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Comparison of the age distributions of GPCRs vs. the "downstream genes" provided a more detailed view of the duplication-divergence process along the time axis in the context of major speciation events in vertebrates.
However, these studies did not provide information as to how the duplication-divergence process [ 5] proceeded along the time axis during major speciation events, such as the emergence of vertebrates, as their model species were all invertebrates.
If the CASP hypothesis is correct, then major speciation events are driven not by "periodic infestations" by TEs [ 8] but by subdivisions of populations into small subpopulations, some of which may become founder populations for new species.
However, previous studies were mostly based on gene networks in invertebrate species, and they had the inherent shortcoming of not being able to provide information on how the duplication-divergence process proceeded along the time axis during major speciation events.
This suggests earlier major speciation events in rabbits, associated with amplification of older families of TEs, consistent with phylogenetic analysis based on activities of SINE elements [ 70]. Figure 3 shows the number of different families of TEs in rabbit (yellow) and in pika (blue) for three different time intervals measured by sequence similarity to consensus.
Our results also suggest that most major speciation events within Melanohalea occurred during the Miocene and Pliocene, and were likely the result of complex patterns associated with new habitats formed during Miocene orogeny events, major climatic changes, and global shifts in vegetation.
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Most likely it originated as a major speciation event, a star-burst, from which all lineages have diverged at similar rates with several of those lineages also forming small sub-lineages.
It may be possible that introgressions occurred soon after the major speciation event, which may not be distinguishable from the stochastic variation of the distribution of coalescence times in the ancestral population.
These results suggest that genome plasticity is a major force behind speciation events separating the great ape lineages.
Our study in the genus Brachycaudus suggests an additional diversification scenario, in which re-acquisitions of heteroecy have probably played a major role in speciation events.
Inter- and postglacial isolation processes due to fragmented distribution areas and restriction to glacial refugia are thought to be a major driving force for younger speciation events in the European fauna [27].
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