Basal (phylogenetics)

In phylogenetics, basal is the direction of the base (or root) of a 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. Each node in the tree corresponds to a clade; i.e., clade C may be described as basal within a larger clade D if its root is directly linked to the root of D. The terms deep-branching or early-branching are similar in meaning.

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[n 1] and/or species diversity. If C is a basal clade within D that has the lowest rank of all basal clades within D, C may be described as the basal taxon of that rank within D. Greater diversification may be associated with more evolutionary innovation, but ancestral characters should not be imputed to the members of a less species-rich basal clade without additional evidence, as there can be no assurance such an assumption is valid.[1][2][3][n 2]

In general, clade A is more basal than clade B if B is a subgroup of the sister group of A. Within large groups, "basal" may be used loosely to mean 'closer to the root than the great majority of', and in this context terminology such as "very basal" may arise. A 'core clade' is a clade representing all but the basal clade(s) of lowest rank within a larger clade; e.g., core eudicots.

Usage

A basal group in the stricter sense forms a sister group to the rest of the larger clade, as in the following case:

Root 

 Basal clade #1

 Non-basal clade #1

 Non-basal clade #2  

 Non-basal clade #3

Basal clade #2

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 assumed in this example that the terminal branches of the cladogram depict all the extant taxa of a given rank within the clade; otherwise, the diagram could be highly deceptive. Additionally, this qualification does not ensure that the diversity of extinct taxa (which may be poorly known) is represented.

In phylogenetics, the term basal can be objectively applied to clades of organisms, but tends to be applied selectively and more controversially to groups or lineages[n 3] thought to possess ancestral characters, or to such presumed ancestral traits themselves. In describing characters, "ancestral" or "plesiomorphic" are preferred to "basal" or "primitive", the latter of which may carry false connotations of inferiority or a lack of complexity.

Despite the ubiquity of the usage of basal, some systematists believe its application to extant groups is unnecessary and misleading.[6] 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.[3] 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). Other famous examples of this phenomenon are the oviparous reproduction and nipple-less lactation of monotremes, a basal clade of mammals[7] with just five species, and the archaic anatomy of the tuatara,[8] a basal clade of lepidosaurian with a single species.

Examples

Flowering plants

The flowering plant family Amborellaceae, restricted to New Caledonia in the southwestern Pacific,[n 4] is a basal clade of extant angiosperms, consisting of the most basal species, genus, family and order within the group (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 tracheids), of any living angiosperm" as well as "simple, separate flower parts of indefinite numbers, and unsealed carpels."[9] 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).[9]

Amborellales

Monocots

Magnoliids

Eudicots

Great apes

Within the primate family Hominidae (great apes), gorillas (eastern and western) are a sister group to common chimpanzees, bonobos and humans. These five species form a clade, the subfamily Homininae (African apes), of which Gorilla is the basal genus. However, if the analysis is not restricted to genera, the Homo plus Pan clade is also basal.

Humans (Homo sapiens)

Bonobos (Pan paniscus)

Common chimpanzees (Pan troglodytes)

Eastern gorillas (Gorilla beringei)

Western gorillas (Gorilla gorilla)

Moreover, 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.)

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.

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.[10] Orangutans also differ from African apes in their more highly arboreal lifestyle, a trait generally viewed as ancestral among the apes.[11][12]

Relevance to biogeographic history

Noctilionoidea phylogeny PLoS ONE 2014-02-04
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.

Given that the deepest phylogenetic split in a widely dispersed group is likely to have occurred in its region of origin, identification of the most basal clade(s) in such a group can provide valuable insight into its biogeographic history. For example:

  • Spiders of the genus Amaurobioides are present in South Africa, Australia, New Zealand and Chile.[13][14] The most basal clade is South African; DNA sequence evidence indicates that after their South American ancestors reached South Africa, they dispersed eastward all the way back to South America over an interval of about 8 million years.[14]
  • Iguanid lizards (sensu lato) are distributed throughout the Americas, on Madagascar, and on Fiji and Tonga in the western South Pacific. The Malagasy forms are basal, with an estimated divergence date from the others of ~162 million years, not long before the time of Madagascar's separation from Africa.[15] This suggests that iguanids once had a widespread Gondwanan distribution; after the Malagasy and New World representatives were isolated by vicariance, the remaining Gondwanan iguanids became extinct through competition with other Old World lizard groups. In contrast, western Pacific iguanids are nested deeply within American iguanids,[16] having apparently colonized their isolated range after a remarkable 10,000 km rafting event.[17][18]
  • Coral snakes comprise 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.[19]
  • 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 a basal position (the most basal species, genus, family and order) in the superorder is an important clue that its origin was in South America.[20][n 5]
  • 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[21] suggests, in combination with the fossil record, that the superfamily originated in Africa.[22]

Notes

  1. ^ Meaning the lowest taxonomic ranks of the respective clades (see Amborella example); the highest ranks should be the same.
  2. ^ For example, the giant panda represents the most basal extant species, genus and subfamily within Ursidae,[4] but its specializations for a bamboo diet are not ancestral ursid characters.[5]
  3. ^ 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 origin of life. Thus, from a phylogenetic standpoint, the notion of a lineage being basal is nonsensical. However, in genetics, basal lineage refers to a lineage connecting a common ancestor with a single variant allele to a branch ancestor with two descendant variants.
  4. ^ New Caledonia is viewed as a 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.
  5. ^ 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.[20]

References

  1. ^ Baum, D. A. (4 November 2013). "Phylogenetics and the History of Life". The Princeton Guide to Evolution. Princeton University Press. p. 57. ISBN 978-1-4008-4806-5. OCLC 861200134.
  2. ^ Crisp, M. D.; Cook, L. G. (March 2005). "Do early branching lineages signify ancestral traits?". Trends in Ecology & Evolution. 20 (3): 122–128. doi:10.1016/j.tree.2004.11.010. PMID 16701355.
  3. ^ a b Jenner, Ronald A (2006). "Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney". Development Genes and Evolution. 216 (7–8): 385–394. doi:10.1007/s00427-006-0084-5. PMID 16733736.
  4. ^ Krause, J.; Unger, T.; Noçon, A.; Malaspinas, A.; Kolokotronis, S.; Stiller, M.; Soibelzon, L.; Spriggs, H.; Dear, P. H.; Briggs, A. W.; Bray, S. C. E.; O'Brien, S. J.; Rabeder, G.; Matheus, P.; Cooper, A.; Slatkin, M.; Pääbo, S.; Hofreiter, M. (2008). "Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary". BMC Evolutionary Biology. 8 (220): 220. doi:10.1186/1471-2148-8-220. PMC 2518930. PMID 18662376.
  5. ^ McLellan, Bruce; Reiner, David C. (1994). "A Review of Bear Evolution". Bears: Their Biology and Management. 9 (1): 85–96. doi:10.2307/3872687. JSTOR 3872687.
  6. ^ Krell, Frank T.; Cranston, Peter S. (2004). "Which side of the tree is more basal?". Systematic Entomology. 29 (3): 279–281. doi:10.1111/j.0307-6970.2004.00262.x.
  7. ^ Van Rheede, Teun (2005). "The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians". Molecular Biology and Evolution. 23 (3): 587–597. doi:10.1093/molbev/msj064. PMID 16291999.
  8. ^ Herrera-Flores, J. A.; Stubbs, T. L.; Benton, M. J.; Ruta, M. (2017). "Macroevolutionary patterns in Rhynchocephalia: is the tuatara (Sphenodon punctatus) a living fossil?". Palaeontology. 60 (3): 319–328. doi:10.1111/pala.12284.
  9. ^ a b Essig, F. B. (2014-07-01). "What's so primitive about Amborella?". Botany Professor. Retrieved 2014-10-04.
  10. ^ Moya-Sola, S.; Alba, D. M.; Almecija, S.; Casanovas-Vilar, I.; Kohler, M.; De Esteban-Trivigno, S.; Robles, J. M.; Galindo, J.; Fortuny, J. (2009-06-16). "A unique Middle Miocene European hominoid and the origins of the great ape and human clade". PNAS. 106 (24): 9601–9606. doi:10.1073/pnas.0811730106. PMC 2701031. PMID 19487676..
  11. ^ MaClatchy, L.; Gebo, D.; Kityo, R.; Pilbeam, D. (2000). "Postcranial functional morphology of Morotopithecus bishopi, with implications for the evolution of modern ape locomotion". Journal of Human Evolution. 39 (2): 159–183. doi:10.1006/jhev.2000.0407. PMID 10968927.
  12. ^ Thorpe, S. K. S.; Crompton, R. H. (2006). "Orangutan positional behavior and the nature of arboreal locomotion in Hominoidea". American Journal of Physical Anthropology. 131 (3): 384–401. doi:10.1002/ajpa.20422. PMID 16617429.
  13. ^ Kukso, F. (2016-11-08). "Seafaring Spiders Made It around the World—in 8 Million Years". Scientific American. Retrieved 2016-11-10.
  14. ^ a b Kuntner, M.; Ceccarelli, F. S.; Opell, B. D.; Haddad, C. R.; Raven, Robert J.; Soto, E. M.; Ramírez, M. J. (2016-10-12). "Around the World in Eight Million Years: Historical Biogeography and Evolution of the Spray Zone Spider Amaurobioides (Araneae: Anyphaenidae)". PLOS ONE. 11 (10): e0163740. doi:10.1371/journal.pone.0163740. PMC 5061358. PMID 27732621.
  15. ^ Okajima, Y.; Kumazawa, Y. (2009-07-15). "Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines". Gene. 441 (1–2): 28–35. doi:10.1016/j.gene.2008.06.011. PMID 18598742.
  16. ^ Schulte, J. A.; Valladares, J. P.; Larson, A. (September 2003). "Phylogenetic Relationships Within Iguanidae Inferred Using Molecular and Morphological Data and a Phylogenetic Taxonomy of Iguanian Lizards". Herpetologica. 59 (3): 399–419. doi:10.1655/02-48.
  17. ^ Gibbons, J. R. H. (1981-07-31). "The Biogeography of Brachylophus (Iguanidae) including the Description of a New Species, B. vitiensis, from Fiji". Journal of Herpetology. 15 (3): 255–273. doi:10.2307/1563429. JSTOR 1563429.
  18. ^ Keogh, J. S.; Edwards, D. L; Fisher, R. N; Harlow, P. S (2008). "Molecular and morphological analysis of the critically endangered Fijian iguanas reveals cryptic diversity and a complex biogeographic history". Philosophical Transactions of the Royal Society B: Biological Sciences. 363 (1508): 3413–3426. doi:10.1098/rstb.2008.0120. PMC 2607380. PMID 18782726.
  19. ^ 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.
  20. ^ a b Nilsson, M. A.; Churakov, G.; Sommer, M.; Van Tran, N.; Zemann, A.; Brosius, J.; Schmitz, J. (2010-07-27). Penny, David (ed.). "Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions". PLoS Biology. 8 (7): e1000436. doi:10.1371/journal.pbio.1000436. PMC 2910653. PMID 20668664.
  21. ^ 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.
  22. ^ 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. PMC 3913578. PMID 24504061.

External links

Basal

Basal or basilar is a term meaning base, bottom, or minimum.

Cladogram

A cladogram (from Greek clados "branch" and gramma "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed; nevertheless, many evolutionary trees can be inferred from a single cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

Primitive (phylogenetics)

In phylogenetics, a primitive (or ancestral) character, trait, or feature of a lineage or taxon is one that is inherited from the common ancestor of a clade (or clade group) and has undergone little change since. Conversely, a trait that appears within the clade group (that is, is present in any subgroup within the clade but not all) is called advanced or derived. A clade is a group of organisms that consists of a common ancestor and all its lineal descendants.

A primitive trait is the original condition of that trait in the common ancestor; advanced indicates a notable change from the original condition. These terms in biology contain no judgement about the sophistication, superiority, value or adaptiveness of the named trait. "Primitive" in biology means only that the character appeared first in the common ancestor of a clade group and has been passed on largely intact to more recent members of the clade. "Advanced" means the character has evolved within a later subgroup of the clade.

Cladograms are important for scientists as they allow them to classify and hypothesize the origin and future of organisms. Cladograms allow scientists to propose their evolutionary scenarios about the lineage from a primitive trait to a derived one. By understanding how the trait came to be, scientists can hypothesize the environment that specific organism was in and how that affected the evolutionary adaptations of the trait that came to be.Other, more technical, terms for these two conditions—for example, "plesiomorphic" and "synapomorphic"—are frequently encountered; see the table below.

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