3.8 | Population structure of B. schroederipopulations
We carried out whole-genome resequencing of 266 samples, including 240
from captive pandas of the Sichuan subspecies and 26 samples from
individuals of the wild Qinling panda subspecies (Fig. 6a). The average
sequencing coverage and sequencing depth reached 97.91% and 41-fold,
respectively (Table S1 and S13). A total of 6.32 million SNPs were
obtained after filtering (see methods). Principal components analysis
(PCA) supported the clear separation between B. schroederi from
the captive Sichuan and the wild Qinling panda subspecies (Fig. 6b),
with PC1 separating the Qinling and Sichuan populations and PC2
separating the Sichuan population into two clusters
(P <0.05). We constructed a phylogenetic tree using the
maximum likelihood (ML) method, which showed two distinct clusters in
the whole population, with all Qinling individuals forming a single
cluster and all Sichuan individuals forming another single cluster (Fig.
6c). In addition, the results of structure analyses also indicated that
there were almost no shared ancestral components between the Qinling and
Sichuan populations, supporting the results from the phylogenetic tree
and the PCA (Fig. 6d). Although the two populations showed extremely
similar genetic diversity (Fig. S14 and Fig. S15), our results
consistently supported two distinct groups corresponding to the Sichuan
and Qinling populations.
3.9 | Recent positive selections in theB. schroederipopulations
We used integrated haplotype score (iHS) to detect genes under recent
natural selection in the captive and wild populations. A total of 29,553
SNPs in captive and 18,953 SNPs in wild were identified within the top
1% iHS scores. By extending the 25 kb distance around the top 1% SNPs,
filtering out SNPs in the non-gene regions, a total of 518 and 370 genes
were located in the positively selected regions in captive and wild
populations, respectively (Supplementary Data 3b and 3c). We further
calculated the distribution of nucleotide diversity on the 21
superscaffolds (Fig S15), and
found that the genetic diversity in some regions was significantly lower
than in the flanking genome regions such as glutamate-gated chloride
channel alpha (glc-1 , a receptor for anthelmintic ivermectin
(Cook et al., 2006)), nose resistant to fluoxetine protein 6
(nrf-6 , a fluoxetine (Prozac) resistance gene (Choy, Kemner, &
Thomas, 2006; Fares & Grant, 2002)), ABC transporter ced-7
(ced-7 , phagocyte corpse) (Wu & Horvitz, 1998) and
β-1,4-N-acetylgalactosaminyltransferase bre-4 (bre-4 , resistance
to pore-forming toxin (Griffitts et al., 2003)) genes (Fig. 7b).
Interestingly, the four genes were only found under positive selection
in the captive population, but not in the wild population. In addition,
we also used the cross-population extended haplotype homozygosity
(XP-EHH) method (Pardis C Sabeti et al., 2007) to screen for genes that
might have been positively selected by different deworming selection
pressures by comparing the captive and wild populations (Fig. S16, Fig
S17, Supplementary Data 3d). Similarly, the genes encoding the multidrug
resistance protein pgp-3 (Xu et al., 1998) which is related to
ivermectin resistance, glc-1 , nrf-6 , cytochrome p450
(CYP ) family members and other drug resistance related genes,
were also observed to be under strong positive selection in the captive
population (Fig. 7c).