Alleles are one or two forms of the same gene. Plants and animals have two alleles for each trait. Only the dominant allele is noticed. If a recessive gene develops a mutation, it won't affect the species until members of the species receive two of the recessive, mutant genes. Even after the mutation becomes apparent, it may not be absolutely positive or negative. After all, some traits are good in one situation and bad in another. For example, vegetables can be large or small. Large vegetables may be tougher and overtake smaller ones when growing wild. Smaller vegetables usually are tastier, however, so farmers prefer to grow smaller varieties.
Theoretically, genes mutate very slowly, over long periods of time. As the mutations become more pronounced and the mutated members of the species reproduce, they slowly become significantly different from the original species. At some point the mutated members of the species may be so different that they're a unique species. In reality, however, if you were to take a bunch of poodles and isolate them for a number of years so that any mutations would be propagated through interbreeding, over time, they might not be compatible with other poodles - - or even other dogs. You might have a new distinct species.
One cornerstone of evolutionary theory is that species can spontaneously develop new chromosomes. This doesn't seem to bear out, however. After all, no new species seem to have appeared in the past hundreds of years. Scientists are trying to find concrete evidence of this theory by studying transposons, which are genes that can move from one chromosome to another. Transposons also can copy themselves onto different chromosomes. Scientists also are researching whether polyploidy, or the process by which a chromosome duplicates itself, might have played a role in the evolution of different species. Polyploidy allows for the duplication of all of an organism's chromosomes. Plants often undergo polyploidy, which is why plants can have 100 chromosomes.
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