Polytomy
Encyclopedia
A polytomy pəˈlɪtəmi, meaning many temporal based branches, is a section of a phylogeny in which the evolution
ary relationships can not be fully resolved to dichotomies. In a phylogenetic tree
, a polytomy is represented as a node which has more than two immediate descending branches. They present an analytical problem, but can usually be better studied by utilizing more flexible phylogenetic network
software such as SplitsTree
, which can represent some polytomies as median networks.
On the contrary, hard polytomies represents several speciation
or lineage divergence events occurring at the same time, i.e. without their ancestral population, lineage or gene pool
evolving in between, the resultant daughter species are equally distant from each other. While some researchers doubt that hard polytomies occur at all, there is little reason to assume that they don't. In particular situations they may even be not uncommon, for example when a species that has rapidly expanded its range and/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 species.
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. As 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).
Note that "speciation or lineage divergence events occurring at the same time" refers to evolutionary time measured in generation
s, as this is the only means that novel traits (e.g. germline
point mutation
s) can be passed on. Also note that in practical terms, our ability to distinguish between hard and soft polytomies is limited: if for example a kilobase of DNA sequence
s which mutate approximately 1% per million years is analysed, lineages diverging from the same ancestor within the same 100,000 years cannot be reliably distinguished as to which one diverged first.
In that respect, it is also important to realize that founder effect
s 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.
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary relationships can not be fully resolved to dichotomies. In a 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...
, a polytomy is represented as a node which has more than two immediate descending branches. They present an analytical problem, but can usually be better studied by utilizing more flexible phylogenetic network
Phylogenetic network
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species . They are employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are...
software such as SplitsTree
SplitsTree
SplitsTree is a popular program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees...
, which can represent some polytomies as median networks.
Soft polytomies vs. hard polytomies
Two types of polytomies are recognised, soft and hard polytomies. Soft polytomies are the result of insufficient phylogenetic information: though the lineages diverged at different times – meaning that some of them are closer relatives than others – the available data does not allow to recognize this.On the contrary, hard polytomies represents several 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...
or lineage divergence events occurring at the same time, i.e. without their ancestral population, lineage or gene pool
Gene pool
In population genetics, a gene pool is the complete set of unique alleles in a species or population.- Description :A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection...
evolving in between, the resultant daughter species are equally distant from each other. While some researchers doubt that hard polytomies occur at all, there is little reason to assume that they don't. In particular situations they may even be not uncommon, for example when a species that has rapidly expanded its range and/or is highly panmictic undergoes peripatric speciation
Peripatric speciation
Peripatric and peripatry are terms from biogeography, referring to organisms whose ranges are closely adjacent but do not overlap, being separated where these organisms do not occur – for example a wide river or a mountain range. Such organisms are usually closely related Peripatric and...
in different regions.
An example is the Drosophila simulans species complex
Drosophila melanogaster species subgroup
The Drosophila melanogaster species subgroup contains 9 species, including the best known species Drosophila melanogaster and D. simulans. The subgroup belongs to the Drosophila melanogaster species group within the subgenus Sophophora....
. Here, the ancestor seems to have colonized two islands at the same time but independently, yielding two equally old but divergently evolved species.
Recognizing hard polytomies
As DNA sequenceDNA 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...
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
Population
A population is all the organisms that both belong to the same group or species and live in the same geographical area. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals...
is considered. As 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
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of each individual organism is considered, but rather widespread on the population genetical
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...
level if entire 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...
are considered as interbreeding populations (see also species concept).
Note that "speciation or lineage divergence events occurring at the same time" refers to evolutionary time measured in generation
Generation
Generation , also known as procreation in biological sciences, is the act of producing offspring....
s, as this is the only means that novel traits (e.g. germline
Germline
In biology and genetics, the germline of a mature or developing individual is the line of germ cells that have genetic material that may be passed to a child.For example, gametes such as the sperm or the egg, are part of the germline...
point mutation
Point mutation
A point mutation, or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA. Often the term point mutation also includes insertions or deletions of a single base pair...
s) can be passed on. Also note that in practical terms, our ability to distinguish between hard and soft polytomies is limited: if for example a kilobase 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 which mutate approximately 1% per million years is analysed, lineages diverging from the same ancestor within the same 100,000 years cannot be reliably distinguished as to which one diverged first.
In that respect, it is also important to realize that founder effect
Founder effect
In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall...
s and genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
may result in different rates of evolution. This can easily confound molecular clock
Molecular clock
The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...
algorithms to the point where hard polytomies become unrecognizable as such.