Morphotypes,varieties, or subspecies?: genetic diversity and differentiation of four Saintpaulia (Gesneriaceae) morphotypes from the East Usambara Mountains,Tanzania

Saintpaulia (H. Wendl.) is a forest-dependent, endangered plant genus endemic to Tanzania and Kenya. The taxonomy of Saintpaulia from the Usambara Mountains and adjacent lowlands in north-eastern Tanzania is problematic because of the morphological similarity of the species and the presence of considerable intraspecific variation. Conventional molecular phylogenetic methods have failed to reveal the genetic structure of this Saintpaulia complex. In this study, we assessed the genetic composition of 12 Saintpaulia populations, representing four different morphotypes, from the East Usambara Mountains using inter-simple sequence repeat (ISSR) markers. Relatively high genetic diversities were observed within populations (mean h  = 0.320), indicating their adaptive potential. Little genetic differentiation amongst populations (mean F _st  = 0.063) and the genetic divergence of the rosulate and trailing morphotypes support the hypothesis of ongoing divergent evolution within the East Usambara metapopulation(s) of Saintpaulia .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 347–355.     

656. TWO NEW SPECIES OF SAINTPAULIA FROM THE ULUGURU MOUNTAINS, TANZANIA

Two new endemic species of Saintpaulia, S. ulugurensis Haston and S. watkinsii Haston (Gesneriaceae) are described from the Uluguru Mountains. Their discovery emphasises the need for additional floristic work to be carried out in this area and supports the calls for strong conservation measures for the fragile forest habitats of Tanzania.     

Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences

Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia.     

Reproductive ecology of three endangered African violet (Saintpaulia H. Wendl.) species in the East Usambara Mountains, Tanzania

Knowledge of the reproductive biology of endangered plants is essential for their effective conservation. It also provides important information for understanding the evolutionary processes that affect speciation, thus helping the definition of proper units for conservation in endangered plants with problematic taxonomy. We studied the reproductive potential and possibility for hybridization in the endangered genus Saintpaulia (Gesneriaceae) by examining flowering phenology, flower and seed production and pollination of three sympatric cross‐compatible Saintpaulia species in the East Usambara Mts., Tanzania. The synchrony observed in flowering in S. confusa and S. difficilis may enable hybridization between these two species, whereas partial phenological separation may contribute to the integrity of S. grotei. Although the level of flower abortion is high in S. confusa, each pollinated flower yields about 1000 seeds. Saintpaulia confusa produces fruits following both self‐ and cross‐pollination but spontaneous self‐pollination seems not to occur. Thus, seed production depends on sufficient pollinator service. Floral heteromorphy (i.e. enantiostyly) and bee pollination are likely to further enhance cross‐pollination, suggesting that the genus predominantly outcrosses. Thus, Saintpaulia populations are likely to suffer from negative effects of inbreeding if they become small and isolated.     

A new species of Zenkerella (Leguminosae-Caesalpinioideae) from Tanzania

Zenkerella perplexa sp. nov. from the Uluguru Mts in Tanzania is described and illustrated. Differences between this species and Z. egregia are pointed out.     

Amphibian Diversity in East African Biodiversity Hotspots: Altitudinal and latitudinal Patterns

The Eastern Arc mountain chain and adjoining coastal forests of Tanzania and Kenya have been listed as world biodiversity hotspots. We report on an ongoing attempt to estimate amphibian diversity on the three best studied mountains of the Eastern Arc, the East Usambara, Uluguru and Udzungwa mountains of Tanzania, complemented by an estimate of diversity on the adjoining coastal lowland. This proves to be a complex task, which introduces a note of caution into evaluating global biodiversity estimates. Most amphibian species in eastern Tanzania occur on the coastal lowlands and are widely distributed, extending at least north or south of Tanzania and, to a variable extent, westwards to the elevated interior. Diversity patterns along the length of the lowlands are complex, with the presence of a Sahelian element in the extreme north. On the three Eastern Arc mountains studied, species turnover associated with rising altitude is greater than turnover associated with latitudinal distance between the mountain blocks, leading to greater altitudinal than latitudinal diversity in this equatorial region. A long-standing divergence is indicated between montane and lowland endemics. Although forest-associated species are not the largest contributor to the eastern Tanzanian total species diversity (some 48%), the uniqueness of these species both in lowland and montane forests, combined with their evident vulnerability to disturbance, makes them a subject for particular conservation concern, and justifies hotspot status for both montane and lowland forests.     

A revision of the genus Lasianthus (Rubiaceae) in Africa, excluding Madagascar

23 species, one subspecies and three varieties have been described or named for the pan-tropical genus Lasianthus Jack (Rubiaceae) in continental Africa. In the present revision thirteen species, five subspecies and one variety are recognized; additionally two hybrids are proposed. Of the previously named taxa, the subspecies is raised to species rank whereas two species are degraded to subspecies and variety status, respectively. Five species are synonymised including two varieties, and four are left with uncertain status, including one variety. The distribution of the genus in Africa consists of two distinct elements: one component is found in the Guineo-Congolian regional centre of endemism and one in the eastern part of Afiomontane Archipelago-like regional centre of endemism. A centre of species diversity is found in Eastern Arc Mts., where six endemic species occur together with L. laxinervis and the more widespread L. kilimandscharicus. Four of the species are strict endemics of the Uluguru Mts. In addition to the presentation of the new section: Lasianthus Sectio Membranacei, sect. nov., this revision contain two hybrids from Uluguru Mts.: L. macrocalyx × pedunculatus and L. cereifizorus × pedunculatus, and following new taxa and new combinations: L. africanus ssp. biokoensis, subsp. nov.; L. africanus ssp. mayumbensis, comb. et stat. nov.; L. kilimandscharicus ssp. glabrescens, ssp. nov.; L. kilimandscharicus ssp. glabrescens var. xanthospermus, comb. et stat. nov.; L. kilimandscharicus ssp. hirsutus, ssp. nov.; L. laxinervis, stat. nov.; L. pedunculatus ssp. angustisepalus, ssp. nov.     

A newStylochiton species (Araceae) from East Africa

Stylochiton crassispathus J.Bogner, spec. nova of sect.Stylochiton, is only known from the type locality in the Usambara Mts., Tanzania. It is compared withS. puberulus andS. cuculliferus.     

Radiation of the endemic genus Dendroseris (Asteraceae) on the Juan Fernandez Islands: evidence from sequences of the its regions of nuclear ribosomal DNA

Phylogenetic relationships among nine of the 11 species of the endemic genus Dendroseris on the Juan Fernandez Islands were inferred from nucleotide sequences of the internal transcribed spacer regions (ITS) of the 18-26S nuclear ribosomal DNA. Sequences were determined for 15 populations of Dendroseris and one population for each of two outgroups from the genera Sonchus and Sventenia. Little length variation was detected in the ITS regions of Dendroseris, with ITS 1 253 or 254 bp long and ITS 2 224 or 225 bp. The sequence data provide strong support for the holophyly of Dendroseris despite the distinct morphological differences among the three subgenera. The molecular data also indicate that subg. Dendroseris and Phoenicoseris are holophyletic, but do not support holophyly of subg. Rea. The ITS sequences did not resolve relationships among subgenera, supporting the hypothesis of rapid adaptive radiation of Dendroseris on the islands. Relative rate tests indicate that rates of nucleotide substitutions in the ITS regions are not significantly different among the different lineages of Dendroseris following adaptive radiation. Comparisons of average pairwise sequence divergence of Dendroseris species in the ITS regions and chloroplast genome indicated that ITS sequences have evolved about 38 times faster than cpDNA in the genus. Rates of ITS sequence divergence of Dendroseris were estimated to be faster than (3.94 ± 0.10) × 10^-9 per site per year, and likely (6.06 ±0.15) × 10^-9 per site per year.     

The use of mitochondrial and nuclear sequence data in assessing the taxonomic status of the endangered Uluguru Bush Shrike Malaconotus alius

The endangered Uluguru Bush Shrike Malaconotus alius is a large, black-headed bush shrike, strictly endemic to the Uluguru Mountains in Tanzania. It has recently been suggested that this species has been misplaced within the genus Malaconotus and might instead be related to Malagasy Vangidae. To assess its systematic affinities, we analysed 1518 bp of sequence data obtained from a nuclear intron (myoglobin intron-2) and a mitochondrial protein-coding gene (ND2) using parsimony, maximum likelihood and Bayesian inference. Both genes strongly support the traditional placement within the genus Malaconotus , suggesting that similarities between the Uluguru Bush Shrike and the Vangidae are due to convergence. These results caution that taxonomic changes should not be made without a proper character analysis (i.e. assignment of character homology).     

Molecular phylogeny of the endemic East African flightless grasshoppers Altiusambilla Jago, Usambilla (Sjöstedt) and Rhainopomma Jago (Orthoptera: Acridoidea: Lentulidae)

Abstract.  A molecular phylogeny of endemic flightless grasshoppers is presented for the three Lentulidae genera Altiusambilla Jago, 1981 , Usambilla Sjöstedt, 1909 and Rhainopomma Jago, 1981 based on DNA sequences (16S rRNA locus). Parsimony, distance and likelihood reconstructions were performed using different assumptions on sequence evolution. The generated phylogenies agree in almost all parts of the calculated trees and support the monophyly of the observed genera. It was shown that Usambilla and Rhainopomma are more closely related to each other, Altiusambilla being a separate clade. However, the investigated East African lentulid genera are clearly separated from South African taxa, underlining the monophyly of East African genera. Usambilla olivacea is re-established. Populations of Rhainopomma montanum from the Taita Hills of Kenya and from the West Usambara mountains of Tanzania are two separate species not closely related to each other. Rhainopomma samples from the North Pare mountains of Tanzania belong to a hitherto undescribed species.     

Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot

Aim East Africa is one of the most biologically diverse regions, especially in terms of endemism and species richness. Hypotheses put forward to explain this high diversity invoke a role for forest refugia through: (1) accumulation of new species due to radiation within refugial habitats, or (2) retention of older palaeoendemic species in stable refugia. We tested these alternative hypotheses using data for a diverse genus of East African forest chameleons, Kinyongia. Location East Africa. Methods We constructed a dated phylogeny for Kinyongia using one nuclear and two mitochondrial markers. We identified areas of high phylogenetic diversity (PD) and evolutionary diversity (ED), and mapped ancestral areas to ascertain whether lineage diversification could best be explained by vicariance or dispersal. Results Vicariance best explains the present biogeographic patterns, with divergence between three major Kinyongia clades (Albertine Rift, southern Eastern Arc, northern Eastern Arc) in the early Miocene/Oligocene (> 20 Ma). Lineage diversification within these clades pre‐dates the Pliocene (> 6 Ma). These dates are much older than the Plio‐Pleistocene climatic shifts associated with cladogenesis in other East African taxa (e.g. birds), and instead point to a scenario whereby palaeoendemics are retained in refugia, rather than more recent radiations within refugia. Estimates of PD show that diversity was highest in the Uluguru, Nguru and East Usambara Mountains and several lineages (from Mount Kenya, South Pare and the Uluguru Mountains) stand out as being evolutionarily distinct as a result of isolation in forest refugia. PD was lower than expected by chance, suggesting that the phylogenetic signal is influenced by an unusually low number of extant lineages with long branch lengths, which is probably due to the retention of palaeoendemic lineages. Main conclusions The biogeographic patterns associated with Kinyongia are the result of long evolutionary histories in isolation. The phylogeny is dominated by ancient lineages whose origins date back to the early Miocene/Oligocene as a result of continental wide forest fragmentation and contraction due to long term climatic changes in Africa. The maintenance of palaeoendemic lineages in refugia has contributed substantially to the remarkably high biodiversity of East Africa.     

Molecular and Cytogenetic Characterization of Wild Musa Species

The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world''s largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.     

Trypanosome Diversity in Wildlife Species from the Serengeti and Luangwa Valley Ecosystems

Background

The importance of wildlife as reservoirs of African trypanosomes pathogenic to man and livestock is well recognised. While new species of trypanosomes and their variants have been identified in tsetse populations, our knowledge of trypanosome species that are circulating in wildlife populations and their genetic diversity is limited.

Methodology/Principal Findings

Molecular phylogenetic methods were used to examine the genetic diversity and species composition of trypanosomes circulating in wildlife from two ecosystems that exhibit high host species diversity: the Serengeti in Tanzania and the Luangwa Valley in Zambia. Phylogenetic relationships were assessed by alignment of partial 18S, 5.8S and 28S trypanosomal nuclear ribosomal DNA array sequences within the Trypanosomatidae and using ITS1, 5.8S and ITS2 for more detailed analysis of the T. vivax clade. In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.

Conclusions/Significance

Wildlife carries a wide range of trypanosome species. The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania. Since conventional species-specific primers may not amplify all trypanosomes of interest, the use of ITS PCR primers followed by sequencing is a valuable approach to investigate diversity of trypanosome infections in wildlife; amplification of sequences outside the T. brucei clade raises concerns regarding ITS primer specificity for wildlife samples if sequence confirmation is not also undertaken.     

The phylogeny of the genus Indoplanorbis (Gastropoda,Planorbidae) from Africa and the French West Indies

Indoplanorbis exustus is a freshwater snail known as the intermediate host of various trematode parasites, including different species of the genus Schistosoma. Although its genetic diversity is well described in Asia, the phylogenetic diversity of strains from Africa and Guadeloupe (French West Indies) and their relationship to Asian and South‐East Asian strains remain unknown. To tackle this issue, we sampled individuals from Africa and Guadeloupe, and we computed phylogenetic reconstructions using five molecular markers: partial sequences of two mitochondrial genes, cox1 and 16S, and three nuclear markers, ITS1, ITS2 (Internal Transcribed Spacer 1 and 2) and 5.8S. Our results suggest that strains in Africa and Guadeloupe come from Asia and that they all belong to a single clade that is widespread around the globe.     

The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.     

New evolutionary lineages, unexpected diversity, and host specificity in the parabasalid genus Tetratrichomonas

We studied morphological and molecular polymorphism of 53 Tetratrichomonas isolates obtained from amphibian, reptilian, mammalian hosts, and from a slug with the aid of protargol staining and analyses of ITS1-5.8S rRNA-ITS2, SSU rRNA, and alpha-tubulin gene sequences. The phylogenetic tree based on the concatenate of all sequences showed the monophyly of the genus Tetratrichomonas with respect to the genus Trichomonas. Our data suggest that two parabasalid genera, Pentatrichomonoides and Trichomonoides, may belong to the genus Tetratrichomonas. Tetratrichomonas isolates were divided into 16 robust host-specific and monophyletic groups that probably represent separate, mostly new, species. As only five Tetratrichomonas species were described from the examined host taxa so far, our study uncovered considerable species diversity within the genus. The wide host range, high level of species-specific host specificity, and newly revealed biodiversity make the genus Tetratrichomonas a valuable model for studying evolution of parasites.     

An ITS region phylogeny of Siderastrea (Cnidaria: Anthozoa): is S. glynni endangered or introduced?

The genus Siderastrea contains only five extant species, including Siderastrea glynni, which is one of the few recognized species of endangered stony coral. Cloned sequences of the internal transcribed spacer (ITS) region had low levels of intragenomic nucleotide diversity, and few alignment ambiguities, which allowed for the first species-level phylogenetic analysis of the genus. Results indicated an unexpected deep divergence between the Western-Pacific and Atlantic species. ITS region sequences indicated that S. glynni is not derived from S. savignyana, as previously thought. Instead, S. glynni shared identical sequence types with S. siderea in the Caribbean. Given a range of previously published evolutionary rates for the ITS region, it is unlikely that S. glynni represents the remnants of a population that was divided by the closure of the Central American Seaway (approximately 3–3.8 MYA). It is more likely that S. glynni originated by a breach of the Isthmus (approximately 2 MYA), or a contemporary introduction by ship.