The identity of Albuca caudata Jacq. (Hyacinthaceae) and a description of a new related species : A. bakeri
- Martinez-Azorin, Mario, Cresbo, Manuel B, Dold, Anthony P, Barker, Nigel P
- Authors: Martinez-Azorin, Mario , Cresbo, Manuel B , Dold, Anthony P , Barker, Nigel P
- Date: 2011
- Language: English
- Type: Article
- Identifier: vital:6528 , http://hdl.handle.net/10962/d1005969
- Description: The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin´s concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker´s concept of Albuca caudata are described as a new related species: Albuca bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed.
- Full Text:
- Date Issued: 2011
- Authors: Martinez-Azorin, Mario , Cresbo, Manuel B , Dold, Anthony P , Barker, Nigel P
- Date: 2011
- Language: English
- Type: Article
- Identifier: vital:6528 , http://hdl.handle.net/10962/d1005969
- Description: The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin´s concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker´s concept of Albuca caudata are described as a new related species: Albuca bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed.
- Full Text:
- Date Issued: 2011
Using molecules and morphology to infer the phylogenetic relationships and evolutionary history of the Dirini (Nymphalidae: Satyrinae), a tribe of butterflies endemic to Southern Africa
- Price, Benjamin W, Villet, Martin H, Walton, Shaun M, Barker, Nigel P
- Authors: Price, Benjamin W , Villet, Martin H , Walton, Shaun M , Barker, Nigel P
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442397 , vital:73981 , https://doi.org/10.1111/j.1365-3113.2010.00560.x
- Description: The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I (COI) and the nuclear genes elongation factor 1α (EF1α) and wingless (WG) (totalling 1734 bp) were used to infer the relationships of the in‐group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in‐group genus were strongly supported. Key findings are the sister‐taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans‐Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid–late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early‐middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C4 grasses over the C3 grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate-related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis.
- Full Text:
- Date Issued: 2011
- Authors: Price, Benjamin W , Villet, Martin H , Walton, Shaun M , Barker, Nigel P
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442397 , vital:73981 , https://doi.org/10.1111/j.1365-3113.2010.00560.x
- Description: The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I (COI) and the nuclear genes elongation factor 1α (EF1α) and wingless (WG) (totalling 1734 bp) were used to infer the relationships of the in‐group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in‐group genus were strongly supported. Key findings are the sister‐taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans‐Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid–late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early‐middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C4 grasses over the C3 grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate-related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis.
- Full Text:
- Date Issued: 2011
A watershed study on genetic diversity phylogenetic analysis of the Platypleura plumosa (Hemiptera Cicadidae) complex reveals catchment-specific lineages
- Price, Benjamin W, Barker, Nigel P, Villet, Martin H
- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2010
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441711 , vital:73909 , https://doi.org/10.1016/j.ympev.2009.10.011
- Description: Historical biogeography studies have at their disposal a small suite of vicariance models to explain genetic differentiation within and between species. One of these processes involves the role of river catchments and their associated watersheds, in driving diversification and is applicable to both aquatic and terrestrial organisms. Although the idea of catchments structuring the genetic history of aquatic organisms is reasonably well understood, their effect on terrestrial organisms has largely been overlooked, with relevant studies being limited in scope. South Africa presents a perfect test-bed for elucidating this mechanism of diversification due to its rich biodiversity, range of climatic environments and many large river catchments. Here we use the cicadas of the Platypleura plumosa complex to highlight the importance of catchments and their associated watersheds in driving diversification of terrestrial invertebrates that lack an aquatic life-stage. Population structure was found to correspond to primary and in some cases secondary catchments; highlighting the need to include information on catchment structure when formulating hypotheses of population diversification. Recognizing that climate change in the near future is likely to alter the environment, and particularly precipitation patterns, insight into recent patterns of population change related to catchments may be useful in a conservation context.
- Full Text:
- Date Issued: 2010
- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2010
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441711 , vital:73909 , https://doi.org/10.1016/j.ympev.2009.10.011
- Description: Historical biogeography studies have at their disposal a small suite of vicariance models to explain genetic differentiation within and between species. One of these processes involves the role of river catchments and their associated watersheds, in driving diversification and is applicable to both aquatic and terrestrial organisms. Although the idea of catchments structuring the genetic history of aquatic organisms is reasonably well understood, their effect on terrestrial organisms has largely been overlooked, with relevant studies being limited in scope. South Africa presents a perfect test-bed for elucidating this mechanism of diversification due to its rich biodiversity, range of climatic environments and many large river catchments. Here we use the cicadas of the Platypleura plumosa complex to highlight the importance of catchments and their associated watersheds in driving diversification of terrestrial invertebrates that lack an aquatic life-stage. Population structure was found to correspond to primary and in some cases secondary catchments; highlighting the need to include information on catchment structure when formulating hypotheses of population diversification. Recognizing that climate change in the near future is likely to alter the environment, and particularly precipitation patterns, insight into recent patterns of population change related to catchments may be useful in a conservation context.
- Full Text:
- Date Issued: 2010
A tropical/subtropical biogeographic disjunction in southeastern Africa separates two evolutionarily significant units of an estuarine prawn
- Teske, Peter R, Winker, A Henning, McQuaid, Christopher D, Barker, Nigel P
- Authors: Teske, Peter R , Winker, A Henning , McQuaid, Christopher D , Barker, Nigel P
- Date: 2009
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445407 , vital:74383 , https://doi.org/10.1007/s00227-009-1168-3
- Description: Recent phylogeographic research has indicated that biodiversity in the sea may be considerably greater than previously thought. However, the majority of phylogeographic studies on marine invertebrates have exclusively used a single locus (mitochondrial DNA), and it is questionable whether the phylogroups identified can be considered distinct species. We tested whether the mtDNA phylogroups of the southern African sandprawn Callianassa kraussi Stebbing (Decapoda: Thalassinidea) are also recovered using nuclear sequence data. Four mtDNA phylogroups were recovered that were each associated with one of South Africa’s four major biogeographic provinces. Three of these were poorly differentiated, but the fourth (tropical) group was highly distinct. The nuclear phylogeny recovered two major clades, one present in the tropical region and the other in the remainder of South Africa. Congruence between mitochondrial and nuclear DNA indicates that the species comprises two Evolutionarily Significant Units sensu Moritz (1994). In conjunction with physiological data from C. kraussi and morphological, ecological and physiological data from other species, this result supports the notion that at least some of the mtDNA phylogroups of coastal invertebrates whose distributions are limited.
- Full Text:
- Date Issued: 2009
- Authors: Teske, Peter R , Winker, A Henning , McQuaid, Christopher D , Barker, Nigel P
- Date: 2009
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445407 , vital:74383 , https://doi.org/10.1007/s00227-009-1168-3
- Description: Recent phylogeographic research has indicated that biodiversity in the sea may be considerably greater than previously thought. However, the majority of phylogeographic studies on marine invertebrates have exclusively used a single locus (mitochondrial DNA), and it is questionable whether the phylogroups identified can be considered distinct species. We tested whether the mtDNA phylogroups of the southern African sandprawn Callianassa kraussi Stebbing (Decapoda: Thalassinidea) are also recovered using nuclear sequence data. Four mtDNA phylogroups were recovered that were each associated with one of South Africa’s four major biogeographic provinces. Three of these were poorly differentiated, but the fourth (tropical) group was highly distinct. The nuclear phylogeny recovered two major clades, one present in the tropical region and the other in the remainder of South Africa. Congruence between mitochondrial and nuclear DNA indicates that the species comprises two Evolutionarily Significant Units sensu Moritz (1994). In conjunction with physiological data from C. kraussi and morphological, ecological and physiological data from other species, this result supports the notion that at least some of the mtDNA phylogroups of coastal invertebrates whose distributions are limited.
- Full Text:
- Date Issued: 2009
Phylogeny, biogeography and classification of the snake superfamily Elapoidea a rapid radiation in the late Eocene
- Kelly, Christopher M R, Barker, Nigel P, Villet, Martin H, Broadley, Donald G
- Authors: Kelly, Christopher M R , Barker, Nigel P , Villet, Martin H , Broadley, Donald G
- Date: 2009
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442267 , vital:73971 , https://doi.org/10.1111/j.1096-0031.2008.00237.x
- Description: The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid‐Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models.
- Full Text:
- Date Issued: 2009
- Authors: Kelly, Christopher M R , Barker, Nigel P , Villet, Martin H , Broadley, Donald G
- Date: 2009
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442267 , vital:73971 , https://doi.org/10.1111/j.1096-0031.2008.00237.x
- Description: The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid‐Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models.
- Full Text:
- Date Issued: 2009
Tri-locus sequence data reject a Gondwanan origin hypothesis for the African/South Pacific crab genus Hymenosoma
- Teske, Peter R, McLay, Colin L, Sandoval-Castillo, Jonathan, Papadopoulos, Isabelle, Newman, Brent K, Griffiths, Charles L, McQuaid, Christopher D, Barker, Nigel P, Borgonie, Gaetan, Beheregaray, Luciano B
- Authors: Teske, Peter R , McLay, Colin L , Sandoval-Castillo, Jonathan , Papadopoulos, Isabelle , Newman, Brent K , Griffiths, Charles L , McQuaid, Christopher D , Barker, Nigel P , Borgonie, Gaetan , Beheregaray, Luciano B
- Date: 2009
- Language: English
- Type: Article
- Identifier: vital:6547 , http://hdl.handle.net/10962/d1006003
- Description: Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.
- Full Text:
- Date Issued: 2009
- Authors: Teske, Peter R , McLay, Colin L , Sandoval-Castillo, Jonathan , Papadopoulos, Isabelle , Newman, Brent K , Griffiths, Charles L , McQuaid, Christopher D , Barker, Nigel P , Borgonie, Gaetan , Beheregaray, Luciano B
- Date: 2009
- Language: English
- Type: Article
- Identifier: vital:6547 , http://hdl.handle.net/10962/d1006003
- Description: Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.
- Full Text:
- Date Issued: 2009
Coastal topography drives genetic structure in marine mussels
- Nicastro, Katy R, Zardi, Gerardo I, McQuaid, Christopher D, Teske, Peter R, Barker, Nigel P
- Authors: Nicastro, Katy R , Zardi, Gerardo I , McQuaid, Christopher D , Teske, Peter R , Barker, Nigel P
- Date: 2008
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445634 , vital:74409 , https://doi.org/10.3354/meps07607
- Description: Understanding population connectivity is fundamental to ecology, and, for sedentary organisms, connectivity is achieved through larval dispersal. We tested whether coastal topography influences genetic structure in Perna perna mussels by comparing populations inside bays and on the open coast. Higher hydrodynamic stress on the open coast produces higher mortality and thus genetic turnover. Populations on the open coast had fewer private haplotypes and less genetic endemism than those inside bays. Gene flow analysis showed that bays act as source populations, with greater migration rates out of bays than into them. Differences in genetic structure on scales of 10s of kilometres show that coastal configuration strongly affects selection, larval dispersal and haplotype diversity.
- Full Text: false
- Date Issued: 2008
- Authors: Nicastro, Katy R , Zardi, Gerardo I , McQuaid, Christopher D , Teske, Peter R , Barker, Nigel P
- Date: 2008
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445634 , vital:74409 , https://doi.org/10.3354/meps07607
- Description: Understanding population connectivity is fundamental to ecology, and, for sedentary organisms, connectivity is achieved through larval dispersal. We tested whether coastal topography influences genetic structure in Perna perna mussels by comparing populations inside bays and on the open coast. Higher hydrodynamic stress on the open coast produces higher mortality and thus genetic turnover. Populations on the open coast had fewer private haplotypes and less genetic endemism than those inside bays. Gene flow analysis showed that bays act as source populations, with greater migration rates out of bays than into them. Differences in genetic structure on scales of 10s of kilometres show that coastal configuration strongly affects selection, larval dispersal and haplotype diversity.
- Full Text: false
- Date Issued: 2008
Oceanic dispersal barriers, adaptation and larval retention: an interdisciplinary assessment of potential factors maintaining a phylogeographic break between sister lineages of an African prawn
- Teske, Peter R, Papadopoulos, Isabelle, Newman, Brent K, Dworschak, Peter C, McQuaid, Christopher D, Barker, Nigel P
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Newman, Brent K , Dworschak, Peter C , McQuaid, Christopher D , Barker, Nigel P
- Date: 2008
- Language: English
- Type: Article
- Identifier: vital:6546 , http://hdl.handle.net/10962/d1006002 , http://dx.doi.org/10.1186/1471-2148-8-341
- Description: Background. Genetic breaks separating regional lineages of marine organisms with potentially high broadcasting abilities are generally attributed either to dispersal barriers such as currents or upwelling, or to behavioural strategies promoting self-recruitment. We investigated whether such patterns could potentially also be explained by adaptations to different environmental conditions by studying two morphologically distinguishable genetic lineages of the estuarine mudprawn Upogebia africana across a biogeographic disjunction in south-eastern Africa. The study area encompasses a transition between temperate and subtropical biotas, where the warm, southward-flowing Agulhas Current is deflected away from the coast, and its inshore edge is characterised by intermittent upwelling. To determine how this phylogeographic break is maintained, we estimated gene flow among populations in the region, tested for isolation by distance as an indication of larval retention, and reared larvae of the temperate and subtropical lineages at a range of different temperatures. Results. Of four populations sampled, the two northernmost exclusively included the subtropical lineage, a central population had a mixture of both lineages, and the southernmost estuary had only haplotypes of the temperate lineage. No evidence was found for isolation by distance, and gene flow was bidirectional and of similar magnitude among adjacent populations. In both lineages, the optimum temperature for larval development was at about 23°C, but a clear difference was found at lower temperatures. While larvae of the temperate lineage could complete development at temperatures as low as 12°C, those of the subtropical lineage did not complete development below 17°C. Conclusion. The results indicate that both southward dispersal of the subtropical lineage inshore of the Agulhas Current, and its establishment in the temperate province, may be limited primarily by low water temperatures. There is no evidence that the larvae of the temperate lineage would survive less well in the subtropical province than in their native habitat, and their exclusion from this region may be due to a combination of upwelling, short larval duration with limited dispersal potential near the coast, plus transport away from the coast of larvae that become entrained in the Agulhas Current. This study shows how methods from different fields of research (genetics, physiology, oceanography and morphology) can be combined to study phylogeographic patterns.
- Full Text:
- Date Issued: 2008
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Newman, Brent K , Dworschak, Peter C , McQuaid, Christopher D , Barker, Nigel P
- Date: 2008
- Language: English
- Type: Article
- Identifier: vital:6546 , http://hdl.handle.net/10962/d1006002 , http://dx.doi.org/10.1186/1471-2148-8-341
- Description: Background. Genetic breaks separating regional lineages of marine organisms with potentially high broadcasting abilities are generally attributed either to dispersal barriers such as currents or upwelling, or to behavioural strategies promoting self-recruitment. We investigated whether such patterns could potentially also be explained by adaptations to different environmental conditions by studying two morphologically distinguishable genetic lineages of the estuarine mudprawn Upogebia africana across a biogeographic disjunction in south-eastern Africa. The study area encompasses a transition between temperate and subtropical biotas, where the warm, southward-flowing Agulhas Current is deflected away from the coast, and its inshore edge is characterised by intermittent upwelling. To determine how this phylogeographic break is maintained, we estimated gene flow among populations in the region, tested for isolation by distance as an indication of larval retention, and reared larvae of the temperate and subtropical lineages at a range of different temperatures. Results. Of four populations sampled, the two northernmost exclusively included the subtropical lineage, a central population had a mixture of both lineages, and the southernmost estuary had only haplotypes of the temperate lineage. No evidence was found for isolation by distance, and gene flow was bidirectional and of similar magnitude among adjacent populations. In both lineages, the optimum temperature for larval development was at about 23°C, but a clear difference was found at lower temperatures. While larvae of the temperate lineage could complete development at temperatures as low as 12°C, those of the subtropical lineage did not complete development below 17°C. Conclusion. The results indicate that both southward dispersal of the subtropical lineage inshore of the Agulhas Current, and its establishment in the temperate province, may be limited primarily by low water temperatures. There is no evidence that the larvae of the temperate lineage would survive less well in the subtropical province than in their native habitat, and their exclusion from this region may be due to a combination of upwelling, short larval duration with limited dispersal potential near the coast, plus transport away from the coast of larvae that become entrained in the Agulhas Current. This study shows how methods from different fields of research (genetics, physiology, oceanography and morphology) can be combined to study phylogeographic patterns.
- Full Text:
- Date Issued: 2008
The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera
- Kelly, Christopher M R, Barker, Nigel P, Villet, Martin H, Broadley, Donald G, Branch, William R
- Authors: Kelly, Christopher M R , Barker, Nigel P , Villet, Martin H , Broadley, Donald G , Branch, William R
- Date: 2008
- Language: English
- Type: Article
- Identifier: vital:6522 , http://hdl.handle.net/10962/d1005953
- Description: This study constitutes the first evolutionary investigation of the snake family Psammophiidae—the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa's familylevel snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis 'sibilans' species complex into two monophyletic entities, provisionally named the 'phillipsii' and 'subtaeniatus' complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris.
- Full Text:
- Date Issued: 2008
- Authors: Kelly, Christopher M R , Barker, Nigel P , Villet, Martin H , Broadley, Donald G , Branch, William R
- Date: 2008
- Language: English
- Type: Article
- Identifier: vital:6522 , http://hdl.handle.net/10962/d1005953
- Description: This study constitutes the first evolutionary investigation of the snake family Psammophiidae—the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa's familylevel snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis 'sibilans' species complex into two monophyletic entities, provisionally named the 'phillipsii' and 'subtaeniatus' complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris.
- Full Text:
- Date Issued: 2008
Climate change, genetics or human choice: why were the shells of mankind’s earliest ornament larger in the Pleistocene than in the Holocene?
- Teske, Peter R, Papadopoulos, Isabelle, McQuaid, Christopher D, Newman, Brent K, Barker, Nigel P
- Authors: Teske, Peter R , Papadopoulos, Isabelle , McQuaid, Christopher D , Newman, Brent K , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6952 , http://hdl.handle.net/10962/d1011984
- Description: The southern African tick shell, Nassarius kraussianus (Dunker, 1846), has been identified as being the earliest known ornamental object used by human beings. Shell beads dated from ~75,000 years ago (Pleistocene era) were found in a cave located on South Africa's south coast. Beads made from N. kraussianus shells have also been found in deposits in this region dating from the beginning of the Holocene era (<10,000 years ago). These younger shells were significantly smaller, a phenomenon that has been attributed to a change in human preference. We investigated two alternative hypotheses explaining the difference in shell size: a) N. kraussianus comprises at least two genetic lineages that differ in size; b) the difference in shell size is due to phenotypic plasticity and is a function of environmental conditions. To test these hypotheses, we first reconstructed the species' phylogeographic history, and second, we measured the shell sizes of extant individuals throughout South Africa. Although two genetic lineages were identified, the sharing of haplotypes between these suggests that there is no genetic basis for the size differences. Extant individuals from the cool temperate west coast had significantly larger shells than populations in the remainder of the country, suggesting that N. kraussianus grows to a larger size in colder water. The decrease in fossil shell size from Pleistocene to Holocene was likely due to increased temperatures as a result of climate change at the beginning of the present interglacial period. We hypothesise that the sizes of N. kraussianus fossil shells can therefore serve as indicators of the climatic conditions that were prevalent in a particular region at the time when they were deposited. Moreover, N. kraussianus could serve as a biomonitor to study the impacts of future climate change on coastal biota in southern Africa.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Papadopoulos, Isabelle , McQuaid, Christopher D , Newman, Brent K , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6952 , http://hdl.handle.net/10962/d1011984
- Description: The southern African tick shell, Nassarius kraussianus (Dunker, 1846), has been identified as being the earliest known ornamental object used by human beings. Shell beads dated from ~75,000 years ago (Pleistocene era) were found in a cave located on South Africa's south coast. Beads made from N. kraussianus shells have also been found in deposits in this region dating from the beginning of the Holocene era (<10,000 years ago). These younger shells were significantly smaller, a phenomenon that has been attributed to a change in human preference. We investigated two alternative hypotheses explaining the difference in shell size: a) N. kraussianus comprises at least two genetic lineages that differ in size; b) the difference in shell size is due to phenotypic plasticity and is a function of environmental conditions. To test these hypotheses, we first reconstructed the species' phylogeographic history, and second, we measured the shell sizes of extant individuals throughout South Africa. Although two genetic lineages were identified, the sharing of haplotypes between these suggests that there is no genetic basis for the size differences. Extant individuals from the cool temperate west coast had significantly larger shells than populations in the remainder of the country, suggesting that N. kraussianus grows to a larger size in colder water. The decrease in fossil shell size from Pleistocene to Holocene was likely due to increased temperatures as a result of climate change at the beginning of the present interglacial period. We hypothesise that the sizes of N. kraussianus fossil shells can therefore serve as indicators of the climatic conditions that were prevalent in a particular region at the time when they were deposited. Moreover, N. kraussianus could serve as a biomonitor to study the impacts of future climate change on coastal biota in southern Africa.
- Full Text:
- Date Issued: 2007
Implications of life history for genetic structure and migration rates of southern African coastal invertebrates: planktonic, abbreviated and direct development
- Teske, Peter R, Papadopoulos, Isabelle, Zardi, Gerardo I, McQuaid, Christopher D, Edkins, M T, Griffiths, C L, Barker, Nigel P
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Zardi, Gerardo I , McQuaid, Christopher D , Edkins, M T , Griffiths, C L , Barker, Nigel P
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445447 , vital:74388 , https://doi.org/10.1007/s00227-007-0724-y
- Description: The amount of genetic structure in marine invertebrates is often thought to be negatively correlated with larval duration. However, larval retention may increase genetic structure in species with long-lived planktonic larvae, and rafting provides a means of dispersal for species that lack a larval dispersal phase. We compared genetic structure, demographic histories and levels of gene flow of regional lineages (in most cases defined by biogeographic region) of five southern African coastal invertebrates with three main types of larval development: (1) dispersal by long-lived planktonic larvae (mudprawn Upogebia africana and brown mussel Perna perna), (2) abbreviated larval development (crown crab Hymenosoma orbiculare) and (3) direct development (estuarine isopod Exosphaeroma hylecoetes and estuarine cumacean Iphinoe truncata). We hypothesized that H. orbiculare, having abbreviated larval development, would employ a strategy of larval retention, resulting in genetic structure comparable to that of the direct developers rather than the planktonic dispersers.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Zardi, Gerardo I , McQuaid, Christopher D , Edkins, M T , Griffiths, C L , Barker, Nigel P
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445447 , vital:74388 , https://doi.org/10.1007/s00227-007-0724-y
- Description: The amount of genetic structure in marine invertebrates is often thought to be negatively correlated with larval duration. However, larval retention may increase genetic structure in species with long-lived planktonic larvae, and rafting provides a means of dispersal for species that lack a larval dispersal phase. We compared genetic structure, demographic histories and levels of gene flow of regional lineages (in most cases defined by biogeographic region) of five southern African coastal invertebrates with three main types of larval development: (1) dispersal by long-lived planktonic larvae (mudprawn Upogebia africana and brown mussel Perna perna), (2) abbreviated larval development (crown crab Hymenosoma orbiculare) and (3) direct development (estuarine isopod Exosphaeroma hylecoetes and estuarine cumacean Iphinoe truncata). We hypothesized that H. orbiculare, having abbreviated larval development, would employ a strategy of larval retention, resulting in genetic structure comparable to that of the direct developers rather than the planktonic dispersers.
- Full Text:
- Date Issued: 2007
Lack of genetic differentiation among four sympatric southeast African intertidal limpets (Siphonariidae): phenotypic plasticity in a single species?
- Teske, Peter R, Barker, Nigel P, McQuaid, Christopher D
- Authors: Teske, Peter R , Barker, Nigel P , McQuaid, Christopher D
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445461 , vital:74390 , https://doi.org/10.1093/mollus/eym012
- Description: Specimens of four sympatric intertidal limpet species (Siphonaria dayi, S. tenuicostulata, S. anneae and S. nigerrima) were collected from four localities on the east coast of South Africa and southern Mozambique. Their phylogenetic relationships were investigated using sequences of the mitochondrial COI gene and the intron-containing nuclear ATPSβ gene. Two closely related lineages were recovered, which grouped specimens on the basis of geography rather than morphology. One lineage was associated with the subtropical coastline of South Africa's east coast and the other with the tropical coastline of northeastern South Africa and southern Mozambique. This genetic discontinuity coincides with a biogeographic boundary located in the vicinity of Cape St Lucia. Combined genetic diversity of the four species was lower than that of three other southern African congeners, and fell within the range determined for single southern African marine mollusc species. We suggest that the four limpet species are in fact different morphotypes of a single species.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Barker, Nigel P , McQuaid, Christopher D
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445461 , vital:74390 , https://doi.org/10.1093/mollus/eym012
- Description: Specimens of four sympatric intertidal limpet species (Siphonaria dayi, S. tenuicostulata, S. anneae and S. nigerrima) were collected from four localities on the east coast of South Africa and southern Mozambique. Their phylogenetic relationships were investigated using sequences of the mitochondrial COI gene and the intron-containing nuclear ATPSβ gene. Two closely related lineages were recovered, which grouped specimens on the basis of geography rather than morphology. One lineage was associated with the subtropical coastline of South Africa's east coast and the other with the tropical coastline of northeastern South Africa and southern Mozambique. This genetic discontinuity coincides with a biogeographic boundary located in the vicinity of Cape St Lucia. Combined genetic diversity of the four species was lower than that of three other southern African congeners, and fell within the range determined for single southern African marine mollusc species. We suggest that the four limpet species are in fact different morphotypes of a single species.
- Full Text:
- Date Issued: 2007
Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa
- Price, Benjamin W, Barker, Nigel P, Villet, Martin H
- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6964 , http://hdl.handle.net/10962/d1012027
- Description: Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.
- Full Text:
- Date Issued: 2007
- Authors: Price, Benjamin W , Barker, Nigel P , Villet, Martin H
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6964 , http://hdl.handle.net/10962/d1012027
- Description: Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.
- Full Text:
- Date Issued: 2007
Phylogeographic structure of Octopus vulgaris in South Africa revisited: identification of a second lineage near Durban harbor
- Teske, Peter R, Oosthuizen, A, Papadopoulos, Isabelle, Barker, Nigel P
- Authors: Teske, Peter R , Oosthuizen, A , Papadopoulos, Isabelle , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6544 , http://hdl.handle.net/10962/d1006000
- Description: In a previous study that investigated genetic structure of Octopus vulgaris along the South African coast by sequencing the mitochondrial cytochrome oxidase III gene (COIII), all sequences generated were identical. Such a finding is unusual, because mitochondrial DNA mutates quickly, and several marine invertebrates present in southern Africa show considerable genetic variation and structure. We reanalysed the samples using two different mitochondrial markers, namely cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA). Sequences of both these markers showed variation. The conclusion of the previous study, that South Africa’s O. vulgaris population is characterised by a lack of genetic structure along the coast, is rejected. Some specimens from Durban (southeast Africa) were genetically more different from those found in the remainder of the country than were specimens from other regions (Tristan da Cunha and Senegal). We suggest that the lineage in Durban may have been recently introduced.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Oosthuizen, A , Papadopoulos, Isabelle , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6544 , http://hdl.handle.net/10962/d1006000
- Description: In a previous study that investigated genetic structure of Octopus vulgaris along the South African coast by sequencing the mitochondrial cytochrome oxidase III gene (COIII), all sequences generated were identical. Such a finding is unusual, because mitochondrial DNA mutates quickly, and several marine invertebrates present in southern Africa show considerable genetic variation and structure. We reanalysed the samples using two different mitochondrial markers, namely cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA). Sequences of both these markers showed variation. The conclusion of the previous study, that South Africa’s O. vulgaris population is characterised by a lack of genetic structure along the coast, is rejected. Some specimens from Durban (southeast Africa) were genetically more different from those found in the remainder of the country than were specimens from other regions (Tristan da Cunha and Senegal). We suggest that the lineage in Durban may have been recently introduced.
- Full Text:
- Date Issued: 2007
Phylogeographic structure of the caridean shrimp Palaemon peringueyi in South Africa: further evidence for intraspecific genetic units associated with marine biogeographic provinces
- Teske, Peter R, Froneman, P William, Barker, Nigel P, McQuaid, Christopher D
- Authors: Teske, Peter R , Froneman, P William , Barker, Nigel P , McQuaid, Christopher D
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445486 , vital:74392 , https://doi.org/10.2989/AJMS.2007.29.2.9.192
- Description: Recent genetic studies have shown that most widely distributed, passively dispersing invertebrates in southern Africa have regional intraspecific units that are associated with the three main marine biogeographic provinces (cool-temperate, warm-temperate and subtropical). The caridean shrimp Palaemon peringueyi also occurs in all three provinces, but the fact that it can disperse both actively and passively (i.e. larval drifting, adult walking/swimming and potential adult rafting by means of floating objects) suggests that the amount of gene flow between regions may be too high for evolutionary divergence to have taken place. Samples of P. peringueyi were collected throughout South Africa and an intraspecific phylogeny was reconstructed using mitochondrial COI and 16S rRNA sequences. Three major clades were recovered, which were broadly associated with the three biogeographic regions. This suggests that, even though P. peringueyi can disperse actively, the fact that neither larvae nor adults are strong swimmers has resulted in genetic subdivisons comparable to those of passively dispersing coastal invertebrates in southern Africa.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Froneman, P William , Barker, Nigel P , McQuaid, Christopher D
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445486 , vital:74392 , https://doi.org/10.2989/AJMS.2007.29.2.9.192
- Description: Recent genetic studies have shown that most widely distributed, passively dispersing invertebrates in southern Africa have regional intraspecific units that are associated with the three main marine biogeographic provinces (cool-temperate, warm-temperate and subtropical). The caridean shrimp Palaemon peringueyi also occurs in all three provinces, but the fact that it can disperse both actively and passively (i.e. larval drifting, adult walking/swimming and potential adult rafting by means of floating objects) suggests that the amount of gene flow between regions may be too high for evolutionary divergence to have taken place. Samples of P. peringueyi were collected throughout South Africa and an intraspecific phylogeny was reconstructed using mitochondrial COI and 16S rRNA sequences. Three major clades were recovered, which were broadly associated with the three biogeographic regions. This suggests that, even though P. peringueyi can disperse actively, the fact that neither larvae nor adults are strong swimmers has resulted in genetic subdivisons comparable to those of passively dispersing coastal invertebrates in southern Africa.
- Full Text:
- Date Issued: 2007
Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage
- Teske, Peter R, Hamilton, Healy, Matthee, Conrad A, Barker, Nigel P
- Authors: Teske, Peter R , Hamilton, Healy , Matthee, Conrad A , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6549 , http://hdl.handle.net/10962/d1006005
- Description: The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns.
- Full Text:
- Date Issued: 2007
- Authors: Teske, Peter R , Hamilton, Healy , Matthee, Conrad A , Barker, Nigel P
- Date: 2007
- Language: English
- Type: Article
- Identifier: vital:6549 , http://hdl.handle.net/10962/d1006005
- Description: The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns.
- Full Text:
- Date Issued: 2007
Unexpected genetic structure of mussel populations in South Africa: indigenous Perna perna and invasive Mytilus galloprovincialis
- Zardi, Gerardo I, McQuaid, Christopher D, Teske, Peter R, Barker, Nigel P
- Authors: Zardi, Gerardo I , McQuaid, Christopher D , Teske, Peter R , Barker, Nigel P
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445564 , vital:74401 , doi:10.3354/meps337135
- Description: Genetic structure of sedentary marine organisms with planktonic larvae can be influenced by oceanographic transport, larval behaviour and local selection. We analysed the population genetic structure (based on mtDNA) of the invasive mussel Mytilus galloprovincialis and the indigenous mussel Perna perna along the southern African coastline. Low genetic divergence of M. galloprovincialis confirms its recent arrival in South Africa. In contrast, the genetic structure of P. perna revealed strong divergence on the south-east coast, forming a western and an eastern lineage. The distribution of the 2 lineages is extraordinary. They overlap for ca. 200 km on the south-east coast, and the western lineage includes animals occurring on either side of a 1000 km break in distribution across the Benguela upwelling system. In cluster analyses, animals on the south coast grouped with others 1000s of km to the west, rather than with those only 200 km to the east.
- Full Text: false
- Date Issued: 2007
- Authors: Zardi, Gerardo I , McQuaid, Christopher D , Teske, Peter R , Barker, Nigel P
- Date: 2007
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445564 , vital:74401 , doi:10.3354/meps337135
- Description: Genetic structure of sedentary marine organisms with planktonic larvae can be influenced by oceanographic transport, larval behaviour and local selection. We analysed the population genetic structure (based on mtDNA) of the invasive mussel Mytilus galloprovincialis and the indigenous mussel Perna perna along the southern African coastline. Low genetic divergence of M. galloprovincialis confirms its recent arrival in South Africa. In contrast, the genetic structure of P. perna revealed strong divergence on the south-east coast, forming a western and an eastern lineage. The distribution of the 2 lineages is extraordinary. They overlap for ca. 200 km on the south-east coast, and the western lineage includes animals occurring on either side of a 1000 km break in distribution across the Benguela upwelling system. In cluster analyses, animals on the south coast grouped with others 1000s of km to the west, rather than with those only 200 km to the east.
- Full Text: false
- Date Issued: 2007
A technique for evaluating species richness maps generated from collections data
- Robertson, Mark P, Barker, Nigel P
- Authors: Robertson, Mark P , Barker, Nigel P
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6538 , http://hdl.handle.net/10962/d1005979
- Description: There is considerable pressure on conservation planners to use existing data from herbarium and museum collections for planning and monitoring, despite the weaknesses of such data. It is thus important to be able to assess the quality of this information. One application of these data is the production of species richness maps. However, sampling effort is generally not consistent throughout a region for maps generated from collections data, and it is thus desirable to identify geographic grid cells (such as quarter degree squares: QDS) for which there has been low sampling effort. We describe a technique that can be used to identify QDS that are likely to have low species richness that is due to insufficient sampling effort rather than to low actual species richness. The technique exploits relationships between climate and species richness to detect QDS that are poorly sampled. This approach offers advantages over the current practice of applying a single threshold across the entire map region to detectQDSthat are poorly sampled. Here we report on the application of our technique to plant species richness data in the PRECIS database. Results reveal that the majority of QDS in the Flora of Southern Africa region can be considered to be poorly sampled, even when using conservative thresholds for richness values. The advantages and weaknesses of the technique are discussed and issues requiring further investigation are highlighted.
- Full Text:
- Date Issued: 2006
- Authors: Robertson, Mark P , Barker, Nigel P
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6538 , http://hdl.handle.net/10962/d1005979
- Description: There is considerable pressure on conservation planners to use existing data from herbarium and museum collections for planning and monitoring, despite the weaknesses of such data. It is thus important to be able to assess the quality of this information. One application of these data is the production of species richness maps. However, sampling effort is generally not consistent throughout a region for maps generated from collections data, and it is thus desirable to identify geographic grid cells (such as quarter degree squares: QDS) for which there has been low sampling effort. We describe a technique that can be used to identify QDS that are likely to have low species richness that is due to insufficient sampling effort rather than to low actual species richness. The technique exploits relationships between climate and species richness to detect QDS that are poorly sampled. This approach offers advantages over the current practice of applying a single threshold across the entire map region to detectQDSthat are poorly sampled. Here we report on the application of our technique to plant species richness data in the PRECIS database. Results reveal that the majority of QDS in the Flora of Southern Africa region can be considered to be poorly sampled, even when using conservative thresholds for richness values. The advantages and weaknesses of the technique are discussed and issues requiring further investigation are highlighted.
- Full Text:
- Date Issued: 2006
Impacts of marine biogeographic boundaries on phylogeographic patterns of three South African estuarine crustaceans
- Teske, Peter R, McQuaid, Christopher D, Froneman, P William, Barker, Nigel P
- Authors: Teske, Peter R , McQuaid, Christopher D , Froneman, P William , Barker, Nigel P
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6548 , http://hdl.handle.net/10962/d1006004 , http://dx.doi.org/10.3354/meps314283
- Description: The South African coastline comprises 3 main biogeographic provinces: (1) the cool-temperate west coast, (2) the warm-temperate south coast, and (3) the subtropical east coast. The boundaries between these regions are defined by changes in species compositions and hydrological conditions. It is possible that these affect phylogeographic patterns of coastal organisms differently, depending on the species’ ecologies and modes of dispersal. In the present study, genealogies of 3 estuarine crustaceans, each characterized by a different mode of passive dispersal and present in more than one biogeographic province, were reconstructed using mtDNA COI sequences, and the impacts of biogeographic boundaries on their phylogeographic patterns were compared. The species were (mode of dispersal in brackets): (1) the mudprawn Upogebia africana (planktonic larvae), (2) the isopod Exosphaeroma hylecoetes (adult rafting), and (3) the cumacean Iphinoe truncata (adult drifting). Two major mtDNA lineages with slightly overlapping distributions were identified in U. africana (the species with the highest dispersal potential). The other 2 species had 3 mtDNA lineages each, which were characterized by strict geographic segregation. Phylogeographic breaks in U. africana and E. hylecoetes coincided with biogeographic boundaries, whereas the phylogeographic patterns identified in I. truncata may reflect persistent palaeogeographic patterns. Ecological factors and modes of dispersal are likely to have played a role in both cladogenesis of the different lineages and in the establishment of their present-day distribution patterns.
- Full Text:
- Date Issued: 2006
- Authors: Teske, Peter R , McQuaid, Christopher D , Froneman, P William , Barker, Nigel P
- Date: 2006
- Language: English
- Type: Article
- Identifier: vital:6548 , http://hdl.handle.net/10962/d1006004 , http://dx.doi.org/10.3354/meps314283
- Description: The South African coastline comprises 3 main biogeographic provinces: (1) the cool-temperate west coast, (2) the warm-temperate south coast, and (3) the subtropical east coast. The boundaries between these regions are defined by changes in species compositions and hydrological conditions. It is possible that these affect phylogeographic patterns of coastal organisms differently, depending on the species’ ecologies and modes of dispersal. In the present study, genealogies of 3 estuarine crustaceans, each characterized by a different mode of passive dispersal and present in more than one biogeographic province, were reconstructed using mtDNA COI sequences, and the impacts of biogeographic boundaries on their phylogeographic patterns were compared. The species were (mode of dispersal in brackets): (1) the mudprawn Upogebia africana (planktonic larvae), (2) the isopod Exosphaeroma hylecoetes (adult rafting), and (3) the cumacean Iphinoe truncata (adult drifting). Two major mtDNA lineages with slightly overlapping distributions were identified in U. africana (the species with the highest dispersal potential). The other 2 species had 3 mtDNA lineages each, which were characterized by strict geographic segregation. Phylogeographic breaks in U. africana and E. hylecoetes coincided with biogeographic boundaries, whereas the phylogeographic patterns identified in I. truncata may reflect persistent palaeogeographic patterns. Ecological factors and modes of dispersal are likely to have played a role in both cladogenesis of the different lineages and in the establishment of their present-day distribution patterns.
- Full Text:
- Date Issued: 2006
A yellowwood by any other name: molecular systematics and the taxonomy of Podocarpus and the Podocarpaceae in southern Africa
- Barker, Nigel P, Muller, E M, Mill, R R
- Authors: Barker, Nigel P , Muller, E M , Mill, R R
- Date: 2004
- Language: English
- Type: Article
- Identifier: vital:6495 , http://hdl.handle.net/10962/d1004488
- Description: We briefly review the taxonomic history of the Podocarpaceae, with an emphasis on the recognition of numerous segregate genera out of Podocarpus sensu lato. Despite some controversy over the recognition of these genera, molecular data (DNA sequences) provide evidence that supports this taxonomy. The implications for African Podocarpaceae are discussed. In particular, molecular data support the recognition of Afrocarpus as distinct from Podocarpus. Additional taxonomic problems concerning the possible segregation of Podocarpus milanjianus from P. latifolius are addressed using DNA sequence data from the nuclear internal transcribed spacer 2 (ITS2) region. Results of this are inconclusive, and suggest that alternative DNA-based evidence, such as from AFLPs or microsatellites, may be more informative in resolving such species complexes in African Podocarpus.
- Full Text:
- Date Issued: 2004
- Authors: Barker, Nigel P , Muller, E M , Mill, R R
- Date: 2004
- Language: English
- Type: Article
- Identifier: vital:6495 , http://hdl.handle.net/10962/d1004488
- Description: We briefly review the taxonomic history of the Podocarpaceae, with an emphasis on the recognition of numerous segregate genera out of Podocarpus sensu lato. Despite some controversy over the recognition of these genera, molecular data (DNA sequences) provide evidence that supports this taxonomy. The implications for African Podocarpaceae are discussed. In particular, molecular data support the recognition of Afrocarpus as distinct from Podocarpus. Additional taxonomic problems concerning the possible segregation of Podocarpus milanjianus from P. latifolius are addressed using DNA sequence data from the nuclear internal transcribed spacer 2 (ITS2) region. Results of this are inconclusive, and suggest that alternative DNA-based evidence, such as from AFLPs or microsatellites, may be more informative in resolving such species complexes in African Podocarpus.
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- Date Issued: 2004