Paternal leakage of plastids rescues inter-lineage hybrids in Silene nutans

BACKGROUND AND AIMS

Organelle genomes are usually maternally inherited in angiosperms. However, biparental inheritance has been observed, especially in hybrids resulting from crosses between divergent genetic lineages. When it concerns the plastid genome, this exceptional mode of inheritance might rescue inter-lineage hybrids suffering from plastid-nuclear incompatibilities. Genetically differentiated lineages of Silene nutans exhibit strong postzygotic isolation owing to plastid-nuclear incompatibilities, highlighted by inter-lineage hybrid chlorosis and mortality. Surviving hybrids can exhibit variegated leaves, which might indicate paternal leakage of the plastid genome. We tested whether the surviving hybrids inherited the paternal plastid genome and survived thanks to paternal leakage.

METHODS

We characterized the leaf phenotype (fully green, variegated or white) of 504 surviving inter-lineage hybrids obtained from a reciprocal cross experiment among populations of four genetic lineages (W1, W2, W3 and E1) of S. nutans from Western Europe and genotyped 560 leaf samples (both green and white leaves for variegated hybrids) using six lineage-specific plastid single nucleotide polymorphisms.

KEY RESULTS

A high proportion of the surviving hybrids (≤98 %) inherited the paternal plastid genome, indicating paternal leakage. The level of paternal leakage depended on cross type and cross direction. The E1 and W2 lineages as maternal lineages led to the highest hybrid mortality and to the highest paternal leakage from W1 and W3 lineages in the few surviving hybrids. This was consistent with E1 and W2 lineages, which contained the most divergent plastid genomes. When W3 was the mother, more hybrids survived, and no paternal leakage was detected.

CONCLUSIONS

By providing a plastid genome potentially more compatible with the hybrid nuclear background, paternal leakage has the potential to rescue inter-lineage hybrids from plastid-nuclear incompatibilities. This phenomenon might slow down the speciation process, provided hybrid survival and reproduction can occur in the wild.

Comprehensive analysis of floral scent and fatty acids in nectar of Silene nutans through modern analytical gas chromatography techniques

The aim of this work was to show the potential of multidimensional gas chromatography combined with mass spectrometry and suitable chemometrics means based on untargeted and profiling data analysis to strengthen the information provided by floral scent and nectar fatty acids of four genetically differentiated lineages (E1, W1, W2, and W3) of the nocturnal moth-pollinated herb Silene nutans. Volatile organic compounds emitted by flowers were trapped for a total of 42 samples by in-vivo sampling dynamic head space for analysing floral scent by untargeted approach, while 37 samples of nectar were collected for analysing fatty acids through profiling analysis. The resulting data from floral scent analysis were aligned and compared using a tile-based methodology followed by data mining to access high-level information. Based on floral scent and nectar fatty acid results, it was possible to distinguish E1 from the W lineages, and W3 from W1 and W2. This work puts the bases for a larger study aiming to clarify the existence of prezygotic barriers involved in speciation among lineages of S. nutans, and thus the possible implication of different flower scents and nectar compositions in this phenomenon.

Pollinator sharing between reproductively isolated genetic lineages of Silene nutans

High reciprocal pollination specialization leading to pollinator isolation can prevent interspecific pollen transfer and competition for pollinators. Sharing pollinators may induce mating costs, but it may also increase pollination services and pollen dispersal and offer more resources to pollinators, which may be important in case of habitat fragmentation leading to pollination disruption. We estimated pollen dispersal and pollinator isolation or sharing between two reproductively isolated genetic lineages of Silene nutans (Caryophyllaceae), which are rare and occur in parapatry in southern Belgium, forming two edaphic ecotypes. As inter-ecotypic crosses may lead to pollen wastage and inviable progeny, pollinator isolation might have evolved between ecotypes. Silene nutans is mainly pollinated by nocturnal moths, including nursery pollinators, which pollinate and lay their eggs in flowers, and whose caterpillars feed on flowers and seeds. Pollinator assemblages of the two ecotypes are largely unknown and inter-ecotypic pollen flows have never been investigated. Fluorescent powdered dyes were used as pollen analogues to quantify intra- and inter-ecotypic pollen transfers and seeds were germinated to detect chlorotic seedlings resulting from inter-ecotypic pollination. Nocturnal pollinators were observed using infrared cameras on the field, and seed-eating caterpillars were collected and reared to identify nursery pollinator species. No pollinator isolation was found: we detected long-distance (up to 5 km) inter-ecotypic dye transfers and chlorotic seedlings, indicating inter-ecotypic fertilization events. The rare moth Hadena albimacula, a nursery pollinator specialized on S. nutans, was found on both ecotypes, as well as adults visiting flowers (cameras recordings) as seed-eating caterpillars. However, S. nutans populations harbor different abundance and diversity of seed predator communities, including other rare nursery pollinators, suggesting a need for distinct conservation strategies. Our findings demonstrate the efficiency of moths, especially of nursery pollinators, to disperse pollen over long distances in natural landscapes, so to ensure gene flow and population sustainability of the host plant. Seed-predator specificities between the two reproductively isolated genetic lineages of S. nutans, and pollinator sharing instead of pollinator isolation when plants occur in parapatry, suggest that conservation of the host plant is also essential for sustaining (rare) pollinator and seed predator communities.

The Diversity of Lichenized Trentepohlioid Algal (Ulvophyceae) Communities is Driven by Fungal Taxonomy and Ecological Factors

Trentepohliales are a group of both free-living and lichenized algae, with most diversity occurring in tropical regions. Recent studies showed that the abundance of lichens with a trentepohlioid photobiont has been increasing in temperate habitats, probably because of global warming, which makes them an interesting study case. A detailed molecular study of the diversity of lichenized Trentepohliales, epiphytic as well as epilithic, was performed in three forests of north-western Europe. Additional samples of lichens of the Arthoniales order (associating essentially with a trentepohlioid photobiont) from other European regions and from other continents were also sequenced. A total of 195 algal sequences were obtained. Phylogenetic analyses with rbcL and ITS loci were performed and associations between phylogenetic distances of photobionts and ecological factors (substratum, climate or Wirth indices, mycobiont taxonomy, and geographic location) were tested by variation partitioning and phylogenetic signal analyses. The high number of rbcL algal haplotypes found in some lichens or on different substrata revealed that the Trentepohliales diversity in extratropical regions was underestimated. The phylogenetic patterns showed selectivity of some photobionts in their fungal partner choice and vice-versa, while others were linked with several haplotypes. Photobionts seemed to be less selective than mycobionts. The main factors influencing lichenized algal community were climate and mycobiont species. Coevolution between mycobionts and photobionts as well as switching between free living and lichenized lifestyles appeared to drive the evolution of Trentepohliales and might explain the high cryptic diversity observed, which might be changing in some regions due to climate change.

Assessing Population Genetic Status for Designing Plant Translocations

Assisted gene flow interventions such as plant translocations are valuable complementary techniques to habitat restoration. Bringing new genetic variants can contribute to increasing genetic diversity and evolutionary resilience, counteract inbreeding depression and improve plant fitness through heterosis. Large, highly genetically variable populations are usually recommended as sources for translocation. Unfortunately, many critically endangered species only occur as small populations, which are expected to show low genetic variation, high inbreeding level, paucity of compatible mates in self-incompatible species, and increased genetic divergence. Therefore, assessment of population genetic status is required for an appropriate choice of the source populations. In this paper, we exemplify the different analyses relevant for genetic evaluation of populations combining both molecular (plastid and nuclear) markers and fitness-related quantitative traits. We assessed the genetic status of the adult generation and their seed progeny (the potential translocation founders) of small populations of Campanula glomerata (Campanulaceae), a self-incompatible insect-pollinated herbaceous species critically endangered in Belgium. Only a few small populations remain, so that the species has been part of a restoration project of calcareous grasslands implementing plant translocations. In particular, we estimated genetic diversity, inbreeding levels, genetic structure in adults and their seed progeny, recent bottlenecks, clonal extent in adults, contemporary gene flow, effective population size (Ne), and parentage, sibship and seed progeny fitness variation. Small populations of C. glomerata presented high genetic diversity, and extensive contemporary pollen flow within populations, with multiple parentage among seed progenies, and so could be good seed source candidates for translocations. As populations are differentiated from each other, mixing the sources will not only optimize the number of variants and of compatible mates in translocated populations, but also representativeness of species regional genetic diversity. Genetic diversity is no immediate threat to population persistence, but small Ne, restricted among-population gene flow, and evidence of processes leading to genetic erosion, inbreeding and inbreeding depression in the seed progeny require management measures to counteract these trends and stochastic vulnerability. Habitat restoration facilitating recruitment, flowering and pollination, reconnecting populations by biological corridors or stepping stones, and creating new populations through translocations in protected areas are particularly recommended.

Guidelines for genetic monitoring of translocated plant populations

Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.

Evidence of spontaneous selfing and disomic inheritance in Geranium robertianum

Knowing species' breeding system and mating processes occurring in populations is important not only for understanding population dynamics, gene flow processes, and species' response to climate change, but also for designing control plans of invasive species. Geranium robertianum, a widespread biennial herbaceous species showing high morphological variation and wide ecological amplitude, can become invasive outside its distribution range. A mixed-mating system may be expected given the species' floral traits. However, autonomous selfing is considered as a common feature. Genetic variation and structure, and so population mating processes, have not been investigated in wild populations. We developed 15 polymorphic microsatellite markers to quantify genetic variation and structure in G. robertianum. To investigate whether selfing might be the main mating process in natural conditions, we sampled three generations of plants (adult, F1, and F2) for populations from the UK, Spain, Belgium, Germany, and Sweden, and compared open-pollinated with outcrossed hand-pollinated F2 progeny. The highly positive Wright's inbreeding coefficient (F IS) values in adults, F1, and open-pollinated F2 progeny and the low F IS values in outcross F2 progeny supported autonomous selfing as the main mating process for G. robertianum in wild conditions, despite the presence of attractive signals for insect pollination. Genetic differentiation among samples was found, showing some western-eastern longitudinal trend. Long-distance seed dispersal might have contributed to the low geographic structure. Local genetic differentiation may have resulted not only from genetic drift effects favored by spontaneous selfing, but also from ecological adaptation. The presence of duplicate loci with disomic inheritance is consistent with the hypothesis of allotetraploid origin of G. robertianum. The fact that most microsatellite markers behave as diploid loci with no evidence of duplication supports the hypothesis of ancient polyploidization. The differences in locus duplication and the relatively high genetic diversity across G. robertianum range despite spontaneous autonomous selfing suggest multiple events of polyploidization.

Mixing gene pools to prevent inbreeding issues in translocated populations of clonal species

Assisted gene flow by plant translocations is increasingly implemented for restoring populations of critically endangered species. The success in restoring genetically healthy populations may depend on translocation design, in particular the choice of the source populations. Highly clonal populations may show low genetic diversity despite large census sizes, and disrupted and geitonogamous pollination may result in selfing and inbreeding issues in the offspring intended for translocation. We carried out a genetic monitoring of translocated populations of the clonal Dianthus deltoides using 14 microsatellite markers and quantified fitness traits over two generations (transplants, F1 seed progeny and newly established individuals). Inbreeding levels were higher in the offspring used as transplants than in the adult generation of the source populations, as a result of high clonality and pollination disruption leading to self-pollination. The F1 generation in translocated populations showed high genetic diversity maintained across generations, diminished inbreeding levels, low genetic differentiation, pollen flow and genetic mixing between the four sources. New individuals were established from seed germination. Fitness patterns were a combination of inbreeding depression in inbred transplants and F1 progeny, heterosis in admixed F1 progeny, source population adaptive capacities, phenotypic plasticity, maternal effects and site environmental specificities. The strategy in the translocation design to mix several local sources, combined with large founding population sizes and ecological management has proved success in initiating the processes leading to the establishment of genetically healthy populations, even when source populations are highly clonal with low genetic diversity leading to inbreeding issues in the transplants.

Genetic monitoring of translocated plant populations in practice

Plant translocations allow the restoration of genetic diversity in inbred and depauperate populations and help to prevent the extinction of critically endangered species. However, the successes of plant translocations in restoring genetically viable populations and the possible associated key factors are still insufficiently evaluated. To fill this gap, we carried out a thorough genetic monitoring of three populations of Arnica montana that were created or reinforced by the translocation of plants obtained from seeds of two large natural source populations from southern Belgium. We genotyped nine microsatellite markers and measured fitness quantitative traits over two generations (transplants, F1 seed progeny and newly established F1 juveniles). Two years after translocation, the genetic restoration had been effective, with high genetic diversity and low genetic differentiation across generations, extensive contemporary pollen flow, admixture between seed sources in the F1 generation and recruitment of new individuals from seeds. We detected site, seed source and maternal plant effects on plant fitness. The results also suggest that phenotypic plasticity may favour short-term individual survival and long-term adaptive capacity and enhance the evolutionary resilience of the populations to changing environmental conditions. We found no sign of heterosis or outbreeding depression at early life stages in the F1 generation. Our findings emphasize the importance of the translocation design (700 transplants of mixed sources, planted at high density) as well as the preparatory site management for the successful outcome of the translocations, which maximized flowering, random mating, and recruitment from seeds in the first years after translocation.

Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry

Reproductive isolation can rise either as a consequence of genomic divergence in allopatry or as a byproduct of divergent selection in parapatry. To determine whether reproductive isolation in gynodioecious Silene nutans results from allopatric divergence or from ecological adaptation following secondary contact, we investigated the pattern of postzygotic reproductive isolation and hybridization in natural populations using two phylogeographic lineages, western (W1) and eastern (E1). Experimental crosses between the lineages identified strong, asymmetric postzygotic isolation between the W1 and the E1 lineages, independent of geographic overlap. The proportion of ovules fertilized, seeds aborted, and seeds germinated revealed relatively little effect on the fitness of hybrids. In contrast, hybrid mortality was high and asymmetric: while half of the hybrid seedlings with western lineage mothers died, nearly all hybrid seedlings with E1 mothers died. This asymmetric mortality mirrored the proportion of chlorotic seedlings, and is congruent with cytonuclear incompatibility. We found no evidence of hybridization between the lineages in regions of co-occurrence using nuclear and plastid markers. Together, our results are consistent with the hypothesis that strong postzygotic reproductive isolation involving cytonuclear incompatibilities arose in allopatry. We argue that the dynamics of cytonuclear gynodioecy could facilitate the evolution of reproductive isolation.

Fine-scale genetic structure of the common Primula elatior (Primulaceae) at an early stage of population fragmentation

Many rare species are threatened by habitat fragmentation; however, less is known about effects of fragmentation on common species, despite their potential role in ecosystem productivity and functioning. We identified key factors and processes influencing gene flow in a large population of Primula elatior, a common distylous perennial herb, at an early stage of the fragmentation process, i.e., when fragmentation is taking place. Using 19 allozyme loci, we investigated genetic variation and fine-scale spatial genetic structure (SGS) at seedling and adult life stages in relation to fragmentation history (recent bottlenecks), selection, clonal propagation, sexual reproduction (seed and pollen dispersal, distyly), and patchy structure (patch size, plant density, and morph ratio). The main factors contributing to the strong SGS are seed and (to a lesser extent) pollen dispersal, through a spatial Wahlund effect and biparental inbreeding. Significant differences in allele frequencies between seedlings and adults indicate a temporal Wahlund effect. Patch plant density and biased morph ratio also affect the genetic patterns. Our results show that if P. elatior populations evolve into patchworks of small, isolated remnants, genetic erosion, reduced gene flow, and increased inbreeding can be expected, suggesting that such common plant species might require large population sizes to remain viable.

Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species

Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.