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An internal node of a phylogenetic tree is described as a polytomy or multifurcation if (i) it is in a rooted tree and is linked to three or more child subtrees or (ii) it is in an unrooted tree and is attached to four or more branches. [1] [2] A tree that contains any multifurcations can be described as a multifurcating tree.
Two types of polytomies are recognized, soft and hard polytomies. [3] [4]
Soft polytomies are the result of insufficient phylogenetic information: though the lineages diverged at different times – meaning that some of these lineages are closer relatives than others, and the available data does not allow recognition of this. Most polytomies are soft, meaning that they would be resolved into a typical tree of dichotomies if better data were available. [5]
In contrast, a hard polytomy represents a true divergence event of three or more lineages.
Interpretations for a polytomy depend on the individuals that are represented in the phylogenetic tree.
If the lineages in the phylogenetic tree stand for species, a polytomy shows the simultaneous speciation of three or more species. [6] In particular situations, they may be common, for example when a species that has rapidly expanded its range or is highly panmictic undergoes peripatric speciation in different regions.
An example is the Drosophila simulans species complex. Here, the ancestor seems to have colonized two islands at the same time but independently, yielding two equally old but divergently evolved daughter species
If a phylogenetic tree is reconstructed from DNA sequence data of a particular gene, a hard polytomy arises when three or more sampled genes trace their ancestry to a single gene in an ancestral organism. In contrast, a soft polytomy stems from branches on gene trees of finite temporal duration but for which no substitutions have occurred. [7]
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As DNA sequence evolution is usually much faster than evolution of complex phenotypic traits, it may be that genetic lineages diverge a short time apart from each other, while the actual organism has not changed if the whole ancestral population is considered. Since few if any individuals in a population are genetically alike in any one population – especially if lineage sorting has not widely progressed – it may be that hard polytomies are indeed rare or nonexistent if the entire genome of each individual organism is considered, but rather widespread on the population genetical level if entire species are considered as interbreeding populations (see also species concept).
"Speciation or lineage divergence events occurring at the same time" refers to evolutionary time measured in generations, as this is the only means that novel traits (e.g. germline point mutations) can be passed on. In practical terms, the ability to distinguish between hard and soft polytomies is limited: if for example a kilobase of DNA sequences that mutate approximately 1% per million years is analyzed, lineages diverging from the same ancestor within the same 100,000 years cannot be reliably distinguished as to which one diverged first.
Founder effects and genetic drift may result in different rates of evolution. This can easily confound molecular clock algorithms to the point where hard polytomies become unrecognizable as such.
Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.
Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed on to their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.
Cladogenesis is an evolutionary splitting of a parent species into two distinct species, forming a clade.
Anagenesis is the gradual evolution of a species that continues to exist as an interbreeding population. This contrasts with cladogenesis, which occurs when there is branching or splitting, leading to two or more lineages and resulting in separate species. Anagenesis does not always lead to the formation of a new species from an ancestral species. When speciation does occur as different lineages branch off and cease to interbreed, a core group may continue to be defined as the original species. The evolution of this group, without extinction or species selection, is anagenesis.
In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA), of a set of organisms is the most recent individual from which all the organisms of the set are descended. The term is also used in reference to the ancestry of groups of genes (haplotypes) rather than organisms.
Ailuridae is a family in the mammal order Carnivora. The family consists of the red panda and its extinct relatives.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).
An evolutionary lineage is a temporal series of populations, organisms, cells, or genes connected by a continuous line of descent from ancestor to descendant. Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics.
Evidence of common descent of living organisms has been discovered by scientists researching in a variety of disciplines over many decades, demonstrating that all life on Earth comes from a single ancestor. This forms an important part of the evidence on which evolutionary theory rests, demonstrates that evolution does occur, and illustrates the processes that created Earth's biodiversity. It supports the modern evolutionary synthesis—the current scientific theory that explains how and why life changes over time. Evolutionary biologists document evidence of common descent, all the way back to the last universal common ancestor, by developing testable predictions, testing hypotheses, and constructing theories that illustrate and describe its causes.
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood, parsimony, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space.
Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave rise to the human genome, and its current effects. Differences between genomes have anthropological, medical, historical and forensic implications and applications. Genetic data can provide important insights into human evolution.
The chimpanzee–human last common ancestor (CHLCA) is the last common ancestor shared by the extant Homo (human) and Pan genera of Hominini. Estimates of the divergence date vary widely from thirteen to five million years ago.
Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.
The following outline is provided as an overview of and topical guide to evolution:
Multispecies Coalescent Process is a stochastic process model that describes the genealogical relationships for a sample of DNA sequences taken from several species. It represents the application of coalescent theory to the case of multiple species. The multispecies coalescent results in cases where the relationships among species for an individual gene can differ from the broader history of the species. It has important implications for the theory and practice of phylogenetics and for understanding genome evolution.
This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.
The Elapoidea are a superfamily of snakes in the clade Colubroides, traditionally comprising the families Lamprophiidae and Elapidae. Advanced genomic sequence studies, however, have found lamprophiids to be paraphyletic in respect to elapids, and anywhere between four and nine families are now recognized.
Genetic saturation is the result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred. When comparing two or more genetic sequences consisting of single nucleotides, differences in sequence observed are only differences in the final state of the nucleotide sequence. Single nucleotides that undergoing genetic saturation change multiple times, sometimes back to their original nucleotide or to a nucleotide common to the compared genetic sequence. Without genetic information from intermediate taxa, it is difficult to know how much, or if any saturation has occurred on an observed sequence. Genetic saturation occurs most rapidly on fast-evolving sequences, such as the hypervariable region of mitochondrial DNA, or in short tandem repeats such as on the Y-chromosome.
In phylogenetics, reconciliation is an approach to connect the history of two or more coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree representing the evolution of an entity can be drawn within another phylogenetic tree representing an encompassing entity to reveal their interdependence and the evolutionary events that have marked their shared history. The development of reconciliation approaches started in the 1980s, mainly to depict the coevolution of a gene and a genome, and of a host and a symbiont, which can be mutualist, commensalist or parasitic. It has also been used for example to detect horizontal gene transfer, or understand the dynamics of genome evolution.