I am very interested in the evolution of the evolution process itself. There are of course a lot of things that influence how evolution will work, but for this question, I am interested in things that are only related to the evolution process. Examples could be increase chance of mutations in newborns, change in reproduction age, and similar. I am specifically interested in observation where the evolution process itself has adapted to a change in the environment.
Bacteria such as E. coli are known to increase their mutation rate (by switching to a more error prone polymerase among other things) when under stress. This can mean being placed in a medium where it's not adapted to grow (http://www.micab.umn.edu/courses/8002/Rosenberg.pdf) or when treated with antibiotics (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088971/?tool=pmcentrez).
The "change in reproduction age" you mention is one major aspect of life history evolution.
A massive literature exists on this topic, including several books: e.g., The evolution of life histories: Theory and analysis (Roff, 1992) and The evolution of life histories (Stearns, 1992).
Reznick and various colleagues have carried out extensive studies of experimental life history evolution in Trinidadian guppies going back ~30 years. For example:
- Reznick, D.N. and Endler, J.A. 1982. The impact of predation on life history evolution in Trindadian guppies (Poecilia reticulata). Evolution 36:160-177.
- Reznick, D.N. and Bryga, H. 1987. Life-history evolution in guppies. 1. Phenotypic and genotypic changes in an introduction experiment. Evolution 41:1370-1385.
- Reznick, D.N. 1989. Life history evolution in guppies. 2. Repeatability of field observations and the effects of season on life histories. Evolution 43:1285-1297.
- Reznick, D.N., Shaw, F.H., Rodd, F.H. and Shaw, R.G. 1997. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata). Science 275: 1934-1937.
- Reznick, D.N. 1997. Life history evolution in guppies (Poecilia reticulata): guppies as a model for studying the evolutionary biology of aging. Experimental Gerontology 32:245-258.
Life history evolution has also been documented in response to human pressures. Fisheries stocks are evolving in response to overfishing. For example:
- Walsh, M.R., Munch, S.B., Chiba, S. and Conover, D.O. 2006. Maladaptive changes in multiple traits caused by fishing: impediments to population recovery. Ecology Letters 9:142-148.
- Conover, D.O., Arnott, S.A., Walsh, M.R. and Munch, S.B.. 2005. Darwinian Fishery Science: lessons from the Atlantic silverside. Canadian Journal of Fisheries and Aquatic Science 62:730-737.
I think this falls into your criteria but correct me if i'm wrong :).
The HIV reverse transcriptase protein has evolved to have relatively low fidelity (leading to a high mutation rate in replicated virus particles). Reverse transcriptase is also recombinogenic, ie. it can switch templates during replication leading to even more variability. Combined, these two properties lead to each individual having a large number of variant viral genomes, which leads to increased resistance to antiretroviral drugs etc.
I thought of influenza as a second example. The viral genome has evolved to be fragmented into 7-8 pieces of RNA, which can be swapped with other strains during co-infection of a single cell. This can lead to more virulent or transmissible strains of influenza; these can also be helpful to create new strains that influenza vaccines are no longer useful against.
Species have been observed in controlled experiments to use different sources of energy, for instance axenic E. coli cultures picking up citrate metabolism in Lenski's Lab at MSU. They have also shown that mutations to the mutator gene mutT can accelerate the process of evolution, though it's evolution directed by fitness in a very specific setting.
How about species actively changing the factors that play a role in the selection process?
Humans are a species that have heavily modified this process. In the western world, we have gone away from selection by survival skills and genetic fitness to move to a social selection, where genome is secondary to social skills and adaptation to fashion, which are acquired skills.
Pigliucci gives a good review of some aspects of this topic in "Is evolvability evolvable?" (2008). He sees what you're asking about, which he calls "evolvability", as one of the key topics for the future of the study of evolution.
It's very conceptually dense evo-devo-theory, so I'll probably do a poor job trying to explain it, but he tries to set up a framework that deals not just with things like life-history (per kmm's answer) and mutation/recombination rate (low fidelity in HIV per GWW's answer, and, I suppose, the evolution of sex itself), but also with constraints that evolve at various levels to "positively channel" mutation (that is, the understanding that while mutations are effectively random, the phenotypes that emerge, and are acted upon by natural selection, are not random, but are channelled by the developmental system of the organism).
He also includes the role of development in opening up "phenotypic space" into which a lineage may evolve. For instance, single-celled organisms have a limit on size and complexity, the evolution of multicellularity opens up this huge zone of evolvability. In a sense, this is also the "evolution of evolution".
- Pigliucci M. 2008. Is evolvability evolvable? Nat Rev Genet 9: 75–82. Behind paywall, but free pdf here
The following paper published on August 25, 2015 claims that there are indeed directed mutations. Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005477