Ecological genetics and seed transfer guidelines for Pinus albicaulis (Pinaceae)

Whitebark pine (Pinus albicaulis Engelm.) has greatly declined throughout its range as a result of introduced disease, fire suppression, and other factors, and climate change is predicted to accelerate this decline. Restoration is needed; however, no information regarding the degree of local adaptation is available to guide these efforts. A seedling common-garden experiment was employed to assess genetic diversity and geographic differentiation (Q(ST)) of whitebark pine for traits involved in growth and adaptation to cold and to determine climatic variables revealing local adaptation. Seedlings from 48 populations were grown for two years and measured for height increment, biomass, root to shoot ratio, date of needle flush, fall and spring cold injury, and survival. Significant variation was observed among populations for most traits. The Q(ST) was low (0.07-0.14) for growth traits and moderate (0.36-0.47) for cold adaptation related traits, but varied by region. Cold adaptation traits were strongly correlated with mean temperature of the coldest month of population origins, while growth traits were generally correlated with growing season length. We recommend that seed transfer for restoration favor seed movement from milder to colder climates to a maximum of 1.9°C in mean annual temperature in the northern portion of the species range, and 1.0°C in the U. S. Rocky Mountains to avoid maladaptation to current conditions yet facilitate adaptation to future climates.     

Development of microsatellite loci for Pinus koraiensis (Pinaceae)

? Premise of the study: Microsatellite markers were developed for Pinus koraiensis to characterize its genetic diversity and understand its population structure. ? Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) Repeats protocol, 20 primer sets were developed in Chinese populations of P. koraiensis. Three of the markers showed polymorphism with two alleles per locus when assessed in a sample of two populations of P. koraiensis from the Changbai Mountain in the Jilin Province of China. Five and three loci were successfully amplified in P. taiwanensis and P. massoniana, respectively. The amplification size of these loci matches those in P. koraiensis. ? Conclusions: These markers may be useful for further investigation of population genetics of P. koraiensis.     

Cone and seed trait variation in whitebark pine (Pinus albicaulis; Pinaceae) and the potential for phenotypic selection

Phenotypic variation among individuals is necessary for natural selection to operate and is therefore essential for adaptive evolution. However, extensive variation within individuals can mask variation among individuals and weaken the potential for selection. Here we quantify variation among and within individuals in female cone and seed traits of whitebark pine (Pinus albicaulis). In many plants, the production of numerous reproductive structures creates the potential for considerable variation within a plant, but these same traits should also undergo strong selection because of their direct link to plant fitness. We found about twice as much variation among individuals (overall mean = 65.3 ± 4.5% SE) than within individuals (overall mean = 34.7 ± 4.5%). One only needs to sample three to five cones per tree to accurately assess variation among trees in most cone and seed traits. The ease at which trees can be assessed helps account for the strong and consistent patterns of phenotypic selection exerted by seed predators and dispersers of whitebark pine and many other conifers. In contrast, the few traits where variation within trees equaled or exceeded that among trees underwent weak if any phenotypic selection.     

Biodiversity of Pinus (Pinaceae) in Mexico: speciation and palaeo-endemism

Mexico, with 43 species of Pinus recognized in the most recent revision for Flora Neotropica, is the richest centre of diversity for the genus. Other centres are California and south-east U.S.A. In comparison, Eurasian pine regions are less diverse. This biogeography, combined with the virtual absence of fossil evidence in Mexico, has led to the consensus that Pinus is a relative newcomer to the region and that 'recent' speciation accounts for its diversity. Phylogenetic analysis indicates that several of the oldest and most primitive members of the genus may have originated in this part of the continent and coexist with the species resulting from more recent radiation.     

Morphological evaluation of the Pinus kesiya complex (Pinaceae)

The main aim of this study is to compare all taxa from the Pinus kesiya complex and related P. tabuliformis using statistical, ordination and discrimination techniques focusing on ten most discriminating morphological traits. Special emphasis was placed on the recently described taxa Pinus densata subsp. tibetica and P. × naxiorum (=P. yunnanensis × P. densata). Population comparisons of the particular main geographic distribution areas of Pinus kesiya, P. densata subsp. tibetica and P. yunnanensis were also conducted separately within each mentioned taxon using the same data. Pinus densata subsp. tibetica proved to be sufficiently morphologically differentiated from subsp. densata as well as from other species of the P. kesiya complex and P. tabuliformis. The recently originating hybrid P. × naxiorum appears to be intermediate between its parents. The unique shrubby taxon P. densata var. pygmaea is clearly closer to P. densata than to P. yunnanensis, to which it has been classified in Chinese floras. Populations of four distant Pinus kesiya geographic distribution areas lack substantial differences that would support the recognition of infraspecific taxa such as subsp. insularis or var. langbianensis. Pinus yunnanensis is very similar to P. kesiya, with only one trait, leaf length, being significantly different.     

Taxonomic Revision of Pinus fujiii (Yasui) Miki (Pinaceae) and Its Implications for the Phytogeography of the Section Trifoliae in East Asia

Pinus trifolia Miki 1939 (Pinaceae) was originally proposed based on seed cones from the upper Miocene of Aichi and Gifu Prefectures, central Japan. However, before the publication of P. trifolia, a different name (Pinus fujiii (Yasui) Miki) was given to a female cone with the same morphology. On the other hand, P. fujiii auct. non (Yasui) Miki has been used for seed cones with different morphologies from Yasui’s holotype, i.e., apophyses arranged in 5:8 parastichies and a perexcentromucronate slightly-pointed umbo. As a result of re-examination on the Miki and Yasui specimens, we concluded that P. trifolia was a synonym for P. fujiii and proposed here Pinus mikii sp. nov. for cones assigned to P. fujiii auct. non (Yasui) Miki. We also emended the diagnosis of P. fujiii based on these specimens. Pinus fujiii is characterized by a large female cone in which the apophyses with a centromucronate prickle-like umbo are arranged in 8:13 parastichies, and deciduous seed wings. These characters suggest that P. fujiii belongs to the section Trifoliae of the subgenus Pinus, which is now restricted to North and Central America and the Caribbean islands. Fossil data suggest that the P. fujiii lineage firstly appeared in Japan around the Eocene/Oligocene boundary. We speculate that the P. fujiii lineage might have moved southward to Japan from a refugium located elsewhere in high-latitude areas in response to the late Eocene cooling event, as occurred with other Trifoliae species in North America.     

Hypotheses for the evolution of dioecy in seed plants

Over the last decade, new hypotheses have been proposed for the evolution of dioecy in plants. Most of the selective mechanisms invoked have been suggested and supported by phylogenetic correlations. Here we review (1) the validity of the correlations (especially in light of recent critiques of the comparative method), and (2) the conformity of the proposed mechanisms to empirical data. None of the hypotheses can be flatly rejected on existing evidence, but the strength of their support varies. Future correlational studies must explicitly consider phylogeny; more importantly, such broad studies should also be supplemented by detailed studies of particular transitions to dioecy (e.g. within genera) - studies of the sort that have clarified analogous issues such as heterostyly.     

Pinus baileyi (section Pinus, Pinaceae) from the Paleogene of Idaho, USA

Pinus baileyi from the Paleogene of Idaho was initially related to the bristlecone pine P. longaeva (subgen. Strobus, sect. Parrya, subsect. Balfourianae) from western North America. Unlike the centromucronate condition in P. longaeva, P. baileyi cones have raised umbos that are excentromucronate, i.e., the mucro positioned in the upper umbo field above the keel. Cone size and scale morphology shows that P. baileyi more closely resembles excentromucronate pines of subsects. Halepenses and Pinus sensu Gernandt et al. (2005, Taxon 54: 29-42), but is most similar to P. resinosa, P. kesiya, and P. massoniana of subsect. Pinus. Morphologically, P. baileyi resembles the fossil species P. princetonensis and P. arnoldii from the Eocene Princeton Chert, British Columbia, Canada. Pinus baileyi extends the western North American range of ovulate cones resembling subsect. Pinus from the middle Eocene of British Columbia, Canada and Washington, USA to the Oligocene of Idaho, USA. Pinus baileyi, and possibly P. princetonensis and P. arnoldii, indicates the presence of early populations of subsect. Pinus-type pines in the western cordillera of North America, raising the possibility that P. resinosa and P. tropicalis may have evolved from this group.     

Allozyme diversity in Pinus virginiana (Pinaceae): intraspecific and interspecific comparisons

Two of the four members of subsection Contortae of the genus Pinus occur in the southeastern United States: Pinus virginiana, which ranges throughout the southern and central Appalachian Mountains, and P. clausa, which is restricted to Florida and southern Alabama. We examined allozyme variation within P. virginiana and genetic relationships between this species and the two varieties of P. clausa (var. clausa and var. immuginata). P. virginiana maintains more genetic diversity at both the species (Hes = 0.139) and population (Hep = 0.128) levels than the other three species in the subsection, which may reflect the combination of its widespread distribution and the absence of cone serotiny. Genetic differentiation among populations in P. virginiana was relatively low (GST = 0.053), but significant contrasts in allozyme frequencies and genetic diversity were apparent between populations to the northwest vs. outheast of the Appalachian Mountains. These regional differences likely resulted initially from historical processes that occurred during the Pleistocene and early Holocene, and have been reinforced by modern selective pressures and barriers to gene flow. The mean genetic distance between populations of P. virginiana and P. clausa (D = 0.071) was greater than that between populations of the two varieties of P. clausa (D = 0.012), which suggests that the two varieties diverged at some point after the separation of the two species.     

Population divergence for heteroblasty in the Canary Island pine (Pinus canariensis, Pinaceae)

A heteroblastic (or vegetative phase) change is an abrupt manifestation in the general heteroblastic development during the ontogeny of plants. The Canary Island pine undergoes an especially marked and delayed heteroblastic change, including both the formation of secondary needles on dwarf shoots and the onset of preformed growth. To assess genetic and environmental effects on the heteroblastic change in this species, we followed plants from 19 populations at a dry site and a wetter site. Comparing juvenile and adult needles from the same individuals, the adult had a significantly lower rate of water loss and higher leaf mass per area. Pooling data from all seed sources, the heteroblastic change took place when plants reached a critical height, on average, at 4 years of age at the dry site and 1 year earlier at the wet site. Within a subsample of individuals of equal size, mortality was significantly higher in juvenile plants than in mature plants. However, the juvenile phase was longer in plants from dry regions when compared to plants from highly productive, wet regions. This apparent contradiction might be explained through differential resource allocation and the cost of sclerophylly and resprouting ability. Considering the life strategy of the Canary Island pine, we interpret the prolonged juvenile phase as an unavoidable trade-off for the high tolerance of adults to harsh environments.     

Variation among individuals in cone production in Pinus palustris (Pinaceae)

? Premise of the study: Reproductive output varies considerably among individuals within plant populations, and this is especially so in cone production of conifers. While this variation can have substantial effects on populations, little is known about its magnitude or causes. ? Methods: We studied variation in cone production for 2 years within a population of Pinus palustris Mill. (longleaf pine; Pinaceae). Using hurdle models, we evaluated the importance of burn treatments, tree size (dbh), canopy status (open, dominant, subordinate), and number of conspecific neighbors within 4 m (N(4)). ? Key results: Cone production of individuals-even after accounting for other variables-was strongly correlated between years. Trees in plots burned every 1, 2, or 5 years produced more cones than those burned every 7 years, or unburned. Larger trees tend to produce more cones, but the large effects of the other factors studied caused substantial scatter in the dbh-cone number relationship. Among trees in the open, dbh had little explanatory power. Subordinate trees with three neighbors produced no cones. ? Conclusions: Tree size alone was a weak predictor of cone production. Interactions with neighbors play an important role in generating reproductive heterogeneity, and must be accounted for when relating cone production to size. The strong between-year correlation, together with the large variance in cone production among trees without neighbors, suggests that still more of the variance may be explainable, but requires factors outside of our study.     

Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome

The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.     

EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): Implications for the evolution of green plants (Viridiplantae)

Background  

The Viridiplantae (land plants and green algae) consist of two monophyletic lineages, the Chlorophyta and the Streptophyta. The Streptophyta include all embryophytes and a small but diverse group of freshwater algae traditionally known as the Charophyceae (e.g. Charales, Coleochaete and the Zygnematales). The only flagellate currently included in the Streptophyta is Mesostigma viride Lauterborn. To gain insight into the genome evolution in streptophytes, we have sequenced 10,395 ESTs from Mesostigma representing 3,300 independent contigs and compared the ESTs of Mesostigma with available plant genomes (Arabidopsis, Oryza, Chlamydomonas), with ESTs from the bryophyte Physcomitrella, the genome of the rhodophyte Cyanidioschyzon, the ESTs from the rhodophyte Porphyra, and the genome of the diatom Thalassiosira.     

Genetic variation of Pinus uncinata (Pinaceae) in the Pyrenees determined with cpSSR markers

The genetic variation within and between 13 populations (385 individuals) of Pinus uncinata was analyzed with ten chloroplast microsatellite markers. Both the infinite allele mutation and stepwise mutation model (SMM) have been applied to the analysis of the genetic structure and the geographical distribution of haplotypic variation. High level of genetic diversity and low but significant differentiation among compared population were found. Three marginal populations, Sierra de Cebollera, Margaride Mountains and Sierra de Gúdar are strongly differentiated from the rest. Mutations following SMM-like process contributed significantly to the regional differentiation. The pattern of genetic structure observed in mountain pine is common in conifers with a wide distribution range. Lack of significant genetic structuring may be a result of a recent fragmentation of a historically larger population and/or interspecific hybridization and introgression. The southernmost populations from the Sierra Cebollera and the Sierra de Gúdar are the most genetically distinct. This suggests a long period of spatial isolation and/or origin from different ancestral populations.     

Contribution to the taxonomy of Pinus uncinata (Pinaceae) based on cone characters

Eight natural populations of Pinus uncinata Ramond from the Spanish Pyrenees, five of P. mugo Turra from the Carpathians, the Sudethians and Abruzzian Apennines, three of P. sylvestris L. from the Central-European Lowland and the Iberian Peninsula and one of P. uliginosa Neumann from SW Poland have been compared biometrically in 16 cone characters. P. uncinata appears the most distant from all other taxa, differing by having the largest and most asymmetric cones and the thickest apophyses with the most prominent umbo. In cone characters, P. mugo is more similar to P. sylvestris than to P. uncinata. Nevertheless, P. mugo and P. sylvestris remain distant from each other in a number of morphological characters examined. P. uliginosa has cones intermediate between the other three taxa and is moreover very variable. The locality of P. uliginosa in the Silesian Lowland may be of a relict character and conserve genes from P. uncinata.     

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton,Pinaceae)

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP–climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.