1 Introduction
Biological invasion denotes the phenomenon that an alien species spreads
outside its natural range and proliferates and persists in new habitats.
This is increasingly occurring as a result of human activities and
causes negative impacts on native ecosystems (Mack et al., 2000; Reid et
al., 2005). Nevertheless, invasive populations are also interesting
models to investigate rapid genetic response and adaptation to novel
environments, thus providing valuable insights into basic biological
processes (Prentis et al., 2008; Sakai et al., 2001). In general, an
introduced population tends to lose its genetic diversity because of
bottlenecks which can reduce the fitness and evolutionary potential
(Lee, 2002). The genetic paradox of invasion appears when a bottlenecked
introduced population becomes invasive (Estoup et al., 2016). However,
recent studies provide evidence that the genetic paradox of invasion is
to a large extent overrated. In some cases, no paradox exists, as
introduced populations shows no loss of genetic diversity possibly owing
to multiple introductions, or no adaptive challenge in the introduced
habitat (Blumenfeld et al., 2021; Facon et al., 2006; Rius et al.,
2015). In other cases, an apparent paradox is spurious, when the loss in
genetic diversity of introduced populations mainly occurs at neutral
genetic markers which are not reflected in adaptive traits, or the
diversity loss is a consequence of a successful response to strong
selection (Dlugosch & Parker, 2008; Estoup et al., 2016; Gonzalez et
al., 2013). Genetic analysis of the genetic architecture and composition
of introduced populations would provide insights into the evolutionary
mechanisms facilitating the invasion success.
High-throughput sequencing technologies, such as whole genome
resequencing and reduced representation sequencing, provide huge number
of molecular markers for genome-wide population genetic studies in
non-model organisms (Ellegren, 2014). Genome-wide markers, such as
single nucleotide polymorphisms (SNPs), can be used for accurately
estimating genome-wide genetic diversity both within individuals and at
population levels and provide powerful tools to uncover population
genetic structure and reconstruct invasion history (Austin et al., 2006;
Baltazar-Soares et al., 2020; Le Moan et al., 2021; Liu et al., 2018).
Moreover, genome scans allow detecting possible footprints of selection
associated with local adaptation, albeit not without challenges (Haasl
& Payseur, 2016). Finally, significant progress has been made in using
genomic data for reconstructing long-term demographic history and
estimating genomic inbreeding level and recent demographic history which
affect genetic diversity (Beichman et al., 2018; Ceballos et al., 2018;
Dong et al., 2021).
The Tibetan Plateau is one of the largest and highest plateaus on Earth.
The fish diversity of the Tibetan Plateau is very sensitive and
vulnerable to biological invasion due to the fragile ecosystem and
unique fish fauna (Favre et al., 2015; He et al., 2020; Jia et al.,
2019; Tao et al., 2018). One of the most widespread invasive species in
the region is the goldfish Carassius auratus which is originally
distributed throughout the East Asian region except for the Tibetan
Plateau (Luo & Yue, 2000). It represents a remarkable species complex
containing individuals with different ploidy levels in natural waters
(mainly diploid and triploid, and in rare cases tetraploid) (Liu et al.,
2017b; Xiao et al., 2011). They have different reproduction modes, with
diploids exhibiting sexual reproduction and triploids exhibiting
unisexual gynogenesis (Gui & Zhou, 2010; Zhou et al., 2000). Triploids
produce chromosome number-unreduced eggs by suppression of the first
meiotic division. Eggs are subsequently activated by the sperm of
sympatric sexual species to initiate embryogenesis, resulting in clonal
offspring from their mothers (Wang et al., 2022). Such parthenogenesis
in vertebrates is also observed in a few other fishes, such asPoecilia formosa (Warren et al., 2018) and Phoxinus
eos-neogaeus (Angers & Schlosser, 2007). Unisexual vertebrates are
generally predicted to have low evolutionary potentials due to lack of
meiotic recombination which thus result in the accumulation of
deleterious mutations and hindrance of the creation of genetic diversity
(Butlin, 2002). On the other hand, asexual organisms may have advantages
to be better colonizers than sexual organisms, because they can populate
new habitats without mates thus avoiding inbreeding (Avise, 2008). The
unisexual triploid C. auratus derives from sympatric diploids by
multiple independent polyploidization events and possesses a comparable
or slightly higher genetic diversity compared with diploids (Liu et al.,
2017c; Luo et al., 2014; Ren et al., 2018). If both sexual diploids and
unisexual triploids have been introduced into the Tibetan Plateau, this
raises an interesting possibility to compare the genetic responses of
the two forms.
C. auratus is one of the most popular fishes in Tibet markets and
are bought and released into local waters for religious reasons (Jia et
al., 2019), resulting in repeated introductions of the species into the
waters of Tibet. Based on our preliminary market survey (data not
published), C. auratus in Tibet is directly imported from the
aquatic product markets in Ningxia (NX: located on the upper Yellow
River) and Sichuan (SC: located on the upper Yangtze River) Provinces
mainly by the two main transportation routes (Qinghai-Tibet Highway and
Sichuan-Tibet Highway) connecting Tibet and its east (Figure 1). In
addition, C. auratus in Ningxia was also imported from the
central and eastern regions along the Yangtze River and Huai River.
Hence, invasive populations of C. auratus in Tibet came from
diverse sources which may be genetically distinct. Previous studies of
multiple invasive species have shown that multiple
introductions from the same or
distinct source populations may have prevented or even reversed loss of
genetic diversity within the invasive range owing to founder events
(Blumenfeld et al., 2021; Kelager et al., 2013; van Boheemen et al.,
2017). However, given the extreme environmental conditions on the
Tibetan Plateau (Feng et al., 2019), this begs the question to which
extent genetic diversity of C. auratus has been shaped by the
extreme environments that it has been transplanted into during multiple
introductions.
In this study, by analyzing whole-genome sequence data of 151 goldfish
individuals from two invasive and 11 native populations,
we investigated how genomic
changes occurred in invasive populations in Tibet derived from diverse
sources. We specifically tested the hypothesis that different genetic
imprints of the colonization process would be detected between invasive
diploid and triploid populations, with loss of variation and inbreeding
occurring in diploids, but with no loss of variation in triploids. To
address this, we first determined the ploidy levels of each individual
and called SNPs for diploids and triploids separately. Subsequently,
genetic diversity and population genetic structure were analyzed in both
invasive and native populations, with a specific focus on detecting
inbreeding and footprints of recent founder events in invasive
populations. Finally, putative signatures of selection in invasive
populations were analyzed, with the expectation that such patterns would
be evident only in diploids. Our results provide insights into
evolutionary processes facilitating the invasion success in Tibet and
also insights into different genetic responses to novel habitats between
sexual and asexual forms of vertebrate species.