Basal (phylogenetics)

{{Short description|Root of a phylogenetic tree}} In [[phylogenetics]], '''basal''' is the direction of the ''base'' (or root) of a [[phylogenetic tree#Rooted tree|rooted phylogenetic tree]] or [[cladogram]]. The term may be more strictly applied only to nodes adjacent to the root, or more loosely applied to nodes regarded as being close to the root. Extant taxa that lie on branches connecting directly to the root are not more closely related to the root than any other extant taxa.<ref name=":0">{{Cite web |last=Smith |first=Stacey |date=2016-09-19 |title=For the love of trees: The ancestors are not among us |url=https://for-the-love-of-trees.blogspot.com/2016/09/the-ancestors-are-not-among-us.html |access-date=2022-03-07 |website=For the love of trees}}</ref><ref name=":1">{{cite journal |author=Crisp, Michael D. |author2=Cook, Lyn G |date=2005 |title=Do early branching lineages signify ancestral traits? |journal=[[Trends in Ecology & Evolution]] |volume=20 |issue=3 |pages=122–128 |doi=10.1016/j.tree.2004.11.010|pmid=16701355 |s2cid=82371239 |doi-access=free }}</ref><ref name=":2">{{cite journal |author=Krell, Frank-T |author2=Cranston, Peter S. |date=2004 |title=Which side of the tree is more basal? |journal=[[Systematic Entomology]] |volume=29 |issue=3 |pages=279–281 |doi=10.1111/j.0307-6970.2004.00262.x |bibcode=2004SysEn..29..279K }}</ref>

While there must always be two or more equally "basal" clades sprouting from the root of every cladogram, those clades may differ widely in [[taxonomic rank]],{{refn|group=n|Meaning the lowest taxonomic ranks of the respective clades; the highest ranks should be the same (assuming they are ranked).}} [[Phylogenetic diversity|species diversity]], or both.{{refn|group=n|See the [[#Flowering plants|''Amborella'' example]], in which one basal clade is a single extant [[species]] (that is also the sole living representative of an [[order (biology)|order]], [[Amborellales]]). Meanwhile, the other (unranked) sister basal clade has about 250,000 species.}} If ''C'' is a basal clade within ''D'' that has the lowest rank of all basal clades within ''D'',{{refn|group=n|For example, ''C'' might be a [[genus]] and the other basal clade(s) might have the higher ranks of [[subfamily]] or [[Family (taxonomy)|family]].}} ''C'' may be described as ''the'' basal [[taxon]] of that rank within ''D''.{{refn|group=n|In the [[#Great apes|great apes example]], ''Gorilla'' is the basal genus of subfamily Homininae, while ''Pongo'' is the basal genus of family Hominidae. The two basal clades of the latter both have the highest rank of subfamily, i.e. Homininae and Ponginae.}} The concept of a '[[key innovation]]' implies some degree of correlation between evolutionary innovation and [[cladogenesis|diversification]].<ref name="Heard1995">{{Cite journal |author=Heard, S.B.|author2= Hauser, D.L.|title= Key evolutionary innovations and their ecological mechanisms |journal= Historical Biology|volume= 10|year= 1995|pages= 151–173|doi= 10.1080/10292389509380518 |issue= 2|bibcode= 1995HBio...10..151H}}</ref><ref name="Engel2004">{{cite journal|last1= Engel|first1= M.S.|last2= Grimaldi|first2= D.A.|title= New light shed on the oldest insect |journal= Nature|volume= 427|issue= 6975|year= 2004|pages= 627–630|doi= 10.1038/nature02291|pmid= 14961119|bibcode= 2004Natur.427..627E|s2cid= 4431205}}</ref><ref name="Fernández-Mazuecos2019">{{cite journal|last1= Fernández-Mazuecos|first1= M.|last2= Blanco-Pastor|first2= J.L.|last3= Juan|first3= A.|last4= Carnicero|first4= P.|last5= Forrest|first5= A.|last6= Alarcón|first6= M.|last7= Vargas|first7= P.|last8= Glover|first8= B.J.|title= Macroevolutionary dynamics of nectar spurs, a key evolutionary innovation |journal= New Phytologist |volume= 222|issue= 2|year= 2019|pages= 1123–1138|doi= 10.1111/nph.15654|pmid= 30570752|bibcode= 2019NewPh.222.1123F|hdl= 10045/89954|s2cid= 58567195|hdl-access= free}}</ref>{{refn|group=n|Greater diversification of a clade may also be associated with colonization of a new land mass, especially if larger or less competitive than the ancestral land mass; see the [[#Relevance to biogeographic history|coral snake, marsupial and noctilionoid bat examples]].}} However, such a correlation does not make a given case predicable, so [[Cladistics#Terminology for character states|ancestral characters]] should not be imputed to the members of a less species-rich basal clade without additional evidence.<ref name=":0" /><ref name=":1" /><ref name="Baum2013">{{cite book|author1=Baum, D. A.|chapter= Phylogenetics and the History of Life|title=The Princeton Guide to Evolution|chapter-url= https://books.google.com/books?id=_XitAAAAQBAJ&pg=PA57|date=4 November 2013|publisher= Princeton University Press|isbn=978-1-4008-4806-5|page=57| oclc= 861200134}}</ref><ref name = "Jenner2006"/>{{refn|group=n|For example, the [[giant panda]] represents the most basal extant species, genus and subfamily within [[Ursidae]],<ref name="krause2008">{{Cite journal | last=Krause | first=J. | author2=Unger, T. | author3=Noçon, A. | author4=Malaspinas, A. | author5=Kolokotronis, S. | author6=Stiller, M. | author7=Soibelzon, L. | author8=Spriggs, H. | author9=Dear, P. H. | author10=Briggs, A. W. | author11=Bray, S. C. E. | author12=O'Brien, S. J. | author13=Rabeder, G. | author14=Matheus, P. | author15=Cooper, A. | author16=Slatkin, M. | author17=Pääbo, S. | author18=Hofreiter, M. | title=Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary | journal=BMC Evolutionary Biology | volume=8 | issue=220 | page=220 | year=2008 | pmid=18662376 | pmc=2518930| doi=10.1186/1471-2148-8-220 | bibcode=2008BMCEE...8..220K | doi-access=free }}</ref> but its specializations for a bamboo diet are not ancestral ursid characters.<ref>{{cite journal | last1 = McLellan | first1 = Bruce | last2 = Reiner | first2 = David C. | year = 1994 | title = A Review of Bear Evolution | journal = Bears: Their Biology and Management | volume = 9 | issue = 1| pages = 85–96 | doi=10.2307/3872687| jstor = 3872687 }}</ref>}}

In general, clade ''A'' is more basal than clade ''B'' if ''B'' is a subgroup of the [[sister group]] of ''A'' or of ''A'' itself.{{refn|group=n|That is, in the diagram below, both basal clades #1 and #2 are more basal than non-basal clade #1, which in turn is more basal than non-basal clades #2 and #3.}} In the context of large groups, the term "basal" is often used loosely to refer to positions closer to the root than the majority, and in such cases, expressions like "very basal" can appear. A 'core clade' refers to the grouping that encompasses all constituent clades except for the basal clade(s) of the lowest rank within a larger clade, exemplified by [[core eudicots]]. No extant taxon is closer to the root of life than any other.

==Usage== A basal group in the stricter sense forms a sister group to the rest of the larger clade,{{cn|date=November 2021}} as in the following case: {{barlabel |size=4 |at1=3 |color=red |label1=Basal clade #2 |cladogram= {{clade |label1=[[Phylogenetic tree#Rooted tree|Root]] |{{clade |1=<span style="color:red;">Basal clade #1</span> |2={{clade|barbegin1=red |1=Non-basal clade #1 |2={{clade |1=Non-basal clade #2|bar1=red |2=Non-basal clade #3|barend2=red }} }} }} }} }}

While it is easy to identify a basal clade in such a cladogram, the appropriateness of such an identification is dependent on the accuracy and completeness of the diagram. It is often assumed in this example that the terminal branches of the cladogram depict ''all'' the extant taxa of a given rank within the clade; this is one reason the term basal is highly deceptive, as the lack of additional species in one clade is taken as evidence of morphological affinity with ancestral taxa. Additionally, this qualification does not ensure that the diversity of extinct taxa (which may be poorly known) is represented.{{cn|date=November 2021}}

In phylogenetics, the term ''basal'' cannot be objectively applied to clades of organisms, but tends to be applied selectively and more controversially to groups or [[Lineage (evolution)|lineages]]{{refn|group=n|Since a lineage is a linear chain of descent, all lineages within a clade can be traced back not only to the root, but to the [[LUCA#Location of the root|origin of life]]. Thus, from a phylogenetic standpoint, the notion of a lineage being basal is nonsensical. However, in genetics, ''[[Lineage (genetic)#Basal lineage|basal lineage]]'' refers to a lineage connecting a common ancestor with a single variant [[allele]] to a branch ancestor with two descendant variants.}} thought to possess ancestral characters, or to such presumed ancestral [[Phenotypic trait|traits]] themselves. In describing characters, "ancestral" or "[[plesiomorphic]]" are preferred to "basal" or "[[primitive (phylogenetics)|primitive]]", the latter of which may carry false connotations of inferiority or a lack of complexity.<ref name=":0" /> The terms <nowiki>''</nowiki>deep-branching<nowiki>''</nowiki> or <nowiki>''</nowiki>early-branching<nowiki>''</nowiki> are similar in meaning, and equally may misrepresent extant taxa that lie on branches connecting directly to the root node as having more ancestral character states.<ref name=":0" /><ref name=":1" />

Despite the ubiquity of the usage of ''basal'', [[systematics|systematists]] try to avoid its usage because its application to extant groups is unnecessary and misleading.<ref name=":2" /> The term is more often applied when one branch (the one deemed "basal") is less diverse than another branch (this being the situation in which one would expect to find a basal taxon of lower ''minimum'' rank). The term may be equivocal in that it also refers to the direction of the root of the tree, which represents a hypothetical ancestor; this consequently may inaccurately imply that the sister group of a more species-rich clade displays ancestral features.<ref name = "Jenner2006">{{cite journal|last=Jenner|first=Ronald A|title=Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney|journal=Development Genes and Evolution|year=2006|volume=216|issue=7–8|pages=385–394|doi=10.1007/s00427-006-0084-5|pmid=16733736|bibcode=2006DGEvo.216..385J |s2cid=23140594}}</ref> An extant basal group may or may not resemble the [[last common ancestor]] of a larger clade to a greater degree than other groups, and is separated from that ancestor by the same amount of time as all other extant groups. However, there are cases where the unusually small size of a sister group does indeed correlate with an unusual number of ancestral traits, as in ''[[Amborella]]'' (see below). This is likely a source of the mis-use of the term. Other famous examples of this phenomenon are the [[oviparous]] reproduction and nipple-less [[lactation]] of [[monotreme]]s, a clade of mammals<ref name = "Rheede2005">{{cite journal | last1 = Van Rheede | first1 = Teun | year = 2005 | title = The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians | journal = Molecular Biology and Evolution | volume = 23 | issue = 3| pages = 587–597 | doi=10.1093/molbev/msj064 | pmid=16291999| title-link = Theria | doi-access = free }}</ref> with just five species, and the archaic anatomy of the [[tuatara]],<ref name="Flores2017">{{cite journal|last1= Herrera-Flores|first1=J. A.|last2= Stubbs|first2=T. L.|last3= Benton|first3=M. J.|last4= Ruta|first4= M.|title= Macroevolutionary patterns in Rhynchocephalia: is the tuatara (''Sphenodon punctatus'') a living fossil?|journal= Palaeontology|volume= 60|issue= 3|year= 2017|pages= 319–328|doi= 10.1111/pala.12284|bibcode=2017Palgy..60..319H |doi-access= free|hdl= 1983/940fdc51-30db-47c0-9ac6-97fda3c2ea01|hdl-access= free}}</ref> a basal clade of [[lepidosauria]]n with a single species.

==Examples== ===Flowering plants=== [[File:Amborella2.jpg|thumb|''[[Amborella trichopoda]]'', the most basal extant angiosperm]] The [[flowering plant]] family [[Amborellaceae]], restricted to [[Biodiversity of New Caledonia|New Caledonia]] in the southwestern Pacific,{{refn|group=n|New Caledonia is viewed as a [[Refugium (population biology)|refugium]]; i.e., in this case the geographic location of the basal clade is not thought to provide evidence for the locale in which angiosperms originated.}} is a [[Basal angiosperms|basal clade of extant angiosperms]],<ref name="Li2019">{{cite journal|last1= Li|first1=H.-T.|last2= Yi|first2=T.-S.|last3= Gao|first3=L.-M.|last4= Ma|first4=P.-F.|last5= Zhang|first5=T.|last6= Yang|first6=J.-B.|last7= Gitzendanner|first7=M.A.|last8= Fritsch|first8=P.W.|last9= Cai|first9=J.|last10= Luo|first10=Y.|last11= Wang|first11=H.|last12=van der Bank|first12=M.|last13= Zhang|first13=S.-D.|last14= Wang|first14=Q.-F.|last15= Wang|first15=J.|last16= Zhang|first16=Z.-R.|last17= Fu|first17=C.-N.|last18= Yang|first18=J.|last19= Hollingsworth|first19=P.M.|last20= Chase|first20=M.W.|last21= Soltis|first21=D.E.|last22= Soltis|first22=P.S.|last23= Li|first23=D.-Z.|title= Origin of angiosperms and the puzzle of the Jurassic gap|journal= Nature Plants |volume= 5|issue= 5|year= 2019|pages= 461–470|doi= 10.1038/s41477-019-0421-0|pmid=31061536|bibcode=2019NatPl...5..461L |s2cid=146118264}}</ref> consisting of the most species, genus, family and order within the group that are sister to all other angiosperms (out of a total of about 250,000 angiosperm species). The traits of ''Amborella trichopoda'' are regarded as providing significant insight into the evolution of flowering plants; for example, it has "the most primitive wood (consisting only of [[tracheid]]s), of any living angiosperm" as well as "simple, separate flower parts of indefinite numbers, and unsealed carpels".<ref name = "Essig2014"/> However, those traits are a mix of archaic and [[apomorphic]] (derived) features that have only been sorted out via comparison with other angiosperms and their positions within the phylogenetic tree (the [[fossil record]] could potentially also be helpful in this respect, but is absent in this case).<ref name = "Essig2014">{{cite web | last = Essig | first = F. B. | title = What's so primitive about ''Amborella''? | work = Botany Professor | date = 2014-07-01 | url = https://botanyprofessor.blogspot.com/2014/07/whats-so-primitive-about-amborella.html | access-date = 2014-10-04 }}</ref> The cladogram below is based on Ramírez-Barahona ''et al.'' (2020),<ref name="Ramírez-Barahona2020">{{cite journal|last1= Ramírez-Barahona|first1= S.|last2= Sauquet|first2= H.|last3= Magallón|first3= S.|title=The delayed and geographically heterogeneous diversification of flowering plant families |journal= Nature Ecology & Evolution |year= 2020|volume= 4|issue= 9|pages= 1232–1238|doi= 10.1038/s41559-020-1241-3|pmid= 32632260|bibcode= 2020NatEE...4.1232R|s2cid= 220375828}}</ref> with species counts taken from the source indicated.

{{barlabel |size=8 |at1=2 |color=green |label='[[Basal angiosperm]]s'|cladogram= {{clade|label1=[[Angiosperms]] |{{Clade|[[Amborellales]] (1 species)<ref name="Palmer2004">{{cite journal|last1= Palmer|first1=J.D.|last2= Soltis|first2=D.E.|last3= Chase|first3=M.W.|title=The plant tree of life: an overview and some points of view|journal= American Journal of Botany|volume= 91|issue= 10|year= 2004|pages= 1437–1445|doi= 10.3732/ajb.91.10.1437|pmid=21652302|bibcode=2004AmJB...91.1437P |doi-access= free}}</ref>|bar1=green |{{Clade|[[Nymphaeales]] (about 90 species)<ref name="Christenhusz-Byng2016">{{cite journal |author1=Christenhusz, M. J. M. |author2=Byng, J. W. | year = 2016 | title = The number of known plants species in the world and its annual increase | journal = Phytotaxa | volume = 261 | pages = 201–217 | url = http://biotaxa.org/Phytotaxa/article/download/phytotaxa.261.3.1/20598 | doi = 10.11646/phytotaxa.261.3.1 | issue = 3 |bibcode=2016Phytx.261..201C | doi-access = free }}</ref>|bar1=green |{{Clade|[[Austrobaileyales]] (about 95 species)<ref name="Christenhusz-Byng2016" />|bar1=green |{{Clade |1={{Clade |1=[[Magnoliid]]s (about 9,000 species)<ref name="Palmer2004" /> |2={{Clade |1=[[Chloranthales]] (about 80 species)<ref name="Christenhusz-Byng2016" /> |2=[[Monocot]]s (about 70,000 species)<ref name="Palmer2004" /> }} }} |2={{Clade |1=[[Ceratophyllales]] (about 6 species)<ref name="Palmer2004" /> |2=[[Eudicot]]s (about 175,000 species)<ref name="Palmer2004" /> }} }} }}}}}}}}}}

===Great apes=== {{more inline|section|date=November 2021}} Within the [[great ape]]s, [[gorilla]]s (eastern and western) are a sister group to [[chimpanzee]]s, [[bonobo]]s and [[human]]s. These five species form a clade, the subfamily [[Homininae]] (African apes), of which '' Gorilla'' has been termed the basal genus. However, if the analysis is not restricted to genera, the ''[[Homo]]'' plus ''[[Pan (genus)|Pan]]'' clade is also basal.

[[File:Phylogenetic tree of marsupials derived from retroposon data - journal.pbio.1000436.g002.png|thumb|The [[phylogenetic tree]] of marsupials derived from [[retroposon]] data shows the basal position of South American [[Didelphimorphia]] within [[Marsupialia]], and the basal position of South American ''[[Dromiciops]]'' within otherwise Australasian [[Australidelphia]].<ref name = "Nilsson2010"/>]] [[File:Noctilionoidea phylogeny PLoS ONE 2014-02-04.png|thumb|Relationship of biogeography and phylogeny of bat superfamily [[Noctilionoidea]] inferred from nuclear DNA sequence data, showing the basal position of the Malagasy family [[Myzopodidae]]. Locations with only fossil members are indicated by red stars.]]

{{clade|label1=[[Homininae]]|1={{clade|{{Clade|[[Human]]s (''Homo sapiens'')|{{clade|[[Bonobo]]s (''Pan paniscus'')|[[Chimpanzee]]s (''Pan troglodytes'')}}}}|{{clade|[[Eastern gorilla]]s (''Gorilla beringei'')|[[Western gorilla]]s (''Gorilla gorilla'')}}}}}}

Moreover, [[orangutan]]s are a sister group to Homininae and are the basal genus in the great ape family [[Hominidae]] as a whole.

{{clade|label1=[[Hominidae]]|1={{clade|label1=[[Ponginae]]|[[Orangutan]]s (''Pongo'' spp.)|label2=Homininae|2={{clade|1={{Clade|Humans (''[[Homo sapiens]]'')|[[Chimpanzee]]s (''Pan'' spp.)}}|2=[[Gorilla]]s (''Gorilla'' spp.)}}}}}}

Subfamilies Homininae and [[Ponginae]] are both basal within Hominidae, but given that there are no nonbasal subfamilies in the cladogram it is unlikely the term would be applied to either. In general, a statement to the effect that one group (e.g., orangutans) is basal, or branches off first, within another group (e.g., Hominidae) may not make sense unless the appropriate taxonomic level(s) (genus, in this case) is specified. If that level cannot be specified (i.e., if the clade in question is unranked) a more detailed description of the relevant sister groups may be needed. As can be seen, the term is not reflective of ancestral states or proximity to the common ancestor of extant species.

In this example, orangutans differ from the other genera in their Asian range. This fact plus their basal status provides a hint that the most recent common ancestor of extant great apes may have been Eurasian (see below), a suggestion that is consistent with other evidence.<ref name="Moya-Sola2009">{{Cite journal |last1=Moya-Sola|first1=S.|last2=Alba|first2=D. M.|last3=Almecija|first3=S.|last4=Casanovas-Vilar|first4=I.|last5=Kohler|first5=M.|last6=De Esteban-Trivigno|first6=S.|last7=Robles|first7=J. M.|last8=Galindo|first8=J.|last9=Fortuny|first9=J.|title=A unique Middle Miocene European hominoid and the origins of the great ape and human clade |journal=[[Proceedings of the National Academy of Sciences|PNAS]] |volume=106 |issue=24 |pages=9601–9606 |date = 2009-06-16 |doi= 10.1073/pnas.0811730106 |pmid= 19487676 |pmc= 2701031|bibcode=2009PNAS..106.9601M|doi-access=free}}.</ref> (Of course, [[lesser ape]]s are entirely Asiatic.) However, orangutans also differ from African [[ape]]s in their more highly [[arboreal]] lifestyle, a trait generally viewed as ancestral among the apes.<ref name="MaClatchy2000">{{cite journal|last1= MaClatchy|first1= L.|last2= Gebo|first2= D.|last3= Kityo|first3= R.|last4= Pilbeam|first4= D.|title= Postcranial functional morphology of ''Morotopithecus bishopi'', with implications for the evolution of modern ape locomotion|journal=Journal of Human Evolution|volume= 39|issue= 2|year= 2000|pages= 159–183|doi= 10.1006/jhev.2000.0407|pmid= 10968927|bibcode= 2000JHumE..39..159M}}</ref><ref name="Thorpe2006">{{cite journal|last1= Thorpe|first1=S. K. S.|last2= Crompton|first2=R. H.|title= Orangutan positional behavior and the nature of arboreal locomotion in Hominoidea|journal=American Journal of Physical Anthropology|volume= 131|issue= 3|year= 2006|pages= 384–401|doi= 10.1002/ajpa.20422|pmid=16617429|bibcode=2006AJPA..131..384T |doi-access= free}}</ref>

==Relevance to biogeographic history== Given that the deepest phylogenetic split in a group is likely to have occurred early in its history, identification of the most basal subclade(s) in a widely dispersed taxon or clade can provide valuable insight into its region of origin; however, the lack of additional species in a clade is not evidence that it carries the ancestral state for most traits. Most deceptively, people often believe that the direction of migration away from the area of origin can also be inferred (as in the ''Amaurobioides'' and Noctilionoidea cases below). As with all other traits, the phylogeographic location of one clade that connects to the root does not provide information about the ancestral state. Examples where such unjustified inferences may have been made include:

* Spiders of the genus ''[[Amaurobioides]]'' are present in South Africa, Australia, New Zealand and Chile.<ref name = "Kukso2016">{{cite web | url = https://www.scientificamerican.com/article/seafaring-spiders-made-it-around-the-world-in-8-million-years/ | title = Seafaring Spiders Made It around the World—in 8 Million Years | last = Kukso | first = F. | date = 2016-11-08 | website = [[Scientific American]] | access-date = 2016-11-10}}</ref><ref name="Kuntner2016">{{cite journal|last1= Kuntner|first1=M.|last2= Ceccarelli|first2=F. S.|last3= Opell|first3=B. D.|last4= Haddad|first4=C. R.|last5= Raven|first5=Robert J.|last6= Soto|first6=E. M.|last7= Ramírez|first7=M. J.|title=Around the World in Eight Million Years: Historical Biogeography and Evolution of the Spray Zone Spider ''Amaurobioides'' (Araneae: Anyphaenidae)|journal=PLOS ONE|volume= 11|issue= 10|date= 2016-10-12|article-number= e0163740|doi= 10.1371/journal.pone.0163740|pmid=27732621|pmc=5061358|bibcode=2016PLoSO..1163740C|doi-access=free}}</ref> The most basal clade is South African; DNA sequence evidence indicates that after their South American ancestors reached South Africa, they [[oceanic dispersal|dispersed eastward]] all the way back to South America over an interval of about 8&nbsp;million years.<ref name="Kuntner2016" /> * [[Iguanid]] lizards (''[[sensu lato]]'') are distributed throughout the Americas, on [[Madagascar]], and on [[Fiji]] and [[Tonga]] in the western South Pacific. The [[Opluridae|Malagasy forms]] (Opluridae) were previously thought to be basal, with an estimated divergence date from the others of ~162&nbsp;million years, not long before the time of Madagascar's separation from Africa.<ref name="Okajima2009">{{Cite journal |last1 =Okajima |first1 =Y.|last2= Kumazawa|first2= Y.|title= Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines |journal= [[Gene (journal)|Gene]]| volume= 441|issue =1–2|pages = 28–35| date= 2009-07-15 | doi = 10.1016/j.gene.2008.06.011 |pmid= 18598742}}</ref> This suggested that iguanids once had a widespread [[Gondwanan]] distribution; after the Malagasy and New World representatives were separated by [[vicariance]], less isolated Old World iguanids became extinct through competition with other lizard groups (e.g., [[agamid]]s). In contrast, [[Brachylophus|western Pacific iguanids]] are nested deeply within American iguanids,<ref name="Schulte2003">{{cite journal|last1= Schulte|first1=J. A.|last2= Valladares|first2=J. P.|last3=Larson|first3=A.|title=Phylogenetic Relationships Within Iguanidae Inferred Using Molecular and Morphological Data and a Phylogenetic Taxonomy of Iguanian Lizards|journal= Herpetologica|volume= 59|issue=3|date= September 2003|pages= 399–419|doi=10.1655/02-48|bibcode=2003Herpe..59..399S |s2cid=56054202}}</ref> having apparently colonized their isolated range after an epic 10,000&nbsp;km [[rafting event]].<ref name="Gibbons">{{Cite journal | last = Gibbons | first = J. R. H. | title = The Biogeography of ''Brachylophus'' (Iguanidae) including the Description of a New Species, ''B. vitiensis'', from Fiji | journal = Journal of Herpetology | volume = 15 | issue = 3 | pages = 255–273 | date = 1981-07-31 | doi = 10.2307/1563429 | jstor = 1563429 | bibcode = 1981JHerp..15..255G }}</ref><ref name="Keogh2008">{{cite journal|last1= Keogh|first1=J. S.|last2= Edwards|first2=D. L|last3= Fisher|first3=R. N|last4= Harlow|first4=P. S|title= Molecular and morphological analysis of the critically endangered Fijian iguanas reveals cryptic diversity and a complex biogeographic history|journal= Philosophical Transactions of the Royal Society B: Biological Sciences|volume= 363|issue= 1508|year= 2008|pages= 3413–3426|doi= 10.1098/rstb.2008.0120|pmid=18782726|pmc=2607380}}</ref> However, a 2022 study found oplurids to be closely allied with the American iguanians [[Leiosauridae]], having only diverged 60 million years ago following a likely rafting event of their own.<ref>{{Cite journal |last1=Welt |first1=Rachel S. |last2=Raxworthy |first2=Christopher J. |date=2022-02-01 |title=Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar |journal=Molecular Phylogenetics and Evolution |language=en |volume=167 |article-number=107345 |doi=10.1016/j.ympev.2021.107345 |pmid=34748875 |bibcode=2022MolPE.16707345W |s2cid=243821392 |issn=1055-7903|doi-access=free }}</ref> Due to this, neither of the Old World "iguanids" are thought to represent basal lineages. * [[Coral snake]]s comprise about 16 species in Asia and over 65 species in the Americas. However, none of the American clades are basal, implying that the group's ancestry was in the Old World.<ref name = "Slowinski2001">{{cite journal |last1=Slowinski |first1=J. B. |author-link1=Joseph Bruno Slowinski |last2=Boundy |first2=J. |last3=Lawson |first3=R. |title=The Phylogenetic Relationships of Asian Coral Snakes (Elapidae: Calliophis and Maticora) Based on Morphological and Molecular Characters |date=June 2001 |journal=Herpetologica |volume=57 |issue=2 | pages=233–245 |jstor=3893186}}</ref> * Extant australidelphian marsupials constitute about 240 species in Australasia and one species (the [[monito del monte]]) in South America. The fact that the monito del monte occupies a basal position (the most basal species, genus, family and order) in the superorder [[Australidelphia]] is an important clue that its origin was in South America. This conclusion is consistent with the fact that the South American order [[Didelphimorphia]] is basal within infraclass [[Marsupialia]]; i.e., extant marsupials as a whole also appear to have originated in South America.<ref name = "Nilsson2010">{{Cite journal |editor1-last=Penny |editor1-first=David |last1=Nilsson |first1=M. A. |last2=Churakov |first2=G. |last3=Sommer |first3=M. |last4=Van Tran |first4=N. |last5=Zemann |first5=A. |last6=Brosius |first6=J. |last7=Schmitz |first7=J. |title=Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions |journal=[[PLOS Biology]] |volume=8 |issue=7 |article-number=e1000436 |date=2010-07-27 |doi=10.1371/journal.pbio.1000436 |pmid=20668664 |pmc=2910653 |doi-access=free }}</ref>{{refn|group=n|These conclusions have been supported by the finding of [[Eocene]] fossil remains of the [[microbiotheria]]n ''[[Woodburnodon]] casei'' in [[Seymour Island|Antarctica]],<ref name = "Goin">{{cite journal | last1 = Goin | first1 = F. J. | last2 = Zimicz | first2 = N. | last3 = Reguero | first3 = M. A. | last4 = Santillana | first4 = S. N. | last5 = Marenssi | first5 = S. A. | last6 = Moly | first6 = J. J. | title = New marsupial (Mammalia) from the Eocene of Antarctica, and the origins and affinities of the Microbiotheria | journal = Revista de la Asociación Geológica Argentina | volume = 62 | issue = 4 | pages = 597–603 | date = 2007 | url = https://www.researchgate.net/publication/262722641 | access-date = 2016-07-17}}</ref> which is presumed to have served as a way station on the migration route to Australia before the final breakup of [[Gondwana]].}}{{refn|group=n|Similarly, among australobatrachian frogs, the South American family [[Calyptocephalellidae]], with 5 extant species (living in the same [[Valdivian temperate rain forest|Valdivian forest]] as the monito del monte), is basal to the Australasian families [[Limnodynastidae]] and [[Myobatrachidae]],<ref name="Pyron2011">{{cite journal|last1= Pyron|first1= R.A.|last2= Wiens|first2= J.J.|title=A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians |journal= Molecular Phylogenetics and Evolution |volume= 61|issue= 2|year= 2011|pages= 543–583|doi= 10.1016/j.ympev.2011.06.012|pmid= 21723399|bibcode= 2011MolPE..61..543A|doi-access= free}}</ref> with about 120 extant species, suggesting a South American origin for the group.<ref name="Feng2017">{{cite journal|last1= Feng|first1= Y.-J.|last2= Blackburn|first2= D.C.|last3= Liang|first3= D.|last4= Hillis|first4= D.M.|last5= Wake|first5= D.B.|last6= Cannatella|first6= D.C.|last7= Zhang|first7= P.|title= Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary |journal= Proceedings of the National Academy of Sciences |volume= 114|issue= 29|year= 2017|pages= E5864–E5870|doi= 10.1073/pnas.1704632114|pmid= 28673970|pmc= 5530686|bibcode= 2017PNAS..114E5864F|doi-access= free}}</ref> This is consistent with the finding of a fossil from the South American family in Antarctica.<ref name="Mörs2020">{{cite journal|last1= Mörs|first1= T.|last2= Reguero|first2= M.|last3= Vasilyan|first3= D.|title=First fossil frog from Antarctica: implications for Eocene high latitude climate conditions and Gondwanan cosmopolitanism of Australobatrachia |journal= Scientific Reports |volume= 10|issue= 1|year= 2020|page= 5051|doi= 10.1038/s41598-020-61973-5|pmid= 32327670|pmc= 7181706|bibcode= 2020NatSR..10.5051M|doi-access= free}}</ref>}}{{refn|group=n|[[Ratite]]s may have similarly traveled overland from South America to colonize Australia;<ref name="Yonezawa2017">{{cite journal|last1= Yonezawa|first1=T.|last2= Segawa|first2=T.|last3= Mori|first3=H.|last4= Campos|first4=P. F.|last5= Hongoh|first5=Y.|last6= Endo|first6=H.|last7= Akiyoshi|first7=A.|last8= Kohno|first8=N.|last9= Nishida|first9=S.|last10= Wu|first10=J.|last11= Jin|first11=H.|last12= Adachi|first12=J.|last13= Kishino|first13=H.|last14= Kurokawa|first14=K.|last15= Nogi|first15=Y.|last16= Tanabe|first16=H.|last17= Mukoyama|first17=H.|last18= Yoshida|first18=K.|last19= Rasoamiaramanana|first19=A.|last20= Yamagishi|first20=S.|last21= Hayashi|first21=Y.|last22= Yoshida|first22=A.|last23= Koike|first23=H.|last24= Akishinonomiya|first24=F.|last25= Willerslev|first25=E.|last26= Hasegawa|first26=M.|title=Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites|journal= Current Biology|volume= 27|issue= 1|date= 2016-12-15|pages= 68–77|doi= 10.1016/j.cub.2016.10.029|pmid=27989673|doi-access= free}}</ref> a fossil ratite is known from Antarctica,<ref name = "Tambussi1994">{{cite journal|last1= Tambussi|first1= C.P.|last2= Noriega|first2= J.I.|last3= Gazdzicki|first3= A.|last4= Tatur|first4= A.|last5= Reguero|first5= M.A.|last6= Vizcaino|first6= S.F.|title= Ratite bird from the Paleogene La Meseta Formation, Seymour Island, Antarctica|journal= Polish Polar Research|volume= 15|issue= 1–2|pages= 15–20|date= 1994|url= http://polar.pan.pl/ppr15/1994-1-2_015-020.pdf|access-date= 28 December 2019|archive-date= 2019-12-28|archive-url= https://web.archive.org/web/20191228235043/http://polar.pan.pl/ppr15/1994-1-2_015-020.pdf}}</ref> and South American rheas are more basal within the group than Australo-Pacific ratites.<ref name="Yonezawa2017" />}} * While the bat superfamily [[Noctilionoidea]] has over 200 species in the Neotropics, [[Mystacinidae|two in New Zealand]], and [[Myzopodidae|two in Madagascar]], the basal position of the Malagasy family<ref name="Teeling2005">{{Cite journal | last1 = Teeling | first1 = E. C. | last2 = Springer | first2 = M. | last3 = Madsen | first3 = O. | last4 = Bates | first4 = P. | last5 = O'Brien | first5 = S. | last6 = Murphy | first6 = W. | title = A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record | doi = 10.1126/science.1105113 | journal = Science | volume = 307 | issue = 5709 | pages = 580–584 | date = 2005-01-28| pmid = 15681385| bibcode = 2005Sci...307..580T | s2cid = 25912333 }}</ref> suggests, in combination with the fossil record and the next-most-basal placement of the New Zealand family, that the superfamily originated in Africa and then migrated eastward to South America, proliferating there but surviving in the Old World only in [[Refugium (population biology)|refugia]].<ref name="Gunnell2014">{{Cite journal | last1 = Gunnell | first1 = G. F. | last2 = Simmons | first2 = N. B. | last3 = Seiffert | first3 = E. R. | date = 2014-02-04 | title = New Myzopodidae (Chiroptera) from the Late Paleogene of Egypt: Emended Family Diagnosis and Biogeographic Origins of Noctilionoidea | journal = [[PLoS ONE]] | volume = 9 | issue = 2 | article-number = e86712 | doi = 10.1371/journal.pone.0086712 | pmid=24504061 | pmc=3913578| bibcode = 2014PLoSO...986712G | doi-access = free }}</ref> * The genus ''[[Urocyon]]'' (gray and island foxes) is basal in the [[Caninae|canine subfamily]],<ref name=Lindblad-Toh2005>{{cite journal|doi= 10.1038/nature04338|pmid= 16341006|title= Genome sequence, comparative analysis and haplotype structure of the domestic dog|journal= Nature|volume= 438|issue= 7069|pages=803–819 |year= 2005|last1= Lindblad-Toh|first1= K.|last2= Wade|first2= C.M.|last3= Mikkelsen|first3= T.S.|last4= Karlsson|first4= E.K.|last5= Jaffe|first5= D.B.|last6= Kamal|first6= M.|last7= Clamp|first7= M.|last8= Chang|first8= J.L.|last9= Kulbokas|first9= E.J.|last10= Zody|first10= M.C.|last11= Mauceli|first11= E.|last12= Xie|first12= X.|last13= Breen|first13= M.|last14= Wayne|first14= R.K.|last15= Ostrander|first15= E.A.|last16= Ponting|first16= C.P.|last17= Galibert|first17= F.|last18= Smith|first18= D.R.|last19= Dejong|first19= P.J.|last20= Kirkness|first20= E.|last21= Alvarez|first21= P.|last22= Biagi|first22= T.|last23= Brockman|first23= W.|last24= Butler|first24= J.|last25= Chin|first25= C.-W.|last26= Cook|first26= A.|last27= Cuff|first27= J.|last28= Daly|first28= M.J.|last29= Decaprio|first29= D.|last30= Gnerre|first30= S.|display-authors= 29|bibcode= 2005Natur.438..803L|doi-access= free}}</ref> suggesting a North American origin of the nearly worldwide group. This is consistent with fossil evidence indicating a North American origin for the [[Canidae|canid family]] as a whole (the other two canid subfamilies, the extinct [[Borophaginae]]<ref name="Wang1999">{{Cite journal |last1=Wang |first1=Xiaoming |last2=Tedford |first2=Richard |last3=Taylor |first3=Beryl |date=1999-11-17 |title= Phylogenetic systematics of the Borophaginae (Carnivora, Canidae) |journal=Bulletin of the American Museum of Natural History |volume=243 |hdl=2246/1588}}</ref> and [[Hesperocyoninae]],<ref name=Wang2008>{{cite book |last1= Wang |first1= X.| last2= Tedford | first2= R.H.| date= 2008 |title= Dogs, Their Fossil Relatives and Evolutionary History |publisher= Columbia University Press |pages = 23–31 |isbn= 978-0-231-13528-3 |url= https://books.google.com/books?id=degwyTaHLt8C&pg=PA23}}</ref> the latter being basal in Canidae, were both [[endemic]] to North America).

== See also == * [[Primitive (phylogenetics)]]

== Notes == {{reflist|group=n}}

==References== {{reflist}}

==External links== * {{cite web |title=Interpreting the Tree Diagram or List of Subgroups on a Tree of Life Page |publisher=[[Tree of Life Web Project]] |url=http://tolweb.org/tree/home.pages/treeinterpret.html}}

{{Phylogenetics}}

[[Category:Phylogenetics]]