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.

Figure 1. The distribution of sampling localities (details in Table 1).

Red triangles — Lissotriton montandoni (Lm); green circles— L. vulgaris (Lv); two symbols superimposed — syntopic locality where both species co-occur; T – localities from which six Lm individuals were sampled for liver transcriptomes. The distribution of Lm (Zavadil et al. 2003 and own unpublished data) is hatched. Areas above 500 m a.s.l. are shaded.

Figure 2. Genetic differentiation within L. montandoni.

(a) Non-metric two-dimensional scaling of the pairwise F _ST matrix; orange – populations from the northern group; blue – populations from the southern group; (b) Principal Component Analysis (PCA) performed on individual genotypes; in parentheses percentage of variance explained by principal components; orange – individuals from the northern group; blue – individuals from the southern group.

Figure 3. Relationships among populations.

A neighbor-joining tree was constructed from the matrix of pairwise F _ST; syntopic populations were excluded. Robustness of relationships was tested with 1000 bootstrap replicates. Red – L. montandoni: orange – northern, blue – southern group; green – L. vulgaris: yellow – populations in the Carpathian Basin, violet – populations outside the Carpathian Basin.

Figure 4. Genetic structure of L. montandoni inferred by Structure for K = 2 groups.

For each population pie charts show the fraction of the genes from the northern (orange) and southern (blue) groups.

Figure 5. Genetic differentiation between L. montandoni (Lm) and L. vulgaris (Lv).

(a) Non-metric two-dimensional scaling of the matrix of pairwise F _ST between populations; red triangles – Lm; green circles – Lv; grey diamonds – syntopic populations; (b) and (c) Principal Component Analysis (PCA) performed on individual genotypes; in parentheses percentage of variance explained by principal components; red triangles – Lm; green circles – Lv; grey diamonds – individuals from syntopic populations.

Figure 6. Genetic differentiation and admixture between L. montandoni and L. vulgaris inferred by Structure for K = 2 groups.

For each population pie charts show the fraction of L. montandoni (red) and L. vulgaris (green) genes.

Figure 7. Detection of outlier loci from genome scans.

(a) F _ST outliers in L. montandoni, (b) F _CT outliers in L. montandoni, (c) F _CT outliers in interspecific analysis – markers at the extremes of interspecific differentiation.