4.1 Mito-nuclear discordance and sex-biased dispersal
At the inter-lineage scale, we observed more genetic structure at
mitochondrial than at nuclear loci. This dissimilarity has been observed
for numerous Procellariiformes species (e.g. Gangloff et al. 2013, Silva
et al. 2015, Welch et al. 2011) as well as other organisms (see Toews &
Brelsford 2012 for a review). One likely explanation is a difference in
the pace of molecular evolution between mitochondrial and nuclear
markers, with the latter having a slower substitution rate than the
former, and the former being more polymorphic at the intra-specific
scale (see Brown 1985), at least in birds (Helm-Bychowski 1984; Mindel
et al. 1996). However, we did observe high levels of intra-lineage
diversity for some nuclear loci such as βfib (see also Gangloff
et al. 2013, Silva et al. 2015), and therefore the difference of
structuration cannot be solely attributed to a difference of marker
variability. We therefore suspect that incomplete lineage sorting and
retention of ancestral polymorphisms at nuclear loci also contribute.
Indeed, effective population size of mitochondrial DNA is four times
smaller than that of nuclear DNA due to uniparental inheritance. Lineage
sorting will therefore be faster in mtDNA than in nuDNA, being inversely
proportional to the effective population size (Funk & Omland 2003).
Incomplete lineage sorting is actually thought to be the main cause of
mito-nuclear discordance when associated to a pattern of loss of
geographic differentiation on nuclear markers (McKay & Zink 2010; Toews
& Brelsford 2012). We also found patterns suggestive of introgression
in nuclear markers. Hybridisation with introgression has been documented
in shearwaters (Genovart et al. 2007, Gómez-Díaz et al. 2009), other
Procellariiformes (Brown et al. 2010,) and other seabirds (Gay et al.
2009; Morris-Pocock et al. 2011; Pons et al. 2014). The likelihood of
Indian Ocean petrels visiting breeding Atlantic Petrels may be supported
by recent tracking of Pterodroma arminjoniana breeding on Round
Island (Mauritius), which showed that some individuals foraged around
South Trinidad Is, off Brazil, and even in the northern Atlantic (Booth
Jones et al. 2017), although flight capacities of Pterodroma are
far higher than Puffinus . Introgression can also blur
phylogeographic signals by mixing alleles from distinct populations, and
is considered as the second main cause of mito-nuclear discordance
(McKay & Zink 2010). Incomplete lineage sorting and introgression are
however difficult to distinguish, and additional unlinked markers would
be required to disentangle these phenomena. Finally, as the
mitochondrial markers represent only the female evolutionary history,
sex-biased dispersal favoring females may alternatively explain why the
population structure inferred based on nuclear markers conflicts with
female-inherited mtDNA markers (see Petit & Excoffier (2009). These
authors suggested that the markers associated with the most dispersing
sex should better delimitate species, as they will show stronger
intra-specific gene flow from colonizing lineages, reducing the effects
of genetic drift and lowering the probability of fixating introgressed
alleles. Dispersal was indeed stronger in females in some populations,
particularly in the larger and the putatively ancestral lineage,nicolae . Sex-biased dispersal was however more uncertain forlherminieri and boydi , while for baroli dispersal
was inferred to be male-biased. The sample size for baroli was
theoretically large enough to robustly detect a bias inF ST, F Is, and Relatedness
(Goudet et al. 2002). Sex-biased dispersal may therefore have further
contributed to the observed mito-nuclear discordance, at least in some
lineages.