Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA:
- Matumba, Tshifhiwa G, Oliver, Jody, Barker, Nigel P, McQuaid, Christopher D, Teske, Peter R
- Authors: Matumba, Tshifhiwa G , Oliver, Jody , Barker, Nigel P , McQuaid, Christopher D , Teske, Peter R
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/160401 , vital:40442 , https://doi.org/10.12688/f1000research.23635.2
- Description: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality.
- Full Text:
- Date Issued: 2020
- Authors: Matumba, Tshifhiwa G , Oliver, Jody , Barker, Nigel P , McQuaid, Christopher D , Teske, Peter R
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/160401 , vital:40442 , https://doi.org/10.12688/f1000research.23635.2
- Description: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality.
- Full Text:
- Date Issued: 2020
Biomes, geology and past climate drive speciation of laminate-toothed rats on South African mountains (Murinae: Otomys)
- Taylor, Peter J, Kearney, Theresa, Dalton, Desire L, Chakona, Gamuchirai, Kelly, Christopher M R, Barker, Nigel P
- Authors: Taylor, Peter J , Kearney, Theresa , Dalton, Desire L , Chakona, Gamuchirai , Kelly, Christopher M R , Barker, Nigel P
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453158 , vital:75227 , xlink:href="https://doi.org/10.1093/zoolinnean/zlz134"
- Description: Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).
- Full Text:
- Date Issued: 2020
- Authors: Taylor, Peter J , Kearney, Theresa , Dalton, Desire L , Chakona, Gamuchirai , Kelly, Christopher M R , Barker, Nigel P
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453158 , vital:75227 , xlink:href="https://doi.org/10.1093/zoolinnean/zlz134"
- Description: Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).
- Full Text:
- Date Issued: 2020
Out of Africa?: a dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot and Audinet‐Serville
- Price, Benjamin W, Marshall, David C, Barker, Nigel P, Simon, Chris, Villet, Martin H
- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
- Full Text:
- Date Issued: 2019
- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
- Full Text:
- Date Issued: 2019
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
Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa:
- Taylor, Chantal L, Barker, Nigel P, Barber-James, Helen M, Villet, Martin H, Pereira-da-Conceicoa, Lyndall L
- Authors: Taylor, Chantal L , Barker, Nigel P , Barber-James, Helen M , Villet, Martin H , Pereira-da-Conceicoa, Lyndall L
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/149314 , vital:38824 , https://doi.org/10.3897/zookeys.936.38587
- Description: This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA.
- Full Text:
- Date Issued: 2020
- Authors: Taylor, Chantal L , Barker, Nigel P , Barber-James, Helen M , Villet, Martin H , Pereira-da-Conceicoa, Lyndall L
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/149314 , vital:38824 , https://doi.org/10.3897/zookeys.936.38587
- Description: This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA.
- Full Text:
- Date Issued: 2020
Rules of attraction: the role of bait in small mammal sampling at high altitude in South Africa
- Kok, Armand D, Parker, Daniel M, Barker, Nigel P
- Authors: Kok, Armand D , Parker, Daniel M , Barker, Nigel P
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443936 , vital:74173 , https://doi.org/10.1080/15627020.2013.11407571
- Description: Baits or lures are commonly used for surveying small mammal communities, not only because they attract large numbers of these animals, but also because they provide sustenance for trapped individuals. In this study we used Sherman live traps with five bait treatments to sample small mammal populations at three high-altitude sites (>1700 m) in the Sneeuberg Mountain Complex of the Eastern Cape Province, South Africa.We investigated the influence of bait treatment on three parameters commonly recorded in small mammal surveys. In addition, we investigated how different bait treatments vary in measuring species richness using the Chao 2 species richness estimator together with rarefaction curves. Overall, 12 small mammal species were sampled. A combination of birdseed and banana captured the highest number of species (11) but the most successful bait overall was peanut butter and oats (greatest number of captures, recaptures, number of individuals and highest Shannon diversity). The Chao 2 richness estimator indicated that four of the five bait treatments reached their sampling capacity. Rarefaction curves indicated that all bait treatments are similar with regard to species accumulation. This could possibly be explained by odours left behind in traps as even un-baited traps (i.e. controls) captured seven different small mammal species. We conclude that the most suitable bait for surveying small mammals at high altitude in South Africa is peanut butter and oats. However, using peanut butter and oats in combination with other bait treatments will improve estimates of diversity when surveying small mammal communities.
- Full Text:
- Date Issued: 2013
- Authors: Kok, Armand D , Parker, Daniel M , Barker, Nigel P
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443936 , vital:74173 , https://doi.org/10.1080/15627020.2013.11407571
- Description: Baits or lures are commonly used for surveying small mammal communities, not only because they attract large numbers of these animals, but also because they provide sustenance for trapped individuals. In this study we used Sherman live traps with five bait treatments to sample small mammal populations at three high-altitude sites (>1700 m) in the Sneeuberg Mountain Complex of the Eastern Cape Province, South Africa.We investigated the influence of bait treatment on three parameters commonly recorded in small mammal surveys. In addition, we investigated how different bait treatments vary in measuring species richness using the Chao 2 species richness estimator together with rarefaction curves. Overall, 12 small mammal species were sampled. A combination of birdseed and banana captured the highest number of species (11) but the most successful bait overall was peanut butter and oats (greatest number of captures, recaptures, number of individuals and highest Shannon diversity). The Chao 2 richness estimator indicated that four of the five bait treatments reached their sampling capacity. Rarefaction curves indicated that all bait treatments are similar with regard to species accumulation. This could possibly be explained by odours left behind in traps as even un-baited traps (i.e. controls) captured seven different small mammal species. We conclude that the most suitable bait for surveying small mammals at high altitude in South Africa is peanut butter and oats. However, using peanut butter and oats in combination with other bait treatments will improve estimates of diversity when surveying small mammal communities.
- Full Text:
- Date Issued: 2013
Coastal dunefields maintain pre‐Holocene genetic structure in a rocky shore red alga
- Mmonwa, Kolobe L, Barker, Nigel P, McQuaid, Christopher D, Teske, Peter R
- Authors: Mmonwa, Kolobe L , Barker, Nigel P , McQuaid, Christopher D , Teske, Peter R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444784 , vital:74298 , https://doi.org/10.1111/jpy.13182
- Description: Most intertidal algae have limited dispersal potential, and areas that lack hard substratum suitable for attachment are thus expected to isolate regional populations from each other. Here, we used nuclear and mitochondrial genetic data to compare genetic structure in two co‐distributed intertidal red algae with different dispersal potential along the South African coastline. Gelidium pristoides is divided into a south‐eastern and a south‐western evolutionary lineage separated by extensive, continuous sandy shoreline habitat adjacent to coastal dunefields. In contrast, Hypnea spicifera is genetically homogeneous throughout its range. In G. pristoides, the genetic breaks are associated with contemporary coastal dunefields. The age of the divergence event suggests that this may reflect the effect of older dispersal barriers, and that genetic structure was subsequently maintained by the formation of contemporary coastal dunefields.
- Full Text:
- Date Issued: 2021
- Authors: Mmonwa, Kolobe L , Barker, Nigel P , McQuaid, Christopher D , Teske, Peter R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444784 , vital:74298 , https://doi.org/10.1111/jpy.13182
- Description: Most intertidal algae have limited dispersal potential, and areas that lack hard substratum suitable for attachment are thus expected to isolate regional populations from each other. Here, we used nuclear and mitochondrial genetic data to compare genetic structure in two co‐distributed intertidal red algae with different dispersal potential along the South African coastline. Gelidium pristoides is divided into a south‐eastern and a south‐western evolutionary lineage separated by extensive, continuous sandy shoreline habitat adjacent to coastal dunefields. In contrast, Hypnea spicifera is genetically homogeneous throughout its range. In G. pristoides, the genetic breaks are associated with contemporary coastal dunefields. The age of the divergence event suggests that this may reflect the effect of older dispersal barriers, and that genetic structure was subsequently maintained by the formation of contemporary coastal dunefields.
- Full Text:
- Date Issued: 2021
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
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
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
Mitonuclear discordance in genetic structure across the Atlantic/Indian Ocean biogeographical transition zone
- Teske, Peter R, Papadopoulos, Isabelle, Barker, Nigel P, McQuaid, Christopher D, Beheregaray, Luciano B
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Barker, Nigel P , McQuaid, Christopher D , Beheregaray, Luciano B
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444832 , vital:74301 , https://doi.org/10.1111/jbi.1220
- Description: Based on mitochondrial DNA (mtDNA) data, many organisms with ranges spanning multiple biogeographical regions exhibit genetic structure across the transition zones between these regions, while others appear to be genetically homogenous. No clear link has been found between the presence or absence of such spatial genetic discontinuities and species' dispersal potential, confounding the formulation of general predictions concerning genetic structure. The fact that discrepancies between mtDNA and nuclear markers are common across semi‐permeable barriers suggests that a lack of structure could be attributable to mtDNA‐specific properties of inheritance. We re‐examined genetic structure in the coastal crab Hymenosoma orbiculare, a species that is represented by a single mtDNA lineage across the Atlantic/Indian Ocean biogeographical transition zone, by comparing mtDNA data with nuclear DNA data.
- Full Text:
- Date Issued: 2014
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Barker, Nigel P , McQuaid, Christopher D , Beheregaray, Luciano B
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444832 , vital:74301 , https://doi.org/10.1111/jbi.1220
- Description: Based on mitochondrial DNA (mtDNA) data, many organisms with ranges spanning multiple biogeographical regions exhibit genetic structure across the transition zones between these regions, while others appear to be genetically homogenous. No clear link has been found between the presence or absence of such spatial genetic discontinuities and species' dispersal potential, confounding the formulation of general predictions concerning genetic structure. The fact that discrepancies between mtDNA and nuclear markers are common across semi‐permeable barriers suggests that a lack of structure could be attributable to mtDNA‐specific properties of inheritance. We re‐examined genetic structure in the coastal crab Hymenosoma orbiculare, a species that is represented by a single mtDNA lineage across the Atlantic/Indian Ocean biogeographical transition zone, by comparing mtDNA data with nuclear DNA data.
- Full Text:
- Date Issued: 2014
Evolution of foraging behaviour: Deep intra-generic genetic divergence between territorial and non-territorial southern African patellid limpets
- Mmonwa, Kolobe L, Teske, Peter R, McQuaid, Christopher D, Barker, Nigel P
- Authors: Mmonwa, Kolobe L , Teske, Peter R , McQuaid, Christopher D , Barker, Nigel P
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444798 , vital:74299 , https://doi.org/10.1016/j.ympev.2017.05.024
- Description: Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSβ intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient. Maximum Likelihood and Bayesian Inference phylogenetic analyses revealed that the species sharing a foraging type are monophyletic in both genera. Territoriality is a derived character, as the clades with this foraging type are nested within a tree that otherwise comprises non-territorial taxa. These include Helcion, which was recovered as sister to the Cymbula/Scutellastra clade, and the next basal genus, Patella, which is ancestral to all southern African patellogastropods. Deep genetic divergence between the two foraging traits reflects strong adaptive effects of resource partitioning in the evolution of southern African patellid limpets.
- Full Text:
- Date Issued: 2017
- Authors: Mmonwa, Kolobe L , Teske, Peter R , McQuaid, Christopher D , Barker, Nigel P
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444798 , vital:74299 , https://doi.org/10.1016/j.ympev.2017.05.024
- Description: Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSβ intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient. Maximum Likelihood and Bayesian Inference phylogenetic analyses revealed that the species sharing a foraging type are monophyletic in both genera. Territoriality is a derived character, as the clades with this foraging type are nested within a tree that otherwise comprises non-territorial taxa. These include Helcion, which was recovered as sister to the Cymbula/Scutellastra clade, and the next basal genus, Patella, which is ancestral to all southern African patellogastropods. Deep genetic divergence between the two foraging traits reflects strong adaptive effects of resource partitioning in the evolution of southern African patellid limpets.
- Full Text:
- Date Issued: 2017
Historical demography of southern African patellid limpets: congruence of population expansions, but not phylogeography
- Mmonwa, Kolobe L, Teske, Peter R, McQuaid, Christopher D, Barker, Nigel P
- Authors: Mmonwa, Kolobe L , Teske, Peter R , McQuaid, Christopher D , Barker, Nigel P
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444814 , vital:74300 , https://doi.org/10.2989/1814232X.2015.1009165
- Description: Global climatic oscillations have shaped the contemporary genetic structure of marine taxa in different ways. Previous demographic studies have indicated that various intertidal marine species display genetic signatures of demographic expansion that either pre- or postdate the Last Glacial Maximum. Such expansions and the ability of species to colonise new habitats will influence their genetic structure, but the link between scales of larval dispersal and the strength of phylogeographic structure is not always clear. We analysed a fragment of the mitochondrial COI gene of 11 sympatric species of intertidal southern African patellid limpets to investigate how ancient oceanographic dynamics have shaped and maintained their contemporary spatial genetic variation. Our data show that the patellid limpets investigated display congruent evidence of spatial expansion during the Late Pleistocene or Early Holocene, which corresponds with the establishment of the contemporary southern African shoreline. We argue that closely related and co-distributed southern African intertidal invertebrates responded to ancient climatic oscillations as a cohesive group. In contrast, contemporary oceanographic circulation has shaped the phylogeographic patterns of these limpets in different ways. We show close relationships between phylogeography and biogeography for some species, but not for others, despite the similarities in their life histories and exposure to the same climatic changes.
- Full Text:
- Date Issued: 2015
- Authors: Mmonwa, Kolobe L , Teske, Peter R , McQuaid, Christopher D , Barker, Nigel P
- Date: 2015
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444814 , vital:74300 , https://doi.org/10.2989/1814232X.2015.1009165
- Description: Global climatic oscillations have shaped the contemporary genetic structure of marine taxa in different ways. Previous demographic studies have indicated that various intertidal marine species display genetic signatures of demographic expansion that either pre- or postdate the Last Glacial Maximum. Such expansions and the ability of species to colonise new habitats will influence their genetic structure, but the link between scales of larval dispersal and the strength of phylogeographic structure is not always clear. We analysed a fragment of the mitochondrial COI gene of 11 sympatric species of intertidal southern African patellid limpets to investigate how ancient oceanographic dynamics have shaped and maintained their contemporary spatial genetic variation. Our data show that the patellid limpets investigated display congruent evidence of spatial expansion during the Late Pleistocene or Early Holocene, which corresponds with the establishment of the contemporary southern African shoreline. We argue that closely related and co-distributed southern African intertidal invertebrates responded to ancient climatic oscillations as a cohesive group. In contrast, contemporary oceanographic circulation has shaped the phylogeographic patterns of these limpets in different ways. We show close relationships between phylogeography and biogeography for some species, but not for others, despite the similarities in their life histories and exposure to the same climatic changes.
- Full Text:
- Date Issued: 2015
Climate‐driven genetic divergence of limpets with different life histories across a southeast African marine biogeographic disjunction: different processes, same outcome
- Teske, Peter R, Papadopoulos, Isabelle, Mmonwa, Kolobe L, Matumba, Tshifhiwa G, McQuaid, Christopher D, Barker, Nigel P, Beheregaray, Luciano B
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Mmonwa, Kolobe L , Matumba, Tshifhiwa G , McQuaid, Christopher D , Barker, Nigel P , Beheregaray, Luciano B
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445420 , vital:74385 , https://doi.org/10.1111/j.1365-294X.2011.05307.x
- Description: Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis.
- Full Text:
- Date Issued: 2011
- Authors: Teske, Peter R , Papadopoulos, Isabelle , Mmonwa, Kolobe L , Matumba, Tshifhiwa G , McQuaid, Christopher D , Barker, Nigel P , Beheregaray, Luciano B
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445420 , vital:74385 , https://doi.org/10.1111/j.1365-294X.2011.05307.x
- Description: Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis.
- Full Text:
- Date Issued: 2011
Identification of a uniquely southern African clade of coastal pipefishes Syngnathus spp.
- Mwale, Monica, Kaiser, Horst, Barker, Nigel P, Wilson, A B, Teske, Peter R
- Authors: Mwale, Monica , Kaiser, Horst , Barker, Nigel P , Wilson, A B , Teske, Peter R
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445499 , vital:74393 , https://doi.org/10.1111/jfb.12130
- Description: The taxonomic status of two southern African coastal pipefish species, Syngnathus temminckii and Syngnathus watermeyeri, was investigated using a combination of morphological and genetic data. Morphological data showed that S. temminckii is distinct from the broadly distributed European pipefish Syngnathus acus, and a molecular phylogeny reconstructed using mitochondrial DNA recovered S. temminckii and S. watermeyeri as sister taxa. The southern African species share an evolutionary origin with north‐eastern Atlantic Ocean and Mediterranean Sea species, including S. acus. These data support the existence of a distinct southern African clade of Syngnathus pipefishes that has diverged in situ to form the two species present in the region today.
- Full Text:
- Date Issued: 2013
- Authors: Mwale, Monica , Kaiser, Horst , Barker, Nigel P , Wilson, A B , Teske, Peter R
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445499 , vital:74393 , https://doi.org/10.1111/jfb.12130
- Description: The taxonomic status of two southern African coastal pipefish species, Syngnathus temminckii and Syngnathus watermeyeri, was investigated using a combination of morphological and genetic data. Morphological data showed that S. temminckii is distinct from the broadly distributed European pipefish Syngnathus acus, and a molecular phylogeny reconstructed using mitochondrial DNA recovered S. temminckii and S. watermeyeri as sister taxa. The southern African species share an evolutionary origin with north‐eastern Atlantic Ocean and Mediterranean Sea species, including S. acus. These data support the existence of a distinct southern African clade of Syngnathus pipefishes that has diverged in situ to form the two species present in the region today.
- Full Text:
- Date Issued: 2013
Biomes, geology and past climate drive speciation of laminate-toothed rats on South African mountains (Murinae: Otomys)
- Taylor, Peter J, Kearney, Theresa, Dalton, Desire L, Chakona, Gamuchirai, Kelly, Christopher M R, Barker, Nigel P
- Authors: Taylor, Peter J , Kearney, Theresa , Dalton, Desire L , Chakona, Gamuchirai , Kelly, Christopher M R , Barker, Nigel P
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425481 , vital:72249 , xlink:href="https://doi.org/10.1093/zoolinnean/zlz134"
- Description: Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).
- Full Text:
- Date Issued: 2020
- Authors: Taylor, Peter J , Kearney, Theresa , Dalton, Desire L , Chakona, Gamuchirai , Kelly, Christopher M R , Barker, Nigel P
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425481 , vital:72249 , xlink:href="https://doi.org/10.1093/zoolinnean/zlz134"
- Description: Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).
- Full Text:
- Date Issued: 2020
Microbial Community Responses to Alterations in Historical Fire Regimes in Montane Grasslands
- Gokul, Jarishma K, Matcher, Gwynneth, Dames, Joanna F, Nkangala, Kuhle, Gordijn, Paul J, Barker, Nigel P
- Authors: Gokul, Jarishma K , Matcher, Gwynneth , Dames, Joanna F , Nkangala, Kuhle , Gordijn, Paul J , Barker, Nigel P
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440366 , vital:73777 , https://doi.org/10.3390/d15070818
- Description: The influence of fire regimes on soil microbial diversity in montane grasslands is a relatively unexplored area of interest. Understanding the belowground diversity is a crucial stepping-stone toward unravelling community dynamics, nutrient sequestration, and overall ecosystem stability. In this study, metabarcoding was used to unravel the impact of fire disturbance regimes on bacterial and arbuscular mycorrhizal fungal community structures in South African montane grasslands that have been subjected to an intermediate (up to five years) term experimental fire-return interval gradient. Bacterial communities in this study exhibited a shift in composition in soils subjected to annual and biennial fires compared to the controls, with carbon and nitrogen identified as significant potential chemical drivers of bacterial communities. Shifts in relative abundances of dominant fungal operational taxonomic units were noted, with Glomeromycota as the dominant arbuscular mycorrhiza observed across the fire-return gradient. A reduction in mycorrhizal root colonisation was also observed in frequently burnt autumnal grassland plots in this study. Furthermore, evidence of significant mutualistic interactions between bacteria and fungi that may act as drivers of the observed community structure were detected. Through this pilot study, we can show that fire regime strongly impacts bacterial and fungal communities in southern African montane grasslands, and that changes to their usually resilient structure are mediated by seasonal burn patterns, chemical drivers, and mutualistic interactions between these two groups.
- Full Text:
- Date Issued: 2023
- Authors: Gokul, Jarishma K , Matcher, Gwynneth , Dames, Joanna F , Nkangala, Kuhle , Gordijn, Paul J , Barker, Nigel P
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440366 , vital:73777 , https://doi.org/10.3390/d15070818
- Description: The influence of fire regimes on soil microbial diversity in montane grasslands is a relatively unexplored area of interest. Understanding the belowground diversity is a crucial stepping-stone toward unravelling community dynamics, nutrient sequestration, and overall ecosystem stability. In this study, metabarcoding was used to unravel the impact of fire disturbance regimes on bacterial and arbuscular mycorrhizal fungal community structures in South African montane grasslands that have been subjected to an intermediate (up to five years) term experimental fire-return interval gradient. Bacterial communities in this study exhibited a shift in composition in soils subjected to annual and biennial fires compared to the controls, with carbon and nitrogen identified as significant potential chemical drivers of bacterial communities. Shifts in relative abundances of dominant fungal operational taxonomic units were noted, with Glomeromycota as the dominant arbuscular mycorrhiza observed across the fire-return gradient. A reduction in mycorrhizal root colonisation was also observed in frequently burnt autumnal grassland plots in this study. Furthermore, evidence of significant mutualistic interactions between bacteria and fungi that may act as drivers of the observed community structure were detected. Through this pilot study, we can show that fire regime strongly impacts bacterial and fungal communities in southern African montane grasslands, and that changes to their usually resilient structure are mediated by seasonal burn patterns, chemical drivers, and mutualistic interactions between these two groups.
- Full Text:
- Date Issued: 2023
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
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
"Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions
- Teske, Peter R, Ruis, Marc, McQuaid, Christopher D, Styan, Craig A, Piggott, Maxine P, Benhissoune, Saïd, Fuentes-Grünewald, Claudio, Walls, Kathy, Page, Mike, Attard, Catherine R M, Cooke, Georgina M, McClusky, Claire F, Banks, Sam C, Barker, Nigel P, Beheregaray, Luciano B
- Authors: Teske, Peter R , Ruis, Marc , McQuaid, Christopher D , Styan, Craig A , Piggott, Maxine P , Benhissoune, Saïd , Fuentes-Grünewald, Claudio , Walls, Kathy , Page, Mike , Attard, Catherine R M , Cooke, Georgina M , McClusky, Claire F , Banks, Sam C , Barker, Nigel P , Beheregaray, Luciano B
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445529 , vital:74396 , https://doi.org/10.1186/1471-2148-11-176
- Description: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit.
- Full Text:
- Date Issued: 2011
- Authors: Teske, Peter R , Ruis, Marc , McQuaid, Christopher D , Styan, Craig A , Piggott, Maxine P , Benhissoune, Saïd , Fuentes-Grünewald, Claudio , Walls, Kathy , Page, Mike , Attard, Catherine R M , Cooke, Georgina M , McClusky, Claire F , Banks, Sam C , Barker, Nigel P , Beheregaray, Luciano B
- Date: 2011
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/445529 , vital:74396 , https://doi.org/10.1186/1471-2148-11-176
- Description: Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit.
- Full Text:
- Date Issued: 2011