Evolution in subdivided plant populations: concepts, recent advances and future directions

Natural Populations of Astrocaryum aculeatum Meyer in Amazonia: Genetic Diversity and Conservation

Astrocaryum aculeatum, a palm tree incipiently domesticated from upland ecosystems in the Brazilian Amazon, is especially adapted to anthropized areas. The pulp of the fruit, obtained by extractivism, is consumed fresh by the Amazonian population. The objective of the study is to evaluate the diversity and genetic structure of the natural populations of A. aculeatum, exploited by extractive farmers in Amazonas, Brazil, seeking to suggest conservation and management strategies for this species. A total of 218 plants were sampled in 15 populations in 14 municipalities in the state of Amazonas, evaluated by 12 microsatellite loci. A total of 101 alleles were observed. The means of the observed heterozygosities (H_O = 0.6390) were higher than expected (H_E = 0.557), with high levels of heterozygotes in the populations. The fixation index in the loci and populations was negative. The F_ST (0.07) and AMOVA showed moderate population structure. Bayesian analysis indicated the grouping k = 4 as the most adequate. There is a high genetic diversity in populations, with a moderate genetic structure due to possible historical events, which could be related to the process of subpopulation formation, possibly presenting three historical moments: before and after the beginning of deforestation and today. The conservation and management policies of this species must be carried out at a watershed level.

Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics - and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.

The Genomic Selfing Syndrome Accompanies the Evolutionary Breakdown of Heterostyly

The evolutionary transition from outcrossing to selfing can have important genomic consequences. Decreased effective population size and the reduced efficacy of selection are predicted to play an important role in the molecular evolution of the genomes of selfing species. We investigated evidence for molecular signatures of the genomic selfing syndrome using 66 species of Primula including distylous (outcrossing) and derived homostylous (selfing) taxa. We complemented our comparative analysis with a microevolutionary study of P. chungensis, which is polymorphic for mating system and consists of both distylous and homostylous populations. We generated chloroplast and nuclear genomic data sets for distylous, homostylous, and distylous–homostylous species and identified patterns of nonsynonymous to synonymous divergence (d_N/d_S) and polymorphism (π_N/π_S) in species or lineages with contrasting mating systems. Our analysis of coding sequence divergence and polymorphism detected strongly reduced genetic diversity and heterozygosity, decreased efficacy of purifying selection, purging of large-effect deleterious mutations, and lower rates of adaptive evolution in samples from homostylous compared with distylous populations, consistent with theoretical expectations of the genomic selfing syndrome. Our results demonstrate that self-fertilization is a major driver of molecular evolutionary processes with genomic signatures of selfing evident in both old and relatively young homostylous populations.

Genetic diversity and structure of Saussurea polylepis (Asteraceae) on continental islands of Korea: Implications for conservation strategies and management

Saussurea polylepis Nakai is an herbaceous perennial endemic to Korea and is highly restricted to several continental islands in the southwestern part of the Korean Peninsula. Given its very narrow geographical distribution, it is more vulnerable to anthropogenic activities and global climate changes than more widely distributed species. Despite the need for comprehensive genetic information for conservation and management, no such population genetic studies of S. polylepis have been conducted. In this study, genetic diversity and population structure were evaluated for 97 individuals from 5 populations (Gwanmaedo, Gageodo, Hongdo, Heusando, and Uido) using 19 polymorphic microsatellites. The populations were separated by a distance of 20–90 km. We found moderate levels of genetic diversity in S. polylepis (Ho = 0.42, He = 0.43). This may be due to long lifespans, outcrossing, and gene flow, despite its narrow range. High levels of gene flow (Nm = 1.76, mean Fst = 0.09), especially from wind-dispersed seeds, would contribute to low levels of genetic differentiation among populations. However, the small population size and reduced number of individuals in the reproductive phase of S. polylepis can be a major threat leading to inbreeding depression and genetic diversity loss. Bayesian cluster analysis revealed three significant structures at K = 3, consistent with DAPC and UPGMA. It is thought that sea level rise after the last glacial maximum may have acted as a geographical barrier, limiting the gene flow that would lead to distinct population structures. We proposed the Heuksando population, which is the largest island inhabited by S. polylepis, as a source population because of its large population size and high genetic diversity. Four management units (Gwanmaedo, Gageodo, Hongdo-Heuksando, and Uido) were suggested for conservation considering population size, genetic diversity, population structure, unique alleles, and geographical location (e.g., proximity).

Genetic consequences of being a dwarf: do evolutionary changes in life-history traits influence gene flow patterns in populations of the world's smallest goldenrod?

BACKGROUND AND AIMS

Contrasting life-history traits can evolve through generations of dwarf plant ecotypes, yet such phenotypic changes often involve decreased plant size and reproductive allocation, which can configure seed dispersal patterns and, subsequently, population demography. Therefore, evolutionary transitions to dwarfism can represent good study systems to test the roles of life-history traits in population demography by comparing genetic structure between related but phenotypically divergent ecotypes.

METHODS

In this study, we examined an ecotypic taxon pair of the world's smallest goldenrod (stem height 2.6 cm) in alpine habitats and its closely related lowland taxon (30-40 cm) found on Yakushima Island, Japan. Genetic variation in chloroplast DNA sequences, nuclear microsatellites and genome-wide single-nucleotide polymorphisms were used to investigate 197 samples from 16 populations, to infer the population genetic demography and compare local genetic structure of the ecotypes.

KEY RESULTS

We found a pronounced level of genetic differentiation among alpine dwarf populations, which were much less geographically isolated than their lowland counterparts. In particular, several neighbouring dwarf populations (located ~500 m apart) harboured completely different sets of chloroplast haplotypes and nuclear genetic clusters. Demographic modelling revealed that the dwarf populations have not exchanged genes at significant levels after population divergence.

CONCLUSIONS

These lines of evidence suggest that substantial effects of genetic drift have operated on these dwarf populations. The low-growing stature and reduced fecundity (only 3.1 heads per plant) of the dwarf plants may have reduced gene flow and rare long-distance seed dispersal among habitat patches, although the effects of life-history traits require further evaluation using ecological approaches.

Allele Frequency Changes Provide Evidence for Selection and Identification of Candidate Loci for Survival in Red Clover (Trifolium pratense L.)

Survivor populations of red clover (Trifolium pratense L.) from plots in a field experiment in southern Norway were genetically characterized using genotyping by sequencing, and compared with the original population and each other. Genetic differentiation between populations was characterized on the basis of allele frequencies of single nucleotide polymorphisms (SNPs), using principal component analysis. SNPs that had been under selection, i.e., SNPs with significantly different allele frequencies in survivor populations relative to the original population, or between survivor populations that had received different treatments, were identified by analysis of F _ST values, using BayeScan and a simple and stringent F _ST-based test utilizing replicate populations from the field experiment. In addition, we tested the possibility of pooling DNA samples prior to sequencing, and pooling leaf samples prior to DNA extraction and sequencing, followed by allele frequency estimation on the basis of number of variant reads. Overall, survivor populations were more different from each other than from the original population, indicating random changes in allele frequency, selection in response to local variation in conditions between plots in the field experiment, or sampling error. However, some differentiation was observed between plots sown as pure stands or species mixtures, plots sown at different densities, and plots subjected to different harvesting regimes. Allele frequencies could be accurately estimated from pooled DNA, and SNPs under selection could be identified when leaf samples were pooled prior to DNA extraction. However, substantial sampling error required replicate populations and/or a high number of sampled individuals. We identified a number of chromosomal loci that had been under selection in pure stand plots relative to the original sown population, and loci that had been under differential selection in pure stands of red clover vs. red clover grown in species mixtures. These are all candidate loci for establishment success or persistence in red clover.

Paternity analysis, pollen flow, and spatial genetic structure of a natural population of Euterpe precatoria in the Brazilian Amazon

Euterpe precatoria, known as açaí do Amazonas, is a regionally important palm of the Amazon rainforest for the fruit production through extractive agriculture. Little information is available with regard to genetic diversity, gene flow, and spatial genetic structure (SGS) of açaí populations, which are essential for the use, management, and conservation of genetic resources of the species. This research aimed to assess the genetic diversity, inbreeding level, SGS, and gene flow in four ontogenetic stages of a natural E. precatoria population in the Brazilian Amazon, based on 18 microsatellite loci. The study was carried out in a natural population dispersed in an area of about 10 ha. Leaf tissues of 248 plants were mapped and sampled and classified into four ontogenetic stages: reproductive (59), immature (70), young (60), and seedling (59). Genetic diversity indices were high for all ontogenetic stages. The fixation index (F) for all ontogenetic stages was not significantly different from zero, indicating the absence of inbreeding. A significant SGS was found for all ontogenetic stages (68-110 m), indicating seed dispersal over short distances. Paternity analysis detected pollen immigration of 39.1%, a selfing rate of 4.2%, and a mean pollen dispersal distance within the population of 531 m. The results indicate substantial allele input in the population via pollen immigration, contributing to the maintenance of the genetic diversity of the population. However, within a population, the renewal with new progenies selected from seed plants spaced at least 110 m apart is important to avoid collecting seeds from related plants.

Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb

Background

Due to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range.

Methods

For each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (F_ST) and quantitative (P_ST) genetic differentiation of populations.

Results

The populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed P_ST < F_ST, indicating convergent selection.

Discussion

The variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.

Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long-distance dispersal in North American palms

Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genomewide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognized species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genomewide divergence mediated by multiple effectors.

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)

Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.

Invasions and extinctions through the looking glass of evolutionary ecology

Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Limiting inbreeding in disjunct and isolated populations of a woody shrub

Pollen movements and mating patterns are key features that influence population genetic structure. When gene flow is low, small populations are prone to increased genetic drift and inbreeding, but naturally disjunct species may have features that reduce inbreeding and contribute to their persistence despite genetic isolation. Using microsatellite loci, we investigated outcrossing levels, family mating parameters, pollen dispersal, and spatial genetic structure in three populations of Hakea oldfieldii, a fire-sensitive shrub with naturally disjunct, isolated populations prone to reduction in size and extinction following fires. We mapped and genotyped a sample of 102 plants from a large population, and all plants from two smaller populations (28 and 20 individuals), and genotyped 158-210 progeny from each population. We found high outcrossing despite the possibility of geitonogamous pollination, small amounts of biparental inbreeding, a limited number of successful pollen parents within populations, and significant correlated paternity. The number of pollen parents for each seed parent was moderate. There was low but significant spatial genetic structure up to 10 m around plants, but the majority of successful pollen came from outside this area including substantial proportions from distant plants within populations. Seed production varied among seven populations investigated but was not correlated with census population size. We suggest there may be a mechanism to prevent self-pollination in H. oldfieldii and that high outcrossing and pollen dispersal within populations would promote genetic diversity among the relatively small amount of seed stored in the canopy. These features of the mating system would contribute to the persistence of genetically isolated populations prone to fluctuations in size.

Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)

Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD) were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation.

Cuticular waxes in alpine meadow plants: climate effect inferred from latitude gradient in Qinghai-Tibetan Plateau

Alpine meadow ecosystems are susceptible to climate changes. Still, climate impact on cuticular wax in alpine meadow plants is poorly understood. Assessing the variations of cuticular wax in alpine meadow plants across different latitudes might be useful for predicting how they may respond to climate change. We studied nine alpine meadows in a climate gradient in the east side of Qinghai-Tibetan Plateau, with mean annual temperature ranging from -7.7 to 3.2°C. In total, 42 plant species were analyzed for cuticular wax, averaged 16 plant species in each meadow. Only four plant species could be observed in all sampling meadows, including Kobresia humilis,Potentilla nivea,Anaphalis lacteal, and Leontopodium nanum. The amounts of wax compositions and total cuticular wax in the four plant species varied among sampling meadows, but no significant correlation could be observed between them and temperature, precipitation, and aridity index based on plant species level. To analyze the variations of cuticular wax on community level, we averaged the amounts of n-alkanes, aliphatic acids, primary alcohols, and total cuticular wax across all investigated plant species in each sampling site. The mean annual temperature, mean temperature in July, and aridity index were significantly correlated with the averaged amounts of wax compositions and total cuticular wax. The average chain length of n-alkanes in both plant and soil linearly increased with increased temperature, whereas reduced with increased aridity index. No significant correlation could be observed between mean annual precipitation and mean precipitation from June to August and the cuticular wax amounts and average chain length. Our results suggest that the survival of some alpine plants in specific environments might be depended on their abilities in adjusting wax deposition on plant leaves, and the alpine meadow plants as a whole respond to climate change, benefiting the stability of alpine meadow ecosystem.

Genomic patterns of species diversity and divergence in Eucalyptus

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.

The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations

The transition from outcrossing to selfing is predicted to reduce the genome-wide efficacy of selection because of the lower effective population size (Ne) that accompanies this change in mating system. However, strongly recessive deleterious mutations exposed in the homozygous backgrounds of selfers should be under strong purifying selection. Here, we examine estimates of the distribution of fitness effects (DFE) and changes in the magnitude of effective selection coefficients (Nes) acting on mutations during the transition from outcrossing to selfing. Using forward simulations, we investigated the ability of a DFE inference approach to detect the joint influence of mating system and the dominance of deleterious mutations on selection efficacy. We investigated predictions from our simulations in the annual plant Eichhornia paniculata, in which selfing has evolved from outcrossing on multiple occasions. We used range-wide sampling to generate population genomic datasets and identified nonsynonymous and synonymous polymorphisms segregating in outcrossing and selfing populations. We found that the transition to selfing was accompanied by a change in the DFE, with a larger fraction of effectively neutral sites (Nes < 1), a result consistent with the effects of reduced Ne in selfers. Moreover, an increased proportion of sites in selfers were under strong purifying selection (Nes > 100), and simulations suggest that this is due to the exposure of recessive deleterious mutations. We conclude that the transition to selfing has been accompanied by the genome-wide influences of reduced Ne and strong purifying selection against deleterious recessive mutations, an example of purging at the molecular level.

Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.

Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase F_ST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. F_ST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.

Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait

BACKGROUND AND AIMS

Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST-FST comparison).

METHODS

A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h(2)) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an 'animal model' fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance.

KEY RESULTS

Serotiny showed a significant narrow-sense heritability (h(2)) of 0·20 (credible interval 0·09-0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites.

CONCLUSIONS

Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and supporting the role of fire in generating genetic divergence for adaptive traits.

Is gene flow the most important evolutionary force in plants?

Although theory has demonstrated rather low levels of gene flow are sufficient to counteract opposing mutation, drift, and selection, widespread recognition of the evolutionary importance of gene flow has come slowly. The perceived role of gene flow as an evolutionary force has vacillated over the last century. In the last few decades, new methods and analyses have demonstrated that plant gene flow rates vary tremendously-from nil to very high-depending on the species and specific populations involved, and sometimes over time for individual populations. In many cases, the measured gene flow rates are evolutionarily significant at distances of hundreds and sometimes thousands of meters, occurring at levels sufficient to counteract drift, spread advantageous alleles, or thwart moderate levels of opposing local selection. Gene flow in plants is likely to often act as a cohesive force, uniting individual plant species into real evolutionary units. Also, gene flow can evolve under natural selection, decreasing or increasing. The fact of frequent, but variable, plant gene flow has important consequences for applied issues in which the presence or absence of gene flow might influence the outcome of a policy, regulatory, or management decision. Examples include the unintended spread of engineered genes, the evolution of invasiveness, and conservation. New data-rich genomic techniques allow closer scrutiny of the role of gene flow in plant evolution. Most plant evolutionists now recognize the importance of gene flow, and it is receiving increased recognition from other areas of plant biology as well.

Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana

Plants may escape unfavorable environments by dispersing to new sites, or by remaining in an ungerminated state at a given site until environmental conditions become favorable. There is limited evidence regarding the occurrence, interplay and relative importance of dispersal processes in time and space in plant populations. Thirty-six natural populations of the annual ruderal species Arabidopsis thaliana were monitored over five consecutive years, sampling both seed bank and above-ground cohorts. We show that immigration rates are considerably higher than previously inferred, averaging 1.7% per population yr(-1). On the other hand, almost one-third of the individuals in a given above-ground cohort result from seeds shed 2 or 3 yr back in time in 10 of the studied populations. Populations that disappeared one year were recolonized by regeneration from the seed bank the subsequent year. Thus, dispersal in both time and space is an important contributor to the structuring of genetic variability in natural populations of A. thaliana, where a high dispersal rate in time may partly counteract the homogenizing effects of spatial seed and pollen dispersal.

Adaptations between ecotypes and along environmental gradients in Panicum virgatum

Determining the patterns and mechanisms of natural selection in the wild is of fundamental importance to understanding the differentiation of populations and the evolution of new species. However, it is often unknown the extent to which adaptive genetic variation is distributed among ecotypes between distinct habitats versus along large-scale geographic environmental gradients, such as those that track latitude. Classic studies of selection in the wild in switchgrass, Panicum virgatum, tested for adaptation at both of these levels of natural variation. Here we review what these field experiments and modern agronomic field trials have taught us about natural variation and selection at both the ecotype and environmental gradient levels in P. virgatum. With recent genome sequencing efforts in P. virgatum, it is poised to become an excellent system for understanding the adaptation of grassland species across the eastern half of North America. The identification of genetic loci involved in different types of adaptations will help to understand the evolutionary mechanisms of diversification within P. virgatum and provide useful information for the breeding of high-yielding cultivars for different ecoregions.