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Chao1 richness is estimated to be 10 times that estimated for MLSA if every difference is considered unique and is very likely a dramatic underestimation of diversity due to undersampling [31].
Thus, the underestimation of interspecific differentiation and the underestimation of C. maxima within diversity with the CHet markers explain the underestimation of diversity and heterozygosity of the above mentioned secondary species.
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Furthermore, the exact microbial concentration cannot be determined using only cultivation dependent methods since microbes may be viable but non-cultivable and culturing usually leads to underestimation of microbial diversity and concentration [22 26].
The identical COI sequence may be the result of mitochondrial introgression caused by ongoing hybridization or, alternatively, by maternally inherited symbionts such as Wolbachia, which may result in a considerable underestimation of species diversity using DNA barcoding [40].
Underestimation of haplotype diversity due to homoplasy reduced their power to detect population expansion in a simulated data set.
Any underestimation of genetic diversity within 2003 samples would actually dampen the pattern of decline in these parameters after 2003.
This may lead to an underestimation of nucleotide diversity but assures that false positives will be discarded.
Conversely, morphological conservatism (primarily among surface-dwellers) has also led to underestimation of species diversity [ 10, 20].
The use of feces to obtain genetic data could lead to an underestimation of genetic diversity values if several samples of the same individual are used.
This new sampling and data revealed a striking instance of severe underestimation of phylogenetic diversity, with important ramifications for conservation and understanding the environmental history of Australia.
It is notable that more than a half of the 983 sequences are less than 300 bp in length (Table S1), which may result in underestimation of the diversity of the recombination NoVs in China.
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