Single Nucleotide Polymorphisms Reveal Genetic Structuring of the Carpathian Newt and Provide Evidence of Interspecific Gene Flow in the Nuclear Genome

Abstract

Genetic variation within species is commonly structured in a hierarchical manner which may result from superimposition of processes acting at different spatial and temporal scales. In organisms of limited dispersal ability, signatures of past subdivision are detectable for a long time. Studies of contemporary genetic structure in such taxa inform about the history of isolation, range changes and local admixture resulting from geographically restricted hybridization with related species. Here we use a set of 139 transcriptome-derived, unlinked nuclear single nucleotide polymorphisms (SNP) to assess the genetic structure of the Carpathian newt (Lissotriton montandoni, Lm) and introgression from its congener, the smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of Lm populations likely originated from separate refugia, both located in the Eastern Carpathians. The colonization of the present range in north-western and south-western directions was accompanied by a modest loss of variation; admixture between the two groups has occurred in the middle of the Eastern Carpathians. Local, apparently recent introgression of Lv alleles into several Lm populations was detected, demonstrating increased power for admixture detection in comparison to a previous study based on a limited number of microsatellite markers. The level of introgression was higher in Lm populations classified as admixed than in syntopic populations. We discuss the possible causes and propose further tests to distinguish between alternatives. Several outlier loci were identified in tests of interspecific differentiation, suggesting genomic heterogeneity of gene flow between species.

Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

“…; Zielinski et al . ). Previous studies have shown that polyploidy (LLR and LRR, very rarely tetraploidy) in P. esculentus occurs frequently and across different population systems (including mixed systems with P. lessonae and P. ridibundus , or both) in Ukraine and Russia (Borkin et al .…”

Divergence history of the Carpathian and smooth newts modelled in space and time

“…; Zieliński et al . , ). While Lm is also genetically structured, this structure is relatively shallow (Zieliński et al .…”

“…While Lm is also genetically structured, this structure is relatively shallow (Zieliński et al . , ), and thus, here we consider all Lm as a single genetic lineage. To minimize the confounding effects of population structure, we randomly subsampled one gene copy per population, resulting in 26 Lm and 32 Lv gene copies per locus in the ABC data set.…”

“…Evidence from a panel of SNP markers (Zieliński et al . ) and MHC class II genes (Nadachowska‐Brzyska et al . ) points to limited, genomically and spatially heterogeneous interspecific gene flow in the nuclear genome.…”

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

“…There is little evidence for genetic exchange between them after the divergence dated to the Pliocene (Nadachowska-Brzyska et al 2012; Pabijan et al 2015). Lissotriton montandoni has however exchanged genes with other evolutionary lineages of L. vulgaris (Lv, Babik et al 2005; Nadachowska-Brzyska et al 2012; Zieliński et al 2013, 2014, 2016). The higher MHC class II variation in Lm has been attributed to introgression from Lv (Nadachowska-Brzyska et al 2012).…”