South African Genus Research Articles

Phylogeny of Pelargonium (Geraniaceae) based on DNA sequences from three genomes

AbstractPhylogenetic hypotheses for the largely South African genus Pelargonium L'Hér. (Geraniaceae) were derived based on DNA sequence data from nuclear, chloroplast and mitochondrial encoded regions. The datasets were unequally represented and comprised cpDNA trnL­F sequences for 152 taxa, nrDNA ITS sequences for 55 taxa, and mtDNA nad 1 b/c exons for 51 taxa. Phylogenetic hypotheses derived from the separate three datasets were overall congruent. A single hypothesis synthesising the information in the three datasets was constructed following a total evidence approach and implementing dataset specific stepmatrices in order to correct for substitution biases. Pelargonium was found to consist of five main clades, some with contrasting evolutionary patterns with respect to biogeographic distributions, dispersal capacity, pollination biology and karyological diversification. The five main clades are structured in two (subgeneric) clades that correlate with chromosome size. One of these clades includes a "winter rainfall clade" containing more than 70% of all currently described Pelargonium species, and all restricted to the South African Cape winter rainfall region. Apart from (woody) shrubs and small herbaceous rosette subshrubs, this clade comprises a large "xerophytic" clade including geophytes, stem and leaf succulents, harbouring in total almost half of the genus. This clade is considered to be the result of in situ proliferation, possibly in response to late­Miocene and Pliocene aridification events. Nested within it is a radiation comprising c. 80 species from the geophytic Pelargonium section Hoarea, all characterised by the possession of (a series of) tunicate tubers.

Phylogeny of Pelargonium (Geraniaceae) Based on DNA Sequences from Three Genomes

Phylogenetic hypotheses for the largely South African genus Pelargonium L'Her. (Geraniaceae) were derived based on DNA sequence data from nuclear, chloroplast and mitochondrial encoded regions. The datasets were unequally represented and comprised cpDNA trnL-F sequences for 152 taxa, nrDNA ITS sequences for 55 taxa, and mtDNA nad1 b/c exons for 51 taxa. Phylogenetic hypotheses derived from the separate three datasets were overall congruent. A single hypothesis synthesising the information in the three datasets was constructed following a total evidence approach and implementing dataset specific stepmatrices in order to correct for substitution biases. Pelargonium was found to consist of five main clades, some with contrasting evolutionary patterns with respect to biogeographic distributions, dispersal capacity, pollination biology and karyological diversification. The five main clades are structured in two (subgeneric) clades that correlate with chromosome size. One of these clades includes a rainfall containing more than 70% of all currently described Pelargonium species, and all restricted to the South African Cape winter rainfall region. Apart from (woody) shrubs and small herbaceous rosette subshrubs, this clade comprises a large xerophytic clade including geophytes, stem and leaf succulents, harbouring in total almost half of the genus. This clade is considered to be the result of in situ proliferation, possibly in response to late-Miocene and Pliocene aridification events. Nested within it is a radiation comprising c. 80 species from the geophytic Pelargonium section Hoarea, all characterised by the possession of (a series of) tunicate tubers.

Evidence for the Polyphyly of Haworthia (Asphodelaceae Subfamily Alooideae; Asparagales) Inferred from Nucleotide Sequences of rbcL, matK, ITS1 and Genomic Fingerprinting with ISSR‐PCR

Abstract: Four molecular markers have been studied to examine the phylogenetic position of the South African plant genus Haworthia Duval within the succulent Asphodelaceae. Sequence data of the chloroplast genes matK and rbcL were compared to the nuclear markers ITS1 and ISSR (Inter Simple Sequence Repeat) analysis. Both lines of molecular data, chloroplast and nuclear DNA, indicate that Haworthia is polyphyletic, forming two distinct clades. Most taxa previously combined as Haworthia subgenus Haworthia branch off early in the alooid chloroplast trees forming a strongly monophyletic group, whereas subgenus Hexangulares forms a polyphyletic assemblage comprising other alooid genera. The nuclear markers ITS1 and ISSR fingerprinting support the two groups as distinctly different, therefore confirming the division seen in chloroplast DNA. The practical implication is that the generic concept of Haworthia may have to be restricted to H. subgenus Haworthia or alternatively, that the groups of Haworthia be treated as infrageneric taxa within a broadened (Linnaean) concept of Aloe.

Revision of the South African endemic genus Edenophorus Smith (Diptera: Empididae)

Revision of the South African endemic genus Edenophorus Smith (Diptera: Empididae)

Phylogenetic Relationships in Burseraceae Based on Plastid rps16 Intron Sequences

Summary. The intron of the plastid rpsl6 gene was sequenced for 13 species in 11 genera of Burseraceae and three genera of Anacardiaceae. Parsimony analysis produced just three strongly supported trees. Canarieae and Protieae are shown to be monophyletic with 100% bootstrap support. Bursereae, however, are paraphyletic with two distinct clades corresponding to the subtribes. The hypothesised, but never formally recognised, close association between the genera Garuga and Boswellia is reinforced. The close association between the South American genus Bursera and African genus Commiphora is clearly demonstrated. The position of the recently discovered Beiselia is resolved as a distant sister to the rest of

The Early Triassic ‘lizard’Colubrifer Campi: A Reassessment

Colubrifer campi Carroll, 1982 is a small reptile represented by a single skeleton from the Lower Triassic of South Africa. Carroll attributed the genus to the Squamata, proposing that it was a derived lizard with reduced limbs. Re‐examination of the specimen permits a rather different interpretation of the skull. The holotype of Colubrifer is the skeleton of a small primitive procolophonian, almost certainly referable to the established South African genus Owenetta.

A comprehensive phylogeny of the Phaeophyceae based on nrDNA sequences resolves the earliest divergences

The present study is the first comprehensive phylogeny of the class of the Phaeophyceae. For 67 species representing all orders of the class, the sequences of the 3’-end of the small and the 5ˈ-end of the large subunit nrRNA genes were aligned and analysed. A further analysis based on sequences of the 3’-end of the small and of the complete sequences of the 28S gene of the large subunits was also performed, but for only eight taxa. In both analyses, Tribonema marinum (Xanthophyceae) was used as outgroup. The analyses showed the Dictyotales as diverging first, followed by the Sphacelariales, then the Syringodermatales. Most of the orders currently accepted were confirmed as monophyletic groups but the Laminariales and Tilopteridales remained polyphyletic. The relationships of the remaining orders to each other were not resolved with the present data set. Ascoseira, included for the first time in a molecular study, appeared as a separate lineage without any clear relationship with other algae possessing conceptacles ( Splachnidium and Fucales). Algae with stellate plastids, never studied in a global context, were polyphyletic; this result is consistent with their plastid ultrastructure and is discussed in detail. As further result of the present study, the South African genus Bifurcariopsis appeared as the sister taxon of the North Atlantic genus Himanthalia, and Xiphophora appeared as the sister taxon of Hormosira rather than as a member of the Fucaceae; the taxonomic position of these genera is discussed.

Subtribe Astephaninae (Apocynaceae-Asclepiadoideae) Reconsidered: New Evidence Based on cpDNA Spacers

The circumscription of the subtribe Astephaninae has a complex and convoluted history due in part to a scarcity of readily observed distinctive morphological characters. In this study the subtribe Astephaninae, as hitherto defined by morphological characters, is reexamined using sequences of the tmT-L and trnL-F spacer, as well as the trnL intron for 12 of its 15 genera. Eustegia is found to occupy an isolated basal position in the tribe Asclepiadeae, and Schizostephanus is transferred to the Metastelminae. The remaining 10 genera fall into two only distantly related clades of 3 and 7 genera, respectively. The Astephaninae s. str. comprise only 3 South African genera, Astephanus s. str., Microloma, and Oncinema. The other 7 genera form a well-supported clade, the subtribe Tylophorinae. Both groups comprise only Old World genera. All New World taxa studied, even those that have never been formally excluded from Astephanus, are found in a distinct, well-supported New World Metastelminae clade. Based on the results presented here one of the key characters of the asclepiads-the corona-has been lost independently at least twice: once in the south African Astephaninae, and once in the New World Metastelminae. This once again underscores the extreme lability of this morphologically complex organ, as well as the difficulties in assessing homology in the asclepiads. A corollary classification of the Asclepiadeae is provided as an Appendix.

Molecular Systematics of Cyperaceae Tribe Cariceae Based on Two Chloroplast DNA Regions: ndhF and trnL Intron-Intergenic Spacer

A phylogenetic analysis of Cyperaceae tribe Cariceae was conducted using chloroplast DNA sequences from the gene ndhF and trnL intron and trnL-trnF intergenic spacer. Twenty nine taxa within Cariceae, four outgroup genera, and approximately 3,000 bp of cpDNA were included in the study. Our analysis reveals a monophyletic Cariceae with 100% bootstrap support. Within Cariceae, the South African genus Schoenoxiphium forms a clade that is sister to the rest of the tribe. Our results indicate that genus Carex is paraphyletic with respect to Kobresia, Cymophyllus, and Uncinia. Cymophyllus and Uncinia are nested within an assemblage containing Kobresia, Cymophyllus, and several unispicate Carex species. At the subgeneric level within Carex, only Carex subgenus Vignea appears monophyletic. Several well supported clades were iden- tified within the Cariceae, including the Schoenoxiphium clade, Uncinia clade, Carex subgenus Indocarex/Carex clade, and subgenus Vignea clade; however, relationships among some clades are only moderately supported. Interpretation of the phylogenetic patterns and an account of past phylogenetic hypotheses with respect to the new data are provided.

Molecular Phylogeny and Biogeography of Tribe Anthemideae (Asteraceae), Based on Chloroplast Gene ndhF

Anthemideae (Asteraceae) is primarily a north temperate, Old World tribe of 109 genera and approximately 1740 species. We sequenced a 1200-bp portion of chloroplast gene ndhF for representative genera and subtribes and constructed a phylogeny for the tribe. There is support for monophyly of subtribes Chrysantheminae and Gonosperminae and for portions of some subtribes. However, our molecular phylogeny differs significantly from traditional classifications and from previously published morphological phylogenies of the tribe. Many South African genera from several different subtribes form a basal grade, indicating multiple, relictual lineages. Eurasian genera form a recently derived clade that includes the Mediterranean genera of the Iberian Peninsula and North Africa. There is little resolution or support for the placement of eastern Asian genera. Apparently, the tribe originated in the Southern Hemisphere, presumably in Africa, with the Eurasian and Mediterranean members being derived from a common ancestor.

Molecular Phylogeny and Biogeography of the Native Rodents of Madagascar (Muridae: Nesomyinae): A Test of the Single-Origin Hypothesis.

Complete nucleotide sequences from the mitochondrial cytochrome b gene (1143 bp) were used to investigate the phylogenetic relationships among the native rodents of Madagascar. Specifically, this study examines whether the nine genera of nesomyines form a monophyletic group relative to other Old World murids. All nine of the nesomyine genera, including multiple individuals from 15 of the 21 described species, were included in the analysis, and their monophyly was assessed relative to the murid subfamilies Mystromyinae, Petromyscinae, Dendromurinae, Cricetomyinae, Murinae, Rhizomyinae, and Calomyscinae. Phylogenetic analysis of the resulting 95 taxa and 540 characters resulted in 502 equally parsimonious cladograms. The strict consensus tree weakly refutes the monophyly of Nesomyinae and suggests that the Malagasy rodents form a clade with dendromurines (as represented by Steatomys) and the African rhizomyine Tachyoryctes. The cladogram strongly refutes the association of the South African genus Mystromys with the Malagasy genera and suggests that Petromyscus and Mystromys form a monophyletic group. We provide the first explicitly phylogenetic scenario for the biogeographic history of nesomyine rodents. Our phylogenetic hypothesis indicates: (1) rodents invaded Madagascar only once, (2) they came from Asia not from Africa as is commonly assumed, and (3) there was a secondary invasion of rodents from Madagascar into Africa.

The Phylogenetic Position of Prionium (Juncaceae) within the Order Juncales Based on Morphological and rbcL Sequence Data

In this study we estimate the phylogenetic position of the South African genus Prionium within the order Juncales. Prionium is traditionally included within the family Juncaceae. However, trees based on rbcL sequence data have indicated that Juncaceae is paraphyletic because Prionium is not included within Jun- caceae. Morphological and rbcL sequence data are analyzed separately and then in a combined data set to assess the phylogenetic position of Prionium. Each of these analyses supports a basal position of Prionium within Juncales. The monophyly of Juncaceae sensu lato is not corroborated by the morphological data set, the rbcL data set, or the combined data set, while Cyperaceae is monophyletic. Based on these results, Jun- caceae s.l. can no longer be recognized without raising Prionium to family level. Juncales may consist of four families, the Prioniaceae, Thurniaceae, Juncaceae (excluding Prionium), and Cyperaceae. The basal position of Prionium within Juncales is supported by several unique features. Therefore, it is suggested that a new fam- ily should be erected for Prioniuim and be given the name Prioniaceae.

Transfers from Amaryllis to Hippeastrum (Amaryllidaceae)

SummaryMeerow, A. W., Van Scheepen, J. & Dutilh, J. H. A.: Transfers from Amaryllis to Hippeastrum (Amaryllidaceae). – Taxon 46: 15‐19. 1997. – ISSN 0040‐0262.42 species transfers are made from Amaryllis to Hippeastrum in accord with the decision, at the Fourteenth International Botanical Congress in 1987, on the application of the former name to a South African genus. This completes the validation of combinations required in Hippeastrum, and will thus aid nomenclatural clarity and enable botanists and horticulturists to refer to these species by their correct names.

Parental care inHemisus(Anura: Hemisotidae)

Accounts of parental care in Anura frequently include mention of the South African frog genus Hemisus and derive their infonnation from what was written by the late Vincent Wager, An analysis is given of what exactly is known and what has been written, either from original observations or derived from other publications. S, Afr. J, Zool. 1997,32(2)

Trachyandra triquetra (Asphodelaceae), a new species from the Horn of Africa

The new species Trachyandra triquetra, from shady limestone rocks in north‐eastem Somalia, is described and illustrated. This apparently narrow endemic is the only member of this mainly South African genus in eastern and north‐eastem tropical Africa except for the widespread T. saltii.

Relatively recent evolution of an unusual pattern of early embryonic development (long germ band?) in a South African onychophoran, Opisthopatus cinctipesPurcell (Onychophora: Peripatopsidae)

During embryonic development the process of segment formation in both families of the Onychophora, the Peripatidae and the Peripatopsidae, follows an essentially similar pattern with the exception of the South African peripatopsid, Opisthopatus cinctipesPurcell. In all other species in which development has been described, paired lateral halves of the embryo, separated by extra-embryonic ectoderm, develop as thickened bands on the surface of the blastoderm coincident with the appearance of the mouth and anus. The bands quickly differentiate paired segmental swellings with intersegmental grooves. The body elongates by proliferation from a posterior growth zone. During this process, presumptive mesoderm, located posteriorly in the early embryo, proliferates and moves anteriorly to form two lateral bands of mesodermal cells which segment during their forward growth into an anterior-posterior sequence of paired somites. In O. cinctipesthe embryo elongates without any visible external or internal segment boundaries. In the elongating embryo only ectoderm and endoderm layers are present. Only after elongation has occurred are mesodermal somites formed. Allozyme analysis indicates that O. cinctipesdiverged from the other South African genus PeripatopsisPocock, with in the last 30 Myr.

Relatively recent evolution of an unusual pattern of early embryonic development (long germ band?) in a South African onychophoran, Opisthopatus cinctipes Purcell (Onychophora: Peripatopsidae)

Abstract During embryonic development the process of segment formation in both families of the Onychophora, the Peripatidae and the Peripatopsidae, follows an essentially similar pattern with the exception of the South African peripatopsid, Opisthopatus cinctipes Purcell. In all other species in which development has been described, paired lateral halves of the embryo, separated by extra-embryonic ectoderm, develop as thickened bands on the surface of the blastoderm coincident with the appearance of the mouth and anus. The bands quickly differentiate paired segmental swellings with intersegmental grooves. The body elongates by proliferation from a posterior growth zone. During this process, presumptive mesoderm, located posteriorly in the early embryo, proliferates and moves anteriorly to form two lateral bands of mesodermal cells which segment during their forward growth into an anterior-posterior sequence of paired somites. In O. cinctipes the embryo elongates without any visible external or internal segment boundaries. In the elongating embryo only ectoderm and endoderm layers are present. Only after elongation has occurred are mesodermal somites formed. Allozyme analysis indicates that O. cinctipes diverged from the other South African genus Peripatopsis Pocock, with in the last 30 Myr.

Phylogeny of the African Genera Anomatheca and Freesia (Iridaceae: Ixioideae), and a New Genus Xenoscapa

Anomatheca and Freesia, African genera of Iridaceae subfamily Ixioideae, are currently thought to be closely related, but until now the exact nature of their alliance has been difficult to determine. Cladistic analysis has provided one means of assessing their relationship. Using 25 characters found to be useful for phylogenetic analysis, including traditional morphological features as well as original data from pollen morphology, leaf anatomy, embryology, and seed development, Freesia appears to be monophyletic but nested in Anomatheca sect. Anomatheca, one of two sections of the genus. A second section, Xenoscapa, which includes one named species and a second one described here, comprises a well-supported clade that is probably only distantly related to Freesia plus sect. Anomatheca. We herein unite Anomatheca and Freesia, but under the later name Freesia. Because Freesia is already a conserved name and because it is a well-known and horticulturally important genus, Anomatheca has been formally rejected in favor of Freesia. We raise sect. Xenoscapa to generic rank and transfer A. fistulosa to it, describe the new species, X. uliginosa, and provide new combinations in Freesia for the species until now included in Anomatheca. Anomatheca Ker-Gawl. (1805), a tropical and southern African genus currently including five species, and Freesia Klatt (1863), a South African genus of 11 species, are closely related members of Ixieae, one of three tribes of the Old World and largely African subfamily Ixioideae (Goldblatt 1990, 1991) of the Iridaceae. Anomatheca was later treated as a subgenus of Lapeirousia Pouret by Baker (1896, 1898). Lewis (1954), however, disagreed with Baker's circumscription of Lapeirousia and suggested that Anomatheca might be better regarded as a separate genus, which she believed was most closely allied to Freesia. Lewis placed the two genera on the same branch of a phylogenetic tree some distance from Lapeirousia in subtribe Watsoniinae. Goldblatt (1971, 1972) also recognized Anomatheca and removed both it and Freesia from Watsoniinae and treated them as the sole genera of a subtribe Freesiinae. In this paper we explore the relationships of Freesia and Anomatheca and, as a result, propose some changes to the taxonomy of Ixieae. MATERIALS AND METHODS Taxa and Characters. Characters selected for inclusion in the analysis and their states and polarization are discussed in Appendix 1. Data for Anomatheca were largely taken from a study by Goldblatt (1972) and for Freesia from a revision by Goldblatt (1982). Data on leaf anatomy were obtained from work by Rudall and Goldblatt (1991) and supplemented by additional observations for species not known anatomically. Pollen characters, taken from a study by Goldblatt et al. (1990), were also supplemented by original observations presented in Table 1. Chromosome numbers were determined for the new species, confirmed for A. grandiflora Bak. and A. fistulosa (Spreng. ex Klatt) Goldblatt by M. Takei, and will be reported fully elsewhere (Goldblatt and Takei, in mss). Seed characters are taken from ongoing studies (Manning and Goldblatt unpubl. data) of seed development in Ixioideae.

The cicada genusStagean. gen. (Homoptera Tibicinidae): systematics

The monotypic genus Stagea n. gen. and the species S. platyptera n. sp. are described. The type was caught in Natal, South Africa. The genus shares several characters with the endemic South African genera Stagira Stal 1861 and Bavea Distant 1905.

The Erythrothrips complex of tropical Aeolothripidae (Thysanoptera) with new taxa from Australia and South Africa

AbstractThe New World genus Erythrothrips is redefined and a key to the species provided. A new genus and species, Erythridothrips cubilis, is described from Australian tropical rain-forest. The South African genus Audiothrips is withdrawn from synonymy with Erythrothrips and a new species, A. senckenbergiana, is described. The sole African species in the American genus Stomatothrips is transferred to the African genus Allelothrips. The relationships of these taxa are discussed, together with reasons for questioning the validity of the tribe Orothripini.