Genetic variability of Siberian fir <Emphasis Type="Italic">Abies sibirica</Emphasis> Ledeb. inferred from AFLP markers

Genetic variability of AFLP markers was studied in 20 populations of Siberian fir (Abies sibirica, Pinaceae) and in two populations of Far-Eastern species Manchurian fir A. nephrolepis and Sakhalin fir A. sachalinensis each. Four pairs of selective primers were used. In total, 168 samples from three fir species were genotyped for 117 polymorphic loci. According to the AMOVA results, the variability proportion characterizing the differences among three Abies species was several times higher (F _CT = 0.53) than that acounting for population differences within the species (F _SC = 0.125). Differentiation of the A. sibirica populations based on AFLP markers exceeded 14% (F _ST = 0.141). Significant correlation between the genetic distances calculated from the AFLP data and the geographic distances between populations was found. The results of AFLP variability analysis supported and supplemented the conclusions inferred previously from allozyme and cpSSR data: several genetically similar geographic groups of Siberian fir were identified. These groups differ both in allele frequencies and in the levels of genetic variation.     

The diversity of chloroplast microsatellite loci in Siberian fir (Abies sibirica Ledeb.) and two Far East fir species A. nephrolepis (Trautv.) Maxim. and A. sachalinensis Fr. Schmidt

The genetic variability in 29 populations of Abies sibirica, three of A. nephrolepis, and seven of A. sachalinensis was studied using SSR markers of chloroplast DNA. Among ten primer pairs examined, pairs Pt71936 and Pt30204 gave stable amplification and polymorphic products (with nine and fourteen alleles, respectively). Totally, 70 haplotypes were found, 43 in A. sibirica, 49 in A. sachalinensis, and 31 in A. nephrolepis. The highest values of genetic diversity parameters were observed in A. sachalinensis, and the lowest in A. sibirica. The Siberian fir differs from Far East species by the uneven multimodal frequency distributions of allele length in both cpSSR loci, which is explained by the presence of few separated from each other dominating haplotypes. This fact indicates that A. sibirica and the Far East species have different demographic histories. In A. sibirica, the proportion of diversity between populations in the total genetic diversity, calculated taking into account the differences between haplotypes (R _ST) was 8.34 and 4.42% without accounting for haplotypes differences (R _ST > G _ST, P = 0.01). The pairwise G _ST correlate significantly with geographic distances between the populations A. sibirica and with genetic distances D calculated from allozyme data. No such correlations were found with the R _ST parameter. The results of cpSSR variability analysis strongly support the conclusions inferred from allozyme data: several geographic groups of comparatively genetically close populations are identified, which may be explained by the history of colonization of the present-day Siberian fir range. Original Russian Text ? S.A. Semerikova, V.L. Semerikov, 2007, published in Genetika, 2007, Vol. 43, No. 12, pp. 1637–1646.     

Identification and characterization of nuclear microsatellite loci in Abies alba Mill.

Eleven polymorphic nuclear microsatellite markers for Abies alba Mill. were developed from an enriched genomic library. An average of 5.2 alleles per locus and a mean expected heterozygosity of 0.532 were found in a sample of 24 Abies alba individuals from different populations within Europe. These loci can be used in studies of genetic diversity for parentage analysis and for estimation of gene flow in silver fir populations. Moreover, successful amplifications were obtained for eight other Mediterranean Abies species, suggesting that these loci may be useful for similar applications in other fir species.     

DIFFERENTIATION OF MITOCHONDRIAL DNA POLYMORPHISMS IN POPULATIONS OF FIVE JAPANESE ABIES SPECIES

Mitochondrial DNA polymorphism of 40 populations of five Abies species was investigated using PCR-amplified coxI and coxIII gene probes. Using four combinations of probe and restriction enzyme, we detected three major haplotypes and 15 total haplotypes. We also found varied levels of gene diversity for the different species: 0.741, 0.604, 0.039, 0.000, and 0.292 for A. firma, A. homolepis, A. veitchii, A. mariesii, and A. sachalinensis, respectively. The marginal and southern populations of A. firma and A. homolepis have unique haplotypes, especially the Kyushu, Shikoku, and Kii Peninsula populations, which inhabit areas coinciding with probable refugia of the last glacial period and possess high levels of mtDNA genetic diversity. The haplotypes in some populations suggested mtDNA capture also occurred between species through introgression/hybridization. The strong mtDNA population differentiation in Abies is most likely due to the maternal inheritance of mitochondria and restricted seed dispersal. A phenetic tree based on the genetic similarity of the mtDNA suggests that some species are polyphyletic. Based on mtDNA variation, the five Abies species could be divided roughly into three groups: (1) A. firma and A. homolepis, (2) A. veitchii and A. sachalinensis, and (3) A. mariesii. However, we found that all these Abies species, except A. mariesii, are genetically very closely related according to an analysis of their cpDNA sequences. This showed that the chloroplast rbcL gene differed by only one base substitutions among the four species. We believe that the mtDNA variation and cpDNA similarity clearly reflect relationships among, and the dissemination processes affecting these Abies species since the last glacial period.     

Development and characterization of microsatellite markers in Abies firma and interspecific amplification in other Japanese Abies species

Abies firma is a dominant coniferous tree species endemic to Japan. We isolated eight microsatellite loci from needles of this tree species and tested their polymorphism among 26 A. firma individuals. Six of them showed polymorphism, with two to 16 alleles per locus. Their expected heterozygosities ranged from 0.075 to 0.922. Moreover, interspecific amplification among Abies sachalinensis, Abies mariesii and Abies veitchii was successful in majority of the isolated loci, suggesting that these loci may be useful for characterization of other fir species.     

Crossability relationships between Korean firs Abies koreana , A. nephrolepis and A. holophylla and some other representatives of the genus Abies

Artificial crossing experiments involving 3 Abies species native to Korean peninsula and 5 other representatives of Abies revealed a high hybridological affinity between Abies koreana and A. nephrolepis. Both these species are reproductively isolated from A. holophylla. All the three Korean species were found to exhibit incompatible relationships with the North American species A. concolor. The species A. holophylla and A. koreana differ also in their abilities to intercross with the Mediterranean firs. The former has been successfully crossed with A. nordmanniana, A. alba and A. cilicica exhibiting 19.1–55.3% crossability, whereas the latter produced filled seeds only with A. nordmanniana reaching 46.4% crossability. A considerable differentiation is postulated to exist between the pair of species A. koreana and A. nephrolepis on the one side and A. holophylla on the other side.     

Fossil wood of <Emphasis Type="Italic">Abietoxylon shakhtnaense</Emphasis> sp. nov. (Pinaceae) from the Upper Oligocene-Lower Miocene deposits of Southeastern Sakhalin

A new species, Abietoxylon shakhtnaense (Pinaceae), was erected on the basis of fossil wood anatomical characters from the Upper Oligocene-Lower Miocene deposits of Southeastern Sakhalin. A. shakhtnaense is similar to wood of firs Abies sachalinensis, A. magnifica, and A. grandis. Fossil wood with features characterizing fir anatomical structure was found in Sakhalin for the first time.     

High level of variation at Abies alba chloroplast microsatellite loci in Europe

Based on two polymorphic chloroplast microsatellites that had been previously identified and sequence characterized in the genus Abies, genetic variation was studied in a total of 714 individuals from 17 European silver fir (Abies alba Mill.) populations distributed all over the natural range. We found eight and 18 different length variants at each locus, respectively, which combined into 90 different haplotypes. Genetic distances between most populations were high and significant. There is also evidence for spatial organization of the distribution of haplotypes, as shown by permutation tests, which demonstrate that genetic distances increase with spatial distances. A large heterogeneity in levels of diversity across populations was observed. Furthermore, there is good congruence in the levels of allelic richness of the two loci across populations. The present organization of levels of allelic richness across the range of the species is likely to have been shaped by the distribution of refugia during the last glaciation and the subsequent recolonization processes.     

Epiphytic lichen diversity and its dependence on bark chemistry in the northern Mongolian dark taiga

Epiphytic lichen diversity was studied in a dark taiga forest of Pinus sibirica, Abies sibirica and Picea obovata in the western Khentey Mountains, northern Mongolia. Though most lichen species occurred on all three tree species, lichen diversity was higher on Abies and Picea than on Pinus. On branches, lichen vegetation differed less between tree species than on the trunk. The occurrence of many Parmeliaceae species with a hydrophilic surface and of many species producing the dibenzofuran usnic acid gives evidence of the low deposition of acidic pollutants in the study area. The Mn content of bark, which is known to limit at high values the abundance of epiphytic lichens in coniferous forests of Europe and North America, is apparently not controlling the spatial distribution of epiphytic lichens in the dark taiga of Mongolia. This is attributed to the dry and cold winters in Mongolia, as high Mn is especially leached from the surface of trees under moist conditions at temperatures around the freezing point, when the contact between water droplets and the tree surface is particularly intensive. Such moist and cold weather conditions are frequent in most parts of the northern coniferous forests of Europe and North America, but are rare events in the most continental parts of Asia, i.e. in Mongolia and eastern Siberia.     

Evolutionary history of two endemic Appalachian conifers revealed using microsatellite markers

Fraser fir (Abies fraseri [Pursh] Poir.) and intermediate fir (Abies balsamea [L.] Mill. var. phanerolepis Fern.) exist in small populations in the Appalachian highlands of the southeastern United States. We used ten nuclear microsatellite markers to quantify genetic variation within Fraser fir and intermediate fir, and to examine their evolutionary relationships with the widespread balsam fir (Abies balsamea [L.] Mill.). We found little genetic differentiation among these taxa, suggesting that Fraser fir might best be classified as a variety of balsam fir. The results further appear to reject the hypothesis that intermediate fir was of hybrid origin between two comparatively distantly related species. Low levels of genetic diversity suggest that intermediate fir and Fraser fir have undergone at least some genetic degradation since post-Pleistocene isolation. The results may prove important for in situ and ex situ gene conservation efforts for Fraser fir and intermediate fir, which are imperiled by an exotic insect and by global climate change.     

Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae)

The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the Structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.     

Genetic variability of Siberian fir (Abies sibirica Ledeb.) inferred from AFLP markers

Genetic variability of AFLP markers was studied in 20 populations of Siberian fir (Abies sibirica (Pinaceae) and in two populations of Far-Eastern Manchurian fir A. nephrolepis and Sakhalin fir A. sachalinensis each. Four pairs of selective primers were used. In total, 168 samples from three fir species were genotyped for 117 polymorphic loci. According to the AMOVA results, the variability proportion characterizing the differences between three Abies species was several times higher (F(CT) = 0.53) than that accounting for among-population differences within the species (F(SC) = 0.125). Differentiation of the A. sibirica populations based on AFLP markers exceeded 14% (F(ST) = 0.141). Significant correlation between the genetic distances calculated from the AFLP data and the geographic distances between populations was found. The results of AFLP variability analysis supported and supplemented the conclusions inferred previously from allozyme and cpSSR data: several genetically similar geographic groups of Siberian fir were identified. These groups differ both in allele frequencies and in the levels of genetic variation.     

Genetic variation at chloroplast microsatellites (cpSSRs) in Abies nebrodensis (Lojac.) Mattei and three neighboring Abies species

Abies nebrodensis (Lojac.) Mattei (Sicilian fir) is an endangered species represented by only one population of 29 adult individuals occurring in a limited area of the Madonie Range in northern Sicily (Italy). Taxonomic boundaries between this taxon and the neighboring Abies species are not clear. In this study, we used six chloroplast simple-sequence repeats (cpSSRs) to investigate the population genetic structure and the distribution of chloroplast haplotypic variation in A. nebrodensis and three of the neighboring Abies species: Abies alba (Mill.), Abies numidica (De Lann) and Abies cepha-lonica (Loud.). Our aims were to quantify the level of cpDNA differentiation within the Abies populations and to shed light on the history of A. nebrodensis. Diversity levels based on the haplotype frequency at six cpSSRs were high, especially in A. alba and A. cephalonica. In all, we found 122 haplotypes among the 169 individuals analyzed, and the four species were distinguished from each other by their haplotype composition. The majority of the haplotypes (76%) were detected only once, but in A. nebrodensis seven individuals (41% of the sample population) shared the same haplotype. Moreover, the seven A. nebrodensis individuals with an identical haplotype showed a tendency to be geographically grouped within the population"s limited range. The analysis of molecular variance (AMOVA) showed a significant difference in the level of apportionment of gene diversity between the species A. alba and A. cephalonica (F_ST=0.191 and 0.012, respectively). AMOVA analysis conducted over all populations from the four species showed that 19% of the total cpSSR variation was attributable to differences among species, 6% was due to differences among populations within species, and 74% to differences within populations. The high percentage of unique haplotypes identified confirms the power of cpSSR haplotype analysis for identifying individual trees in individual Abies populations. Our results indicate that A. nebrodensis differs from the other three Abies species investigated and support its classification as an independent taxon. The results also showed a decreased level of variation in A. nebrodensis and suggested that the species has experienced a genetic bottleneck during the last two centuries. Received: 10 April 2000 / Accepted: 13 July 2000     

Microsatellite markers for Sachalin fir (Abies sachalinensis Masters)

We developed eight polymorphic microsatellite markers from the Sachalin fir (Abies sachalinensis Masters). The number of alleles per locus ranged from eight to 31, with an average of 21.4. The observed and expected heterozygosities ranged from 0.656 to 0.937 and from 0.710 to 0.945, respectively. These markers will be available for population genetic studies and parentage analysis.     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Genetic variation and population differentiation in Siberian fir Abies sibirica ledeb. inferred from allozyme markers

Genetic variation in 24 populations of Siberian fir Abies sibirica Ledeb. from the Urals, West Siberia, East Siberia, South Siberia, and the Baikal region were examined using allozyme markers. Three out of fifteen allozyme loci proved to be polymorphic. Heterozygosity H _e was 6.6–9.6%, which is substantially lower than that in other widely spread boreal conifers. Our results suggest that the Siberian fir populations are subdivided into four geographic groups: (1) the Baikal Lake group, (2) the Sayan and the Altai group, (3) the Middle and Southern Urals group, and (4) Subpolar and Northern Urals group. This pattern of geographic differentiation may be explained by the preservation of the Siberian fir during the last glacial maximum (18 000–22 000 years B.P.) in isolated refugia with subsequent recolonization of the present area. F _ST in the populations examined was 10.16%, which is comparable to the estimate for Larix sibirica (7.9%), a conifer species having a similar range and pattern of geographic population differentiation.     

Spatial pattern dynamics over 10 years in a conifer/broadleaved forest,northern Japan

The present study investigated stand dynamics during 10-year period in a conifer/broadleaved mixed forest in Hokkaido, northern Japan, focusing on spatially dependent recruitment, mortality and growth of two growth-form groups, deciduous broadleaved species and the dominant evergreen conifer Abies sachalinensis. The stand-level basal area was maintained over the 10-year period, while a compositional equilibrium at the individual species level was not confirmed. Univariate and bivariate spatial analyses revealed clustering of many of the constituent species. The absence of single-species patches suggested an ambiguous mosaic formed by co-occurrence of Abies and broadleaved trees. The trend towards an aggregated distribution of Abies and broadleaved trees was caused by spatially dependent recruitment rather than mortality. New recruits of broadleaved species were spatially associated with surviving broadleaved trees, while this was not the case for Abies. The degree of competitive effects on growth was not consistent over the 10-year period. Abies showed between-groups competition, but not within-group competition. In contrast, we found asymmetric competitions between the broadleaved trees. Our results suggest that Abies is not sufficiently competitively dominant to exclude broadleaved trees, and that the co-occurrence of the two growth-form groups might be maintained.     

Allelic sequence polymorphisms in the intron region of the nuclear-encoded GapC gene preceded the speciation of three closely related Abies species (Pinaceae)

The DNA sequences of GapC intron 8 were determined for three closely related Abies species, Abies firma, Abies homolepis and Abies veitchii, and ten alleles were identified. Although, in most cases, an allele was specifically detected in one species, some rare alleles were found in two species. The phylogenetic analysis of those alleles showed that they trace back to different ancestral sequences, and that a species possessed the different originated alleles. The polymorphism of the GapC gene observed in the three Abies species seemed to have preceded their evolutionary divergence. Received: 1 February 2000 / Accepted: 10 May 2000     

Stand structure and dynamics of wave-typeAbies sachalinensis coastal forest

Stand structure and regeneration pattern were examined inAbies sachalinensis coastal forest in northern Hokkaido. In the forest a similar phenomenon to the wave regeneration in subalpine forests has been found. Wave regeneration has been reported for montaneAbies forests in central Japan and North America. Differences and similarities between wave-type stands in this coastal forest and wave-regenerated montane forests were clarified. The shift of dead tree zone, stand structure and regeneration pattern in wave-type stands are the same as in subalpine wave-regenerated forests. High density of individuals is considered to be an internal factor which causes stand-level dieback and also enables the stands to persist in the severe environment in both forests. A difference between wave-regenerated forests andA. sachalinensis wave-type stands is the number of dead tree zones, which is only one in wave-type stands. Changes of regeneration patterns ofAbies sachalinensis with environmental gradient from seaward to inland were related to this difference.     

Isolation and characterization of microsatellite markers in Fraser fir (Abies fraseri)

We describe the isolation and characterization of 14 microsatellite loci from Fraser fir (Abies fraseri). These markers originated from cloned inserts enriched for DNA sequences containing tandem di‐ and tri‐nucleotide repeats. In total, 36 clones were selected, sequenced and evaluated. Polymerase chain reaction (PCR) primers for 14 of these sequences consistently produced simple PCR profiles and were found to be polymorphic among 13 Fraser fir samples. In addition, more than half of these loci were found to amplify a wide range of samples from several Abies taxa.