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Abstract
Traditionally, information on the postglacial history of plant species has been gained
from the analysis of fossil pollen data. More recently, surveys of present patterns of
genetic variation have given valuable insights into species phylogeography. The genus
Alnus, based on fossil data, is known to have had at least four glacial refugia. A survey of
chloroplast DNA (cpDNA) diversity in populations of black alder (A. glutinosa) was
undertaken in order to gain more insight into its postglacial history. This revealed a high
degree of structuring of 13 cpDNA haplotypes on a European scale which indicated that
most of northern and central Europe was colonized from a refuge in the Carpathian
Mountains. Based on the distribution of two common cpDNA haplotypes, colonization
routes from this refuge can be determined. The locations of other previously identified
refugia are confirmed and two formerly unconfirmed refugial areas for alder (southern
Spain and Turkey) are proposed.
Keywords: Betulaceae, black alder, PCRÐRFLP, polymorphism, postglacial history, refugia
Received 5 December 1997; revision received 17 February 1998; accepted 2 March 1998
the Bay of Biscay region. To this may be added refugia in were rocked gently to aid precipitation of the DNA. The
southern Italy and Greece (Bennett et al. 1991). Alder DNA was washed in an ethanol wash buffer (76%
pollen has also been found in late glacial deposits from ethanol, 10 mM ammonium acetate), air dried at room
southwest Turkey (Van Zeist et al. 1975) and northern Iran temperature for a few minutes and then dissolved in
(Van Zeist & Bottema 1977). 50Ð100 µL of TE (Tris-EDTA buffer, pH 8).
A previous study of isozyme variation in A. glutinosa
(Prat et al. 1992) demonstrated strong differentiation
PCR amplification
between populations that was attributed to both ecologi-
cal and historical events affecting population evolution. cpDNA was amplified using the universal primers of
This contrasts with the results of Bousquet et al. (1990) Taberlet et al. (1991) and Demesure et al. (1995) (Table 1).
who found very little population differentiation in the Reactions were carried out in a total volume of 25 µL con-
North American A. sinuata and A. crispa. sisting of 17.55 µL of double-distilled water, 2.5 µL of 10×
The extent to which the different putative refugia have PCR buffer (Bioline), 1.25 µL of dNTPs (2 mM), 1 µL of
contributed to the present European distribution of alder MgCl2 (50 mM), 0.5 µL of each of the forward and reverse
is unknown and thus it was decided to study the chloro- primers (10 µM), 1 unit of BIOTAQ DNA polymerase
plast DNA phylogeography of A. glutinosa using a (Bioline) and 1.5 µL of genomic DNA. PCR amplifications
PCRÐRFLP (polymerase chain reactionÐrestriction frag- were performed in a DNA thermal cycler (Perkin Elmer
ment length polymorphism) approach. Using these Cetus). An initial 5 min denaturation at 94 ¡C was fol-
results, it should be possible to identify glacial refugia and lowed by 30 cycles of 94 ¡C for 30 s, annealing at 54Ð62 ¡C
relate observed patterns of cpDNA variation to possible for 30 s and extension at 72 ¡C for from 90 s to 3 mins.
postglacial migration routes. Annealing temperature was dependent upon primers
used and extension time was dependent on the length of
the PCR product (Table 1). Reactions were given a final
Materials and methods 10 min extension time at 72 ¡C.
Plant material
Two sources of Alnus glutinosa were used in the study. Seed RFLP analysis
material was obtained from the International Alder Seed PCR product (10 µL) was restricted overnight with either
Bank at Geraardsbergen, Belgium. Seeds were germinated one or two restriction enzymes following the methods of
on damp compost and harvested for DNA extraction when Ferris et al. (1993, 1995). Initially, each of the nine PCR
4Ð6-weeks old. Alternatively, fresh leaf material was col- products from six individuals of A. glutinosa were
lected in the field and either snap-frozen in liquid nitrogen digested with six 4-bp cutting and two 6-bp cutting
or dried over silica gel (Chase & Hills 1991). Where possi- restriction enzymes (AluI, CfoI, EcoRI, HaeIII, HindIII,
ble, a minimum of three nonadjacent trees per population HinfI, MboI and RsaI; Gibco BRL). Restriction digests were
were sampled. The total sample consisted of 217 individual run on either 6% polyacrylamide or 1.6% agarose gels and
trees from 101 populations covering the entire natural visualized by staining with ethidium bromide
range of the species within Europe. Details of site location (0.5 µg/mL). Polymorphisms were scored visually and
and sample size per site are given in Appendix 1. numbered in order of decreasing molecular weight.
Bands were scored as presence (1) vs. absence (0) of the
band. In order to determine the nature of each mutation,
DNA extraction
amplicons were digested with several restriction enzyme
DNA was extracted from frozen or dried material using combinations. Size variation was assumed when similar
the CTAB method of Doyle & Doyle (1990) with the addi- patterns were observed with different enzymes.
tion of fine sand to aid grinding of the leaf material and
substituting PVPP (polyvinyl polypyrrolidone) in place
Data analysis
of PVP. For seedling material, a miniprep modification of
the CTAB method was used. Leaf material (0.1 g) was Each polymorphism was scored as an unordered multi-
ground with fine sand in liquid nitrogen, added to 500 µL state character and subjected to phylogenetic analysis
of 2× CTAB in a 1.5 mL centrifuge tube and incubated at using the heuristic search option of PAUP version 3.1.
60 ¡C for 30Ð60 min. A volume of 500 µL of 24:1 chloro- (Swofford 1993). The number of mutational differences
form:iso-amyl alcohol was added, the tubes were mixed between haplotypes was calculated and analysed using
and spun at 13 000 rpm for 10 min in a bench-top cen- M I N S P N E T (Excoffier & Smouse 1994) to produce a
trifuge. The top layer was then pipetted into a clean tube minimum-spanning tree of haplotypes found. This proce-
to which 250 µL of isopropanol was added. The tubes dure is used to connect points, in this case haplotypes, by
direct links having the smallest possible total length (Prim primers pairs proved sufficient to identify all haplotypes
1957). Minimum-spanning networks are alternatives to found. Numerous mutations were detected (Table 2,
Wagner parsimony trees, but better convey the connec- Fig. 1). In all, a total of 13 cpDNA haplotypes were found
tions between haplotypes (Excoffier & Smouse 1994). and these are described in Table 3.
The level of population subdivision for a cytoplasmi- The geographical distribution of these haplotypes is
cally inherited genome using unordered alleles (GSTc) was highly structured (Fig. 2). Southeast Europe is a major area
calculated following the method of Pons & Petit (1995) for cpDNA variation with a total of seven haplotypes being
using the computer program H A P L O I D I V . NSTc, the level found in an area covering Bulgaria, Greece, Turkey,
of population subdivision for ordered alleles was calcu- Georgia and the Ukraine. Southern Europe possesses a fur-
lated using the program H A P L O N S T (Pons & Petit 1996). ther three haplotypes (one each in southern Italy, Corsica
A ratio of seed to pollen flow was calculated using the and Spain). Most of central and northern European popula-
equation: tions are comprised of one or the other of two common
(1/GSTb Ð 1) Ð 2 (1/GSTc Ð 1) haplotypes, with a third rare haplotype restricted to a sin-
(pollen flow/seed flow = ÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐÐ gle population in central Norway. The area around
(1/GSTc Ð 1)
Hungary and northern Croatia is polymorphic.
were GSTb is the level of population subdivision based on Due to the low number of variable and phylogeneti-
biparentally (nuclear) inherited genomes. For this study, cally informative mutations and the presence of homo-
GSTb is taken from Prat et al. (1992) This is a modification plasy in the data set a reliable phylogeny of haplotypes
of the equation of Ennos (1994) with the substitution of could not be found using parsimony analysis. Using PAUP
GST values for FST values. (Swofford 1993), a total of 638 trees of length 17
(C.I. = 0.842) were found. Haplotype relatedness was rep-
resented using the M I N S P N E T (Excoffier & Smouse 1994)
Results
program (Fig. 3) which clearly indicates four groupings.
An initial screen of nine pairs of universal chloroplast The seven southeast European haplotypes (Fig. 2) are split
primers with eight restriction enzymes revealed variation into two groups, one containing haplotypes A, B, C and D,
in six Alnus glutinosa fragments (Table 1). Only those the other L, M and N. The Corsican (K) and Spanish (J)
primerÐenzyme combinations that gave easily scorable haplotypes form their own grouping, as do the remaining
variation were used in the full survey. Four of these European haplotypes (E, F, G and H).
Table 2 Summary of sizes and RFLP differences found in cpDNA PCR fragments of European Alnus glutinosa and restriction enzymes
used in this study. Primer codes correspond to those given in Table 1
A total of 217 individual trees from 101 populations was northward and westward from this refugial area, reach-
analysed. Only populations where three or more individ- ing western Europe by 10 000 BP (Huntley & Birks 1983),
uals could be obtained were used in the H A P L O I D I V and and arrived in Fennoscandia around 8500 BP (Tallantire
H A P L O N S T analyses. As single plants represented popu- 1974). Colonization of Britain took place about 8000 BP
lations from Istanbul, Kvam and southern Italy their rep- (Birks 1989). No data are available on the postglacial his-
resentative haplotypes were omitted from the analysis. Of tory of alder in Spain or Turkey. We undertook this pre-
the 43 populations used, seven were polymorphic. The sent study to compare molecular phylogenetic data with
level of population subdivision within A. glutinosa was what is known from fossil analysis and to gain further
high, GSTc = 0.866 (hs = 0.103; ht = 0.773). For the NSTc anal- insights into the postglacial history of black alder. By
ysis, a distance matrix derived from the pairwise number combining both approaches we get a very good picture of
of mutational differences between haplotypes was used. the glacial/postglacial history of species.
Again, the level of population subdivision was high, The geographical distribution of the 13 alder haplotypes
NSTc = 0.905 (vs = 0.190: vt = 2.00). is highly structured (Fig. 2). From the present study, the dis-
Combining GSTc with the value of subdivision for nuclear tribution of cpDNA haplotypes confirms that most of
markers (GSTb = 0.204; Prat et al. 1992) gives effective gene northern Europe was colonized from a refuge in the area of
flow via pollen ≈ 23 times greater than that via seed. the Carpathian Mountains (present-day Hungary and
Romania). The initial westward migration identified by
Huntley & Birks (1983) apparently involved haplotype G,
Discussion
while the migration into northern Europe and
A general knowledge of the postglacial history of alder is Fennoscandia comprised haplotype F. The presence of hap-
known from fossil pollen analysis. Restricted to south- lotype F in central and southwest France and haplotype G
eastern Europe at 13 000 BP, Alnus glutinosa migrated in southern Norway is thought to be due to long-distance
Table 3 Catalogue of cpDNA haplotypes for Alnus glutinosa. Mutations are scored in order of decreasing molecular weight. A 0 represents
the complete absence of a restriction fragment from its expected position on a gel
A 1 1 2 1 3 3 1 1
B 3 1 1 1 3 3 1 1
C 3 1 1 1 4 3 1 1
D 4 1 1 1 5 3 1 1
E 3 0 2 1 4 2 1 1
F 3 0 2 1 1 2 1 1
G 3 0 2 1 2 2 1 1
H 3 0 2 0 2 2 1 1
J 2 0 2 1 3 2 1 1
K 2 0 2 1 0 1 1 1
L 1 0 2 1 2 2 2 1
M 1 0 2 1 3 2 2 1
N 1 0 2 1 3 2 2 0
subdivision for a cytoplasmically inherited genome, for taken with caution. This is the first reported pollen/seed
both ordered and unordered alleles, where the values for flow value for a tree species adapted to aquatic seed dis-
NSTc of 0.905 and GSTc of 0.866 indicate a high degree of persal. Higher pollen-to-seed-flow values have so far only
isolation between populations in terms of seed flow. The been found in Pinus contorta (24), Fagus sylvatica (84), Q.
significantly higher value of NSTc relative to GSTc indi- robur (286) and Q. petraea (500). Not surprisingly, these are
cates some correspondence between haplotype phy- all wind-pollinated species.
logeny and the geographical distribution of haplotypes The findings of this study clearly demonstrate that a
(Pons & Petit 1996). molecular phylogenetic approach can compliment the
The high degree of isolation between populations is findings of earlier fossil-based studies on plant popula-
unexpected due to the high potential for seed dispersal in tion history. With better sampling in southeast Europe,
alder via water. Although on some islands of the UK alder the Ukraine and North Africa we will be able to gain a
is now extinct, fossil pollen and macrofossil evidence, e.g. clearer picture of the migration and colonization of alder
Fossitt (1996), have shown that it was able to disperse in these areas after the last ice age.
over 70 km of open sea and colonize these islands in post-
glacial times (Bennett 1995). Alder seedlings are shade
Acknowledgements
intolerant (McVean 1956) and will not readily invade
wooded areas despite having the capability to disperse Financial support from the University of Leicester is gratefully
over long distances. acknowledged. The authors wish to thank K. Ashburner, J. Bailey,
R. Brooks, P. Catalan, P. H. Salvesen, C. Stace and R. VŠinšlŠ for
Range expansion can establish patterns of genetic vari-
collection of material for this study, T. Glover for computing
ation that can persist for hundreds or thousands of gener-
assistance, B. Michiels of the International Alder Seed Bank and
ations (Nichols & Hewitt 1994). Initially, both nuclear and the Royal Botanic Garden, Kew and Ness Botanical Gardens,
chloroplast genomes will exhibit the same geographical Wirral for access to their living collections.
patterns of variation. Over time, especially in species with
high pollen-flow to seed-flow ratios, nuclear patterns will
become much less distinct. The present highly structured References
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Appendix 1 Continued
Sample
Site size Haplotype
Wasserburg 1 1G
Greece
Sperkihos River Valley 4 2 B, 2 D
Hungary
Homokszenty 1 1F
Mike 1 1F
Nagykorp‡d 3 1 F, 2 G
…tvšskrp‡d 3 3 G,
Somogys‡rd 2 2G
Italy
Lagonegro 1 1E
Lasila 1 1E
S. Antonio di Susa 3 3G
Viterbo 3 3G
Latvia
Balofi 2 2F
Lithuania
Benderka Forest, Dzirmiskes 4 4F
Kaunas Lagoon, Girionys 1 1F
Netherlands
Korenburgerveen 3 3F
Lg. Singraven, Denekamp 1 1F
Wageningen, Binnenveld 3 3G
Weerribben 1 1G
Norway
EidesŒsen, Odda, Hordaland county 1 1F
Fron, Kvam 1 1H
Gilje, Sandnes, Rogaland county 1 1G
Jarlsberg, T¯nsberg, Vestfold county 5 5G
J¯rstad, SnŒsa, Nord-T¯ndelag county 1 1F
Laukhammer, Tysnes, Hordaland county 3 3F
Lyngneset, Tysnes, Hordaland county 2 2F
Poland
Biala Podlaska, Kloda 1 1F
Forest Karcz, Sulecha 1 1F
Kurowo, Wlolawek 4 4F
Wichrowo, Smolajny 4 4F
Wyszkow, Fidest 1 1F
Romania
Satu Mare, Tibenn 1 1G
Scotland
Glen Barrisdale, Knoydart 3 3F
Slovakia
Gabcokovo 2 1 F, 1 G
Spain
Asturias, Covadonga 2 2J
Malaga 4 4J
Vizcaya-Bizkaia, Col Barazar 3 3F
Sweden
Boserup 1 1F
Bubbetorp 1 1F
Uppsala 1 1F
Vanneberga 1 1F
Turkey
Dereli, Giresun 5 2 L, 3 N
East Anatolia 1 1L
Gatak, Giresun 3 3L
Gšktas, Artvin 1 1C
Appendix 1 Continued
Sample
Site size Haplotype
Hopa, Artvin 4 1 C, 3 L
Istanbul 1 1M
Kapili Dag River, N.E. of Borcka 1 1C
Kesap, Giresun 1 1N
Ma•ka, Trabzon 4 4L
Mesudiye, Ordu 4 4L
Tirebolu, Giresun 3 3L
Ulubey, Ordu 4 4L
Vakfikebir, Trabzon 3 3C
Ukraine
Yalta 2 2C
Wales
River Twyi 2 2G