Basal (phylogenetics)

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In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. Basal (phylogenetics)_sentence_0

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. Basal (phylogenetics)_sentence_1

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. Basal (phylogenetics)_sentence_2

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, species diversity, or both. Basal (phylogenetics)_sentence_3

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. The concept of a 'key innovation' implies some degree of correlation between evolutionary innovation and diversification. Basal (phylogenetics)_sentence_4

However, such a correlation does not make a given case predicable, so ancestral characters should not be imputed to the members of a less species-rich basal clade without additional evidence. Basal (phylogenetics)_sentence_5

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. Basal (phylogenetics)_sentence_6

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. Basal (phylogenetics)_sentence_7

A 'core clade' is a clade representing all but the basal clade(s) of lowest rank within a larger clade; e.g., core eudicots. Basal (phylogenetics)_sentence_8

Usage Basal (phylogenetics)_section_0

A basal group in the stricter sense forms a sister group to the rest of the larger clade, as in the following case: Basal (phylogenetics)_sentence_9

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. Basal (phylogenetics)_sentence_10

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. Basal (phylogenetics)_sentence_11

Additionally, this qualification does not ensure that the diversity of extinct taxa (which may be poorly known) is represented. Basal (phylogenetics)_sentence_12

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 thought to possess ancestral characters, or to such presumed ancestral traits themselves. Basal (phylogenetics)_sentence_13

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. Basal (phylogenetics)_sentence_14

Despite the ubiquity of the usage of basal, some systematists believe its application to extant groups is unnecessary and misleading. Basal (phylogenetics)_sentence_15

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). Basal (phylogenetics)_sentence_16

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. Basal (phylogenetics)_sentence_17

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. Basal (phylogenetics)_sentence_18

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). Basal (phylogenetics)_sentence_19

Other famous examples of this phenomenon are the oviparous reproduction and nipple-less lactation of monotremes, a basal clade of mammals with just five species, and the archaic anatomy of the tuatara, a basal clade of lepidosaurian with a single species. Basal (phylogenetics)_sentence_20

Examples Basal (phylogenetics)_section_1

Flowering plants Basal (phylogenetics)_section_2

The flowering plant family Amborellaceae, restricted to New Caledonia in the southwestern Pacific, 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). Basal (phylogenetics)_sentence_21

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". Basal (phylogenetics)_sentence_22

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). Basal (phylogenetics)_sentence_23

The cladogram below is based on Ramírez-Barahona et al. Basal (phylogenetics)_sentence_24

(2020), with species counts taken from the source indicated. Basal (phylogenetics)_sentence_25

Great apes Basal (phylogenetics)_section_3

Within the great apes, gorillas (eastern and western) are a sister group to common chimpanzees, bonobos and humans. Basal (phylogenetics)_sentence_26

These five species form a clade, the subfamily Homininae (African apes), of which Gorilla is the basal genus. Basal (phylogenetics)_sentence_27

However, if the analysis is not restricted to genera, the Homo plus Pan clade is also basal. Basal (phylogenetics)_sentence_28

Moreover, orangutans are a sister group to Homininae and are the basal genus in the great ape family Hominidae as a whole. Basal (phylogenetics)_sentence_29

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. Basal (phylogenetics)_sentence_30

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. Basal (phylogenetics)_sentence_31

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. Basal (phylogenetics)_sentence_32

In this example, orangutans differ from the other genera in their Asian range. Basal (phylogenetics)_sentence_33

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. Basal (phylogenetics)_sentence_34

(Of course, lesser apes are entirely Asiatic.) Basal (phylogenetics)_sentence_35

Orangutans also differ from African apes in their more highly arboreal lifestyle, a trait generally viewed as ancestral among the apes. Basal (phylogenetics)_sentence_36

Relevance to biogeographic history Basal (phylogenetics)_section_4

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. Basal (phylogenetics)_sentence_37

In some situations where it might not otherwise be obvious, the direction of migration away from the area of origin can also be inferred (as in the Amaurobioides and Noctilionoidea cases below). Basal (phylogenetics)_sentence_38

Examples include: Basal (phylogenetics)_sentence_39

Basal (phylogenetics)_unordered_list_0

  • Spiders of the genus Amaurobioides are present in South Africa, Australia, New Zealand and Chile. 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.Basal (phylogenetics)_item_0_0
  • 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. This suggests 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., agamids). In contrast, western Pacific iguanids are nested deeply within American iguanids, having apparently colonized their isolated range after an epic 10,000 km rafting event.Basal (phylogenetics)_item_0_1
  • Coral snakes 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.Basal (phylogenetics)_item_0_2
  • 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.Basal (phylogenetics)_item_0_3
  • 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 family 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 refugia.Basal (phylogenetics)_item_0_4
  • The genus Urocyon (gray and island foxes) is basal in the canine subfamily, suggesting a North American origin of the nearly worldwide group. This is consistent with fossil evidence indicating a North American origin for the canid family as a whole (the other two canid subfamilies, the extinct Borophaginae and Hesperocyoninae, the latter being basal in Canidae, were both endemic to North America).Basal (phylogenetics)_item_0_5

Credits to the contents of this page go to the authors of the corresponding Wikipedia page: (phylogenetics).