Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae)

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Genetic and biophysical models help define marine conservation focus areas

Ecological and environmental variables play a major role in the genetic structure of marine populations, but how oceanography affects their dispersal and associated connectivity remains far from being understood. To account for the effect of different dispersal strategies in terms of pelagic larvae and non-pelagic reproduction, we utilize the power of comparative phylogeographic analyses of five phylogenetically and functionally diverse intertidal species along the west coast of South Africa using population genetics and biophysical models within the Benguela Current system. Some broadcast spawners exhibit genetic panmixia, others show genetic structure similar to direct-developing species, suggesting complex recruitment patterns in rocky shore environments. Patterns of genetic structure do not correspond with pelagic larval competency period, with a broadcast spawning urchin displaying the highest levels of population structure. Biophysical models of larval dispersal reveal mixed dispersal patterns, with the strongest connections in a northward direction following the Benguela Current, yet most modeled species also show the capacity for southward (albeit weaker) migration among some sample localities. Some sites, particularly the most northern areas, show very low levels of potential connectivity. Lastly, we synthesized our results to highlight key areas for the development of Marine Protected Areas (MPAs) that capture the evolutionary patterns of marine species of the west coast and find that the results from our molecular and biophysical analyses are coherent with previous suggestions for a network of protected areas

Multilocus phylogenetic analysis of the genus Atherina (Pisces: Atherinidae)

Sand-smelts are small fishes inhabiting inshore, brackish and freshwater environments and with a distribution in the eastern Atlantic and Mediterranean Sea, extending south into the Indian Ocean. Here, we present a broad phylogenetic analysis of the genus Atherina using three mitochondrial (control region, 12S and 16S) and two nuclear markers (rhodopsin and 2nd intron of S7). Phylogenetic analyses fully support the monophyly of the genus. Two anti-tropical clades were identified, separating the South African Atherina breviceps from the north-eastern Atlantic and Mediterranean Atherina’ species. In European waters, two groups were found. The first clade formed by a well supported species-pair: Atherina presbyter (eastern Atlantic) and Atherina hepsetus (Mediterranean), both living in marine waters; a second clade included Atherina boyeri (brackish and freshwater environments) and two independent lineages of marine punctated and non-punctated fishes, recently proposed as separate species. Sequence divergence values strongly suggest multiple species within the A. boyeri complex

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future

Environmental DNA biomonitoring in biodiversity hotspots: A case study of fishes of the Okavango Delta

The Okavango Delta is the largest freshwater wetland in southern Africa and a recognized biodiversity hotspot and UNESCO World Heritage Site. The region is extremely rich in floral and faunal diversity, including a fish fauna of ~90 species in 15 families, that also support recreational and subsistence fishing. Anthropogenic pressures and invasive species threaten the unique biodiversity and ecosystem services that the Delta provides, necessitating biomonitoring tools that can provide broad community-level diversity insights. Here, we utilize environmental DNA metabarcoding of aquatic eDNA using the MiFish 12S rRNA primers, to investigate fish communities and also sequenced 211 mtDNA 12S barcodes for 74 species across 36 genera of fishes from the region. Metabarcoding recovered 11 of 15 families, with 40 species detected across 23 genera, representing ~50% of known diversity, with the mtDNA 12S fragment able to delineate all genera (except for the cichlid genera Serranochromis and Pharyngochromis that comprised a single clade) and most species, except for some in the Clarias, Enteromius, Labeo, Lacustricola, and Petrocephalus genera. Generally, abundant and wide-spread taxa such as Clarias spp. and Marcusenius altisambesi, amongst others, were often detected in the surveys, with other species, including Zaireichthys kavangoensis, Schilbe intermedius, and Labeo sp. detected less frequently. Dissolved oxygen, temperature, and dissolved organic solids were positively correlated with community diversity, highlighting the influence of environmental factors in shaping fish communities in the region. Further, there was strong variability in the eDNA signal across only 1000 m, suggesting that future surveys need to consider spatio-temporal aspects of sample collection. Our study highlights the potential of eDNA metabarcoding for surveying aquatic biodiversity in the Okavango Delta, particularly within the context of baseline biodiversity inventories, that underpin conservation and management initiatives. As such, we provide a number of recommendations that can help structure future sampling efforts in the region

Evolving coral reef conservation with genetic information

Targeted conservation and management programs are crucial for mitigating anthropogenic threats to declining biodiversity. Although evolutionary processes underpin extant patterns of biodiversity, it is uncommon for resource managers to explicitly consider genetic data in conservation prioritization. Genetic information is inherently relevant to management because it describes genetic diversity, population connectedness, and evolutionary history; thereby typifying their behavioral traits, physiological climate tolerance, evolutionary potential, and dispersal ability. Incorporating genetic information into spatial conservation prioritization starts with reconciling the terminology and techniques used in genetics and conservation science. Genetic data vary widely in analyses and their interpretations can be challenging even for experienced geneticists. Therefore, identifying objectives, decision rules, and implementations in decision support tools specifically for management using genetic data is challenging. Here, we outline a framework for eight genetic system characteristics, their measurement, and how they could be incorporated in spatial conservation prioritization for two contrasting objectives: biodiversity preservation vs maintaining ecological function and sustainable use. We illustrate this framework with an example using data from Tridacna crocea (Lamarck, 1819) (boring giant clam) in the Coral Triangle. We find that many reefs highlighted as conservation priorities with genetic data based on genetic subregions, genetic diversity, genetic distinctness, and connectivity are not prioritized using standard practices. Moreover, different characteristics calculated from the same samples resulted in different spatial conservation priorities. Our results highlight that omitting genetic information from conservation decisions may fail to adequately represent processes regulating biodiversity, but that conservation objectives related to the choice of genetic system characteristics require careful consideration

The application of genetics to marine management and conservation: examples from the Indo-Pacific

Molecular tools and analyses have played pivotal roles in uncovering the processes and patterns of biodiversity in the Indian and Pacific oceans. However, integrating genetic results into management and conservation objectives has been challenging, with few examples that show practical applicability. This review aims to address some of the perceived barriers to an enhanced approach that integrates molecular data into management and conservation goals, by reviewing papers relevant to both conservation and fisheries management in the Indo-Pacific region, particularly with respect to phylogeography, connectivity, and species identification, as well as stock delineation, restoration of depleted wild stocks, mislabeled marine resources and "molecular forensics." We also highlight case studies from each of these areas that illustrate how molecular analyses are relevant to conservation and management in the Indo- Pacific, spanning a variety of vertebrate and invertebrate species. We discuss the application of genetic data to the design and evaluation of the effectiveness of marine protected area networks, stock delineation, and restoration and the usage of exclusion tests and parentage analyses for fisheries management. We conclude that there is a distinct need for increasing public awareness and ownership of genetically unique lineages and, ultimately, the increased inclusion of genetic research into management policy and conservation. Finally, we make a case for the importance of clear and effective communication for promoting public awareness, public ownership, and for achieving conservation goals within the region

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

Phylogeography Unplugged: Comparative Surveys in the Genomic Era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ( unplugged ) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches