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.
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Secret sex lives in the intertidal: insights into the mating systems of clinid fishes from molecular parentage analyses
- Authors: Scheeper, Martinus Johannes
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72438 , vital:30048
- Description: Expected release date-April 2020
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Morphological and genetic variation of Gymnothorax undulatus (Anguilliformes: Muraenidae) in the Western Indian Ocean
- Authors: Sithole, Yonela
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63722 , vital:28476
- Description: Expected release date-April 2019
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Genetic structure and biogeography of three wrasse species (Labridae) within the Western Indian Ocean
- Authors: Mayekiso, Sisanda
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1114 , vital:20021
- Description: The biogeography of wrasses within the Western Indian Ocean (WIO) is poorly understood, with regard to origins and genetic differentiation or connectivity among the regions of the WIO. This region is a good model for studying the influence of physical complexities and biogeographic breaks in shaping patterns of differentiation in wrasses. Three reef-associated fish species, Cheilio inermis, Thalassoma hebraicum and T. lunare, were selected to examine the factors that have influenced patterns of differentiation across the WIO. Each species was sampled from various localities of the WIO, the Red Sea and Indo-West Pacific Islands. Sequence data were generated from two mitochondrial gene fragments (cytochrome b and ATPase 6) and one nuclear locus (the first intron of the ribosomal protein S7 gene). Genetic analyses were used to calculate genetic diversity indices within species, which were then compared among species. The relationships among haplotypes and alleles were constructed using median-joining networks. Where necessary, neighbour-joining trees (NJ) were constructed to examine relationships among haplotypes and alleles for the Thalassoma species. Population structure was analysed using AMOVA and pairwise ФST to compare and calculate differentiation between the WIO localities. Mismatch distributions were used to examine population growth and decline or stability, and demographic parameters were used to calculate time of population expansion. There was high haplotype (h = 0.88 to 0.98) and low nucleotide diversities (π = 0.003 to 0.008) among all species for mitochondrial markers. For S7 intron I, high allelic (A = 0.95 to 0.98) and low nucleotide diversities (π = 0.002 to 0.014) were observed for all species. The pairwise ФST values revealed little to great (ФST = -0.02 to 0.67) genetic differentiation between localities, across all species for the three gene regions. The pairwise comparisons indicated the differentiation in C. inermis of Tanzania and Kenya from Mozambique and Nosy Be (Madagascar). The widespread C. inermis also revealed the differentiation of Kenya and Tanzania. For C. inermis, the AMOVAs of ATPase 6 and cytochrome b data indicated high differentiation among defined locality groups. The groups were defined according to geographic proximity. However, the AMOVA of the nuclear gene (S7 intron I) did not find variation among defined locality groups. Cheilio inermis revealed a sequence divergence of 0.4%. The divergence that was found in C. inermis was not enough to suggest a cryptic species within the WIO. Overall, the widespread and monotypic C. inermis revealed genetic differentiation within the WIO. Thalassoma hebraicum generally revealed little genetic differentiation across the WIO. The AMOVAs of the three gene regions showed no variation among specimens of the defined locality groups. However, some differentiation was found between localities. The pairwise comparisons of T. hebraicum revealed the differentiation of Seychelles from the African mainland and Madagascar. Southern Africa was observed to be differentiated from Nosy Be and Zanzibar. The observed differentiation could be caused by oceanic barriers such as the South Equatorial Current (SEQC), East African Coastal Current (EACC), and the Comoros Gyres and eddies in the Mozambique Channel, and Agulhas Current. Thalassoma lunare revealed genetic isolation between the WIO and the Red Sea as well as within the WIO. The genetic isolation between the WIO and the Red Sea is probably due to the historical isolation by the Bab al Mandab and contemporary barriers such as the cold upwelling cells in Somalia. The differentiation of Maldives from the African mainland and Seychelles could be due to distance and the upwelling cells created by monsoon winds. Mismatch distributions suggested that C. inermis and T. hebraicum had undergone demographic expansion during the Pleistocene (92 678 to 40 219 years ago). The results of the current study are similar to those from previous studies of WIO reef fish species, and the results of the present study could have potential implications for conservation and fisheries management. Single genetic markers and single species studies do not detect all barriers to dispersal in the WIO, thus they are insufficient to inform conservation management. Thus, the use of multispecies and genetic markers in the current study can be adopted by other studies of the marine taxa of the WIO.
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Regional connectivity, differentiation and biogeography of three species of the genus Lutjanus in the western Indian Ocean
- Authors: Morallana, Jonas Moqebelo
- Date: 2014
- Subjects: Lutjanus -- Indian Ocean , Biogeography -- Indian Ocean , Phylogeography -- Indian Ocean , Lutjanus -- Geographical distribution , Lutjanus -- Variation , Mitochondrial DNA , Animal genetics , Variation (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5369 , http://hdl.handle.net/10962/d1013293
- Description: Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.
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Movement patterns and genetic stock delineation of an endemic South African sparid, the Poenskop, Cymatoceps nasutus (Castelnau, 1861)
- Authors: Murray, Taryn Sara
- Date: 2013
- Subjects: Fish stock assessment -- South Africa , Sparidae -- South Africa , Fishes -- Reproduction -- South Africa , Fishing -- South Africa , Fish populations -- South Africa , Fishes -- Behavior -- South Africa , Marine fishes -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5178 , http://hdl.handle.net/10962/d1001514 , Fish stock assessment -- South Africa , Sparidae -- South Africa , Fishes -- Reproduction -- South Africa , Fishing -- South Africa , Fish populations -- South Africa , Fishes -- Behavior -- South Africa , Marine fishes -- South Africa
- Description: Poenskop Cymatoceps nasutus (Pisces: Sparidae), an endemic South African sparid, is an important angling species being predominantly targeted by the recreational shore and skiboat sector. This species is slow-growing, long-lived, late-maturing and sex-changing, making poenskop acutely sensitive to over-exploitation. Despite interventions, such as the imposition of size and bag limits (currently 50 cm TL and one per licensed fisher per day) by authorities, catch-per-unit-effort trends reflect a severe and consistent stock decline over the last two decades. Poenskop has been identified as a priority species for research and conservation. Although the biology and population dynamics of this species have been well-documented, little is known about the movement behaviour of poenskop. Furthermore, there is a complete lack of information on its genetic stock structure. This thesis aimed to address the current knowledge gaps concerning movement behaviour and genetic stock structure of poenskop, making use of a range of methods and drawing on available information, including available fishery records as well as published and unpublished survey and research data, and data from long-term monitoring programmes. Analysis of available catch data (published and unpublished) revealed a decline in the number of poenskop caught as well as size of fish taken over the last two decades, ultimately reflecting the collapse of the stock (estimated to be at 20% of their pristine level). Improved catch-per-unit-effort data from the Tsitsikamma National Park Marine Protected Area (MPA), and larger poenskop being caught in the no-take areas than adjacent exploited areas of the Pondoland MPA confirmed that MPAs can be effective for the protection and management of poenskop. The current MPA network in South Africa is already wellestablished, and encompasses considerable reef areas, being preferable for poenskop habitation. Conventional dart tagging and recapture information from three ongoing, long-term fishtagging projects, conducted throughout the poenskop’s distribution, indicated high levels of residency at all life-history stages. Coastal region, seasonality and time at recapture did not appear to have a significant effect on the level of movement or distance moved. However, on examining the relationship among coastal movements and fish size and ages, larger and older fish (adults) moved greater distances, with juveniles and sub-adults showing high degrees of residency. An estimation of home-range size indicated smaller poenskop to hold smaller home-ranges, while larger poenskop hold larger home-ranges. Large easterly displacements of a number of adult poenskop is in accordance with previous findings that this species may undertake a unidirectional migration up the coastline of South Africa where they possibly settle in Transkei waters for the remainder of their lives. This high level of residency makes poenskop vulnerable to localised depletion, although they can be effectively protected by suitable MPAs. Despite considerable tagging effort along the South African coastline (2 704 poenskop tagged with 189 recaptures, between 1984 and 2010), there remains limited information on the connectivity of different regions along the South African coastline. This was addressed using mitochondrial DNA sequencing. The mitochondrial DNA control region was used due to its high substitution rate, haploid nature, maternal inheritance and absence of recombination. The mtDNA sequencing showed no evidence of major geographic barriers to gene flow in this species. Samples collected throughout the core distribution of poenskop showed high genetic diversity (h = 0.88, π = 0.01), low genetic differentiation among regions, no spatial structure (ɸST = 0.012, p = 0.208) and no evidence of isolation by distance. The collapsed stock status of poenskop as well as the fact that it is being actively targeted by recreational and commercial fishers suggests that this species requires improved management, with consideration given to its life-history style, residency and poor conservation status. Management recommendations for poenskop, combined with increasing South Africa’s existing MPA network, include the possibility of setting up a closed season (during known spawning periods) as well as the decommercialisation of this species. The techniques used and developed in this study can also be adopted for other overexploited linefish species.
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Comparative biogeography and ecology of freshwater fishes in the Breede and associated river systems, South Africa
- Authors: Chakona, Albert
- Date: 2012
- Subjects: Freshwater fishes -- South Africa -- Breede River , Freshwater fishes -- South Africa -- Geographical distribution , Freshwater fishes -- Ecology , Feshwater fishes -- Genetics
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5372 , http://hdl.handle.net/10962/d1015694
- Description: Distribution patterns and levels of genetic diversity in extant taxa are a product of complex palaeogeographic processes and climatic oscillations as well as the species’ intrinsic ecological adaptations. The Cape Floristic Region of South Africa presents a unique system for studying the processes that promote species diversification and distribution patterns. This region has a high degree of endemism of both terrestrial and aquatic biota and is clearly isolated from neighbouring areas by the Cape Fold Mountains and the Great Escarpment. The objective of this study was to firstly examine the ecology of freshwater fishes belonging to the genera Galaxias, Pseudobarbus and Sandelia in the south-western CFR. This was followed by an assessment of the genetic diversity of these taxa. Unique lineages were identified and their distribution was mapped. The work aimed to explore the role of the region’s complex palaeogeographic and climatic history as well as the role of the species’ ecological adaptations in driving lineage diversification and shaping contemporary distribution patterns. The four main components of the study can be summarised as follows: 1. Habitat associations of three widely distributed lineages of Galaxias zebratus Pseudobarbus burchelli and Sandelia capensis were evaluated at multiple localities in minimally disturbed mountain tributaries of the Breede, Duiwenhoks and Goukou River systems. The lineages have distinct habitat associations which were related to differences in their morphological traits. The slender-bodied Galaxias ‘nebula’ and the fusiform-shaped Pseudobarbus ‘Breede’ are capable of exploiting upper reaches with faster water velocity. By contrast, the laterally compressed Sandelia ‘eastern’ is restricted to lower reaches, making this lineage more susceptible to a wide array of impacts. 2. A recently discovered lineage of Galaxias zebratus, (Galaxias ‘nebula’), was found to be capable of tolerating emersion for a prolonged period of time. This is the first time that such capabilities have been documented in an African galaxiid. These adaptations have implications for the interpretation of Galaxias ‘nebula’s wide distribution range. 3. The phylogeography of Galaxias ‘nebula’ across its entire distribution range was investigated using two mitochondrial genes (cytochrome c oxidase subunit I (COI) and cytochrome b (cyt b)). This lineage has a complex evolutionary history that was influenced by both intrinsic and extrinsic factors. Rare events such as episodic drainage connections during Pleistocene and Holocene pluvial periods, possibly augmented by river confluences during periods of lower sea-levels and river capture events seem to be the most credible explanation for the extensive contemporary distribution and the relatively shallow genetic divergence between different river systems. 4. Mitochondrial cyt b sequences were used (i) to assess genetic diversity in G. zebratus, P. burchelli and S. capensis from the south-western CFR and (ii) to determine the roles of intrinsic ecological adaptations and extrinsic landscape and climatic changes in promoting genetic diversification and shaping present day distribution patterns of lineages in the three taxa. Marine incursions during periods of major sea-level transgressions are proposed to have isolated populations in upland refugia, thereby driving allopatric divergence in these species. Subsequent connections of rivers during wetter periods and lower sea-levels are proposed to have facilitated post-speciation dispersal of lineages to attain present day distribution patterns. While detailed morphological studies and further genetic analysis are needed to substantiate the taxonomic status of the newly discovered lineages of Galaxias zebratus, Pseudobarbus burchelli and Sandelia capensis, results of the present study indicate that the south-western CFR represents a previously unrecognised centre of freshwater fish diversity and microendemism in the broader Cape Floristic Region. Accurate identification of lineages and comprehensive mapping of their distribution is a fundamental pre-requisite for ecological studies, assessing conservation status and implementation of appropriate conservation measures.
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