Discussion
The integration of genetic, morphological and ecological data, provide
support to the hypothesis that even the barrier-free sea environment
maintains a vast potential for ecological specialization. We delimited
three independent clades of S. schlegeli by genomic data, and
observed that this differentiation was mirrored in the morphological
divergence of local populations. A similar phylogeographical pattern
have been documented in the northwestern Pacific using fishes, molluscs,
and crustaceans (Liu et al. 2007; Ni et al. 2012; Wilsonet al. 2020; Xu et al. 2009).
In marine environments, worldwide glaciation is confirmed to be the most
efficient way in generating intraspecific genetic splits (Hewitt 2000),
as well as shaping the present-day phylogeographical pattern of marine
species (Dong et al. 2012; Wilson et al. 2020). Example of
this have been found in different biogeographic realms, from the
Indo-West Pacific to the Atlantic and Mediterranean basins (Cunhaet al. 2008; Ni et al. 2014). Pleistocene sea level
fluctuation resulted in the isolation of marginal seas; for instance,
sea level during the LGM decreased in the marginal seas of northwestern
Pacific (approximately 100–120 m drop in the SCS, and 130–150 m drop
in the ECS) (Wang & Sun 1994). Therefore, along with the sea level
dropping, the ECS was reduced to an elongated trough, the Okinawa
Trough, while the SCS became a semi-enclosed sac-shaped gulf connected
with the Pacific mainly through the Bashi Strait (Wang & Sun 1994).
These sea basins served as separate refuges for different geographic
populations of local marine species. Clearly, the present genetic data
suggests a relatively deep genetic split between the ECS-YS and SCS
lineages, which has also been reported in other marine fishes (Liuet al. 2007). A few genomic regions in S. schlegeli showed
high differentiation while the rest of the genome was very similar, as
indicated by F ST analysis between North and SCS
populations. Such a heterogeneous genome divergence has been commonly
described in situations where differentiated genomes have experienced
differential introgression following secondary contact (Xu et al.2009). Postglacial range expansions of marine species may bring formerly
isolated populations into secondary contact at suture zones between seas
including ECS/SCS (Ni et al. 2014). In fact, paleo habitat
suitability projections showed a clear geographical separation between
south and north populations during the LGM, which provide ecological
support for the observed differentiation of ECS-YS and SCS lineages ofS. schlegeli . We hypothesize that Taiwan Strait land bridge may
have served as a barrier to the dispersal of coastal marine species
during the glacial periods, favouring inter-population genetic
divergences.
Gene exchange among YS and ECS populations of S. schlegeliappears to be relatively frequent, as revealed by the genetic ancestry
analyses, despite the fact that ECS and YS populations are clearly
separated based on the PCA and phylogenetic tree clustering. During
glacial periods, the northern regions of the YS were covered by land,
and the ECS populations of S. schlegeli may have experienced
expansion concomitant with a rise in sea level during interglacial
periods, leading to genetic exchange between the ECS and YS populations
(Chen et al. 2006; Yu & Zhou 2001). In parallel, genetic breaks
may be attributed to
freshwater outflow
from rivers, as demonstrated, for example, in the Amazon basin (Rochaet al. 2002). As the third largest river in the world, Yangtze
(Changjiang) River pours into the ECS with an average annual discharge
of 924 billion m3 (Ni et al. 2012). While the
barrier effect of the huge freshwater outflow on gene flow of coastal
species is still a controversial issue, we suggest that the freshwater
outflow may have affected the gene change of marine species in a more
recent historical scale following potential changes in the estuary and
variable river discharges. Given the fact that the freshwater outflow
seems to affect mostly intertidal species with a strong habitat
specificity (Dong et al. 2012), and SDM projections suggest that
a large part of coastal areas of China, Japan, and Korea are suitable
for S. schlegeli , we are inclined to believe that the
phylogeographical pattern of S. schlegeli is largely explained by
the historical glaciation.
It is worth noting that pipefishes are unique among fishes in that the
males have a brood pouch and are ovoviviparous. Moreover, they are
generally considered to be slow swimmers. These life history traits
render them sensitive to environmental change (Vincent et al.2011; Wilson et al. 2003; Zhang et al.2017).
Compared with other marine fishes, environmental heterogeneity is
considered more likely to affect the S. schlegeli population
structure due to local adaptation and the limited gene flow between
different geographical populations. Hypervolume analysis indicated thatS. schlegeli from different geographic regions diverge in their
realized niche, implying that the three clades have adapted to largely
distinct environmental conditions including temperature and salinity. A
recent study of Syngnathus typhle based on geometric
morphometrics, prey availability, and dietary composition, demonstrated
a pronounced variation in snout morphology across its distribution
range, which may contribute to its adaptation in novel environments
(Wilson et al. 2020). In the present study, a north-to-south
variation of cranial morphology was detected in different S.
schlegeli populations, which indicates that the individuals in the
south of the distributional range (SCS) have smaller eye, and the
opposite patterns are observed in the north (ECS and YS). The
differences detected in the eye phenotype of pipefish from different
populations may be related to differences in various environmental
conditions, such as sea water turbidity, and food type and availability.
Divergent selection resulted from the diverse environmental conditions
could constitute barriers to gene flow (Tobler et al.2008),
and identification of loci or genes under natural selection is important
for determining the genetic basis of local adaptation affecting
fitness traits (Zardi et
al. 2013). A total number of 143 genes were annotated from the selected
genome regions revealed by genome scan method, among which many key
genes are involved in growth (pax7 ) (Akolkar et al. 2016),
cold adaptation (csde1 ) (Yang et al. 2012), and eye
development (eys , rx3 ) (Loosli et al. 2003; Yuet al. 2016). Accordingly, local populations of S.
schlegeli may benefit from the adaptive variation to improve fitness of
this species to local environments.
Despite the fact that marine fish generally show high genetic diversity
and shallow population structure (Takahashi et al. 2015; Utter &
Seeb
2010),
the results of this study confirm that S. schlegeli has obvious
geographical population structures along its distribution range in
northwestern Pacific. The divergence among the different geographical
populations may be related to the geological events, as well as
adaptation to the habitat heterogeneity across the latitudinal
gradients.