Incomplete lineage sorting, also termed hemiplasy, deep
coalescence
Coalescence may refer to:
* Coalescence (chemistry), the process by which two or more separate masses of miscible substances seem to "pull" each other together should they make the slightest contact
* Coalescence (computer science), the merging of ...
, retention of ancestral
polymorphism, or trans-species polymorphism, describes a phenomenon in
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...
when ancestral gene copies fail to coalesce (looking backwards in time) 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
In botany, a tree is a perennial plant with an elongated stem, or trunk, usually supporting branches and leaves. In some usages, the definition of a tree may be narrower, including only woody plants with secondary growth, plants that are ...
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.
Concept
![Non-hemiplasy example](https://upload.wikimedia.org/wikipedia/commons/5/51/Non-hemiplasy_example.svg)
The concept of incomplete lineage sorting has some important implications for phylogenetic techniques. The persistence of
polymorphisms across different
speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
events can cause incomplete lineage sorting. Suppose two subsequent speciation events occur where an ancestor species gives rise firstly to species A, and secondly to species B and C. When studying a single gene, it can have multiple versions (
allele
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
s) causing different characters to appear (polymorphisms). In the example shown in Figure 1, the gene G has two versions (alleles), G0 and G1. The ancestor of A, B and C originally had only one version of gene G, G0. At some point, a mutation occurred and the ancestral population became polymorphic, with some individuals having G0 and others G1. When species A split off, it retained only G1, while the ancestor of B and C remained polymorphic. When B and C diverged, B retained only G1 and C only G0; neither were now polymorphic in G. The tree for gene G shows A and B as sisters, whereas the species tree shows B and C as sisters. If the phylogeny of these species is based on gene G, it will not represent the actual relationships between the species. In other words, the most related species will not necessarily inherit the most related genes. This is of course a simplified example of incomplete lineage sorting, and in real research it is usually more complex containing more genes and species.
However, other mechanisms can lead to the same apparent discordancy, for example, alleles can move across species boundaries via hybridization, and DNA can be transferred between species by viruses. This is illustrated in Figure 2. Here the ancestor of A, B and C, and the ancestor of B and C, had only the G0 version of gene G. A mutation occurred at the divergence of B and C, and B acquired a mutated version, G1. Some time later, the arrow shows that G1 was transferred from B to A by some means (e.g. hybridization or horizontal gene transfer). Studying only the final states of G in the three species makes it appear that A and B are sisters rather than B and C, as in Figure 1, but in Figure 2 this is not caused by incomplete lineage sorting.
Implications
Incomplete lineage sorting has important implications for phylogenetic research. There is a chance that when creating a phylogenetic tree it may not resemble actual relationships because of this incomplete lineage sorting. However, gene flow
In population genetics, gene flow (also known as gene migration or geneflow and allele flow) is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent a ...
between lineages by hybridization or horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
may produce the same conflicting phylogenetic tree. Distinguishing these different processes may seem difficult, but much research and different statistical approaches are (being) developed to gain greater insight in these evolutionary dynamics. One of the resolutions to reduce the implications of incomplete lineage sorting is to use multiple genes for creating species or population phylogenies. The more genes used, the more reliable the phylogeny becomes.
In
diploid
Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectively ...
organisms
Incomplete lineage sorting commonly happens with sexual reproduction
Sexual reproduction is a type of reproduction that involves a complex life cycle in which a gamete ( haploid reproductive cells, such as a sperm or egg cell) with a single set of chromosomes combines with another gamete to produce a zygote tha ...
because the species cannot be traced back to a single person or breeding pair. When organism tribe populations are large (i.e. thousands) each gene has some diversity and the gene tree consists of other pre-existing lineages. If the population is bigger these ancestral lineages are going to persist longer. When you get large ancestral populations together with closely timed speciation events these different pieces of DNA retain conflicting affiliations. This makes it hard to determine a common ancestor or points of branching.
In primate evolution
When studying primates, chimpanzees and bonobos are more related to each other than any other taxa and are thus sister taxa
In phylogenetics, a sister group or sister taxon, also called an adelphotaxon, comprises the closest relative(s) of another given unit in an evolutionary tree.
Definition
The expression is most easily illustrated by a cladogram:
Taxon A and ...
. Still, for 1.6% of the bonobo genome, sequences are more closely related to homologues of humans than to chimpanzees, which is probably a result of incomplete lineage sorting. A study of more than 23,000 DNA sequence alignments in the family Hominidae
The Hominidae (), whose members are known as the great apes or hominids (), are a taxonomic family of primates that includes eight extant species in four genera: '' Pongo'' (the Bornean, Sumatran and Tapanuli orangutan); ''Gorilla'' (the ea ...
(great apes, including humans) showed that about 23% did not support the known sister relationship of chimpanzees and humans.[
]
In human evolution
In human evolution, incomplete lineage sorting is used to diagram hominin lineages that may have failed to sort out at the same time that speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
occurred in prehistory. Due to the advent of genetic testing and genome sequencing, researchers found that the genetic relationships between hominin lineages might disagree with previous understandings of their relatedness based on physical characteristics. Moreover, divergence of the last common ancestor
In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA) or concestor, of a set of organisms is the most recent individual from which all the organisms of the set are descended. The ...
(LCA) may not necessarily occur at the same time as speciation. Lineage sorting is a method that allows paleoanthropologists to explore the genetic relationships and divergences that may not fit with their previous speciation models based on phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
alone.
Incomplete lineage sorting of the human family tree is an area of great interest. There are a number of unknowns when considering both the transition from archaic humans
A number of varieties of ''Homo'' are grouped into the broad category of archaic humans in the period that precedes and is contemporary to the emergence of the earliest early modern humans (''Homo sapiens'') around 300 ka. Omo-Kibish I (Omo I) f ...
to modern humans and divergence of the other great apes from the hominin lineage.
Ape and hominin / human divergence
Incomplete lineage sorting means that the average divergence time between genes may differ from the divergence time between species. Models suggest that the average divergence time between the genes in the human and chimpanzee genome is older than the split between humans and gorillas. What this means is the common ancestor of humans and chimpanzees has left traces of genetic material that was present in the common ancestor of humans, chimpanzees, and gorillas. However, the genetic tree slightly differs from that of the species or phylogeny tree. In the phylogeny tree when we look at the evolutionary relationship between the human, bonobo
The bonobo (; ''Pan paniscus''), also historically called the pygmy chimpanzee and less often the dwarf chimpanzee or gracile chimpanzee, is an endangered great ape and one of the two species making up the genus '' Pan,'' the other being the comm ...
chimpanzee, and gorilla, the results show that the separation of bonobo and chimpanzee transpired in a close proximity of time to the common ancestor of the bonobo-chimpanzee ancestor and humans, indicating that humans and chimpanzees shared a common ancestor for several million years after separation from gorillas. This creates the phenomenon that is incomplete lineage sorting. Today researchers are relying on DNA fragments in order to study the evolutionary relationships among humans and their counterparts in the hope that it will provide information about speciation and ancestral processes from genomes from different types of humans.
In viruses
Incomplete lineage sorting is a common feature in viral phylodynamics Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies.
Since the coining of the term in 2004, research on viral phylodynamics has foc ...
, where the phylogeny represented by transmission of a disease from one person to the next, which is to say the population level tree, often doesn't correspond to the tree created from a genetic analysis due to the population bottleneck
A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide, widespread violen ...
s that are an inherent feature of viral transmission of disease. Figure 3 illustrates how this can occur. This has relevance to criminal transmission of HIV
Criminal transmission of HIV is the intentional or reckless infection of a person with the human immunodeficiency virus (HIV). This is often conflated, in laws and in discussion, with criminal exposure to HIV, which does not require the transm ...
where in some criminal cases, a phylogenetic analysis of one or two genes from the strains from the accused and the victim have been used to infer transmission; however, the commonality of incomplete lineage sorting means that transmission cannot be inferred solely on the basis of such a basic analysis.
In
linguistics
Linguistics is the scientific study of human language. It is called a scientific study because it entails a comprehensive, systematic, objective, and precise analysis of all aspects of language, particularly its nature and structure. Linguis ...
Jacques and List (2019) show that the concept of incomplete lineage sorting can be applied to account for non-treelike phenomena in language evolution. Kalyan and François
François () is a French masculine given name and surname, equivalent to the English name Francis.
People with the given name
* Francis I of France, King of France (), known as "the Father and Restorer of Letters"
* Francis II of France, Kin ...
(2019), proponents of the method of historical glottometry Historical Glottometry is a method used in historical linguistics. It is a quantitative, non-cladistic approach to language subgrouping.
The aim of Historical Glottometry (HG) is to address the limitations of the tree model when applied to dialec ...
, a model challenging the applicability of the tree model in historical linguistics, concur that "Historical Glottometry does not challenge the family tree model once incomplete lineage sorting has been taken into account."
See also
* Gibbon–human last common ancestor
The phylogenetic split of the superfamily Hominoidea (apes) into the Hylobatidae (gibbons) and Hominidae (great apes) families (also dubbed "gibbon–human last common ancestor", GHLCA) is dated to the early Miocene, roughly .
Hylobatidae ha ...
* Laggar falcon
The laggar falcon (''Falco jugger''), also known as the lugger falcon or jugger (from Hindi जग्गर — jaggar, “falcon”) is a mid-sized bird of prey which occurs in the Indian subcontinent from extreme southeastern Iran, southeaste ...
* Coalescent theory
Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, m ...
* Multispecies coalescent process 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 speci ...
* Lineage (evolution)
An evolutionary lineage is a temporal series of populations, organisms, cells, or genes connected by a continuous line of descent from ancestor to descendant.The Oxford English Dictionary defines biological lineage as "a sequence of species each of ...
References
External links
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* {{cite journal , last1=Scornavacca , first1=C. , last2=Galtier , first2=N. , year=2017 , title=Incomplete lineage sorting in mammalian phylogenomics , journal=Systematic Biology , volume=66 , issue=1 , pages=112–120 , doi=10.1093/sysbio/syw082, pmid=28173480 , doi-access=free
Phylogenetics
Population genetics