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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- Date Issued: 2020
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
- Full Text: false
- Date Issued: 2019
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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- Date Issued: 2018
Potential effects of different salinities on the survival of the mangrove crab, Uca urvillei and its associated chemoautotrophic bacterial symbionts
- Authors: Mbobo, Tumeka https://orcid.org/0000-0002-0159-6569
- Date: 2015-06
- Subjects: Mangrove ecology http://id.loc.gov/authorities/subjects/sh85080528 , Crabs--South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/19225 , vital:43033
- Description: The ability of natural populations to maintain fitness is important to their long-term persistence and has further relevance in the light of climate change scenarios. Fitness is however also influenced strongly by interactions with other species of the community. It is, therefore, important to focus on how environmental change can alter key biological interactions. The present study aimed to investigate the effects of different salinity levels on one species of mangrove crab, Uca urvillei and the associated chemoautotrophic bacterial symbionts, from the Mngazana estuary, South Africa. To examine the influence of different salinities over time on the symbiotic bacterial community, salinity experiments were set up, choosing three salinity exposures (5, 20 and 35percent) and four time exposures (3, 7, 14 and 21 days). The results showed that microbial community associated with U. urvillei was generally stable throughout the three salinity treatments, while the survival of the host (crab), was influenced by high salinities, particularly after day 14. Overall, the results of this study suggest that over time, environmental salinity (35percent) has the potential to affect significantly the physiology of U. urvillei, but this might not necessarily be the case for the associated microbial communities. The modes at which the significant symbionts are transferred from mother to offspring were also investigated by analysing the bacterial profiles from eggs, ovigerous and non-ovigerous females, along with mud. The results were fairly complex, but with significant differences in the bacterial communities of eggs from mud and females. These differences were driven mostly by two dominant phyla: Actinobacteria and Proteobacteria. The presence of both these phyla throughout the categories (even though in different percentages) suggest that U. urvillei might employ a mixed mode strategy of acquiring and maintaining the bacterial symbionts. Overall, this study contributes to further understand the dynamic and complex effects of environmental Abstract ii change on symbiotic communities, with overall potential cascading repercussions to the persistence of mangrove systems. , Thesis (MSc) (Zoology) -- Faculty of Science and Agriculture, 2015
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- Date Issued: 2015-06