Phenetics
Encyclopedia
In biology
, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology
or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy
which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath
and Robert R. Sokal
. Their books are still primary references for this sub-discipline, although now somewhat dated and out of print
Phenetics has largely been superseded by cladistics
for research into evolutionary relationships among species. However, certain phenetic methods, such as neighbor-joining
, have found their way into cladistics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference
) are too computationally expensive.
Phenetic techniques include various forms of clustering and ordination. These are sophisticated ways of reducing the variation displayed by organisms to a manageable level. In practice this means measuring dozens of variables, and then presenting them as two or three dimensional graphs. Much of the technical challenge in phenetics revolves around balancing the loss of information in such a reduction against the ease of interpreting the resulting graphs.
and adaptive radiation
. A typical error occurring in phenetic analysis is that basal evolutionary grade
s - which retain many plesiomorphies compared to more advanced lineages - appear to be monophyletic.
Consider for example songbird
s. These can be divided into two groups - Corvida
, which retains ancient characters in phenotype
and genotype
, and Passerida
, which has more modern traits. But only the latter are a group of closest relatives; the former are numerous independent and ancient lineages which are about as distantly related to each other as each single one of them is to the Passerida. In a phenetic analysis, the large degree of overall similarity found among the Corvida will make them appear to be monophyletic too, but their shared traits were present in the ancestors of all songbirds already. It is the loss of these ancestral traits rather than their presence that signifies which songbirds are more closely related to each other than to other songbirds.
But the two methodologies need not be mutually exclusive. In general, phenetics is today recognized to provide too much unreliable information about the evolutionary relationships among taxa to remain a mainstay method. But there is no reason why e.g. species identified using phenetics cannot subsequently be subjected to cladistic analysis, to determine their evolutionary relationships. Phenetic methods can also be superior to cladistics when only the distinctness of related taxa is important, as the computational requirements are lower. On the other hand, whenever information on the evolutionary history of taxa is needed for a study, a researcher of today will generally try to analyze using cladistic methods.
for bird
s. Highly controversial at its time, some of its findings (e.g. the Galloanserae) have been vindicated, while others (e.g. the all-inclusive "Ciconiiformes
" or the "Corvida
") have been rejected. However, with computers growing increasingly powerful and widespread, more refined cladistic algorithm
s became available and could put the suggestions of Willi Hennig
to the test; as it turned out, the results of cladistic analyses turned out to be superior to those of phenetic methods - at least when it came to resolving phylogenies.
Many systematists continue to use phenetic methods, particularly in addressing species-level questions. While the ultimate goal of taxonomy includes describing the 'tree of life' - the evolutionary path connecting all species - in fieldwork one needs to be able to separate one taxon
from another. Classifying diverse groups of closely related organisms that differ by very subtle differences is difficult using a cladistic approach. Phenetics provides numerical tools for examining overall patterns of variation, allowing researchers to identify discrete groups that can be classified as species.
Modern applications of phenetics are common in botany
, and some examples can be found in most issues of the journal Systematic Botany. Indeed, due to the effects of horizontal gene transfer
, polyploid complex
es and other peculiarities of plant genomics
, phenetic techniques in botany - though less informative altogether - are also less prone to errors compared with cladistic analysis of DNA sequence
s.
In addition, many of the techniques developed by phenetic taxonomists have been adopted and extended by community ecologists, due to a similar need to deal with large amounts of data.
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy
Numerical taxonomy
Numerical taxonomy is a classification system in biological systematics which deals with the grouping by numerical methods of taxonomic units based on their character states.. It aims to create a taxonomy using numeric algorithms like cluster analysis rather than using subjective evaluation of...
which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath
Peter Sneath
Peter Henry Andrews Sneath FRS, MD was a microbiologist who co-founded the field of numerical taxonomy, together with Robert R. Sokal. Sneath and Sokal wrote Principles of Numerical Taxonomy, revised in 1973 as Numerical taxonomy...
and Robert R. Sokal
Robert R. Sokal
Robert Reuven Sokal is an Austrian-American biostatistician and anthropologist. Distinguished Professor Emeritus at the State University of Stony Brook, New York, Sokal is a member of the National Academy of Sciences and the American Academy of Arts and Sciences...
. Their books are still primary references for this sub-discipline, although now somewhat dated and out of print
Phenetics has largely been superseded by cladistics
Cladistics
Cladistics is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants . For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade...
for research into evolutionary relationships among species. However, certain phenetic methods, such as neighbor-joining
Neighbor-joining
In bioinformatics, neighbor joining is a bottom-up clustering method for the creation of phenetic trees , created by Naruya Saitou and Masatoshi Nei...
, have found their way into cladistics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference
Bayesian inference
In statistics, Bayesian inference is a method of statistical inference. It is often used in science and engineering to determine model parameters, make predictions about unknown variables, and to perform model selection...
) are too computationally expensive.
Phenetic techniques include various forms of clustering and ordination. These are sophisticated ways of reducing the variation displayed by organisms to a manageable level. In practice this means measuring dozens of variables, and then presenting them as two or three dimensional graphs. Much of the technical challenge in phenetics revolves around balancing the loss of information in such a reduction against the ease of interpreting the resulting graphs.
Difference from cladistics
Phenetic analyses do not distinguish between plesiomorphies - traits that are inherited from an ancestor (and therefore phylogenetically uninformative) - and apomorphies - traits that evolved anew in one or several lineages. Consequently, phenetic analyses are liable to be misled by convergent evolutionConvergent evolution
Convergent evolution describes the acquisition of the same biological trait in unrelated lineages.The wing is a classic example of convergent evolution in action. Although their last common ancestor did not have wings, both birds and bats do, and are capable of powered flight. The wings are...
and adaptive radiation
Adaptive radiation
In evolutionary biology, adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Starting with a recent single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different...
. A typical error occurring in phenetic analysis is that basal evolutionary grade
Evolutionary grade
In alpha taxonomy, a grade refers to a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.-Definition:...
s - which retain many plesiomorphies compared to more advanced lineages - appear to be monophyletic.
Consider for example songbird
Songbird
A songbird is a bird belonging to the suborder Passeri of the perching birds . Another name that is sometimes seen as scientific or vernacular name is Oscines, from Latin oscen, "a songbird"...
s. These can be divided into two groups - Corvida
Corvida
The "Corvida" were one of two "parvorders" contained within the suborder Passeri, as proposed in the Sibley-Ahlquist taxonomy. Standard taxonomic practice would place them at the rank of infraorder....
, which retains ancient characters in phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
and genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...
, and Passerida
Passerida
Passerida is under the Sibley-Ahlquist taxonomy, one of two "parvorders" contained within the suborder Passeri...
, which has more modern traits. But only the latter are a group of closest relatives; the former are numerous independent and ancient lineages which are about as distantly related to each other as each single one of them is to the Passerida. In a phenetic analysis, the large degree of overall similarity found among the Corvida will make them appear to be monophyletic too, but their shared traits were present in the ancestors of all songbirds already. It is the loss of these ancestral traits rather than their presence that signifies which songbirds are more closely related to each other than to other songbirds.
But the two methodologies need not be mutually exclusive. In general, phenetics is today recognized to provide too much unreliable information about the evolutionary relationships among taxa to remain a mainstay method. But there is no reason why e.g. species identified using phenetics cannot subsequently be subjected to cladistic analysis, to determine their evolutionary relationships. Phenetic methods can also be superior to cladistics when only the distinctness of related taxa is important, as the computational requirements are lower. On the other hand, whenever information on the evolutionary history of taxa is needed for a study, a researcher of today will generally try to analyze using cladistic methods.
Phenetics today
Traditionally there was a great deal of heated debate between pheneticists and cladists, as both methods were initially proposed to resolve evolutionary relationships. Perhaps the "high-water mark" of phenetics were the DNA-DNA hybridization studies by Charles G. Sibley, Jon E. Ahlquist and Burt L. Monroe Jr., from which resulted the 1990 Sibley-Ahlquist taxonomySibley-Ahlquist taxonomy
The Sibley-Ahlquist taxonomy is a bird taxonomy proposed by Charles Sibley and Jon Edward Ahlquist. It is based on DNA-DNA hybridization studies conducted in the late 1970s and throughout the 1980s....
for bird
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...
s. Highly controversial at its time, some of its findings (e.g. the Galloanserae) have been vindicated, while others (e.g. the all-inclusive "Ciconiiformes
Ciconiiformes
Traditionally, the order Ciconiiformes has included a variety of large, long-legged wading birds with large bills: storks, herons, egrets, ibises, spoonbills, and several others. Ciconiiformes are known from the Late Eocene...
" or the "Corvida
Corvida
The "Corvida" were one of two "parvorders" contained within the suborder Passeri, as proposed in the Sibley-Ahlquist taxonomy. Standard taxonomic practice would place them at the rank of infraorder....
") have been rejected. However, with computers growing increasingly powerful and widespread, more refined cladistic algorithm
Algorithm
In mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...
s became available and could put the suggestions of Willi Hennig
Willi Hennig
Emil Hans Willi Hennig was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics. With his works on evolution and systematics he revolutionised the view of the natural order of beings...
to the test; as it turned out, the results of cladistic analyses turned out to be superior to those of phenetic methods - at least when it came to resolving phylogenies.
Many systematists continue to use phenetic methods, particularly in addressing species-level questions. While the ultimate goal of taxonomy includes describing the 'tree of life' - the evolutionary path connecting all species - in fieldwork one needs to be able to separate one taxon
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
from another. Classifying diverse groups of closely related organisms that differ by very subtle differences is difficult using a cladistic approach. Phenetics provides numerical tools for examining overall patterns of variation, allowing researchers to identify discrete groups that can be classified as species.
Modern applications of phenetics are common in botany
Botany
Botany, plant science, or plant biology is a branch of biology that involves the scientific study of plant life. Traditionally, botany also included the study of fungi, algae and viruses...
, and some examples can be found in most issues of the journal Systematic Botany. Indeed, due to the effects of horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
, polyploid complex
Polyploid complex
A polyploid complex is a group of interrelated and interbreeding plants that also have differing levels of ploidy that can allow genetic exchanges between unrelated species.The polyploid complex was first described by E. B. Babcock and G...
es and other peculiarities of plant genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
, phenetic techniques in botany - though less informative altogether - are also less prone to errors compared with cladistic analysis of DNA sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
s.
In addition, many of the techniques developed by phenetic taxonomists have been adopted and extended by community ecologists, due to a similar need to deal with large amounts of data.