scholarly journals Integrating population genomics and biophysical models towards evolutionary-based fisheries management

2018 ◽  
Vol 75 (4) ◽  
pp. 1245-1257 ◽  
Author(s):  
Miguel Baltazar-Soares ◽  
Hans-Harald Hinrichsen ◽  
Christophe Eizaguirre
Keyword(s):  
Fisheries Management ◽  
Population Genomics ◽  
Adaptive Potential ◽  
Adaptive Genetic Variation ◽  
Evolutionary Potential ◽  
Management Tools ◽  
Species Response ◽  
Selective Pressures ◽  
Connectivity Patterns ◽  
Biophysical Modelling

Abstract Overfishing and rapid environmental shifts pose severe challenges to the resilience and viability of marine fish populations. To develop and implement measures that enhance species’ adaptive potential to cope with those pressures while, at the same time, ensuring sustainable exploitation rates is part of the central goal of fisheries management. Here, we argue that a combination of biophysical modelling and population genomic assessments offer ideal management tools to define stocks, their physical connectivity and ultimately, their short-term adaptive potential. To date, biophysical modelling has often been confined to fisheries ecology whereas evolutionary hypotheses remain rarely considered. When identified, connectivity patterns are seldom explored to understand the evolution and distribution of adaptive genetic variation, a proxy for species’ evolutionary potential. Here, we describe a framework that expands on the conventional seascape genetics approach by using biophysical modelling and population genomics. The goals are to identify connectivity patterns and selective pressures, as well as putative adaptive variants directly responding to the selective pressures and, ultimately, link both to define testable hypotheses over species response to shifting ecological conditions and overexploitation.

Molecular basis of adaptive evolution of sperm motility involved in in vivo fertilization of terrestrial animals

Impact ◽  
2020 ◽  
Vol 2020 (6) ◽  
pp. 73-75
Author(s):  
Akihiko Watanabe
Keyword(s):  
Sexual Reproduction ◽  
Sperm Motility ◽  
Asexual Reproduction ◽  
Acrosome Reaction ◽  
Sperm Morphology ◽  
Adaptive Potential ◽  
Selective Pressures ◽  
The Face ◽  
Genetic Profiles

One of the unifying traits of life on this planet is reproduction, or life's ability to make copies of itself. The mode of reproduction has evolved over time, having almost certainly begun with simple asexual reproduction when the ancestral single celled organism divided into two. Since these beginnings' life has tried out numerous strategies, and perhaps one of the most important and successful has been sexual reproduction. This form of reproduction relies on the union of gametes, otherwise known as sperm and egg. Evolutionarily, sexual reproduction allows for greater adaptive potential because the genes of two unique individuals have a chance to recombine and mix in order to produce a new individual. Unlike asexual reproduction which produces genetically-identical clones of the parent individual, sex produces offspring with novel genes and combinations of genes. Therefore, in the face of new selective pressures there is a higher chance that one of these novel genetic profiles will produce an adaptation that is advantageous in the new circumstances. Dr Akihiko Watanabe is a reproductive biologist based in the Department of Biology, Faculty of Science Yamagata University in Japan, he is currently working on three research projects; a comparative study on the signalling pathways for inducing sperm motility and acrosome reaction in amphibians, the mechanism behind the adaptive modification of sperm morphology and motility, and the origin of sperm motility initiating substance (SMIS).

scholarly journals Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andras Balogh ◽  
Lam Ngo ◽  
Kirk S. Zigler ◽  
Groves Dixon
Keyword(s):  
Genetic Divergence ◽  
Population Genomics ◽  
Sample Sizes ◽  
Dense Region ◽  
Evolutionary Processes ◽  
Cumberland Plateau ◽  
Selective Pressures ◽  
Genome Wide ◽  
Good Sample ◽  
Limited Dispersal

Abstract Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.

scholarly journals Effective fisheries management instrumental in improving fish stock status

2020 ◽  
Vol 117 (4) ◽  
pp. 2218-2224 ◽  
Author(s):  
Ray Hilborn ◽  
Ricardo Oscar Amoroso ◽  
Christopher M. Anderson ◽  
Julia K. Baum ◽  
Trevor A. Branch ◽  
...  
Keyword(s):  
Fisheries Management ◽  
Marine Fish ◽  
Food System ◽  
Fish Stock ◽  
Management Tools ◽  
Fish Stocks ◽  
Fisheries Science ◽  
The World ◽  
Fish Catch ◽  
Intensively Managed

Marine fish stocks are an important part of the world food system and are particularly important for many of the poorest people of the world. Most existing analyses suggest overfishing is increasing, and there is widespread concern that fish stocks are decreasing throughout most of the world. We assembled trends in abundance and harvest rate of stocks that are scientifically assessed, constituting half of the reported global marine fish catch. For these stocks, on average, abundance is increasing and is at proposed target levels. Compared with regions that are intensively managed, regions with less-developed fisheries management have, on average, 3-fold greater harvest rates and half the abundance as assessed stocks. Available evidence suggests that the regions without assessments of abundance have little fisheries management, and stocks are in poor shape. Increased application of area-appropriate fisheries science recommendations and management tools are still needed for sustaining fisheries in places where they are lacking.

scholarly journals A typology of fisheries management tools: using experience to catalyse greater success

2016 ◽  
Vol 18 (3) ◽  
pp. 543-570 ◽  
Author(s):  
Elizabeth R Selig ◽  
Kristin M Kleisner ◽  
Oren Ahoobim ◽  
Freddy Arocha ◽  
Annabelle Cruz-Trinidad ◽  
...  
Keyword(s):  
Fisheries Management ◽  
Management Tools

Primacy of bottom-up effects on a butterflyfish assemblage

2016 ◽  
Vol 67 (8) ◽  
pp. 1175 ◽  
Author(s):  
Susannah M. Leahy ◽  
Garry R. Russ ◽  
Rene A. Abesamis
Keyword(s):  
Climate Change ◽  
Water Quality ◽  
Coral Reefs ◽  
Fisheries Management ◽  
Negative Association ◽  
Feeding Guilds ◽  
Top Down ◽  
Management Tools ◽  
Bottom Up ◽  
Anthropogenic Stressors

The question of whether biological systems are maintained by top-down versus bottom-up drivers is a recurring one in ecology. It is a particularly important question to address in the management of coral reefs, which are at risk from a variety of anthropogenic stressors. Here, we explicitly test whether the abundance of different feeding guilds of coral-associated Chaetodon butterflyfishes are controlled by top-down or bottom-up drivers, and we assess the relative influence of all statistically significant drivers. We find that the abundance and species richness of Chaetodon butterflyfishes are predominately determined by bottom-up drivers. The abundance of corallivores is primarily driven by availability of branching and tabular live corals, whereas the abundance of generalists is most strongly influenced by a negative association with macroalgal cover. We also find evidence of weak top-down control on the abundance of corallivorous butterflyfish by gape-limited mesopredators, but no such effects on generalist butterflyfish. Our findings indicate that conservation of coral reefs for Chaetodon butterflyfishes must include management at a larger spatial scale in order to reduce the effect of coral reef stressors such as declining water quality and climate change, but should also include implementation of fisheries management tools in order to increase local herbivory.

scholarly journals Ecological niche models as hypothesis generators of functional genetic differentiation and potential local adaptation in a Mediterranean alpine ecosystem

2020 ◽  
Author(s):  
Javier Morente-López ◽  
Jamie M. Kass ◽  
Carlos Lara-Romero ◽  
Josep María Serra-Diaz ◽  
José Carmen Soto-Correa ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Ecological Niche ◽  
Conservation Value ◽  
Ecological Niche Models ◽  
Evolutionary Potential ◽  
Marginal Populations ◽  
Phenotypic Differentiation ◽  
Selective Pressures ◽  
Marginal Areas ◽  
Niche Models

AbstractGeographically disparate populations within a species’ range may show important differences including variation in ecological, demographic, genetic and phenotypic characteristics. Based on the Center-Periphery Hypothesis, it is often assumed that environmental conditions are optimal in the geographic center of the range and stressful or suboptimal at the periphery, implying ecological marginality is concordant with geographic periphery. But this assumption has been challenged as geographical and ecological gradients are not necessarily concordant. The conservation value of populations inhabiting environmentally marginal areas is still under debate and is closely related with their evolutionary potential. Strong selective pressures caused by stressful conditions may generate novel adaptations in marginal areas, conferring these populations distinct evolutionary potential. But populations inhabiting marginal areas may also show reductions in neutral and adaptive genetic diversity via drift and inbreeding.In this work we explore the potential of ecological niche models (ENMs) to identify environmentally optimal and marginal areas, as well as the principal putative selective pressures likely to act. To do so, we built a carefully parameterized ENM of Silene ciliata, a dominant plant species of Mediterranean alpine habitats. Complementarily, we selected wild populations inhabiting contrasting environmental conditions and carried out common garden experiments to detect genetic differentiation among populations associated with functional traits. With the resulting information, we tested whether environmentally marginal populations defined by the ENM had genetically differentiated phenotypes that are potentially adaptive and, thus, of conservation value.We found genetically based phenotypic differentiation of phenological traits between populations inhabiting areas identified by the ENM as marginal and optimal, as well as between populations with different habitat suitability values. Results supported ENMs as powerful tools for determining environmental marginality and identifying selection pressures, and thus also as hypothesis generators for divergent selection. Furthermore, genetically based phenotypic differentiation found underlines the potential adaptive value of populations inhabiting marginal areas. The approach developed here provides a theoretically justified and practical way to study adaptive processes and provide insights about the conservation value of marginal populations.

scholarly journals Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

2018 ◽  
Author(s):  
Marco A. Escalante ◽  
Charles Perrier ◽  
Francisco J. García-De León ◽  
Arturo Ruiz-Luna ◽  
Enrique Ortega-Abboud ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Local Adaptation ◽  
Population Genomics ◽  
Landscape Heterogeneity ◽  
Genotyping By Sequencing ◽  
Anthropogenic Factors ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Potential

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

scholarly journals Balancing positive and negative selection: in vivo evolution of Candida lusitaniae MRR1

2020 ◽  
Author(s):  
Elora G. Demers ◽  
Jason Stajich ◽  
Alix Ashare ◽  
Patricia Occhipinti ◽  
Deborah A. Hogan
Keyword(s):  
Hydrogen Peroxide ◽  
Population Genomics ◽  
Microbial Evolution ◽  
Chronic Infections ◽  
Gain Of Function ◽  
Multiple Alleles ◽  
Selective Pressures ◽  
Candida Lusitaniae ◽  
Bacterial Products

AbstractThe evolution of pathogens in response to selective pressures present during chronic infections can influence persistence, virulence, and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally-derived Clavispora (Candida) lusitaniae isolates from a single chronic lung infection with a striking enrichment in the number of alleles of MRR1. Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity suggesting the presence of counteracting selective pressures. Our studies demonstrated tradeoffs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation of MDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multiple Candida species and in serial analysis of populations from this individual collected over three years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population.ImportanceUnderstanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multiple MRR1 alleles in isolates from a single Clavispora (Candida) lusitaniae infection revealed the selection for both high and low Mrr1 activity. Our studies reveal tradeoffs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution, and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.

scholarly journals (In)exhaustible suppliers for evolution? Epistatic selection tunes the adaptive potential of non-genetic inheritance

2018 ◽  
Author(s):  
Etienne Rajon ◽  
Sylvain Charlat
Keyword(s):  
Dna Sequences ◽  
Future Generations ◽  
Genetic Mutations ◽  
Combined Effects ◽  
Genetic Contribution ◽  
Adaptive Potential ◽  
Genetic Inheritance ◽  
Modifier Locus ◽  
Selective Pressures ◽  
Variable Environments

Non-genetic inheritance media, from methyl-accepting cytosines to culture, tend to ‘mutate’ more frequently than DNA sequences. Whether or not this makes them inexhaustible suppliers for adaptive evolution will depend on the effect of non-genetic mutations (hereafter epimutations) on fitness-related traits. Here we investigate how the magnitude of these effects might themselves evolve. More specifically, we examine the hypothesis that natural selection could set boundaries to the adaptive potential of non-genetic inheritance media due to their higher mutability. In our model, the genetic and epigenetic contributions to a non-neutral phenotype are controlled by an epistatic modifier locus, which we let evolve under the combined effects of drift and selection, in stable and in variable environments. We show that a pure genetic control evolves when the environment is stable, provided that the population is large enough, such that the phenotype becomes robust to frequent epimutations. When the environment fluctuates, however, the direction of selection on the modifier locus also fluctuates and can overall produce a large non-genetic contribution to the phenotype, especially when the epimutation rate matches the rate of environmental variation. We further show that selection on the modifier locus is mostly direct – i.e. it does not rely on subsequent effects in future generations – as our results are generally insensitive to recombination. These results suggest that unstable inheritance media might significantly contribute to fitness variation of traits subject to highly variable selective pressures, but little to traits responding to scarcely variable aspects of the environment, which likely represent a majority. More generally, our study demonstrates that the rate of mutation and the adaptive potential of any inheritance media should not be seen as independent properties.

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