Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs

The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

Intraspecific phylogeny of a Patagonian fescue: differentiation at molecular markers and morphological traits suggests hybridization at peripheral populations

BACKGROUND AND AIMS

Grasses of the Festuca genus have complex phylogenetic relations due to morphological similarities among species and interspecific hybridization processes. Within Patagonian fescues, information concerning phylogenetic relationships is very scarce. In Festuca pallescens, a widely distributed species, the high phenotypic variability and the occurrence of interspecific hybridization preclude a clear identification of the populations. Given the relevance of natural rangelands for livestock production and their high degradation due to climate change, conservation actions are needed and knowledge about genetic variation is required.

METHODS

To unravel the intraspecific phylogenetic relations and to detect genetic differences, we studied 21 populations of the species along its natural geographical distribution by coupling both molecular [internal transcribed spacer (ITS) and trnL-F markers] and morpho-anatomical analyses. Bayesian inference, maximum likelihood and maximum parsimony methods were applied to assemble a phylogenetic tree, including other native species. The morphological data set was analysed by discriminant and cluster analyses.

KEY RESULTS

The combined information of the Bayesian tree (ITS marker), the geographical distribution of haplotype variants (trnL-F marker) and the morpho-anatomical traits, distinguished populations located at the margins of the distribution. Some of the variants detected were shared with other sympatric species of fescues.

CONCLUSIONS

These results suggest the occurrence of hybridization processes between species of the genus at peripheral sites characterized by suboptimal conditions, which might be key to the survival of these populations.

Assessing signals of selection and historical demography to develop conservation strategies in the Chilean emblematic Araucaria araucana

Loss of genetic diversity reduces the ability of species to evolve and respond to environmental change. Araucaria araucana is an emblematic conifer species from southern South America, with important ethnic value for the Mapuche people (Pehuenche); the Chilean Government has catalogued its conservation status as vulnerable. Climatic fluctuations were potentially a major impact in the genetic variation within many tree species. In this context, the restricted geographic distribution of A. araucana in Chile appears to be a consequence of the Last Glacial Maximum (LGM). During the past two centuries, strong human intervention has also affected the geographical distribution and population sizes of A. araucana. Reduction of population size may cause loss of genetic diversity, which could affect frequency of adaptive loci. The aims of this study were to know the existence of potential loci under selection and populations with genetic, demographic disequilibrium in the Chilean distribution of A. araucana. Based on 268 polymorphic AFLP loci, we have investigated potential loci under selection and genetic, demographic disequilibrium within seven Chilean populations of Araucaria araucana. Correlation of 41 outlier loci with the environmental variables of precipitation and temperature reveals signatures of selection, whereas 227 neutral loci provide estimates of demographic equilibrium and genetic population structure. Three populations are recommended as priorities for conservation.

Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation

Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.

How do cold-sensitive species endure ice ages? Phylogeographic and paleodistribution models of postglacial range expansion of the mesothermic drought-tolerant conifer Austrocedrus chilensis

In view of global climate change, it is important to understand the responses of tree species to climate changes in the past. Combinations of phylogeographic analysis of genetic evidence, coupled with species distribution models (SDMs), are improving our understanding on this subject. We combined SDMs and microsatellite data from populations of the entire range of Austrocedrus chilensis, a dominant mesotherm (cold-sensitive) conifer of dryland forests of the southern Andes, to test the hypothesis of long-distance postglacial migration from northern and warmer refugia at the Last Glacial Maximum (LGM). The SDM indicated suitable conditions for Austrocedrus in northern Chile (western) at the LGM and largely unsuitable conditions in Argentina (eastern). Population genetic diversity and effective population sizes within populations decreased southward along the Andes, consistent with the hypothesis of long-distance dispersal from a northern refugium. Results support the hypothesis of one (or a few) warmer (low latitude) refugia in Chile for Austrocedrus. On balance, the evidence suggests that in contrast to cold-tolerant tree taxa with the capacity to fast-track postglacial warming thanks to local refugia, cold-sensitive species might have undergone long-distance range expansion, lagging behind progressive climate change throughout the Holocene.

Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species

BACKGROUND

New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia.

RESULTS

The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations.

CONCLUSIONS

The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.

Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data

The effect of glaciation on the levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly, complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant communities. We therefore studied the population genetics of three closely related, hybridizing species of Nothofagus (N. obliqua, N. alpina, and N. glauca, all of subgenus Lophozonia; Nothofagaceae) from Chile. To estimate population genetic parameters and infer the influence of the last ice age on the spatial and genetic distribution of these species, we examined and analyzed genetic variability at seven polymorphic microsatellite DNA loci in 640 individuals from 40 populations covering most of the ranges of these species in Chile. Populations showed no significant inbreeding and exhibited relatively high levels of genetic diversity (H_E = 0.502–0.662) and slight, but significant, genetic structure (R_ST = 8.7–16.0%). However, in N. obliqua, the small amount of genetic structure was spatially organized into three well-defined latitudinal groups. Our data may also suggest some introgression of N. alpina genes into N. obliqua in the northern populations. These results allowed us to reconstruct the influence of the last ice age on the genetic structure of these species, suggesting several centers of genetic diversity for N. obliqua and N. alpina, in agreement with the multiple refugia hypothesis.

Genetic evidence for glacial refugia of the temperate tree Eucryphia cordifolia (Cunoniaceae) in southern South America

PREMISE OF THE STUDY

The temperate forests of southern South America were greatly affected by glaciations. Previous studies have indicated that some cold-tolerant tree species were able to survive glacial periods in small, ice-free patches within glaciated areas in the Andes and in southern Patagonia. Here we asked whether populations of the mesothermic species Eucryphia cordifolia also were able to survive glaciations in these areas or only in unglaciated coastal areas.

METHODS

The chloroplast intergenic spacer trnV-ndhC was sequenced for 150 individuals from 22 locations. Genetic data were analyzed (standard indexes of genetic diversity, a haplotype network, and genetic differentiation) in a geographical context.

KEY RESULTS

Two of the nine haplotypes detected were widespread in high frequency across the entire range of the species. The highest levels of genetic diversity were found around 40°S, decreasing sharply northward and more moderately southward. No differences in genetic diversity were found between Andean and coastal populations. Notably, seven haplotypes were found in a small area of the Coast Range known as the Cordillera Pelada (40°S). The differentiation coefficients G(ST) and N(ST) revealed that most of the genetic variation detected was due to variation within populations.

CONCLUSIONS

The low levels of population differentiation and the high genetic diversity found in the Cordillera Pelada suggest that this area was the main refugium for E. cordifolia during glaciations. Nevertheless, given the high levels of genetic diversity found in some Andean populations, we cannot discount that some local populations also survived the glaciation in the Andes.

Range-wide genetic structure and diversity of the endemic tree line species Polylepis australis (Rosaceae) in Argentina

PREMISE OF THE STUDY

Knowledge on the range-wide distribution of genetic structure and diversity is required to facilitate the understanding of historical tree migration and for predicting responses to current climate change. With respect to post-glacial migration patterns known from the northern hemisphere, we tested the prediction that the southernmost populations of a subtropical tree line species have lower within-population genetic diversity and higher genetic differentiation than the central and northernmost populations.

METHODS

We used AFLP to assess the genetic structure of 18 populations of the wind-pollinated Polylepis australis (Rosaceae) sampled over its entire distributional range in three Argentinean high mountain regions. Genetic diversity was calculated as a percentage of polymorphic bands (P) and Nei's expected heterozygosity (He); genetic differentiation was assessed using AMOVA, Φ(ST)--statistics, and Bayesian cluster analysis.

KEY RESULTS

Contrary to our expectations, the northernmost Polylepis australis stands had lower within-population genetic diversity and higher genetic differentiation than the central and southernmost stands. Populations grouped into two major clusters, the first containing the southern populations and four central populations and the second containing the northern and one central population.

CONCLUSIONS

Patterns of Polylepis australis genetic structure and diversity differ from historical migration scenarios observed for the northern hemisphere. The decline in genetic diversity toward the north may point to an equatorward migration following past climatic changes. Populations within the south and central part appear to be connected by effective long-distance pollination while gene flow in the northern part is probably hampered by geographic isolation.

Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa

While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.

Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa

The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (F(ST) = 0.21; R(ST) = 0.28; R(ST) > R(ST) (permuted)) and chloroplast simple sequence repeats (SSRs) (G(ST) = 0.81; N(ST) = 0.90; N(ST) > N(ST) (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa.

Genetic diversity and differentiation in Dalbergia sissoo (Fabaceae) as revealed by RAPD

Dalbergia sissoo, a wind-dispersed tropical tree, is one of the most preferred timber tree species of South Asia. Genetic diversity and differentiation among natural populations of D. sissoo were examined for the first time. We found a relatively high level of genetic diversity in D. sissoo, both at the species level (percentage of polymorphic bands = 89.11%; H = 0.2730; I = 0.4180) and the population level (percentage of polymorphic bands = 68.7%; H = 0.239; I = 0.358), along with a relatively low degree of differentiation among populations (GST = 0.1311; AMOVA = 14.69%). Strong gene flow among populations was estimated, N(m) = 3.3125. The Mantel test suggested that genetic distances between populations were weakly correlated with geographic distances (R = 0.3702, P = 0.1236). The high level of genetic diversity, low degree of differentiation, strong gene flow, and weak correlation between genetic and geographic distances can be explained by its biological character and wide-spread planting. This information will be useful for the introduction, conservation and further studies of D. sissoo and related species.

Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert.) O. Kuntze relict populations

Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five “genetic clusters” (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three “genetic clusters”. These results are in agreement with the pattern of geographic distribution of the studied populations.

Plastid DNA variation in highly fragmented populations of Microbiota decussata Kom. (Cupressaceae), an endemic to Sikhote Alin Mountains

Microbiota decussata Kom. (Cupressaceae) is a subalpine species endemic to the Sikhote Alin Mountains with populations scattered throughout the range. We used sequence data for four noncoding regions of chloroplast DNA to characterize the genetic diversity in populations sampled from different parts of M. decussata natural range. No variation was observed in the trnT-trnF region, whereas the trnH-psbA, trnS-trnfM, and trnS-trnG regions showed polymorphisms. At the species level, we found a low nucleotide diversity (pi = 0.0009) and high haplotype diversity (h = 0.981) as well as high differentiation (Phi(ST) = 0.420). N(ST) and G(ST) values suggested the existence of a phylogeographic structure in M. decussata. The observed patterns of diversity could be explained in part by ecological features of the species and its long-term persistence throughout the range with population expansion, successive fragmentation and isolation.

Fruit properties and genetic diversity of five ber (Ziziphus mauritiana Lamk) cultivars

The present study was conducted on five ber (Ziziphus mauritiana Lamk) cultivars (Komethry, Pakstany, Um-sulaem, Toffahy and Peyuan) grown in Saudi Arabia during 2005 and 2006 seasons. The aim of the present study was to investigate fruit properties (fruit weight, length, diameter, shape, specific gravity, seed weight, pulp percentage, total soluble solids (TSS), acidity percentage, TSS/acid, vitamin C content total, reducing and non-reducing sugars). Peyuan cv. had the heaviest fruit weight, fruit volume and reducing sugar content however, it was the lowest in pulp percentage and non-reducing sugars among the five cultivars in both seasons. Toffahy cv. had highest fruit diameter and seed weight while, had lowest TSS %, vitamin C and total sugars values. Um-sulaem cv. had highest acidity percentage and vitamin C content and lowest fruit weight, length and TSS/acid. On the other hand, Pakstany cv. had highest percentage of both pulp percentage, TSS, total and non-reducing sugars. Finally, Komethry had the longest fruit. The molecular characterization and fingerprint identification of the ber cultivars was conducted using the ISSR (Inter-Simple Sequence Repeats) technique. The ISSR technique was able to uniquely characterize and differentiate between the five ber genotypes. Moreover, the genetic similarity tree showed that the cultivar Um-slaem is genetically distant from the other four cultivars and the two cultivars Pakstany and Komethry were genetically identical.

Genetic structure of Araucaria angustifolia (Araucariaceae) populations in Brazil: implications for the in situ conservation of genetic resources

The distribution of the genetic variation within and among natural populations of A. ANGUSTIFOLIA growing in different regions in Brazil was assessed at microsatellite and AFLP markers. Both markers revealed high gene diversity ( H = 0.65; AR = 9.1 for microsatellites and H = 0.27; P = 77.8 % for AFLPs), moderate overall differentiation ( RST = 0.13 for microsatellites and FST = 0.10 for AFLPs), but high divergence of the northernmost, geographically isolated population. In a Bayesian analysis, microsatellite data suggested population structure at two levels: at K = 2 and at K = 3 in agreement to the geographical distribution of populations. This result was confirmed by the UPGMA dendrogram based on microsatellite data (bootstrap support > 95 %). Non-hierarchical AMOVA revealed high variation among populations from different A POSTERIORI defined geographical groups. The genetic distance between sample locations increased with geographical distance for microsatellites ( R = 0.62; P = 0.003) and AFLPs ( R = 0.32; P = 0.09). This pattern of population differentiation may be correlated with population history such as geographical isolation and postglacial colonization of highlands. Implications of the population genetic structure for the conservation of genetic resources are discussed.

Genetic diversity of the shea tree (Vitellaria paradoxa C.F. Gaertn), detected by RAPD and chloroplast microsatellite markers

RAPDs and chloroplast microsatellites were used to quantify the genetic variation of Vitellaria paradoxa (an economically important tree species in sub-Saharan Africa, north of the equator) and to analyse the geographic distribution of diversity in relation to the refuge theory. A total of 13 locations were sampled in eight countries, covering most of the natural range from Senegal to Uganda. A total of 67 polymorphic and 15 monomorphic RAPD loci were detected in 179 individuals. No relationship was identified between diversity and longitude or latitude. An unrooted neighbour-joining tree suggested a western group and an eastern group, representing 7% (P = 0.000) of the total variation. A Mantel test suggested that genetic distances between populations were correlated to geographic distances (R = 0.88, P = 0.001). The three-chloroplast microsatellite primers, assayed in 116 individuals, revealed 10 different alleles and seven chlorotypes. Most of the populations comprised a single haplotype. It is proposed from these results that the difference between western and eastern populations results from putative refugia separated by the current 'Dahomey Gap' (a semiarid zone that meets the coast around the Ghana-Togo-Benin-Nigeria borders), an area that may have been exceptionally dry during glacial periods. In addition, it is suggested that the haplotype distribution and frequency in the western populations could be due to the more recent impact of humans, particularly shea tree selection and dispersal during traditional agroforestry.

Comparative genetic study confirms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae)

The Wollemi pine, Wollemia nobilis (Araucariaceae), was discovered in 1994 as the only extant member of the genus, previously known only from the fossil record. With fewer than 100 trees known from an inaccessible canyon in southeastern Australia, it is one of the most endangered tree species in the world. We conducted a comparative population genetic survey at allozyme, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) loci in W. nobilis, Araucaria cunninghamii and Agathis robusta - representatives of the two sister genera. No polymorphism was detected at 13 allozyme loci, more than 800 AFLP loci or the 20 SSR loci screened in W. nobilis. In Ag. robusta only one of 12 allozyme loci, five of 800 AFLP loci and none of the 15 SSR loci were variable. For A. cunninghamii, 10 of > 800 AFLP loci and five of 20 SSR loci were variable. Thus low genetic diversity characterizes all three species. While not ruling out the existence of genetic variation, we conclude that genetic diversity is exceptionally low in the Wollemi pine. To our knowledge this is the most extreme case known in plants. We conclude that the combination of small population effects, clonality and below-average genetic variation in the family are probable contributing factors to the low diversity. The exceptionally low genetic diversity of the Wollemi pine, combined with its known susceptibility to exotic fungal pathogens, reinforces current management policies of strict control of access to the pines and secrecy of the pine locations.

Patterns of genetic variation in Pinus chiapensis, a threatened Mexican pine, detected by RAPD and mitochondrial DNA RFLP markers

Pinus chiapensis (Pinaceae) is a large conifer, endemic to central and southern Mexico and north-western Guatemala. In order to assess the extent of genetic variation within and between populations of this species, samples were obtained from throughout the natural range and analysed using random amplified polymorphic DNA (RAPD) and mtDNA RFLPs markers. Probes for the CoxI mitochondrial gene enabled two mitotypes to be observed. Populations from the eastern and western limit of the range of the species were fixed for one mitotype ('A'), whereas two populations distributed near the centre of the range were fixed for another ('B'). When the samples were screened with eight 10-mer RAPD primers, a total of 12 polymorphic bands were detected. The proportion of polymorphic bands was unusually low (24.5%) compared with other tree species. AMOVA analysis indicated that a significant proportion of the variation (P < 0.002) was distributed between populations; the extent of population differentiation detected (Phi(st) = 0.226; G(ST ) = 0.194) was exceptionally high for a pine species. Pair-wise comparison of Phi(st) values derived from AMOVA indicated that populations were significantly (P < 0.05) different from each other in virtually every case. These results are interpreted in the context of the evolutionary history of the species, and the implications for its in- and ex situ conservation are discussed.