Genetic population structure and tools for the management of European sprat (Sprattus sprattus)

2020 ◽  
Vol 77 (6) ◽  
pp. 2134-2143
Author(s):  
Niall J McKeown ◽  
Piera Carpi ◽  
Joana F Silva ◽  
Amy J E Healey ◽  
Paul W Shaw ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Population Connectivity ◽  
Ne Atlantic ◽  
Genetic Population ◽  
Sprattus Sprattus ◽  
Population Average ◽  
Outlier Loci ◽  
Baltic Population ◽  
Assisted Management ◽  
Mixed Stock

Abstract This study used RAD-seq-derived SNPs to explore population connectivity, local adaptation, and individual assignment in European sprat (Sprattus sprattus) and inform the alignment of management units with biological processes. FST, clustering, and outlier analyses support a genetically cohesive population spanning the Celtic Sea-English Channel-North Sea-Kattegat (NE Atlantic) region. The lack of structure among the NE Atlantic samples indicates connectivity across current management boundaries. However, the assumption of demographic panmixia is cautioned against unless verified by a multidisciplinary approach. The data confirm high genetic divergence of a Baltic population (average FST vs. NE Atlantic samples = 0.051) with signatures compatible with local adaptation in the form of outlier loci, some of which are shown to occur within exonic regions. The outliers permit diagnostic assignment of individuals between the NE Atlantic and Baltic populations and thus represent a “reduced panel” of markers for monitoring a potential mixed stock fishery within the western Baltic. Overall, this study provides information that may help refine spatial management boundaries of sprat and resources for genetic-assisted management.

scholarly journals Genomic analysis reveals multiple mismatches between biological and management units in yellowfin tuna (Thunnus albacares)

2018 ◽  
Vol 75 (6) ◽  
pp. 2145-2152 ◽  
Author(s):  
Rachel B Mullins ◽  
Niall J McKeown ◽  
Warwick H H Sauer ◽  
Paul W Shaw
Keyword(s):  
Indian Ocean ◽  
Genomic Analysis ◽  
Yellowfin Tuna ◽  
Thunnus Albacares ◽  
Management Units ◽  
Spawning Site ◽  
Asymmetric Dispersal ◽  
Outlier Loci ◽  
The Indian Ocean ◽  
Mixed Stock

Abstract 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.

scholarly journals Evidence for divergent selection and spatial differentiation in a putative zona pellucida gene is indicative of local adaptation in Pacific cod

2021 ◽  
Author(s):  
Ingrid Spies ◽  
Daniel Drinan ◽  
Eleni Petrou ◽  
Rory Spurr ◽  
Theodore Hartinger ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Zona Pellucida ◽  
Atlantic Cod ◽  
Spatial Differentiation ◽  
Marine Species ◽  
Genomic Region ◽  
Divergent Selection ◽  
Pacific Cod ◽  
Sperm Binding ◽  
Outlier Loci

Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist. The study of highly differentiated outlier loci can provide information on how genetic variation might contribute to local adaptation. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod was previously identified in Pacific cod populations as a high differentiation outlier. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, but the function of this genomic region is not understood in Pacific cod. We sequenced a 544 bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. Here we show that ZP3 haplotypes exhibit strong spatial structure and there is evidence for divergent selection at this locus in samples collected from the Bering Sea region. The potential for adaptation to different thermal regimes is particularly relevant given that Pacific cod have demonstrated high natural mortality during recent ocean warming events.

scholarly journals Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex

2021 ◽  
Author(s):  
Deborah Leigh ◽  
Heidi Lischer ◽  
Frédéric Guillaume ◽  
Christine Grossen ◽  
Torsten Günther
Keyword(s):  
Local Adaptation ◽  
Genetic Drift ◽  
False Positive ◽  
Conservation Management ◽  
Detection Methods ◽  
True Positive ◽  
Alpine Ibex ◽  
Snp Data ◽  
Outlier Loci ◽  
Management Plans

Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role in species management plans, assessments of adaptive capacity, and looking for responses to climate change. Yet, the allele frequency changes exploited in selection detection methods are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods have across bottlenecked populations. In this study, simulations were used to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). The meticulously recorded demographic history of the Alpine ibex was used to generate comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in outliers identified in empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more methods were combined. True positive rates were consistently low and became negligible with increased stringency. Despite finding many outlier loci in the empirical Alpine ibex SNPs, none could be distinguished from genetic drift-driven false positives. Unfortunately, the low true positive rate also prevents the exclusion of recent local adaptation within the Alpine ibex. The baselines and stringent approach outlined here should be applied to other bottlenecked species to ensure the risk of false positive, or negative, signals of selection are accounted for in conservation management plans.

scholarly journals Novel Insights Into the Genetic Population Connectivity of Transient Whale Sharks (Rhincodon typus) in Pacific Panama Provide Crucial Data for Conservation Efforts

2021 ◽  
Vol 8 ◽  
Author(s):  
Héctor M. Guzmán ◽  
Caitlin E. Beaver ◽  
Edgardo Díaz-Ferguson
Keyword(s):  
Genetic Diversity ◽  
Gulf Of California ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Population Connectivity ◽  
Region Gene ◽  
Genetic Population ◽  
Regional Patterns ◽  
Rhincodon Typus ◽  
Whale Sharks

The whale shark (Rhincodon typus) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity (Hd = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2, were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3, PTY4, and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

scholarly journals Depletion of coastal predatory fish sub-stocks coincided with the largest sea urchin grazing event observed in the NE Atlantic

AMBIO ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 163-173 ◽  
Author(s):  
Kjell Magnus Norderhaug ◽  
Kjell Nedreaas ◽  
Mats Huserbråten ◽  
Even Moland
Keyword(s):  
Sea Urchin ◽  
Sea Urchins ◽  
Local Population ◽  
Population Connectivity ◽  
Strongylocentrotus Droebachiensis ◽  
Predatory Fish ◽  
Ne Atlantic ◽  
Laminaria Hyperborea ◽  
Fish Stocks ◽  
Coastal Fisheries

AbstractIn this contribution, we propose fishery driven predator release as the cause for the largest grazing event ever observed in the NE Atlantic. Based on the evolving appreciation of limits to population connectivity, published and previously unpublished data, we discuss whether overfishing caused a grazer bloom of the sea urchin (Strongylocentrotus droebachiensis) resulting in overgrazing of more than 2000 km2 kelp (Laminaria hyperborea) forest along Norwegian and Russian coasts during the 1970 s. We show that coastal fisheries likely depleted predatory coastal fish stocks through modernization of fishing methods and fleet. These fish were important predators on urchins and the reduction coincided with the urchin bloom. From this circumstantial evidence, we hypothesize that coastal predatory fish were important in regulating sea urchins, and that a local population dynamics perspective is necessary in management of coastal ecosystems.

scholarly journals Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

2019 ◽  
Vol 110 (6) ◽  
pp. 707-719 ◽  
Author(s):  
Jared J Homola ◽  
Cynthia S Loftin ◽  
Kristina M Cammen ◽  
Caren C Helbing ◽  
Inanc Birol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Parallel Evolution ◽  
Urban Environments ◽  
Wood Frogs ◽  
Urban Populations ◽  
Genome Wide ◽  
Outlier Loci ◽  
Selection Factors ◽  
Fst Outlier

Abstract Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

scholarly journals Genetic population structure constrains local adaptation in sticklebacks

2021 ◽  
Author(s):  
Petri Kemppainen ◽  
Zitong Li ◽  
Pasi Rastas ◽  
Ari Löytynoja ◽  
Bohao Fang ◽  
...  
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Genetic Population Structure ◽  
Genetic Population

scholarly journals Seascape genomics reveals population structure and local adaptation in a widespread coral reef snail, Coralliophila violacea (Kiener, 1836)

2021 ◽  
Author(s):  
Sara E. Simmonds ◽  
Samantha H. Cheng ◽  
Allison L. Fritts-Penniman ◽  
Gusti Ngurah Mahardika ◽  
Paul H. Barber
Keyword(s):  
Coral Reef ◽  
Local Adaptation ◽  
Geographic Range ◽  
Sea Surface ◽  
Population Divergence ◽  
Evolutionary Divergence ◽  
Coral Host ◽  
Ocean Climate ◽  
Outlier Loci ◽  
Annual Range

Local adaptation to different environments may reinforce neutral evolutionary divergence, especially in populations in the periphery of a species' geographic range. Seascape genomics (high-throughput genomics coupled with ocean climate databases) facilitates the exploration of neutral and adaptive variation in concert, developing a clearer picture of processes driving local adaptation in marine populations. This study used a seascape genomics approach to test the relative roles of neutral and adaptive processes shaping population divergence of a widespread coral reef snail, Coralliophila violacea. We collected C. violacea from colonies of their coral host (Porites spp.) at ten locations spanning a large portion of their geographic range. We used RAD-seq to investigate possible local adaptation via genetic-environmental associations with five ocean climate variables. Four genetic partitions were concordant with regions previously observed in mtDNA (Indian Ocean, Coral Triangle, and Hawaiian Islands), with the addition of Vietnam and varying isolation and admixture levels. We identified outlier loci (FDR = 0.10, N = 72) among individual localities and between regions (FDR = 0.10, N = 34), suggesting that some loci are putatively under divergent selection. Association analyses showed that the two strongest drivers of local adaptation were the annual range and mean of sea surface temperature. Populations that experience lower sea surface temperatures at the periphery of C. violacea's geographic range drive these associations. Our results show that local adaptation to different environments likely reinforces neutral divergence, especially in peripheral populations.

scholarly journals High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments

2016 ◽  
Author(s):  
Clément Goubert ◽  
Hélène Henri ◽  
Guillaume Minard ◽  
Claire Valiente Moro ◽  
Patrick Mavingui ◽  
...  
Keyword(s):  
Transposable Element ◽  
Local Adaptation ◽  
Adaptive Evolution ◽  
High Throughput ◽  
Asian Tiger Mosquito ◽  
Virtual Absence ◽  
Asian Tiger ◽  
Outlier Loci ◽  
Tiger Mosquito

AbstractInvasive species represent unique opportunities to evaluate the role of local adaptation during colonization of new environments. Among these species, the Asian tiger mosquito, Aedes albopictus, is a threatening vector of several human viral diseases, including dengue and chikungunya, and raises concerns about the Zika fever. Its broad presence in both temperate and tropical environments has been considered the reflection of great “ecological plasticity”. However, no study has been conducted to assess the role of adaptive evolution in the ecological success of Ae. albopictus at the molecular level. In the present study, we performed a genomic scan to search for potential signatures of selection leading to local adaptation in one-hundred-forty field-collected mosquitoes from native populations of Vietnam and temperate invasive populations of Europe. High-throughput genotyping of transposable element insertions led to the discovery of more than 120 000 polymorphic loci, which, in their great majority, revealed a virtual absence of structure between the bio-geographic areas. Nevertheless, 92 outlier loci showed a high level of differentiation between temperate and tropical populations. The majority of these loci segregates at high insertion frequencies among European populations, indicating that this pattern could have been caused by recent adaptive evolution events in temperate areas. An analysis of the overlapping and neighboring genes highlighted several candidates, including diapause, lipid and juvenile hormone pathways.

Sign in / Sign up

Export Citation Format

Share Document