Evolutionary history of Podarcis tiliguerta on Corsica and Sardinia

Background

Podarcis tiliguerta is a wall lizard endemic to the Mediterranean islands of Corsica and Sardinia. Previous findings of high mtDNA and morphological diversity have led to the suggestion that it may represent a species complex. Here, we analysed mitochondrial and nuclear markers (mtDNA, 3110 bp; 6 nDNA loci, 3961 bp) in P. tiliguerta sampled from thirty-two localities across Corsica and Sardinia.

Results

We find much greater intraspecific genetic divergence than between sister species of other Mediterranean island Podarcis, i.e., between P. lilfordi and P. pityusensis. We detected three mtDNA clusters in Corsica (North, South-East and South-West) and either two or three in Sardinia (North vs. South) depending on the clustering method. Only one or two nDNA groups were identified within each main island (again, depending on the method). A Bayesian time-calibrated multispecies coalescent tree was obtained from mtDNA and provided statistical support for a Miocene origin of the species (13.87 Ma, 95% HPD: 18.30–10.77 Ma). The posterior mean divergence time for the Corsican and Sardinian lineages was 12.75 Ma ago (95% HPD: 16.94–9.04 Ma).

Conclusion

The results support the evolutionary distinctiveness of Corsican and Sardinian populations and also indicate a lack of post-divergence migration despite periods of contact being possible. Further to this, species delimitation analyses of Corsican and Sardinian lineages provided statistical support for their recognition as distinct (sister) taxa. Our results provide new insights into the biogeography of the Mediterranean biodiversity hotspot, and contribute important findings relevant to the systematics and evolution of this speciose lizard genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0860-4) contains supplementary material, which is available to authorized users.

Variability of the mc1r gene in melanic and non-melanic Podarcis lilfordi and Podarcis pityusensis from the Balearic archipelago

The association between polymorphism at the mc1r locus and colour variation was studied in two wall lizard species (Podarcis lilfordi and P. pityusensis) from the Balearic archipelago. Podarcis lilfordi comprises several deep mitochondrial lineages, the oldest of which originated in the Pliocene, while much shallower mitochondrial lineages are found in P. pityusensis. Here, we examined whether specific substitutions were associated with the melanic colouration found in islet populations of these species. Homologous nuclear sequences covering most of the mc1r gene were obtained from 73 individuals from melanic and non-melanic Podarcis from different populations (the entire gene was also sequenced in six selected individuals). MtDNA gene trees were also constructed and used as a framework to assess mc1r diversity. Mc1r showed greater polymorphism in P. lilfordi than in P. pityusensis. However, we observed no substitutions that were common to all melanic individuals across the two species. Only one significant association was detected in the mc1r partial sequence, but this was a synonymous A/G mutation with A alleles being more abundant in melanic populations. In addition, there were no associations between the main dominant phenotypes (green and brown, blue and yellow spots and ventral colour) and synonymous or non-synonymous substitutions in the mc1r gene. There was no statistical evidence of selection on mc1r. This study suggests no relationship between mc1r polymorphism and colour variation in Balearic Podarcis.

Allele frequencies of 15 STRs in the Calchaqui Valleys population (North-Western Argentina)

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a sample of 110 individuals from the Calchaqui Valleys population (North-Western Argentina). The combined power of exclusion and combined power of discriminating for the 15 tested STR loci were 0.999964 and 0.9999999999999998, respectively. Matching probability was 1 in 4.58 × 10(15). Therefore, it may be concluded that the set of 15 STRs included in the AmpF STR Identifiler kit, represents a powerful tool for forensic applications, paternity testing and population genetics studies in the Calchaqui Valleys population.

Mitochondrial DNA effects on fitness in Drosophila subobscura

We tested different fitness components on a series of conspecific mtDNA haplotypes, detected by RFLPs in Drosophila subobscura. Additionally, haplotype VIII, endemic to the Canary Islands, was tested upon its own native nuclear DNA background and upon that of the rest of mtDNAs tested herein. We found that both nuclear and mitochondrial DNA can have a significant effect upon their hosts' fitness, and that negative selection is one of the mechanisms that can intervene in this species' mtDNA haplotype pattern. We discuss the importance of this mechanism in relation to genetic drift, in the form of periodic population bottlenecks, and how the latter can enhance the former. We also detected a significant positive effect of haplotype VIII upon fitness that could explain in part the dominance of this endemic haplotype on some of the Canary Islands, and a mitochondrial heterosis involving this haplotype when on a foreign nuclear DNA background.

Clinic and genetic evaluation of variegate porphyria (VP) in a large family from the Balearic Islands

Variegate porphyria (VP) (an autosomal dominant disease), is clinically characterized by skin photosensitivity and/or acute neurovisceral crises and biochemically by high levels of faecal protoporphyrin and coproporphyrin. It results from the partial deficiency of protoporphyrinogen oxidase (PPOX gene). Genetic heterogeneity has been reported in this gene, although no genotype-phenotype correlation has been evidenced. We have sequenced 27 members of a single large Majorcan family with several individuals that exhibit VP symptoms: two of the eight patients had only skin symptoms (25%), one patient had only acute visceral crises (12.5%), one patient had both manifestations (12.5%) and the rest were completely asymptomatic (50%). In eight individuals, a T>A transversion at the intron 6 consensus splicing site was found (IVS6+2T>A), but only four of them presented clinical symptoms. We have also detected four polymorphic positions, three non-coding and one non-synonymous coding: c.-414A>C; IVS2+121G>C; c.1188G>A and IVS12+34C>T. Although IVS12+34C>T change has been reported to cause VP, generalized linear model (GLM) analyses showed no significant association between these SNPs and phenotypic manifestations. Only three mtDNA haplogroups were detected in this family: H, K and U(5a1). Two of them are relatively common in Balearic Islands. Our family evidenced a positive correlation between the clinically overt VP and haplogroup H. Thus, it seems that, in this family, the haplogroup H could be involved in the expression of the disease. The GLM analyses evidenced an association between haplogroup H, mutation IVS6+2T>A and clinically overt variegate porphyria.

Mitochondrial DNA sequence variation in Jewish populations

Sequence analysis of HVRI and HVRII mitochondrial DNA was carried out on 107 Jewish samples from Ashkenazi, Oriental, North African, and Sephardic origins. Control region sequences were assigned to a haplogroup by means of the analysis of the RFLP motif -7025 AluI or by using sequence motifs. A total of 88 different haplotypes were observed with a lower incidence of unique haplotypes (68.2%) than in other populations. Four individuals with one position of sequence heteroplasmy at nucleotides 16093, 16134, 16169, and 235, respectively, were detected. The mean pairwise difference in the Jewish population was 9.7 nucleotides. The gene diversity was 0.996, and the random match probability was 1.3%. When the data were compared with the autosomal and Y-chromosome markers previously studied in these populations, sex-specific differences could be observed in the Jewish populations. This fact must be taken into account for choosing suitable databases to correctly weigh the value of the evidence of a mtDNA and/or Y profile match.

Differential maternal and paternal contributions to the genetic pool of Ibiza Island, Balearic Archipelago

We report on a comparison of the genetic diversity between Ibiza and the population of the other Balearic islands and also between the archipelago with respect to circum-Mediterranean populations. For such a comparison, autosomal and Y-chromosome STRs, as well as mtDNA sequence data analyzed from the same individuals, were studied. Analysis of 14 autosomal STRs showed that Ibiza had significant differentiation with respect to other Balearic populations and also with respect to insular and continental populations from the Mediterranean area. Nevertheless, the results obtained from the analysis of eight Y-STRs showed a high level of genetic homogeneity for eight western Mediterranean populations. On the other hand, these populations did not show a compacted group when mtDNA diversity was analyzed, since they showed genetic differentiation among them. The analyses of haplotypes shared between populations indicated that mtDNA haplotypes have drifted to higher frequencies than the Y chromosome. This fact could be due to a shared recent history between Ibiza and other western Mediterranean populations, with numerous male displacements originated by wars and, especially, commercial relations. The results of mtDNA from the Ibiza population could be due to a maternal Carthaginian/Phoenician founder effect, together with genetic drift, in accordance with the historical and demographic data of the area.

Prevalence of HFE C282Y and H63D in Jewish populations and clinical implications of H63D homozygosity

The frequencies of C282Y and H63D mutations of the HFE gene vary between different populations. A previous study showed an unexpectedly high H63D frequency in Chuetas (a population of Jewish descent). The present study addressed the question of the distribution of these mutations in Jewish populations from different origins and studied the possible causes of the high H63D frequency in Chuetas. Moreover, to improve the understanding of the controversial relationship between H63D homozygosity and iron overload, a group of patients with altered iron metabolism were studied. The high frequency of H63D mutation in Chuetas is not due to a high prevalence of this mutation in Sephardic Jews. Jewish populations have low C282Y and moderate H63D frequencies, suggesting slight gene flow from their surrounding populations. In accordance with historical and demographic data, genetic drift is the most probable cause for the singular H63D frequency in Chuetas. Clinically, this study of H63D homozygotes supports the conclusion that this genotype must be taken into account, because it confers an increased risk of iron overload and therefore genetic susceptibility to developing hereditary hemochromatosis or to aggravating other diseases.

Mitochondrial DNA HVRI variation in Balearic populations

The Balearic archipelago (Majorca, Minorca, and Ibiza islands and the Chuetas, a small and inbred community of descendants of Sephardic Jews) and Valencia were studied by means of the sequencing of a 404-bp segment of hypervariable region I (HVRI) mtDNA in 231 individuals. In total, 127 different haplotypes defined by 92 variable positions were identified. The incidence of unique haplotypes was very low, especially in Ibiza and the Chuetas. A remarkable observation in the Chueta community was the high frequency (23%) of preHV-1, a Middle Eastern lineage that is closely related, though not identical, to many others found at high frequencies in different Jewish populations. The presence of this haplogroup convincingly supported the Jewish origin of the Chueta community. The studied populations showed a reduced African contribution, and no individuals were detected with North African haplogroup U6, indicating a lack of maternal contribution from the Moslem settlement to these populations. Only Ibiza showed a lower diversity, indicating a possible genetic drift effect, also supported by the historical information known about this island. The variability in the sequence of mtDNA hypervariable region I correlated well with the existing information from the populations, with the exception of that of the Y-chromosome, which could indicate a differential contribution of the maternal and paternal lineages to the genetic pool of the Balearic Islands. The phylogenetic trees showed the intermediate position of the Chueta population between the Middle Eastern and Majorcan samples, confirming the Jewish origin of this population and their Spanish admixture.

Fitness and life-history traits of the two major mitochondrial DNA haplotypes of Drosophila subobscura

Mitochondrial DNA restriction site analyses on natural populations of Drosophila subobscura have proved the existence of two common, coexisting haplotypes (I and II), as well as a set of less frequent ones derived from them. To explain this distribution, experiments to date point practically to all possible genetic mechanisms being involved in the changes of gene frequencies (cytonuclear coadaptation, direct natural selection on mtDNA and genetic drift). In an attempt to find differences that help to understand the dynamics of these haplotypes and to detect the effect of selection, we measured certain fitness components and life-history traits (egg-larva and larva-adult viabilities and developmental times, longevity, resistance to desiccation and optimal density) of the two main haplotypes I and II when maintained in laboratory population cages. As a general trend, haplotype II showed a higher net fitness than haplotype I, which explains the superiority of haplotype II over haplotype I in experimental populations but not their coexistence in nature, where additional factors must be considered.

Linkage disequilibria between mtDNA haplotypes and chromosomal arrangements in a natural population of Drosophila subobscura

The association between mtDNA haplotypes and chromosomal arrangements in a natural population of Drosophila subobscura from Calvia (Balearic Islands, Spain) was studied in order to search for linkage disequilibria, in an attempt to explain the populational dynamics of the mtDNA haplotypes of this species in nature. The presence of Wolbachia was not detected. Two main haplotypes (I and II) were found, as well as a series of less common ones. The Tajima D-test seemed to indicate some kind of seasonal population bottleneck. An analysis of linkage disequilibrium and factorial analysis of correspondences detected an association between haplotype I and the J(ST) inversion and haplotype II and the J(1) inversion.

Genetic variability at 14 STR loci in the Puna population of north western Argentina

Frequency data of the short tandem repeat (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, HUMTH01, D4S243, D18S535, HUMF13A1 and D12S391 were determined in the Puna population (Andean region from north western Argentina). In this study, 5 out of the 14 loci did not meet Hardy-Weinberg expectations. The excess of homozygotes observed in most of the markers could be due to a Wahlund effect and/or inbreeding. The frequencies were significantly different from those of other compared populations from Europe and America. Forensic parameters indicated that the 14 loci studied in the Puna region are highly discriminating, but the lack of Hardy-Weinberg equilibrium in some of the markers must be taken into account in the application of these results to paternity and forensic casework.

Distribution of HFE C282Y and H63D mutations in the Balearic Islands (NE Spain)

The HFE gene contains two main missense mutations: C282Y and H63D. Individuals with these mutations carry a risk of developing hereditary haemochromatosis (HH). The common form of this disease is due to homozygosity for the C282Y mutation. Population studies have shown the variation of the prevalence of these mutations in different countries and ethnic groups. The purposes of this current study were to determine the prevalence of the C282Y and H63D mutations in the Balearic Islands and the genotypic characterization of patients diagnosed with HH, as well as those with iron overload and liver diseases. A total of 1330 Balearic chromosomes were analyzed. The results showed that the populations of the Balearic Islands were not homogeneous. No C282Y carriers were observed in a group of descendants of Majorcan Jews (Chuetas) and the frequency was very low in Minorca (1.2%) in comparison with the other islands of Majorca (4.7%) and Ibiza (6.5%). The carrier frequency of the H63D mutation was similar in the three islands and very high (43.1%) in the descendants of Majorcan Jews. The study of patients was carried out in 129 individuals. The homozygous C282Y genotype was the principal one involved in hereditary haemochromatosis (90%), whereas the other HH patients were C282Y/H63D compound heterozygous and H63D homozygous.

Y-chromosome polymorphism data in Majorcan, Minorcan and Valencian populations (eastern Spain)

Frequency data of the six STRs: (1) DYS19; (2) DYS389I; (3) DYS389II; (4) DYS390; (5) DYS391 and (6) DYS393, and the DYS287 polymorphism (YAP) were determined in a sample of 117 unrelated males from three eastern Spanish populations: 53 from Majorca, 40 from Minorca and 24 from Valencia.

Genetic analyses in five western Mediterranean populations: variation at five tetrameric short tandem repeat loci

A population study of the Balearic (Majorca, Minorca, Ibiza, Chueta) and Valencia populations was carried out using the short tandem repeat loci HUMTHO1, D4S243, HUMF13A1, D18S535, and D12S391. All the populations sampled were found to be in Hardy-Weinberg equilibrium for the five markers analyzed. Several statistical analyses showed a clear displacement of the Chueta and Ibiza populations from the other populations sampled. These results are in agreement with those obtained from the analysis of classical markers and mitochondrial DNA restriction fragment length polymorphisms, as well as with the history of these populations. A comparative study performed with other European populations using three of the five markers selected for this study (HUMTHO1, HUMF13A1, and D12S391) revealed a clear differentiation only of the Chueta population. We detected a tendency for a west-east clinal distribution in the frequency of the HUMTH01*6 allele in the European and Mediterranean area. This distribution could reflect some of the migratory events that have happened throughout that area's history. The forensic usefulness of these markers can be judged by their highly combined power of discrimination (0.999997).

Genetic variability at nine STR loci in the Chueta (Majorcan Jews) and the Balearic populations investigated by a single multiplex reaction

A study of the genetic variability in the Chueta (Majorcan Jews) and the Balearic (Majorca and Minorca Islands) populations was carried out using a multiplex system containing the nine tetrameric STRs D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. The Chueta population has remained isolated because intermarriage with non-Jews did not take place until the middle of this century, which has resulted in it being a small inbred community. The results indicate the existence of HW equilibrium for the Chueta and Balearic populations. No pair-wise correlation was observed between the nine markers. Consequently, they seem to comprise a suitable group of markers for population genetics purposes and for paternity and forensic testing.

Prevalence of the C282Y mutation for haemochromatosis on the Island of Majorca

The C282Y mutation of the HFE gene has been reported to be present in most of the patients with hereditary haemochromatosis (HH) of Northern European ancestry. HH affects approximately 1/300 individuals, but it is not evenly distributed in the different European countries. In the present study, polymerase chain reaction (PCR) and restriction-enzyme digestion were used to analyse the frequency of the most important mutation in haemochromatosis (C282Y) in subjects from Majorca (Balearic Islands, Spain) and patients with haemochromatosis. The results were compared with other studies from Spain and Europe. A total of 420 Majorcan chromosomes were analysed and the C282Y mutation was observed at a frequency of 2.62%+/-0.8 (11 heterozygotes: eight men and three women). In the group of hereditary haemochromatosis probands, 13 out of 14 were homozygous for the C282Y mutation. In the distribution of the C282Y mutation, a north-west to south-east cline was detected, supporting the Celtic origin of this mutation.

Orosomucoid (ORM1) polymorphism in Arabs and Jews of Israel: more evidence for a middle eastern origin of the Jews

A study of 8 Israeli population groups for the ORM1 polymorphism included 1242 serum samples: 156 samples from Arab Moslems, 139 from Arab Druzes, and 947 from 6 Jewish groups. The two most frequent alleles in Europeans and Asians, ORM1*F1 (ORM1*1) and ORM1*S (ORM1*2) were found in Jews and Arabs at frequencies similar to those in Europe. Unique to Arab and Jewish populations were polymorphic frequencies of two ORM1 slow electrophoretic variants, designated ORM1*S1 and ORM1*S2. These were formerly observed only in Europe, where two individuals with *S1 and two with *S2 have been observed so far. The Chueta community of converted Majorcan Jews is the only previously studied group that, like the other studied Jewish groups, has polymorphic frequencies of both ORM1*S1 and ORM1*S2. In this study we associate the Chuetas with the Israeli groups, as a population of Middle Eastern origin. Published data on ORM1 in Europe and East Asia together with the present data, making a total of 47 populations, were subjected to a discriminant analysis that resulted in a correct classification of 93.6% of the populations. Results of this analysis suggest that ORM1 is a useful polymorphic marker for anthropological studies.

Serum protein polymorphism in Chuetas (Majorcan Jews)--GC, A2HS, ORM, ITI and HP

A sample of 140 Chuetas (descendants of Majorcan Jews) were typed for the GC, A2HS, ORM, ITI and HP serum proteins. Studies on ORM and ITI markers have not yet been reported in other Jewish populations. The allele frequencies obtained were: GC*1 = 0.610; A2HS*1 = 0.787; ORM*F1 = 0.339; ORM*S = 0.497; ITI*1 = 0.581; ITI*2 = 0.414; HP*2FS = 0.625; HP*1S = 0.230; HP*1F = 0.135. Some rare variants were found in polymorphic frequencies (ORM*S1 = 0.043; ORMS*S2 = 0.096; A2HS*10 = 0.015). These results have been compared with those found in other Jewish and non-Jewish European populations. The relatively high frequency of the HP*2FS allele and the presence of ORM*S1 and ORM*S2 variants in Chuetas show the Jewish origin of this population. The frequencies of GC and A2HS in Chuetas are similar to those found in other surrounding non-Jewish populations. ITI results are similar to those found in the two European populations studied. HP frequencies suggest a Spanish admixture.

PI and TF subtypes in Chuetas (Majorcan Jews)

PI and TF subtypes were studied in a sample of 137 individuals of the Chueta population. In addition to the PI*M alleles, PI*S, PI*Z, and PI*F were observed in the PI system. In the TF system no TF*B or TF*D alleles were found. PI results were compared with those of some Jewish and non-Jewish populations. The relatively high frequency of PI*S is indicative of a substantial Spanish influence. There are no previous data available on TF*C subtypes in Jews. The very low TF*C3 frequency in Chuetas (lower than in Spain) indicates that this allele may be extremely rare or absent in other Jewish populations.

Blood groups in the Chueta community (Majorcan Jews)

A sample of 443 Chuetas (descendents of Majorcan Jews) was typed for the ABO, Rh, Lewis, Duffy, MNSs, Kell and P blood groups. Significant deviations from the Hardy-Weinberg equilibrium were observed in the MNSs and Duffy systems with a deficiency of heterozygotes. The gene frequencies were compared with those of the Balearic non-Jewish populations and significant differences were found. Genetic distances and cluster analysis demonstrated that the Chuetas resemble more their neighboring non-Jewish populations than other Jewish populations. Discriminant analyses showed that the Chuetas and other Jews considered in this study do not resemble each other but their host peoples with respect to these markers.

Enzymatic polymorphisms in the Jewish community (Chuetas) from the Majorca Island

The genetic polymorphism of four red cell enzymatic systems (ESD, ACP1, GLO1 and PGD) has been studied in the "Chueta" community (descendants of converted Jews from Majorca Island). The results have been compared with those of the population of Majorca that has no Jewish origin, and with other Jewish and non-Jewish Mediterranean populations. For these comparisons the following methods were used: chi 2 test, Wright's F, Nei's identities and distances and a dendrogram based on Nei's measures. The results obtained indicate that the Chueta community differs form the non-Chueta Majorcan population, although it resembles this non-Chueta population more closely than it does other Jewish ones.

Red cell enzyme polymorphisms in the Balearic Islands. II. A comparison based on multivariate analyses

A sample of 2143 individuals from Mallorca, coming from six geographic regions of this island: "Es Raiguer", "La Muntanya", "Es Plà", "Mijgorn", "Llevant" and "Palma", as well as 390 individuals from Eivissa island have been studied for the following six red cell enzyme systems: Esterase-D (ESD), acid phosphatase-1 (ACP1), glyoxalase-I (GLO1) 6-phosphogluconate dehydrogenase (PGD), phosphoglucomutase-1 (PGM1) and adenylate-kinase (AK1). The data were processed by means of multivariate statistical procedures: principal components, factorial correspondence and cluster analyses. The results indicate that ACP1 and ESD were the most suitable systems for the characterization of these caucasian populations, while GLO1 was important when different ethnic groups were included in the analyses. The Balearic gene frequencies fell within the European standard. Slight genetic distances were detected among the different Balearic populations, notably with the exception of the high differentiation of "La Muntanya".