Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones

Abstract

Background: The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species.

Results: Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry.

Conclusions: The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.

Figure 1

Map of the Iberian Peninsula showing the current distribution of Lacerta lepida and sampled localities. a) Distribution of the recognized continental subspecies of Lacerta lepida (L. lepida. iberica, L. lepida lepida and L. lepida nevadensis). b) Sampling localities. Numbers are as in Additional file 1, Table S1. Shaded areas denote altitude gradients, with darker areas representing higher altitudes.

Figure 2

Phylogenetic relationships among cytochrome b sequences (627 bp). Fifty percent majority-rule consensus phylogram from the Bayesian inference analysis. Numbers above branches represent posterior probabilities. Haplotype numbers are the same as in Figure 3 and as in Additional file, Table S1. Colours represent the geographic distribution of haplotypes as in Figure 5.

Figure 3

Statistical Parsimony network of Lacerta lepida cytochrome b haplotypes from 312 samples. Open circles with no numbers represent unsampled or extinct haplotypes. L1, L2, L3, L4, L5 and N represent different mitochondrial phylogroups. The ancestral haplotype within each phylogroup is marked with an asterisk. Phylogroup N connects to the main network through 65 mutations, represented by an interrupted line.

Figure 4

Distribution of Lacerta lepida mitochondrial phylogroups based on 627 bp of the cytochrome b gene. Colours are the same as in Figures 2 and 3. Filled red circles represent populations where divergent haplotypes from two or more phylogroups were detected in sympatry. Numbers correspond to sampling localities as in Figure 1 and Additional file 1, Table S1.

Figure 5

Statistical Parsimony network of Lacerta lepida β-Fibrinogen intron 7 alleles from 104 samples. Open circles with no numbers represent unsampled or extinct alleles, and the filled black circle represents the outgroup (Lacerta pater). Pie chart shading represents the proportion of each allele found within each mitochondrial phylogroup. Colours in pie charts are the same as those used to represent mitochondrial phylogroups in Figure 3. Dashed lines represent ambiguities in the network.

Figure 6

Mismatch distribution of mtDNA haplotypes for each of the 6 Lacerta lepida phylogroups. The expected frequency is based on a population growth-decline model, determined using DnaSP v4.50 [69] and is represented by a continuous line. The observed frequency is represented by a dotted line.

Figure 7

Bayesian skyline plots showing the historical demographic trends for each Lacerta lepida mitochondrial phylogroup detected using cytochrome b sequences. Along the y-axis is the expressed population size estimated in units of N_eμ (N_e: effective population size, μ: mutation rate per haplotype per generation). The y-axis is in a log-scale. Solid lines represent median estimates and shaded areas represent confidence intervals.

Figure 8

Observed and null model expected distances of haplotypes from the MRCA in southern and northern regions of phylogroups L3 and L5. Null model distributions were generated by randomising the geographic states of alleles (see text for details). Arrows indicate observed distances. For both phylogroups the average distance of southern haplotypes from the MRCA is significantly less than would be expected by chance, and the average distance of northern haplotypes from the MRCA is significantly greater than would be expected by chance. L3 southern populations: 78, 81, 82, 83, 85, 93 and 94; L3 northern populations: 87, 89, 90, 91 and 92; L5 southern: 15, 17, 18, 19, 20, 21, 22, 53, 95, 96, 97, 98, 99 and 100; L5 northern populations: 56, 58, 78, 79, 82, 101, 102, 103, 104, 105, 106 and 108.