Contrasting patterns of genetic admixture explain the phylogeographic history of Iberian high mountain populations of midwife toads

Abstract

Multiple Quaternary glacial refugia in the Iberian Peninsula, commonly known as “refugia within refugia”, allowed diverging populations to come into contact and admix, potentially boosting substantial mito-nuclear discordances. In this study, we employ a comprehensive set of mitochondrial and nuclear markers to shed light onto the drivers of geographical differentiation in Iberian high mountain populations of the midwife toads Alytes obstetricans and A. almogavarii from the Pyrenees, Picos de Europa and Guadarrama Mountains. In the three analysed mountain regions, we detected evidence of extensive mito-nuclear discordances and/or admixture between taxa. Clustering analyses identified three major divergent lineages in the Pyrenees (corresponding to the eastern, central and central-western Pyrenees), which possibly recurrently expanded and admixed during the succession of glacial- interglacial periods that characterised the Late Pleistocene, and that currently follow a ring-shaped diversification pattern. On the other hand, populations from the Picos de Europa mountains (NW Iberian Peninsula) showed a mitochondrial affinity to central-western Pyrenean populations and a nuclear affinity to populations from the central Iberian Peninsula, suggesting a likely admixed origin for Picos de Europa populations. Finally, populations from the Guadarrama Mountain Range (central Iberian Peninsula) were depleted of genetic diversity, possibly as a consequence of a recent epidemic of chytridiomycosis. This work highlights the complex evolutionary history that shaped the current genetic composition of high mountain populations, and underscores the importance of using a multilocus approach to better infer the dynamics of population divergence.

Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)

“…1). In fact, we detected introgression in populations that were supposedly pure according to microsatellite analyses (Maia-Carvalho et al, 2018;Lucati et al, 2022). Even the holotype of A. a. inigoi featured A. a. almogavarii alleles (15 %), which causes a nomenclatural problem (see also the case of Triturus arntzeni, Wielstra and Arntzen, 2014).…”

“…For instance, ~4kb of intron sequences branched A. a. inigoi with the lineages assigned to A. obstetricans (Maia-Carvalho et al, 2014). Microsatellite analyses of northeastern Iberian populations grouped A. a. almogavarii and A. a. inigoi together but nested them within the high diversity of A. o. obstetricans/pertinax in this part of the range, and in a different order depending on analyses (Lucati et al, 2022). All these observations emphasize the potential unreliability of conventional markers for phylogenetic inferences, including introns when they are used in low numbers (e.g., Cruaud et al, 2014), and especially microsatellites, which are known to retain high ancestral polymorphism that confounds lineage-diagnostic alleles (van Oppen et al, 2000).…”

“…Although many phylogeographic studies on Alytes were conducted over the last decades, based on allozymes (García-París, 1995;Arntzen and García-París, 1995), mitochondrial sequences (Gonçalves et al, 2007(Gonçalves et al, , 2015, nuclear intron sequences (Maia-Carvalho et al, 2014;Gonçalves et al, 2015), or microsatellites (Maia-Carvalho et al, 2018;Lucati et al, 2022), a fully resolved species tree for the genus has so far eluded herpetologists. Genetic relationships in the A. obstetricans complex are particularly puzzling.…”

The limits of mtDNA analysis for determining the provenance of invasive species: a midwife toad example

“…) almogavarii; Dufresnes and Martínez-Solano, 2020). Mito-nuclear discordance is rampant, with nuclear DNA-defined clades not recovered as monophyletic with mtDNA and extensive geographical mismatch between nuclear DNA and mtDNA (Maia-Carvalho et al, 2014;Gonçalves et al, 2015;Dufresnes and Martínez-Solano, 2020;Dufresnes and Hernandez, 2021;Lucati et al, 2022;Ambu et al, submitted). Despite the complicated evolutionary and taxonomical history of A. obstetricans, the geographical genetic structure of its mtDNA facilitates testing the provenance of introduced populations.…”