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Lastly, the greater variability of nuclear genes makes them desirable markers for phylogenetic studies, but the high frequency of heterozygotes and long coalescence times (which result in the shared retention of ancient alleles in many species) will likely limit their utility in analyses of closely related species.
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This process has generated a large fraction of algal biodiversity, but the cryptomonads and the chlorarachniophytes are unusual in their shared retention of the algal endosymbiont nucleus, which has been lost in all other secondary plastid-bearing algae, such as diatoms and haptophytes (Archibald 2009a, 2009b).
Although phylogenetic analysis of many species of organisms often yields some conflict in resolution of the placement of some of the species in the system, this is always considered an error of analysis of confusing true shared evolutionary novelties with homoplasy; instances of shared retention of primitive similarities or the independent acquisition of confusingly similar structures.
Thus the Quichean Mamean grouping can be said to rest mostly on shared retentions rather than innovations.
For example, the geographic distribution of highest intakes from East Asia to Eastern and Central Europe suggests a 'Silk Road' pattern, implying shared retentions from past transportation and food cultures such as use of salt for food preservation.
This may be why some banks now speak of "retention bonuses" rather than performance bonuses, but the idea that retention bonuses are needed depends on the shared myth of skill, and since the myth is known to be a myth, the system is profoundly dishonest – unless the dart-throwing monkeys are going to be cut in.
Similarly on BTA29 we observed 215 different retention patterns, 193 unique retention patterns and 60 shared compatible retention patterns, out of 253 loci tested.
On BTA19, we observed 455 different retention patterns, 390 unique retention patterns and 165 shared compatible retention patterns, out of 555 loci tested.
The loci sharing compatible retention patterns suggest that they were so close that radiation could not induce any chromosomal break between them.
A total of 191 loci displayed unique retention patterns, whereas 46 shared identical retention patterns with at least one other locus indicating no obligate chromosome breaks between them (see Additional file 2).
The microsatellite analysis evidenced shared allelic retentions and loss among the epithelial and the mesenchymal neoplastic counteparts.
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