. The fish industry has reported a significant impact on fish yield and the conflict between pelicans and fishermen has escalated so that hundreds of pelicans have died in recent years from shooting or accidental electrocution. We approached this management problem by studying the energy requirements of the Great White Pelican during migration and while wintering in Israel, under different feeding regimes (fish or chicks) and in different seasons, in captivity. The results show that a captive bird consumes 1.1 kg of fish per day. The basal metabolic rate and apparent metabolized energy of the Great White Pelican are both higher than predicted from allometric equations. Energetic demands were quite stable on both diets (fish and chicks) and during both seasons (winter and summer). The fat deposits of migrating pelicans averaged 313.5 g compared with 480 g in wintering birds (3.4% and 5.4% of body mass, respectively). Based on these fat contents and on the measured daily energy consumption, we calculated that birds that do not feed in Israel can fly only up to 1620 km from Israel southward and could not cover the distance to their likely wintering grounds in the Sudd area in southern Sudan. However, birds that replenish their fuel reserves could fly up to 2460 km and hence could reach this area. Therefore, we conclude that Great White Pelicans must feed in Israel during the autumn migration in order to complete their journey to Africa. One solution to the conflict between pelicans and fishermen could be to combine deterrents preventing pelicans from feeding in fish‐ponds with the provision of attractive alternative reservoirs, to ensure regular food supplies during autumn.     

Satelliten-Telemetrie beim Wei?storchCiconia ciconia: Wanderung eines Ost-Storchs westlich bis Nigeria

A male White Stork, for the first time equipped with a mini-transmitter operated by a solar battery, was tracked on the eastern migration route from E Germany to central African winter quarters and during part of the return migration, for a total distance of about 10 000 km. The individual moved westward into Nigeria, i.e. into the wintering area of western Storks. Since a number of other eastern Storks were tracked as far as Chad, the possibility is discussed that individuals migrating to central Africa along the eastern or western route may eventually return on the opposite route when attracted to flocks of the population from the other side of the migration divide. Some ringing recoveries are consistent with a U-shaped abmigration.     

Onchocerca volvulus: genetic diversity of parasite isolates from Sudan

Onchocerciasis in Sudan exists in three distinct foci which exhibit differing clinical presentations. Previous studies have demonstrated that a tandemly repeated Onchocerca sequence family with a unit repeat length of 150 bp (the O-150 family) is a useful marker for deducing relationships among different O. volvulus populations. In the current study, the O-150 repeat families of O. volvulus from Sudan were analyzed and compared to each other and to those of parasites from West Africa. Similar to West African and American O. volvulus, the O-150 families of the Sudanese parasites could be divided into clusters within which little or no intracluster variation was evident, suggesting that the O-150 family in these parasites was subject to the forces of concerted evolution. Statistical analysis of the O-150 families from the different Sudanese parasite isolates, employing a nested algorithm based on an analysis of variance, revealed that O. volvulus endemic to the northern focus at Abu Hamed were significantly different from all other O. volvulus populations examined to date. In contrast, parasites from the southern and eastern foci of Sudan were indistinguishable from those endemic to the West African savanna. The significance of these data are discussed in light of knowledge of the biogeography and biology of transmission of O. volvulus in Africa.     

Environmental Kuznets Curve hypothesis and the role of globalization in selected African countries

The present study incorporates globalization and energy intensity into the CO₂ emissions function and investigates the presence of Environmental Kuznets Curve (EKC) in 19 African countries for the time period of 1971–2012. We have applied the ARDL bounds testing approach for cointegration to examine the long run relationship in the variables. Our results confirmed the presence of cointegration between the series in Africa, Algeria, Angola, Cameroon, Congo Republic, Ghana, Kenya, Libya, Morocco, Nigeria, South Africa, Sudan, Tanzania, Togo, Tunisia, Zambia and Zimbabwe. The results indicated the positive effect of energy intensity on CO₂ emissions in Africa, Algeria, Angola, Cameroon, Congo Republic, Ghana, Kenya, Libya, Morocco, Nigeria, South Africa, Sudan, Togo, and Tunisia while energy intensity declines CO₂ emissions in the case of Zambia and Zimbabwe. Globalization decreases CO₂ emissions in Africa, Angola, Cameroon, Congo Republic, Egypt, Kenya, Libya, Tunisia and Zambia but increases CO₂ emissions in Ghana, Morocco, South Africa, Sudan and Tanzania. The EKC exists in Africa, Algeria, Cameroon, Congo Republic, Morocco, Tunisia and Zambia but U-shaped relationship is found between economic growth and CO₂ emissions in Sudan and Tanzania.     

XLV.—Systematic Notes on East African Birds.

T he authors of these notes are engaged upon a work to be called 'The African Handbook of Birds,' the first part of which covers that area of eastern Africa which includes the Sudan, Eritrea, Abyssinia, the Somalilands, Uganda, Kenya Colony, Tanganyika Territory, Belgian Ruanda and Urundi, the part of Nyasaland east of Lake Nyasa and the Shirté River, the part of Portuguese East Africa north of the Zambesi, and the islands adjacent to the mainland, including Socotra, Abd-el-Kuri, Pemba, and Zanzibar.     

Isozyme variation inFaidherbia albida (Leguminosae, Mimosoideae)

Genetic variation has been assessed in 30 populations (931 families) ofFaidherbia albida (Leguminosae, Mimosoideae) from across its entire African range, using six isozyme loci identified by five enzyme systems. Among the populations studied a null allele was proposed to explain the absence ofLap-1 activity in populations from southern and eastern Africa. The mean percentage of polymorphic loci per population, the mean number of alleles per locus and the mean genetic diversity within populations were 31.7%, 1.6 and 0.127 respectively. Genetic diversity was greatest in populations from West Africa and lowest in populations from eastern/southern Africa, with Ethiopian/Sudanese populations intermediate. The overall degree of genetic differentiation between populations (G_ST) indicated that approximately 56% of the enzyme variation resided within populations. Clustering of Nei's unbaised genetic distances calculated between all populations produced a dendrogram that generally followed the geographic distribution of the populations. Two major groups were identified that may be considered the eastern/southern African and the Ethiopian/West African clusters. Within the Ethiopian/West African cluster two subclusters could be recognised, one broadly corresponding to those populations from Ethiopia/Sudan and the other to those populations from West Africa. The implications of these results for theories regarding the origin ofF. albida in Africa are discussed.     

Molecular relationships in Encephalartos (Zamiaceae, Cycadales) based on nucleotide sequences of nuclear ITS 1&2, rbcL, and genomic ISSR fingerprinting

The cycad genus Encephalartos is restricted to Africa and is threatened with extinction in most of its range. Total DNA was extracted from 51, i.e., 78 %, of the described species of Encephalartos. The accessions were sampled from the furthest western occurrence of the genus in Nigeria, via Sudan and Uganda, to southern South Africa. The sequences of nuclear ribosomal internal transcribed spacer regions 1 and 2 (ITS 1&2), the chloroplast encoded rbcL gene, and ISSR genomic fingerprinting were employed to resolve the molecular history and the relationships within the genus. Sequence alignment, as well as ISSR fingerprinting, data show low genetic variation among all analysed accessions, indicating diversification within the Pliocene/Pleistocene. ITS 1&2 data agree well with morphological and geographical characters and resolved three major genetic clusters with overlapping distribution ranges in eastern South Africa. This area, that contains the largest diversity of genotypes of Encephalartos, may have served as a Pliocene/Pleistocene refugium.     

Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography

Abstract.— A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species. We estimated the phylogeny and lineage divergence times within one such angiosperm group, the acridocarpoid clade (Malpighiaceae), with combined ITS, ndhF , and trnL-F data from 15 species that encompass the range of morphological and geographic variation within the group. Dispersal-vicariance analysis and divergence-time estimates suggest that the basal acridocarpoid divergence occurred between African and Southeast Asian lineages approximately 50 million years ago (mya), perhaps after a southward ancestral retreat from high-latitude tropical forests in response to intermittent Eocene cooling. Dispersion of Acridocarpus from Africa to Madagascar is inferred between approximately 50 and 35 mya, when lowland humid tropical forest was nearly continuous between these landmasses. A single dispersal event within Acridocarpus is inferred from western Africa to eastern Africa between approximately 23 and 17 mya, coincident with the widespread replacement of humid forests by savannas in eastern Africa. Although the spread of xeric environments resulted in the extinction of many African plant groups, our data suggest that for others it provided an opportunity for further diversification.     

Morphometric and molecular differentiation of Phlebotomus (Phlebotomus) sandflies

The closely related sandfly species of the subgenus Phlebotomus namely, Phlebotomus papatasi (Scopoli, 1786), Phlebotomus duboscqi Neveu‐Lemair, 1906 and Phlebotomus bergeroti Parrot, 1934 (Diptera: Psychodidae), are major vectors of Leishmania major (Kinetoplastida: Trypanosomatidae), the causative agent of cutaneous leishmaniasis in the Old World. Although allopatric in most of their distribution, the three species exist sympatrically in many places in central and eastern Sudan. Males of the three species can be distinguished using morphological characters; however, females are much harder to identify, thus complicating epidemiological studies. We carried out a morphometric and a molecular study to determine reliable morphological features and develop a polymerase chain reaction (PCR) assay for distinguishing females of these species. Males and females from each species were collected from sites in Sudan, East Africa and from one site in Mali, West Africa. Males were analysed morphologically and 20 characters and 10 character ratios were used in a stepwise discriminant analysis. This led to the identification of four characters with high discriminant loading scores sufficient for accurate male species identification. Male DNA was then used for the development of a PCR‐based species diagnostic based on the second internal transcribed spacer (ITS2) of the ribosomal DNA. A set of four primers was developed to generate fragment sizes that are specific to each species and can reliably identify females as well as hybrid DNA. Both the morphometric and the molecular findings of this study have important applications for studies of the epidemiology of cutaneous leishmaniasis.     

Genetic Diversity of Schistosoma haematobium Eggs Isolated from Human Urine in Sudan

The genetic diversity of Schistosoma haematobium remains largely unstudied in comparison to that of Schistosoma mansoni. To characterize the extent of genetic diversity in S. haematobium among its definitive host (humans), we collected S. haematobium eggs from the urine of 73 infected schoolchildren at 5 primary schools in White Nile State, Sudan, and then performed a randomly amplified polymorphic DNA marker ITS2 by PCR-RFLP analysis. Among 73 S. haematobium egg-positive cases, 13 were selected based on the presence of the S. haematobium satellite markers A4 and B2 in their genomic DNA, and used for RFLP analysis. The 13 samples were subjected to an RFLP analysis of the S. haematobium ITS2 region; however, there was no variation in size among the fragments. Compared to the ITS2 sequences obtained for S. haematobium from Kenya, the nucleotide sequences of the ITS2 regions of S. haematobium from 4 areas in Sudan were consistent with those from Kenya (> 99%). In this study, we demonstrate for the first time that most of the S. haematobium population in Sudan consists of a pan-African S. haematobium genotype; however, we also report the discovery of Kenyan strain inflow into White Nile, Sudan.     

Population Dynamics of Intermediate-Host Snails in the White Nile River,Sudan: A Year-Round Observational Descriptive Study

We aimed to explore the population dynamics of snail in 3 sites of the White Nile in Sudan. More specifically, we aimed to investigate the annual patterns of snail populations that act as intermediate hosts of schistosomes and monthly snail infection rates and ecological characteristics presumably related to snail populations. We collected snails for 1 year monthly at 3 different shore sites in the vicinity of El Shajara along the White Nile river in Khartoum State, Sudan. In addition, we measured air and water temperatures, water turbidities, vegetation coverages, and water depths and current speeds. Most of the collected snails were Biomphalaria pfeifferi and Bulinus truncatus. The population densities of snails and their infection rates varied across survey sites. The collected snails liberated S. mansoni and S. haematobium cercariae as well as Amphistome and Echinostome cercariae. Infected snails were found during March–June. The ecological characteristics found to be associated with the absence of snails population were: high turbidity, deep water, low vegetation coverage (near absence of vegetation), high water temperature, and high current speed. To our knowledge, this is the first longitudinal study of the snail population and ecological characteristics in the main basin of the White Nile river.     

Microbotanical Evidence of Domestic Cereals in Africa 7000 Years Ago

The study of plant exploitation and early use of cereals in Africa has seen over the years a great input from charred and desiccated macrobotanical remains. This paper presents the results of one of the few examples in Africa of microbotanical analyses. Three grave contexts of phytolith-rich deposits and the dental calculus of 20 individuals were analysed from two Neolithic cemeteries in North and Central Sudan. The radiocarbon-dated phytoliths from the burial samples show the presence of Near East domestic cereals in Northern Sudan at least 7000 years ago. Phytoliths also indicate the exploitation of wild, savannah-adapted millets in Central Sudan between 7500 and 6500 years ago. The calculus samples contained starch grains from wheat/barley, pulses and millets, as well as panicoid phytoliths. This evidence shows that Near East domestic cereals were consumed in Northern Africa at least 500 years earlier than previously thought.     

Genetic variation in Rhipicephalus appendiculatus (Acari: Ixodidae) from Zambia: correlating genetic and ecological variation with Rhipicephalus appendiculatus from eastern and southern Africa.

Based on their ecology, Rhipicephalus appendiculatus ticks from eastern and southern Africa have been divided into three groups. We investigated how two geographic genetically differentiated stocks of R. appendiculatus from the southern and the eastern provinces of Zambia, representing two ecological groups, i.e., southern African and transition groups, respectively, genetically compare to stocks from east Africa (Rwanda) and southern Africa (Zimbabwe and South Africa). The ITS2 and two mitochondrial genes segments, 12s rDNA and COI, were used in the investigations. The ITS2 tree did not show support for differentiation into any groups, while the two mitochondrial genes trees (12s rDNA and COI) showed two genetically differentiated groups: an east African genetic group which included specimens from Rwanda and the plateau area of the eastern province of Zambia, and a southern African genetic group represented by specimens from South Africa, Zimbabwe and specimens collected on the fringes of the eastern province plateau in the Nyimba district of Zambia. This suggests that the two geographically differentiated stocks of the southern and eastern provinces of Zambia might be part of two wider geographic genetically differentiated R. appendiculatus groups that extend beyond Zambia. Stocks of "transition" ecology (eastern province) belong to the east African genetic group and the differences in ecology within this genetic grouping may be due to genetic polymorphism, phenotypic plasticity, and other local factors.     

Cytogenetics of the Anopheles gambiae complex in Sudan, with special reference to An. arabiensis: relationships with East and West African populations

The species composition of malaria vector mosquitoes belonging to the Anopheles gambiae complex (Diptera: Culicidae) from >40 localities in Sudan, representing most ecological situations, was determined by analysis of ovarian polytene chromosomes. Of 2162 females, 93% were identified as An. arabiensis Patton and 7% were An. gambiae Giles sensu stricto. No hybrids were found between the two species. Anopheles arabiensis occurred in all but two sites, whereas An. gambiae s.s. was effectively limited to the southernmost, more humid localities. For chromosomal paracentric inversions, the degree of polymorphism was low in An. gambiae s.s. (inversions 2La, 2Rb and 2Rd), higher in An. arabiensis (inversions Xe, 2Ra, b, bc, d1, s; 3Ra, d). Anopheles gambiae samples from Sudan were all apparently panmictic, i.e. they did not show restricted gene flow such as observed among West African populations (interpreted as incipient speciation). Chromosomal inversion patterns of An. gambiae in southern Sudan showed characteristics of intergrading Savanna/Forest populations similar to those observed in comparable eco-climatic situations of West Africa. Anopheles arabiensis was polymorphic for inversion systems recorded in West Africa (2Ra, 2Rb, 2Rdl, 3Ra) and for a novel 2Rs polymorphism, overlapping with inversion systems 2Rb and 2Rd1. Samples carrying the 2Rs inversion were mostly from Khashm-el-Girba area in central-eastern Sudan. In the great majority of the samples all polymorphic inversions were found to be in Hardy-Weinberg equilibrium. Sudan populations of An. arabiensis should therefore be considered as generally panmictic. Anopheles arabiensis shows more inversion polymorphism in west than in east African populations. Sudan populations have more evident similarities with those from westwards than those from eastwards of the Great Rift Valley. The possible influence of the Rift on evolution of An. arabiensis is discussed.     

Satelliten-Telemetrie der Jahreswanderungen eines Wei?storchsCiconia ciconia und Diskussion der Orientierungsmechanismen des Heimzugs

In a female White Stork the complete migration cycle could be tracked by satellite from the nesting site to the wintering grounds in the Sudan and Tanzania and back to the nest. The migration route extended over 16 000 km, autumn migration lasted 100 days, homeward migration 70 days, wintering 58 and 41 days in northeastern and southeastern Africa, respectively. The maximum daily route was about 350 km. Up to Turkey the bird migrated together with its male. Homeward migration was performed within a relatively narrow corridor in which autumn migration took place, but in detail the routes of the two migratory seasons showed substantial differences. These data together with those from some raptors in which complete annual migration cycles could be tracked indicate that homeward migration is based on navigation (vector navigation and/or true navigation) rather than on route reversal.     

A Diet High in Saturated Fat and Sucrose Alters Glucoregulation and Induces Aortic Fatty Streaks in New Zealand White Rabbits

A new and convenient animal model for studying peripheral vascular and coronary artery disease in diabetes was established in this study. Male New Zealand White rabbits weighing approximately 2 kg were divided into 2 groups: a normal control group fed standard laboratory chow and a diabetogenic diet–fed group received a high-fat/high-sucrose diet. The high-fat/high-sucrose diet (contained 10% lard and 37% sucrose) feeding was maintained for 6 months. Plasma total cholesterol, high-density lipoprotein (HDL) cholesterol, triglyceride, superoxide dismutase, nitric oxide, nitric oxide synthase, insulin, and glucose were quantitated at monthly or bimonthly intervals. The aortic fatty streak lesions were quantified following lipid staining with Sudan IV. The aortic samples were observed by electron microscopy. High plasma triglyceride and glucose concentrations were induced. At the end of 6 months, the aortic fatty streak lesions were present in the animals'' vascular specimens. As far as we know, this is the first report that demonstrates that New Zealand White rabbits can develop obvious aortic fatty streaks by feeding a high-fat/high-sucrose diet. Our results suggest that NewZealand White rabbits fed a high-fat/high-sucrose diet would provide a convenient model for studying peripheral vascular and coronary artery disease in diabetes.     

Study on the Floristic Composition Similarity of Mangrove Among Their Global Distribution Regions

Based on set theory, the similarity and disparity indices among plant distribution regions were defined with the Jaccard’s similarity index. The similarity among six mangrove distribution regions in the world was analysed. The results showed that the region most similar to the eastern coast of Africa was the coast of Oceania, the region most similar to the coast of Asia and the eastern Pacific Archipelago was the coast of Oceania, the region most similar to the western coast of America was the western coast of Africa, the region most similar to the western coast of Africa was the eastern coast of America. By cluster analysis of the six mangrove distribution regions, the western coast of Africa and the eastern coast of America, the coast of Asia and eastern Pacific Archipelago and the coast of Oceania, were merged into two large regions respectively. The six mangrove distribution regions were further merged into two large regions which were consistent with the east central group and the west central group.