Hybridization is now common in plants and animals with the development of sequencing technology. Regarding the hybridization event, I have several questions that confused me.
1. I am confused about how to separate genetic introgression events from multiple generations of hybridization (such as F2, F3, and F4) at the genomic level. Is there any software that can deal with this?
2. What is the definition of a hybrid swarm? A region with ongoing hybridization events? what about a region that has an ancient hybridization event, but then been isolated?
3. How to confirm a hybridization speciation event? To what extent does the genome of the hybrids differ from that of the parent, we can define the hybrid as a new hybridization speciation event.
Thank you!
Jun
1. I do not know but before "the development of seq technology" they used Article A Model-Based Method for Identifying Species Hybrids Using M...
2."There are indeed various definitions for a hybrid swarm, some of which would encompass many cases of introgressive hybridization and even unimodal hybrid zones (sensu Jiggins & Mallet 2000, e.g. Rhymer & Simberloff 1996). Here we can however, refer to a stricter concept of such a swarm as a randomly mating hybrid population that is independent of further outside recruitment (cf. Arnold 1993)." 3. Depends on your favorite species concept (I don't know). But it seems to me that the degree to which the genome of hybrid taxon differs from the genomes of parental species is hardly an important criterion.
From my point of view, the difference between hybridisation and introgression really lies in the length of the time scale. Hybridisation places more emphasis on more recent events, whereas introgression emphasises the time of ancient hybridisation that occurred early in the process of species formation.
Therefore, if we understand them from the branch length of the phylogenetic tree, hybrids are generally closer to or even consistent with existing genotypes, so the branch length of the phylogenetic tree is shorter. Inrogression, on the other hand, occurs in the ancient times, so it will show the ancestral form in the branch length, and the branch length is longer than hybridisation (software like BLT , QuIBL and PhyloNet, but these software just tell you the gene flow happened).
In terms of size, mosaic regions resulting from hybridisation are usually more evenly distributed across genomic regions. In contrast, mosaic regions of introgression are continually removed due to the effects of species formation, eventually forming chimeric structures (like Darwin's finch).
In terms of software use, genomic data at the individual level can be simulated using G-Phocs and BPP, which gives the time at which gene flow occurs, while simulations at the population level give the time at which gene flow occurs using simulations such as momi2, fastsimocal2, dadi2, and so on.
Overall, the distinction between hybrids and introgression can be made in terms of mosaic areas, branch lengths, etc., but only if there are corresponding parental data to illustrate the point.
here some paper about speciation, may help you to understand.
1.Extensive gene flow in secondary sympatry after allopatric speciation
2. Genomic evidence for homoploid hybrid speciation between ancestors of two different genera
3. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera
4. Hybrid speciation via inheritance of alternate alleles of parental isolating genes
5. Toward understanding the genetic mechanisms of speciation: Fine-grained introgressions between species
6. Replies to the commentaries on the question of ‘Is it time to abandon the biological species concept?’
7. Genes and speciation – Is it time to abandon the Biological Species Concept?
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