In biology, phylogenetics ()from Greek φυλή/φῦλον [] "tribe, clan, race", and γενετικός [] "origin, source, birth" is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, protein structure, and morphology. The results are a phylogenetic tree—a diagram depicting the hypothetical relationships among the organisms, reflecting their inferred evolutionary history.
The tips of a phylogenetic tree represent the observed entities, which can be living taxa or fossils. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the taxa represented on the tree. An unrooted tree diagram (a network) makes no assumption about directionality of character state transformation, and does not show the origin or "root" of the taxa in question.
In addition to their use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among genes or individual organisms. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes.
Phylogenetics is a component of systematics that uses similarities and differences of the characteristics of species to interpret their evolutionary relationships and origins.
In the field of cancer research, phylogenetics can be used to study the clonal evolution of tumors and molecular chronology, predicting and showing how cell populations vary throughout the progression of the disease and during treatment, using whole genome sequencing techniques. Because cancer cells reproduce mitotically, the evolutionary processes behind cancer progression are quite different from those in sexually-reproducing species. These differences manifest in several areas: the types of aberrations that occur, the rates of mutation, the high heterogeneity (variability) of tumor cell subclones, and the absence of genetic recombination.
Phylogenetics can also aid in drug design and discovery. Phylogenetics allows scientists to organize species and can show which species are likely to have inherited particular traits that are medically useful, such as producing biologically active compounds - those that have effects on the human body. For example, in drug discovery, venom-producing animals are particularly useful. Venoms from these animals produce several important drugs, e.g., ACE inhibitors and Prialt (Ziconotide). To find new venoms, scientists turn to phylogenetics to screen for closely related species that may have the same useful traits. The phylogenetic tree shows venomous species of fish, and related fish they may also contain the trait. Using this approach, biologists are able to identify the fish, snake and lizard species that may be venomous. In forensic science, phylogenetic tools are useful to assess DNA evidence for court cases. Phylogenetic analysis has been used in criminal trials to exonerate or hold individuals.
HIV forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples. HIV forensics have limitations, i.e., it cannot be the sole proof of transmission between individuals, and phylogenetic analysis which shows transmission relatedness does not indicate direction of transmission.
Taxonomy and classification
Taxonomy is the identification, naming, and classification of organisms. The Linnaean classification system developed in the 1700s by Carolus Linnaeus is the foundation for modern classification methods. Linnaean classification traditionally relied on the phenotypes or physical characteristics of organisms to group species. With the emergence of biochemistry, classifications of organisms are now often based on DNA sequence data or a combination of DNA and morphology. Many systematists contend that only monophyletic taxa should be recognized as named groups.
The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (synapomorphies); evolutionary taxonomy tries to take into account both the branching pattern and "degree of difference" to find a compromise between inferred patterns of common ancestry and evolutionary distinctness.
Inference of a phylogenetic tree
Usual methods of phylogenetic inference involve computational approaches implementing an optimality criterion and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the relative probabilities of character state transformation within and among the characters observed.
Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or similar observable traits which was often assumed to approximate phylogenetic relationships. Neighbor Joining is a phenetic method that is often used for building similarity trees for DNA barcodes.
Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods were often ambiguous and lacked explicit criteria for evaluating alternative hypotheses.Richard C. Brusca & Gary J. Brusca (2003). Invertebrates (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. .Bock, W. J. (2004). Explanations in systematics. Pp. 49–56. In Williams, D. M. and Forey, P. L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.Auyang, Sunny Y. (1998). Narratives and Theories in Natural History. In: Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics. Cambridge, U.K.; New York: Cambridge University Press.
Impacts of taxon sampling In phylogenetic analysis, taxon sampling selects a small group of exemplar taxa to infer the evolutionary history of a clade. This process is also known as stratified sampling or clade-based sampling. Judicious taxon sampling is important, given limited resources to compare and analyze every species within a diverse clade, and also given the computational limits of phylogenetic software. Poor taxon sampling may result in incorrect phylogenetic inferences. Long branch attraction, in which nonrelated branches are incorrectly grouped by shared, homoplastic nucleotide sites, is a theoretical cause for inaccuracy
There are debates if increasing the number of taxa sampled improves phylogenetic accuracy more than increasing the number of genes sampled per taxon. Differences in each method's sampling impact the number of nucleotide sites utilized in a sequence alignment, which may contribute to disagreements. For example, phylogenetic trees constructed utilizing a more significant number of total nucleotides are generally more accurate, as supported by phylogenetic trees' bootstrapping replicability from random sampling.
The graphic presented in Taxon Sampling, Bioinformatics, and Phylogenomics, compares the correctness of phylogenetic trees generated using fewer taxa and more sites per taxon on the x-axis to more taxa and fewer sites per taxon on the y-axis. With fewer taxa, more genes are sampled amongst the taxonomic group; in comparison, with more taxa added to the taxonomic sampling group, fewer genes are sampled. Each method has the same total number of nucleotide sites sampled. Furthermore, the dotted line represents a 1:1 accuracy between the two sampling methods. As seen in the graphic, most of the plotted points are located below the dotted line, which indicates gravitation toward increased accuracy when sampling fewer taxa with more sites per taxon. The research performed utilizes four different phylogenetic tree construction models to verify the theory; neighbor-joining (NJ), minimum evolution (ME), unweighted maximum parsimony (MP), and maximum likelihood (ML). In the majority of models, sampling fewer taxon with more sites per taxon demonstrated higher accuracy.
Generally, with the alignment of a relatively equal number of total nucleotide sites, sampling more genes per taxon has higher bootstrapping replicability than sampling more taxa. However, unbalanced datasets within genomic databases make increasing the gene comparison per taxon in uncommonly sampled organisms increasingly difficult.
History
Overview The term "phylogeny" derives from the German , introduced by Haeckel in 1866, and the Darwinian approach to classification which became known as the "phyletic" approach. It can be traced back to Aristotle, who wrote in his Posterior Analytics, "We may assume the superiority ceteris paribus [other things being equal] of the demonstration which derives from fewer postulates or hypotheses."
Ernst Haeckel's recapitulation theory
The modern concept of phylogenetics evolved primarily as a disproof of a previously widely accepted theory. During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely popular. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected.Blechschmidt, Erich (1977) The Beginnings of Human Life. Springer-Verlag Inc., p. 32: "The so-called basic law of biogenetics is wrong. No buts or ifs can mitigate this fact. It is not even a tiny bit correct or correct in a different form, making it valid in a certain percentage. It is totally wrong."Ehrlich, Paul; Richard Holm; Dennis Parnell (1963) The Process of Evolution. New York: McGraw–Hill, p. 66: "Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology. The resemblance of early vertebrate embryos is readily explained without resort to mysterious forces compelling each individual to reclimb its phylogenetic tree." Instead, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.
Timeline of key points
14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan friar, but the idea actually goes back to Aristotle, as a precursor concept. He introduced the concept of Occam's razor, which is the problem solving principle that recommends searching for explanations constructed with the smallest possible set of elements. Though he did not use these exact words, the principle can be summarized as "Entities must not be multiplied beyond necessity." The principle advocates that when presented with competing hypotheses about the same prediction, one should prefer the one that requires fewest assumptions. 1763, Bayesian probability, Rev. Thomas Bayes, a precursor concept. Bayesian probability began a resurgence in the 1950s, allowing scientists in the computing field to pair traditional Bayesian statistics with other more modern techniques. It is now used as a blanket term for several related interpretations of probability as an amount of epistemic confidence.