Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.

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Short-scale temporal variability of physical, biological and biogeochemical processes in the NW Mediterranean Sea: an introduction

Biogeosciences Discussions ◽

10.5194/bgd-5-5233-2008 ◽

2008 ◽

Vol 5 (6) ◽

pp. 5233-5251 ◽

Cited By ~ 6

Author(s):

V. Andersen ◽

M. Goutx ◽

L. Prieur ◽

J. R. Dolan

Keyword(s):

Mediterranean Sea ◽

Time Course ◽

Special Section ◽

Zooplankton Community ◽

Spatial Dimension ◽

Western Mediterranean ◽

Major Product ◽

Data Set ◽

Nw Mediterranean ◽

Nw Mediterranean Sea

Abstract. In the framework of the PROOF-PECHE project (www.obs-vlfr.fr/proof/vt/op/ec/peche/pec.htm) a multi-disciplinary team performed experiments and collected samples during the DYNAPROC2 cruise aboard the RV Thalassa from September to October in 2004. The cruise provided data on the functioning of the pelagic food web by sampling over a month long period in the NW Mediterranean Sea at a fixed station subject to weak horizontal advection currents during a period of hydrological stability. This paper describes the background of the cruise and provides an overview of the results derived from the campaign which constitute the special section. The major objective of the cruise was to assess the relative importance and variability of the pathways of carbon in the open ocean. Intensive sampling through 4 periods of 5 days each was accomplished a site near the DYFAMED time-series site. The site was near stable in terms of hydrodynamics as there was some evidence of an intrusion of low-salinity coastal water. One major product of the cruise was a comprehensive data set data set acquired by sampling at high frequencies (ranging from every 3, 6, 12 and/or 24 h) and over a vertical spatial dimension so far never explored (0–1000 m) in the North Western Mediterranean Sea. Parameters investigated included the biochemical composition of DOM (lipids), and the structure of bacterial communities, phytoplankton and zooplankton community compositions and abundances, as well as zooplankton metabolism, and particulate organic carbon fluxes. Nearly all the parameters described in this section, as well as reports appearing elsewhere, showed time-course variabilities of similar magnitude to those known from a previous study of the spring-summer seasonal transition, a period of marked hydrological change, at the same study site.

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Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

Frontiers in Plant Science ◽

10.3389/fpls.2021.700161 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaojuan Wang ◽

Hua Rao ◽

Jianxiang Ma ◽

Xiaodan Chen ◽

Guanglin Li ◽

...

Keyword(s):

Stress Tolerance ◽

Local Adaptation ◽

Molecular Mechanisms ◽

Natural Populations ◽

Northern China ◽

Genomic Variation ◽

Forward Genetics ◽

Local Adaptations ◽

Salt Cress ◽

Eutrema Salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

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Biogeography of acoustic biodiversity of NW Mediterranean coralligenous reefs

Scientific Reports ◽

10.1038/s41598-021-96378-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lucia Di Iorio ◽

Manon Audax ◽

Julie Deter ◽

Florian Holon ◽

Julie Lossent ◽

...

Keyword(s):

Large Scale ◽

Spatial Scales ◽

Western Mediterranean ◽

Ecosystem Functions ◽

Marine Biodiversity ◽

Predator Species ◽

The North ◽

Mediterranean Habitats ◽

Geographical Regions ◽

Nw Mediterranean

AbstractMonitoring the biodiversity of key habitats and understanding the drivers across spatial scales is essential for preserving ecosystem functions and associated services. Coralligenous reefs are threatened marine biodiversity hotspots that are challenging to monitor. As fish sounds reflect biodiversity in other habitats, we unveiled the biogeography of coralligenous reef sounds across the north-western Mediterranean using data from 27 sites covering 2000 km and 3 regions over a 3-year period. We assessed how acoustic biodiversity is related to habitat parameters and environmental status. We identified 28 putative fish sound types, which is up to four times as many as recorded in other Mediterranean habitats. 40% of these sounds are not found in other coastal habitats, thus strongly related to coralligenous reefs. Acoustic diversity differed between geographical regions. Ubiquitous sound types were identified, including sounds from top-predator species and others that were more specifically related to the presence of ecosystem engineers (red coral, gorgonians), which are key players in maintaining habitat function. The main determinants of acoustic community composition were depth and percentage coverage of coralligenous outcrops, suggesting that fish-related acoustic communities exhibit bathymetric stratification and are related to benthic reef assemblages. Multivariate analysis also revealed that acoustic communities can reflect different environmental states. This study presents the first large-scale map of acoustic fish biodiversity providing insights into the ichthyofauna that is otherwise difficult to assess because of reduced diving times. It also highlights the potential of passive acoustics in providing new aspects of the correlates of biogeographical patterns of this emblematic habitat relevant for monitoring and conservation.

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From Genetics to Genomics of Epilepsy

Neurology Research International ◽

10.1155/2012/876234 ◽

2012 ◽

Vol 2012 ◽

pp. 1-18 ◽

Cited By ~ 7

Author(s):

Silvio Garofalo ◽

Marisa Cornacchione ◽

Alfonso Di Costanzo

Keyword(s):

Dna Sequencing ◽

Dna Microarrays ◽

Molecular Cytogenetics ◽

Entire Genome ◽

Sequencing Technologies ◽

Genomic Approach ◽

Molecular Karyotype ◽

High Throughput Dna Sequencing ◽

Laboratory Technology ◽

Near Future

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

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The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

10.1101/340992 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ahmed R. Hasan ◽

Rob W. Ness

Keyword(s):

Chlamydomonas Reinhardtii ◽

Recombination Rate ◽

Natural Populations ◽

Gc Content ◽

Sexual Cycle ◽

Rate Variation ◽

Effective Population ◽

Entire Genome ◽

Recombination Rate Variation ◽

Linked Selection

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.

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Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants

10.1101/385377 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sara Marin ◽

Juliette Archambeau ◽

Vincent Bonhomme ◽

Mylène Lascoste ◽

Benoit Pujol

Keyword(s):

Local Adaptation ◽

Natural Populations ◽

Common Garden ◽

Global Scale ◽

Structured Populations ◽

Adaptive Divergence ◽

Adaptation To Climate Change ◽

Phenotypic Differentiation ◽

Multiple Populations ◽

Environmental Demand

ABSTRACTPhenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.

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Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

10.21203/rs.3.rs-35039/v3 ◽

2020 ◽

Author(s):

Erica Nielsen ◽

Romina Henriques ◽

Maria Beger ◽

Robert Toonen ◽

Sophie von der Heyden

Keyword(s):

Global Change ◽

Outlier Detection ◽

Genomic Variation ◽

Sea Surface ◽

Environmental Drivers ◽

Comparative Approach ◽

Evolutionary Potential ◽

Environmental Selection ◽

Outlier Loci ◽

Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

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Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

10.21203/rs.3.rs-35039/v1 ◽

2020 ◽

Author(s):

Erica Nielsen ◽

Romina Henriques ◽

Maria Beger ◽

Robert Toonen ◽

Sophie von der Heyden

Keyword(s):

Global Change ◽

Outlier Detection ◽

Genomic Variation ◽

Sea Surface ◽

Environmental Drivers ◽

Comparative Approach ◽

Evolutionary Potential ◽

Environmental Selection ◽

Outlier Loci ◽

Isolation By Environment

Abstract Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare the dominant environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin ( Parechinus angulosus ), Common shore crab ( Cyclograpsus punctatu s), and Granular limpet ( Scutellastra granularis ). Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus . Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus , but not for C. punctatus . Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses better predict evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

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Intraspecific genomic variation and local adaptation in a young hybrid species

10.1101/732313 ◽

2019 ◽

Author(s):

Angélica Cuevas ◽

Mark Ravinet ◽

Glenn-Peter Sætre ◽

Fabrice Eroukhmanoff

Keyword(s):

Genetic Variation ◽

Local Adaptation ◽

Climatic Variation ◽

Genomic Variation ◽

Population Divergence ◽

Parent Species ◽

Evolutionary Potential ◽

Variable Environment ◽

Hybrid Species ◽

Species Population

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

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