4.4. Signature of genomic diversification of P. lilfordipopulations
Local adaptation in effectively closed populations is a trade-off
between genetic drift and selective pressures (Savolainen et al., 2013).
The two processes are intrinsically associated with the island surface
and its exposure to open sea, both affecting the impact of environmental
stochasticity (stronger in smaller islets) and resource availability
(reduced in smaller islands). Particularly, the vegetation cover, highly
correlated to the island size, provides a strong cascade effect on
lizard resource availability, including pollen and fruits production,
insect visitor frequency and diversity, and even seabirds presence, all
potential sources of dietary items (Pérez-Mellado et al., 2008; Ruiz De
Infante Anton et al., 2013; Salvador, 2009; Santamaría et al., 2020).
Along with stochasticity, this gives rise to a heterogeneous landscape
across islands, which is expected to drive independent processes of
lizard phenotypic diversification.
We explored the signature of genomic diversification that might underpin
this lizard phenotypic diversity through outlier analysis. Outlier
distribution showed a clearly skewed chromosome representation, with
most outliers falling within the sexual chromosome Z, consistently for
all datasets analyzed (Figure 7A). Recent studies in birds and lizards
showed that closely related species often present high differentiation
on the Z chromosome (Kulikova et al., 2022; Rovatsos et al., 2019), a
pattern that is typically explained as faster Z evolution and lower
recombination rates (Irwin, 2018; Lima, 2014; Mank et al., 2010; Wright
et al., 2015). The existence of potential ”islands of differentiation”
within the sexual chromosomes has also been hypothesized (Lavretsky et
al., 2019). At present, detection of such “islands” in P.
lilfordi Z chromosome would require a higher sequencing coverage than
the one currently provided by GBS and RADseq (i.e., genome
resequencing).
Most outliers fell within protein-coding genes, although the large
majority were intronic (Figure 7A). Substantial evidence supports the
notion that introns have a crucial and evolutionarily conserved function
in controlling gene expression in eukaryotes (Kumari et al., 2022; Rose,
2019), providing a particularly rapid mechanism for increasing variation
in proteome variance by production of a diverse array of alternative
splicing variants (AS) (Reixachs‐Solé and Eyras, 2022; Wang et al.,
2015). Moreover, most genes with outliers were associated with protein
binding and catalytic activities and were involved in metabolic and
growth processes (Figure S3), critical molecular functions for gene
expression regulation and phenotypic diversification (Van Nostrand et
al., 2020). In small, isolated populations, extensive modulation of gene
expression conferring phenotypic plasticity could represent a major
mechanism to counteract the loss of genetic diversity (Fulgione et al.,
2023; Sherpa et al., 2023), a hypothesis that needs to be validated by
whole transcriptome and epigenome data (Chapelle and Silvestre, 2022;
Fulgione et al., 2023).
We found a subset of protein-coding genes targets of multiple outliers
according to both independent sequencing methods, GBS and RADSeq (Figure
7B), which might represent interesting candidates for further
exploration of population genomic diversification in P. lilfordi .
Of these proteins, few represented potassium and calcium channels, which
could hint to an important regulatory role of osmotic pressure in
lizards (Dantzler and Bradshaw, 2008). We also highlight the cullin-1
protein, with a shared outlier SNP detected by all datasets. The protein
is known to be involved in ubiquitination and subsequent proteasomal
degradation of target proteins (Duan et al., 2011; Gao et al., 2011;
Scott et al., 2016). Recent evidence indicates a critical role of this
protein in modulation of the transcription factor c-MYC, a major
regulator of gene expression and cell proliferation (Sweeney et al.,
2020). While there are no specific studies on cullin-1 protein in
lizards, c-MYC was linked to the cellular regenerative response after
tail amputation (Alibardi, 2017). The gradual loss of tail autotomy
ability in insular lizards is a hallmark of their reduced antipredator
response following insular adaptation (part of the island syndrome)
(Cooper et al., 2004; Pafilis et al., 2009; Perez-Mellado, 1997).
Exploration of the major variables driving outlier genotypes primarily
recovered a signature of past geographic separation between Menorca and
Cabrera/Mallorca, with a large proportion of loci presenting fixed
allelic differences between archipelagos (Figure 7C). These SNPs are
putatively derived from a past founder effect that occurred during
initial colonization of the Menorca archipelago (Brown et al., 2008;
Terrasa et al., 2009) or the result of unclear selective forces,
including potential selective sweeps (Brown et al., 2023; Campagna et
al., 2022; Stephan, 2019). In all cases, they support no recent
secondary contact between Archipelagos, in line with previous
mtDNA-based phylogeographic reconstructions (Terrasa et al., 2009). We
note that given the major confounding effect of archipelago, the
significance/impact of other environmental variables in driving genome
diversification cannot be reliably assessed with the current sampling
design (Bassitta et al. 2021). Additional sampling, along with
phenotypic data are required to clarify the putative adaptive role of
these genomic changes.