Influence of the Benguela Current in genetic sub-structuring of commercially exploited fish species

Oceanographic features such as currents, fronts and upwelling cells have been recognised as possible factors driving population differentiation within species. The Benguela Current is one of the oldest upwelling systems in the world, located off the west coast of Southern Africa, and represents a biogeographical boundary between the Atlantic and Indo-Pacific Oceans. Previous studies have reported the influence of this system in isolating several marine taxa between the two oceans. However, few have been conducted within the Benguela Current boundaries, in order to understand its role in shaping population genetic structure of fish species at a regional level. The present study documents the influence of the Benguela Current oceanographic features on the genetic differentiation, population connectivity and evolutionary history of five coastal fish species (Diplodus capensis, Argyrosomus inodorus, Argyrosomus coronus, Atractoscion aequidens and Lichia amia), and one oceanic pelagic fish species (Thunnus albacares). Results for both mitochondrial and nuclear marker variation in all coastal species revealed a similar geographical pattern of population genetic structuring despite distinct differences in life history features. The oceanic species exhibited shallow population differentiation between Atlantic and Indian Oceans. For coastal species, different depths of differentiation were observed, ranging from speciation events (A. aequidens, A. coronus and A. japonicus) to shallow structuring (A. inodorus and T. albacares). Furthermore, in these cases, population structures were coincident with the Benguela Current oceanographic features, suggesting that the system may represent a vicariant barrier to dispersal of coastal fish species. Congruence between mitochondrial and nuclear markers suggests that population isolation was not a single historical event, but has persisted over large timescales and is still active. The existence of cryptic speciation events, and the high levels of genetic diversity and differentiation documented make the Benguela Current a natural laboratory to study evolutionary mechanisms shaping biodiversity and genetic population structure of marine fish species

Incipient genetic isolation of a temperate migratory coastal Sciaenid fish (Argyrosomus inodorus) within the Benguela Cold Current system

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

Population Connectivity and Phylogeography of a Coastal Fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current Region: Evidence of an Ancient Vicariant Event

Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φ (ST) = 0.902, microsatellite F (ST) = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species

Molecular genetic, life-history and morphological variation in a coastal warm-temperature sciaenid fish:Evidence for an upwelling-driven speciation event

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)

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

All data is available via data Dryad : Dryad doi https://doi.org/10.5061/dryad.z08kprrmw.DATA AVAILABILITY : Data will be made available on request.In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259–11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.The National Research Foundation and the Oppenheimer Foundation.https://www.elsevier.com/locate/ympevhj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species

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

Molecular ecology meets systematic conservation planning

Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the ‘why’) to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the ‘how’), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.Environment and Climate Change Canada (ECCC); Nature Conservancy of Canada; NERC Wallacea Programme Strategic Grant; an individual research contract by Fundação para a Ciência e Tecnologia; the National Research Foundation; a European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement.https://www.cell.com/trends/ecology-evolution/homeam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Ocean warming favours a northern Argyrosomus species over its southern congener, whereas preliminary metabolic evidence suggests that hybridization may promote their adaptation

DATA AVAILABILITY : The data underlying this article are available in the article and in its online supplementary material.Anthropogenic-induced climate change is having profound impacts on aquatic ecosystems, and the resilience of fish populations will be determined by their response to these impacts. The northern Namibian coast is an ocean warming hotspot, with temperatures rising faster than the global average. The rapid warming in Namibia has had considerable impacts on marine fauna, such as the southern extension of the distribution of Argyrosomus coronus from southern Angola into northern Namibian waters, where it now overlaps and hybridizes with the closely related Namibian species, A. inodorus. Understanding how these species (and their hybrids) perform at current and future temperatures is vital to optimize adaptive management for Argyrosomus species. Intermittent flow-through respirometry was used to quantify standard and maximum metabolic rates for Argyrosomus individuals across a range of temperatures. The modelled aerobic scope (AS) of A. inodorus was notably higher at cooler temperatures (12, 15, 18 and 21°C) compared with that of A. coronus, whereas the AS was similar at 24°C. Although only five hybrids were detected and three modelled, their AS was in the upper bounds of the models at 15, 18 and 24°C. These findings suggest that the warming conditions in northern Namibia may increasingly favour A. coronus and promote the poleward movement of the leading edge of their southern distribution. In contrast, the poor aerobic performance of both species at cold temperatures (12°C) suggests that the cold water associated with the permanent Lüderitz Upwelling Cell in the south may constrain both species to central Namibia. This is most concerning for A. inodorus because it may be subjected to a considerable coastal squeeze.The National Research Foundation—National Commission on Research Science and Technology, South Africa—Namibia Agreement on Cooperation in Science and Technology.https://academic.oup.com/conphysam2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-14:Life below wate