scholarly journals Evolutionary capacitance emerges spontaneously during adaptation to environmental changes

2017 ◽  
Author(s):  
Paul G Nelson ◽  
Joanna Masel
Keyword(s):  
Environmental Change ◽  
Environmental Changes ◽  
Model System ◽  
Error Rates ◽  
Yeast Prion ◽  
A Genome ◽  
Low Levels ◽  
Selection For ◽  
Open Question ◽  
Evolutionary Capacitance

ABSTRACTAll biological populations are to a greater or lesser degree evolvable, but the forces that shape evolvability, especially the evolution of evolvability as an adaptive response to a changing environment, have been a source of controversy. One source of enhanced evolvability is the benign status of “cryptic sequences” typically expressed at low levels due to molecular errors, but with the potential to be expressed more fully following mutational co-option. A genome enriched for benign cryptic sequences has a more benign mutational neighborhood, via the possibility of co-option, and thus enhanced evolvability. Whether selection for evolvability itself can be the cause of a more benign mutational neighborhood remains an open question. Here, we show that environmental change can cause the evolution of increased evolvability, despite our use of a strong-selection weak mutation regime that precludes, by design, the adaptive evolution of evolvability. Instead, enhanced evolvability arises as a byproduct of environmental change via a novel mechanism that we call “emergent evolutionary capacitance”. When the environment changes, increased molecular error rates evolve as a strategy to rapidly change phenotypes, with the side effect of purging deleterious cryptic sequences and enhancing the mutational neighborhood for future adaptation. The behavior is strikingly similar to that seen in a model system for capacitance, the yeast prion [PSI+].

scholarly journals A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

Genetics ◽  
2013 ◽  
Vol 196 (3) ◽  
pp. 829-840 ◽  
Author(s):  
Timothy M. Beissinger ◽  
Candice N. Hirsch ◽  
Brieanne Vaillancourt ◽  
Shweta Deshpande ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Maize Population ◽  
Genome Wide ◽  
A Genome ◽  
Selection For ◽  
Ear Number ◽  
Genome Wide Scan

Pleistocene–Holocene environmental change in the Canary Archipelago as inferred from the stable isotope composition of land snail shells

2011 ◽  
Vol 75 (3) ◽  
pp. 658-669 ◽  
Author(s):  
Yurena Yanes ◽  
Crayton J. Yapp ◽  
Miguel Ibáñez ◽  
María R. Alonso ◽  
Julio De-la-Nuez ◽  
...  
Keyword(s):  
Environmental Change ◽  
Canary Islands ◽  
Environmental Changes ◽  
Isotope Composition ◽  
Moving Average ◽  
Land Snail ◽  
Balance Model ◽  
Low Latitude ◽  
The Times

AbstractThe isotopic composition of land snail shells was analyzed to investigate environmental changes in the eastern Canary Islands (28–29°N) over the last ~ 50 ka. Shell δ13C values range from −8.9‰ to 3.8‰. At various times during the glacial interval (~ 15 to ~ 50 ka), moving average shell δ13C values were 3‰ higher than today, suggesting a larger proportion of C4 plants at those periods. Shell δ18O values range from −1.9‰ to 4.5‰, with moving average δ18O values exhibiting a noisy but long-term increase from 0.1‰ at ~ 50 ka to 1.6–1.8‰ during the LGM (~ 15–22 ka). Subsequently, the moving average δ18O values range from 0.0‰ at ~ 12 ka to 0.9‰ at present. Calculations using a published snail flux balance model for δ18O, constrained by regional temperatures and ocean δ18O values, suggest that relative humidity at the times of snail activity fluctuated but exhibited a long-term decline over the last ~ 50 ka, eventually resulting in the current semiarid conditions of the eastern Canary Islands (consistent with the aridification process in the nearby Sahara). Thus, low-latitude oceanic island land snail shells may be isotopic archives of glacial to interglacial and tropical/subtropical environmental change.

scholarly journals Synchronization-induced persistence versus selection for habitats in spatially coupled ecosystems

2013 ◽  
Vol 10 (87) ◽  
pp. 20130559 ◽  
Author(s):  
Adam Lampert ◽  
Alan Hastings
Keyword(s):  
Phase Transitions ◽  
Stochastic Systems ◽  
Environmental Changes ◽  
Heterogeneous Environments ◽  
Migration Rates ◽  
Stochastic Fluctuations ◽  
Key Factor ◽  
Spatially Extended ◽  
Unique Method ◽  
Selection For

Critical population phase transitions, in which a persistent population becomes extinction-prone owing to environmental changes, are fundamentally important in ecology, and their determination is a key factor in successful ecosystem management. To persist, a species requires a suitable environment in a sufficiently large spatial region. However, even if this condition is met, the species does not necessarily persist, owing to stochastic fluctuations. Here, we develop a model that allows simultaneous investigation of extinction due to either stochastic or deterministic reasons. We find that even classic birth–death processes in spatially extended ecosystems exhibit phase transitions between extinction-prone and persistent populations. Sometimes these are first-order transitions, which means that environmental changes may result in irreversible population collapse. Moreover, we find that higher migration rates not only lead to higher robustness to stochastic fluctuations, but also result in lower sustainability in heterogeneous environments by preventing efficient selection for suitable habitats. This demonstrates that intermediate migration rates are optimal for survival. At low migration rates, the dynamics are reduced to metapopulation dynamics, whereas at high migration rates, the dynamics are reduced to a multi-type branching process. We focus on species persistence, but our results suggest a unique method for finding phase transitions in spatially extended stochastic systems in general.

A model system for rapid selection for resistance and investigation of resistance mechanisms in Fusarium wilt of oil palm

1995 ◽  
Vol 44 (4) ◽  
pp. 749-755 ◽  
Author(s):  
R. MEPSTED ◽  
J. FLOOD ◽  
T. PAUL ◽  
C. AIREDE ◽  
R. M. COOPER
Keyword(s):  
Fusarium Wilt ◽  
Oil Palm ◽  
Resistance Mechanisms ◽  
Model System ◽  
Selection For

scholarly journals Local genic base composition impacts protein production and cellular fitness

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4286 ◽  
Author(s):  
Erik M. Quandt ◽  
Charles C. Traverse ◽  
Howard Ochman
Keyword(s):  
Escherichia Coli ◽  
Base Composition ◽  
Protein Production ◽  
Purifying Selection ◽  
Specific Protein ◽  
Compositional Variation ◽  
Terminal Portion ◽  
A Genome ◽  
Selection For ◽  
Protein Feature

The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence fromEscherichia colidemonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.

scholarly journals An early signaling transcription factor regulates differentiation in Giardia

2021 ◽  
Author(s):  
Han-Wei Shih ◽  
Germain C.M. Alas ◽  
Daria S. Rydell ◽  
Bailin Zhang ◽  
Greyson A. Hamilton ◽  
...  
Keyword(s):  
Giardia Lamblia ◽  
Environmental Changes ◽  
Early Response ◽  
Restriction Point ◽  
Cyst Production ◽  
Cyst Viability ◽  
M Phase ◽  
Parasitic Pathogens ◽  
Open Question ◽  
Stimulation Of

Transcriptional regulation of differentiation is critical for parasitic pathogens to adapt to environmental changes and regulate transmission. How early signaling transcription factors (TF) activate signal transduction to initiate encystation remains an open question in Giardia. Here, we generate a CasRX-mediated knockdown system, together with an established CRISPRi system to screen early signaling TFs in Giardia lamblia. We identified an early response TF, GARP4 that regulates cyst wall protein (CWP) levels during encystation. Depletion of GARP4 increases encystation efficiency resulting in increased cyst production. Interestingly, cyst viability and CWP1 trafficking are not altered in GARP4 knockdowns, suggesting GARP4 regulates the restriction point controlling the portion of cells that terminally differentiate into cysts. Consistent with previous studies, we find that stimulation of encystation shifts the distribution of cells to the G2/M phase and these cells exhibits higher levels of CWP1, indication that entry into the encystation pathway is cell cycle regulated. Key to this increase of CWP1 in G2/M cells is activation of MYB2, a TF commonly observed during the early phase of encystation in Giardia. Remarkably, activated GARP4 only exhibits in G1/S cells, suggesting it has a role in preventing encystation until G2/M. Furthermore, we demonstrate that depletion of GARP4 activates MYB2 and overexpression of GARP4 represses MYB2. Our findings provide the first molecular mechanism underlying the restriction point regulating differentiation during early signaling of encystation in Giardia lamblia.

scholarly journals Expressions of climate perturbations in western Ugandan crater lake sediment records during the last 1000 yr

2013 ◽  
Vol 9 (5) ◽  
pp. 5183-5226 ◽  
Author(s):  
K. Mills ◽  
D. B. Ryves ◽  
N. J. Anderson ◽  
C. L. Bryant ◽  
J. J. Tyler
Keyword(s):  
Environmental Change ◽  
East Africa ◽  
Environmental Changes ◽  
Sediment Cores ◽  
Ice Age ◽  
Ecosystem Response ◽  
Large Lakes ◽  
Crater Lakes ◽  
Continental Scale ◽  
Western Uganda

Abstract. Equatorial East Africa has a complex, regional patchwork of climate regimes, with multiple interacting drivers. Recent studies have focussed on large lakes and reveal signals that are smoothed in both space and time, and, whilst useful at a continental scale, are of less relevance when understanding short-term, abrupt or immediate impacts of climate and environmental changes. Smaller-scale studies have highlighted spatial complexity and regional heterogeneity of tropical palaeoenvironments in terms of responses to climatic forcing (e.g. the Little Ice Age [LIA]) and questions remain over the spatial extent and synchroneity of climatic changes seen in East African records. Sediment cores from paired crater lakes in western Uganda were examined to assess ecosystem response to long-term climate and environmental change as well as testing responses to multiple drivers using redundancy analysis. These archives provide annual to sub-decadal records of environmental change. The records from the two lakes demonstrate an individualistic response to external (e.g. climatic) drivers, however, some of the broader patterns observed across East Africa suggest that the lakes are indeed sensitive to climatic perturbations such as a dry Mediaeval Climate Anomaly (MCA; 1000–1200 AD) and a relatively drier climate during the main phase of the LIA (1500–1800 AD); though lake levels in western Uganda do fluctuate. The relationship of Ugandan lakes to regional climate drivers breaks down c. 1800 AD, when major changes in the ecosystems appear to be a response to sediment and nutrient influxes as a result of increasing cultural impacts within the lake catchments. The data highlight the complexity of individual lake response to climate forcing, indicating shifting drivers through time. This research also highlights the importance of using multi-lake studies within a landscape to allow for rigorous testing of climate reconstructions, forcing and ecosystem response.

Future Environments of South America

2007 ◽  
Author(s):  
Thomas T. Veblen ◽  
Kenneth R. Young
Keyword(s):  
South America ◽  
Environmental Change ◽  
Environmental Changes ◽  
Human Impacts ◽  
Southern Oscillation ◽  
Physical Geography ◽  
Tierra Del Fuego ◽  
South American ◽  
Policy Options ◽  
Natural Processes

An important goal of this book has been to provide a comprehensive understanding of the physical geography and landscape origins of South America as important background to assessing the probabilities and consequences of future environmental changes. Such background is essential to informed discussions of environmental management and the development of policy options designed to prepare local, national, and international societies for future changes. A unifying theme of this book has been the elucidation of how natural processes and human activities have interacted in the distant and recent past to create the modern landscapes of the continent. This retrospective appreciation of how the current landscapes have been shaped by nature and humans will guide our discussion of possible future trajectories of South American environments. There is abundant evidence from all regions of South America, from Tierra del Fuego to the Isthmus of Panama, that environmental change, not stasis, has been the norm. Given that fact, the history, timing, and recurrence intervals of this dynamism are all crucial pieces of information. The antiquity and widespread distribution of changes associated with the indigenous population are now well established. Rates and intensities of changes related to indigenous activities varied widely, but even in regions formerly believed to have experienced little or no pre-European impacts we now recognize the effects of early humans on features such as soils and vegetation. Colonization by Europeans mainly during the sixteenth century modified or in some cases replaced indigenous land-use practices and initiated changes that have continued to the present. Complementing these broad historical treatments of human impacts, other chapters have examined in detail the environmental impacts of agriculture (chapter 18) and urbanism (chapter 20), and the disruptions associated with El Niño–Southern Oscillation events. The goal of this final synthesis is to identify the major drivers of change and to discuss briefly their likely impacts on South American environments and resources in the near and medium-term future. Our intent is not to make or defend predictions, but rather to identify broad causes and specific drivers of environmental change to inform discussions of policy options for mitigating undesirable changes and to facilitate potential societal adaptations to them.

Can the planet be saved in Time? On the temporalities of socionature, the clock and the limits debate

2019 ◽  
Vol 3 (3) ◽  
pp. 904-926 ◽  
Author(s):  
Vijay Kolinjivadi ◽  
Diana Vela Almeida ◽  
Jonathan Martineau
Keyword(s):  
Environmental Change ◽  
Environmental Changes ◽  
Food Sovereignty ◽  
System Change ◽  
Rice Production ◽  
Clock Time ◽  
Limits To Growth ◽  
Economic Productivity ◽  
Linear Representations ◽  
Political Act

The tendency of capitalist modernity to impose predictable, homogenous and linear representations of time for economic productivity has made it increasingly difficult, if not impossible, to effectively respond to catastrophic environmental changes that are emergent, sudden, non-linear and unpredictable. A confusion between the actions and consequences of environmental change, and socialized representations of time and space within which humans must respond to such changes, not only paralyses possible solutions within fixed imaginaries but is also out of synch with the perpetual coming-into-being of socionature entanglements. The multiple temporalities coordinating interactions of humans and non-human natures are instead fetishized and made governable, commensurable and reproducible through the mechanistic intervals of the clock. We argue that the desire for transformative system change can be found in temporal desynchronizations to clock Time (capital T) and that political strategies to responding to socio-ecological crises reside in alter-temporalities (lower t time) of emergent socionature relations. Through an example of the desynchronized temporalities of tinawon rice production, we show how alter-temporalities emerge to reclaim cultural and food sovereignty from the otherwise flattening effects of modernity. We highlight the futuring potentials of such temporalities and their implication within ongoing debates between ecomodernists and those advocating limits to growth. Given that continuing to act in the Time of capital evidently fails to bring about system change and even aids in perpetuating our crises, we claim that responding in time (lower t) is itself a political act in raising the possibility for more convivial and life-affirming futures.

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