Reticulate evolution

Last updated May 02, 2023

Reticulate evolution, or network evolution is the origination of a lineage through the partial merging of two ancestor lineages, leading to relationships better described by a phylogenetic network than a bifurcating tree.^[1] Reticulate patterns can be found in the phylogenetic reconstructions of biodiversity lineages obtained by comparing the characteristics of organisms.^[2] Reticulation processes can potentially be convergent and divergent at the same time.^[3] Reticulate evolution indicates the lack of independence between two evolutionary lineages.^[1] Reticulation affects survival, fitness and speciation rates of species.^[2]

Reticulate evolution can happen between lineages separated only for a short time, for example through hybrid speciation in a species complex. Nevertheless, it also takes place over larger evolutionary distances, as exemplified by the presence of organelles of bacterial origin in eukaryotic cells.^[2]

Reticulation occurs at various levels:^[4] at a chromosomal level, meiotic recombination causes evolution to be reticulate; at a species level, reticulation arises through hybrid speciation and horizontal gene transfer; and at a population level, sexual recombination causes reticulation.^[1]

The adjective reticulate stems from the Latin words reticulatus, "having a net-like pattern" from reticulum, "little net."^[5]

Underlying mechanisms and processes

Since the nineteenth century, scientists from different disciplines have studied how reticulate evolution occurs. Researchers have increasingly succeeded in identifying these mechanisms and processes. It has been found to be driven by symbiosis, symbiogenesis (endosymbiosis), lateral gene transfer, hybridization and infectious heredity.^[2]

Symbiosis

Symbiosis is a close and long-term biological interaction between two different biological organisms.^[6] Often, both of the organisms involved develop new features upon the interaction with the other organism. This may lead to the development of new, distinct organisms.^[7]^[8] The alterations in genetic material upon symbiosis can occur via germline transmission or lateral transmission.^[2]^[9]^[10] Therefore, the interaction between different organisms can drive evolution of one or both organisms.^[6]

Symbiogenesis

Symbiogenesis (endosymbiosis) is a special form of symbiosis whereby an organism lives inside another, different organism. Symbiogenesis is thought to be very important in the origin and evolution of eukaryotes. Eukaryotic organelles, such as mitochondria, have been theorized to have been originated from cell-invaded bacteria living inside another cell.^[11]^[12]

Lateral gene transfer

Lateral gene transfer, or horizontal gene transfer, is the movement of genetic material between unicellular and/or multicellular organisms without a parent-offspring relationship. The horizontal transfer of genes results in new genes, which could give new functions to the recipient and thus could drive evolution.^[13]

Hybridization

In the neo-Darwinian paradigm, one of the assumed definition of a species is that of Mayr's, which defines species based upon sexual compatibility.^[14] Mayr's definition therefore suggests that individuals that can produce fertile offspring must belong to the same species. However, in hybridization, two organisms produce offspring while being distinct species.^[2] During hybridization the characteristics of these two different species are combined yielding a new organism, called a hybrid, thus driving evolution.^[15]

Infectious heredity

Infectious agents, such as viruses, can infect the cells of host organisms. Viruses infect cells of other organisms in order to enable their own reproduction. Hereto, many viruses can insert copies of their genetic material into the host genome, potentially altering the phenotype of the host cell.^[16]^[17]^[18] When these viruses insert their genetic material in the genome of germ line cells, the modified host genome will be passed onto the offspring, yielding genetically differentiated organisms. Therefore, infectious heredity plays an important role in evolution,^[2] for example in the formation of the female placenta.^[19]^[20]

Models

Reticulate evolution has played a key role in the evolution of some organisms such as bacteria and flowering plants.^[21]^[22] However, most methods for studying cladistics have been based on a model of strictly branching cladogeny, without assessing the importance of reticulate evolution.^[23] Reticulation at chromosomal, genomic and species levels fails to be modelled by a bifurcating tree.^[1]

According to Ford Doolittle, an evolutionary and molecular biologist: “Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree”.^[24]

Reticulate evolution refers to evolutionary processes which cannot be successfully represented using a classical phylogenetic tree model,^[25] as it gives rise to rapid evolutionary change with horizontal crossings and mergings often preceding a pattern of vertical descent with modification.^[26] Reconstructing phylogenetic relationships under reticulate evolution requires adapted analytical methods.^[27] Reticulate evolution dynamics contradict the neo-Darwininan theory, compiled in the Modern Synthesis, by which the evolution of life occurs through natural selection and is displayed with a bifurcating or branching pattern. Frequent hybridisation between species in natural populations challenges the assumption that species have evolved from a common ancestor by simple branching, in which branches are genetically isolated.^[27]^[28] The study of reticulate evolution is said to have been largely excluded from the modern synthesis.^[4] The urgent need for new models which take reticulate evolution into account has been stressed by many evolutionary biologists, such as Nathalie Gontier who has stated "reticulate evolution today is a vernacular concept for evolutionary change induced by mechanisms and processes of symbiosis, symbiogenesis, lateral gene transfer, hybridization, or divergence with gene flow, and infectious heredity". She calls for an extended evolutionary synthesis that integrates these mechanisms and processes of evolution.^[26]

Applications

Reticulate evolution has been extensively applied to plant hybridization in agriculture and gardening. The first commercial hybrids appeared in the early 1920s.^[29] Since then, many protoplast fusion experiments have been carried out, some of which were aimed at improvement of crop species.^[30] Wild types possessing desirable agronomic traits are selected and fused in order to yield novel, improved species. The newly generated plant will be improved for traits such as better yield, greater uniformity, improved color, and disease resistance.^[31]

Examples

Reticulate evolution is regarded as a process that has shaped the histories of many organisms.^[32] There is evidence of reticulation events in flowering plants, as the variation patterns between angiosperm families strongly suggests there has been widespread hybridisation.^[33] Grant^[21] states that phylogenetic networks, instead of phylogenetic trees, arise in all major groups of higher plants. Stable speciation events due to hybridisation between angiosperm species supports the occurrence of reticulate evolution and highlights the key role of reticulation in the evolution of plants.^[34]

Genetic transfer can occur across wide taxonomic levels in microorganisms and become stably integrated into the new microbial populations,^[35]^[36] as has been observed through protein sequencing.^[37] Reticulation in bacteria usually only involves the transfer of only a few genes or parts of these.^[23] Reticulate evolution driven by lateral gene transfer has also been observed in marine life.^[38] Lateral genetic transfer of photo-response genes between planktonic bacteria and Archaea has been evidenced in some groups, showing an associated increase in environmental adaptability in organisms inhabiting photic zones.^[39]

Moreover, in the well-studied Darwin finches signs of reticulate evolution can be observed. Peter and Rosemary Grant, who carried out extensive research on the evolutionary processes of the Geospiza genus, found that hybridization occurs between some species of Darwin finches, yielding hybrid forms. This event could explain the origin of intermediate species.^[40] Jonathan Weiner ^[41] commented on the observations of the Grants, suggesting the existence of reticulate evolution: "To the Grants, the whole tree of life now looks different from a year ago. The set of young twigs and shoots they study seems to be growing together in some seasons, apart in others. The same forces that created these lines are moving them toward fusion and then back toward fission."; and "The Grants are looking at a pattern that was once dismissed as insignificant in the tree of life. The pattern is known as reticulate evolution, from the Latin reticulum, diminutive for net. The finches' lines are not so much lines or branches at all. They are more like twiggy thickets, full of little networks and delicate webbings."

Related Research Articles

In biology, evolution is the change in heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination. Evolution occurs when evolutionary processes such as natural selection and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation.

Heredity, also called inheritance or biological inheritance, is the passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic information of their parents. Through heredity, variations between individuals can accumulate and cause species to evolve by natural selection. The study of heredity in biology is genetics.

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection, gene flow and genetic drift. This change happens over a relatively short amount of time compared to the changes termed macroevolution.

Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.

In population genetics, gene 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 allele frequencies and therefore can be considered a single effective population. It has been shown that it takes only "one migrant per generation" to prevent populations from diverging due to drift. Populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity among populations, by modifying allele frequencies. High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaptation. In some cases dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population

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 onto 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.

This is a list of topics in evolutionary biology.

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).

Introgression, also known as introgressive hybridization, in genetics is the transfer of genetic material from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species. Introgression is a long-term process, even when artificial; it may take many hybrid generations before significant backcrossing occurs. This process is distinct from most forms of gene flow in that it occurs between two populations of different species, rather than two populations of the same species.

A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.

The following outline is provided as an overview of and topical guide to genetics:

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

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.

<span class="mw-page-title-main">Outline of evolution</span>

The following outline is provided as an overview of and topical guide to evolution:

The extended evolutionary synthesis consists of a set of theoretical concepts argued to be more comprehensive than the earlier modern synthesis of evolutionary biology that took place between 1918 and 1942. The extended evolutionary synthesis was called for in the 1950s by C. H. Waddington, argued for on the basis of punctuated equilibrium by Stephen Jay Gould and Niles Eldredge in the 1980s, and was reconceptualized in 2007 by Massimo Pigliucci and Gerd B. Müller. Notably, Dr. Müller concluded from this research that Natural Selection has no way of explaining speciation, saying: “selection has no innovative capacity...the generative and the ordering aspects of morphological evolution are thus absent from evolutionary theory.”

Hermann Reinheimer also known as Harry Ryner was a British biologist and early science writer who proposed cooperation in evolution and symbiogenesis.

This glossary of evolutionary biology is a list of definitions of terms and concepts used in the study of evolutionary biology, population biology, speciation, and phylogenetics, as well as sub-disciplines and related fields. For additional terms from related glossaries, see Glossary of genetics, Glossary of ecology, and Glossary of biology.

Eukaryote hybrid genomes result from interspecific hybridization, where closely related species mate and produce offspring with admixed genomes. The advent of large-scale genomic sequencing has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number.

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.

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