Abundance,diversity and geographic distribution of cassava mosaic disease pandemic‐associated Bemisia tabaci in Tanzania

Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae), one of the most economically important agricultural pests worldwide, is the vector of cassava mosaic geminiviruses that cause cassava mosaic disease (CMD). In East and Central Africa, a severe CMD pandemic that spread from Uganda in the late 1980s still continues to devastate cassava crops. To assess the association of distinct B. tabaci genetic groups with the CMD pandemic, mitochondrial cytochrome oxidase I gene sequences were analysed from whiteflies collected during surveys conducted from 2010 to 2013 in Tanzania. Four genetic groups – Sub‐Saharan Africa 1 (SSA1), Mediterranean, Indian Ocean and East Africa 1, and a group of unknown whitefly species were identified. SSA1 comprised four subgroups: SSA1‐SG1, SSA1‐SG2, SSA1‐SG1/2 and SSA1‐SG3. SSA1‐SG1 was confined to the pandemic‐affected north‐western parts of Tanzania whilst SSA1‐SG2 and SSA1‐SG3 were found in the central and eastern parts not yet affected by the pandemic. The CMD pandemic front was estimated to lie in Geita Region, north‐western Tanzania, and to be spreading south‐east at a rate of ca 26 km/year. The pandemic‐associated B. tabaci SSA1‐SG1 predominated up to 180 km ahead of the CMD front indicating that changes in whitefly population characteristics precede changes in disease characteristics.     

Diversity of symbiotic bacteria associated with Bemisia tabaci (Homoptera: Aleyrodidae) in cassava mosaic disease pandemic areas of Tanzania

All Bemisia tabaci individuals harbour an obligate bacterial symbiont (Portiera aleyrodidarum), and many also harbour non‐essential facultative symbionts. The association of symbiotic bacteria with the various genetic groups of B. tabaci remains unknown for East Africa. This study aimed to assess any association between the various whitefly genetic groups and the endosymbionts they harbour; to investigate if a unique endosymbiont is associated with super‐abundant whiteflies, and to provide baseline information on endosymbionts of whiteflies for a part of East Africa. Whiteflies collected during surveys in Tanzania were genotyped and screened for the presence of the obligate and six secondary symbionts (SS): Rickettsia (R), Hamiltonella (H), Arsenophonus (A), Wolbachia (W), Cardinium (C) and Fritschea (F). The results revealed the presence of Mediterranean (MED), East Africa 1 (EA1), Indian Ocean (IO) and Sub‐Saharan Africa 1 (SSA1) genetic groups of Bemisia tabaci, with SSA1 further clustered into four sub‐groups: SSA1‐SG1, SSA1‐SG2, SSA1‐SG1/2 and SSA1‐SG3. F was completely absent from all of the whiteflies tested while R was always found in double or multiple infections. In general, no particular symbiont appeared to be associated with the super‐abundant SSA1‐SG1 B. tabaci, although A or AC infections were common among infected individuals. The most striking feature of these super‐abundant whiteflies, dominating cassava mosaic disease pandemic areas, was the high prevalence of individuals uninfected by any of the six SS tested. This study of the endosymbionts of B. tabaci in East Africa showed contrasting patterns of infection in crop and weed hosts.     

Whole-genome single nucleotide polymorphism and mating compatibility studies reveal the presence of distinct species in sub-Saharan Africa Bemisia tabaci whiteflies

In sub-Saharan Africa cassava growing areas, two members of the Bemisia tabaci species complex termed sub-Saharan Africa 1 (SSA1) and SSA2 have been reported as the prevalent whiteflies associated with the spread of viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics. At the peak of CMD pandemic in the late 1990s, SSA2 was the prevalent whitefly, although its numbers have diminished over the last two decades with the resurgence of SSA1 whiteflies. Three SSA1 subgroups (SG1 to SG3) are the predominant whiteflies in East Africa and vary in distribution and biological properties. Mating compatibility between SSA1 subgroups and SSA2 whiteflies was reported as the possible driver for the resurgence of SSA1 whiteflies. In this study, a combination of both phylogenomic methods and reciprocal crossing experiments were applied to determine species status of SSA1 subgroups and SSA2 whitefly populations. Phylogenomic analyses conducted with 26 548 205 bp whole genome single nucleotide polymorphisms (SNPs) and the full mitogenomes clustered SSA1 subgroups together and separate from SSA2 species. Mating incompatibility between SSA1 subgroups and SSA2 further demonstrated their distinctiveness from each other. Phylogenomic analyses conducted with SNPs and mitogenomes also revealed different genetic relationships among SSA1 subgroups. The former clustered SSA1-SG1 and SSA1-SG2 together but separate from SSA1-SG3, while the latter clustered SSA1-SG2 and SSA1-SG3 together but separate from SSA1-SG1. Mating compatibility was observed between SSA1-SG1 and SSA1-SG2, while incompatibility occurred between SSA1-SG1 and SSA1-SG3, and SSA1-SG2 and SSA1-SG3. Mating results among SSA1 subgroups were coherent with phylogenomics results based on SNPs but not the full mitogenomes. Furthermore, this study revealed that the secondary endosymbiont—Wolbachia—did not mediate reproductive success in the crossing assays carried out. Overall, using genome wide SNPs together with reciprocal crossings assays, this study established accurate genetic relationships among cassava-colonizing populations, illustrating that SSA1 and SSA2 are distinct species while at least two species occur within SSA1 species.     

Microbiome diversity and reproductive incompatibility induced by the prevalent endosymbiont Arsenophonus in two species of African cassava Bemisia tabaci whiteflies

A minimum of 13 diverse whitefly species belonging to the Bemisia tabaci (B. tabaci) species complex are known to infest cassava crops in sub‐Saharan Africa (SSA), designated as SSA1‐13. Of these, the SSA1 and SSA2 are the predominant species colonizing cassava crops in East Africa. The SSA species of B. tabaci harbor diverse bacterial endosymbionts, many of which are known to manipulate insect reproduction. One such symbiont, Arsenophonus, is known to drive its spread by inducing reproductive incompatibility in its insect host and are abundant in SSA species of B. tabaci. However, whether Arsenophonus affects the reproduction of SSA species is unknown. In this study, we investigated both the reproductive compatibility between Arsenophonus infected and uninfected whiteflies by inter‐/intraspecific crossing experiments involving the sub‐group three haplotypes of the SSA1 (SSA1‐SG3), SSA2 species, and their microbial diversity. The number of eggs, nymphs, progenies produced, hatching rate, and survival rate were recorded for each cross. In intra‐specific crossing trials, both male and female progenies were produced and thus demonstrated no reproductive incompatibility. However, the total number of eggs laid, nymphs hatched, and the emerged females were low in the intra‐species crosses of SSA1‐SG3A+, indicating the negative effect of Arsenophonus on whitefly fitness. In contrast, the inter‐species crosses between the SSA1‐SG3 and SSA2 produced no female progeny and thus demonstrated reproductive incompatibility. The relative frequency of other bacteria colonizing the whiteflies was also investigated using Illumina sequencing of 16S rDNA and diversity indices were recorded. Overall, SSA1‐SG3 and SSA2 harbored high microbial diversity with more than 137 bacteria discovered. These results described for the first time the microbiome diversity and the reproductive behaviors of intra‐/inter‐species of Arsenophonus in whitefly reproduction, which is crucial for understanding the invasion abilities of cassava whiteflies.     

Genetic identification of members of the Bemisia tabaci cryptic species complex from South Africa reveals native and introduced haplotypes

The whitefly Bemisia tabaci cryptic species complex contains some important agricultural pest and virus vectors. Members of the complex have become serious pests in South Africa (SA) because of their feeding habit and their ability to transmit begomovirus species. Despite their economic importance, studies on the biology and distribution of B. tabaci in SA are limited. To this end, a survey was made to investigate the diversity and distribution of B. tabaci cryptic species in eight geographical locations (provinces) in SA, between 2002 and 2009, using the mitochondrial cytochrome oxidase I (mtCOI) sequences. Phylogenetic analysis revealed the presence of members from two endemic sub‐Saharan Africa (SSAF) subclades coexisting with two introduced putative species. The SSAF‐1 subclade includes cassava host‐adapted B. tabaci populations, whereas the whiteflies collected from cassava and non‐cassava hosts formed a distinct subclade, referred to as SSAF‐5, and represent a new subclade among previously recognized southern Africa clades. Two introduced cryptic species, belonging to the Mediterranean and Middle East–Asia minor 1 clades, were identified and include the B and Q types. The B type showed the widest distribution, being present in five of the eight provinces explored in SA, infesting several host plants and predominating over the indigenous haplotypes. This is the first report of the occurrence of the exotic Q type in SA alongside the more widely distributed B type. Furthermore, mtCOI PCR‐RFLP was developed for the SA context to allow rapid discrimination between the B, Q and SSAF putative species. The capacity to manage pests and disease effectively relies on knowledge of the identity of the agents causing the damage. Therefore, this study contributes to the understanding of South African B. tabaci species diversity, information needed for the development of knowledge‐based disease management practices.     

Application of hydrolysis probe analysis to identify clade types of the malaria vector mosquito Anopheles funestus sensu stricto from Muheza,northeastern Tanzania

A hydrolysis probe analysis (TaqMan assay) was used to study clade types in Anopheles funestus sensu stricto Giles, a major malaria vector in sub‐Saharan Africa, with specimens collected from Muheza in Tanga, northeastern Tanzania. A total of 186 An. funestus specimens were analysed, revealing that 176 (94.6%) were of clade I and 10 (5.4%) of clade II. These findings extend the distribution of clade type II from southern Mozambique and northern Zambia to northeastern Tanzania. The technique used can also be of great value in assessing the role and contribution of these clade types in malaria transmission and insecticide resistance frequencies for An. funestus s.s.     

New insights into the mitochondrial phylogeny of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in the Mediterranean Basin

The whitefly Bemisia tabaci is vector of plant infecting viruses and it is considered as one of the most important agricultural pests around the Mediterranean basin. At present, five biotypes of B. tabaci have been reported in the Mediterranean Basin: B, Q, S, T and M. To establish the phylogeographic relationship of these Mediterranean biotypes with others, 54 samples collected in Europe and Africa were analysed by sequencing the mitochondrial cytochrome oxidase I gene (mtCOI). The phylogeny showed that Spanish samples corresponding to the biotype S were related to the haplotype Uganda 2 of the African clade, associated with recent epidemic upsurges of cassava mosaic virus (CMD) in that country. This phylogeographic relationship gave support to a distinct subgroup revealed within the African clade. Bemisia tabaci collected from Euphorbia plants in Italy (biotype T) formed one of the three distinct subgroups existing within the Southeast/Far East Asian clade, while samples from Turkey (biotype M) clustered together with reference mitochondrial sequences from whiteflies from Pakistan and Thailand. Recent reports indicate that Bemisia populations corresponding to the biotypes S and T are distributed in areas larger than those initially delimited. Other results indicated that samples collected in Sudan grouped within the Mediterranean–North Africa clade together with reference sequences of the biotype Q corresponding to insects collected in Spain and Morocco. Mitochondrial haplotypes of B. tabaci samples collected on sweet potato in Ghana clustered with reference sequences of samples from Cameroon corresponding to one of the five Sub-Saharan subgroups already described in the African clade. These data extends the phylogenetic information of the B. tabaci species complex and present new questions to be investigated.     

Reproductive incompatibility and cytochrome oxidase I gene sequence variability amongst host-adapted and geographically separate Bemisia tabaci populations (Hemiptera: Aleyrodidae)

Abstract. Reciprocal‐crossing experiments were carried out and mitochondrial cytochrome oxidase I gene (mtCOI) sequences were compared for allopatric and sympatric Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) populations collected from Africa and India, and from the host‐plants cassava, sweet‐potato and a common weed, Euphorbia geniculata. Three incompatible mating groups were discovered, which involved the cassava B. tabaci colonies from Africa and India, the cassava and sweet‐potato B. tabaci populations from Uganda, and the cassava and E. geniculata B. tabaci from India. Successful reciprocal mating occurred between cassava‐specific B. tabaci from Uganda, Tanzania and Ghana, and between two Indian cassava B. tabaci populations. The parsimony and neighbour‐joining analyses of 699 bp mtCOI gene sequences divided the colonies primarily into those originating from Africa and India. Further subgrouping corresponded to host‐plant specialization. Cassava‐specific Ugandan, Tanzanian and Ghanaian colonies formed a single group and the sympatric sweet‐potato colony from Uganda grouped separately from them. The two geographically distant Indian cassava B. tabaci populations were similar and formed a single group, whereas the sympatric E. geniculata colony formed a sister clade. The clades generated by the phylogenetic analyses were maintained, with highly supported bootstrap values, when other published mtCOI gene sequences were included in the tree‐building process and the divisions matched those revealed by the reciprocal‐crossing experiments. These data suggest that biologically discrete populations exist within B. tabaci (sensu Russell, 1957 ).     

Occurrence of Bondar's Nesting Whitefly,Paraleyrodes bondari (Hemiptera: Aleyrodidae), on cassava in Uganda

Cassava is a valued calorific source to millions of Africans who eat it daily and a vital staple for their food security. One of the key constraints to this crop is whiteflies which are both a vector of viral diseases and a direct pest. Although the African cassava whitefly is known to cause physical damage on cassava with considerable tuberous yield loss, a recent whitefly outbreak caused unusually severe damage, which prompted the current reported investigation. Molecular identification of whitefly adults sampled from the affected cassava field revealed the presence of a new whitefly species, Paraleyrodes bondari. This communication is the first report of the occurrence of P. bondari on cassava in Uganda.     

Colonization of non-cassava plant species by cassava whiteflies (Bemisia tabaci) in Uganda

Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae) is the vector of cassava mosaic geminiviruses (CMGs), which are the main production constraint to cassava [Manihot esculenta Crantz (Euphorbiaceae)], both in Uganda and elsewhere in Africa. Two B. tabaci genotype clusters, Ug1 and Ug2, differentiated at 8% nucleotide (nt) divergence within the mitochondrial cytochrome oxidase I (mtCOI) gene, have been shown to occur on cassava in Uganda. However, the role of alternative hosts in the ecology of cassava B. tabaci genotypes and their possible involvement in the epidemiology of cassava mosaic disease (CMD) in Uganda remain unknown. In this study, we investigated the restriction of cassava B. tabaci genotypes to cassava and the colonization of alternative host species in select cassava‐growing areas of the country in 2003 and 2004. Bemisia tabaci adults and 4th instar nymphs were collected from cassava and 11 other cultivated and uncultivated species occurring adjacent to the sampled cassava fields. Phylogenetic analysis of mtCOI sequences revealed that only a single genotype cluster, Ug1, was present on both cassava and non‐cassava plant species sampled in this study. The Ug1 genotypes (n = 49) shared 97–99% nt identity with the previously described cassava‐associated B. tabaci populations in southern Africa, and were ～8% and ～13% divergent from Ug2 and the ‘Ivory Coast cassava’ genotypes in Uganda and Ivory Coast, respectively. The Ug1 genotypes occurred (as adults) on all 12 source‐plant species sampled. However, based on the presence of B. tabaci 4th instar nymphs, the Ug1 genotypes (n = 13) colonized cassava and five other non‐cassava plant species: Manihot glaziovii, Jatropha gossypifolia, Euphorbia heterophylla, Aspilia africana, and Abelmoschus esculentus, suggesting that cassava B. tabaci (Ug1 genotypes) are not restricted to cassava in Uganda. No Ug2‐like genotypes were detected on any of the plant species sampled, including cassava, in this study. The identification of additional hosts for at least one genotype cluster, Ug1, known also to colonize cassava, and which was hitherto thought to be ‘cassava‐restricted’ may have important epidemiological significance for the spread of CMGs in Uganda.     

Altitudinal species turnover in southern Tanzania shown by anurans: Some zoogeographical considerations

A transect was used to investigate the pattern of altitudinal species turnover shown by the rich fauna of frogs and toads in southeastern Tanzania, and to compare the pattern with those shown by transects taken further south. The transect, taken from the Udzungwa range to the southeastern coast, was divided into 50 m intervals. As with the southern transects, there appears to be a major grouping into lowland and highland sets, with opposing and overlapping subtraction margins that form a replacement‐transition zone. A distributionally complex assemblage of species occurs in this zone. When a similarity value (the Dice‐S?rensen index, expressed as a percentage) taken between the montane ridge and lowland faunas was compared with those of the southern transects, a markedly higher species turnover (low similarity value) is shown in Tanzania. Both lowland and highland faunas have more species than equivalent faunas to the south; the highland fauna is particularly rich in genera not known to occur further south. Yet overall, the pattern of altitudinal turnover shown in the Tanzanian transect is in agreement with the pattern shown in the southern transects. The transects discussed in this paper, combined with other evidence, suggest a need for re‐evaluating the common practice of including all sub‐Saharan Africa in a single so‐called Afrotropical Region.     

Genetic diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) populations and presence of the B biotype and a non-B biotype that can induce silverleaf symptoms in squash, in Uganda

The extent of genetic variability and host‐plant distribution of Bemisia tabaci (Gennadius) genotypes colonising cultivated and uncultivated plant species occurring adjacent to cassava fields in selected cassava‐producing areas of Uganda in 2003/04 were investigated using the mitochondrial cytochrome oxidase I (mtCOI) gene as the molecular marker. Eight genotype clusters, Ug1–Ug8, which are supported by high bootstrap values (≥80), at 3–18% nt divergence, were revealed among the collective Ugandan B. tabaci populations. Ug1 and Ug2 (both cassava‐associated) and Ug8 (sweetpotato‐associated) have been reported previously in Uganda. Ug3 was genetically dissimilar to B. tabaci described elsewhere and colonised a single species, Ocimum gratissimum. Ug4–Ug7 formed four closely related subclusters (93–97% nt identity) and diverged by 15–18% from Ug1, Ug2, Ug3 and Ug8, respectively. Ug4 had as its closest relatives (at 97–99% nt identity) the Ivory Coast okra biotype, whereas genotypes Ug5 and Ug6 had as their closest relatives (at 95–99% and 99% nt identity, respectively) the Mediterranean–North Africa–Middle East (MED‐NAFR‐ME) biotypes, which also include the well‐studied B and Q biotypes. Ug7 was closely related (at 98–99% nt identity) to biotype Ms from the Reunion Island in the Indian Ocean. Ug4 colonised Cucurbita pepo, Cucurbita sativus, Leonotis nepetifolia and Pavonia urens, while Ug7 colonised Commelina benghalensis, Gossypium hirsutum and Phaseolus vulgaris. Ug6, the B‐biotype‐like genotype colonised Abelmoschus esculentus and C. benghalensis only. None of Ug4–Ug7 genotypes was found associated with, or colonising, cassava or sweetpotato plants. In addition to colonising sweetpotato, the Ug8 genotypes colonised Lycopersicon esculentum and L. nepetifolia. Ug6 and Ug7, both members of the B biotype/B‐like cluster, induced silverleaf symptoms on Cucurbita sp. The discovery of five previously identified B. tabaci genotype clusters, Ug3–Ug7, in Uganda, among which are some of the world's most economically important biotypes, namely B and Q, is particularly significant in the spread of geminiviruses with devastating effects to crop production in Africa.     

Occurrence and distribution of cassava begomoviruses in Kenya

A survey for cassava mosaic disease (CMD) was conducted in Kenya, to investigate the factors contributing to the generally increased incidence and severity of CMD in the cassava growing regions and to study the distribution of the disease's causal begomoviruses, African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) and their strains. Special emphasis was given to the occurrence of the destructive recombinant Uganda variant strain of EACMV (EACMV-UG2). Samples from 91 farmers' fields in the main cassava-growing areas of coastal and western Kenya were collected and subjected to ELISA and PCR for detection and typing of the begomoviruses present. CMD incidence was highest in western Kenya (80–100%) and lowest in the Coast province (25–50%). In Western and Nyanza provinces, 52% of the samples tested contained EACMV-UG2, 22% ACMV and 17% contained both ACMV and EACMV-UG2. EACMV was found in four cases at different sites. In cassava samples from the coast province, only EACMV with DNA-A sequences similar to EACMV strains present in Kenya and Tanzania was found. East African cassava mosaic Zanzibar virus (EACMZV) was present in several farms in the Kilifi district. In 15% of all cassava samples with CMD symptoms, flexuous, filamentous virus-like particles were also found, providing evidence for a more complex virus situation in cassava grown at the Kenyan coast. In western Kenya, where intense cassava cultivation takes place, CMD is rampant and EACMV-UG2 was found in mixed virus infections with ACMV driving the epidemics. In coastal areas, where farms are scattered and in isolation, EACMV is endemic, however, with a lower disease incidence and with a limited impact to cassava production.     

Genetic diversity, geographical range and origin of Bemisia tabaci (Hemiptera: Aleyrodidae) Indian Ocean Ms

The whitefly Bemisia tabaci is a pest vector of begomoviruses on crops worldwide. Bemisia tabaci is composed of a complex of cryptic species which barely interbreed. An exception is the Ms from the South West Indian Ocean (SWIO), which crosses in low proportions with the exotic B. The Ms, together with B and Q is part of the same phylogenetic clad. To infer the genetic structure, the geographical range and putative origin of this putative species, microsatellite data and mitochondrial DNA (cytochrome oxydase I) sequences were analysed on an extensive sample set, including all the islands of the region and samples from mainland Africa. Only B and Ms populations were detected across these islands. The exotic B was found only on the islands of Réunion and Mauritius, whereas the Ms is found on all the SWIO islands. Very high isolation by distance was found for the Ms populations between islands of the SWIO, suggesting a long period of presence in this region. Ms populations from mainland Africa had a higher COI diversity than the Ms of the SWIO islands. This diversity is correlated with size and geological ages of the SWIO islands. The population genetic data obtained are in accordance with an origin of Ms in Africa, followed by its expansion and evolution across the SWIO islands prior to human arrival, confirming the status of Ms as indigenous in the SWIO islands.     

Taxonomy and diversity of Afroalpine Chironomidae (Insecta: Diptera) on Mount Kenya and the Rwenzori Mountains, East Africa

Aim Anthropogenic climate change is expected to result in the complete loss of glaciers from the high mountains of tropical Africa, with profound impacts on the hydrology and ecology of unique tropical cold‐water lakes located downstream from them. This study examines the biodiversity of Chironomidae (Insecta: Diptera) communities in these scarce Afroalpine lake systems, in order to determine their uniqueness in relation to lowland African lakes and alpine lakes in temperate regions, and to evaluate the potential of Afroalpine Chironomidae as biological indicators to monitor future changes in the ecological integrity of their habitat. Location Mount Kenya (Kenya) and Rwenzori Mountains (Uganda). Methods The species composition of Afroalpine chironomid communities was assessed using recent larval death assemblages extracted from the surface sediments of 11 high‐mountain lakes between 2900 and 4575 m. Results were compared with similar faunal data from 68 East African lakes at low and middle elevation (750–2760 m), and with literature records of Chironomidae species distribution in sub‐Saharan Africa, the Palaearctic region and elsewhere. All recovered taxa were fully described and illustrated. Results The 11‐lake analysis yielded 1744 subfossil chironomid larvae belonging to 16 distinct taxa of full‐grown larvae, and three taxa of less differentiated juveniles. Eleven of these 16 are not known to occur in African lakes at lower elevation, and eight taxa (or 50% of total species richness) appear restricted to the specific habitat of cold lakes above 3900 m, where night‐time freezing is frequent year‐round. The faunal transition zone coincides broadly with the Ericaceous zone of terrestrial vegetation (c. 3000–4000 m). Snowline depression during the Quaternary ice ages must have facilitated dispersion of cold‐stenothermous species among the high mountains of equatorial East Africa, but less so from or to the Palaearctic region via the Ethiopian highlands. Main conclusions Chironomid communities in glacier‐fed lakes on Africa's highest mountains are highly distinct from those of lowland African lakes, and potentially unique on a continental scale. By virtue of excellent preservation and their spatial and temporal integration of local community dynamics, chironomid larval death assemblages extracted from surface sediments are powerful biological indicators for monitoring the hydrological and ecological changes associated with the current retreat and loss of Africa's glaciers.     

A distinct Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodidae) genotype cluster is associated with the epidemic of severe cassava mosaic virus disease in Uganda

During the 1990s, an epidemic of cassava mosaic virus disease caused major losses to cassava production in Uganda. Two factors associated with the epidemic were the occurrence of a novel recombinant begomovirus, EACMV-Ug, and unusually high populations of the whitefly vector, Bemisia tabaci. Here we present molecular evidence for the occurrence of two cassava-colonizing B. tabaci genotype clusters, Ug1 and Ug2, one of which, Ug2, can be consistently associated with the CMD epidemic in Uganda at the time of collection in 1997. By contrast, a second genotype cluster, Ug1, only occurred 'at' or 'ahead of' the epidemic 'front', sometimes in mixtures with Ug2. Comparison of mitochondrial cytochrome oxidase I gene sequences for Ug1 and Ug2 and well-studied B. tabaci reference populations indicated that the two Ugandan populations exhibited approximately 8% divergence, suggesting they represent distinct sub-Saharan African lineages. Neither Ugandan genotype cluster was identified as the widely distributed, polyphagous, and highly fecund B biotype of Old World origin, with which they both diverged by approximately 8%. Within genotype cluster divergence of Ug1 at 0.61 +/- 0.1% was twice that of Ug2 at 0.35 +/- 0.1%. Mismatch analysis suggested that Ug2 has undergone a recent population expansion and may be of nonUgandan origin, whereas Ug1 has diverged more slowly, and is likely to be an indigenous genotype cluster.     

Rethinking the evolution of extant sub‐Saharan African suids (Suidae,Artiodactyla)

Gongora, J., Cuddahee, R. E., do Nascimento, F. F., Palgrave, C. J., Lowden, S., Ho, S. Y. W., Simond, D., Damayanti, C. S., White, D. J., Tay, W. T., Randi, E., Klingel, H., Rodrigues‐Zarate, C. J., Allen, K., Moran, C. & Larson, G. (2011). Rethinking the evolution of extant sub‐Saharan African suids (Suidae, Artiodactyla). —Zoologica Scripta, 40, 327–335. Although African suids have been of scientific interest for over two centuries, their origin, evolution, phylogeography and phylogenetic relationships remain contentious. There has been a long‐running debate concerning the evolution of pigs and hogs (Suidae), particularly regarding the phylogenetic relationships among extant Eurasian and African species of the subfamily Suinae. To investigate these issues, we analysed the mitochondrial and nuclear DNA sequences of extant genera of Suidae from Eurasia and Africa. Molecular phylogenetic analyses revealed that all extant sub‐Saharan African genera form a monophyletic clade separate from Eurasian suid genera, contradicting previous attempts to resolve the Suidae phylogeny. Two major sub‐Saharan African clades were identified, with Hylochoerus and Phacochoerus grouping together as a sister clade to Potamochoerus. In addition, we find that the ancestors of extant African suids may have evolved separately from the ancestors of modern day Sus and Porcula in Eurasia before they colonised Africa. Our results provide a revision of the intergeneric relationships within the family Suidae.     

Pliocene isolation of a north‐west Saharan cichlid fish

The evolutionary origin of the only north‐west Saharan haplochromine cichlid, Astatotilapia desfontainii, was explored using mitochondrial DNA sequences. Phylogenetic analyses revealed that this species belonged to the main East African–Nilotic haplochromine clade, but was a distinct lineage that diverged from modern haplochromines in the Pliocene. The results suggest that A. desfontainii is a relict haplochromine lineage that has endured major climate fluctuations in North Africa.