Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines

New Insight into Genetic Structure and Diversity of Scots Pine (Pinus sylvestris L.) Populations in Lithuania Based on Nuclear, Chloroplast and Mitochondrial DNA Markers

We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (FST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed.

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.

Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America

The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.

Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species

Background and Aims

Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis.

Methods

Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species.

Key Results and Conclusion

Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.

Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation

It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China.

Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival

The dynamics of forest ecosystems depend largely on the survival of seedlings in their understories, but seedling survival is known to be limited by preemption of light and soil resources by overstory trees. It has been hypothesized that "common mycorrhizal networks," wherein roots of seedlings are linked to overstory trees by symbiotic mycorrhizal fungi, offset some or all of the negative effects of trees on seedlings. Here we report the results of an unambiguous experimental test of this hypothesis in a monodominant Pinus radiata forest. We also tested the hypothesis that adaptive differentiation among plant populations causes local plant genotypes to respond more positively to mycorrhizal networks than nonlocal plant genotypes. Our results demonstrate large positive effects of overstory mycorrhizal networks on seedling survival, along with simultaneous negative effects of tree roots, regardless of whether plant genotypes were locally derived. Physiological and leaf-chemistry measurements suggest that seedlings connected to common mycorrhizal networks benefited from increased access to soil water. The similar magnitude of the positive and negative overstory effects on seedlings and the ubiquity of mycorrhizal networks in forests suggest that mycorrhizal networks fundamentally influence the demographic and community dynamics of forest trees.

Interactions of biotic and abiotic environmental factors in an ectomycorrhizal symbiosis, and the potential for selection mosaics

BACKGROUND

Geographic selection mosaics, in which species exert different evolutionary impacts on each other in different environments, may drive diversification in coevolving species. We studied the potential for geographic selection mosaics in plant-mycorrhizal interactions by testing whether the interaction between bishop pine (Pinus muricata D. Don) and one of its common ectomycorrhizal fungi (Rhizopogon occidentalis Zeller and Dodge) varies in outcome, when different combinations of plant and fungal genotypes are tested under a range of different abiotic and biotic conditions.

RESULTS

We used a 2 x 2 x 2 x 2 factorial experiment to test the main and interactive effects of plant lineage (two maternal seed families), fungal lineage (two spore collections), soil type (lab mix or field soil), and non-mycorrhizal microbes (with or without) on the performance of plants and fungi. Ecological outcomes, as assessed by plant and fungal performance, varied widely across experimental environments, including interactions between plant or fungal lineages and soil environmental factors.

CONCLUSION

These results show the potential for selection mosaics in plant-mycorrhizal interactions, and indicate that these interactions are likely to coevolve in different ways in different environments, even when initially the genotypes of the interacting species are the same across all environments. Hence, selection mosaics may be equally as effective as genetic differences among populations in driving divergent coevolution among populations of interacting species.

Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala

The genus Abies has a complex history in southern México and Guatemala. In this region, four closely related species, Abies flinckii, A. guatemalensis, A. hickelii, and A. religiosa, are distributed in fragmented and isolated montane populations. Range-wide genetic variation was investigated across species using cytoplasmic DNA markers with contrasted inheritance. Variation at two maternally inherited mitochondrial DNA markers was low. All species shared two of the nine mitotypes detected, while the remaining seven mitochondrial DNA types were restricted to a few isolated stands. Mitochondrial genetic differentiation across taxa was high (G(ST) = 0.933), it was not related to the taxonomic identity (amova; P > 0.05) of the populations, and it was not phylogeographically structured (G(ST) approximately N(ST)). In contrast, variation at three paternally inherited chloroplast DNA microsatellites was high. Chloroplast genetic differentiation was lower (G(ST) = 0.402; R(ST) = 0.547) than for mitochondrial DNA, but it was significantly related to taxonomy (amova; P < 0.001), and exhibited a significant phylogeographical structure (G(ST) < R(ST)). Different analyses of population structure indicated that A. flinckii was the most divergent taxon, while the remaining three species formed a relatively homogeneous group. However, a small number of the populations of these three taxa, all located at the limits of their respective ranges or in the Transverse Volcanic Belt, diverged from this main cluster. These trends suggest that the Mesoamerican Abies share a recent common ancestor and that their divergence and speciation is mainly driven by genetic drift and isolation during the warm interglacial periods.

Organellar genome analysis of rye (Secale cereale) representing diverse geographic regions

Rye (Secale cereale) is an important diploid (2n = 14, RR) crop species of the Triticeae and a better understanding of its organellar genome variation can aid in its improvement. Previous genetic analyses of rye focused on the nuclear genome. In the present study, the objective was to investigate the organellar genome diversity and relationships of 96 accessions representing diverse geographic regions using chloroplast (cp) and mitochondrial (mt) DNA PCR-RFLPs. Seven cpDNA and 4 mtDNA coding and noncoding regions were amplified using universal cpDNA and mtDNA primer pairs. Each amplified fragment was digested with 13 different restriction enzymes. mtDNA analysis indicated that the number of polymorphic loci (20) was low and genetic differentiation (GST) was 0.60, excluding the outgroups (hexaploid wheat, Triticum aestivum, 2n = 6x = 42, AABBDD; triticale, xTriticosecale Wittmack, 2n = 6x = 42, AABBRR). cpDNA analysis revealed a low level of polymorphism (40%) among the accessions, and GST was 0.39. Of the 96 genotypes studied, 70 could not be differentiated using cpDNA PCR-RFLPs even though they are from different geographic regions. This is most likely due to germplasm exchange, indicating that genotypes might have a common genetic background. Two cpDNA and 3 mtDNA fragments were significantly correlated to the site of germplasm collection. However, there was no clear trend. These results indicate that the level of organellar polymorphism is low among the cultivated rye genotypes. The cpDNA and mtDNA PCR-RFLP markers used in the present study could be used as molecular markers in rye genetics and breeding programs.

Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor

BACKGROUND

At the last glacial maximum, Fennoscandia was covered by an ice sheet while the tundra occupied most of the rest of northern Eurasia. More or less disjunct refugial populations of plants were dispersed in southern Europe, often trapped between mountain ranges and seas. Genetic and paleobotanical evidences indicate that these populations have contributed much to Holocene recolonization of more northern latitudes. Less supportive evidence has been found for the existence of glacial populations located closer to the ice margin. Scots pine (Pinus sylvestris L.) is a nordic conifer with a wide natural range covering much of Eurasia. Fractures in its extant genetic structure might be indicative of glacial vicariance and how different refugia contributed to the current distribution at the continental level. The population structure of Scots pine was investigated on much of its Eurasian natural range using maternally inherited mitochondrial DNA polymorphisms.

RESULTS

A novel polymorphic region of the Scots pine mitochondrial genome has been identified, the intron 1 of nad7, with three variants caused by insertions-deletions. From 986 trees distributed among 54 populations, four distinct multi-locus mitochondrial haplotypes (mitotypes) were detected based on the three nad7 intron 1 haplotypes and two previously reported size variants for nad1 intron B/C. Population differentiation was high (GST = 0.657) and the distribution of the mitotypes was geographically highly structured, suggesting at least four genetically distinct ancestral lineages. A cosmopolitan lineage was widely distributed in much of Europe throughout eastern Asia. A previously reported lineage limited to the Iberian Peninsula was confirmed. A new geographically restricted lineage was found confined to Asia Minor. A new lineage was restricted to more northern latitudes in northeastern Europe and the Baltic region.

CONCLUSION

The contribution of the various ancestral lineages to the current distribution of Scots pine was asymmetric and extant endemism reflected the presence of large geographic barriers to migration. The results suggest a complex biogeographical history with glacial refugia shared with temperate plant species in southern European Peninsulas and Asia Minor, and a genetically distinct glacial population located more North. These results confirm recent observations for cold tolerant species about the possible existence of refugial populations at mid-northern latitudes contributing significantly to the recolonization of northern Europe. Thus, Eurasian populations of nordic plant species might not be as genetically homogenous as assumed by simply considering them as offsets of glacial populations located in southern peninsulas. As such, they might have evolved distinctive genetic adaptations during glacial vicariance, worth evaluating and considering for conservation.

Geographic structure in a widespread plant?mycorrhizal interaction: pines and false truffles

Mutualistic interactions are likely to exhibit a strong geographic mosaic in their coevolutionary dynamics, but the structure of geographic variation in these interactions is much more poorly characterized than in host-parasite interactions. We used a cross-inoculation experiment to characterize the scales and patterns at which geographic structure has evolved in an interaction between three pine species and one ectomycorrhizal fungus species along the west coast of North America. We found substantial and contrasting patterns of geographic interaction structure for the plants and fungi. The fungi exhibited a clinal pattern of local adaptation to their host plants across the geographic range of three coastal pines. In contrast, plant growth parameters were unaffected by fungal variation, but varied among plant populations and species. Both plant and fungal performance measures varied strongly with latitude. This set of results indicates that in such widespread species interactions, interacting species may evolve asymmetrically in a geographic mosaic because of differing evolutionary responses to clinally varying biotic and abiotic factors.

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalo grass evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.

Organelle DNA haplotypes reflect crop-use characteristics and geographic origins of Cannabis sativa

Comparative sequencing of cannabis individuals across 12 chloroplast and mitochondrial DNA loci revealed 7 polymorphic sites, including 5 length variable regions and 2 single nucleotide polymorphisms. Simple PCR assays were developed to assay these polymorphisms, and organelle DNA haplotypes were obtained for 188 cannabis individuals from 76 separate populations, including drug-type, fibre-type and wild populations. The haplotype data were analysed using parsimony, UPGMA and neighbour joining methods. Three haplotype groups were recovered by each analysis method, and these groups are suggestive of the crop-use characteristics and geographical origin of the populations, although not strictly diagnostic. We discuss the relationship between our haplotype data and taxonomic opinions of cannabis, and the implications of organelle DNA haplotyping to forensic investigations of cannabis.

Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range-wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (G(ST) = N(ST) = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (G(ST) = 0.362; R(ST) = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (G(ST) > R(ST); and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation-drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.

Rangewide molecular structuring in the Utah sucker (Catostomus ardens)

The Utah sucker (Catostomus ardens) is endemic to the Bonneville Basin and the upper Snake River drainage in western North America, and is thought to hybridize with the federally endangered June sucker (Chasmistes liorus mictus) in Utah Lake (Bonneville Basin). Here we describe the discovery of a major subdivision in Utah suckers (4.5% mitochondrial sequence divergence) between the ancient Snake River drainage and the Bonneville Basin. This boundary has not previously been recognized in Utah suckers based on morphologic variation, but has been recently described in two endemic cyprinids in the region. Populations in valleys east of the Wasatch Mountains in Utah clustered with the Snake River populations, suggesting that these valleys may have had an ancient hydrologic connection to the Snake River. We also found evidence of population isolation within the Bonneville Basin, corresponding to two Pleistocene sub-basins of the ancient Lake Bonneville. In contrast, we found no molecular evidence for deep divergence between Utah suckers and June suckers in Utah Lake or for a history of hybridization between divergent lineages in that population, although we recognize that demographic events may have obscured this signal. These findings suggest that the morphological differences between Utah and June suckers in Utah Lake may be the result of strong, and relatively recent, ecological selection. In summary, morphological and molecular characters seem to vary along different axes in different portions of the range of this taxon, providing an interesting system for studying the contributions of neutral and adaptive variation to species diversity.

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.

A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer

Jack pine (Pinus banksiana Lamb.) is a broadly distributed North American conifer and its current range was covered by the Laurentian ice sheet during the last glacial maximum. To infer about the history and postglacial colonization of this boreal species, range-wide genetic variation was assessed using a new and highly variable minisatellite-like marker of the mitochondrial genome. Among the 543 trees analysed, 14 distinct haplotypes were detected, which corresponded to different repeat numbers of the 32-nucleotide minisatellite-like motif. Several haplotypes were rare with limited distribution, suggesting recent mutation events during the Holocene. At the population level, an average of 2.6 haplotypes and a mean haplotype diversity (H) of 0.328 were estimated. Population subdivision of genetic diversity was quite high with G(ST) and R(ST) values of 0.569 and 0.472, respectively. Spatial analyses identified three relatively homogeneous groups of populations presumably representative of genetically distinct glacial populations, one west and one east of the Appalachian Mountains in the United States and a third one presumably on the unglaciated northeastern coastal area in Canada. These results indicate the significant role of the northern part of the US Appalachian Mountains as a factor of vicariance during the ice age. A fourth distinct group of populations was observed in central Québec where the continental glacier retreated last. It included populations harbouring haplotypes present into the three previous groups, and it had higher level of haplotype diversity per population (H = 0.548) and lower population differentiation (G(ST) = 0.265), which indicates a zone of suture or secondary contact between the migration fronts of the three glacial populations. Introgression from Pinus contorta Dougl. var. latifolia Engelm. was apparent in one western population from Alberta. Altogether, these results indicate that the mitochondrial DNA variation of jack pine is geographically highly structured and it correlates well with large-scale patterns emerging from recent phylogeographical studies of other tree boreal species in North America.

Understanding ploidy complex and geographic origin of the Buchloe dactyloides genome using cytoplasmic and nuclear marker systems

Characterizing and inferring the buffalograss [Buchloe dactyloides (Nutt.) Engelm.] genome organization and its relationship to geographic distribution are among the purposes of the buffalograss breeding and genetics program. This buffalograss study was initiated to: (1) better understand the buffalograss ploidy complex using various marker systems representing nuclear and organelle genomes; (2) determine whether the geographic distribution was related to nuclear and organelle genome variation; and (3) compare the genetic structure of accessions with different ploidy levels. The 20 buffalograss genotypes (15 individuals from each genotype) that were studied included diploid, tetraploid, pentaploid, and hexaploid using nuclear (intersimple sequence repeat (ISSRs), simple sequence repeat (SSRs), sequence related amplified polymorphism (SRAPs), and random amplified polymorphic DNA (RAPDs)) and cytoplasmic markers (mtDNA and cpDNA). There was a significant correlation between the ploidy levels and number of alleles detected using nuclear DNA (ISSR, SSR, and SRAP, r = 0.39, 0.39, and 0.41, P<0.05, respectively), but no significant correlation was detected when mitochondrial (r = 0.17, P<0.05) and chloroplast (r = 0.11, P < 0.05) DNA data sets were used. The geographic distribution of buffalograss was not correlated with nuclear and organelle genome variation for the genotypes studied. Among the total populations sampled, regression analysis indicated that geographic distance could not explain genetic differences between accessions. However, genetic distances of those populations from the southern portion of buffalograss adaptation were significantly correlated with geographic distance (r= 0.48, P<0.05). This result supports the hypothesis that genetic relationship among buffalograss populations cannot be estimated based only on geographic proximity.

Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer

Range-wide genetic variation of black spruce (Picea mariana) was studied using polymerase chain reaction-random fragment length polymorphism markers of the mitochondrial genome. Four polymorphic mitochondrial DNA (mtDNA) loci were surveyed and two or three alleles were detected at each locus, resulting in 10 multilocus mtDNA types or mitotypes. A significant subdivision of population genetic diversity was detected (GST = 0.671; NST = 0.726), suggesting low levels of gene flow among populations. The distribution of mitotypes was not random (NST > GST; P < 0.05) and revealed four partially overlapping zones, presumably representative of different glacial populations. Comparison of the genetic structure derived from mtDNA markers and the colonization paths previously deduced from the fossil and pollen records allow us to infer at least three southern and one northeastern glacial populations for black spruce. The patterns revealed in this study suggest that black spruce shares its biogeographical history with other forest-associated North American species.

Chloroplast and mitochondrial molecular tests identify European x Japanese larch hybrids

Hybrids between European and Japanese larches combine the properties of both parental species (drought resistance, canker resistance, stem straightness) and exhibit a fast growth rate. They are produced in seed orchards, generally by natural pollination. Seeds are collected and used for afforestation as interspecific hybrids. However, there are no convenient tests to assess the interspecific hybrid proportion. In the present study, we developed diagnostic molecular markers suitable for the individual identification of hybrids, whatever their developmental stage. Our strategy involved testing a combination of maternally inherited markers from the mitochondrial genome (mtDNA) and paternally inherited markers from the chloroplast genome (cpDNA). Hybrids were then identified by the presence of a mitochondrial sequence inherited from one parental species and a chloroplast sequence inherited from the other parental species. To achieve this aim, markers discriminating both parental species were first sought. Amplifications of mitochondrial and chloroplast sequences were performed using specific PCR primers. After testing 33 primer pairs in combination with nine restriction enzymes, we detected one mitochondrial marker, f13 which was amplified in Japanese larch and absent in European larch, and one chloroplast marker, ll- TaqI which showed different restriction patterns depending on the species. A restriction fragment of 601 bp was obtained in Japanese larch while two fragments of 120 bp and 481 bp were observed in European larch. These patterns were found in all 197 individuals tested from the two pure species. These markers were then used for the evaluation of the hybrid proportion in a seed lot produced from seed orchards; this was assessed as between 43% and 53% depending on the parental species. The male and female parental species could be determined for each progeny.

Genetic diversity of nuclear and mitochondrial genomes in Pinus parviflora Sieb. & Zucc. (Pinaceae) populations

Genetic diversities of the nuclear and mitochondrial genomes in Pinus parviflora were studied in 16 populations, which were distributed across most of the species' range in Japan. Six mitochondrial DNA haplotypes were identified among the 16 populations. The intrapopulation diversity of allozymes was similar to that of other endemic woody species (H(S)=0.259). Although P. parviflora is distributed in discrete populations, differentiation between these was very low (G(ST)=0.044). In addition, the extent of genetic differentiation between two varieties (var. pentaphylla and var. parviflora) was extremely low (G(VT)=0.001). Intrapopulation diversity of mitochondrial DNA was also very low (H(S)=0.098), but population differentiation was high (G(ST)=0.863). Moreover, the distribution of haplotypes reflected the taxonomic differences between P. parviflora var. pentaphylla and var. parviflora. The populations of var. pentaphylla and var. parviflora contained different haplotypes. Differing modes of inheritance may account for the differences in nuclear and mitochondrial genetic diversity.

Evidence for the existence of some dissociation in an otherwise strong linkage disequilibrium between mitochondrial and chloroplastic genomes in Cyclobalanopsis glauca

Variations in mitochondrial DNA in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst. were studied in 140 trees from 32 populations collected from within the tree's natural range. By sequencing two mitochondrial DNA intron fragments (nad4/3-nad4/4r and nad7/2-nad7/3r), we revealed a total of 1788 bp and five polymorphic sites which allowed us to distinguish six mitotypes. The mitochondrial DNA markers provided replicated data to support population phylogeographical scenarios suggested previously using chloroplastic DNA markers. The gene genealogical tree of mitochondrial DNA was partially congruent with the chloroplastic DNA tree owing to the slower mutation rate and different mutational direction. Significant linkage disequilibrium existed between the two organellar genomes. Further paring analyses between fragments synthesized using different primers, accompanied by exclusion of polymorphic sites, showed that the random association could be attributed specifically to one of the polymorphic sites of the petG-trnP fragment of the chloroplastic genome, and the three polymorphic sites of the nad4/3-nad4/4r fragment of the mitochondrial genome. The former was inferred to derive from paternal leakage, and the latter from recurrent mutation. These polymorphic sites were also responsible for uncoupling of the combined gene tree of mitotype and chlorotype. In conclusion, specific fragments found in this study contribute to the incomplete congruence of the two organellar lineages that otherwise associate well phylogeographically.

Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa)

The evolutionary history of a wild-cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty-two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.

Characterization of a mosaic minisatellite locus in the mitochondrial DNA of Norway spruce [Picea abies (L.) Karst.]

A mosaic minisatellite region has been identified in the mitochondrial genome of Norway spruce (Picea abies). The array was composed of three tandem repeats PaTR1 (32 bp), PaTR2a (26 bp) and PaTR2b (26 bp). PaTR2a and PaTR2b differed by one base substitution. The analysis of 92 trees covering the whole natural distribution area of the species allowed detection of 11 length variants ranging from 131 bp to 447 bp. This high intra-specific polymorphism relies on variation in the number of the tandem repeats. Population genetic parameters estimated among 14 populations suggested high population differentiation (Gst=0.749). The phylogenetic analysis of the 11 sequenced length variants has been performed using a parsimony approach. The topology of the tree showed a good association of groups with geographical origin and a low level of size homoplasy. The phylogenetic reconstruction also suggests that this minisatellite locus has mainly evolved by an increase in the repeat copy number.

Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea

Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect sequence-tagged-site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others ( nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L- orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L- orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.

Wind-dispersed pollen mediates postglacial gene flow among refugia

A long-term genetic legacy of refugial isolation has been postulated and was demonstrated for maternal refugial lineages for numerous plant and animal species. The lineages were assumed to have remained separated from each other for several glacial periods. The conifer Abies alba Miller, silver fir, is an excellent model to test whether pollen-mediated gene flow may eliminate the genetic imprints of Pleistocene refugial isolation. Two DNA markers with contrasting modes of inheritance were applied to 100 populations covering the entire range of silver fir in Europe. The markers exhibited each two highly conserved alleles based on an insertion/deletion of 80 bp in the fourth intron of the mitochondrial nad5 gene and on a synonymous substitution in the chloroplast psbC gene. The geographical distribution of the maternally inherited mitochondrial variation supported the existence of at least two refugia with two recolonizing maternal lineages remaining largely separated throughout the range. The cline of the nad5 allele frequencies was much steeper than the one of the two psbC alleles. The psbC cline was as wide as the whole range of the species. Our results provide striking evidence that even a species with very long generation times and heavy pollen grains was able to establish a highly efficient pollen-mediated gene flow between refugia. Therefore we postulate that an exchange of genetic information between refugia by range-wide paternal introgression is possible in wind-pollinated plant species.

Ascertaining maternal and paternal lineage within Musa by chloroplast and mitochondrial DNA RFLP analyses

In banana, the maternal transmission of chloroplast DNA and paternal transmission of the mitochondrial DNA provides an exceptional opportunity for studying the maternal and paternal lineage of clones. In the present study, RFLP combined with hybridization of heterologous mitochondrial and chloroplastic probes have been used to characterize 71 wild accessions and 131 diploid and 103 triploid cultivated clones. In additon to Musa acuminata and Musa balbisiana, other species from the four Musa sections were studied to investigate their contribution to the origin of cultivated bananas. These molecular analyses enable the classification of the Musa complex to be discussed. Results ascertain relationships among and between the wild accessions and the mono- and interspecific diploid and triploid bananas, particularly for the acuminata genome. Parthenocarpic varieties are shown to be linked to M. acuminata banksii and M. acuminata errans, thus suggesting that the first center of domestication was in the Philippines - New Guinea area.

Mitochondrial DNA diversity, population structure, and gender association in the gynodioecious plant Silene vulgaris

A highly variable mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) locus is used to assess the population structure of mitochondrial genomes in the gynodioecious plant Silene vulgaris at two spatial scales. Thirteen mtDNA haplotypes were identified within 250 individuals from 18 populations in a 20-km diameter region of western Virginia. The population structure of these mtDNA haplotypes was estimated as thetaST = 0.574 (+/- 0.066 SE) and, surprisingly, genetic differentiation among populations was negatively correlated with geographic distance (Mantel r = -0.246, P < 0.002). Additionally, mtDNA haplotypes were spatially clumped at the scale of meters within one population. Gender in S. vulgaris is determined by an interaction between autosomal male fertility restorers and cytoplasmic male sterility (CMS) factors, and seed fitness is affected by an interaction between gender and population sex ratio; thus, selection acting on gender could influence the distribution of mtDNA RFLP haplotypes. The sex ratio (females:hermaphrodites) varied among mtDNA haplotypes across the entire metapopulation, possibly because the haplotypes were in linkage disequilibrium with different CMS factors. The gender associated with some of the most common haplotypes varied among populations, suggesting that there is also population structure in male fertility restorer genes. In comparison with reports of mtDNA variation from other published studies, we found that S. vulgaris exhibits a large number of mtDNA haplotypes relative to that observed in other species.

DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis)

Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species. Analyses provide evidence for an ancestral haplotype and two derived mtDNA haplotypes with distinct regional distributions. An abrupt contact zone between mtDNA haplotypes in the Cascade Range suggests postglacial biogeographic movements. Among three cpSSR loci, 42 haplotypes were detected within 28 cpSSR sample populations that were aggregated into six regions. Analysis of molecular variance (amova) was used to determine the hierarchical genetic structure of cpSSRs. amova and population pairwise comparisons (FST ) of cpSSR, and geographical distribution of mtDNA haplotypes provide insights into historical changes in biogeography. The genetic data suggest that whitebark pine has been intimately tied to climatic change and associated glaciation, which has led to range movements facilitated by seed dispersal by Clark's nutcracker (Nucifraga columbiana Wilson). The two hypotheses proposed to explain the genetic structure are: (i) a northward expansion into Canada and the northern Cascades in the early Holocene; and (ii) historical gene flow between Idaho and the Oregon Cascades when more continuous habitat existed in Central Oregon during the late Pleistocene. Genetic structure and insights gained from historical seed movements provide a basis on which to develop recovery plans for a species that is at risk from multiple threats.

Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes in Silene vulgaris

Both the chloroplast and mitochondrial genomes are used extensively in studies of plant population genetics and systematics. In the majority of angiosperms, the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) are each primarily transmitted maternally, but rare biparental transmission is possible. The extent to which the cpDNA and mtDNA are in linkage disequilibrium is argued to be dependent on the fidelity of co-transmission and the population structure. This study reports complete linkage disequilibrium between cpDNA and mtDNA haplotypes in 86 individuals from 17 populations of Silene vulgaris, a gynodioecious plant species. Phylogenetic analysis of cpDNA and mtDNA haplotypes within 14 individuals supports a hypothesis that the evolutionary histories of the chloroplasts and mitochondria are congruent within S. vulgaris, as might be expected if this association persists for long periods. This provides the first documentation of the evolutionary consequences of long-term associations between chloroplast and mitochondrial genomes within a species. Factors that contribute to the phylogenetic and linkage associations, as well as the potential for intergenomic hitchhiking resulting from selection on genes in one organellar genome are discussed.

Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations

Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost 'ideal' tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction-restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence-tagged-site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (PhiST = 0.59; P < or = 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.

Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNA

To make inferences about the glacial refugia that harboured the limber pine, Pinus flexilis James, we examined the range-wide population structure of mitochondrial DNA (mtDNA) with eight size variants in the second intron of nad1. The data consisted of haplotypes from 704 trees collected from 40 localities. The value of FST for these populations was 0.80, which is a much larger value than has been reported for allozymes and chloroplast DNA (cpDNA) in limber pine, and it suggests that the number of seeds moving among localities per generation is approximately 0.12. Gene flow of this magnitude would allow mutation and subsequent genetic drift to have a substantial impact on the population structure of mtDNA. The majority of the mtDNA haplotypes are restricted to minor portions of the geographical range. The data are consistent with mtDNA differentiation in seven glacial refugia, followed by dispersal out of those refugia.

Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers

We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13 populations were analyzed at 32-36 allozyme loci, using a published data set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were found to be homologous by Southern hybridization in all three species. Using an enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpDNA) library as probes, two fragments of cpDNA origin, and one of mtDNA origin present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene diversity and substantially higher total genetic diversity and population differentiation than did allozyme markers for each species. We performed a simulation study using allozyme data, which showed that the dominant and biallelic nature of RAPD markers could explain the differences observed in differentiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Results of joint phylogenetic analyses of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata pines, and south-to-north migration histories for all three species.Key words: allozymes, dominance, gene diversity, Pinus attenuata, Pinus muricata, Pinus radiata, phylogeny, RAPDs.