Basal (phylogenetics)

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In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. A basal clade is the earliest clade (of a given taxonomic rank[a]) to branch within a larger clade. More generally, clade A is basal to clade B if B is a subset of the sister group of A.

Examples[edit]

A basal group forms a sister group to the rest of the larger clade, such as in the following example:



Basal group




Non-basal group




Non-basal group



Non-basal group





The word "basal" is preferred to the term "primitive", which may carry false connotations of inferiority or a lack of complexity.

The term basal can only be correctly applied to clades of organisms, not to individual traits possessed by the organisms—although it may be misused in this manner in technical literature. While the term "basal" applies to clades, characters or traits are usually considered derived if they are absent in a basal group, but present in other groups. This assumption only holds true if the basal group is a good analogy for the last common ancestor of the group.

The flowering plant family Amborellaceae, restricted to New Caledonia in the southwestern Pacific, is considered the most basal clade (the most basal species, genus, family and order) of extant angiosperms.



Amborellales




Monocots



Magnoliids



Eudicots




Within the primate family Hominidae, gorillas (eastern and western) are a sister group to common chimpanzees, bonobos and humans. These five species form a clade, the subfamily Homininae, of which Gorilla is the basal genus.




Humans (Homo sapiens)




Bonobos (Pan paniscus)



Common chimpanzees (Pan troglodytes)






Eastern gorillas (Gorilla beringei)



Western gorillas (Gorilla gorilla)




However, orangutans are a sister group to Homininae and are the basal genus in the family as a whole.



Orangutans (Pongo spp.)






Humans (Homo sapiens)



Chimpanzees (Pan spp.)




Gorillas (Gorilla spp.)





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.

Criticism[edit]

Despite the ubiquity of the usage of the term, some systematists believe it is unnecessary and misleading.[1] This is because a pair of sister branches of a phylogenetic tree are equally ranked and can be freely rotated about their last common node. The term tends to be applied when one branch (the one deemed "basal") is less diverse than another branch. This raises an equivocal usage for this term in that it also refers to the direction of the root of the tree. As the root represents a hypothetical ancestor, this consequently may carry misleading connotations that the sister group of a more species-rich clade is primitive.[2]

Relevance to biogeographic history[edit]

Identification of the most basal clade(s) in a widely dispersed group can provide valuable insight into the group's biogeographic history. For example, extant australidelphian marsupials constitute about 238 species in Australasia and one species (the monito del monte) in South America. The fact that the monito del monte occupies the basal position (the most basal species, genus, family and order) in the superorder is an important clue that its origin was in South America.[3][b] Also, while the bat superfamily Noctilionoidea has over 200 species in the Neotropics, two in New Zealand, and two in Madagascar, the basal position of the Malagasy genus and family[4] suggests (in combination with the fossil record) that the superfamily originated in Africa.[5] Similarly, while coral snakes comprise 16 species in Asia and over 65 species in the Americas, the fact that none of the American clades are basal implies that the group's ancestry was in the Old World.[6]

Notes[edit]

  1. ^ Without this qualification there must, of course, be two or more equally basal clades branching off from the root of every cladogram.
  2. ^ This conclusion is consistent with the fact that Didelphimorphia is the basal order within Marsupialia; i.e., extant marsupials as a whole also appear to have originated in South America.[3]

References[edit]

  1. ^ Krell, Frank T.; Cranston, Peter S. (2004). "Which side of the tree is more basal?". Systematic Entomology 29: 279–281. doi:10.1111/j.0307-6970.2004.00262.x. 
  2. ^ Jenner, Ronald A (2006). "Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney". Development Genes and Evolution 216: 385–394. doi:10.1007/s00427-006-0084-5. 
  3. ^ a b Nilsson, M. A.; Churakov, G.; Sommer, M.; Van Tran, N.; Zemann, A.; Brosius, J.; Schmitz, J. (2010-07-27). "Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions". In Penny, David. PLoS Biology (Public Library of Science) 8 (7): e1000436. doi:10.1371/journal.pbio.1000436. PMC 2910653. PMID 20668664. 
  4. ^ Teeling, E. C.; Springer, M.; Madsen, O.; Bates, P.; O'Brien, S.; Murphy, W. (2005-01-28). "A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record". Science 307 (5709): 580–584. doi:10.1126/science.1105113. PMID 15681385.  edit
  5. ^ Gunnell, G. F.; Simmons, N. B.; Seiffert, E. R. (2014-02-04). "New Myzopodidae (Chiroptera) from the Late Paleogene of Egypt: Emended Family Diagnosis and Biogeographic Origins of Noctilionoidea". PLoS ONE 9 (2): e86712. doi:10.1371/journal.pone.0086712. Retrieved 2014-02-05.  edit
  6. ^ Slowinski, J. B.; Boundy, J.; Lawson, R. (June 2001). "The Phylogenetic Relationships of Asian Coral Snakes (Elapidae: Calliophis and Maticora) Based on Morphological and Molecular Characters". Herpetologica 57 (2): 233–245. JSTOR 3893186.