What is the reason for the low bootstrap value of the phylogenetic tree I constructed?

Hello! First of all, it's probably because the sequences are highly homologous. It's not always better to have more homology when you're building phylogenetic relationships, the data set you choose depends on how different your molecular data are. Tree construction is essentially a kind of clustering analysis, which gathers the ones with high similarity and arranges the near and far relationships with the ones with low similarity according to the degree of difference. Mega software defines branches as binary. That is, no matter how similar the sequence is, it will default to the binary scale. The result is that if the sequence differences are just right, the tree will be fine, and if the sequence differences are not right, the tree will be very wrong. In addition, the Bootstrap method is not equal to the level of sequence homology. If the level of homology is not high, the Bootstrap value may also be high, without the necessary correlation between the two. Wish you all the best!