My epigenetics article

Epigenetics are Not Always Adaptive

Epigenetics is the branch of biology that studies how the environmental conditions experienced by one generation can have a non-genetic influence on their offspring. The vast majority of epigenetic research demonstrates how this phenomenon can increase the survivorship and fitness of offspring, however Leung et al. (2013) clearly exposed the possibility for epigenetics to be non-adaptive. In their study, parent organisms of marine tubeworms Hydroides elegans and Hydroides diramphus were exposed to hypoxic (low oxygen level) or normoxic (normal oxygen level) conditions. After 2 weeks of hypoxia, both species produced significantly fewer eggs than those in normoxic conditions. Such decreases in fecundity can directly reduce the future success of a species. Furthermore, after the hypoxia treatment, H. elegans produced eggs with slower growth, and embryonic abnormalities that would prevent their future development; however these disadvantages were not observed for H. diramphus. These differences in tolerance to hypoxia led the authors to suggest that H. diramphus could completely displace H. elegans if ocean oxygen concentrations continue to decrease as a result of climate change. This study illustrates how environmental changes experienced at one time can negatively affect the number and quality of offspring in the future, thus prolonging the effect. This influences the success of the affected species, its competitors, and those within the associated food webs, and therefore has evolutionary importance. This research has established the potential for climate change to trigger epigenetic effects capable of dictating the patterns of success, decline, and extinction that ultimately drive evolution.

Word Count: 248

REFERENCES

Leung, J. Y. S., Cheung, S. G., Qiu, J. W., Ang, P. O., Chiu, J. M. Y., Thiyagarajan, V. and Shin, P. K. S. (2013).  Effect of parental hypoxic exposure on embryonic development of the offspring of two serpulid polychaetes: Implication for transgenerational epigenetic effect. Marine Pollution Bulletin, 74. 149-155.

Paradigm shift! or not...whatever

Pigliucci argues that there is no, and will be no paradigm shift regarding the modern synthesis. He states that current evolutionary theory should shift to form (plasticity, epigentic inheritance) instead of a focus on genetic theory.
He goes on to propose as Extended Evolutionary Synthesis (EES), and how he expects it to come to fruition and become fairly expected over the next decade or so.
The modern synthesis is lacking, in terms of not including anything on form, as well as developmental biology, which wasn't include in 'evolutionary theory' until 1977 (Gould) in a paper called Ontogeny and Phylogeny. Followed by the Evo-Devo thing in the 1990's.
PLASTICITY
In terms of plasticity; there is no longer just the topic of 'heritability' in its basic form. There is an enormous dependence on genotype-interactions (these can be studied/investigated by looking at the reactions norm that Simon was talking about) - plasticity exists in almost every species that it has been investigated for. Pigliucci also says, like Simon also showed today, that plasticity can lean towards evolutionary change, preceding genetic change itself.
EPIGENETICS
Pigluicci states that epigenetics is not a contradiction to genetic inheritance (and so the Modern Synthesis) but instead is an extremely complex extension of the field.
COMPLEXITY THEORY
He uses this term to highlight the idea that natural selection may not be the only 'organizing principal' available to explain the complexity of biological systems. Natural selection would not be ignored or thought of as a secondary role, just interact with the theory of form.

http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2007.00246.x/pdf

What we are to do. Our official topic title and questions we should aim to understand and discuss by reading around our topic

Official title of our topic is:
Natural variation and knock-out techniques as probes of Darwinian fitness (incorporating Noble's review of the link between physiology and genetics).

Question 1. What are the proposals of Noble's review of the link between physiology and genetics?

Question 2. Considering Denis Noble; what are the applications and limitations of genetic knock-out experiments as probes of Darwinian fitness?

Question 3. Considering Denis Noble; what are the applications and limitations of experimental manipulations of natural variation as probes of Darwinian fitness?

Aim to read at least 1 paper about both genetic knock-outs and experimental manipulations applications/limitations.

HUMMINGBIRDS

 It is established that genome, nucleus and red blood cell size are all correlated in vertebrates. Since larger cells have lower surface area to volume ratios, they are less efficient at gas exchange; which means that high metabolisms are constrained to small cells, which must therefore have small genomes. Powered flight is metabolically expensive, so birds are predicted to have smaller average genomes compared to all other vertebrates. Saurischian dinosaurs underwent a genome reduction before they evolved powered flight and gave rise to birds; within birds genome size tends to be smaller with increasing flying ability.

This study compares 37 species of hummingbirds in terms of nucleus, red blood cell and genome size, as well as other physiological parameters such as cardiac mass, haemoglobin concentration, body mass, wing loading and elevation, taking phylogeny into account. Genome size of hummingbirds was found to be constrained similarly to other vertebrates. Genome size across hummingbird species was found to have low variation and did not correlate with body size, but was positively correlated with heart size. The results generated two important questions which could be extrapolated to other groups; 1) is genome size a derived or ancestral feature? and 2) why do some species within a clade have larger genomes?

Hummingbirds diverged from nightjars; a group which have larger genome sizes than hummingbirds, so genome reduction must have occurred after this divergence and is therefore not an ancestral feature. Hummingbird species with the largest genomes were all from the upper tropical zone in 900-1600 m humid evergreen forests; these species are not close relatives, so the secondary change in genome size (the primary change being the reduction following divergence from nightjars) makes the relationship between phylogeny and genome size not as clear as the relationship between environment and genome size. Thus this study provides a strong example of evolution influenced by interactions between the genome and the environment.

HO, BURGGREN, & Interactions between the epigenome and the genome

I think this will be a useful paper
"Epigenetics and transgenerational transfer: a physiological perspective"- (Ho & Burggren, 2010)
Here is the link: http://jeb.biologists.org/content/213/1/3.full

I will go through it fully and summarise next week, unless anybody wants to beat me to it or read themselves!


This figure could be a good topic for discussion. 

Maternal Effects

Definition of Maternal Effects: a non-genetic influence on the offspring phenotype, based on the environmental conditions experienced by the mother organism. Maternal effects are a type of epigenetic effect.

Mechanisms:
----Through variations in resource/energy allocation
----Oviposition site (where the mother releases her progeny has an effect on its life history eg. next to food = better, next to other offspring = worse as they are competitors for resources)
----Hormones (hormone levels during oogeneis affect embryo)

(Fowler, 2005): Looked at aphids (greenflies) - found that under a certain predator-induced stress cue, the mothers produced winged offspring. This gave them advantage with dispersibility and fitness through escaping the predator.
----->> mother experience (predator cue) -------->> changes offspring phenotype 
this is relevant to evolution because it influences the dispersibility, gives it a competitive advantage (can get resources easier due to wings) (also can escape predator) - therefore affect other populations through out-competing other species or organism. Also, affect food availability to the predator.... if all offspring are winged and fly away then new food source?
This phenotypic change influences population dynamics and evolution.

Relevance to our Topic: Having the focus of scientific experiments on genetic knock-out and trying to compose genomes will not give us a FULL understanding of organisms, their ecology and evolution. This is (what I think) Denis Noble is saying. Maternal effects are sort of a more knowledgable version of Lamarck's idea about inherited acquired characteristics. Maternal effects mean that two hypothetical offspring of the same species could have the same genes and yet they could develop differently through maternal effects (or any epigenetic effect for that matter). 

Marine example (Campbell et al., 1992): when female rainbow trouts experienced confinement during oogeneis they had higher levels of cortisol (stress hormone) and this resulted in smaller offspring with increased mortality rates. The environmental conditions experiences by the mother affect her offspring mortality ./ life history (smaller offspring = less successful, less likely to outcompete, more likely to be predated, perhaps less resource allocation so less efficient.... etc)

WHAT IS OUR TOPIC ABOUT

I am confused about what our topic is about...

  I get genetic knock out and experimental manipulation... however I don't clearly understand the bridge between them?
Can anybody shed some light?

From what I gather, the big QUESTION presented in our topic is:

 How useful is genetic knock out / experimental manipulation research in our understanding of evolutionary physiology... since Denis Noble points out a number of other non-genetic influences on this.

Please feel free to correct me!


PS - in Noble's paper he posts this table... I feel like it summarises his main points - "the paradigm shift."