Sicily represents the Italian reservoir of chloroplast DNA diversity of Quercus ilex L. (Fagaceae)
Ann. For. Sci.
Sicily represents the Italian reservoir of chloroplast DNA diversity of Quercus ilex L. (Fagaceae)
Silvia FINESCHI 3
Salvatore COZZOLINO 1
Marianna MIGLIACCIO 1
Aldo MUSACCHIO 2
Michela INNOCENTI 0
Giovanni G. VENDRAMIN 0
0 CNR Istituto di Genetica Vegetale , Sezione di Firenze , Italy
1 Dipartimento Biologia Vegetale, Università di Napoli Federico II , Italy
2 Dipartimento di Ecologia, Università della Calabria , Arcavacata di Rende - CS , Italy
3 Consiglio Nazionale delle Ricerche, Istituto per la Protezione delle Piante, Polo Scientifico Sesto Fiorentino , Via Madonna del Piano, Edificio E, 50019 Sesto Fiorentino, Firenze , Italy
- Chloroplast DNA polymorphism was analysed in forty-four Italian holm oak populations. Results obtained with different markers (PCR-RFLP and SSR) were congruent, showing a clear geographic structure of genetic diversity and high value of genetic differentiation (GST = 0.80). By combining PCR-RFLP and SSR, eight haplotypes were identified in Italy, six of them in Sicily. Most populations were fixed for one haplotype. Some populations from the extreme West Mediterranean (Morocco) and the extreme East Mediterranean areas (Crete) were interpreted as reproductively isolated populations because they had completely different haplotypes. These results strongly support the hypothesis of glacial refugia existing in southern Italy, and underline the high conservation value of natural tree populations in Sicily, in which most diversity was detected.
Lumaret et al. [
] recently analysed the variation of
chloroplast DNA in Quercus ilex over its whole distribution range.
Their results indicated that post-glacial recolonisation probably
started from the three Mediterranean peninsulas, as already
suggested and demonstrated for several animal and plant
2, 15, 16, 30
] including deciduous oaks [
3, 10, 13, 21, 24
In the study by Lumaret et al. [
], which is based on RFLP
of the whole chloroplast genome, Italy and south-eastern
France appeared to have been colonised by one major
haplotype. Additional haplotypes were rarely detected in continental
Italy and in the islands of Corsica and Sicily, and no Balkan
haplotype was detected along the Italian Adriatic coast.
Opposite to that, deciduous oaks phylogeography has shown that the
Italian and the Balkan peninsulas share two major haplotypes,
whose occurrence in the different areas may be ascribed either
to the presence of the same haplotype in the two different
refugia, or to the migration that took place through the Adriatic
bridge during glacial period [
On the basis of the results by Lumaret et al. [
] we analysed
in more detail the chloroplast DNA diversity in Italy and
particularly in Sicily. As compared to that study we wanted to
investigate more deeply the haplotype distribution within the
Italian peninsula in order to identify the potential refugial areas
of holm oak. Our sampling was particular intense in Sicily
because this island is characterised by elevated biodiversity and
a high number of endemic species [
Among the European evergreen oaks, holm oak is the most
widely distributed species; in the Italian peninsula it is
widespread from north to south along both the Tyrrhenian and the
Adriatic coasts, and in the main islands Sicily and Sardinia.
According to Huntley and Birks [
], the history of
European evergreen oaks during the last interglacial is not well
known; however, fossil pollen records suggest that this group
of oaks was present around the Mediterranean during the last
interglacial, where it survived throughout the last glacial
period. In the late glacial and early Holocene (10 000 years BP)
colonisation probably started from the Eastern Mediterranean
refugia, and increased rapidly as climate improved. In the last
2000 years a decline of pollen records was registered, which
might result from anthropogenic clearance of the
Mediterranean regions [
In this work we analysed Italian holm oak populations with
chloroplast (PCR-RFLP and SSR) markers. Additional
populations sampled in other countries (Crete, Croatia, Slovenia,
and Morocco) were also included in this study. The main
objectives were: (i) to quantify the chloroplast genetic diversity of
this species and its geographic distribution in Italy; (ii) to verify
if Sicily represents a hotspot of diversity for holm oak, and to
test its possible role in the migration history along the Italian
2. MATERIALS AND METHODS
Forty four holm oak populations were collected in Italy, eighteen
of them in Sicily. Each population was represented by 3 to 11
individuals (the island of Vulcano was represented by only one individual). Name
of locations, geographic co-ordinates, and number of individuals per
population are indicated in Table I. In addition, one Q. ilex population
from the island of Crete, two from Morocco, one from Slovenia, and
two from Croatia were also analysed.
Total DNA was extracted from frozen leaves using QIAGEN
Dnaeasy Plant kit. All populations were analysed by chloroplast
(PCRRFLP and SSR) markers.
Chloroplast DNA was amplified using universal primers (fragment
]; fragments CD, DT, AS, HK, K1K2, CS: [
]; fragment FV:
]). Amplification, digestion, and electrophoretic procedures are
described in Demesure et al. [
] and Fineschi et al. [
Six chloroplastic microsatellite regions were amplified using
specific primer pairs (ccmp2, ccmp3, ccmp4, ccmp5, ccmp7, ccmp10)
]. PCR amplifications and sizing of the fragments were performed
as described by Vendramin and Ziegenhagen [
fragments of the two polymorphic chloroplast microsatellites were cloned
into plasmid vectors using the Invitrogen TOPO cloning kit and then
sequenced from both ends using an automatic sequencer Alf Express
(Pharmacia). Each fragment was sequenced twice.
Diversity and differentiation parameters were calculated according
to Pons and Petit [
] using the software PERMUT (http://
www.pierroton.inra.fr/genetics/labo/Software): the average within
population gene diversity (hS), the total gene diversity (hT), and the
differentiation for unordered alleles (GST) and for ordered alleles (NST).
Thousand random permutations of haplotypes identities were made,
keeping the haplotype frequencies and the matrix of pairwise haplotype
differences as in the original study . For this analysis only populations
represented by more than two individuals were considered (the
population from Vulcano was excluded). The distribution of values
obtained by permutation was compared with the observed values. For
the NST analysis, a distance matrix derived from the pairwise number
of mutational differences between haplotypes was used. According to
Pons and Petit [
] significantly higher values for NST than for GST
indicate the existence of a phylogeographic structure.
Statistical parsimony was used to reconstruct phylogenetic
relationships between haplotypes (TCS, version 1.06, [
]) by combining
PCR-RFLP and microsatellite data.
Six out of sixteen primer-enzyme combinations were
polymorphic and led to the identification of eleven different
PCRRFLP haplotypes (Tabs. I and II). All mutations were caused
by insertion/deletion, no point mutation was detected. Two
microsatellite regions out of six showed polymorphysm in Q. ilex:
ccmp4 and ccmp10, which displayed three variant each.
Sequencing revealed that the three SSR haplotypes differed in
the number of repeats within the microsatellite regions
(accession numbers: AY465917, AY465918, AY465919, AY465920,
By combining PCR-RFLP and SSR, eight haplotypes were
identified in Italy (Fig. 1), six of them in Sicily (haplotypes
number 1, 2, 3, 6, 7, and 8). Additional haplotypes were detected
in the island of Crete (9 and 10), and in Morocco (haplotype 11).
Some Italian haplotypes were very rare and restricted to
Sicily (number 1, 7, and 8). Haplotype 5, the most frequent one
(0.36), was widely distributed over the whole Italian peninsula
and in Sardinia, but it was absent in Sicily. Among the most
frequent haplotypes (number 3: 0.25, number 2: 0.15, and
number 6: 0.14) only haplotype 3 was distributed outside of
Sicily. Haplotype 4 was detected only in Calabria.
Most populations (12 out of 18 in Sicily and 23 Italian,
Slovenian, Croatian, and Moroccan populations out of 31) were
monomorphic. In the most polymorphic sites (populations 16:
Monte Pellegrino, 17: San Rizzo, 19: Reggio Calabria, and 28:
Avellino) three haplotypes were identified.
The presence of haplotype 2 in one Apennine population
(32: Larino) has to be interpreted as an artificial introduction:
indeed such haplotype occurs only in Sicily and particularly in
the south-eastern part of the island, close to the Etna region.
Haplotype 6 characterises the south-western part of Sicily,
including the island of Pantelleria. One individual having this
haplotype was identified in population 28 (Avellino): this result
is not surprising because historical records report evidences of
some artificial seed transfer in this area from Sicily [
The analysis of genetic diversity revealed high value of
genetic differentiation: GST = 0.802 (se = 0.047). The
coefficient of genetic differentiation for ordered alleles NST = 0.811
(se = 0.056) was not significantly different from GST. Average
genetic diversity within populations (hS) and total genetic
diversity (hT) were equal to 0.153 (se = 0.038) and 0.774 (se =
The cladogram of cpDNA haplotypes, as inferred using
statistical parsimony, indicated that haplotypes 1 and 2 were the
most divergent among the Italian ones. The haplotypes detected
in Crete (9 and 10) and in Morocco (11) clearly belonged to
different lineages (Fig. 1).
The coefficient of population subdivision calculated in this
study for Q. ilex (GST = 0.80) is of the same order of magnitude
than the mean value reported for maternal inherited genomes
in angiosperm tree species: GST = 0.73 [
], and very close to
that calculated for sessile oak, GST = 0.83 [
In oaks, organelle genomes are maternally inherited [
seeds are dispersed mostly by gravity around the mother tree,
and by animals (acorns are cached by birds and small
mammals). Consequently, high levels of differentiation among
populations are expected. Indeed, the GST value measured in the
present study for holm oak populations is consistent with
estimates reported for other oak species [
], although Lumaret
et al. [
] obtained higher value of population subdivision (GST =
0.92) over the whole distribution of Q. ilex.
On the other hand, GST value calculated for Moroccan holm
oak was lower: GST = 0.33 [
]. According to the authors, such
low value might be caused by the limited sample size (165
individuals), the low levels of cpDNA diversity of this species in
Morocco, and the occasional but incomplete introgression with
Q. suber detected in sympatric populations [
Six out of eight Italian haplotypes were detected in Sicily,
and one of them (haplotype 3) was also found in peninsular
Italy. Results by Lumaret et al. [
] demonstrated that a single
haplotype, out of three detected in Sicily, was also present in
the whole Italian peninsula, in the islands of Sardinia and
Corsica, and in south-eastern France. It should be taken into
account that different methods for hapotype identification were
applied in the survey by Lumaret et al. [
] (RFLP after
digestion with 6- and 4-cutter endonucleases) and in the present
study (PCR-RFLP). Therefore, our haplotypes number 3, 4, and
5 likely represent haplotype 4 described by Lumaret et al. [
On the base of molecular data and in the absence of
macrofossil evidences, the direction of the migration followed by
holm oak after the last glacial period can only be based on
assumptions. In fact, a migration from potential central Italian
refugia towards north but also towards south is not unlikely,
because the presence of holm oak in this part of the peninsula
during previous interglacial (250 000 years BP) is recorded
Our haplotype number 3 might have migrated from the
southern Italian refugium at the end of last glacial period
colonising new areas. Alternatively, and most likely, penisular
Italy could have been colonized from local refugia, well
documented in southern and central Italy, as remnants of a
widespread diffusion of Q. ilex during the last interglacial [
age of the postglacial spread of holm oak in southern France
], clearly younger than in central Italy, where it started
already in the late glacial [
], rules out that haplotypes 3
and 5 migrated from France southward into central Italy.
In contrast to the significant expansions of Q. ilex that took
place in Italy, the Sicilian private haplotypes (1, 2, 6, 7, and 8)
might be the remnant of a more ancient Q. ilex distribution that
did not appreciably expand during the postglacial and so did
not contribute to the colonisation of the peninsula. In fact,
according to Sadori and Narcisi [
] the presence of holm oak
in Sicily was conspicuous already at the beginning of Holocene.
The general picture obtained by our study seems to support
the hypothesis formulated by Lumaret et al. [
] about the
colonisation processes of the Italian peninsula; moreover, it gives
evidence about the importance of Sicily for the conservation of
haplotype diversity. In this sense, it is worth to underline the
haplotype richness detected in Sicily. Three haplotypes (1, 7,
and 8) are very rare and appear only in few populations.
However, the artificial introduction of these haplotypes from other
Italian regions can be excluded because of their absence
elsewhere. On the other hand, haplotypes 2 and 6 are more frequent
(0.15 and 0.14) despite the fact that their occurrence is limited
It is further worth stressing that the geographic structure of
haplotype distribution in Sicily was maintained in spite of the
range fragmentation and the intense human impact on the forest
and agricultural landscape experienced by the island during the
On the basis of our results we can conclude that Sicily
represents the Italian reservoir for holm oak haplotypic diversity,
thus increasing the conservation value of this area. The analysis
of nuclear markers (isozymes) over the whole species
distribution revealed that some Sicilian populations were characterised
by the occurrence of private alleles [
]. Such evidences
underline the need to increase conservation efforts for the
preservation of biodiversity in this area, also considering that in Sicily
unique tree species like Abies nebrodensis and Zelkova sicula
survived as relict. It should be stressed that chloroplast diversity
is not necessarily related to adaptive variation, i.e. the
component of genetic diversity that should be conserved to maintain
high adaptive potential. In this contest, the conservation value
of Sicilian holm oak populations should be confirmed by
studies on adaptive diversity.
Acknowledgements: We are grateful to A. Bevacqua. D. Salvini, and
D. Taurchini for their help. We acknowledge: A. Cabiddu, S. Delfine,
A. de Leonardis, T. La Mantia, D.S. La Mela Veca, M. Michelozzi,
P. Nascetti, R. Papa, M.H. Pemonge, D. Slade, L. Todaro, F. Talone,
V. Vremech, and the Italian Forest Service (CFS) from Bosco Mesola
and Peri for collecting and sending Quercus ilex material. We warmly
thank Roselyne Lumaret (Montpellier), M. Lascoux (Uppsala), and
Donatella Magri (Rome), for critical reading of the manuscript. This
research was partly supported by the European Union (FESR Fondo
Europeo Sviluppo Regionale).
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