Hybrid Speciation

Homoploid hybrid speciation – that is, the origin of a new species via hybridization between two species without a alter in chromosome number – is one of the near spectacular outcomes of hybridization (Rieseberg and Willis, 2007).

From: Encyclopedia of Biodiversity (Second Edition) , 2013

Hybrid Speciation

B.A. Counterman , in Encyclopedia of Evolutionary Biology, 2016

What Is Hybrid Speciation?

Hybrid speciation can exist broadly defined as the hybridization betwixt two or more distinct lineages that contributes to the origin of a new species. More than specifically, hybridization must result in a hybrid population that is at least partially reproductively isolated from the parental species. Recently, three criteria were established to demonstrate hybrid speciation: (1) there must exist show of hybridization between species, (ii) the hybrids must exist reproductively isolated from the parental species, and (3) in that location should be evidence that hybridization is the cause of the isolation ( Schumer et al., 2014). Studies of potential examples of hybrid speciation in nature and the lab over the past 100 years accept shown that in that location are several ways that hybridization can atomic number 82 to origin of a new hybrid species.

The nigh well-known route to hybrid speciation is through the doubling of chromosome numbers in hybrids (allopolyploidy), and so hybrids have twice the number of chromosomes every bit their parents. These allopolyploid hybrids can be reproductively isolated from the progenitor species that accept a different ploidy, due to improper chromosome pairing during meiosis (Grant, 1981) and genetic incompatibilities between the hybridizing genomes (Abbott et al., 2013). Therefore, the doubling of chromosomes offers a rapid route to hybrid speciation. Examples of allopolyploidy provide some of the clearest evidence of hybrid speciation, since the increased ploidy of hybrids resulting from hybridization straight causes reproductive isolation.

Hybrid speciation can also occur with no change in chromosome number, which is referred to equally homoploid hybrid speciation (HHS) (also known every bit recombinational speciation, encounter Grant, 1981). In HHS, feasible, true-breeding hybrids evolve that are reproductively isolated from the parental species. Homoploid hybrids do not take the reward of existence immediately isolated from the parent species, like allopolyploids do. Therefore, HHS requires the evolution of reproduction isolation while gene menstruation is ongoing with the parental species, which may explicate why HHS is unlikely or more difficult to demonstrate than allopolyploid hybrid speciation (Barton, 2001; Coyne and Orr, 2004).

Information technology is as well important to understand what hybrid speciation is non. Hybrid speciation is non simply the production of F1 or backcross offspring between distinct species, as information technology requires the establishment of a 3rd, distinct species. Therefore, interspecific hybrids such every bit ligers and geeps, which are sterile like mules and cannot persist beyond a single generation, are not examples of hybrid species. Similarly, hybridogenesis, a reproductive strategy that involves backcrossing between hybrids and a parental species with different ploidy (as seen in edible European frog Rana esculenta (Tunner and Nopp, 1979)), does not authorize equally hybrid speciation since the hybrids are patently not reproductively isolated from the parental species. Additionally, hybrid speciation should also be considered distinct from reinforcement where natural selection against deleterious hybridization drives the evolution of increased reproductive isolation. Although reinforcement involves both hybridization and speciation, it does not necessarily involve the origin of a new, hybrid species.

The concept of hybrid speciation may seem counterintuitive to some. If species are divers every bit reproductively isolated groups, then by definition, hybridization should not occur. Hybrid speciation requires that the reproductive barrier between the parental species is either incomplete or has been lost, so that hybridization can occur. When considering hybrid speciation, it may be more than useful to ascertain species as distinguishable groups of individuals with clusters of shared genotypes that remain distinct in the face of cistron flow (Mallet, 1995). Importantly, this definition, referred to as the Genotypic Cluster Species Concept, acknowledges that divergence and speciation can occur even with hybridization and gene menses.

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Hybridization in Plants

Pamela S. Soltis , in Encyclopedia of Biodiversity (2nd Edition), 2013

Hybrid Speciation

Homoploid hybrid speciation – that is, the origin of a new species via hybridization betwixt two species without a change in chromosome number – is one of the most spectacular outcomes of hybridization ( Rieseberg and Willis, 2007). This mode of speciation has been a staple of plant evolutionary biology for decades, simply despite its conceptual framework, very few cases of homoploid hybrid speciation have been unequivocally demonstrated. The model of hybridization, followed by the sorting of a unique phenotype that moves into a novel habitat and therefore becomes isolated from its parents, is straightforward. Notwithstanding, the number of putative hybrid species greatly outnumbers those that have been analyzed in item; and of those analyzed, very few provide convincing evidence of hybrid species formation (perhaps only 20 good examples; Gross and Rieseberg, 2005). Part of the problem is that, even with fantabulous genetic markers, it is difficult to make up one's mind (one) if a population or gear up of populations arose via hybridization between two (or more than) other species and (2) if this set of populations should be recognized as a distinct species (Gallez and Gottlieb, 1982; meet discussion in Soltis and Soltis, 2009).

Hybrid species are often expected to exist "additive" of their parental traits, with this additivity manifested equally intermediacy. Even so, numerous studies have shown that, for a unmarried trait, hybrids may be intermediate, or they may resemble one parent or the other or exhibit a novel phenotype (McDade, 1990; Rieseberg, 1995). When the many traits of a plant are considered, hybrids are probably never truthful intermediates, just mosaics of traits that bridge the range of parental resemblance through intermediacy to novelty. The range of mosaic genotypes – and their expressed phenotypes – may brand hybrid species highly polymorphic, with some genotypes at selective advantages and disadvantages.

The best-studied hybrid species in plants occur in Iris and sunflowers (Helianthus). Studies of the Louisiana Iris group (Riley, 1938; Anderson, 1949) served equally the ground for the development of Anderson's ideas on introgression. 3 hybridizing species – Iris fulva, Iris brevifolia, and Iris hexagona – have contributed to the complex germination of Iris nelsonii (Arnold, 1993). This species complex has provided opportunities for studying the genetic architecture of interspecific traits and adaptation to different habitats.

Multiple and repeated examples of homoploid hybrid speciation have occurred in Helianthus (see Novel Genotypes Through Hybridization and Introgression; Heiser, 1949; Rieseberg et al., 1995, 2006). The widespread cultivated sunflower, H. annuus, has hybridized with Helianthus petiolaris multiple times, and these hybridization events take yielded three hybrid species: H. anomalus, Helianthus deserticola, and H. paradoxus. Although these species share the same parental species, they reverberate separate origins and different combinations of parental genes. The consequence is that each hybrid species is unique, and each occupies a specialized, and environmentally extreme, habitat. H. anomalous occurs on sand dunes in the Southwest, H. paradoxus occurs in saline wetlands in Texas and New Mexico, and H. deserticola is found in the deserts of the Corking Basin (Rieseberg et al., 2007). Despite their departure in ecological tolerances, these three derivative species have undergone concerted chromosomal rearrangements (Rieseberg et al., 1995).

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Speciation, Process of

Guy 50. Bush , in Encyclopedia of Biodiversity, 2001

Iii.C.3.b. Recombinational Hybrid Speciation

A far more mutual mode of hybrid speciation involves the formation and establishment in the progeny of a chromosomally sterile or semisterile species hybrid of a new, structurally homozygous recombination blazon. Individuals are fertile inside the line but isolated from other lines and from the parental species by a chromosomal sterility barrier. It is nearly likely to occur when the hybrid interface is long and the organisms involved are predominantly selfing, relatively fertile, and possess few structural chromosome differences between the parental species.

III.C.three.b.i. Hybrid Speciation in Wild Sunflowers

A molecular study of hybrid speciation in the wild sunflowers Helianthus by Rieseberg et al. (1995) revealed that F1 hybrids of H. annus and H. petiolaris are semisterile with pollen viabilities less than 10% and seed set less than 1%. F2 pollen viability is highly variable, ranging from xiii to 97%. The ii species are distinguished by several morphological and chromosomal features, and based on chloroplast DNA and nuclear ribosomal Deoxyribonucleic acid variation they occur in divergent clades. Although the species are sympatric throughout much of the western Usa, they accept different ecological requirements. Helianthus annus is restricted to heavy, clay soils, whereas H. petiolaris predominantly inhabits dry, sandy soils.

Helianthus anomalus is a rare endemic to xeric habitats in northern Arizona and southern Utah. It is well within range of parental species and is a recombinational hybrid resulting from a cross betwixt H. annus and H. petiolaris. The Fone hybrids with parental species are partially sterile because chromosomal structural differences enhance reproductive isolation. A preliminary survey of 126 loci in natural populations of the parental species indicated that H. anomalus has loci derived from both H. annus and H. petiolaris. Some blocks of markers, perhaps protected from recombination, are transmitted intact.

Helianthus anomalus combines rDNA repeat units and allozymes of H. annus and H. petiolaris equally predicted for diploid hybrid species, although individuals possess chlDNA haplotypes of H. annus and H. petiolaris rather than a unique haplotype. Genetic linkage maps generated for all 3 species using random amplified polymorphic DNA markers reveal loci distributed onto 17 linkage groups corresponding to the haploid chromosome number of the three species. Although levels of polymorphisms vary from 212 in H. annus to 400 in H. petiolaris, map density is similar among species. By comparing genomic location and linear order of homologous markers, chromosomal structural relationships were inferred among the 3 species.

Even though six linkage groups showed no changes in all three species, the remaining xi linkages were not conserved in factor order. The parental species differ from H. anomalus by at least ten separate structural rearrangements, 3 inversions and a minimum of 7 inter-chromosomal translocations. The genome of H. anomalus is thus extensively rearranged relative to its parents. All 7 novel rearrangements in H. anomalus involve linkage groups that are structurally divergent in parental species, suggesting that structural differences may induce additional chromosomal rearrangements upon recombination.

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Speciation Genes

B.Thousand. Blackman , in Encyclopedia of Evolutionary Biology, 2016

Hybridization as a driver of speciation

Reinforcement, allopolyploid speciation, and homoploid hybrid speciation are documented ways that hybridization may foster speciation. Speciation gene sequences have revealed an boosted, mayhap surprising way that hybridization may really promote the cessation of factor flow. In several cases, gene flow has facilitated the spread of alleles contributing to the evolution of RI between lineages. For case, optix sequences involved in wing design divergence accept been passed among Heliconius species and repeatedly reused in the independent evolution of mimetic races (Heliconius Genome Consortium, 2012; Reed et al., 2011). In the threespine stickleback, the Eda allele that confers adaptation to freshwater through loss of lateral plates, and that may contribute to behavioral isolation betwixt marine and freshwater populations due to effects on growth charge per unit in a species that assortatively mates based on size, was likely transported to many freshwater populations worldwide through the marine genetic pool (Barrett et al., 2009; Colosimo et al., 2005; McKinnon et al., 2004; Schluter and Conte, 2009). It remains to be determined whether alleles that initiate or resolve genomic conflicts similarly introgress among species and, if and then, whether cistron flow of such alleles would facilitate or impede the speciation procedure.

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Speciation, Process of

Jeffrey L. Feder , ... Peter J. Meyers , in Reference Module in Life Sciences, 2021

Hybrid, Polyploid, and Homoploid Speciation

Hybridization and polyploidization are two processes that can also facilitate speciation (Arnold, 2006; Mallet, 2007 ). In hybrid speciation, interbreeding betwixt two differentiated populations generates new variation that serves as the ground for creating new forms reproductively isolated from parent populations. In polyploid speciation, changes in the number of whole sets of chromosomes tin cause problems in development or in meiosis in hybrids with parental forms, generating RI. Polyploid speciation appears to be more common in plants ( Jiao et al., 2011) than in animals (Mable, 2004).

Hybrid speciation tin occur past either allopolyploid or homoploid mechanisms. In allopolyploid speciation, hybridization betwixt different taxa is a trigger for polyploidization (Stebbins, 1950; Soltis and Soltis, 2000). The new hybrid polyploid, having a dissimilar chromosomal constitution, is immediately reproductively isolated from parental populations. Subsequent ecological adaptation of the allopolyploid population to novel environmental weather is often required for the new species to persist and not exist displaced by parental forms. It is also possible, however, for polyploidy to occur without hybridization (conspecifically) in a process termed autopolyploidy (when the polyploid event involves individuals belonging to the same population or species) and generate RI leading to speciation (Ramsey and Schemske, 1998).

Homoploid hybrid speciation does non involve ploidy changes. Instead, hybridization produces novel combinations of genes that can adapt hybrids to new habitats or biotic weather condition that cause them to be reproductively isolated from parental populations (Mallet, 2007; Abbott et al., 2010). Divergent ecological accommodation is thought to be crucial in social club for hybrid populations to avoid beingness swamped by gene flow from parental species or being competitively excluded (Coyne and Orr, 2004). A case report in tephritid fruit flies showed that hybridization of Rhagoletis mendax (that infests blueberries) with Rhagoletis zephyria (that lives on snowberries) formed a new hybrid population that attacks Lonicera (honeysuckle) (Schwarz et al., 2005). As a effect, the hybrid fly population tin persist on honeysuckle, sympatric with the parental populations infesting different host plants. Many Heliconius butterflies may accept been formed by hybridization (Mavarèz et al., 2006), involving changes in merely a few genes affecting mimicry (Heliconius Genome Consortium, 2012). Certain Helianthus sunflowers too appear to take originated by hybridization and inhabit novel, often marginal, habitats to which they are divergently adjusted (Gross et al., 2003). In dissimilarity to the butterflies, many genomic components from both parental taxa are present in hybrid sunflower species.

Hybrid and polyploid speciation are now accepted as occurring in nature. Questions remain concerning how frequently homoploid hybrid speciation occurs, although recent studies suggest that it may be more common than previously thought (Gompert et al., 2006; Mallet, 2007; Abbott et al., 2013; Servedio et al., 2013; Nice et al., 2013; Schumer et al., 2014).

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Hybridization, Organismal

G. Macholán , in Brenner's Encyclopedia of Genetics (Second Edition), 2013

Hybridization as an Active Evolutionary Strength

Some authors propose that hybridization between species tin can play a more active role in species evolution than previously acknowledged. For instance, many species of bacteria benefit from gene substitution with distantly related taxa, oft gaining new adaptive traits such every bit resistance to antibiotics. As well, insecticide resistance is thought to be transferred via interspecific factor period in mosquitoes and blackflies. Similar positive effects of hybridization on fettle has been recorded in Darwin's finches, Heliconius and Papilio butterflies equally well as in other organisms. Introgression can increase variation but new combinations of genes that arise can allow colonization of a new habitat ( Figure 1 (d)) and, eventually, lead to the origin of a new species (e.yard., Helianthus sunflowers, Lycaeides and Heliconius collywobbles). Hybrid speciation is usually associated with allopolyploidization (i.e., doubling of the chromosome fix via fusion of two dissimilar genomes). Polyploidy is frequent in plants, whereas in animals it can only be found in some groups with undifferentiated sex chromosomes and/or parthenogenetic reproduction (fish, amphibians).

The origin and development of a new species may non exist restricted to a unique hybridization upshot. Rather it can be dependent on a specific course of long-persisting interspecific hybridization chosen hybridogenesis. For example, the edible frog (Rana esculenta) is formed through crosses betwixt the marsh frog (Rana ridibunda) and the pool frog (Rana lessonae). Whereas both genomes participate in germination of somatic tissues, lessonae chromosomes are eliminated from the germ line in Western European populations (conversely, chromosomes derived from ridibunda are not passed on to gametes in frogs from Eastern Europe). Thus, from the puddle frog's view (in Western populations), its gametes are 'stolen' by R. esculenta and and then the latter species is sometimes called klepton (from Greek kleptein that ways 'to steal') and the whole group of the three forms is chosen synklepton.

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Phylogenetic Tree

A.D. Scott , D.A. Baum , in Encyclopedia of Evolutionary Biological science, 2016

What a Tree Represents

Phylogenetic trees are a convenient mode to represent millions or billions of years of evolution and the shared history of various organisms. So what are the branches and nodes really showing united states of america?

Evolutionary trees are essentially about ancestors and descendants. You are probably familiar with pedigrees, which may be used to trace the ancestry of purebred dogs, tulip varieties, or royal families. Consider for a moment your own ancestry. Your line of ancestry includes your two parents, your four grandparents, and then on. You lot could map out your own ancestry in a family tree, and trace back your line of descent, merely as you go farther back time, the number of individuals tends to airship, at to the lowest degree initially (Figure iii). If you go far enough dorsum in time or include many individuals besides yourself from the current generation it apace becomes hard to map out all of the lines of descent neatly without crisscrossing. At present imagine expanding the pedigree to include every other member of our species. That would be messy and certainly not treelike! The problem is that we are thinking at the wrong timescale.

Figure 3. Image showing the beginnings of one person (Winston Churchill). Visualization tool by Bradford F. Lyon located at https://learnforeverlearn.com/ancestors/.

Development may be inverse over time, but just how much time can exist difficult to grasp. In a curt fourth dimension frame, such as a human lifespan, the relationship amongst most organisms within a species is not treelike at all. However from a 'zoomed-out' view, we can consider the members of a species to exist part of the same 'population lineage.' That is to say that members of a species share genes oft plenty that they evolve more or less every bit a single unit. The branches of a phylogenetic tree stand for these population lineages, which are equanimous of many individuals over many generations (Figure 4). Every then ofttimes in evolution, a single population lineage splits into ii (or more) descendant lineages. This happens when a species is split into two subsets, whose individuals do not exchange genes. When this occurs, the descendant lineages go costless to accumulate differences and, if they don't come back together and fuse, will eventually requite ascension to very different organisms. A node represents such a lineage splitting effect – the breaking of genetic connections that allowed the descendant lineages to accumulate differences and somewhen give rise to distinct descendant clades.

Effigy four. Close-upwardly of lineage splitting on a tree. Lines of descent look sloppy up shut, but are represented as clean lines when considered in evolutionary time.

It is worth noting that even from a zoomed-out perspective, there are cases where a phylogeny does not appear strictly treelike. Branches on the tree of life can sometimes grow together. Such a rendezvous between formerly singled-out lineages is called 'reticulation.' Reticulation can be attributed to a few different biological processes (Figure v ). 'Introgression' happens when hybrids form between 2 distinct lineages and, through subsequent crossing, novel genetic material comes to be transferred from 1 species to another. In some cases, lineages tin can hybridize to grade a new lineage that is distinct from either parental lineage – a procedure known as 'hybrid speciation.' Introgression of very few genes (whether by sexual reproduction or another machinery), called horizontal gene transfer, is usually all-time visualized as a treelike population history with a few genes having a discordant history. Indeed, so long as introgression and hybrid speciation are rare or limited to closely related tips, information technology is appropriate to represent evolutionary relationships using the tree metaphor. However, in extreme cases the tree metaphor may pause down, pregnant that evolutionary relationships are best represented every bit a network.

Figure 5. Processes leading to reticulation. (a) Bidirectional introgression into ii parental lineages. (b) Unidirectional introgression. (c) Hybrid speciation.

If evolution can be summarized as descent with modification, it makes sense that when we talk near evolution, we oft do so in terms of those modifications (i.e., traits). 'Traits' are heritable characteristics of organisms. For example, flowers are a trait shared past all angiosperms, backbones are a trait shared past all vertebrates, and chitin cell walls are a trait shared by all fungi. Molecular characteristics, such as having the amino acid leucine at a sure position in a poly peptide, should besides exist considered equally traits. It is important to empathize how traits evolve on copse, since traits serve as the basis of tree inference (run across other manufactures within the Phylogenetic Methods section for theory and methods of phylogenetic inference).

Traits arise due to evolutionary changes within population lineages (see other articles within the Population Genetics section). Once a new trait arises and becomes fixed in a population lineage all descendant lineages are expected to have that trait, though due to subsequent evolution it might expect quite different. All state vertebrates ('tetrapods'), for example, are descended from an ancestor with four limbs, though the form of their limbs differs greatly among species. Some state vertebrates did evolve a lack of limbs, but this occurred by further modifying the trait out of existence rather than by evolutionarily back-tracking to the precursor condition of having fins (Effigy half dozen).

Figure 6. Cladogram of tetrapods showing trait evolution.

Lineage splitting is frequently mistakenly confused with trait evolution. A lineage splitting consequence is not necessarily accompanied by trait divergence (and even if it did, information technology might involve traits that we don't even know about). It is afterward lineage splitting that descendant lineages accumulate independent mutations, which over time may atomic number 82 to novel traits. For this reason, as in Effigy six, traits are not usually depicted as evolving on nodes just on branches. If a certain clade has a unique trait, then we can infer that the final common ancestor of this clade, represented by the 'crown node,' had the trait. We can besides assume that the last antecedent shared between this clade and its closest relative (its 'sib taxon') represented past the 'stem node' did not have the trait. This follows because, if stalk node individuals had already evolved the trait, so the sister clade should have it likewise. Therefore, the correct mapping of the unique trait is on the 'stem lineage' of the clade, the branch linking its stem and crown nodes (Figure 7).

Figure seven. Trait development and crown/stem terminology.

And so far we take focused on trait evolution along a tree, which may imply that the products of evolution are always visible. It is important to note that evolutionary kinship is non ever apparent just by looking at organisms. For example, the tree in Effigy 6 shows that crocodiles are more closely related to birds than they are to lizards, fifty-fifty though superficially yous might think lizards and crocodiles seem more than like. Relatedness does not equal similarity.

In that location is a specialized group of terms used to describe traits, based on their distribution and origin. 'Synapomorphic' traits are ones that are unique to a item clade. In Figure 6, snakes, lizards, crocodiles, birds, and mammals share the synapomorphy of the amnion, which evolved afterwards the divergence of amphibians; animals-with-amnions corresponds to a monophyletic grouping. 'Plesiomorphic' traits, in contrast, are those shared by a group of taxa that were inherited from an ancestor, where another lineages lost this trait. For example, 'four limbs' is a plesiomorphic trait of tetrapods (Figure 6); vertebrates-with-four-limbs does not stand for to a monophyletic group because some tetrapods, such equally snakes, legless lizards, caecilian, and whales, lack external limbs. If 2 independent lineages evolve a similar trait, they are said to share a homoplasious trait. Homoplasy arises when distinct lineages acquire similar traits.

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Phytochemical and biological research of Polygoneae medicinal resource

Da Cheng Hao , ... Pei Gen Xiao , in Medicinal Plants, 2015

12.5 Phylogeny

The buckwheat family unit Polygonaceae is a diverse grouping of plants and is a good model for investigating biogeography, breeding systems, coevolution with symbionts such as ants and fungi, functional trait evolution, hybridization, invasiveness, morphological plasticity, pollen morphology, and wood anatomy. Age estimates for Polygonaceae were obtained by calibrating a Bayesian phylogenetic analysis (Schuster et al., 2013), using a relaxed molecular clock with fossil data. Eighty-i species of Polygonaceae were analyzed with MrBayes to infer species relationships. One nuclear (nrITS) and 3 chloroplast (cp) markers (the trnL-F spacer region and matK and ndhF genes) were used. Seven calibration points including fossil pollen and a foliage fossil of Muehlenbeckia (a Southern Hemisphere group) were used to infer node ages. Results of the Fauna analyses indicate an age of 110.9/118.7 million years (My) with an uncertainty interval of 90.7–125.0   My for the stalk age of Polygonaceae. This age is older than previously thought (approximately 65.5–lxx.6   My). The estimated deviation time for Muehlenbeckia is 41.0/41.6 (39.6–47.eight)   My and its crown clade is 20.5/22.iii (14.2–33.five)   My. Considering the breakup of Gondwana occurred from 95 to 30   My ago, diversification of Muehlenbeckia is best explained by oceanic long-distance and maybe stepping-stone dispersal rather than vicariance.

Interspecific hybridization and the post-obit polyploidization play a major role in plant diversification, but quantifying the contribution of this machinery to diversification within taxonomically circuitous clades remains difficult. Incongruence amid gene trees can provide critical insights, especially when combined with data on chromosome numbers, morphology, and geography. Molecular phylogenetic studies using three cpDNA regions and nrITS sequences were performed to explore the hybrid speciation in Persicaria (Polygonum, Polygonaceae; Figure 12.4) (Kim and Donoghue, 2008), with an emphasis on sampling inside section Eupersicaria. At that place are major conflicts betwixt the combined cpDNA tree and the nrITS tree; a diverseness of incongruence tests rejected stochastic mistake as the crusade of incongruence in well-nigh cases. Both the tree incongruence results and data on chromosome numbers advise that the origin of 10 polyploid species involved interspecific hybridization. The recognition of several previously named species that accept been treated every bit belonging inside other species was supported. Repeated allotetraploidy (as distinct from radiations at the tetraploid level) might be the cardinal machinery governing the diversification of this taxonomically challenging group.

Figure 12.four. Phylogenetic human relationship of Polygonum and related groups. A, ITS tree inferred from maximum likelihood (ML) method based on GTR   +   I (10.90% sites)   +   G model. The tree is drawn to scale, with co-operative lengths measured in the number of substitutions per site. The assay involved 91 nucleotide sequences. There were a full of 1006 positions in the concluding dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013). B, matK   +   rbcL   +   trnL-F tree inferred from neighbor joining method. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. The analysis involved 46 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a full of 4645 positions in the final dataset.

Multiple instances of allopolyploid speciation were also shown in Persicaria using a low-copy nuclear cistron region (LEAFY 2d intron) (Kim et al., 2008b), which belong to Polygonum in Flora of Communist china. Fifteen species seem to be allopolyploids, which is higher than the number found in previous comparisons of cp DNA and nrITS phylogenies (Kim and Donoghue, 2008). This underestimation of the extent of allopolyploidy is due in at least three cases to homogenization of nrITS toward the maternal lineage. The diploid species, P. lapathifolia, has been involved in at least six cases of allopolyploid speciation. Of the diploids, this species is the virtually widespread geographically and ecologically and also bears more numerous and conspicuous flowers, illustrating ecological factors that may influence hybridization frequency. With a few exceptions, the allopolyploid species as well are widespread, plastic, ecological generalists. Hybridization events fostered by homo introductions may exist fueling the production of new species that have the potential to become aggressive weeds.

ITS sequences from 44 Indian Polygonum taxa were examined to investigate relationships among various sections proposed previously (Choudhary et al., 2012). The maximum parsimony copse obtained from ITS sequences suggested eight major groups of the Indian Polygonum spp. The relationships amidst dissimilar sections were largely congruent with those inferred from morphological characters every bit described by Hooker. The handling of the Persicaria suggested by Haraldson on the ground of anatomical characters proved to be nearly in line with that based on ITS data. A loftier resolution of phylogeny of the Himalayan Polygonum (e.one thousand., P. microcephalum, P. assamicum, P. recumbens, and P. effusum) was provided and merger of the section Amblygonon in the section Persicaria was supported. Molecular differences were detected amidst Persicaria barbata collected from different geographic locations of India, although these were non differentiated at the morphological level.

To examine the phylogenetic relationships of Koenigia (Polygonaceae), 43 samples representing all species of Koenigia and closely related taxa (Aconogonon, Bistorta, and Persicaria) were sequenced for nr ITS and four cp regions (trnL-F, atpB-rbcL, rbcL, and rpl32-trnL(UAG); Fan et al., 2013a,b). Trib. Polygoneae and trib. Rumiceae are recovered on both cp and ITS trees (Figure 12.four), while trib. Atraphaxideae is not. The placement of P. bistorta is uncertain due to conflict between cp and ITS trees (Figure 12.4). It was proposed that the genus Koenigia be circumscribed to include 5 species, that is, perennials (K. forrestii and Yard. nummularifolia) and annuals (Thousand. islandica, K. pilosa, and Thou. nepalensis). Even so, on both cp and ITS trees, One thousand. nepalensis (P. nepalense) is more than closely related to P. capitatum and P. chinense (Effigy 12.4), instead of Koenigia. M. islandica and Yard. fertilis (P. fertile, Figure 12.4a), both of which are from the Himalayan region, can be merged into a single species. P. delicatulum (K. delicatula), P. campanulatum, and P. lichiangense occupy an isolated position at the base of operations of the Polygonaceae (Figure 12.4a), which might be reassigned to a new genus.

The tetraploid P. small-scale (P. minus), which is sister to the P. hydropiperoides complex in the nrITS tree (Kim and Donoghue, 2008), may have arisen through hybridization between an unknown diploid lineage or possibly a tetraploid in the P. hydropiperoides complex and the diploid P. hydropiper. Information technology is not entirely clear that P. hydropiper served as the maternal parent, since the human relationship between P. hydropiper and P. minor is weakly supported in the cpDNA tree (Figure 12.4b). Morphologically, P. minor is more than similar to the diploid P. foliosa (P. foliosum), which should also exist considered equally a possible diploid maternal lineage for P. minor (Kim and Donoghue, 2008).

The pollen apertures likely evolved in parallel in the Aconogonon-Koenigia-Bistorta clade and Persicaria clade (Fan et al., 2013a,b), and tricolpate pollen is probably the ancestral ane. Quincuncial aestivation probable evolved during the early evolution of Koenigia and its close relatives. The uplift of the Himalayas has played a vital role in promoting species diversification of Koenigia. 1000. islandica expanded its range during Pleistocene glacial cycles by tracking changes in newly available habitats.

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Practical Mycology and Biotechnology

Vladimir Makarenkov , ... Pierre Legendre , in Practical Mycology and Biotechnology, 2006

3. Existing Mechanisms of Reticulate Development

Classically, the development of species has been depicted using phylogenetic trees. An example of such a tree, taken from a famous and controversial newspaper past Doolittle (1999). is shown in Fig. four. This manner of representing evolution has been questioned by recent developments in molecular phylogenetics. Every bit pointed out by Doolittle (1999). molecular phylogeneticists volition accept failed to find the true tree of life, not because their methods are inadequate or considering they have chosen the wrong genes, merely because the history of life cannot be properly represented as a tree. Indeed, the mechanisms of horizontal gene transfer, hybridization, homoplasie, and homologous recombination necessitate the apply of network models to illustrate them. Fig. v shows an example of a horizontal gene transfer network involving species from the kingdoms of Bacteria, Eukarya, and Archaea.

Fig. iv. An instance of a phylogenetic tree with a strict hierarchical classification (from Doolittle one 1999).

Fig. 5. A reticulated tree, or species network, which might more than appropriately represent life's history

 (from Doolittle i 1999, Fig. 3).

The fact that almost archaeal and bacterial genomes contain genes from multiple sources is challenging for molecular biologists. Following Sonea and Panisset (1976, 1981, Sonea and Mathieu 2000). who showed that horizontal gene transfer (HGT) was a mutual evolutionary mechanism among bacteria, Doolittle (1999). emphasized the importance of HGT in the evolution of bacteria and higher groups of organisms.

Another reticulate process, hybridization, is prevailing in plants and some groups of animals. In found evolution, hybridization is critically important as a source of novel factor combinations and equally a mechanism of speciation. For instance, in plant breeding desirable traits tin can be moved from one cultivated or fifty-fifty wild species into another cultivated species (Walter et al. 1999). According to i estimate (Stace 1984). there are about 70 000 naturally occurring interspecies found hybrids in the world.

Reticulate evolution shows the lack of independence between lineages. When a reticulation outcome occurs, two or more independent evolutionary lineages interact at some level of biological organization. In this section, we hash out the most of import mechanisms of reticulate development which led to the evolution of the computational methods and software tools that will be described in the next section.

3.1. Horizontal Gene Transfer (HGT)

Horizontal gene transfer is a direct transfer of genetic material from ane lineage to some other. A HGT between the ancestors of Species 3 and 4 took place in the scenario shown in Fig. half dozen. Considering only a few genes, and sometimes only a role of a gene, are transferred from one organism to another, two evolutionary scenarios (Fig. seven) can take identify after a HGT event occurred. The first one, presented in Fig. 7a, is appropriate for the genes acquired through the horizontal transfer shown in Fig. half dozen, whereas the 2d one, shown in Fig. 7b, is plausible for all the other genes inherited from the direct species ancestors.

Fig. half dozen. Horizontal gene transfer.

Fig. 7. Horizontal gene transfer: the two possible gene trees.

Horizontal gene transfer is common among leaner. Bacteria and Archaea developed the ability to accommodate to new environments using the conquering of new genes through horizontal transfer rather than past the amending of factor functions through numerous point mutations. Because they are unable to reproduce sexually, bacterial organisms have adopted several mechanisms to exchange genetic materials. The major mechanisms of HGT are the following:

•

Transformation – This procedure is most common in bacteria that are naturally transformable. Bacteria take upwardly naked DNA fragments from the environment. This is a common way of horizontal gene transfer; it tin mediate the exchange of whatever part of a chromosome. Typically, only short Deoxyribonucleic acid fragments are exchanged in this mode.

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Conjugation – This type of DNA transfer is mediated by conjugal plasmids or conjugal transposons. Even though conjugation requires cell-to-cell contact, information technology tin can occur between distantly related bacteria or even betwixt bacteria and eukaryotes. Long fragments of Deoxyribonucleic acid tin can exist transferred past conjugation.

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Transduction – This is the transfer of DNA by phage. It requires that the donor and recipient share cell surface receptors for phage binding. It is typically limited to closely related bacteria. The length of Dna transferred by transduction is limited by the size of the phage caput.

These mechanisms of horizontal gene transfer can introduce sequences of DNA that have piddling homology with the remaining Deoxyribonucleic acid of the recipient jail cell. If the donor DNA and the recipient chromosome share some homologous sequences, the donor sequences tin can be stably incorporated into the recipient chromosome past homologous recombination. If the homologous sequences are located near sequences that are absent-minded in the recipient, the recipient may learn an insertion from another strain of unrelated bacteria; such insertions can be of any size.

3.ii. Hybridization

Hybridization is another example of reticulate evolution. In Fig. viii, two lineages (Root-Species 2 and Root-Species 3) recombine to create a new species (Species iv). If the new species have the same number of chromosomes every bit the parent species, the process is chosen diploid hybridization. When it has the sum of the number of its parents' chromosomes, it is called polyploid hybridization. The three principal mechanisms of hybridization are the following:

Fig. 8. Hybridization.
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Autopolyploidization is a speciation event involving the doubling of the chromosomes inside a single species. Information technology produces a bifurcating speciation event in a phylogenetic tree.

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Allopolyploidization is a type of hybridization betwixt two species, when an offspring acquires the complete diploid chromosome complements of the two parents. In this case the parents exercise not need to have the same number of chromosomes. Allopolyploidization results in instantaneous speciation considering any backcrossing to the diploid parents is likely to produce a sterile triploid offspring.

•

Diploid hybrid speciation is a normal sexual event taking place between parents from dissimilar only related species. In near all cases, the two parents need to accept the same number of chromosomes. In this case, successful backcrossing to the parents is possible, so the hybrids have to be isolated from the parents to become new species.

In sexually reproducing organisms, hybridization may pb to an entirely female hybrid population. It tin sometimes reproduce either by parthenogenesis, or by gynogenesis, forming a new species consisting merely of females. Gynogenesis, establish amongst fish, amphibians and reptiles, is a mode of reproduction that allows a unisexual female hybrids population to reproduce, using the sperm from a related bisexual ancestor species to stimulate the evolution of the eggs (Dawley 1989).

Consider the trouble of modeling reticulate development after diploid hybrid speciation. In normal diploid organisms, each chromosome consists of a pair of homologs. In the process of diploid hybridization, the hybrid inherits 1 of the two homologs for each chromosome from each of its two parents. Since the genes from both parents are contributed to the hybrid, the evolution of genes inherited from each parent can be represented on separate copse inside a network model. Classical phylogenetic analysis of the iv species involved in a hybrid speciation upshot (Fig. 8) volition produce either the tree in Fig. 9a or the one in Fig. 9b.

Fig. 9. Hybridization: two possible cistron copse for the hybridization event shown in Fig. eight.

Hybridization is very common in plants, fish, amphibians and reptiles, and is near absent-minded in other groups, particularly in birds, mammals, and virtually arthropods. The latter groups are only occasionally affected by hybrid speciation. They usually produce triploids which tin merely reproduce by asexual modes.

three.iii. Homoplasy

Homoplasy is the development of organs or other bodily structures within unlike species, which resemble each other and have the same functions, but did non have a common ancestral origin. These organs arise via convergent evolution and are thus analogous, not homologous to each other. For example, the wings of insects, birds and bats, which are all used for flight, are homoplastic (meaning: similar in form and structure, but not in origin). As shown in Fig. 10, the wings of birds and bats are structurally different: the bird wing (a) is supported past digit number 2, the bat wing (b) past digits 2-5.

Fig. 10. The wings of birds and bats.

1 some other, the add-on of reticulation branches to a tree produces a reticulogram (i.eastward. reticulated cladogram) which describes the data meliorate than a tree would exercise. Fig. eleven, from Makarenkov and Legendre (2000). is an example of a reticulogram built for the primates information originally considered by Hayasaka et al. (1998). First, a distance matrix over 12 species of primates was computed on the base of protein-coding mRNA (898 bases). The phylogenetic tree was synthetic from the distance matrix using the neighbour-joining method (Saitou and Nei 1987). The NJ tree is represented past solid lines in Fig. eleven. Iv groups of primates were plant in the phylogeny. The reticulogram building algorithm (Makarenkov and Legendre 2000). added five reticulation branches (dashed lines) to the primate phylogeny. From the mathematical signal of view, each reticulation co-operative improved the least-squares fit of the distance matrix, compared to the classical phylogenetic tree. From the biological bespeak of view, the reticulation branches are long and they are formed between distant groups, so, they most likely represent homoplasy. For example, consider Tarsius: its position in the phylogeny of primates is uncertain (E. Douzery, personal communication). Tarsius is clustered with Lemur catta in the NJ phylogenetic tree (solid lines), but it is also shut to Hominoidea (reticulation branch between Tarsius and Pongo) and Cercopithecoidea (reticulation branch between Tarsius and Macaca fascicularis). Thus, modeling phylogenetic relationships among primates with reticulograms allowed the authors to depict alternative evolutionary features, homoplasy in this case, which cannot exist represented by means of a classical tree model.

Fig. 11. Reticulogram representing homoplasy among primates (Makarenkov and Legendre2 2000, Fig. 2).

three.iv. Genetic Recombination

Recombination refers to any process that gives rise to new combinations of genetic cloth, such as the reassortment of parental genes through crossing over during meiosis, which leads to the formation of gametes. Recombination creates reticulate evolution within lineages. Homologous chromosomes get paired during the prophase of meiosis, as shown diagrammatically in Fig. 12a. In crossing over, ii homologous chromosomes swap a portion of their genetic cloth (Fig. 12b). Later on separation, each member of a pair of homologues contains parts of its partner's genetic material (Fig. 12c).

Fig. 12. Homologous chromosomes exchanging genetic cloth (their central portions) by crossing over.

The commutation of genetic textile between homologous chromosomes, called homologous genetic recombination (as well known as general recombination or general homologous recombination), may occur at any part of a chromosome. This result can take identify in bacteriophage recombination, in recombination post-obit bacterial conjugation, and during the formation of plasmid multimers. Site-specific recombination involves the exchange of genetic fabric at very specific sites simply. Examples include the integration of a bacteriophage lambda into a host chromosome to class a prophage and the rearrangement of chromosomal Dna prior to expressing antibody genes.

Recombination has an important influence on genomes and on the genetic structure of populations. It affects biological evolution at many different levels and explains a considerable amount of genetic diversity in natural populations of sexually-reproducing species. In general, genes located in regions of the genome with low levels of recombination take low levels of polymorphism. Recombination reshuffles the existing variation and even creates new factor variants at the amino acid level. It shapes the genetic structure of natural populations (Anderson and Kohn 1998; Feil et al. 2001). and the action of natural pick (Marais et al. 2001).

Many applications in biology today are based on the estimation of phylogenetic trees. Since recombination leads to mosaic genes, where dissimilar regions may have different phylogenetic histories, information technology is important to take this procedure into business relationship during the tree reconstruction. A number of statistical methods for the detection of recombination in DNA sequences are available. Their detailed description can be found in Posada and Crandall (2001a). who estimated the performance of xiv different algorithms dealing with recombination.

with low levels of recombination have low levels of polymorphism. Recombination reshuffles the existing variation and even creates new gene variants at the amino acid level. Information technology shapes the genetic structure of natural populations (Anderson and Kohn 1998; Feil et al. 2001). and the action of natural choice (Marais et al. 2001).

Many applications in biological science today are based on the interpretation of phylogenetic trees. Since recombination leads to mosaic genes, where different regions may have dissimilar phylogenetic histories, information technology is important to take this process into account during the tree reconstruction. A number of statistical methods for the detection of recombination in Dna sequences are available. Their detailed description tin exist found in Posada and Crandall (2001a). who estimated the operation of 14 different algorithms dealing with recombination.

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Phylogenetics and speciation

Timothy G. Barraclough , Sean Nee , in Trends in Ecology & Evolution, 2001

Hybrid speciation occurs when hybridization between two species leads to the germination of a new, third species. It has been long considered of import in plants, with 11% of plant species richness attributed to this style by recent authors 19 , merely information technology might too play a role in animals 56 . The master tool of current research is detailed genetic assay, but phylogenetics could play a key function in the futurity resolution of the general prevalence of hybrid speciation. Current work suggests two means in which such tests might proceed. Beginning, extensions of traditional methods of phylogeny reconstruction could be used to reconstruct detailed histories of hybridization and cladogenesis in terms of networks 57,58 . As yet, the practicalities of this approach for large information sets are uncertain: allowing for lateral connections among taxa increases the number of possible solutions among which to search for the optimum. The second approach is to estimate the frequency of hybridization without reconstructing an explicit history of those events. Current methods accept been developed to quantify levels of recombination amidst groups of bacterial and fungal sequences 59,lx , merely like tests could be applied to hybridization between species. A problem common to both approaches is that information technology might be difficult to distinguish hybrid formation of a new species from gene flow between two existing species that does not lead to formation of a tertiary species.

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