Coalescence-based demographic analyses shed light on complex
evolutionary scenarios.
Despite the different analyses that support the presence of three
genetic clusters, one of them potentially resulting from the
hybridisation of the other two, we could not rule out alternative
explanations. To investigate further the underlying processes
responsible for the observed pattern, we conducted a D-statistic test to
differentiate between gene flow and ILS. The results found no
significant support for gene flow between the three genetic clusters.
Moreover, we observed symmetrical counts of the ABBA and BABA patterns,
indicating no excess of shared alleles. Given the lack of evidence for
gene flow, we explored alternative demographic models to understand the
evolutionary history of the lineages better. By considering multiple
evolutionary processes simultaneously, demographic analyses can
disentangle complex scenarios that may produce ambiguous or conflicting
signals, providing deeper insights into the species’ evolutionary
dynamics (Galià-Camps et
al., 2024; Puckett & Munshi-South, 2019). We proposed five scenarios
encompassing the observed patterns in genomic structuring and
D-statistic analyses. These scenarios suggested: the existence of three
recently diverged independent lineages, reflecting the potential effects
of incomplete lineage sorting (Models A and B, Figure S1), ongoing gene
flow as evidenced by the potential hybrids identified in Porto Santo
(Model C, Figure S1), and, finally, we also considered the possibility
that H. insularum PS arose from secondary contact betweenH. insularum MBD and H. maderiana , either episodic,
without contemporary gene flow (Model D), or with contemporary gene flow
(Model E, Figure S1). The scenario of three lineages showing high levels
of co-ancestry was preferred over those involving hybridisation.
Additionally, the effective population size estimation of theHogna lineages, as inferred by the stairway plot 2,
identified an ancestral split on Porto Santo, followed by a similar
pattern of population growth between the two resulting lineages.
Interestingly, the next split, which corresponds to the origin of theH. insularum MDB lineage, shows a much steeper, continuous
population expansion compatible with a bottleneck following the
colonisation of new islands (Madeira, Desertas) from the ancestral Porto
Santo. This founder event inevitably depleted genetic variation
(Cerca, Cotoras, Bieker, et
al., 2023) and helps to explain the exclusive mtDNA haplotypes found in
Desertas and, especially Madeira.
Results of snapp, however, failed to support the topology
selected by the demographic analyses and revealed instead a high level
of discordance among alternative tree topologies of Hogna lineages. High levels of gene-tree discordance suggest the occurrence of
hybridisation and/or ILS
(Mallet et al., 2016). Since
our previous analyses discarded gene flow, we attribute that observed
discordance to the presence of ILS. Short speciation times and large
effective population sizes may result in the retention of ancestral
polymorphisms across species
(Maddison, 1997). Although
they do not directly influence the description of the observed patterns,
it is worth noting that our divergence time estimates differed across
methods and from those based on mitochondrial data by Crespo et al.
(2022) (~1.2 million years ago). These discrepancies could
be attributed to the inherent characteristics of the methods:
StairwayPlot is more informative for events spanning hundreds
of generations, whereas fastsimcoal2 is better suited for
detecting more recent demographic changes
(Lapierre et al., 2017;
Patton et al., 2019).
Regardless of the times, the inferred patterns of ancestral population
sizes reconcile well with the higher levels of retained polymorphisms
observed between H. maderiana and H. insularum PS, and, as
stated above, the reduced polymorphisms in genome-wide data and
mitochondrial haplotypes observed in H. insularum MDS.