Finally, this alignment was used as the input of NeighborNet program in SplitsTree v4. In addition, a statistical analysis was carried out by the pair-wise homoplasy index PHI test Bruen et al. After we constructed the phylogenetic network and carried out the PHI statistical test for recombination, we employed seven different methods, the RDP Martin et al. The breakpoint position of recombination events was determined by RDP4 using a hidden Markov model.
In this process, we identified the recombination events separately for each of eligible multiple alignments. And then, all the outputs of RDP4 were parsed to get the simplified and reliable results, but we only considered those recombination events that at least five out of seven methods showed the significant P -value. Finally, we performed the statistical analysis, as well as the association analysis of recombination with environmental factors. The identification and functional analysis of RDIGs may be important for exploring the biological significance of recombination because recombinational DSBs were previously reported to be an extraordinarily non-random distribution along the whole genome Lam et al.
Here we used the S. In this process, the procedure firstly identified the significantly enriched results according to the P -values by Chi-square test and Fisher exact test. And then, the P -values of gene set enrichment were further adjusted by the default method fdr to filter out those false-positive results. Finally, we took the cutoff of 0. First, orthologous relationships of gene between strains were identified by OrthoMCL software Li et al.
As shown in Supplementary Figure S1, a complex and reticulate tree topology structure was presented, which indicated the presence of significantly conflicting phylogenetic signals. Generally, conflicting signals were caused by genetic recombination. Thus, a more comprehensive assessment of recombination events was necessary for the insight into the underlying biological significance. There were totally blocks after filtering the ineligible blocks. By PHI test analysis, we detected the statistically significant evidence of recombination in the 42 budding yeast strains.
According to the overlapping relationships constructed by Venn diagram, we found very few recombination events with significant signals detected by only one method Fig. Comparison of the results obtained from seven detection methods of recombination. By linear regression analysis, we found that the number of recombination events was positively correlated to the length of chromosomes with a correlation coefficient of 0.
Adaptation - Wikipedia
S3a , but the average length of recombination events had almost no correlation to the length of chromosomes with an insignificant correlation coefficient of 0. Remarkably, in the smallest four chromosomes, the average length of recombination events had an obvious positive correlation to the length of chromosomes, but the number of recombination events had a strong negative correlation to the length of chromosomes, which was in accordance with previous experimental findings on the smallest four chromosomes that the number of recombination events decreased with the length of chromosomes Gerton et al.
In addition, we also estimated the guanine-cytosine GC content of recombination sequences, finding that sequences from recombination events had slightly lower GC contents than those in genomic sequences Supplementary Fig. In order to investigate the correlations between recombination and geographical or environmental factors, we constructed the network relationship of recombination events, which clearly showed the intricate relationship of recombination among strains from different sources.
By this network diagram Supplementary Fig. S5 , we observed that recombination appeared to occur more frequently in clinical strains than non-clinical strains, indicating that these strains in clinical environments suffered from stronger selection pressures, because there always existed a large number of exogenous agents like pharmaceuticals and ionizing radiation.
In order to assess whether the number and length of recombination events in clinical environments differed significantly from those in other environments, we carried out the Wilcoxon test to detect the statistical significance of difference between any two environments. As a result, we found the number of recombination events in clinical environments was obviously more than that in the other two environments wine and other, respectively Fig.
These findings indicated that strains from harmful environments had significantly more genetic combination than those from benign environments, which was in accordance with what had been observed in the fungus Arthrobotrys oligospora Zhang et al. Relationship between environmental factors and recombination. Significance of above two analysis is estimated by the pairwise Wilcoxon test. Clinic, wine and other refer to the clinical, wine and other environments respectively. As a result, we found that DSBs were obviously distributed non-randomly along chromosomes Fig.
Actually, RDIGs were such genes spliced together by different portions of two homologous genes, therefore they also belonged to the mosaic genes. Considering that perfect complementary pairings of invasive strand with template were crucial for the initiation of HR Maher et al. Distribution of DSBs along the genome of strain Sc. And there were two cancer pathways prostate cancer and chemical carcinogenesis, respectively , which was in accordance with previous findings that inaccurate repair of DSBs was related to the development of certain cancer Dexheimer, , and defects of recombination predisposed to cancer Martino et al.
There were also three other disease pathways, the non-alcoholic fatty liver disease, measles, fluid shear stress and atherosclerosis, respectively. Indeed, growing evidence pointed to the association of DNA damages with metabolic syndromes, such as non-alcoholic fatty liver disease and atherosclerosis Gray et al. As to the enrichment of measles pathway, previous experimental study observed a similar result that all the measles cases had an obviously increased frequency of DSBs Koskull et al.
Moreover, there were also five disease-related pathways, namely the IL signaling pathway, oxidative phosphorylation, antigen processing and presentation, Th17 cell differentiation and cardiac muscle contraction, respectively. Moreover, there were also some pathways related to specific adaptability. For instance, estrogen signaling pathway regulated a plethora of physiological processes in mammals including cardiovascular protection, reproduction and behavior Rotroff et al.
Rich factor is the ratio of the number of HRDIGs annotated in this pathway to the number of all genes annotated in this pathway. Climate Risk Management Volume 16 , , Pages Under a Creative Commons license. Abstract The risk of residential overheating and mortality is increasing due to the effects of global warming and the urban heat island effect and needs to be addressed through climate change adaptation.
Keywords Urban climate change adaptation. That is the result of the birth compromise. Much of the problem comes from our upright bipedal stance, without which our pelvis could be shaped more suitably for birth. Neanderthals had a similar problem. As another example, the long neck of a giraffe is a burden and a blessing. However, as previously stated, there is always a trade-off. This long neck is heavy and it adds to the body mass of a giraffe, so the giraffe needs an abundance of nutrition to provide for this costly adaptation. Pre-adaptation occurs when a population has characteristics which by chance are suited for a set of conditions not previously experienced.
For example, the polyploid cordgrass Spartina townsendii is better adapted than either of its parent species to their own habitat of saline marsh and mud-flats. Pre-adaptation may arise because a natural population carries a huge quantity of genetic variability. Features that now appear as adaptations sometimes arose by co-option of existing traits, evolved for some other purpose.
The classic example is the ear ossicles of mammals , which we know from paleontological and embryological evidence originated in the upper and lower jaws and the hyoid bone of their synapsid ancestors, and further back still were part of the gill arches of early fish. Some traits do not appear to be adaptive, that is, they have a neutral or deleterious effect on fitness in the current environment. Because genes have pleiotropic effects, not all traits may be functional: Another possibility is that a trait may have been adaptive at some point in an organism's evolutionary history, but a change in habitats caused what used to be an adaptation to become unnecessary or even maladapted.
Such adaptations are termed vestigial. Many organisms have vestigial organs, which are the remnants of fully functional structures in their ancestors.
As a result of changes in lifestyle the organs became redundant, and are either not functional or reduced in functionality. Since any structure represents some kind of cost to the general economy of the body, an advantage may accrue from their elimination once they are not functional.
If a population cannot move or change sufficiently to preserve its long-term viability, then obviously, it will become extinct, at least in that locale. The species may or may not survive in other locales. Species extinction occurs when the death rate over the entire species exceeds the birth rate for a long enough period for the species to disappear. It was an observation of Van Valen that groups of species tend to have a characteristic and fairly regular rate of extinction.
Just as there is co-adaptation, there is also coextinction, the loss of a species due to the extinction of another with which it is coadapted, as with the extinction of a parasitic insect following the loss of its host, or when a flowering plant loses its pollinator, or when a food chain is disrupted. Adaptation raises philosophical issues concerning how biologists speak of function and purpose, as this carries implications of evolutionary history — that a feature evolved by natural selection for a specific reason — and potentially of supernatural intervention — that features and organisms exist because of a deity's conscious intentions.
On the other hand, biologists want to deny conscious purpose in evolution. The dilemma gave rise to a famous joke by the evolutionary biologist Haldane: Biologists no longer feel obligated to apologize for their use of teleological language; they flaunt it. From Wikipedia, the free encyclopedia. It has been suggested that Niche adaptation be merged into this article. Discuss Proposed since July This article is about the evolutionary process. For other uses, see Adaptation disambiguation.
Not to be confused with Adoption or Acclimatization. Introduction to evolution Evidence of evolution Common descent. History of evolutionary theory. Applications of evolution Biosocial criminology Ecological genetics Evolutionary aesthetics Evolutionary anthropology Evolutionary computation Evolutionary ecology Evolutionary economics Evolutionary epistemology Evolutionary ethics Evolutionary game theory Evolutionary linguistics Evolutionary medicine Evolutionary neuroscience Evolutionary physiology Evolutionary psychology Experimental evolution Phylogenetics Paleontology Selective breeding Speciation experiments Sociobiology Systematics Universal Darwinism.
Evolution as fact and theory Social effects Creation—evolution controversy Objections to evolution Level of support. History of evolutionary thought. The Modern Synthesis . Fitness biology and Fitness landscape. Diversity, Evolution, and Inheritance .
The Modern Synthesis . Spandrel biology and Vestigiality. Adaptationism and Teleology in biology. Adaptive evolution in the human genome Adaptive memory Adaptive mutation Adaptive system Anti-predator adaptation Body reactivity Ecological trap Evolutionary pressure Evolvability Intragenomic conflict Neutral theory of molecular evolution.
How Aristotle Invented Science. Evolution The History of an Idea Revised ed. University of California Press. A Dictionary of Science. Oxford Paperback Reference 6th ed. Any change in the structure or functioning of successive generations of a population that makes it better suited to its environment. Genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes" PDF. Model Systems for Evolutionary Biology". Annual Review of Ecology and Systematics. The niche is the central concept in evolutionary ecology; see especially part II: Analysis of Complex Diseases: Climate Change Impact on Livestock: The Science of Mind and Behaviour 6th ed.
Proceedings of the Royal Society B. The Journal of Experimental Biology. Annual Review of Anthropology. Michael October 12, This sequence tells how Darwin's ideas on adaptation developed as he came to appreciate it as "a continuing dynamic process. University of Chicago Press. Journal of Evolutionary Biology. American Association for the Advancement of Science.
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Journal of Experimental Biology. American Journal of Physical Anthropology. A critique of ideas on the evolution of giraffe".
Journal of Agricultural Research. United States Department of Agriculture. A Dictionary of Genetics 7th ed. Dominance [refers] to alleles that fully manifest their phenotype when present in the heterozygous The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism. Charles Darwin was the first to put forward such ideas. Darwin in tells the story of "a web of complex relations" involving heartsease Viola tricolor , red clover Trifolium pratense , bumblebees , mice and cats. The Journal of Philosophy.
A Dictionary of Zoology.
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Oxford Paperback Reference Reissued with new cover and corrections ed. In Webster, Douglas B. The Evolutionary Biology of Hearing. Charles Darwin's Notebooks, Geology, Transmutation of Species, Metaphysical Enquiries. The History of an Idea 3rd completely rev. Hale ; Ford, E.
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