4.1 Comparison between diploids and triploids in the native
range
Our analyses of genetic diversity and structure between diploid and
triploid C. auratus showed that overall nucleotide diversity of
diploids was comparable to that of triploids based on both mitogenome
and nuclear genome (Table 3). This is inconsistent with results of
previous studies showing a slightly higher genetic diversity in
triploids than diploids (Liu et al., 2017b; Luo et al., 2014). This may
reflect the fact that our sampling work mainly focused on the native
range of source populations for introduction into Tibet, with a higher
percentage of diploids than triploids, while triploids actually have
wider geographic distribution than diploids (Liu et al., 2017b; Liu et
al., 2017c). By using the same procedures of variant calling, total
number of detected SNPs in triploids was slightly higher than that in
diploids, which is consistent with a previous study based on SNPs from
transcriptome data (Ren et al., 2018). Furthermore, at the individual
level, although the mean observed heterozygosity of diploids was
significantly higher than that of triploids when considering ploidy
level (Figure 5), the mean frequency of heterozygous loci across genomes
in diploids was significantly lower than that in triploids. Similarly in
other unisexual organisms that are derived from auto-polyploidization
(uneven ploidy in general), they show levels of genetic diversity close
to that of their sexual diploid counterparts (Joly & Bruneau, 2004; Lee
et al., 2016; Liu et al., 2015b). However, unisexual organisms with
interspecific hybrid origins, such as vertebrate P. formosa andP. eos-neogaeus and some plants, usually have a much higher
genetic diversity than their sexual parental species (Angers &
Schlosser, 2007; Robertson et al., 2010; Vallejo-Marin & Lye, 2013;
Warren et al., 2018). Hence, genetic diversity of unisexual organisms
depends on their specific origin relative to related sexual species.
Previous studies revealed that triploid C. auratus have undergone
multiple independent polyploidy origins from sympatric diploids (Liu et
al., 2017b; Luo et al., 2014). Our results also supported this point by
showing that native diploids were genetically clustered with triploids
within some lineages. Based on mitogenomes, diploids and triploids
coexist in almost each lineages, indicating the same origin within the
species. However, by using genomic SNPs, diploids were clustered with
triploids only within two clusters (Figure 3), and triploids shaped
three more clusters. Given that the genetic variation of triploids
remains almost frozen across generations because of unisexual
gynogenesis (Wang et al., 2022), we assumed that the two shared clusters
reflected recent triploidization events and the three triploid-specific
clusters originated from more ancient triploidization events. Genetic
structure of contemporary diploids linked to a geographical separation
pattern should be shaped by local adaptation or other factors. However,
the genetic structure of triploids is accumulated by previous
triploidization from diploids. Based on results of this study, the
triploid C. auratus has at least five polyploidy origins and
might possess more origins when investigating more samples from a
broader range of locations.