10.5061/DRYAD.GHX3FFBNT
Fan, Ping
0000-0002-3794-4676
Chinese Academy of Sciences
Fjeldså, Jon
University of Copenhagen
Liu, Xuan
Chinese Academy of Sciences
Dong, Yafei
Shaanxi Normal University
Chang, Yongbin
Chinese Academy of Sciences
Qu, Yanhua
Chinese Academy of Sciences
Song, Gang
Chinese Academy of Sciences
Lei, Fumin
Chinese Academy of Sciences
An approach for estimating haplotype diversity from sequences with unequal
lengths
Dryad
dataset
2021
2021-05-14T00:00:00Z
2021-05-14T00:00:00Z
en
240746 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
1. Genetic diversity is an essential component of biodiversity. Developing
robust quantification methods is critically important in depicting the
genetic diversity underlying the geographical distributions of species,
especially for the sequence data with unequal lengths. 2. Traditional
calculation of genetic diversity depends on sequences of equal length.
However, many homologous sequences downloaded from online repositories
vary in length, posing a significant challenge to quantify the genetic
diversity, especially haplotype diversity. We developed a new approach
independent of sequence length by applying the same parameters used in
calculating nucleotide diversity to estimate haplotype diversity. We
compared this novel approach with the calculations by the program DNAsp,
and we used simulation data from terrestrial vertebrates (birds, mammals,
and amphibians) and Homo sapiens to validate the method’s performance. We
further applied this approach to explore the global latitudinal gradients
of haplotype diversity in amphibians, mammals, and birds, and compared the
results by traditional methods. 3. The haplotype diversity calculated by
our novel approach is consistent with the results from DNAsp. The
simulations showed that our approach is robust and has a good estimating
performance for sequence data with unequal lengths. 4. For the datasets of
terrestrial vertebrates and H. sapiens, our approach is capable of
estimating haplotype diversity with unequal intraspecific sequence
lengths. In contrast to patterns based on traditional methods, we observed
different latitudinal patterns of haplotype diversity between the northern
and southern hemispheres for terrestrial vertebrates, which is consistent
with the updated pattern of nucleotide diversity for mammals. The present
work contributes to the development of more precise quantification
methods, which may be broadly applied to assessing biogeographical
patterns of genetic diversity.