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The quagga project has now been in progress for over 20 years. Its aim, given conclusive molecular evidence that the quagga and the plains zebra, Equus quagga, are conspecific, is the retrieval of the pelage characteristics of the quagga by selective breeding from a selected panel of plains zebra Individuals. The programme has now over 25 third generation progeny, and is starting to produce Individuals with a degree of striping reduction shown by none of the original founders and which approximate the striping pattern shown by at least some of the known museum specimens of quagga. These results Indicate that by the fourth generation the project should have largely succeeded in its aim, and will form the basis of a herd of Individuals which can be displayed in the Western Cape as an Illustration of a phenotype which had disappeared from extant populations of plains zebra.

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at approximately 102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5-10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between Gorilla and Pan/Homo at approximately 11.5 MYA and that between Pan and Homo at approximately 8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed approximately 270,000 years ago, i.e. approximately 100,000 years earlier than the traditional age of "Mitochondrial Eve". Comparison between the two new mt genomes of Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera Elephas, Mammuthus and Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.

The world's domestic cats carry patterns of sequence variation in their genome that reflect a history of domestication and breed development. A genetic assessment of 979 domestic cats and their wild progenitors—Felis silvestris silvestris (European wildcat), F. s. lybica (Near Eastern wildcat), F. s. ornata (central Asian wildcat), F. s. cafra (southern African wildcat), and F. s. bieti (Chinese desert cat)—indicated that each wild group represents a distinctive subspecies of Felis silvestris. Further analysis revealed that cats were domesticated in the Near East, probably coincident with agricultural village development in the Fertile Crescent. Domestic cats derive from at least five founders from across this region, whose descendants were transported across the world by human assistance.

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.

A molecular phylogenetic investigation was conducted to examine phylogenetic relationships between various members of the catsharks (Chondrichthyes; Carcharhiniformes; Scyliorhinidae), and is the largest chondrichthyan data set yet analysed, consisting of nearly 130,000 nucleotides. Three mitochondrial DNA genes were used to construct the phylogenies, cytochrome b, NADH-2, and NADH-4, with 41 sequences from 18 taxa being novel. These sequences were either used separately or combined into a single data set, and phylogenies were constructed using various methods, however, only the Bayesian inference tree derived from the cytochrome b data set was resolved sufficiently for phylogenetic inferences to be made. Interestingly, the family Scyliorhinidae was not supported by the results and was found to be paraphyletic. The Scyliorhininae and Pentanchinae were supported, whereas the Pentanchini clade was present, but not well supported. The Halaelurini hypothesis was supported with Holohalaelurus identified as the basal genus of that clade, and Haploblepharus edwardsii identified as the basal taxon for that genus. Elsewhere within the Chondrichthyes, the Carcharhiniformes and the Lamniformes were found to be monophyletic, and the Heterodontiformes was placed within the Squalimorphs. The placement of the skates and rays in these analyses support the Batoidea as being sister to the Elasmobranchii.

The endangered mountain zebra (Equus zebra) is endemic to the semi-arid inhospitable mountainous escarpments of southern Africa. The species is divided taxonomically into two geographically separated subspecies, each with differing recent population histories. In Namibia, Hartmann’s mountain zebra (E. z. hartmannae) is common and occurs in large free-ranging populations, whereas in South Africa, prolonged hunting and habitat destruction over the last 300 years has decimated populations of the Cape mountain zebra (E. z. zebra). In this study, we investigate the consequences of these divergent demographic histories for population genetic diversity and structure. We also examine the phylogeographic relationship between the two taxonomic groups. Genetic information was obtained at 15 microsatellite loci for 291 individuals from a total of 10 populations as well as 445 bp of the mitochondrial control region sequence data from 77 individuals. Both model-based and standard analytical approaches were used to examine the data. Both types of marker returned levels of diversity and structure that were consistent with population history. Low genetic variation within individual Cape mountain zebra populations, the characteristic indicator of population fragmentation and drift, was offset by moderate variation in the entire E. z. zebra sample. This implies that higher levels of diversity still exist within the Cape mountain zebra gene pool. A management strategy that entailed the mixing of aboriginal populations is therefore advocated in order to halt the further loss of Cape mountain zebra genetic diversity. Allele frequencies in Hartmann’s mountain zebra were relatively resilient to demographic fluctuations. Due to the high incidence of mitochondrial haplotype sharing between populations, the hypothesis that Cape and Hartmann’s mountain zebra mitochondrial lineages were reciprocally monophyletic was not supported. However, the presence of private alleles at nuclear loci rendered the two subspecies genetically distinct evolutionary significant units.

The Natal long-fingered bat (Miniopterus natalensis) and lesser long-fingered bat (M. fraterculus) are morphologically almost indistinguishable and occur sympatrically over much of their southern African range. This raises the possibility that they are sister taxa. We employed a multidisciplinary approach to examine their taxonomic relationship to one another and to other Miniopterus species, whose global phylogeny requires review. We examined echolocation, morphological, and dietary differences between M. natalensis and M. fraterculus ,a s well as both nuclear and mitochondrial DNA variation between them in the context of a phylogeny incorporating 13 Miniopterus species and subspecies. Despite similarities in their morphology and distribution, M. natalensis and M. fraterculus echolocate at peak frequencies separated by 12 kHz, and both nuclear and mitochondrial DNA markers confirm they are distinct species. Analysis of cytochrome-b (Cytb) sequences further indicates that M. fraterculus and M. natalensis are not sister taxa; M. fraterculus appears to be more closely related to the greater long-fingered bat (M. inflatus). Examination of the global taxonomy of Miniopterus confirms that Schreibers’s long-fingered bat (M. schreibersii) forms a paraphyletic species complex. Furthermore, the miniopterine bats are divided into 2 geographically isolated monophyletic groups, one containing African and European species, and the other taxa from Australasia and Asia. Cytb sequence divergence also suggests that M. natalensis is distinct from the European M. schreibersii. These results support the elevation of M. natalensis to full species rank.

Microsatellite DNA was used to investigatelevels of genetic variability in severelyfragmented populations of the geometrictortoise, Psammobates geometricus, themost endangered tortoise on mainland Africa.Eight microsatellite markers were used toassess genetic variability within and betweenthree naturally occurring populations of P. geometricus. These populations areseparated by the Cape Fold mountain ranges inthe western Cape region of South Africa. Levels of variability were quantified usingallelic diversity, genotypic frequencies andheterozygosity. Evidence for populationsub-structuring was examined using Fstatistics, Rst and δμ2.High levels of variability were found in allthree populations. Low levels of populationdifferentiation were found suggestingsignificant gene flow between the populations.

Sequence data from the intron and spacer of the trnL-F chloroplast region elucidate the phylogenetic relationships of the tribe Diseae (Orchidoideae: Orchidaceae). Within Diseae, 41 species of Disa, two of Brownleea, three of Satyrium, and two of Corycium were included, with five species ofHabenaria sensu lato (Orchideae) and one epidendroid as outgroups. The sequences revealed substitutions and considerable length variation, due mainly to the presence of repeat motifs. Phylogenetic analysis using parsimony revealed five distinct clades. The branching order of the five weakly supported the paraphyly of Diseae, with the successive divergence of Brownleea, Corycium, Habenaria, Satyrium,and Disa. Within the monophyletic Disa, three main groupings appeared, two strongly supported clades representing sect. Racemosae and sect. Coryphaea and the third grouping containing several clades currently grouped into sections based on morphological phylogenies. Some discrepancies between the molecular phylogeny and the phylogeny based on morphological characters may require reevaluation of some of the morphological characters. The presence of different numbers of repeat motifs, both among different taxa and within taxa, indicates that these characters may be phylogenetically informative at the population level. The tribe Diseae dominates the terrestrial orchid flora of southern Africa including 250 of the 466 orchid species on the subcontinent (Linder and Kurzweil, 1999). Diseae encompasses 54% of all orchids endemic to southern Africa, underlining its importance in the local orchid flora. Linder and Kurzweil (1994) recognize five subtribes in the tribe. Of these, Huttonaeinae and Brownleeinae each contain a single genus. Douzery et al. (1999) corroborated the monophyly of the subtribes with the exception of the Coryciinae, which may be diphyletic, and suggested that the tribe itself may be paraphyletic, with Orchideae embedded in Diseae. Almost half of all species in the Diseae belong to the subtribe Disinae. The subtribe was revised taxonomically by Linder in 1981, resulting in a complicated taxonomy of five genera, and many subgenera, sections, and series. However, attempts to establish a wellresolved phylogeny of the subtribe based on morphological data have been unsuccessful (Linder, 1986; Linder and Kurzweil, 1990). Recent morphological work suggested that Brownleea should be excluded from the subtribe, and that Monadenia and Herschelianthe should be included in Disa, thus reducing the subtribe to two genera: Schizodium with 6 species and Disa with 131 species (Johnson, Linder, and Steiner, 1998; Linder and Kurzweil, 1999). Recently, phylogenetic studies in the Orchidaceae have ben1

The amount of genetic differentiation between the African wild cat (Felis lybica) and the domestic cat (F. catus) in southern Africa is not known, but there is concern that interbreeding between the two may have been sufficiently extensive to threaten the status of the wild cat as a genetically distinct population. Eight hypervariable microsatellite loci were therefore used to determine the genetic relationships within and among wild and domestic cat populations. Measures of genetic differentiation, including FST and RST, confirmed significant differentiation between the wild and domestic cat populations and no significant differentiation between two widely separate domestic cat populations. Our data indicate that the level of genetic introgression is lower than previously thought. This enhances the conservation status of the African wild cat and demonstrates the need for the implementation of feral cat control in and around game reserves and rural areas.

Restriction-endonuclease site maps of mitochondrial DNA were constructed for members of the family Bovidae emphasizing species in the Alcelaphinae, Bovinae, and Aepycerotinae. Cladograms weakly supported sister status of the impala, Aepyceros melampus , relative to the Alcelaphinae, and monophyletic status of the Bovini and Tragelaphini. Four members of the Tragelaphini remained an unresolved quadrichotomy, which would be consistent with the inclusion of the eland, Taurotragus oryx , within Tragelaphus . The restriction data are consistent with a radiation for the Tragelaphini at the end of the Miocene.

Cell cultures have been established from 33 individual black rhinoceroses. These were from wild populations from various localities in southern Africa and include representatives from three geographical regions (southwestern, south-central, and eastern) corresponding to currently accepted conservation units, and include individuals previously attributed to one of the four subspecies, Diceros b. minor, D. b. bicornis, D. b. michaeli, and D. b. chobiensis (du Toit et al. 1987). Comparative mitochondrial DNA restriction maps were constructed using 16 restriction enzymes. These showed in each case two site differences between representative individuals from any two of the above geographical regions. Maps were monomorphic within geographical regions and, therefore, have the potential to provide diagnostic markers. The map from a single individual attributed to the D. b. chobiensis subspecies was identical to other individuals (attributed to D. b. minor) in the south-central geographical region. The low amount of genetic diversity implied by these few differences renders it unlikely that problems with outbreeding depression will arise if, given the continuing decline in numbers of black rhinoceroses, it becomes necessary to supplement wild or captive populations with individuals from a different conservation unit in order to avoid inbreeding depression. Se establecieron cultivos de celulas de 33 rinocerontes negros. Estos provinieron de poblaciones salvajes de varias localidades del sur de Africa e incluyen representantes de tres regiones geograficas (Sudoccidental, Sud-central y Oriental) que corresponden a las unidades de conservacion corrientemente aceptadas e incluyen individuos que previamente fueron atribuidos a otras cuatro subespecies, Diceros b. minor, D. b. bicornis, D. b. michaeli y D. b. chobiensis (du Toit, Foose & Cummings, 1987). Se construyeron mapas de restriccion de ADN mitocondrial comparativos usando 16 enzimas de restriccion. En cada caso estos mostraron diferencias en dos sitios entre individuos representantes de un par cualquiera de las regiones geograficas antes mencionadas. Los mapas fueron monomorficos dentro de cada region geografica y por lo tanto tienen el potencial para proveer marcadores diagnosticos. El mapa de un unico individuo que se atribuia a la subespecie D. b. chobiensis fue identico a otros individuos (atribuidos a D. b. minor), en la region geografica Sud-central. El bajo nivel de diversidad genetica que implican estas pocas differencias hace poco probable que surjan problemas de depresion de exogamia si, dada la declinacion continua en el numero de rinocerontes negros, se hace necesario suplementar las poblaciones salvajes o cautivas con individuos de unidades de conservacion diferentes a los efectos de evitar la depresion de endogamia.

Mitochondrial DNA restriction maps of Diceros bicornis , the black rhinoceros, and Ceratotherium simum , the white rhinoceros, were constructed to provide a basis for population genetic and systematic studies. The sequence divergence between DNA of the two species was calculated to be 6.79% from which it could be estimated that the time of divergence from a common ancestor was ca. 3.4 × 106 years ago. Little intraspecific variation was found in the 24 black rhinoceroses or the 4 white rhinoceroses studied.

The black rhinoceros (Diceros bicornis) is currently one of the most endangered African mammals as a direct result o habitat destruction and intensive poaching. A microsatellite library was constructed to address a number of population genetic questions. This paper describes the isolation of five black rhinoceros microsatellite loci. Three of these loci were found to be polymorphic. In addition, the paper demonstrates the utility for cross-hybridization of these primers in other species of rhinoceros.

Black rhinoceros ( Diceros bicornis ) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

Phylogenetic analysis of 14 cetacean species, including members from two baleen whale families and three toothed whale families, was undertaken using restriction site mapping of mitochondrial DNA and using cladistic and distance measures to infer phylogenies. The amount of between-taxa sequence divergence inferred from the data was lower than expected from the standard interpretation of the fossil record, but more consistent with some recent estimates of sequence divergence in cetacean mitochondrial DNA or nuclear DNA. This implies either that the rate of molecular evolution of cetacean DNA is much lower than that of other mammalian orders or that the fossil record of cetaceans requires reinterpretation. The incompleteness of the cetacean fossil record precludes resolution of the paradox at the present time. However, this discrepancy could in part be attributed to the sampling error inherent in the restriction site mapping technique, as comparative studies using the complete mtDNA genome and restriction site data of the blue and fin whales (genus Balaenoptera) indicate that the restriction site maps underestimate sequence divergence by about 40%. In contrast to a recent study suggesting that toothed whales were paraphyletic, with the sperm whales being more closely related to the rorquals than to the other toothed whales, the restriction data tend to support the monophyly of the baleen and the toothed whales, a finding which is consistent with a recent molecular-based study and with morphological and paleontological data. Topologies of the subfamily and generic levels are generally consistent with morphologically based schemes.

In South Africa, the endemic toad species Bufo pardalis, more commonly known as the leopard toad, was initially described by Hewitt (1935) from Kei Road in the Eastern Cape, as a subspecies of Bufo regularis, Bufo regularis pardalis. It is distributed in two allopatric populations: one that occurs in the extreme southwestern Cape including the Cape Peninsula, Cape Flats and forelands to Hermanus, and the other, larger population that occurs in the Eastern Cape Province from Cape St. Francis to the Kwazulu-Natal border. The smaller Western Cape population is threatened because of the increase in recent years of land development for housing on the peninsula, with corresponding habitat losses (M. I. Cherry, pers. obs.). Hewitt made a distinction between the western and eastern forms based on morphological differences including more brilliant coloration, larger dorsal blotches and broader parotid glands in western specimens. In 1964, Poynton raised Bufo pardalis to specific status but made no comment on Hewitt's distinction between western and eastern forms. Comparisons of laryngeal morphology by Lambiris (1994) provided additional support for species recognition of the two populations. Poynton and Lamibiris (1998) elevated the Western Cape form to specific status as Bufo pantherinus: B. pantherinus was found to have distinctive coloration and markings, as well as unique laryngeal and parotid gland morphology. Differences in call structure have not yet been investigated, but it is intriguing to speculate that the differences in the laryngeal morphology may be reflected by differences in the call structure.

Sequence data from the plastid encoded gene rbcL are used to determine phylogenetic relationships between various lineages in the grasses, with particular emphasis on the subfamily Arundinoideae. Thirty four sequences, producing 155 phylogenetically informative sites, were analysed using both parsimony and distance methods. Cladistic analyses indicate that there are two main lineages: Pooideae (including the Stipeae) and a large clade comprising Panicoideae, Arun- dinoideae, Chloridoideae, and Centothecoideae. The Bambusoideae are unresolved and basal to these two lineages. Relationships within the panicoid, arundinoid, chloridoid, and centothecoid clade indicate that Arundinoideae as presently circumscribed are paraphyletic, as lineages within this subfamily show affinities with all three of the other subfamilies. Despite poor support for some relationships, rbcL appears to be well suited for systematic studies in the Poaceae.

DNA was prepared directly from preparations pf papovavirus excreted in the urine of 2 patients on immunosuppressive therapy, without preliminary amplification in cell cultures. EcoRI, BamHI, and HindIII restriction patterns were typical of BK virus DNA and were identical for the two isolates. However, there were significant differences in the sizes of the HindIII fragments when compared with those of standard cell-culture-adapted BK virus strains.

The nucleic acids of three viruses infecting Heliothis armigera have been studied. A nuclear polyhedrosis virus and granulosis virus contained double-stranded DNA. A cytoplasmic polyhedrosis virus contained double-stranded RNA, and polyacrylamide gel electrophoresis showed that the genome consisted of 10 discrete double-stranded RNA components.

A re-evaluation of the mobility of double-stranded RNA on polyacrylamide gels over a molecular weight range of 0.46–6.3 · 10 6 was carried out using double-stranded RNAs of: bacteriophage Φ6; virus like particles or mycoviruses of Penicillium chrysogenum, Penicillium stoloniferum and Helminthosporium maydis , and reovirus type III. When the relative mobility on polyacrylamide gels was plotted as a function of log molecular weight, a smooth curve could be drawn which passed through all point. The implications of these findings to the determination of molecular weight of double-stranded RNA by polyacrylamide gel electrophoresis are discussed.

The probable extinction of the last confirmed population of northern white rhinoceros (Ceratotherium simum cottoni) in the world has ignited debate regarding its species status compared to the southern white rhinoceros (Ceratotherium simum simum). Previous studies, based on partial mitochondrial sequences, have reported conflicting results regarding the species status of the northern white rhinoceros. We use whole mitochondrial genomes obtained using Next Generation Sequencing of four northern white rhinoceros and three southern white rhinoceros using novel primers in three overlapping fragments. Phylogenetic relationships were constructed, using Maximum Likelihood, and recovered monophyletic clades for northern white rhinoceros and southern white rhinoceros. The divergence time between the two mitochondrial DNA lineages was estimated to be between 0.46 and 0.97 million years ago using Bayesian inferences. Since there are currently only three surviving northern white rhinoceros individuals these results put into sharp focus the ongoing debate regarding the methods of species definition, and in particular the consequences of such definitions in conservation management of endangered species and subspecies. We conclude that the designation of sub-species status is more applicable to northern and southern white rhinoceros.

A BK virus isolate cloned from the urine of an immunosuppressed patient was identified as the WW strain. Fine mapping using four base-pair restriction enzymes identified a number of small deletions and insertions relative to prototype BK. The finding of a transcriptional control region with a structure similar to that of a previous isolate cloned in a similar way demonstrates that this is a reproducible finding and reinforces the hypothesis that the structure is the archetypal form, found when cloned directly from urine, but generally altered when passaged in cell culture. BK virus is a human papovavirus first identified in the urine of a renal allograft patient by Gardner. Several BK strains have been studied in detail by restriction endonuclease mapping or sequencing. Two of these, the Dunlop and the MM strains, have been sequenced in their entirety, and a 400 to 500 base-pair region concerned with the control of transcription and replication has been sequenced in a number of others. All of these BK virus isolates were amplified by passage in cell culture before being characterized, although it often takes many weeks in culture before plaques can be identified and it has been reported that genome changes can occur on passage. Previous to the present isolate, we have identified BK virus in the urine of three local patients, and limited restriction endonuclease analysis of DNA prepared directly from the urine showed that they were similar and represented a new strain (BK-WW).(ABSTRACT TRUNCATED AT 250 WORDS)