Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma:
- Authors: McKeown, Niall J , Gwilliam, Michael P , Healey, Amy J E , Skujina, Ilze , Potts, Warren M , Sauer, Warwick H H , Shaw, Paul W
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158085 , vital:40147 , DOI: 10.1111/jfb.14316
- Description: Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range‐wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters.
- Full Text:
- Date Issued: 2020
Genetic analysis reveals harvested Lethrinus nebulosus in the Southwest Indian Ocean comprise two cryptic species
- Authors: Healey, Amy J E , Gouws, Gavin , Fennessy, Sean T , Kuguru, Baraka , Sauer, Warwick H H , Shaw, Paul W , McKeown, Niall J
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124538 , vital:35626 , https://doi.10.1093/icesjms/fsx245
- Description: This study initially aimed to investigate the genetic population/stock structuring of Lethrinus nebulosus in the Southwest Indian Ocean (SWIO) to inform management practices in light of emerging evidence of overharvesting of this species throughout its distribution. Adult samples were genotyped for 14 nuclear microsatellites and by sequencing fragments of the mtDNA control region and COI gene. A salient feature of the data was the congruent cyto-nuclear partitioning of samples into two high divergent, reciprocally monophyletic groups. This indicates that despite no a priori evidence, hitherto described L. nebulosus in the SWIO comprises two cryptic species that co-occur among southern samples. This intermingling indicates that, at least in southern samples, both species are being indiscriminately harvested, which may severely compromise sustainability. Limited microsatellite differentiation was detected within both species, though there was some evidence of isolation in the Mauritian population. In contrast, mtDNA revealed a pattern consistent with chaotic genetic patchiness, likely promoted by stochastic recruitment, which may necessitate a spatial bet-hedging approach to management to satisfy fishery management and conservation goals.
- Full Text:
- Date Issued: 2018
Genomic analysis reveals multiple mismatches between biological and management units in yellowfin tuna (Thunnus albacares)
- Authors: Mullins, Rachel B , McKeown, Niall J , Sauer, Warwick H H , Shaw, Paul W
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124549 , vital:35627 , https://doi.10.1093/icesjms/fsy102
- Description: The South African (SAF) yellowfin tuna (Thunnus albacares) fishery represents a potential example of misalignment between management units and biological processes. The SAF fishery spans an operational stock with a boundary at 20_E, either side of which fish are considered part of Atlantic or Indian Ocean regional stocks. However, the actual recruitment of fish from Atlantic and Indian Ocean spawning populations into SAF waters is unknown. To address this knowledge gap, genomic analysis (11 101 SNPs) was performed on samples from Atlantic and Indian Ocean spawning sites, including SAF sites spanning the current stock boundary. Outlier loci conferred high discriminatory power to assignment tests and revealed that all SAF fish were assigned to the Indian Ocean population and that no Atlantic Ocean fish appeared in the SAF samples. Additionally, several Indian Ocean migrants were detected at the Atlantic spawning site demonstrating asymmetric dispersal and the occurrence of a mixed-stock fishery in Atlantic waters. This study highlights both the spatial inaccuracy of current stock designations and a misunderstanding of interactions between the underlying biological units, which must be addressed in light of local and global declines of the species. Specifically, the entire SAF fishery must be managed as part of the Indian Ocean stock.
- Full Text:
- Date Issued: 2018
Integrated genetic and morphological data support eco‐evolutionary divergence of Angolan and South African populations of Diplodus hottentotus
- Authors: Gwilliam, Michael P , Winkler, Alexander C , Potts, Warren M , Santos, Carmen V D , Sauer, Warwick H H , Shaw, Paul W , McKeown, Niall J
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124833 , vital:35702 , https://doi.10.1111/jfb.13582
- Description: The genus Diplodus presents multiple cases of taxonomic conjecture. Among these the D. cervinus complex was previously described as comprising three subspecies that are now regarded as separate species: Diplodus cervinus, Diplodus hottentotus and Diplodus omanensis. Diplodus hottentotus exhibits a clear break in its distribution around the Benguela Current system, prompting speculation that Angolan and South African populations flanking this area may be isolated and warrant formal taxonomic distinction. This study reports the first integrated genetic [mitochondrial (mt)DNA and nuclear microsatellite] and morphological (morphometric, meristic and colouration) study to assess patterns of divergence between populations in the two regions. High levels of cytonuclear divergence between the populations support a prolonged period of genetic isolation, with the sharing of only one mtDNA haplotype (12 haplotypes were fully sorted between regions) attributed to retention of ancestral polymorphism. Fish from the two regions were significantly differentiated at a number of morphometric (69·5%) and meristic (46%) characters. In addition, Angolan and South African fish exhibited reciprocally diagnostic colouration patterns that were more similar to Mediterranean and Indian Ocean congeners, respectively. Based on the congruent genetic and phenotypic diversity we suggest that the use of hottentotus, whether for full species or subspecies status, should be restricted to South African D. cervinus to reflect their status as a distinct species-like unit, while the relationship between Angolan and Atlantic–Mediterranean D. cervinus will require further demo-genetic analysis. This study highlights the utility of integrated genetic and morphological approaches to assess taxonomic diversity within the biogeographically dynamic Benguela Current region.
- Full Text:
- Date Issued: 2018
Population connectivity of an overexploited coastal fish, Argyrosomus coronus (Sciaenidae), in an ocean-warming hotspot
- Authors: Henriques, R , Potts, Warren M , Santos, Carmen V D , Sauer, Warwick H H , Shaw, Paul W
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125720 , vital:35811 , https://doi.10.2989/1814232X.2018.1434090
- Description: Anthropogenic activities are recognised as causing significant impacts to marine systems at multiple levels, ranging from habitat disturbance (Pauly et al. 2005) to overfishing (Sala and Knowlton 2006) and loss of genetic diversity (Pinsky and Palumbi 2014). Exploitation and harvesting in particular are known to strongly influence fish populations and their associated ecosystems (Pauly et al. 2005), and in combination with ongoing climate change can have compound effects on the viability and long-term survival of marine fishes (Last et al. 2011). Species can react to the impacts of climate change either by shifting their distributional range or by adapting to changing conditions through individual ecological plasticity and/or local population adaptation (Briggs 2011; Last et al. 2011). However, since ecological plasticity and local adaptation have strong genetic components, overharvesting has the potential to impact the long-term adaptive ability of marine fishes by decreasing the extant genetic diversity (Allendorf et al. 2014). Therefore, understanding the impact of exploitation on genetic diversity and population substructuring is critical for predicting the likely consequences of continued exploitation and climate change.
- Full Text:
- Date Issued: 2018
Spermatophore dimorphism in the chokka squid Loligo reynaudii associated with alternative mating tactics
- Authors: Sato, Noriyosi , Iwata, Yoko , Shaw, Paul W , Sauer, Warwick H H
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/127070 , vital:35952 , https://doi.10.1093/mollus/eyy002
- Description: Chokka squid (Loligo reynaudii) have characteristic alternative mating tactics: ‘consort’ males temporarily pair with and guard a female and transfer spermatophores onto her oviduct opening inside the mantle cavity, whereas ‘sneaker’ males rush towards a mating pair and transfer spermatophores onto the female’s buccal membrane near her sperm storage organ. Differences in mating behaviours and their related sperm-storage sites clearly constrain the fertilization process and can drive dimorphism between consort and sneaker males. The presence and character of male dimorphism has not yet been fully examined in this species, but consort males are commonly much larger than sneaker males. We observed clear dimorphism in spermatangia (the sperm mass ejaculated from the spermatophore), consistently associated with the two alternative sperm storage sites on the female’s body. Observations of spermatophores stored in the Needham’s sac of mature males confirmed that small males produce ‘sneaker-type’ spermatangia whereas larger males produce ‘consort-type’ spermatangia, and no individuals possessed both types. Therefore, by association, the mating tactic adopted (including the sperm deposition site used) by individual males can be determined from observation of their spermatangial type, without requiring direct behavioural observation of mating. This ability to infer information about mating tactic will improve our understanding of the reproductive system and mating dynamics in this species.
- Full Text:
- Date Issued: 2018
Phylogeny of the Sepia officinalis species complex in the eastern Atlantic extends the known distribution of Sepia vermiculata across the Benguela upwelling region
- Authors: Healey, Amy J E , McKeown, Niall J , Potts, Warren M , de Beer, Chénelle L , Sauer, Warwick H H , Shaw, Paul W
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125631 , vital:35802 , https://doi.10.2989/1814232X.2017.1371076
- Description: Accurate species identification and biogeographic characterisation are fundamental for appropriate management of expanding cephalopod fisheries. This study addresses this topic within the common cuttlefish Sepia officinalis species complex (S. officinalis, S. hierredda and S. vermiculata), with an emphasis on occurrence in African waters. Tissue samples from the currently presumed distributions of S. vermiculata and S. hierredda (from South Africa and Ghana/Angola, respectively) were sequenced for the cytochrome c oxidase subunit I (COI) and the cytochrome b (cytb) genes of the mitochondrial genome and then compared to existing S. officinalis sequences. Three highly divergent and reciprocally monophyletic clades, corresponding to S. officinalis, S. hierredda and S. vermiculata, were resolved, representing the first molecular confirmation of the distinct species status of S. hierredda and S. vermiculata. The sequences also revealed that, contrary to expectations based on presently published information, all samples from southern Angola were S. vermiculata. These results indicate that the range of S. vermiculata extends beyond the currently described northern limit and that S. hierredda and S. vermiculata may be indiscriminately harvested in Angolan waters. Finer-scale patterns within S. vermiculata phylogeography also indicate that the Benguela Current System and/or other environmental factors serve to isolate northern and southern stocks.
- Full Text:
- Date Issued: 2017
Molecular genetic, life-history and morphological variation in a coastal warm-temperate sciaenid fish: evidence for an upwelling-driven speciation event
- Authors: Henriques, Romina , Potts, Warren M , Sauer, Warwick H H , Santos, Carmen V D , Kruger, Jerraleigh , Thomas, Jessica A , Shaw, Paul W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125252 , vital:35750 , http://dx.doi.10.1111/jbi.12829
- Description: The marine environment is punctuated by biogeographical barriers that limit dispersal and gene flow in otherwise widespread species (Teske et al., 2011a,b; Briggs & Bowen, 2012; Luiz et al., 2012). These barriers may be physical obstacles such as landmasses (e.g. Isthmus of Panama) or less intuitive features such as deep water (Lessios et al., 2003), freshwater outflows (Floeter et al., 2008) or oceanographic features (Shaw et al., 2004; Galarza et al., 2009; von der Heyden et al., 2011). Upwelling cells and sea surface temperature (SSTs) gradients in particular are known to disrupt gene flow, leading to divergence of allopatric populations and species (Waters & Roy, 2004; Teske et al., 2011a; Henriques et al., 2012, 2014, 2015). However, as oceanographic features are seldom permanent and frequently subject to considerable environmental variability, many barriers often permit some level of permeability to dispersal (Floeter et al., 2008). Other processes may influence the persistence of differentiated allopatric taxa across such physical barriers (Bradbury et al., 2008), with ecological divergence (and diversifying selection) being reported as a major evolutionary process influencing the biogeographical distributions of marine species (Pelc et al., 2009; Teske et al., 2011a; Gaither et al., 2015).
- Full Text:
- Date Issued: 2016
Incipient genetic isolation of a temperate migratory coastal sciaenid fish (Argyrosomus inodorus) within the Benguela Cold Current system
- Authors: Henriques, Romina , Potts, Warren M , Sauer, Warwick H H , Shaw, Paul W
- Date: 2015
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124710 , vital:35652 , https://doi.10.1080/17451000.2014.952309
- Description: The Benguela Cold Current system, located in the south-eastern Atlantic, features cold sea surface temperatures, bounded to the north and south by tropical currents (the Angola and Agulhas Currents, respectively) and a perennial upwelling cell off central Namibia that divides the region into two sub-systems with different characteristics (Shannon 1985; Hutchings et al. 2009). The colder sea surface temperatures of the Benguela Current have been considered an important biogeographic barrier, isolating tropical and warm-temperate fauna of the Atlantic and Indo-Pacific Oceans (Avise 2000; Floeter et al. 2008). However, recent studies revealed that other oceanographic features, such as the perennial upwelling cell, may also play an important role in shaping the population structure of warm temperate fish populations within the Benguela system, as complete disruption of gene flow was documented both in Lichia amia (Linnaeus, 1758) and Atractoscion aequidens (Cuvier, 1830) (Henriques et al. 2012, 2014). Little is known, however, regarding the influence of the Benguela system on genetic population connectivity of cold-water-tolerant species.
- Full Text:
- Date Issued: 2015
Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species
- Authors: Potts, Warren M , Henriques, Romina , Santos, Carmen V D , Munnik, Kate , Ansorge, Isabelle J , Dufois, Francois , Sauer, Warwick H H , Booth, Anthony J , Kirchner, Carola , Sauer, Warwick , Shaw, Paul W
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125375 , vital:35777 , https://doi.10.1111/gcb.12612
- Description: Despite increasing awareness of large-scale climate-driven distribution shifts in the marine environment, no study has linked rapid ocean warming to a shift in distribution and consequent hybridization of a marine fish species. This study describes rapid warming (0.8 °C per decade) in the coastal waters of the Angola-Benguela Frontal Zone over the last three decades and a concomitant shift by a temperature sensitive coastal fish species (Argyrosomus coronus) southward from Angola into Namibia. In this context, rapid shifts in distribution across Economic Exclusive Zones will complicate the management of fishes, particularly when there is a lack of congruence in the fisheries policy between nations. Evidence for recent hybridization between A. coronus and a congener, A. inodorus, indicate that the rapid shift in distribution of A. coronus has placed adults of the two species in contact during their spawning events. Ocean warming may therefore revert established species isolation mechanisms and alter the evolutionary history of fishes. While the consequences of the hybridization on the production of the resource remain unclear, this will most likely introduce additional layers of complexity to their management.
- Full Text:
- Date Issued: 2014
Genetic analysis of the Octopus vulgaris population on the coast of South Africa
- Authors: Oosthuizen, Ané , Jiwaji, Meesbah , Shaw, Paul W
- Date: 2004
- Language: English
- Type: Article
- Identifier: vital:6761 , http://hdl.handle.net/10962/d1007922
- Description: This study on Octopus vulgaris focused on the COIII gene region of mitochondrial DNA. Sequences from 21 samples from the Eastern Cape, and 14 samples from the Western Cape, were compared to determine whether different populations exist along the South African coast. A 380-bp segment of the COIII region of mtDNA was amplified using the polymerase chain reaction with specific designed primers. Phylogenetic inference was made using maximum parsimony (MP), maximum likelihood (ML), and distance based methods. All sequences conformed to a single haplotype. Lack of variation within and between east and west coast samples precluded further population genetic analysis. The sequence obtained in this study was also compared with other sequences lodged in the Genbank database. Phylogenetically, the South African O. vulgaris is closely related to O. vulgaris from Senegal (0.67% divergence) and the Mediterranean (1.51% divergence). Within the Mediterranean group, O. vulgaris from South Africa displayed less sequence divergence from Senegalese and Mediterranean individuals than O. vulgaris from Venezuela (3.85%) and Taiwan (3.87%). These data do not, therefore, refute the hypothesis of a single O. vulgaris genetic population around the coast.
- Full Text:
- Date Issued: 2004