Phylogenetic comparative methods - AbsoluteAstronomy.com

Phylogenetic comparative methods (PCMs) use information on the evolutionary relationships of organisms (phylogenetic trees) to compare species (Harvey and Pagel, 1991). The most common applications are to test for correlated evolutionary changes in two or more traits, or to determine whether a trait contains a phylogenetic signal (the tendency for related species to resemble each other). However, several methods are available to relate particular phenotypic traits to variation in rates of speciation

Speciation

Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...

and/or extinction

Extinction

In biology and ecology, extinction is the end of an organism or of a group of organisms , normally a species. The moment of extinction is generally considered to be the death of the last individual of the species, although the capacity to breed and recover may have been lost before this point...

, including attempts to identify evolutionary key innovations. Although most studies that employ PCMs focus on extant organisms, the methods can also be applied to extinct taxa and can incorporate information from the fossil record.

Owing to their computational requirements, they are usually implemented by computer programs (see list below). PCMs can be viewed as part of evolutionary biology, systematics

Systematics

Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...

, phylogenetics

Phylogenetics

In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

, bioinformatics

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

or even statistics

Statistics

Statistics is the study of the collection, organization, analysis, and interpretation of data. It deals with all aspects of this, including the planning of data collection in terms of the design of surveys and experiments....

, as most methods involve statistical procedures and principles for estimation of various parameters and drawing inferences about evolutionary processes.

What distinguishes PCMs from most traditional approaches in systematics

Systematics

and phylogenetics

Phylogenetics

In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

is that they typically do not attempt to infer the phylogenetic relationships of the species under study. Rather, they use an independent estimate of the phylogenetic tree

Phylogenetic tree

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...

(topology plus branch lengths) that is derived from a separate phylogenetic analysis, such as comparative DNA sequences that have been analyzed by maximum parsimony

Maximum parsimony

Parsimony is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some observed data....

or maximum likelihood

Maximum likelihood

In statistics, maximum-likelihood estimation is a method of estimating the parameters of a statistical model. When applied to a data set and given a statistical model, maximum-likelihood estimation provides estimates for the model's parameters....

methods. PCMs are consumers of phylogenetic trees, not primary producers of them. Accordingly, the list of phylogenetics software shows little overlap with the programs for PCMs (see below).

Comparison of species to elucidate aspects of biology has a long history. Charles Darwin

Charles Darwin

Charles Robert Darwin FRS was an English naturalist. He established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.He published his theory...

relied on such comparisons as a major source of evidence when writing The Origin of Species

The Origin of Species

Charles Darwin's On the Origin of Species, published on 24 November 1859, is a work of scientific literature which is considered to be the foundation of evolutionary biology. Its full title was On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the...

. Many other fields of biology use interspecific comparison as well, including behavioral ecology

Behavioral ecology

Behavioral ecology, or ethoecology, is the study of the ecological and evolutionary basis for animal behavior, and the roles of behavior in enabling an animal to adapt to its environment...

, ethology

Ethology

Ethology is the scientific study of animal behavior, and a sub-topic of zoology....

, ecophysiology

Ecophysiology

Ecophysiology or environmental physiology is a biological discipline which studies the adaptation of organism's physiology to environmental conditions...

, comparative physiology

Comparative physiology

Comparative physiology is a subdiscipline of physiology that studies and exploits the diversity of functional characteristics of various kinds of organisms. It is closely related to evolutionary physiology and environmental physiology. Many universities offer undergraduate courses that cover...

, evolutionary physiology

Evolutionary physiology

Evolutionary physiology is the study of physiological evolution, which is to say, the manner in which the functional characteristics of individuals in a population of organisms have responded to selection across multiple generations during the history of the population.It is a subdiscipline of both...

, functional morphology, comparative biomechanics

Biomechanics

Biomechanics is the application of mechanical principles to biological systems, such as humans, animals, plants, organs, and cells. Perhaps one of the best definitions was provided by Herbert Hatze in 1974: "Biomechanics is the study of the structure and function of biological systems by means of...

, and the study of sexual selection

Sexual selection

Sexual selection, a concept introduced by Charles Darwin in his 1859 book On the Origin of Species, is a significant element of his theory of natural selection...

.

The comparative method

Comparative method

In linguistics, the comparative method is a technique for studying the development of languages by performing a feature-by-feature comparison of two or more languages with common descent from a shared ancestor, as opposed to the method of internal reconstruction, which analyzes the internal...

is also used heavily in linguistics.

Applications

PCMs can be used to analyze the origin and maintenance of biodiversity

Biodiversity

Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...

. Biodiversity is most commonly discussed in terms of the number of species, but it can also be phrased in terms of the amount of phenotypic (e.g., physiological, morphological) space that a given set of species occupies (see also Cambrian explosion

Cambrian explosion

The Cambrian explosion or Cambrian radiation was the relatively rapid appearance, around , of most major phyla, as demonstrated in the fossil record, accompanied by major diversification of other organisms, including animals, phytoplankton, and calcimicrobes...

Phylogenetic comparative methods are commonly applied to such questions as:

What is the slope
Slope
In mathematics, the slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline....

of an allometric scaling relationship?

→ Example: how does brain mass vary in relation to body mass?

Do different clades of organisms differ with respect to some phenotypic trait?

→ Example: do canids have larger hearts than felids?

Do groups of species that share a behavioral or ecological feature (e.g., social system, diet
Diet (nutrition)
In nutrition, diet is the sum of food consumed by a person or other organism. Dietary habits are the habitual decisions an individual or culture makes when choosing what foods to eat. With the word diet, it is often implied the use of specific intake of nutrition for health or weight-management...

) differ in average phenotype?

→ Example: do carnivores have larger home ranges than herbivores?

What was the ancestral state of a trait
Trait
Trait may refer to:* Trait, a characteristic or property of some object* Trait , which involve genes and characteristics of organisms* Trait theory, an approach to the psychological study of personality...

?

→ Example: where did endothermy evolve in the lineage that led to mammals?

→ Example: where, when, and why did placentas
Placenta
The placenta is an organ that connects the developing fetus to the uterine wall to allow nutrient uptake, waste elimination, and gas exchange via the mother's blood supply. "True" placentas are a defining characteristic of eutherian or "placental" mammals, but are also found in some snakes and...

and viviparity evolve?

Does a trait exhibit significant phylogenetic signal in a particular group of organisms? Do certain types of traits tend to "follow phylogeny" more than others?

→ Example: are behavioral traits more labile during evolution?

Do species differences in life history traits
Life history theory
Life history theory posits that the schedule and duration of key events in an organism's lifetime are shaped by natural selection to produce the largest possible number of surviving offspring...

trade-off, as in the so-called fast-slow continuum?

→ Example: why do small-bodied species have shorter life spans

Life expectancy

Life expectancy is the expected number of years of life remaining at a given age. It is denoted by ex, which means the average number of subsequent years of life for someone now aged x, according to a particular mortality experience...

than their larger relatives?

Phylogenetically independent contrasts

Felsenstein (1985) proposed the first general statistical method for incorporating phylogenetic information, i.e., the first that could use any arbitrary topology

Topology

Topology is a major area of mathematics concerned with properties that are preserved under continuous deformations of objects, such as deformations that involve stretching, but no tearing or gluing...

(branching order) and a specified set of branch lengths. The method is now recognized as an 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...

that implements a special case of what are termed phylogenetic generalized least-squares models (Grafen, 1989). The logic

Logic

In philosophy, Logic is the formal systematic study of the principles of valid inference and correct reasoning. Logic is used in most intellectual activities, but is studied primarily in the disciplines of philosophy, mathematics, semantics, and computer science...

of the method is to use phylogenetic information (and an assumed Brownian motion

Brownian motion

Brownian motion or pedesis is the presumably random drifting of particles suspended in a fluid or the mathematical model used to describe such random movements, which is often called a particle theory.The mathematical model of Brownian motion has several real-world applications...

like model of trait evolution) to transform the original tip data (mean values for a set of species) into values that are statistically independent and identically distributed.

The algorithm involves computing values at internal nodes as an intermediate step, but they are generally not used for inferences by themselves. An exception occurs for the basal (root) node, which can be interpreted as an estimate of the ancestral value for the entire tree (assuming that no directional evolutionary trends [e.g., Cope's rule

Cope's rule

Cope's rule states that population lineages tend to increase in body size over evolutionary time. While the rule has been demonstrated in many instances, it does not hold true at all taxonomic levels, or in all clades...

] have occurred) or as a phylogenetically weighted estimate of the mean for the entire set of tip species (terminal taxa). The value at the root is equivalent to that obtained from the "squared-change parsimony" algorithm and is also the maximum likelihood estimate under Brownian motion. The independent contrasts algebra can also be used to compute a standard error

Standard error

Standard error can refer to:* Standard error , the estimated standard deviation or error of a series of measurements* Standard error stream, one of the standard streams in Unix-like operating systems...

or confidence interval

Confidence interval

In statistics, a confidence interval is a particular kind of interval estimate of a population parameter and is used to indicate the reliability of an estimate. It is an observed interval , in principle different from sample to sample, that frequently includes the parameter of interest, if the...

Phylogenetically informed Monte Carlo computer simulations

Martins and Garland (1991) proposed that one way to account for phylogenetic relations when conducting statistical analyses was to use computer simulations to create many data sets that are consistent with the null hypothesis under test (e.g., no correlation between two traits, no difference between two ecologically defined groups of species) but that mimic evolution along the relevant phylogenetic tree. If such data sets (typically 1,000 or more) are analyzed with the same statistical procedure that is used to analyze a real data set, then results for the simulated data sets can be used to create phylogenetically correct (or "PC" [Garland et al., 1993]) null distributions of the test statistic (e.g., a correlation coefficient, t, F). Such simulation approaches can also be combined with methods like phylogenetically independent contrasts (see above).

Related quotations

In addition to having a long and extremely productive history in biology, comparative methods are often controversial. Rather than attempt to recount the various controversies, many of which are ongoing, quotes (in chronological order) are illustrative.

"Ought we, for instance, to begin by discussing each separate species - man, lion, ox, and the like - taking each kind in hand independently of the rest, or ought we rather to deal first with the attributes which they have in common in virtue of some common element of their nature, and proceed from this as a basis for the consideration of the separately?" (Aristotle

Aristotle

Aristotle was a Greek philosopher and polymath, a student of Plato and teacher of Alexander the Great. His writings cover many subjects, including physics, metaphysics, poetry, theater, music, logic, rhetoric, linguistics, politics, government, ethics, biology, and zoology...

, De partibus animalium; quoted in Harvey and Pagel, 1991, p. 35)

"In parallel with laboratory experimental methods, the comparative method increases in value with its sample size, i.e., the number of species

Species

In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...

being compared. When species are few and their phylogenetic relationships are clouded in the distant past of unfossilized ancestors, the comparative method reaps fewer conclusions of trust." (Hailman, 1976, p. 20)

"... there is no easy way, except by comparison, to test most questions about the long-term history of life, or to generate predictions from evolutionary considerations." (Alexander, 1979, p. 13)

"... we must learn to treat comparative data with the same respect as we would treat experimental results ..." (Maynard Smith

John Maynard Smith

John Maynard Smith,His surname was Maynard Smith, not Smith, nor was it hyphenated. F.R.S. was a British theoretical evolutionary biologist and geneticist. Originally an aeronautical engineer during the Second World War, he took a second degree in genetics under the well-known biologist J.B.S....

and Holliday, 1979, p. vii)

"In the past, however, cooperation between systematists and other comparative biologists has been sporadic at best. Most experimental biologists have ignored taxonomy and systematics, some even to the extent of not bothering to provide their animals with proper identifications or scientific names." (Atz et al., 1980, p. 7)

"If we assume that the ... cladogram

Cladogram

A cladogram is a diagram used in cladistics which shows ancestral relations between organisms, to represent the evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational...

.. is correct, we can then hypothesize

Hypothesis

A hypothesis is a proposed explanation for a phenomenon. The term derives from the Greek, ὑποτιθέναι – hypotithenai meaning "to put under" or "to suppose". For a hypothesis to be put forward as a scientific hypothesis, the scientific method requires that one can test it...

what the particular common ancestor must have been like." (Atz et al., 1980, p. 14)

"... biology will never secure fossils of all species in the past because fossilization is such a rare process, requiring just the right physical and chemical conditions. Therefore, in order to trace probable phylogenetic lineages one must reason from the evidence at hand: the characteristics of contemporary animals themselves which are the end-points of phylogeny (evolutionary history)." (Hailman, 1981, p. 93)

"... the comparative method of 1950 was indistinguishable from the comparative method of 350 BC ..." (Ridley, 1983, p. 6)

"Focusing only on highly adapted species may, of course, bring valuable information on extreme situations but might also obscure the basic mechanisms." (Bankir and Rouffignac, 1985, p. R663)

"Most of what we know is based upon comparison. When asked to describe a food not previously tasted or a new kind of music, one often responds that the taste is "like" some other food, or that the sensation "differs" in a particular way from something that is familiar. Indeed, comparison and the similarities and differences it discloses is ingrained in our approach to description of objects, events and processes. Hence the questions "what can we compare?" and its ancillary "how shall we compare?" prove to be the key to any study of natural phenomena." (Gans, 1985, p. 291)

"Some reviewers of this paper felt that the message was "rather nihilistic

Nihilism

Nihilism is the philosophical doctrine suggesting the negation of one or more putatively meaningful aspects of life. Most commonly, nihilism is presented in the form of existential nihilism which argues that life is without objective meaning, purpose, or intrinsic value...

," and suggested that it would be much improved if I could present a simple and robust method that obviated the need to have an accurate knowledge of phylogeny. I entirely sympathize, but do not have a method that solves the problem. The best we can do is perhaps to use pairs of close relatives as suggested above, although this discards at least half of the data. Comparative biologists may understandably feel frustrated upon being told that they need to know the phylogenies of their groups in great detail, when this is not something they had much interest in knowing. Nevertheless, efforts to cope with the effects of the phylogeny will have to be made. Phylogenies are fundamental to comparative biology; there is no doing it without taking them into account." (Felsenstein, 1985, p. 14)

"Comparative biologists tend to suspect comparisons of distantly related species; they hope to base their comparisons on recent evolutionary events that have not been overlaid by much subsequent change." (Felsenstein, 1988, p. 465)

"Yet, one of the most embarrassing things that could be done to a group of respected biologists would be to ask them to spend a few minutes to write down what is meant by the comparative method, and what are the basic goals and principles of biological comparison." (Bock, 1989, p. 18 [cited in Starck, 1998, p. 110])

"As welcome as it is to see the lung

Lung

The lung is the essential respiration organ in many air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located near the backbone on either side of the heart...

successfully employed as a systematic index, it is, on the other hand, unfortunate. Thereby, lungs lose their innocence in the sense that phylogenetic trees and cladograms can no longer be used to help resolve the sequence in the development

Morphogenesis

Morphogenesis , is the biological process that causes an organism to develop its shape...

of lung structure without the danger of circular argumentation." (Perry, 1989, p. 200)

"To be maximally informative, such studies should be undertaken on closely related groups of organisms, so that factors extraneous to the comparison can be minimized ..." (Bennett and Huey

Raymond B. Huey

Raymond B. Huey is a biologist specializing in evolutionary physiology. He has taught at the University of Washington , and he earned his Ph.D. in biology at Harvard University under E. E. Williams. He is currently the chairman of the UW Biology Department.-Education:Huey earned his A.B...

, 1990, p. 272)

"The comparative approach is not new. Indeed, it was Darwin's favoured technique. ... In short, comparative studies have taught us most of what we know about adaptation." (Harvey and Pagel, 1991, p. v)

"In short, all useful comparative methods are based on explicit models of evolutionary change." (Harvey and Pagel, 1991, p. v)

"Adaptation is an inherently comparative idea ..." (Harvey and Pagel, 1991, p. 13)

"The usual symptom of non-independence is that closely related species tend to be more alike than more distantly related species." (Harvey and Pagel, 1991, p. 81)

"... to use species as independent data points in a comparative analysis requires that one ignores phylogenetic relationships." (Harvey and Pagel, 1991, p. 122)

"Because life-history

Life history theory

Life history theory posits that the schedule and duration of key events in an organism's lifetime are shaped by natural selection to produce the largest possible number of surviving offspring...

traits are likely to be correlated with a species' phylogenetic history, unequivocal evidence for adaptation to local environmental conditions may be recognized only after the variation in a trait attributable to phylogeny is removed." (Miles and Dunham, 1992, p. 848)

"Broad-scale comparative evidence from across a large number of taxa may often help set limits to the applicability of hypotheses that have been generated from a particular phenomenon in a particular species." (Moller and Birkhead, 1992, p. 650)

"Any comparative study lacking a phylogenetic perspective now would be incomplete." (Miles and Dunham, 1993, p. 590)

"However, in general, the evolutionary process involves descent with modification, and in the absence of modification, one must conclude that similarities among closely related taxa reflect shared ancestry. Phylogeny, then, is an important explanatory principle for understanding shared characteristics and should be the null hypothesis in all tests of similarity or differentiation among taxa." (Di Fiore and Rendall, 1994, p. 9945)

"Moreover, comparative studies supply only correlational data. Correlation does not demonstrate causation ..." (Garland

Theodore Garland, Jr.

Theodore Garland, Jr. is a biologist specializing in evolutionary physiology. He was on the faculty at the University of Wisconsin–Madison for 14 years, served at the National Science Foundation for one year, and is currently Professor of Biology at the University of California, Riverside. He...

and Adolph, 1994, p. 823)

"In addition to his theory of natural selection, the comparative method is what made Darwin great. If you don't believe this claim, look at any of his major works. They are packed full with interspecific comparisons based on detailed studies and anecdotal observations." (Hauser, 1996, p. 10)

"Population comparisons can provide particularly powerful means of evaluating adaptive hypotheses for two reasons. The first is that there tend to be fewer differences between populations than between species. Consequently, there are fewer covarying traits to confound analyses ... Second, divergent populations are often relatively young and may be more likely to reside in the habitats in which their derived character states evolved than is the case for divergent species with potentially longer intervening histories ..." (Foster and Cameron, 1996, p. 140).

"Naive, prephylogenetic comparative tests should be kept at the other end of a barge pole." (Ridley and Grafen, 1996, p. 87)

"It is the study of the bizarre, the outliers, the freaks, that gives us some of our clearest insights into the hows and whys of evolution." (Torr, 1998, p. 52)

External links

Journals

Software packages (incomplete list)

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