AFLP-based differentiation of tropical African Festuca species compared to the European Festuca complex

For the first time amplified fragment length polymorphism (AFLP) fingerprinting is applied to classify tropical African Festuca species. Five afro-alpine narrow- and two afro-montane broad-leaved species from Uganda and Ethiopia are compared to ten European grass species. A principal coordinate analysis (PCoA) accounts for 62.5% with its first three coordinates. The PCoA and the neighbor-joining (NJ) distinguish the five narrow-leaved African Festuca species from all other species. The broad-leaved African Festuca africana and Festuca simensis are linked to the broad-leaved European species through Festuca altissima and Festuca gigantea, respectively. The narrow- and broad-leaved European species are separated as expected in the NJ. One narrow-leaved African alpine species recently described appears merged (i.e. Festuca richardii with Festuca abyssinica). We provide chromosome numbers for all seven Ugandan species and compare taxonomy and AFLP classification. Our most striking result is that the narrow-leaved African Festuca species are unique and not clustering with the narrow-leaved European species.     

Phylogenetics and seed morphology of African Nymphoides (Menyanthaceae)

We evaluated the boundaries among Nymphoides (Menyanthaceae) species in Africa, a region where the genus has received relatively little attention. We gathered morphological data from seeds using light and scanning electron microscopy, and we conducted molecular phylogenetic analyses using nuclear sequence data from the internal transcribed spacer (ITS) region. Morphological and molecular features distinguished six species and affirmed their respective geographic ranges. No African specimens were attributable to Nymphoides indica, even though this paleotropical species previously had been understood to grow in Africa. We establish the new combination Nymphoides senegalensis (G. Don) Tippery, based on an established African basionym, to accommodate the specimens formerly identified as N. indica. Phylogenetic analyses resolved two distinct clades containing African species. The majority of African species are closely related to neotropical species, with which they share similar petal ornamentation. The morphologically distinct N. ezannoi shares floral and phylogenetic similarity with species from North America and Asia. Results presented here support prior hypotheses that allopolyploid species in the Americas may have originated from one or more parental lineages in Africa. Seed morphological characters remain some of the most reliable features for identifying species, particularly for herbarium specimens lacking observable floral characters.     

Southern African skate biodiversity and distribution

The skates (Family Rajidae) have 12 genera and possibly 28 species off southern Africa (southern Angola, Namibia, South Africa and Mozambique). The geographic and bathymetric distribution and the taxonomic composition of the southern African skate fauna are analysed and the distribution mapped. The southern African skate fauna is best known off the temperate west coast of South Africa from the intertidal to approximately 1,200 meters, but poorly known below 1,200 m and sketchily known in warm-temperate and tropical parts of the area. Southern African skates of the temperate continental shelves above 100 m are not diverse and regularly include one species of the genus Dipturus, one species of Leucoraja, two species of Raja (including R. straeleni, the most abundant skate in southern African waters) and the giant skate Rostroraja alba. All of these skates are ‘shelf overlap’ species that range onto the outer shelves and uppermost slopes, and none are confined to inshore environments. Skate diversity increases on the outer shelves and upper slopes. At least half of the skate species are endemic to the southern African region; other species also occur off East or West Africa, a few extend to European waters, and records of one species, Amblyraja taaf, appear to be of strays from nearby sub-Antarctic seas. The genus Bathyraja and softnose skate group (Arhynchobatinae) are surprisingly limited (a single species) in deep-water off southern Africa (unlike other regions including the Antarctic), and almost all of southern African skates are members of the Rajinae. Amongst rajines, the tribes Amblyrajini (Amblyraja, two species, Leucoraja, two species, and Rajella, five species) Rajini (Dipturus, six species, Okamejei, one species, Raja, two species, and Rostroraja, one species), and Anacanthobatini (Anacanthobatis, two species, and Cruriraja, three species) predominate, while Gurgesiellini has a species of Neoraja and possibly two of Malacoraja.     

Major histocompatibility genes in the Lake Tana African large barb species flock: evidence for complete partitioning of class II B, but not class I, genes among different species

The 16 African large barb fish species of Lake Tana inhabit different ecological niches, exploit different food webs and have different temporal and spatial spawning patterns within the lake. This unique fish species flock is thought to be the result of adaptive radiation within the past 5 million years. Previous analyses of major histocompatibility class II B exon 2 sequences in four Lake Tana African large barb species revealed that these sequences are indeed under selection. No sharing of class II B alleles was observed among the four Lake Tana African large barb species. In this study we analysed the class II B exon 2 sequences of seven additional Lake Tana African large barb species and African large barbs from the Blue Nile and its tributaries. In addition, the presence and variability of major histocompatibility complex class I UA exon 3 sequences in six Lake Tana and Blue Nile African large barb species was analysed. Phylogenetic lineages are maintained by purifying or neutral selection on non-peptide binding regions. Class II B intron 1 and exon 2 sequences were not shared among the different Lake Tana African large barb species or with the riverine barb species. In contrast, identical class I UA exon 3 sequences were found both in the lacustrine and riverine barb species. Our analyses demonstrate complete partitioning of class II B alleles among Lake Tana African large barb species. In contrast, class I alleles remain for the large part shared among species. These different modes of evolution probably reflect the unlinked nature of major histocompatibility genes in teleost fishes.Electronic Supplementary Material Supplementary material is available for this article at .An erratum to this article can be found at     

Cation contents of acrocarpous and pleurocarpous mosses growing on a strontium-rich substratum

Abstract

A new species, Nanobryum thorsbornei, is described from northern Queensland, Australia, and compared with N. dummeri, an African species to which it seems most closely allied. They both have a remarkable persistent protonema which is partly pseudothallose but the leaves of the Australian species are trilobate, a feature lacking in the African species. The relationship of Nanabryum with Fissidens, particularly F. gladiolus, is discussed.     

Mitochondrial DNA sequence and gene order of the Sri Lankan Schistosoma nasale is affiliated to the African/Indian group

A 1.9 kb nucleotide sequence of part of the mitochondrial (mt) genome covering the cox1-trnT-rrnL-trnC-rrnS region, and the order of the remaining mitochondrial protein-coding genes for S. nasale of Sri Lankan origin, has been determined for analysis of the possible placement of this species in the genus Schistosoma. The gene order of this species is similar to that of the African and Indian Schistosoma species, but strikingly different from the East Asian species. Analysis of an alignment of the 1.9 kb sequence with available sequences from other schistosomes indicated affinities with S. spindale (found in Sri Lanka) and African species (in particular S. intercalatum and S. haematobium). Phylogenetic trees inferred from the alignment including 1 kb of RNA (transfer RNA and ribosomal RNA) sequence for 8 other Schistosoma spp. and Fasciola hepatica as an out-group revealed that S. nasale is placed proximally to S. spindale, S. intercalatum, S. haematobium and S. mansoni in the African sub-group while the East Asian species are more distant. S. incognitum lies basal to the combined African/Indian clade. The mtDNA analysis strongly supports the hypothesis that S. nasale is closely affiliated with the African/Indian schistosome group rather than the East Asian Schistosoma species.     

Phylogeography of Mus (Nannomys) minutoides (Rodentia,Muridae) in West Central African savannahs: singular vicariance in neighbouring populations

We studied the phylogeography of the strict savannah pygmy mice Mus (Nannomys) minutoides in West Central Africa. A total of 846 base pairs of the cytochrome b sequence were obtained for 66 individuals collected in Gabon, Cameroon, Republic of Congo and Central African Republic. These sequences were compared to those of M. minutoides from other African countries and to eight other species of the genus Mus. We performed maximum likelihood, Bayesian and nested clade analyses, as well as neutrality tests and time estimates. We show that M. minutoides is a well‐differentiated monophyletic species that separated from other pygmy mice 1.17 Myr ago. A distinct West Central African M. minutoides clade diverged early from the other African populations of the species, with a more recent common ancestor dating 0.14 Myr. West Central African populations are globally homogeneous, despite the present fragmentation of savannahs by the rain forest. However, our analyses show an unexpected vicariance between geographically close savannahs, embedded in the rain forest in Central Gabon. One of these populations is genetically more similar to very distant peripheral populations than to three closely neighbouring populations situated on both sides of the Ogooué River. A non‐river geographical barrier probably persisted in this area, durably isolating these local populations. This hypothesis about the history of the savannah landscape should be testable through the biogeographical analysis of other strict savannah small mammal species.     

Redescription of Ilyocryptus tuberculatus Brehm, 1913 (Anomopoda,Branchiopoda)

The morphology of Ilyocryptus tuberculatus Brehm, 1913 is redescribed, based on material from the Niger basin, Africa. The species name was given by Brehm erroneously, because under an optical microscope he mistook internal structures (the columns between the outer and inner walls of the valves) for the tubercules on the valve surface. But this species is undoubtedly valid, and `incorrect' species names must be conserved. Differences between I. tuberculatus and the most similar I. agilis (probably absent from the majority of African waters), I. spinifer (common in Africa), and some other species are discussed. Currently, I. tuberculatus is known for the Central African Republic, Mali and Niger.     

Identification of a uniquely southern African clade of coastal pipefishes Syngnathus spp

The taxonomic status of two southern African coastal pipefish species, Syngnathus temminckii and Syngnathus watermeyeri, was investigated using a combination of morphological and genetic data. Morphological data showed that S. temminckii is distinct from the broadly distributed European pipefish Syngnathus acus, and a molecular phylogeny reconstructed using mitochondrial DNA recovered S. temminckii and S. watermeyeri as sister taxa. The southern African species share an evolutionary origin with north‐eastern Atlantic Ocean and Mediterranean Sea species, including S. acus. These data support the existence of a distinct southern African clade of Syngnathus pipefishes that has diverged in situ to form the two species present in the region today.     

Deep divergence among mitochondrial lineages in African jackals

Recently, molecular analyses revealed that African and Eurasian golden jackals are distinct species. This finding suggests re‐investigation of the phylogenetic relationships and taxonomy of other African members of the Canidae. Here, we provide a study on the phylogenetic relationship between populations of African jackals Lupulella mesomelas and L. adusta inferred from 962 bp of the mitochondrial cytochrome b (cytb) gene. As expected from its disjunct distribution, with one population in eastern Africa and the other one in southern Africa, we found two mitochondrial lineages within L. mesomelas, which diverged about 2.5 million years ago (Ma). In contrast, in L. adusta with its more continuous distribution in sub‐Saharan Africa, we found only a shallower genetic diversification, with the exception of the West African population, which diverged around 1.4 Ma from the Central and East African populations. Both divergence ages are older than, for example the 1.1–0.9 million years between the grey wolf Canis lupus and the African golden wolf C. lupaster. One taxonomic implication of our findings might be that the two L. mesomelas populations warrant species status. However, genome‐wide data with adequate geographical sampling are needed to substantiate our results.     

A new genus and species of African Phaneropterinae (Orthoptera: Tettigoniidae), with data on its ecology,bioacoustics and chromosomes

A new genus is proposed for a new East African Phaneropterinae species, Lunidia viridis, occurring on Mt. Kilimanjaro, Tanzania. Based on 33 records, notes on distribution and habitat are given, as well as acoustical data provided. Climate and vegetation parameters obtained along several transects on Mt. Kilimanjaro were evaluated describing the ecological niche of the new species. This interdisciplinary approach allows not only a profound characterisation of the ecological demands of the new genus but also predictions of the potential distribution area, which is tested for the first time for an African bush cricket species. Lunidia viridis n. gen. n. sp. occurs within humid and perhumid forests and Chagga home gardens, avoiding subhumid conditions on the mountain. It is found from 1,330 m upwards on the southern slopes, whereas the same ecological conditions are expressed from 1,930 m upwards on the drier northern slopes. Lunidia viridis has an unusually complex and variable song, which is described from field and laboratory recordings. The FISH technique for characterizing chromosomes is applied for the first time for an African species; L. viridis exhibits a karyotype typical for most Tettigoniidae.     

An integrative approach to characterize Malagasy bats of the subfamily Vespertilioninae Gray, 1821, with the description of a new species of Hypsugo

Although important advances have been made in recent years in the taxonomy of different families and subfamilies of Malagasy bats, those belonging to the Vespertilioninae remain partially unresolved. Herein using a mitochondrial marker (cytochrome b) as the point of departure for 76 specimens of Malagasy vespers and appropriate African taxa, we diagnose the six taxa of this subfamily on the island by overlaying different morphological and bioacoustic characters on the clade structure of sequenced animals. The species include: endemic Neoromicia matroka, which is sister to African N. capensis; endemics N. malagasyensis and N. robertsi, which form sister species; a member of the genus Hypsugo, which is sister to African H. anchietae and described herein as new to science; Pipistrellus hesperidus for which Madagascar animals are genetically close but distinct from African populations of the same species; and endemic P. raceyi, which shows segregation of eastern (mesic) and western (dry) populations and its sister species relationships are unresolved. While the external and craniodental measurements, as well as bioacoustic variables, allow only partial differentiation of these six species of Vespertilioninae, molecular characters provide definitive separation of the taxa, as do male bacular morphology. © 2015 The Linnean Society of London     

Molecular systematics of Alethe,Sheppardia and some other African robins (Muscicapoidea)

Phylogenetic relationships between species of akalats (Sheppardia) and alethes (Alethe) were derived from mitochondrial and nuclear sequence data, and phylogeographic pattern was also investigated in three widespread species (two Alethe and one Sheppardia) endemic to the African lowland rainforest biome. Co-distributed species of Alethe and Sheppardia showed similar spatial relationships between the Guineo-Congolian biome and the Western Rift mountains, and preliminary area relationships are shown for species of Sheppardia and Alethe distributed in the Cameroon highlands, the woodland areas north and south of the lowland forest block, and east African montane and lowland forest. Within widespread species, phylogeographic pattern was generally similar, with long branches between Upper and Lower Guinea populations, and between eastern and western Congolian populations. At the interspecific level, the nuclear intron used gave more resolution than the mitochondrial data, which gave poor resolution at basal nodes. While the affinities of some species groups were weakly supported, no support was suggested for the monophyly of Alethe and little for Sheppardia as those genera are currently circumscribed, and taxonomic changes are suggested. As found by previous workers, monophyletic clades corresponding to Muscicapini and Saxicolini of Sibley and Ahlquist (1990) were not recovered, and the membership of any monophyletic 'African forest robin assemblage' needs to be resolved.     

Uncovering the tracks of a recent and rapid invasion: the case of the fruit fly pest Bactrocera invadens (Diptera: Tephritidae) in Africa

Phytophagous insects of the genus Bactrocera are among the most economically important invasive fruit fly pests. In 2003, an unknown Bactrocera species was found in Kenya. First identified as an ‘aberrant form’ of the Asian B. dorsalis complex, it was later recognized as a new species, Bactrocera invadens. Within 2 years of its discovery, the species was recorded in several African countries, becoming an important quarantine pest. As this invasive fly was discovered only recently, no data are available on its invasion pattern in Africa. This pilot study attempts to infer from genetic data the dynamic aspects of the African invasion of this pest. Using microsatellite markers, we evaluated the level of genetic diversity and the extent of common ancestry among several African populations collected across the invaded areas. A sample from the Asian Sri Lankan population was analysed to confirm the Asian origin of this pest. Genetic data cast no doubt that Sri Lanka belongs to the native range, but only a small percentage of its genotypes can be found in Africa. African populations display relatively high levels of genetic diversity associated with limited geographical structure and no genetic footprints of bottlenecks. These features are indicative of processes of rapid population growth and expansion with possible multiple introductions. In the span of relatively few years, the African invasion registered the presence of at least two uncorrelated outbreaks, both starting from the East. The results of the analyses support that invasion started in East Africa, where B. invadens was initially isolated.     

Dispersal and predation of diaspores of Coula edulis Baill. in an evergreen forest of Gabon

The African walnut (Coula edulis) is a tree species of African evergreen forests, the seeds of which are collected and traded by African people. Many animal species consume African walnut diaspores; however, their roles as dispersers or predators have yet to be clarified. In this study, we present observations conducted in two different habitats of a Gabonese region over a 3‐year period. The originality of this research resides in the combination of three complementary approaches: (i) the use of camera‐traps (ii) the exploration of land rodent burrows and (iii) the examination of elephant dung. In total, 408 camera‐trap photographs have shown seven animal species involved in the dispersal/predation of C. edulis. Among these seven frugivorous species, the bush pig was found to be the main consumer and predator of seeds. Land rodents (Muridae) are potential predators, as they damaged the seeds and buried them deep in the soil. They may also play a role in the regeneration process as a result of the loss of seeds during transportation. Finally, no seeds appeared to emerge intact from elephant faeces. These results indicate that the natural regeneration rate of this tree species is low, unless other complex mechanisms are involved.     

Time of diversification in the Cape fauna endemisms,inferred by phylogenetic studies of the genus Iselma (Coleoptera: Meloidae: Eleticinae)

The endemic diversification of the Cape zone fauna and the phylogenetic relationships among the 30 species of the blister beetle genus Iselma are investigated. We analysed morphological, molecular (mtDNA 16S) and combined datasets of characters using a number of approaches (maximum parsimony, maximum likelihood, Bayesian inference analyses). We propose hypotheses of diversification times among taxa from molecular clock analyses. Morphological and molecular analyses produced similar results. According to maximum likelihood molecular studies, radiation within the genus Iselma occurred during the Pliocene and Pleistocene, roughly contemporaneously with the shift in African climate, vegetation and faunal assemblages. Two main lineages, one Namibian and one South African, separated c. 4.9 Ma. Within the South African lineage we identify two groups of endemic species, one in Little Karoo and one that extend towards southern Namaqualand. The remaining South African groups of species are spread through Namaqualand and the southwestern Cape area. These include several endemisms, with different times of diversification during the Pleistocene, probably related in part to glacial cycles. These endemisms are distributed in small areas of the following ecosystems: coastal Strandveld, Succulent Karoo and particularly Fynbos.     

On the systematics and distribution of the molluscan genus Siphonaria in South Africa

Summary A revision of the systematics of the genus Siphonaria found around the South African coast from Port Nolloth on the West coast to Inhaca Island on the East coast is given. Of the twelve species described by Hubendick (1946) as occuring on the South African coast only five are valid. The remainder are reduced to synonyms. Two new species and one new variety are described.The horizontall distribution along the coastline of the valid species is described. Three species are recorded from the cold waters of the West coast while six species are recorded from the East coast. S. deflexa and S. oculus have a western distribution limit in False Bay. While S. dayi sp. nov. is only known from Inhaca Island. S. anneae and S. carbo occur in the subtropical waters near Durban. S. capensis and S. aspera are ubiquitous. S. compressa sp. nov. occurs only on the West coast in the sheltered waters of Langebaan lagoon, Saldanha Bay.Department of Zoology, University of Cape Town     

Home away from home — objective mapping of high-risk source areas for plant introductions

Prevention is the best way to slow the escalation of problems associated with biological invasions. Screening of potential introductions is widely applied for assessing the risk of species becoming invasive. Despite advances in the understanding of the determinants of invasiveness, screening still relies heavily on assessments of the potential of species to ‘fit in’ to the broad environmental conditions of a target region. Most screening systems ask whether species are native to, or are known to be naturalized or invasive in, regions with ‘similar’ climatic/environmental conditions to the target region. The level of similarity required to make the species a high‐risk introduction is generally not specified. This paper describes a protocol for making such assessments more objective, using South Africa as a test case. Using nonparametric niche‐based modelling (generalized additive model; GAM) calibrated on the current distribution of each South African biome, we mapped regions of the world that are climatically similar to South African biomes. Lists were produced of countries with the largest areas climatically similar to South Africa overall, and to each biome separately. Validation of the usefulness of the approach was sought by evaluating whether the main invasive plant species in South African biomes occur naturally, or have adventive ranges, in regions mapped as analogous to South African biomes. A very large part of the world is climatically similar to South Africa, with eight countries having larger areas of land classified as climatically similar to South African biomes than the total area of South Africa. Almost all the most prominent invasive species in South African biomes occur naturally or are invasive outside their natural range in areas with similar climates to those that occur in parts of South Africa. This confirms the value of objective climate matching in screening protocols. We examined climatic conditions for a representative sample of major invasive plants from other parts of the world. The analysis identified several species that are already invasive in regions that have matched climates in South Africa but that are not yet introduced or, if already present, have not yet invaded large areas. For example, the following known invasive species should be considered high‐risk species in South African grasslands: Alliaria petiolata, Cytisus scoparius, Gleditsia triacanthos, Heracleum mantegazzianum, Hieracium pilosella, Juniperus communis, Pinus contorta, P. monticola, P. ponderosa, P. sylvestris, Prunus laurcerasus, and P. serotina. Objectively matched climatic regions are also useful as a first‐cut assessment when evaluating species with no invasive history.