scholarly journals Extinctions in marine plankton preceded by stabilizing selection

2019 ◽  
Author(s):  
Manuel F. G. Weinkauf ◽  
Fabian G. W. Bonitz ◽  
Rossana Martini ◽  
Michal Kučera
Keyword(s):  
Planktonic Foraminifera ◽  
Natural Populations ◽  
Marine Species ◽  
Stabilizing Selection ◽  
Marine Plankton ◽  
Trait Variation ◽  
Trait Divergence ◽  
Quaternary Climate ◽  
Geological Past ◽  
The Face

AbstractUnless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption, increasing trait variation, or stabilisation, decreasing trait variation. In the short term, the more economical response is stabilisation, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalisation is deleterious in the face of persistently increasing stress because it reduces variability and thus decreases the ability to react to further change in stress. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptive reaction of populations facing extinction are rare. In this study, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variance in two species across a salinity rise leading to their local extinction. One species reacted by stabilisation in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remains stable or reacted by further stabilisation. These observations indicate that the default reaction of the studied Foraminifera is stabilisation and that stress escalation did not lead to the local emergence of adapted forms. Inability to breach the global adaptive threshold would explain why communities of Foraminifera, and many other groups of marine plankton, reacted to Quaternary climate change by faithfully tracking their zonally shifting environments. It also means that populations of marine species adapted to response by migration, when exposed to stress outside of the adaptive range, will be at risk of extinction.

scholarly journals The evolution of group differences in changing environments

PLoS Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. e3001072
Author(s):  
Arbel Harpak ◽  
Molly Przeworski
Keyword(s):  
Environmental Effects ◽  
Complex Traits ◽  
Genetic Basis ◽  
Rapid Evolution ◽  
Group Differences ◽  
Stabilizing Selection ◽  
Trait Variation ◽  
Fitness Consequences ◽  
The Face ◽  
Selection For

The selection pressures that have shaped the evolution of complex traits in humans remain largely unknown, and in some contexts highly contentious, perhaps above all where they concern mean trait differences among groups. To date, the discussion has focused on whether such group differences have any genetic basis, and if so, whether they are without fitness consequences and arose via random genetic drift, or whether they were driven by selection for different trait optima in different environments. Here, we highlight a plausible alternative: that many complex traits evolve under stabilizing selection in the face of shifting environmental effects. Under this scenario, there will be rapid evolution at the loci that contribute to trait variation, even when the trait optimum remains the same. These considerations underscore the strong assumptions about environmental effects that are required in ascribing trait differences among groups to genetic differences.

Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae)

2019 ◽  
Vol 191 (1) ◽  
pp. 128-141 ◽  
Author(s):  
Carolina L Pometti ◽  
Cecilia F Bessega ◽  
Ana M Cialdella ◽  
Mauricio Ewens ◽  
Beatriz O Saidman ◽  
...  
Keyword(s):  
Quantitative Traits ◽  
Genetic Basis ◽  
Natural Populations ◽  
Tree Height ◽  
Phenotypic Traits ◽  
Stabilizing Selection ◽  
Trait Variation ◽  
Chaco Region ◽  
Neutral Genetic Variation ◽  
Selection For

Abstract Economically and ecologically important quantitative traits of Acacia aroma are related to life history and the size and shape of fruits and leaves. Substantial variation is observed for these traits in natural populations, suggesting a possible genetic basis that could be useful for selection programmes. Our objective was to detect signals of selection on 12 phenotypic traits in 170 individuals belonging to seven populations of A. aroma in the Chaco Region of Argentina. Phenotypic traits were compared with molecular markers assessed in the same populations. Here, we search for signatures of natural selection by comparing quantitative trait variation to neutral genetic variation through the PST–FST test. We further test for differences among populations for the 12 phenotypic traits, an association of phenotypic variation with environmental variables and geographical distance, and we compare the power of discrimination between the phenotypic and AFLP datasets. The PST–FST test suggested directional selection for tree height and stabilizing selection for the remaining traits. Analyses of variance showed significant differentiation for eight phenotypic traits. These results suggest selecting among provenances as a management strategy to improve tree height (which showed divergent selection), whereas significant genetic gain for the other traits might be obtained by selection within provenances.

The Evolutionary Diversity and Ecological Complexity of Coral Reefs

2011 ◽  
Vol 17 ◽  
pp. 111-120 ◽  
Author(s):  
Nancy Knowlton ◽  
Jeremy Jackson
Keyword(s):  
Coral Reefs ◽  
Small Proportion ◽  
Fossil Record ◽  
Marine Species ◽  
Foreseeable Future ◽  
Ecological Complexity ◽  
The Face ◽  
Open Question ◽  
Trophic Linkages ◽  
Bounce Back

Coral reefs are the most biodiverse marine ecosystems on the planet, with at least one quarter of all marine species associated with reefs today. This diversity, which remains very poorly understood, is nevertheless extraordinary when one considers the small proportion of ocean area that is occupied by coral reefs. Networks of competitive and trophic linkages are also exceptionally complex and dense. Reefs have a long fossil record, although extensive reef building comes and goes. In the present, coral reefs sometimes respond dramatically to disturbances, and collapses are not always followed by recoveries. Today, much of this failure to recover appears to stem from the fact that most reefs are chronically stressed by human activities, judging by observations of recovery at exceptional locations where local human activity is minimal. How long reefs can continue to bounce back in the face of warming and acidification remains an open question. Another big uncertainty is how much loss of biodiversity will occur with the inevitable degradation of coral reefs that will continue in most places for the foreseeable future.

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

2014 ◽  
Vol 203 (2) ◽  
pp. 535-553 ◽  
Author(s):  
Athena D. McKown ◽  
Jaroslav Klápště ◽  
Robert D. Guy ◽  
Armando Geraldes ◽  
Ilga Porth ◽  
...  
Keyword(s):  
Natural Populations ◽  
Genome Wide Association ◽  
Trait Variation ◽  
Genome Wide

scholarly journals Two different epigenetic pathways detected in wild three-spined sticklebacks are involved in salinity adaptation

2019 ◽  
Author(s):  
Melanie J. Heckwolf ◽  
Britta S. Meyer ◽  
Robert Häsler ◽  
Marc P. Höppner ◽  
Christophe Eizaguirre ◽  
...  
Keyword(s):  
Natural Selection ◽  
Gasterosteus Aculeatus ◽  
Natural Populations ◽  
Wild Populations ◽  
Epigenetic Marks ◽  
Transgenerational Plasticity ◽  
The Face ◽  
Adaptation Processes ◽  
Methylation Patterns ◽  
Rapid Emergence

AbstractWhile environmentally inducible epigenetic marks are discussed as one mechanism of transgenerational plasticity, environmentally stable epigenetic marks emerge randomly. When resulting in variable phenotypes, stable marks can be targets of natural selection analogous to DNA sequence-based adaptation processes. We studied both postulated pathways in natural populations of three-spined sticklebacks (Gasterosteus aculeatus) and sequenced their methylomes and genomes across a salinity cline. Consistent with local adaptation, populations showed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. In a two-generation experiment, 62% of these pop-DMS were insensitive to salinity manipulation, suggesting that they could be stable targets for natural selection. Two-thirds of the remaining inducible pop-DMS became more similar to patterns detected in wild populations from the corresponding salinity, and this pattern accentuated over consecutive generations, indicating a mechanism of adaptive transgenerational plasticity. Natural DNA methylation patterns can thus be attributed to two epigenetic pathways underlying the rapid emergence of adaptive phenotypes in the face of environmental change.

Complex Traits in Natural Populations

2020 ◽  
pp. 263-290
Author(s):  
Daniel L. Hartl
Keyword(s):  
Complex Traits ◽  
Population Genomics ◽  
Association Studies ◽  
Natural Populations ◽  
Complex Diseases ◽  
Stabilizing Selection ◽  
Phenotypic Evolution ◽  
Genetic Changes ◽  
Number Of Genes ◽  
Almost All

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

scholarly journals Predicting the Landscape of Recombination Using Deep Learning

2020 ◽  
Vol 37 (6) ◽  
pp. 1790-1808 ◽  
Author(s):  
Jeffrey R Adrion ◽  
Jared G Galloway ◽  
Andrew D Kern
Keyword(s):  
Deep Learning ◽  
Evolutionary History ◽  
Model Misspecification ◽  
Natural Populations ◽  
High Accuracy ◽  
Demographic Model ◽  
Recombination Rates ◽  
Genome Wide ◽  
A Genome ◽  
The Face

Abstract Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERNN), a deep learning method for estimating a genome-wide recombination map that is accurate even with small numbers of pooled or individually sequenced genomes. Rather than use summaries of linkage disequilibrium as its input, ReLERNN takes columns from a genotype alignment, which are then modeled as a sequence across the genome using a recurrent neural network. We demonstrate that ReLERNN improves accuracy and reduces bias relative to existing methods and maintains high accuracy in the face of demographic model misspecification, missing genotype calls, and genome inaccessibility. We apply ReLERNN to natural populations of African Drosophila melanogaster and show that genome-wide recombination landscapes, although largely correlated among populations, exhibit important population-specific differences. Lastly, we connect the inferred patterns of recombination with the frequencies of major inversions segregating in natural Drosophila populations.

scholarly journals Late Quaternary climate change from δ18O records of multiple species of planktonic foraminifera: High-resolution records from the Anoxic Cariaco Basin, Venezuela

1997 ◽  
Vol 12 (3) ◽  
pp. 415-427 ◽  
Author(s):  
Hui-Ling Lin ◽  
Larry C. Peterson ◽  
Jonathan T. Overpeck ◽  
Susan E. Trumbore ◽  
David W. Murray
Keyword(s):  
Climate Change ◽  
High Resolution ◽  
Late Quaternary ◽  
Planktonic Foraminifera ◽  
Cariaco Basin ◽  
Quaternary Climate ◽  
Multiple Species

scholarly journals Integrated modelling to support decision-making for marine social–ecological systems in Australia

2017 ◽  
Vol 74 (9) ◽  
pp. 2298-2308 ◽  
Author(s):  
Jessica Melbourne-Thomas ◽  
Andrew J Constable ◽  
Elizabeth A Fulton ◽  
Stuart P Corney ◽  
Rowan Trebilco ◽  
...  
Keyword(s):  
Decision Making ◽  
Marine Environment ◽  
Marine Species ◽  
Ecological Systems ◽  
System Level ◽  
Integrated Modelling ◽  
Marine Systems ◽  
Social Ecological Systems ◽  
Social Ecological ◽  
The Face

Abstract Policy- and decision-makers require assessments of status and trends for marine species, habitats, and ecosystems to understand if human activities in the marine environment are sustainable, particularly in the face of global change. Central to many assessments are statistical and dynamical models of populations, communities, ecosystems, and their socioeconomic systems and management frameworks. The establishment of a national system that could facilitate the development of such model-based assessments has been identified as a priority for addressing management challenges for Australia’s marine environment. Given that most assessments require cross-scale information, individual models cannot capture all of the spatial, temporal, biological, and socioeconomic scales that are typically needed. Coupling or integrating models across scales and domains can expand the scope for developing comprehensive and internally consistent, system-level assessments, including higher-level feedbacks in social–ecological systems. In this article, we summarize: (i) integrated modelling for marine systems currently being undertaken in Australia, (ii) methods used for integration and comparison of models, and (iii) improvements to facilitate further integration, particularly with respect to standards and specifications. We consider future needs for integrated modelling of marine social–ecological systems in Australia and provide a set of recommendations for priority focus areas in the development of a national approach to integrated modelling. These recommendations draw on—and have broader relevance for—international efforts around integrated modelling to inform decision-making for marine systems.

Asymmetric geographic range expansion explains the latitudinal diversity gradients of four major taxa of marine plankton

Paleobiology ◽  
2017 ◽  
Vol 43 (2) ◽  
pp. 196-208 ◽  
Author(s):  
Matthew G. Powell ◽  
Douglas S. Glazier
Keyword(s):  
Range Expansion ◽  
Biological Diversity ◽  
Close Association ◽  
Planktonic Foraminifera ◽  
Geographic Range ◽  
Temperate Zone ◽  
Latitudinal Gradients ◽  
Polar Regions ◽  
Marine Plankton ◽  
Diversity Gradients

AbstractExtensive investigation of the close association between biological diversity and environmental temperature has not yet yielded a generally accepted, empirically validated mechanism to explain latitudinal gradients of species diversity, which occur in most taxa. Using the highly resolved late Cenozoic fossil records of four major taxa of marine plankton, we show that their gradients arise as a consequence of asymmetric geographic range expansion rather than latitudinal variation in diversification rate, as commonly believed. Neither per capita speciation nor extinction rates trend significantly with temperature or latitude for these marine plankton. Species of planktonic foraminifera and calcareous nannoplankton that originate in the temperate zone preferentially spread toward and arrive earlier in the tropics to produce a normal gradient with tropical diversity peaks; by contrast, temperate-zone originating species of diatoms and radiolarians preferentially spread toward and arrive earlier in polar regions to produce reversed gradients with high-latitude diversity peaks. Our results suggest that temperature affects latitudinal diversity gradients chiefly by its effect on species’ range limits rather than on probabilities of speciation and extinction. We show that this mechanism also appears to operate in various multicellular taxa, thus providing a widely applicable explanation for the origin of latitudinal diversity gradients.

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