Editing Natural selection (section)

==Evolution by means of natural selection==
{{Main|Evolution|Darwinism}}

A prerequisite for natural selection to result in adaptive evolution, novel traits and speciation is the presence of heritable genetic variation that results in fitness differences. Genetic variation is the result of mutations, [[genetic recombination]]s and alterations in the [[karyotype]] (the number, shape, size and internal arrangement of the [[chromosome]]s). Any of these changes might have an effect that is highly advantageous or highly disadvantageous, but large effects are rare. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in [[noncoding DNA]] or resulted in a [[synonymous substitution]]. However, many mutations in [[non-coding DNA]] have deleterious effects.<ref name="NCFitnessEffects">{{cite journal |last1=Kryukov |first1=Gregory V. |last2=Schmidt |first2=Steffen |last3=Sunyaev |first3=Shamil |date=1 August 2005 |title=Small fitness effect of mutations in highly conserved non-coding regions |journal=[[Human Molecular Genetics]] |volume=14 |issue=15 |pages=2221–2229 |doi=10.1093/hmg/ddi226 |pmid=15994173|doi-access=free }}</ref><ref name="NCFitnessEffects2">{{cite journal |last1=Bejerano |first1=Gill |last2=Pheasant |first2=Michael |last3=Makunin |first3=Igor |last4=Stephen |first4=Stuart |last5=Kent |first5=W. James |last6=Mattick |first6=John S. |last7=Haussler |first7=David |display-authors=3 |date=28 May 2004 |title=Ultraconserved Elements in the Human Genome |journal=Science |volume=304 |issue=5675 |pages=1321–1325 |doi=10.1126/science.1098119 |pmid=15131266|url=http://www.bx.psu.edu/~ross/ComparGeno/BejeranoUCEsSci.pdf |bibcode=2004Sci...304.1321B |citeseerx=10.1.1.380.9305 |s2cid=2790337 }}</ref> Although both mutation rates and average fitness effects of mutations are dependent on the organism, a majority of mutations in humans are slightly deleterious.<ref name="Eyre-Walker">{{cite journal |last1=Eyre-Walker |first1=Adam |last2=Woolfit |first2=Megan |last3=Phelps |first3=Ted |date=June 2006 |title=The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans |journal=[[Genetics (journal)|Genetics]] |volume=173 |issue=2 |pages=891–900 |doi=10.1534/genetics.106.057570 |pmc=1526495 |pmid=16547091}}</ref>

Some mutations occur in [[evo-devo gene toolkit|"toolkit" or regulatory genes]]. Changes in these often have large effects on the phenotype of the individual because they regulate the function of many other genes. Most, but not all, mutations in regulatory genes result in non-viable embryos. Some nonlethal regulatory mutations occur in [[Homeobox#Hox genes|HOX genes]] in humans, which can result in a [[cervical rib]]<ref>{{cite journal |last=Galis |first=Frietson |date=April 1999 |title=Why do almost all mammals have seven cervical vertebrae? Developmental constraints, ''Hox'' genes, and cancer |journal=[[Journal of Experimental Zoology]]|volume=285 |issue=1 |pages=19–26 |doi=10.1002/(SICI)1097-010X(19990415)285:1<19::AID-JEZ3>3.0.CO;2-Z |pmid=10327647|bibcode=1999JEZ...285...19G }}</ref> or [[polydactyly]], an increase in the number of fingers or toes.<ref>{{cite journal |last1=Zákány |first1=József |last2=Fromental-Ramain |first2=Catherine |last3=Warot |first3=Xavier |last4=Duboule |first4=Denis |author-link4=Denis Duboule |date=9 December 1997 |title=Regulation of number and size of digits by posterior ''Hox'' genes: A dose-dependent mechanism with potential evolutionary implications |journal=[[Proceedings of the National Academy of Sciences of the United States of America]] |volume=94 |issue=25 |pages=13695–13700 |doi=10.1073/pnas.94.25.13695  |pmc=28368 |pmid=9391088|bibcode=1997PNAS...9413695Z |doi-access=free }}</ref> When such mutations result in a higher fitness, natural selection favours these phenotypes and the novel trait spreads in the population.
Established traits are not immutable; traits that have high fitness in one environmental context may be much less fit if environmental conditions change. In the absence of natural selection to preserve such a trait, it becomes more variable and deteriorate over time, possibly resulting in a [[Vestigiality|vestigial]] manifestation of the trait, also called [[evolutionary baggage]]. In many circumstances, the apparently vestigial structure may retain a limited functionality, or may be co-opted for other advantageous traits in a phenomenon known as [[Exaptation|preadaptation]]. A famous example of a vestigial structure, the eye of the [[Spalax|blind mole-rat]], is believed to retain function in [[Photoperiodism|photoperiod]] perception.<ref name="Sanyal">{{cite journal |last1=Sanyal |first1=Somes |last2=Jansen |first2=Harry G. |last3=de Grip |first3=Willem J. |last4=Nevo |first4=Eviatar |author-link4=Eviatar Nevo |last5=de Jong |first5=Welfried W. |display-authors=4 |date=July 1990 |title=The Eye of the Blind Mole Rat, ''Spalax ehrenbergi''. Rudiment with Hidden Function? |url=http://iovs.arvojournals.org/article.aspx?articleid=2160417 |journal=[[Investigative Ophthalmology & Visual Science]]|volume=31 |issue=7 |pages=1398–1404 |pmid=2142147}}</ref>

===Speciation===
{{Main|Speciation}}
Speciation requires a degree of [[reproductive isolation]]—that is, a reduction in gene flow. However, it is intrinsic to the concept of a [[species]] that [[hybrid (biology)|hybrids]] are selected against, opposing the evolution of reproductive isolation, a problem that was recognised by Darwin. The problem does not occur in [[allopatric]] speciation with geographically separated populations, which can diverge with different sets of mutations. [[E. B. Poulton]] realized in 1903 that reproductive isolation could evolve through divergence, if each lineage acquired a different, incompatible allele of the same gene. Selection against the heterozygote would then directly create reproductive isolation, leading to the [[Bateson–Dobzhansky–Muller model]], further elaborated by [[H. Allen Orr]]<ref>{{cite journal | last1=Orr | first1=H.A. |author-link=H. Allen Orr| title=Dobzhansky, Bateson, and the Genetics of Speciation | journal=Genetics | volume=144 | issue=4 | pages=1331–1335 | year=1996 | doi=10.1093/genetics/144.4.1331 | pmc=1207686 | pmid=8978022 }}</ref> and [[Sergey Gavrilets]].<ref>{{citation |last=Gavrilets |first=S. |title=Fitness Landscapes and the Origin of Species |year=2004 |publisher=Princeton University Press |isbn=978-0-691-11983-0}}</ref> With [[Reinforcement (speciation)|reinforcement]], however, natural selection can favour an increase in pre-zygotic isolation, influencing the process of speciation directly.<ref name="Modes and Mechanisms of Speciation">{{cite journal |title=Modes and Mechanisms of Speciation |author1=Schuler, Hannes |author2=Hood, Glen R. |author3=Egan, Scott P. |author4=Feder, Jeffrey L. | journal=Reviews in Cell Biology and Molecular Medicine | year=2016 | volume=2 | issue=3 | pages=60–93 }}</ref>