Editing Macroevolution (section)

==Macroevolutionary processes==

=== Speciation ===
{{Main|speciation}}
According to the modern definition, the evolutionary transition from the ancestral to the daughter species is microevolutionary, because it results from selection (or, more generally, sorting) among varying organisms.  However, speciation has also a macroevolutionary aspect, because it produces the interspecific variation species selection operates on.<ref name=":1" /> Another macroevolutionary aspect of speciation is the rate at which it successfully occurs, analogous to reproductive success in microevolution.<ref name=":0" />

Speciation is the process in which populations within one species change to an extent at which they become [[Reproductive isolation|reproductively isolated]], that is, they cannot interbreed anymore. However, this classical concept has been challenged and more recently, a phylogenetic or evolutionary [[species]] concept has been adopted. Their main criteria for new species is to be diagnosable and [[Monophyly|monophyletic]], that is, they form a clearly defined lineage.<ref>{{Cite journal |last=Luckow |first=Melissa |date=1995 |title=Species Concepts: Assumptions, Methods, and Applications |url=https://www.jstor.org/stable/2419812 |journal=Systematic Botany |volume=20 |issue=4 |pages=589–605 |doi=10.2307/2419812 |jstor=2419812 |issn=0363-6445|url-access=subscription }}</ref><ref>{{Cite journal |last1=Frost |first1=Darrel R. |last2=Hillis |first2=David M. |date=1990 |title=Species in Concept and Practice: Herpetological Applications |url=https://www.jstor.org/stable/3892607 |journal=Herpetologica |volume=46 |issue=1 |pages=86–104 |jstor=3892607 |issn=0018-0831}}</ref>

[[Charles Darwin]] first discovered that speciation can be extrapolated so that species not only evolve into new species, but also into new [[Genus|genera]], families and other groups of animals. In other words, macroevolution is reducible to microevolution through selection of traits over long periods of time.<ref>{{Cite journal|last=Greenwood|first=P. H.|title=Macroevolution - myth or reality ?|journal=Biological Journal of the Linnean Society|year=1979|volume=12|issue=4|pages=293–304|doi=10.1111/j.1095-8312.1979.tb00061.x}}</ref> In addition, some scholars have argued that selection at the species level is important as well.<ref>{{Cite journal|last=Grantham|first=T A|date=November 1995|title=Hierarchical Approaches to Macroevolution: Recent Work on Species Selection and the "Effect Hypothesis"|journal=Annual Review of Ecology and Systematics|language=en|volume=26|issue=1|pages=301–321|doi=10.1146/annurev.es.26.110195.001505|bibcode=1995AnRES..26..301G |issn=0066-4162}}</ref> The advent of genome sequencing enabled the discovery of gradual genetic changes both during speciation but also across higher taxa. For instance, the evolution of humans from ancestral primates or other mammals can be traced to numerous but individual mutations.<ref>{{Cite journal |last1=Foley |first1=Nicole M. |last2=Mason |first2=Victor C. |last3=Harris |first3=Andrew J. |last4=Bredemeyer |first4=Kevin R. |last5=Damas |first5=Joana |last6=Lewin |first6=Harris A. |last7=Eizirik |first7=Eduardo |last8=Gatesy |first8=John |last9=Karlsson |first9=Elinor K. |last10=Lindblad-Toh |first10=Kerstin |last11=Zoonomia Consortium‡ |last12=Springer |first12=Mark S. |last13=Murphy |first13=William J. |last14=Andrews |first14=Gregory |last15=Armstrong |first15=Joel C. |date=2023-04-28 |title=A genomic timescale for placental mammal evolution |journal=Science |language=en |volume=380 |issue=6643 |pages=eabl8189 |doi=10.1126/science.abl8189 |issn=0036-8075 |pmc=10233747 |pmid=37104581}}</ref>

=== Evolution of new organs and tissues ===
One of the main questions in evolutionary biology is how new structures evolve, such as new [[Organ (biology)|organs]]. Macroevolution is often thought to require the evolution of structures that are 'completely new'. However, fundamentally novel structures are not necessary for dramatic evolutionary change. As can be seen in [[Vertebrate|vertebrate evolution]], most "new" organs are actually not new—they are simply modifications of previously existing organs. For instance, the evolution of [[mammal]] diversity in the past 100 million years has not required any major innovation.<ref>{{Cite journal |last1=Meredith |first1=R. W. |last2=Janecka |first2=J. E. |last3=Gatesy |first3=J. |last4=Ryder |first4=O. A. |last5=Fisher |first5=C. A. |last6=Teeling |first6=E. C. |last7=Goodbla |first7=A. |last8=Eizirik |first8=E. |last9=Simao |first9=T. L. L. |last10=Stadler |first10=T. |last11=Rabosky |first11=D. L. |last12=Honeycutt |first12=R. L. |last13=Flynn |first13=J. J. |last14=Ingram |first14=C. M. |last15=Steiner |first15=C. |date=2011-10-28 |title=Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification |url=https://www.sciencemag.org/lookup/doi/10.1126/science.1211028 |journal=Science |language=en |volume=334 |issue=6055 |pages=521–524 |doi=10.1126/science.1211028 |pmid=21940861 |bibcode=2011Sci...334..521M |s2cid=38120449 |issn=0036-8075|url-access=subscription }}</ref> All of this diversity can be explained by modification of existing organs, such as the evolution of [[Tusk|elephant tusks]] from [[Incisor|incisors]]. Other examples include [[Bird wing|wings]] (modified limbs), [[feather]]s (modified [[reptile scale]]s),<ref>{{Cite journal |last1=Wu |first1=Ping |last2=Yan |first2=Jie |last3=Lai |first3=Yung-Chih |last4=Ng |first4=Chen Siang |last5=Li |first5=Ang |last6=Jiang |first6=Xueyuan |last7=Elsey |first7=Ruth M |last8=Widelitz |first8=Randall |last9=Bajpai |first9=Ruchi |last10=Li |first10=Wen-Hsiung |last11=Chuong |first11=Cheng-Ming |date=2017-11-21 |title=Multiple Regulatory Modules Are Required for Scale-to-Feather Conversion |url=|journal=Molecular Biology and Evolution |volume=35 |issue=2 |pages=417–430 |doi=10.1093/molbev/msx295 |issn=0737-4038 |pmc=5850302 |pmid=29177513}}</ref> [[lung]]s (modified [[swim bladder]]s, e.g. found in [[fish]]),<ref>{{Cite journal |last=Brainerd |first=E. L. |date=1999-12-01 |title=New perspectives on the evolution of lung ventilation mechanisms in vertebrates |url=|journal=Experimental Biology Online |language=en |volume=4 |issue=2 |pages=1–28 |doi=10.1007/s00898-999-0002-1 |bibcode=1999EvBO....4b...1B |s2cid=35368264 |issn=1430-3418}}</ref><ref>{{Cite journal |last1=Hoffman |first1=M. |last2=Taylor |first2=B. E. |last3=Harris |first3=M. B. |date=2016-04-01 |title=Evolution of lung breathing from a lungless primitive vertebrate |journal=Respiratory Physiology & Neurobiology |series=Physiology of respiratory networks of non-mammalian vertebrates |language=en |volume=224 |pages=11–16 |doi=10.1016/j.resp.2015.09.016 |issn=1569-9048 |pmc=5138057 |pmid=26476056}}</ref> or even the [[heart]] (a muscularized segment of a [[vein]]).<ref>{{Cite journal |last1=Jensen |first1=Bjarke |last2=Wang |first2=Tobias |last3=Christoffels |first3=Vincent M. |last4=Moorman |first4=Antoon F. M. |date=2013-04-01 |title=Evolution and development of the building plan of the vertebrate heart |journal=Biochimica et Biophysica Acta (BBA) - Molecular Cell Research |series=Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction |language=en |volume=1833 |issue=4 |pages=783–794 |doi=10.1016/j.bbamcr.2012.10.004 |pmid=23063530 |s2cid=28787569 |issn=0167-4889|doi-access=free }}</ref>

The same concept applies to the evolution of "novel" tissues. Even fundamental tissues such as [[bone]] can evolve from combining existing [[protein]]s ([[collagen]]) with calcium phosphate (specifically, [[Hydroxyapatite|hydroxy-apatite]]). This probably happened when certain cells that make collagen also accumulated calcium phosphate to get a proto-bone cell.<ref>{{Cite journal |last1=Wagner |first1=Darja Obradovic |last2=Aspenberg |first2=Per |date=2011-08-01 |title=Where did bone come from? |url=|journal=Acta Orthopaedica |volume=82 |issue=4 |pages=393–398 |doi=10.3109/17453674.2011.588861 |issn=1745-3674 |pmc=3237026 |pmid=21657973}}</ref>

=== Molecular macroevolution ===
Microevolution is facilitated by [[mutation]]s, the vast majority of which have no or very small effects on gene or protein function. For instance, the activity of an [[enzyme]] may be slightly changed or the stability of a protein slightly altered. However, occasionally mutations can dramatically change the structure and functions of protein. This may be called "molecular macroevolution".

[[File:PDB 2aj4 EBI.png|thumb|The metabolic enzyme [[galactokinase]] can be converted to a [[transcription factor]] (in [[Saccharomyces cerevisiae|yeast]]) by just a 2 amino-acid insertion.]]

'''Protein function'''. There are countless cases in which protein function is dramatically altered by mutations. For instance, a mutation in [[acetaldehyde dehydrogenase]] (EC:1.2.1.10) can change it to a [[4-hydroxy-2-oxovalerate aldolase|4-hydroxy-2-oxopentanoate pyruvate lyase]] (EC:4.1.3.39), i.e., a mutation that changes an [[enzyme]] from one to another [[Enzyme Commission number|EC]] class (there are only 7 main classes of enzymes).<ref>{{Cite journal |last1=Tyzack |first1=Jonathan D |last2=Furnham |first2=Nicholas |last3=Sillitoe |first3=Ian |last4=Orengo |first4=Christine M |last5=Thornton |first5=Janet M |date=2017-12-01 |title=Understanding enzyme function evolution from a computational perspective |journal=Current Opinion in Structural Biology |series=Protein–nucleic acid interactions • Catalysis and regulation |language=en |volume=47 |pages=131–139 |doi=10.1016/j.sbi.2017.08.003 |pmid=28892668 |issn=0959-440X|doi-access=free }}</ref> Another example is the conversion of a [[yeast]] [[galactokinase]] (Gal1) to a [[transcription factor]] (Gal3) which can be achieved by an insertion of only two amino acids.<ref>{{Cite journal |last1=Platt |first1=A. |last2=Ross |first2=H. C. |last3=Hankin |first3=S. |last4=Reece |first4=R. J. |date=2000-03-28 |title=The insertion of two amino acids into a transcriptional inducer converts it into a galactokinase |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=97 |issue=7 |pages=3154–3159 |doi=10.1073/pnas.97.7.3154 |issn=0027-8424 |pmc=16208 |pmid=10737789|bibcode=2000PNAS...97.3154P |doi-access=free }}</ref>

While some mutations may not change the molecular function of a protein significantly, their biological function may be dramatically changed. For instance, most brain receptors recognize specific neurotransmitters, but that specificity can easily be changed by mutations. This has been shown by [[acetylcholine receptor]]s that can be changed to [[serotonin]] or [[glycine receptor]]s which actually have very different functions. Their similar gene structure also indicates that they must have arisen from [[gene duplication]]s.<ref>{{Cite journal |last1=Uetz |first1=Peter |last2=Abdelatty |first2=Fawzy |last3=Villarroel |first3=Alfredo |last4=Rappold |first4=Gudrun |author-link4=Gudrun Rappold |last5=Weiss |first5=Birgit |last6=Koenen |first6=Michael |date=1994-02-21 |title=Organisation of the murine 5-HT 3 receptor gene and assignment tohuman chromosome 11 |journal=FEBS Letters |language=en |volume=339 |issue=3 |pages=302–306 |doi=10.1016/0014-5793(94)80435-4 |pmid=8112471 |s2cid=28979681 |doi-access=free|bibcode=1994FEBSL.339..302U }}</ref>

'''Protein structure'''. Although protein structures are highly conserved, sometimes one or a few mutations can dramatically change a protein. For instance, an [[Insulin-like growth factor-binding protein|IgG-binding]], 4<math>\beta</math>+<math>\alpha</math> fold can be transformed into an [[albumin]]-binding, 3-α fold via a single amino-acid mutation. This example also shows that such a transition can happen with neither function nor native structure being completely lost.<ref>{{Cite journal |last1=Alexander |first1=Patrick A. |last2=He |first2=Yanan |last3=Chen |first3=Yihong |last4=Orban |first4=John |last5=Bryan |first5=Philip N. |date=2009-12-15 |title=A minimal sequence code for switching protein structure and function |journal=Proceedings of the National Academy of Sciences |language=en |volume=106 |issue=50 |pages=21149–21154 |doi=10.1073/pnas.0906408106 |issn=0027-8424 |pmc=2779201 |pmid=19923431|doi-access=free }}</ref> In other words, even when multiple mutations are required to convert one protein or structure into another, the structure and function is at least partially retained in the intermediary sequences. Similarly, [[Protein domain|domains]] can be converted into other domains (and thus other functions). For instance, the structures of [[SH3 domain|SH3]] folds can evolve into [[OB-fold|OB folds]] which in turn can evolve into CLB folds.<ref>{{Cite journal |last1=Alvarez-Carreño |first1=Claudia |last2=Gupta |first2=Rohan J. |last3=Petrov |first3=Anton S. |last4=Williams |first4=Loren Dean |date=2022-12-27 |title=Creative destruction: New protein folds from old |journal=Proceedings of the National Academy of Sciences |language=en |volume=119 |issue=52 |pages=e2207897119 |doi=10.1073/pnas.2207897119 |doi-access=free |pmid=36534803 |pmc=9907106 |bibcode=2022PNAS..11907897A |s2cid=254907939 |issn=0027-8424}}</ref>