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Niche adaptation refers to the ability of some organisms to adapt to changing environments, or niches. Genetic mechanisms of this adaptation include horizontal gene transfer, gene duplication, and gene shuffling. Adaptations are the result of Evolution and allow an organism to live in new environments. All organisms must fill some ecological niche and at some point, species must adapt to fill newer niches if they are to survive in a changing world. Mechanisms involved in evolving new abilities to exploit new environments happen on the genetic scale. Genes mix and match in processes like horizontal gene transfer and gene or genome duplications. Transposable elements and plasmid or phage introduced genomic islands also provide organisms with the genetic tools they need to adapt to newer environments.

Adaptations can result in obviously visible morphological differences or increased metabolic pathways that are not as easily detectable and require genetic analysis to confirm. For pathogenic organisms, this usually means increasing virulence. In the case of wilt-fungi like Verticillium dahliae and Verticillium albo-atrum, the increased virulence is dependent on homologs genes picked up from some incidence of horizontal gene transfer with a bacterium early in its evolutionary history. For ocean dwelling cyanobacteria, adapting to colonize new territories has led to clades of Prochlorococcus becoming specialized to thrive in the low light and colder temperatures of the deeper depths in the ocean. Additionally, resistance to harsh compounds is also important for adaptation. The aerobic ammonia oxidizing bacteria Nitrosomonas eutropha C91 contains genomic islands that house genes important in providing resistance to heavy metals and oxidizing nitrogen. As a result, the species occupies environments with elevated N2 concentrations. Some of these genes are unique to this species, meaning no other ammonia oxidizing bacteria could survive in the climates that N. eutropha C91 does giving it a significant fitness advantage.

Adaptation of Galapagos Finches
The most notable example of niche adaptation comes from the original subject of the topic of evolution, the finches of the Galapagos Islands. The different species of finches that inhabit the different islands were famously one of the main sources of evidence Charles Darwin used when writing his book, On the Origin of Species. Darwin noted that the birds varied in beak size and shape, and that the sizes and shapes of the beaks were perfectly suited to match the source of seeds on the specific islands the birds inhabited. In a recent study by Lamichhaney et. all, the genetic source of this difference was discovered in the form of haplotypes of the ALX1 gene. Using this gene to highlight beak diversity, along with whole genome sequencing of 120 individuals from the different islands, the researchers concluded that individual finches of different species had more similar beak shapes and sizes with birds inhabiting the same islands, and thus feeding from the same sources of food, than with birds of the same species that lived on different islands.

Horizontal Gene Transfer
Horizontal Gene Transfer (HGT) has long been known to contribute to genetic recombination and variation for prokaryotic organisms like bacteria but the extent to which it contributes has been disputed. Recently, experiments have indicated that HGT might be more responsible for more genetic variation than simple accumulation of mutations. Additionally, HGT can occur between any combination of organisms as distantly related as animals, bacteria, archaea, fungi, and plants. Gene cassettes, plasmids, transposons and viruses are all known methods of the transfer of genes between individuals, strains, and species of organisms.

Plasmid Mediated Exchange of Genetic Information
Bacteria can incorporate DNA from many different species into their own genetic libraries. Two of the most common methods involve plasmids and  bacteriophages. Encorporation of DNA from plasmids between two bacterial cells usually involves the creation of a pilus. One bacteria, the donor cell, initiates transmition by extending the pilus to connect with the acceptor cell. The DNA from the plasmid is cut by an endonuclease and a single strand is transfered tot he donor cell. Both cells replicate the single strand into a double strand. Plasmids can become incorporated into the full bacterial chromosome. The restriction sites still exist, meaning various lengths of DNA can be transposed from one cell to another directly from the chromosome. In this way non plasmid bacterial genes neighboring the plasmid genes can also migrate from cell to cell.

Bacteriophages can cause the chromosomes of their infected hosts to break up into segments small enough to fit into the newly constructed viral particles. If some of these bacterial genes are caught up into the phage, they can be released into the next infected individual. This new host can incorporate the DNA from the first bacteria into its own chromosome.

Niche Construction
Many animals use their adaptations not just to survive in their environments, but to modify their surroundings to maximize their abilities to thrive. Humans, earthworms and beavers are good examples.

Human beings have constructed large civilizations in environments we are not perfectly suited for. Insulated homes, extensive piping networks, and air conditioning/ heating units are examples of how cities like Phoenix, Arizona and Fairbanks, Alaska can support human populations year round. Earthworms generally inhabit the topsoil layer of the ground and their lifestyle and metabolic processes work to increase the size of the topsoil layer and improve the quality of the soil they inhabit. This in turn increases the amount of plant matter available to eventually die and decompose and provide the food for the earthworms. Beavers create dams and lodges that dramatically change the ecosystems they inhabit. Families will maintain these changed ecosystems for generations. In all three cases, the construction and maintenance of ecological niches helps drive the continued selection of traditional human, worm, and beaver genes which influences the evolution of the organisms for generations.