Phylogeny and biogeography of African Biomphalaria (Gastropoda: Planorbidae), with emphasis on endemic species of the great East African lakes

The pulmonate snails of the genus Biomphalaria are widely distributed in the tropics, and they are intermediate hosts of the digenean trematode Schistosoma mansoni that causes intestinal schistosomiasis in humans. Recent molecular evidence suggests that Biomphalaria originated in South America, and following a recent transatlantic migration colonized Africa, where it radiated into the currently recognized 12 species. In the present study we further investigate the internal phylogenetic relationships of African Biomphalaria with emphasis on the dispersal and speciation on the continent, especially in the Great Lakes in East Africa. Our results, based on 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and ribosomal internal transcribed spacer I (ITS1), support the monophyly of an African clade with two separate lineages ( Biomphalaria pfeifferi / Biomphalaria camerunensis and the Nilotic species complex/ Biomphalaria angulosa ). Following the initial colonization of Africa, Biomphalaria spread towards the east where a later radiation occurred in the Lake Victoria basin and the Albertine Rift Valley Lakes. With further dispersal along the River Nile, additional speciation took place giving origin to the North-east African species Biomphalaria alexandrina . Our results present almost no support of the species groups of Mandahl-Barth (except for the pfeifferi group), which is in accordance with other molecular appraisals. Our results suggest that Biomphalaria stanleyi , which is endemic to Lake Albert, is not an ecophenotype of the continental B. pfeifferi as previously suggested by other molecular studies. B. angulosa is sequenced for the first time and it is inferred to have an important phylogenetic position as sister group to the Albertine Rift/Lake Victoria basin radiation.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 337–349.     

Recruitment control and production of market-size Oreochromis niloticus with the predator Lates niloticus L. in the Sudan

Experiments were conducted in earth ponds (242–1260m²) to evaluate the Nile perch (Lates niloticus L.) as a predator for recruitment control and the production of marketable Oreochromis niloticus L. in the Sudan. Supply of the predatory fish was maintained by induced spawning of L. niloticus brooders by raising the water level in a 1–0 ha earth pond. Lates niloticus fingerlings (7–5 cm total length) were then stocked with same size O. niloticus at the ratios 1:5, 1:10 and 1:15, Lates:Oreochromis , respectively. Over a period of 7 months Lates niloticus reduced young 50g) Oreochromis population and enhanced the production of preferred-size ( 200 g) Oreochromis. The ratio 1:5 Lates:Oreochromis was established to be the most desirable for Lates -with a total production of 0.2428 kg/m² of O. niloticus with 55.7% (by weight) at the target size averaging 287.5g. The ratios 1:10 and 1:15 produced 0.2106 and 0.2153 kg m² of O. niloticus , with 49.4% and 16.9% averaging 235.0 and 210.0 g, respectively.     

Swimming out of Africa: mitochondrial DNA evidence for late Pliocene dispersal of a cichlid from Central Africa to the Levant

The rich Levantine fauna and flora were shaped by millions of years of migration across the region, from Africa to Eurasia and vice versa. Most large-scale processes that led to this diversity have been relatively well studied. However, small-scale processes, and details such as the area of origin of particular groups, and the route and time of dispersal are often not as clear. This is the case with the endemic Levantine representatives of the fish family Cichlidae. In this work we combine genetic, palaeontological and geological data in an attempt to understand the dispersal of the cichlid fish Astatotilapia flaviijosephi (Lortet, 1883) from sub-Saharan Africa to the Levant. A. flaviijosephi is unique among the Levantine cichlids in being the only non-tilapiine. It is also the only haplochromine cichlid to be found out of Africa. A partial sequence of the control region of the mitochondrial DNA was used to determine A. flaviijosephi 's phylogenetic relationships with other African haplochromines, and to estimate its time of divergence from this group. Combining our findings with palaeontological and geological data, we suggest that A. flaviijosephi separated from the other haplochromines during the middle to late Pliocene (2.5–3.3 Mya) and probably dispersed from Africa to the Levant via the Nile.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 103–109.     

The taxonomy and biology of the centipede Scolopendra amazonicain the Sudan

The life history, reproduction, food and parasites of a population of Scolopendra amazonica Bücherl from the south bank of the Blue Nile at Khartoum, Sudan are described and discussed and Sudanese specimens are compared with Indian S. amazonica and Scolopendra morsitans.     

Systematics and geographic variation of Ethiopian Arvicanthis (Rodentia, Muridae)

Arvicanthis , the unstriped grass-rat, is a widespread genus occurring in many regions of Africa and is major pest in agricultural farmland. Despite its economic importance for developing countries, the taxonomy of the genus is stillin a chaotic state. We used univariate and multivariate morphometrics to investigate two species, A. abyssinicus and A. dembeensis , occurring in Ethiopia. Results show that these taxa are well separated, this contradicting authors who lump all Arvicanthis as A. niloticus . There is a longitudinal cline in the morphology of A. dembeensis from eastern regions along the Rift Valley. Differences between the species in morphlogy seem to reflect adaptation to different ecological niches at high ( A. abyssinicus ) and low ( A. dembeensis ) altitudes.     

mtDNA analysis of Nile River Valley populations: A genetic corridor or a barrier to migration?

To assess the extent to which the Nile River Valley has been a corridor for human migrations between Egypt and sub-Saharan Africa, we analyzed mtDNA variation in 224 individuals from various locations along the river. Sequences of the first hypervariable segment (HV1) of the mtDNA control region and a polymorphic HpaI site at position 3592 allowed us to designate each mtDNA as being of "northern" or "southern" affiliation. Proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the southern Sudan. At slowly evolving sites within HV1, northern-mtDNA diversity was highest in Egypt and lowest in the southern Sudan, and southern-mtDNA diversity was highest in the southern Sudan and lowest in Egypt, indicating that migrations had occurred bidirectionally along the Nile River Valley. Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia. Spatial autocorrelation analysis demonstrates a smooth gradient of decreasing genetic similarity of mtDNA types as geographic distance between sampling localities increases, strongly suggesting gene flow along the Nile, with no evident barriers. We conclude that these migrations probably occurred within the past few hundred to few thousand years and that the migration from north to south was either earlier or lesser in the extent of gene flow than the migration from south to north.     

Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history

We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.     

Circadian rhythm of photosensitivity and the adaptation of reproductive function to the environment in two populations of Arvicanthis niloticus from Mali and Burkina Faso.

Previous studies have shown that there is a circadian rhythm of photosensitivity in different rodent species of the Sahel (Burkina Faso) and that, despite the low amplitude of seasonal variations in daylength, the photoperiod may control reproductive function. The present investigation of Arvicanthis niloticus provides additional support for this hypothesis. Populations of Arvicanthis niloticus from two regions at the same latitude 1000 km apart but with different climates were studied. Oursi, Burkina Faso, has an arid climate (annual rainfall 315 mm) and Kamalé, Mali has a wetter climate (annual rainfall 1114 mm). The circadian rhythm of photosensitivity had the same features in both populations, involving inhibition of testicular activity, but the photosensitive phase began 11 h 30 min after dawn in the population from Burkina Faso and 45 min later in that from Mali. Comparison of these results with the annual variation of daylength showed that the photoperiod inhibits the reproductive activity of A. niloticus from April to December in Burkina Faso and only from mid-May to mid-August in Mali. The population of Arvicanthis niloticus living in an environment with a large and seasonally stable food supply (Mali) thus has a longer reproductive period. This corroborates results from field studies on annual variations of population density.     

Distribution, phenology and demography of sympatric sexual and asexual dandelions (Taraxacum officinale s.l.): geographic parthenogenesis on a small scale

In many plant and animal species, sexual and asexual forms have different geographical distributions ('geographic parthenogenesis'). The common dandelion Taraxacum officinale s.l. provides a particularly clear example of differing distributions: diploid sexuals are restricted to southern and central Europe, while triploid asexuals occur across Europe. To get a better understanding of the factors underlying this pattern, we studied the distribution and demography of sexuals and asexuals in a mixed population that was located at the northern distribution limit of the sexuals. In this population three adjacent, contrasting microhabitats were found: a foreland and south and north slopes of a river dike. Comparative analyses of the distribution, phenology and demography indicated that sexuals had a stronger preference for the south slope than did asexuals. We therefore propose that the large-scale geographic parthenogenesis in T. officinale is shaped by an environmental gradient which acts upon the sexuals.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 205–218.     

Revision of the Micromeria (Labiatae) in tropical to southern Africa and on the Arabian Peninsula

The material of Micromeria s.s. ( M. sect. Micromeria ) from tropical to southern Africa and the Arabian Peninsula is revised. The endemic Ethiopian M. unguentaria Schweinf. is retained as a species, while the other African and Arabian material of Micromeria is included in M. imbricata (Forssk.) C. Chr. M. imbricata is divided into the following three varieties: var. imbricata , which is very polymorphic, widespread in the African highlands, and also occurs in Arabia; var. rhodesiaca (Elly Walther & K.H. Walther) Ryding, which occurs in the highlands of Malawi, Mozambique and Zimbabwe; and var. villosa (Elly Walther & K.H. Walther) Ryding, which occurs in montane to alpine areas of Ethiopia and East Africa. Discontinuities in the variation within var. imbricata , observed at some localities, are suggested to be a result of partial autogamy. Problems with delimitation between M. imbricata , the East Asiatic M. biflora (Buch.-Ham. ex D.Don) Benth. and some Mediterranean species are discussed.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 427–446.     

Dwelling at the oxycline: does increased stratification provide a predation refugium for the Lake Victoria sardine Rastrineobola argentea?

1. We tested the hypothesis that increased hypoxia in Lake Victoria provides a refugium for the cyprinid dagaa ( Rastrineobola argentea ) against hypoxia-sensitive Nile perch ( Lates niloticus ).
2. Hypoxia in the main habitat of dagaa was rare during 1979–80, but lasted 3–5 months in 1987 and 1988, during which time adult dagaa spent the day just above the oxycline instead of near the bottom.
3. Dissolved oxygen concentrations in the layer just above the oxycline were not critical for Nile perch, but a mass kill of this species following a sudden upwelling of hypoxic water suggested that oxycline-dwelling is risky.
4. Our data suggest no difference between dagaa and Nile perch in the level at which dissolved oxygen starts to limit their vertical distribution in the water column, but dagaa seems to be even more sensitive to extreme hypoxia (<1–2 mg O2 L−1) than Nile perch.
5. We argue that oxycline-dwelling dagaa are not seeking a predation refugium but that they are limited by low oxygen levels in reaching their feeding areas near the bottom.     

Modeling the Spatial Spread of Rift Valley Fever in Egypt

Rift Valley fever (RVF) is a severe viral zoonosis in Africa and the Middle East that harms both human health and livestock production. It is believed that RVF in Egypt has been repeatedly introduced by the importation of infected animals from Sudan. In this paper, we propose a three-patch model for the process by which animals enter Egypt from Sudan, are moved up the Nile, and then consumed at population centers. The basic reproduction number for each patch is introduced and then the threshold dynamics of the model are established. We simulate an interesting scenario showing a possible explanation of the observed phenomenon of the geographic spread of RVF in Egypt.     

Phylogeography of the Japanese giant flying squirrel, Petaurista leucogenys (Rodentia: Sciuridae): implication of glacial refugia in an arboreal small mammal in the Japanese Islands

To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel ( Petaurista leucogenys ) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 47–60.     

A new species of Encephalartos (Zamiaceae) in Sudan

Encephalartos mackenziei Newton is described as a new cycad species occurring in south-east Sudan. It is characterized by its branching at the base to produce up to ten trunks per plant and by its broad leaflets, as well as some details of the cone scales. The population is large and widespread, and the presence of small seedlings indicates successful regeneration.  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 187–192.     

Genital morphology and taxonomy of the water strider Aquarius remigis (Say) (Insecta, Hemiptera-Heteroptera: Gerridae)

The shape of the dorsal vesical plate was used to determine the extent of morphological differentiation among populations of the water strider Aquarius remigis (Say) (Hemiptera-Heteroptera: Gerridae), and between species assigned to the A. remigis species group. Populations were sampled throughout North America and Mesoamerica, and included paratypes of A. remigoides Gallant & Fairbairn, and material collected from the type localities of A. amplus (Drake & Harris) and A. nyctalis (Drake & Hottes). If taxonomy is to be inferred from the shape of the dorsal vesical plate, as suggested by previous authors, several taxonomic issues need to be reconsidered. First, there was one species distributed widely across North America and deep into Mexico that is very likely to represent A. remigis , meaning that populations from the western USA previously assigned to ' A. nyctalis ' should be synonymized with this species. Second, A. remigoides as currently defined also includes some populations of A. remigis , and is probably much less widely distributed in the south-eastern USA than previously thought. A hybridization zone in Pennsylvania between A. remigis and A. remigoides , as inferred from measurements of body size and allozyme electrophoresis, is not congruent with data from the male genitalia, which indicated a transition zone between the two forms in Virginia much further to the south. Finally, A. amplus was widespread in Mexico, reaching into Guatemala to the south and into Arizona to the north.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 381–398.     

Chromosomal characterization of Arvicanthis species (Rodentia,Murinae) from western and central Africa: implications for taxonomy

A chromosome study of unstriped grass rats of the genus Arvicanthis (Rodentia, Murinae) in western and central Africa is presented. The observations extend the data available to 242 specimens from 59 localities. All individuals karyotyped belong to four karyotypic forms, or cytotypes, earlier described as ANI-1, ANI-2, ANI-3, and ANI-4 and are presumed to correspond to four distinct species. In order to provide diagnostic characters for these western and one central African Arvicanthis species, we standardized the chromosomal data available and developed a G- and C-banded chromosome nomenclature that allows easy species identification. Each form is characterized by a distinct geographical distribution, roughly following the biogeographical domains of western Africa, although their precise limits remain to be assessed. The sole area of sympatry detected is the region of the inner delta of the Niger River, where both ANI-1 and ANI-3 can be found. It is proposed that the three western African species ANI-1, ANI-3, and ANI-4 be renamed as A. niloticus, A. ansorgei, and A. rufinus, respectively.     

Contrasting temporal dynamics and spatial patterns of population genetic structure correlate with differences in demography and habitat between two closely-related African freshwater snails

The relationship between habitat stability, demography, and population genetic structure was explored by comparing temporal microsatellite variability spanning a decade in two closely-related hermaphroditic freshwater snails from Cameroon, Bulinus forskalii and Bulinus camerunensis . Although both species show similar levels of preferential selfing, microsatellite analysis revealed significantly greater allelic richness and gene diversity in populations of the highly endemic B. camerunensis compared to those of the geographically-widespread B. forskalii . Additionally, B. camerunensis populations showed significantly lower spatial genetic differentiation, higher dispersal rates, and greater temporal stability compared to B. forskalii populations over a similar spatial scale. This suggests that a more stable demography and greater gene flow account for the elevated genetic diversity observed in this geographically-restricted snail. This contrasts sharply with a metapopulation model (which includes extinction/contraction, recolonization/expansion, and passive dispersal) invoked to account for population structuring in B. forskalii . As intermediate hosts for medically important schistosome parasites, these findings have ramifications for determining the scale at which local adaptation may occur in the coevolution of these snails and their parasites.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 747–760.     

A new violet species (Violaceae) from the south-west Alps

Viola laricicola Marcussen sp. nov. is described from collections from four French and Italian localities in the south-west Alps. It is closely related to V. riviniana (section Trigonocarpea ) but differs in a few morphological characters and by the chromosome number 2 n  = 20. Viola laricicola is endemic to the montane and subalpine coniferous forests in the continental parts of the Alps.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 142 , 119–123.     

Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Approximately 1.7 kbp of mitochondrial DNA were sequenced from 29 individuals assignable to 11 Uromastyx species or subspecies and two other agamids. U. ocellata and U. ornata had an insertion between the glutamine and isoleucine tRNA genes, which could be folded into a stable stem-and-loop structure, and the insertion for U. ornata additionally retained a sequence similar to the glutamine tRNA gene. This corroborates the role of tandem duplication in reshaping mitochondrial gene arrangements, and supports the idea that the origin of light-strand replication could be relocated within mitochondrial genomes. Molecular phylogeny from different tree-building methods consistently placed African and Arabian taxa in mutually monophyletic groups, excluding U. hardwickii inhabiting India and Pakistan. Unlike previous studies based on morphology , U. macfadyeni did not cluster with morphologically similar Arabian taxa, suggesting convergent evolution to be responsible for the morphological similarities. Divergence times estimated among the Uromastyx taxa, together with geological and palaeontological evidence, suggest that the Uromastyx agamids originated from Central Asia during the Eocene and colonized Africa after its connection with Eurasia in the early Miocene. Their radiation may have been facilitated by repeated aridification of North Africa since the middle Miocene, and geological events such as the expansion of the Red Sea and the East African Rift Valley.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 247–260.