Editing Common descent (section)

==Evidence==
{{further|Evidence of common descent}}

===Common biochemistry===

All known forms of life are based on the same fundamental biochemical organization: genetic information encoded in [[DNA]], transcribed into [[RNA]], through the effect of [[protein]]- and RNA-[[enzyme]]s, then translated into proteins by (highly similar) [[ribosome]]s, with [[Adenosine triphosphate|ATP]], [[Nicotinamide adenine dinucleotide phosphate|NADPH]] and others as energy sources. Analysis of small sequence differences in widely shared substances such as [[cytochrome c]] further supports universal common descent.<ref name=Knight>{{cite journal |last1=Knight |first1=Robin |last2=Freeland |first2=Stephen J. |last3=Landweber |first3=Laura F. |date=January 2001 |title=Rewiring the keyboard: evolvability of the genetic code |journal=[[Nature Reviews Genetics]] |volume=2 |issue=1 |pages=49–58 |doi=10.1038/35047500 |pmid=11253070 |s2cid=12267003 }}</ref> Some 23 proteins are found in all organisms, serving as [[enzyme]]s carrying out core functions like DNA replication. The fact that only one such set of enzymes exists is convincing evidence of a single ancestry.<ref name="theobald" /><ref name="Than2010">{{cite magazine |last1=Than|first1=Ker |title=All Species Evolved From Single Cell, Study Finds |url=https://news.nationalgeographic.com/news/2010/05/100513-science-evolution-darwin-single-ancestor/ |archive-url=https://web.archive.org/web/20100515123853/http://news.nationalgeographic.com/news/2010/05/100513-science-evolution-darwin-single-ancestor |url-status=dead |archive-date=May 15, 2010 |magazine=National Geographic |access-date=22 November 2017 |date=14 May 2010}}</ref> 6,331 [[gene]]s common to all living animals have been identified; these may have arisen from a single [[Animal#Phylogeny|common ancestor]] that lived [[Cryogenian|650 million years ago]] in the [[Precambrian]].<ref name="NYT-20180504">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=The Very First Animal Appeared Amid an Explosion of DNA |url=https://www.nytimes.com/2018/05/04/science/first-animal-genes-evolution.html |archive-url=https://ghostarchive.org/archive/20220101/https://www.nytimes.com/2018/05/04/science/first-animal-genes-evolution.html |archive-date=2022-01-01 |url-access=limited |date=4 May 2018 |work=[[The New York Times]] |access-date=4 May 2018 }}{{cbignore}}</ref><ref name="NC-20150430">{{cite journal |last1=Paps |first1=Jordi |last2=Holland |first2=Peter W. H. |title=Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty |date=30 April 2018 |journal=[[Nature Communications]] |volume=9 |pages=1730 |number=1730 (2018) |doi=10.1038/s41467-018-04136-5 |pmid=29712911 |pmc=5928047 |bibcode=2018NatCo...9.1730P }}</ref>

===Common genetic code===
{{further|Genetic code}}
{| class="wikitable floatright" style="border: none; text-align: center;"
| '''[[Amino acid]]s'''
| style="background-color:#ffe75f; width: 50px;" | nonpolar
| style="background-color:#b3dec0; width: 50px;" | polar
| style="background-color:#bbbfe0; width: 50px;" | basic
| style="background-color:#f8b7d3; width: 50px;" | acidic
| style="border: none; width: 75px;" |
| style="background-color:#B0B0B0;" | Stop codon
|}

{| class="wikitable floatright"
|+ Standard genetic code
!rowspan=2| 1st<br />base
!colspan=8| 2nd base
|-
!colspan=2| {{{T|T}}}
!colspan=2| C
!colspan=2| A
!colspan=2| G
|-

!rowspan=4| {{{T|T}}}
| {{{T|T}}}{{{T|T}}}{{{T|T}}}
|rowspan=2 style="background-color:#ffe75f" | [[Phenylalanine|Phenyl-<br>alanine]]
| {{{T|T}}}C{{{T|T}}}
|rowspan=4 style="background-color:#b3dec0" | [[Serine]]
| {{{T|T}}}A{{{T|T}}}
|rowspan=2 style="background-color:#b3dec0" | [[Tyrosine]]
| {{{T|T}}}G{{{T|T}}}
|rowspan=2 style="background-color:#b3dec0" | [[Cysteine]]

|-
| {{{T|T}}}{{{T|T}}}C
| {{{T|T}}}CC
| {{{T|T}}}AC
| {{{T|T}}}GC

|-
| {{{T|T}}}{{{T|T}}}A
|rowspan=6 style="background-color:#ffe75f" | [[Leucine]]
| {{{T|T}}}CA
| {{{T|T}}}AA
| style="background-color:#B0B0B0;" | [[Stop codon|Stop]] <!--(''Ochre'')-->
| {{{T|T}}}GA
| style="background-color:#B0B0B0;" | [[Stop codon|Stop]] <!--(''Opal'')-->

|-
| {{{T|T}}}{{{T|T}}}G
| {{{T|T}}}CG
| {{{T|T}}}AG
| style="background-color:#B0B0B0;" | [[Stop codon|Stop]] <!--(''Amber'')-->
| {{{T|T}}}GG
| style="background-color:#ffe75f;" | [[Tryptophan]]&nbsp;<!-- to make the columns roughly the same width -->

|-

! rowspan="4" | C
| C{{{T|T}}}{{{T|T}}}
| CC{{{T|T}}}
|rowspan=4 style="background-color:#ffe75f" | [[Proline]]
| CA{{{T|T}}}
|rowspan=2 style="background-color:#bbbfe0" | [[Histidine]]
|CG{{{T|T}}}
|rowspan=4 style="background-color:#bbbfe0" | [[Arginine]]

|-
|C{{{T|T}}}C
|CCC
|CAC
|CGC

|-
|C{{{T|T}}}A
|CCA
|CAA
|rowspan=2 style="background-color:#b3dec0" | [[Glutamine]]
|CGA

|-
|C{{{T|T}}}G
|CCG
|CAG
|CGG

|-

! rowspan="4" | A
|A{{{T|T}}}{{{T|T}}}
|rowspan=3 style="background-color:#ffe75f" | [[Isoleucine]]
|AC{{{T|T}}}
|rowspan=4 style="background-color:#b3dec0" | [[Threonine]]&nbsp;<!-- to make the columns roughly the same width -->
|AA{{{T|T}}}
|rowspan=2 style="background-color:#b3dec0" | [[Asparagine]]
|AG{{{T|T}}}
|rowspan=2 style="background-color:#b3dec0" | [[Serine]]

|-
|A{{{T|T}}}C
|ACC
|AAC
|AGC

|-
|A{{{T|T}}}A
|ACA
|AAA
|rowspan=2 style="background-color:#bbbfe0" | [[Lysine]]
|AGA
|rowspan=2 style="background-color:#bbbfe0" | [[Arginine]]

|-
|A{{{T|T}}}G
| style="background-color:#ffe75f;" | [[Methionine]]
|ACG
|AAG
|AGG

|-

! rowspan="4" | G
|G{{{T|T}}}{{{T|T}}}
|rowspan=4 style="background-color:#ffe75f" | [[Valine]]
|GC{{{T|T}}}
|rowspan=4 style="background-color:#ffe75f" | [[Alanine]]
|GA{{{T|T}}}
|rowspan=2 style="background-color:#f8b7d3" | [[Aspartic acid|Aspartic<br>acid]]
|GG{{{T|T}}}
|rowspan=4 style="background-color:#ffe75f" | [[Glycine]]

|-
|G{{{T|T}}}C
|GCC
|GAC
|GGC

|-
|G{{{T|T}}}A
|GCA
|GAA
|rowspan=2 style="background-color:#f8b7d3" | [[Glutamic acid|Glutamic<br>acid]]
|GGA

|-
|G{{{T|T}}}G
|GCG
|GAG
|GGG

|-
|}

The [[genetic code]] (the "translation table" according to which DNA information is translated into [[amino acid]]s, and hence proteins) is nearly identical for all known lifeforms, from [[bacteria]] and [[archaea]] to [[animal]]s and [[plant]]s. The universality of this code is generally regarded by biologists as definitive evidence in favor of universal common descent.<ref name=Knight/>

The way that [[Genetic code|codon]]s (DNA triplets) are mapped to [[amino acid]]s seems to be strongly optimised. Richard Egel argues that in particular the [[hydrophobic]] (non-polar) side-chains are well organised, suggesting that these enabled the earliest organisms to create [[peptide]]s with water-repelling regions able to support the essential electron exchange ([[redox]]) reactions for energy transfer.<ref name=Egel>{{cite journal |last1=Egel |first1=Richard |title=Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life |journal=Life |date=March 2012 |volume=2 |issue=1 |pages=170–212 |doi=10.3390/life2010170 |pmc=4187143 |pmid=25382122|bibcode=2012Life....2..170E |doi-access=free }}</ref>

===Selectively neutral similarities===

Similarities which have no adaptive relevance cannot be explained by [[convergent evolution]], and therefore they provide compelling support for universal common descent. Such evidence has come from two areas: [[amino acid]] sequences and DNA sequences. Proteins with the same three-dimensional structure need not have identical amino acid sequences; any irrelevant similarity between the sequences is evidence for common descent. In certain cases, there are several [[Genetic code|codon]]s (DNA triplets) that code redundantly for the same amino acid. Since many species use the same codon at the same place to specify an amino acid that can be represented by more than one codon, that is evidence for their sharing a recent common ancestor. Had the amino acid sequences come from different ancestors, they would have been coded for by any of the redundant codons, and since the correct amino acids would already have been in place, [[natural selection]] would not have driven any change in the codons, however much time was available. [[Genetic drift]] could change the codons, but it would be extremely unlikely to make all the redundant codons in a whole sequence match exactly across multiple lineages. Similarly, shared nucleotide sequences, especially where these are apparently neutral such as the positioning of [[intron]]s and [[pseudogene]]s, provide strong evidence of common ancestry.<ref name="Sharma2005">{{cite book |last=Sharma |first=N. S. |title=Continuity And Evolution Of Animals |url=https://books.google.com/books?id=x7Q47fvCfLIC&pg=PA32 |year=2005 |publisher=Mittal Publications |isbn=978-81-8293-018-6 |pages=32–}}</ref>

===Other similarities===

Biologists often{{quantify|date=March 2018}} point to the universality of many aspects of cellular life as supportive evidence to the more compelling evidence listed above. These similarities include the energy carrier [[adenosine triphosphate]] (ATP), and the fact that all amino acids found in proteins are [[Chirality (chemistry)#In biochemistry|left-handed]]. It is, however, possible that these similarities resulted because of the [[Laws of science|laws of physics and chemistry]] - rather than through universal common descent - and therefore resulted in convergent evolution. In contrast, there is evidence for homology of the central subunits of [[ATPase#Transmembrane ATP synthases|transmembrane ATPases]] throughout all living organisms, especially how the rotating elements are bound to the membrane. This supports the assumption of a LUCA as a cellular organism, although primordial membranes may have been semipermeable and evolved later to the membranes of modern bacteria, and on a second path to those of modern archaea also.<ref>
{{cite book
 |last= Lane |first= Nick |author-link= Nick Lane
 |year= 2015
 |title= The Vital Question: Why Is Life The Way It Is?
 |publisher= Profile Books |isbn= 978-1781250365
 |title-link= The Vital Question
 |page= <!--part 77 of online edition-->
}}
</ref>

===Phylogenetic trees===
{{PhylomapB|size=300px|caption=A [[phylogenetic tree]] based on [[ribosomal RNA]] genes implies a single origin for all life.}}
{{Main |Phylogenetic tree}}
{{See also |Tree of life (biology)}}

Another important piece of evidence is from detailed phylogenetic trees (i.e., "genealogic trees" of species) mapping out the proposed divisions and common ancestors of all living species. In 2010, Douglas L. Theobald published a statistical analysis of available genetic data,<ref name="theobald" /> mapping them to phylogenetic trees, that gave "strong quantitative support, by a formal test, for the unity of life."<ref name="steel" />

Traditionally, these trees have been built using morphological methods, such as appearance, [[embryology]], etc. Recently, it has been possible to construct these trees using molecular data, based on similarities and differences between genetic and protein sequences. All these methods produce essentially similar results, even though most [[genetic variation]] has no influence over external morphology. That phylogenetic trees based on different types of information agree with each other is strong evidence of a real underlying common descent.<ref>{{cite web |url=http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence |title=Prediction 1.3: Consilience of independent phylogenies |last=Theobald |first=Douglas L. |work=29+ Evidences for Macroevolution: The Scientific Case for Common Descent |version=Version 2.89 |publisher=[[TalkOrigins Archive|The TalkOrigins Foundation]] |access-date=2009-11-20}}</ref>