scholarly journals Separate the wheat from the chaff: genomic scan for local adaptation in the red coralCorallium rubrum

2018 ◽  
Author(s):  
M. Pratlong ◽  
A. Haguenauer ◽  
K. Brener ◽  
G. Mitta ◽  
E. Toulza ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Environmental Gradient ◽  
Environmental Gradients ◽  
High Rate ◽  
Corallium Rubrum ◽  
Red Coral ◽  
Geographical Regions ◽  
Adaptive Processes ◽  
Tests Of Association ◽  
Candidate Loci

ABSTRACTGenomic data allow an in-depth and renewed study of local adaptation. The red coral (Corallium rubrum, Cnidaria) is a highly genetically structured species and a promising model for the study of adaptive processes along an environmental gradient. Here, we used RAD-Sequencing in order to study the vertical genetic structure of this species and to search for signals of local adaptation to depth and thermal regime in the red coral. Previous studies have shown different thermotolerance levels according to depth in this species which could correspond to genetic or environmental differences. We designed a sampling scheme with six pairs of ‘shallow vs deep’ populations distributed in three geographical regions as replicates. Our results showed significant differentiation among locations and among sites separated by around 20 m depth. The tests of association between genetics and environment allowed the identification of candidate loci under selection but with a potentially high rate of false positive. We discuss the methodological obstacles and biases encountered for the detection of selected loci in such a strongly genetically structured species. On this basis, we also discuss the significance of the candidate loci for local adaptation detected in each geographical region and the evolution of red coral populations along environmental gradients.A colony of red coral,Corallium rubrum, near Marseille. Photo: F. Zuberer / OSU Pythéas / CNRS

scholarly journals The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

2015 ◽  
Vol 15 (5) ◽  
pp. 1205-1215 ◽  
Author(s):  
M. Pratlong ◽  
A. Haguenauer ◽  
O. Chabrol ◽  
C. Klopp ◽  
P. Pontarotti ◽  
...  
Keyword(s):  
Population Genetics ◽  
Local Adaptation ◽  
Adaptation Studies ◽  
Corallium Rubrum ◽  
Red Coral

scholarly journals Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum

2021 ◽  
Vol 1 ◽  
pp. 1-None
Author(s):  
M. Pratlong ◽  
A. Haguenauer ◽  
K. Brener ◽  
G. Mitta ◽  
E. Toulza ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Corallium Rubrum ◽  
Red Coral

Colonization of plastic debris by the long-lived precious red coral Corallium rubrum: New insights on the “plastic benefits” paradox

2021 ◽  
Vol 165 ◽  
pp. 112104
Author(s):  
Laura Carugati ◽  
Lorenzo Bramanti ◽  
Bruna Giordano ◽  
Lucia Pittura ◽  
Rita Cannas ◽  
...  
Keyword(s):  
Plastic Debris ◽  
Corallium Rubrum ◽  
Red Coral

Landscape genomics and selection signatures of local adaptation of Eritrean indigenous cattle along environmental gradients

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
S. Goitom ◽  
Mathew G. Gicheha ◽  
Francis K. Njonge ◽  
Ngeno Kiplangat
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Selection Signatures ◽  
Indigenous Cattle ◽  
Landscape Genomics

scholarly journals Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Jeroen A. J. M. van de Water ◽  
Rémy Melkonian ◽  
Howard Junca ◽  
Christian R. Voolstra ◽  
Stéphanie Reynaud ◽  
...  
Keyword(s):  
Microbial Community ◽  
Geographic Scale ◽  
Corallium Rubrum ◽  
Red Coral

scholarly journals 3D Photogrammetry Modeling Highlights Efficient Reserve Effect Apparition After 5 Years and Stillness After 40 for Red Coral (Corallium rubrum) Conservation in French MPAs

2021 ◽  
Vol 8 ◽  
Author(s):  
Justine Richaume ◽  
Adrien Cheminée ◽  
Pierre Drap ◽  
Patrick Bonhomme ◽  
Frederic Cadene ◽  
...  
Keyword(s):  
National Park ◽  
Local Level ◽  
Cost Effective ◽  
Maximum Height ◽  
Time Step ◽  
Mechanical Destruction ◽  
Corallium Rubrum ◽  
Red Coral ◽  
Significant Difference ◽  
Precautionary Measures

Imaging the marine environment is more and more useful to understand relationships between species, as well as natural processes. Developing photogrammetry allowed the use of 3D measuring to study populations dynamics of sessile organisms at various scales: from colony to population. This study focuses on red coral (Corallium rubrum), as known as precious coral. Metrics measured at a colony scale (e.g., maximum height, diameter and number of branches) allowed population understanding and a comparison between an old (Cerbère-Banyuls reserve) vs. a new (Calanques National Park) MPA. Our results suggested a 5-year time step allows the appearance of a significant difference between populations inside vs. outside the Calanques National Park no-take zones. Red coral colonies were taller and had more branches inside no-take zones. A significant difference was still observable for the populations inside the Cerbère-Banyuls reserve after 40 years of protection, reflecting the sustainability and effectiveness of precautionary measures set by the reserve. The impacts at the local level (mechanical destruction) and those presumed to occur via global change (climatic variations) underline the need to develop strategies both to follow the evolutions of red coral populations but also to understand their resilience. Photogrammetry induced modeling is a time and cost effective as well as non-invasive method which could be used to understand population dynamics at a seascape scale on coralligenous reefs.

scholarly journals Local adaptation mediated niche expansion in correlation with genetic richness

2021 ◽  
Author(s):  
Masaomi Kurokawa ◽  
Issei Nishimura ◽  
Bei-Wen YING
Keyword(s):  
Escherichia Coli ◽  
Local Adaptation ◽  
High Throughput ◽  
Experimental Evolution ◽  
Environmental Gradient ◽  
Growth Curves ◽  
Quantitative Relationship ◽  
Central Issue ◽  
Wild Type ◽  
Niche Expansion

As a central issue in evolution and ecology, the quantitative relationship among the genome, adaptation and the niche was investigated. Local adaptation of five Escherichia coli strains carrying either the wild-type genome or reduced genomes was achieved by experimental evolution. A high-throughput fitness assay of the ancestor and evolved populations across an environmental gradient of eight niches resulted in a total of 80 fitness curves generated from 2,220 growth curves. Further analyses showed that the increases in both local adaptiveness and niche broadness were negatively correlated with genetic richness. Local adaptation caused common niche expansion, whereas niche expansion for generality or speciality was decided by genetic richness. The order of the mutations accumulated stepwise was correlated with the magnitude of the fitness increase attributed to mutation accumulation. Pre-adaptation probably participated in coordination among genetic richness, local adaptation and niche expansion.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

scholarly journals Do Differences in Latitudinal Distributions of Species and Organelle Haplotypes Reflect Thermal Reaction Norms Within the Emiliania/Gephyrocapsa Complex?

2021 ◽  
Vol 8 ◽  
Author(s):  
Peter von Dassow ◽  
Paula Valentina Muñoz Farías ◽  
Sarah Pinon ◽  
Esther Velasco-Senovilla ◽  
Simon Anguita-Salinas
Keyword(s):  
Local Adaptation ◽  
Coastal Upwelling ◽  
Environmental Gradients ◽  
Reaction Norm ◽  
Emiliania Huxleyi ◽  
Thermal Reaction ◽  
Reaction Norms ◽  
Thermal Niche ◽  
Significant Difference ◽  
The Difference

The cosmopolitan phytoplankter Emiliania huxleyi contrasts with its closest relatives that are restricted to narrower latitudinal bands, making it interesting for exploring how alternative outcomes in phytoplankton range distributions arise. Mitochondrial and chloroplast haplogroups within E. huxleyi are shared with their closest relatives: Some E. huxleyi share organelle haplogroups with Gephyrocapsa parvula and G. ericsonii which inhabit lower latitudes, while other E. huxleyi share organelle haplogroups with G. muellerae, which inhabit high latitudes. We investigated whether the phylogeny of E. huxleyi organelles reflects environmental gradients, focusing on the Southeast Pacific where the different haplogroups and species co-occur. There was a high congruence between mitochondrial and chloroplast haplogroups within E. huxleyi. Haplogroup II of E. huxleyi is negatively associated with cooler less saline waters, compared to haplogroup I, both when analyzed globally and across temporal variability at the small special scale of a center of coastal upwelling at 30° S. A new mitochondrial haplogroup Ib detected in coastal Chile was associated with warmer waters. In an experiment focused on inter-species comparisons, laboratory-determined thermal reaction norms were consistent with latitudinal/thermal distributions of species, with G. oceanica exhibiting warm thermal optima and tolerance and G. muellerae exhibiting cooler thermal optima and tolerances. Emiliania huxleyi haplogroups I and II tended to exhibit a wider thermal niche compared to the other Gephyrocapsa, but no differences among haplogroups within E. huxleyi were found. A second experiment, controlling for local adaptation and time in culture, found a significant difference between E. huxleyi haplogroups. The difference between I and II was of the expected sign, but not the difference between I and Ib. The differences were small (≤1°C) compared to differences reported previously within E. huxleyi by local adaptation and even in-culture evolution. Haplogroup Ib showed a narrower thermal niche. The cosmopolitanism of E. huxleyi might result from both wide-spread generalist phenotypes and specialist phenotypes, as well as a capacity for local adaptation. Thermal reaction norm differences can well explain the species distributions but poorly explain distributions among mitochondrial haplogroups within E. huxleyi. Perhaps organelle haplogroup distributions reflect historical rather than selective processes.

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