Johan C. Groeneveld

Long current to nowhere? — Genetic connectivity of Jasus tristani populations n the southern Atlantic Ocean

The commercially exploited spiny lobster Jasus tristani has a disjunct distribution in the southern Atlantic Ocean, with populations occurring at the Tristan da Cunha Archipelago, Gough Island and on Vema Seamount. A distance of 2 000km separates Vema and the Tristan Archipelago. In order to determine genetic connectivity of lobster between these locations, a region of the cytochrome oxidase II (COII) gene was sequenced for 193 individuals of J. tristani from five sampling sites (Tristan da Cunha, Nightingale, Inaccessible, Gough islands and Vema Seamount). Our results show that J. tristani in the southern Atlantic share a most recent common ancestry that dates back at least one million years. Analyses of molecular variance and pairwise Φst analyses reveal shallow but significant genetic partitioning between Vema Seamount and all other locations. No population differentiation was detected among any of the remaining sampling sites. Coalescent analyses show limited gene flow between Vema and the archipelago (including Gough Island), possibly mediated by larval dispersal in the South Atlantic gyre system. Population divergence between Vema and the other populations, using MDIV, was estimated to be approx. 270 000 years ago. Mismatch distributions, a haplotype network, and Fus Fs test, all suggest that the J. tristani population underwent population expansion between 12 000 and 99 000 years ago.

PHYLOGEOGRAPHY OF THE SCALLOPED SPINY-LOBSTER PANULIRUS HOMARUS RUBELLUS IN THE SOUTHWEST INDIAN OCEAN

The Mozambique Channel between south-east Africa and Madagascar potentially forms a barrier to larval dispersal and thus gene flow across the channel, even in species with long larval lifespans such as spiny lobsters. The DNA of 181 specimens of Panulirus homarus rubellus Berry, 1974, collected from six sites along the African coast and a site in Madagascar, was sequenced (591 base pairs) to investigate gene flow along the coast and across the channel. Bayesian methods were implemented to infer genetic structure and relatedness. A total of 112 haplotypes were recovered, of which 78% were unique. Samples from Africa and Madagascar did not share any haplotypes and differed by 78 mutations and 3% DNA divergence. These distinct lineages suggest an absence of contemporary gene flow across the Mozambique Channel. Shallow genetic structure along approximately 1000 km of African coastline comprised combinations of seven distinct lineages but did not correspond to known biogeographic provinces. The African lineage appeared to be ancestral, and the source population for the Madagascan clade. Genetic isolation in refuges during glacial periods, followed by subsequent range expansions and secondary contact, may account for the high diversity in the African lineages.

High connectivity and lack of mtDNA differentiation among two previously recognized spiny lobster species in the southern Atlantic and Indian Oceans

Abstract Adult spiny lobsters Jasus paulensis and J. tristani inhabit non-emergent seamounts and remote islands in the southern mid-latitude (30–45°S) Indian and Atlantic Oceans. Populations are often thousands of kilometres apart, and metapopulation genetic structure relies on successful exchange of long-lived drifting larvae. Genetic population structure and connectivity were investigated by sequencing the mitochondrial cytochrome oxidase I gene from lobsters collected at two Indian Ocean sites (Seamount 150 and St Paul/Amsterdam Islands) and two Atlantic sites (Vema Seamount and Gough/Inaccessible Islands) between 2006 and 2011. Jasus paulensis and J. tristani individuals share identical haplotypes across the distribution range and Bayesian phylogenetic analyses strongly support the monophyly of all individuals sampled, to the exclusion of all other recognized Jasus species. Analyses of molecular variance revealed no significant population genetic differentiation between sites, and Fus F s and a mismatch distribution suggested demographic expansion, which was estimated to have occurred between 14,000 and 118,000 years ago. The results show an apparent lack of barriers to dispersal and gene flow over thousands of kilometres of the southern Indian and Atlantic Oceans, and suggest that J. paulensis and J. tristani should be synonymized as J. paulensis (Heller, 1862).

Spatial distribution patterns, abundance and population structure of deep-sea crab Chaceon macphersoni, based on complementary analyses of trap and trawl data

Marine species such as deep-sea geryonid crabs often exhibit high spatio-temporal variability in abundance and size over depth, substratum type and season, therefore data collected from a single gear type may not represent the whole population. Complementary data from trawl (soft substratum) and trap (hard substratum) fisheries were analysed within a general linear modelling (GLM) framework to assess distribution, abundance and population structure of Chaceon macphersoni off eastern South Africa. Catch rates, mean size, maturation size and sex ratio were modelled relative to year, month, depth, latitude and gear effects. Trap and trawl analyses indicated higher abundance as depth increased up to 500m, and during the austral spring and summer. The mean size of crabs remained constant at all depths sampled, and sex ratios were skewed towards females. Females were smaller than males, and achieved maturity at a smaller size. A standardised index based on trawl data (1988-2010) showed a long-term decline in abundance, with some recovery after 2002, whereas the trap index showed recent local depletions on hard substrata. Using data from two gear types confirmed broad gradients in abundance, but also emphasised subtle trends, such as local depletions on hard substrata, that would not have been apparent from trawl data only.

Settlement patterns, size and growth of puerulus and juvenile rock lobster Jasus lalandii at an oyster farm in Saldanha Bay, South Africa

Trends in the abundance, size and growth of newly settled pueruli and early juveniles of the rock lobster Jasus lalandii were determined from samples obtained from mesh bags used for oyster mariculture in Saldanha Bay, South Africa. Totals of 3 842 lobster pueruli and 10 158 juveniles were captured between August 2005 and June 2006, and distinct puerulus settlement events were identified in November and January. Juveniles also peaked during these months as well as in March. The size of newly settled pueruli increased significantly between October and March. The carapace length (CL) of pueruli and juveniles overlapped between 8.5 mm (smallest juvenile) and 10.4 mm (largest puerulus), and 50% of pueruli moulted into juveniles by 9.5–9.6 mm CL. There was a size progression in juveniles, with larger individuals in February and March reflecting an accumulation of juveniles from the earlier settlement events. The estimated growth increment from puerulus to first juvenile instar was 0.5–1.5 mm (4.9–16.1%), increasing to 1.4–2.5 mm (14.4–23.3%) for the second instar. Recruitment of J. lalandii pueruli occurred during periods when strong southerly winds prevailed, which results in a general offshore movement of surface waters along the West Coast and upwelling of cold nutrient-rich bottom waters. However, specific settlement events appeared to coincide with a change in wind direction, reduction in upwelling strength and increase in surface water temperatures, implying that larvae may take advantage of landward movements of surface waters during downwelling, or reversal of upwelling, to return them to shallow coastal waters.

Population structure and biology of shortfin mako, Isurus oxyrinchus, in the south-west Indian Ocean

The population structure, reproductive biology, age and growth, and diet of shortfin makos caught by pelagic longliners(2005-10)andbatherprotectionnets(1978-2010)inthesouth-westIndianOceanwereinvestigated.Themean fork length (FL) of makos measured by observers on longliners targeting tuna, swordfish and sharks was similar, and decreased from east to west, with the smallest individuals occurring near the Agulhas Bank edge, June to November. Nearly all makos caught by longliners were immature, with equal sex ratio. Makos caught by bather protection nets were significantlylarger,malesweremorefrequent,and93%ofmalesand55%offemalesweremature.Agewasassessedfrom bandcountsofsectionedvertebrae,andavonBertalanffygrowthmodelfittedtosex-pooledlength-at-agedatapredicteda birth size (L0) of 90cm, maximum FL (LN) of 285cm and growth coefficient (k) of 0.113y � 1 . Males matured at 190cm FL,aged7years,andfemalesat250cm,aged15years.Littersizesrangedfromnineto14pups,andthepresenceofgravid females in bather protection nets suggested that some pupping occurred in shelf waters. Teleosts (mainly Trachurus capensis) occurred in 84% of stomachs collected on longliners, whereas elasmobranchs (63.5%) were most common in samples collected from bather protection nets, followed by teleosts (43.1%) and cephalopods (36.5%). Larger prey size may be a factor that attracts large makos to coastal waters. Additional keywords: demography, GLM, pelagic longline fisheries, shark bycatch, stomach contents.

A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

Genetic population structure and recruitment patterns of three sympatric shallow-water penaeid prawns in Ungwana Bay, Kenya, with implication for fisheries management

Penaeid prawns in Ungwana Bay, Kenya, are heavily exploited by artisanal fishers and industrial bottom trawlers. Human activities in mangrove and estuarine areas may affect prawn nursery habitats and influence juvenile recruitment to fished areas, therefore it was important to investigate recruitment patterns in the bay. To test the hypotheses that single genetic stocks exist, we utilised a combination of mtDNA sequence and microsatellite data. Three dominant sympatric species, Penaeus monodon, Fenneropenaeus indicus and Metapenaeus monoceros were targeted. Sample sites were chosen to represent the bulk of fishery activities, and included estuarine juveniles and offshore adults. An exceptionally high mtDNA haplotype diversity, coupled with low nucleotide diversity was observed for all three species and there was no genetic differentiation among sampling sites. Genetic panmixia was confirmed by the microsatellite analyses of P. monodon. Juveniles that recruit to adult populations in Ungwana Bay most likely originate from local estuaries, and conservation of the prawn nursery habitats along the edges of the bay is advocated. Each of the three species represents a single management unit, and the identification of spatial management strategies to mitigate resource-user conflicts should rather consider other ecological and socio-economic factors than the genetic delineation of stocks.

Abundance and Biology of the Langoustine Metanephrops Mozambicus (Nephropidae) on Deep-Water Trawl Grounds in Eastern South Africa

Abundance trends, population structure, and biology of the langoustine Metanephrops mozambicus (Macpherson, 1990) were investigated, based on commercial logbook information (1988-2010; 49 990 trawls) and biological samples collected off eastern South Africa. A generalized linear model (GLM) framework was used to model variation in catch rates, carapace length (CL), sex ratio, and maturation size. Standardized catch rates were inversely related to fishing effort, gradually increasing between 2002 and 2010, when fishing effort was lower. Catch rates were greatest in trawls made at 300 to 599 m depth and between June and December. Langoustines ranged in size from 17.5 to 72.6 mm CL, and the mean CL decreased with increasing depth. Males predominated in November, but equal numbers of males and females were observed in other months. The smallest egg-bearing female had a CL of 33.5 mm, and L50 was estimated at 49.4 mm, based on the incidence of external eggs. Females with freshly spawned eggs were most abundant in August, and the incidence of egg-bearing remained high until March, where after it declined. Eggs about to hatch occurred mainly in May. Growth parameter estimates (L∞ and K) were 65.5 mm and 0.7 year−1 for sexes combined, based on modal progression and the standard von Bertalanffy growth function, and longevity was estimated to be 3-4 years. Combining analyses of fisheries data with biological samples yielded insights into spatio-temporal population trends, as well as the correlation of reproduction and moulting in M. mozambicus.

Patterns in abundance, population structure and biology of knife prawn Haliporoides triarthrus on deep-water trawl grounds off eastern South Africa

The deep-water trawl fishery along the KwaZulu-Natal coast of South Africa targets several crustacean species, with the knife (or pink) prawn Haliporoides triarthrus contributing most of the catch. Logbook data of fishing effort and catch between 1988 and 2010 were used to assess the distribution and abundance of H. triarthrus on fishing grounds. Generalised linear models were used to quantify the effects of year, month and depth on catch rates. Standardised trends indicated a general decline in abundance between 1990 and 1998, followed by an increase between 2001 and 2008. Catch rates peaked in March, and they were highest between 200 and 499 m depth. Biological samples collected during commercial fishing were used to assess size and sex composition, growth rates and reproductive activity of H. triarthrus. Females became larger than males and mean carapace length (CL) varied by month. The youngest female cohort appeared in November (modal CL of 25 mm), and dissipated after two years (39 mm). Sex ratios were equal for all data combined, but fluctuated by month and CL. Few reproductively active females were recorded. Length-based methods and the standard von Bertalanffy growth function were used to estimate growth parameters (L∞ and K) of females (40.6 mm CL and 1.06 y–1) and males (35.2 mm and 1.27 y–1) respectively. Our findings were compared with information on H. triarthrus from Mozambican waters.