Genetic connectivity of the roundjaw bonefish (Albula glossodonta) in the Southwest Indian Ocean
- Talma, Sheena Claudia Aisa Lydie
- Authors: Talma, Sheena Claudia Aisa Lydie
- Date: 2021-10-29
- Subjects: Bonefish Mauritius , Bonefish Seychelles , Bonefish Genetics , Bonefish Habitat , Bonefish Geographical distribution , Bonefish Larvae Dispersal , Genetic markers , Cytochrome b , Fish populations Mauritius , Fish populations Seychelles , Marine ecotourism , Saltwater fly fishing , Bonefish fisheries Catch effort
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192174 , vital:45202
- Description: The Southwest Indian Ocean (SWIO) islands of Mauritius and Seychelles are both highly dependent on tourism and fisheries for their economies. One of the growing ecotourism sectors is saltwater fly fishing, an industry based on catch-and-release fishing for a host of species, including bonefishes. Bonefishes (Albula spp.) have received significant research attention in the Pacific and Atlantic Oceans, with only sporadic research conducted in the Indian Ocean. My project aimed to investigate the genetic connectivity of the roundjaw bonefish (Albula glossodonta) in two island states (Seychelles and Mauritius) within the SWIO using a mitochondrial genetic marker (cyt-b) and next generation sequencing (ddRADseq). Samples collected were grouped based on their spatial distribution. The Seychelles consisted of four island groups (Inner Island Group, Aldabra Group, Amirantes and Alphonse Group, and Farquhar Group) whereas Mauritius was represented by one island group (Saint Brandon). Genetic analyses were undertaken between and within each of these groups. Mitochondrial cytochrome-b identified two species of bonefish: Albula glossodonta and Albula oligolepis; the latter was only genetically identified from the Inner Island Group. I hypothesise that this is due to habitat partitioning, with A. oligolepis being a deeper dwelling bonefish species compared to A. glossodonta, which occupies shallow water habitats such as sand flats, atoll lagoons and reef flats. Neutral SNP loci revealed a panmictic pattern of distribution for A. glossodonta throughout the Seychelles Island groups but showed a pattern of weak structure between Seychelles and Mauritius. Genetic diversity indices such as allelic richness, showed low diversity across the sampling sites (AR range: 1.761-1.889). Population structure tests such as pairwise FST showed low but significant population structure. The highest FST indices were recorded between the Aldabra and Farquhar Groups, as well as the Aldabra and Saint Brandon Groups (0.044 ± 0.000 and 0.040 ± 0.000, respectively). Descriptive tests such as PCA and DAPC showed similar trends, whereby Saint Brandon clustered separately from the other samples from the Seychelles Island groups. However, these trends were Abstract seen at very low variations (PCA axes 1 and 2 accounted for only 2.0 and 1.9 % of the total variation, respectively). A population assignment test grouped the individuals as one ancestral population. A spatial principal component analysis showed that Saint Brandon was dissimilar to the Seychelles Island groups. Like other Elopomorph species, bonefishes have leptocephalus larvae capable of long-distance dispersal which may explain the well-mixed genetic population observed within the Seychelles islands. Although currents within the Indian Ocean, especially on a mesoscale, are not well understood, the South Equatorial Current likely facilitates connectivity between the Seychelles islands while also limiting gene flow between Seychelles and Mauritius. Understanding population structure is important for informing the appropriate management and conservation strategies, especially in oceanic nations where data informing important industries like tourism and fisheries are often limited. The bonefish fly fishing industry is well-known to be a lucrative sector, generating, for example US$ 1.4 million a year in the Bahamas. This study recognised that there are numerous knowledge gaps relevant to the bonefish industry that need to be addressed, including: 1) understanding the socio-economic importance of fly fishing to island states like Seychelles, 2) estimating the abundance and species distribution of bonefishes within Seychelles, 3) understanding effectiveness of MPAs for recreational fishery species like bonefish and, lastly, 4) generating more fishery-relevant biological information on the heavily targeted fly fishing species within Seychelles. These needs must be met to inform management plans and to better manage the fly fishing ventures that target species like bonefish. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-10-29
- Authors: Talma, Sheena Claudia Aisa Lydie
- Date: 2021-10-29
- Subjects: Bonefish Mauritius , Bonefish Seychelles , Bonefish Genetics , Bonefish Habitat , Bonefish Geographical distribution , Bonefish Larvae Dispersal , Genetic markers , Cytochrome b , Fish populations Mauritius , Fish populations Seychelles , Marine ecotourism , Saltwater fly fishing , Bonefish fisheries Catch effort
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/192174 , vital:45202
- Description: The Southwest Indian Ocean (SWIO) islands of Mauritius and Seychelles are both highly dependent on tourism and fisheries for their economies. One of the growing ecotourism sectors is saltwater fly fishing, an industry based on catch-and-release fishing for a host of species, including bonefishes. Bonefishes (Albula spp.) have received significant research attention in the Pacific and Atlantic Oceans, with only sporadic research conducted in the Indian Ocean. My project aimed to investigate the genetic connectivity of the roundjaw bonefish (Albula glossodonta) in two island states (Seychelles and Mauritius) within the SWIO using a mitochondrial genetic marker (cyt-b) and next generation sequencing (ddRADseq). Samples collected were grouped based on their spatial distribution. The Seychelles consisted of four island groups (Inner Island Group, Aldabra Group, Amirantes and Alphonse Group, and Farquhar Group) whereas Mauritius was represented by one island group (Saint Brandon). Genetic analyses were undertaken between and within each of these groups. Mitochondrial cytochrome-b identified two species of bonefish: Albula glossodonta and Albula oligolepis; the latter was only genetically identified from the Inner Island Group. I hypothesise that this is due to habitat partitioning, with A. oligolepis being a deeper dwelling bonefish species compared to A. glossodonta, which occupies shallow water habitats such as sand flats, atoll lagoons and reef flats. Neutral SNP loci revealed a panmictic pattern of distribution for A. glossodonta throughout the Seychelles Island groups but showed a pattern of weak structure between Seychelles and Mauritius. Genetic diversity indices such as allelic richness, showed low diversity across the sampling sites (AR range: 1.761-1.889). Population structure tests such as pairwise FST showed low but significant population structure. The highest FST indices were recorded between the Aldabra and Farquhar Groups, as well as the Aldabra and Saint Brandon Groups (0.044 ± 0.000 and 0.040 ± 0.000, respectively). Descriptive tests such as PCA and DAPC showed similar trends, whereby Saint Brandon clustered separately from the other samples from the Seychelles Island groups. However, these trends were Abstract seen at very low variations (PCA axes 1 and 2 accounted for only 2.0 and 1.9 % of the total variation, respectively). A population assignment test grouped the individuals as one ancestral population. A spatial principal component analysis showed that Saint Brandon was dissimilar to the Seychelles Island groups. Like other Elopomorph species, bonefishes have leptocephalus larvae capable of long-distance dispersal which may explain the well-mixed genetic population observed within the Seychelles islands. Although currents within the Indian Ocean, especially on a mesoscale, are not well understood, the South Equatorial Current likely facilitates connectivity between the Seychelles islands while also limiting gene flow between Seychelles and Mauritius. Understanding population structure is important for informing the appropriate management and conservation strategies, especially in oceanic nations where data informing important industries like tourism and fisheries are often limited. The bonefish fly fishing industry is well-known to be a lucrative sector, generating, for example US$ 1.4 million a year in the Bahamas. This study recognised that there are numerous knowledge gaps relevant to the bonefish industry that need to be addressed, including: 1) understanding the socio-economic importance of fly fishing to island states like Seychelles, 2) estimating the abundance and species distribution of bonefishes within Seychelles, 3) understanding effectiveness of MPAs for recreational fishery species like bonefish and, lastly, 4) generating more fishery-relevant biological information on the heavily targeted fly fishing species within Seychelles. These needs must be met to inform management plans and to better manage the fly fishing ventures that target species like bonefish. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2021
- Full Text:
- Date Issued: 2021-10-29
Combining DNA barcoding and morphology to identify larval fishes from the nearshore environment off the south-east coast of South Africa
- Authors: Somana, Zinzi Sinazo
- Date: 2020
- Subjects: Fishes -- Larvae -- South Africa -- Identification , Fishes -- Genetics -- Research -- Technique , Fishes -- South Africa -- Classification , Genetic markers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144605 , vital:38362
- Description: The early life history stages of most marine fish species are undescribed. The problem is, most of these fishes have pelagic larvae which are minute, delicate forms. Linking the larval stage to an adult counterpart is extremely challenging as larvae are morphologically different from the adults. Historically, larval fish identification relied solely on distinguishing morphological characteristics and meristic measurements, which has resulted in taxonomic confusion and misidentification. The introduction of the deoxyribonucleic acid (DNA) barcoding technique as an alternative approach has been successful in positively identifying larval fishes. The correct identification of larval specimens is the key to a better understanding of larval ecology, which underpins the success of any adult fish population. This study aimed to positively identify larval fishes of the south-east coast of South Africa using morphological characteristics and DNA barcoding. Larval and eggs specimens for this study were collected from the shallow nearshore waters of the south-east coast of South Africa. A total of 177 larval specimens were used for morphological analysis. Body shape, gut shape, pigmentation and morphometric measurements (such as body depth, preanal length and total body length) were used to identify each specimen to the family level. In addition, a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (COI) was adopted for sequencing to identify larval fish specimens and fish eggs. Sequences generated from this study were compared to those in the Barcode of Life Database (BOLD). When there were no close matches to a sequence, the GenBank nucleic acid sequence database, maintained by the National Center for Biotechnology Information (NCBI), was used as an alternative. A total of 18 different families were identified through morphology. Seventy-seven of the 177 larval specimens were not subjected to morphological identification due to physical damage. The majority of larvae identified using morphological characteristics belonged to either the Sparidae, Tripterygiidae or Gobiesocidae fish families. Through DNA barcoding, 12 fish families, 16 genera and 18 different species were identified. Ten DNA barcodes (categorised as ‘no match’) from 10 different larval specimens were not identified through any of the online databases. Therefore, the 2% threshold value was used to identify members of the same species. The K2P genetic distance relationships were calculated among the no match sequences and downloaded probability matches from NCBI. This resulted in two unknown specimens assigned to the Blenniidae and Gobiidae. All other taxa were identified to species level, except specimens representing the Gobiidae and Tripterygiidae families. Based on the K2P genetic distances Gobiidae representatives were categorised as members of the Caffrogobius genus. Twenty-eight barcodes represented specimens from the Tripterygiidae. DNA barcode data from COI was analysed using the standard phylogenetic procedures in MEGA6 to examine relationships and differentiation among sequences. These could not be identified to the lowest taxonomic rank due to limited sequence data to compare them with. The sequence data from these specimens gave different results in the two online databases. BOLD results were to family level (Tripterygiidae) and NCBI to the species level (Clinidae: Pavoclinus profundus). Results in this study confirmed the efficiency of the DNA barcoding technique in species level identification of fish larvae. The evidence from genetic barcodes of the Tripterygiidae specimens, supported by morphological characteristics, suggests the need for thorough research to identify the individuals to the species level. The fact that this study identified taxonomically problematic Gobiidae and Tripterygiidae specimens suggests that studies similar to this may highlight additional diversity and help to resolve the taxonomy of other species in these families. However, the lack of reference sequence data from the adult specimens, and especially those with cryptic diversity, were both shortcomings for the positive identification of larvae. With that being said, it shows the necessity for more research to be conducted on barcoding of larvae in general as to accommodate all kinds of species from biodiversity to economic perspectives.
- Full Text:
- Date Issued: 2020
- Authors: Somana, Zinzi Sinazo
- Date: 2020
- Subjects: Fishes -- Larvae -- South Africa -- Identification , Fishes -- Genetics -- Research -- Technique , Fishes -- South Africa -- Classification , Genetic markers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144605 , vital:38362
- Description: The early life history stages of most marine fish species are undescribed. The problem is, most of these fishes have pelagic larvae which are minute, delicate forms. Linking the larval stage to an adult counterpart is extremely challenging as larvae are morphologically different from the adults. Historically, larval fish identification relied solely on distinguishing morphological characteristics and meristic measurements, which has resulted in taxonomic confusion and misidentification. The introduction of the deoxyribonucleic acid (DNA) barcoding technique as an alternative approach has been successful in positively identifying larval fishes. The correct identification of larval specimens is the key to a better understanding of larval ecology, which underpins the success of any adult fish population. This study aimed to positively identify larval fishes of the south-east coast of South Africa using morphological characteristics and DNA barcoding. Larval and eggs specimens for this study were collected from the shallow nearshore waters of the south-east coast of South Africa. A total of 177 larval specimens were used for morphological analysis. Body shape, gut shape, pigmentation and morphometric measurements (such as body depth, preanal length and total body length) were used to identify each specimen to the family level. In addition, a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (COI) was adopted for sequencing to identify larval fish specimens and fish eggs. Sequences generated from this study were compared to those in the Barcode of Life Database (BOLD). When there were no close matches to a sequence, the GenBank nucleic acid sequence database, maintained by the National Center for Biotechnology Information (NCBI), was used as an alternative. A total of 18 different families were identified through morphology. Seventy-seven of the 177 larval specimens were not subjected to morphological identification due to physical damage. The majority of larvae identified using morphological characteristics belonged to either the Sparidae, Tripterygiidae or Gobiesocidae fish families. Through DNA barcoding, 12 fish families, 16 genera and 18 different species were identified. Ten DNA barcodes (categorised as ‘no match’) from 10 different larval specimens were not identified through any of the online databases. Therefore, the 2% threshold value was used to identify members of the same species. The K2P genetic distance relationships were calculated among the no match sequences and downloaded probability matches from NCBI. This resulted in two unknown specimens assigned to the Blenniidae and Gobiidae. All other taxa were identified to species level, except specimens representing the Gobiidae and Tripterygiidae families. Based on the K2P genetic distances Gobiidae representatives were categorised as members of the Caffrogobius genus. Twenty-eight barcodes represented specimens from the Tripterygiidae. DNA barcode data from COI was analysed using the standard phylogenetic procedures in MEGA6 to examine relationships and differentiation among sequences. These could not be identified to the lowest taxonomic rank due to limited sequence data to compare them with. The sequence data from these specimens gave different results in the two online databases. BOLD results were to family level (Tripterygiidae) and NCBI to the species level (Clinidae: Pavoclinus profundus). Results in this study confirmed the efficiency of the DNA barcoding technique in species level identification of fish larvae. The evidence from genetic barcodes of the Tripterygiidae specimens, supported by morphological characteristics, suggests the need for thorough research to identify the individuals to the species level. The fact that this study identified taxonomically problematic Gobiidae and Tripterygiidae specimens suggests that studies similar to this may highlight additional diversity and help to resolve the taxonomy of other species in these families. However, the lack of reference sequence data from the adult specimens, and especially those with cryptic diversity, were both shortcomings for the positive identification of larvae. With that being said, it shows the necessity for more research to be conducted on barcoding of larvae in general as to accommodate all kinds of species from biodiversity to economic perspectives.
- Full Text:
- Date Issued: 2020
Determination of the botanical composition of black rhinoceros (Diceros bicornis) dung using the rbcL gene as a molecular marker, and analysis of antioxidant and phenolic content of its browse
- Authors: Bulani, Siyavuya Ishmael
- Date: 2007 , 2013-06-25
- Subjects: Black rhinoceros -- Food , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- Analysis -- South Africa -- Eastern Cape , Plant ecology -- South Africa -- Eastern Cape , Genetic markers , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4070 , http://hdl.handle.net/10962/d1006468 , Black rhinoceros -- Food , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- Analysis -- South Africa -- Eastern Cape , Plant ecology -- South Africa -- Eastern Cape , Genetic markers , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants
- Description: The black rhinoceros remains one of the world's extremely endangered species despite a variety of policies to protect it. The black rhinoceros population at the Great Fish River Reserve (GFRR) in the Eastern Cape in South Africa has increased steadily since their re-introduction in 1986. This megaherbivore is a browser, with a diet obtained largely from the short and medium succulent thicket of the GFRR. Knowledge of the preferential diet of the black rhinoceros on the reserve is an important factor for the effective management of the land and the herbivores that compete for its resources. The dietary preferences of the black rhinoceros at the reserve have been established using backtracking methods. In this study the rbcL gene was used to establish an rbcL gene database of the plants from the GFRR and determine the botanical composition of the black rhinoceros dung from the GFRR. Due to the limited number of rbcL gene plant sequences from the GFRR deposited in the GenBank database, 18 plant species from the GFRR were sequenced. Sequence analyses between the partial rbcL gene sequences generated were able to distinguish between plants down to species level. Plant species from the family Euphorbiaceae and Fabaceae showed sequence variation at intra-specific level compared to those of Tiliaceae which were more conserved. The generated rbcL gene sequences from seasonal dung samples were compared to the rbcL gene sequenced from 18 plant species obtained from the GFRR and those from the GenBank database. A wide range of plant species were identified from the dung samples. There were no major differences in botanical composition between the dung samples, except that Grewia spp. were found to dominate in almost all seasons. The results obtained on the free radical scavenging activity of the extracts against 2,2-Diphenyl-l-picrylhydrazyl (DPPH) increased in the order of methanol > ethyl acetate > chloroform. The DPPH free radical scavenging activity of the methanol plant extracts increased in the order Brachylaena elliptica > Plumbago auriculata > Grewia robusta > Azima tetracantha. Methanol extracts on the TLC plate sprayed with Fe³⁺-2,4,6-Tri-2-pyridyl-s-triazine (TPTZ) showed that the compounds present in the extracts react differently to ferric ion, with most compounds unable to reduce ferric ion. Furthermore the methanol extracts were able to exhibit reduction potentials vs. Ag/AgCl at low concentrations. The compounds in the extracts were shown to be phenolic acids and flavonoid glycosides.
- Full Text:
- Date Issued: 2007
- Authors: Bulani, Siyavuya Ishmael
- Date: 2007 , 2013-06-25
- Subjects: Black rhinoceros -- Food , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- Analysis -- South Africa -- Eastern Cape , Plant ecology -- South Africa -- Eastern Cape , Genetic markers , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4070 , http://hdl.handle.net/10962/d1006468 , Black rhinoceros -- Food , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- Analysis -- South Africa -- Eastern Cape , Plant ecology -- South Africa -- Eastern Cape , Genetic markers , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants
- Description: The black rhinoceros remains one of the world's extremely endangered species despite a variety of policies to protect it. The black rhinoceros population at the Great Fish River Reserve (GFRR) in the Eastern Cape in South Africa has increased steadily since their re-introduction in 1986. This megaherbivore is a browser, with a diet obtained largely from the short and medium succulent thicket of the GFRR. Knowledge of the preferential diet of the black rhinoceros on the reserve is an important factor for the effective management of the land and the herbivores that compete for its resources. The dietary preferences of the black rhinoceros at the reserve have been established using backtracking methods. In this study the rbcL gene was used to establish an rbcL gene database of the plants from the GFRR and determine the botanical composition of the black rhinoceros dung from the GFRR. Due to the limited number of rbcL gene plant sequences from the GFRR deposited in the GenBank database, 18 plant species from the GFRR were sequenced. Sequence analyses between the partial rbcL gene sequences generated were able to distinguish between plants down to species level. Plant species from the family Euphorbiaceae and Fabaceae showed sequence variation at intra-specific level compared to those of Tiliaceae which were more conserved. The generated rbcL gene sequences from seasonal dung samples were compared to the rbcL gene sequenced from 18 plant species obtained from the GFRR and those from the GenBank database. A wide range of plant species were identified from the dung samples. There were no major differences in botanical composition between the dung samples, except that Grewia spp. were found to dominate in almost all seasons. The results obtained on the free radical scavenging activity of the extracts against 2,2-Diphenyl-l-picrylhydrazyl (DPPH) increased in the order of methanol > ethyl acetate > chloroform. The DPPH free radical scavenging activity of the methanol plant extracts increased in the order Brachylaena elliptica > Plumbago auriculata > Grewia robusta > Azima tetracantha. Methanol extracts on the TLC plate sprayed with Fe³⁺-2,4,6-Tri-2-pyridyl-s-triazine (TPTZ) showed that the compounds present in the extracts react differently to ferric ion, with most compounds unable to reduce ferric ion. Furthermore the methanol extracts were able to exhibit reduction potentials vs. Ag/AgCl at low concentrations. The compounds in the extracts were shown to be phenolic acids and flavonoid glycosides.
- Full Text:
- Date Issued: 2007
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