Highly clustered mating networks in naturally fragmented riparian tree populations

Understanding how spatial patterns of mating and gene flow respond to habitat loss and geographical isolation is a crucial aspect of forest fragmentation genetics. Naturally fragmented riparian tree populations exhibit unique characteristics that significantly influence these patterns. In this study, we investigate mating patterns, pollen-mediated gene flow, and genetic diversity in relict populations of Frangula alnus in southern Spain by testing specific hypotheses related to the riparian habitat. We employ a novel approach that combines paternity analysis, particularly suited for small and isolated populations, with complex network theory and Bayesian models to predict mating likelihood among tree pairs. Our findings reveal a prevalence of short-distance pollination, resulting in spatially driven local mating clusters with a distinct subset of trees being highly connected in the mating network. Additionally, we observe numerous pollination events over distances of hundreds of metres and considerable pollen immigration. Local neighbourhood density is the primary factor influencing within-population mating patterns and pollen dispersal; moreover, mating network properties reflect the population's size and spatial configuration. Conversely, among-population pollen dispersal is mainly determined by tree size, which influences floral display. Our results do not support a major role of directional pollen dispersal in longitudinal trends of genetic diversity. We provide evidence that long-term fragmented tree populations persist in unique environments that shape mating patterns and impose constraints to pollen-mediated gene flow. Nevertheless, even seemingly strongly isolated populations can maintain functional connectivity over extended periods, especially when animal-mediated mating networks promote genetic diversity, as in this riparian tree species.

Can natural forest expansion contribute to Europe's restoration policy agenda? An interdisciplinary assessment

Natural forest expansion (NFE), that is, the establishment of secondary forest on non-forested land through natural succession, has substantially contributed to the widespread expansion of forests in Europe over the last few decades. So far, EU policies have largely neglected the potential of NFE for meeting policy objectives on restoration. Synthesising recent interdisciplinary research, this paper assesses the challenges and opportunities of NFE in view of contributing to European forest and ecosystem restoration. Specifically, we discuss the potential for supporting climate change mitigation and adaptation, biodiversity conservation, and forestry and economic use, summarize the current knowledge about societal perceptions and the policymaking on NFE, and make policy recommendations to better use the potential of NFE. We conclude that NFE has the potential to contribute to the European restoration policy agenda if local contexts and possible trade-offs are properly considered.

Revegetation through seeding or planting: A worldwide systematic map

Roughly 2 billion ha of land are degraded and in need of ecological restoration worldwide. Active restoration frequently involves revegetation, which leads to the dilemma of whether to conduct direct seeding or to plant nursery-grown seedlings. The choice of revegetation method can regulate plant survival and performance, with economic implications that ultimately feed back to our capacity to conduct restoration. We followed a peer-reviewed protocol to develop a systematic map that collates, describes and catalogues the available studies on how seeding compares to planting in achieving restoration targets. We compiled a database with the characteristics of all retrieved studies, which can be searched to identify studies of particular locations and habitats, objectives of restoration, plant material, technical aspects, and outcomes measured. The search was made in eight languages and retrieved 3355 publications, of which 178 were retained. The systematic map identifies research gaps, such as a lack of studies in the global South, in tropical rainforests, and covering a long time period, which represent opportunities to expand field-based research. Additionally, many studies overlooked reporting on important technical aspects such as seed provenance and nursery cultivation methods, and others such as watering or seedling protection were more frequently applied for planting than for seeding, which limits our capacity to learn from past research. Most studies measured outcomes related to the target plants but avoided measuring general restoration outcomes or economic aspects. This represents a relevant gap in research, as the choice of revegetation method is greatly based on economic aspects and the achievement of restoration goals goes beyond the establishment of plants. Finally, we identified a substantial volume of studies conducted in temperate regions and over short periods (0-5 y). This research cluster calls for a future in-depth synthesis, potentially through meta-analysis, to reveal the overall balance between seeding and planting and assess whether the response to this question is mediated by species traits, environmental characteristics, or technical aspects. Besides identifying research clusters and gaps, the systematic map database allows managers to find the most relevant scientific literature on the appropriateness of seeding vs. planting for particular conditions, such as certain species or habitats.

Masting is uncommon in trees that depend on mutualist dispersers in the context of global climate and fertility gradients

The benefits of masting (volatile, quasi-synchronous seed production at lagged intervals) include satiation of seed predators, but these benefits come with a cost to mutualist pollen and seed dispersers. If the evolution of masting represents a balance between these benefits and costs, we expect mast avoidance in species that are heavily reliant on mutualist dispersers. These effects play out in the context of variable climate and site fertility among species that vary widely in nutrient demand. Meta-analyses of published data have focused on variation at the population scale, thus omitting periodicity within trees and synchronicity between trees. From raw data on 12 million tree-years worldwide, we quantified three components of masting that have not previously been analysed together: (i) volatility, defined as the frequency-weighted year-to-year variation; (ii) periodicity, representing the lag between high-seed years; and (iii) synchronicity, indicating the tree-to-tree correlation. Results show that mast avoidance (low volatility and low synchronicity) by species dependent on mutualist dispersers explains more variation than any other effect. Nutrient-demanding species have low volatility, and species that are most common on nutrient-rich and warm/wet sites exhibit short periods. The prevalence of masting in cold/dry sites coincides with climatic conditions where dependence on vertebrate dispersers is less common than in the wet tropics. Mutualist dispersers neutralize the benefits of masting for predator satiation, further balancing the effects of climate, site fertility and nutrient demands.

Limits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery

The relationships that control seed production in trees are fundamental to understanding the evolution of forest species and their capacity to recover from increasing losses to drought, fire, and harvest. A synthesis of fecundity data from 714 species worldwide allowed us to examine hypotheses that are central to quantifying reproduction, a foundation for assessing fitness in forest trees. Four major findings emerged. First, seed production is not constrained by a strict trade-off between seed size and numbers. Instead, seed numbers vary over ten orders of magnitude, with species that invest in large seeds producing more seeds than expected from the 1:1 trade-off. Second, gymnosperms have lower seed production than angiosperms, potentially due to their extra investments in protective woody cones. Third, nutrient-demanding species, indicated by high foliar phosphorus concentrations, have low seed production. Finally, sensitivity of individual species to soil fertility varies widely, limiting the response of community seed production to fertility gradients. In combination, these findings can inform models of forest response that need to incorporate reproductive potential.

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.

Globally, tree fecundity exceeds productivity gradients

Lack of tree fecundity data across climatic gradients precludes the analysis of how seed supply contributes to global variation in forest regeneration and biotic interactions responsible for biodiversity. A global synthesis of raw seedproduction data shows a 250-fold increase in seed abundance from cold-dry to warm-wet climates, driven primarily by a 100-fold increase in seed production for a given tree size. The modest (threefold) increase in forest productivity across the same climate gradient cannot explain the magnitudes of these trends. The increase in seeds per tree can arise from adaptive evolution driven by intense species interactions or from the direct effects of a warm, moist climate on tree fecundity. Either way, the massive differences in seed supply ramify through food webs potentially explaining a disproportionate role for species interactions in the wet tropics.

Maintaining forest cover to enhance temperature buffering under future climate change

Forest canopies buffer macroclimatic temperature fluctuations. However, we do not know if and how the capacity of canopies to buffer understorey temperature will change with accelerating climate change. Here we map the difference (offset) between temperatures inside and outside forests in the recent past and project these into the future in boreal, temperate and tropical forests. Using linear mixed-effect models, we combined a global database of 714 paired time series of temperatures (mean, minimum and maximum) measured inside forests vs. in nearby open habitats with maps of macroclimate, topography and forest cover to hindcast past (1970-2000) and to project future (2060-2080) temperature differences between free-air temperatures and sub-canopy microclimates. For all tested future climate scenarios, we project that the difference between maximum temperatures inside and outside forests across the globe will increase (i.e. result in stronger cooling in forests), on average during 2060-2080, by 0.27 ± 0.16 °C (RCP2.6) and 0.60 ± 0.14 °C (RCP8.5) due to macroclimate changes. This suggests that extremely hot temperatures under forest canopies will, on average, warm less than outside forests as macroclimate warms. This knowledge is of utmost importance as it suggests that forest microclimates will warm at a slower rate than non-forested areas, assuming that forest cover is maintained. Species adapted to colder growing conditions may thus find shelter and survive longer than anticipated at a given forest site. This highlights the potential role of forests as a whole as microrefugia for biodiversity under future climate change.

Herbivory on the pedunculate oak along an urbanization gradient in Europe: Effects of impervious surface, local tree cover, and insect feeding guild

Urbanization is an important driver of the diversity and abundance of tree-associated insect herbivores, but its consequences for insect herbivory are poorly understood. A likely source of variability among studies is the insufficient consideration of intra-urban variability in forest cover. With the help of citizen scientists, we investigated the independent and interactive effects of local canopy cover and percentage of impervious surface on insect herbivory in the pedunculate oak (Quercus robur L.) throughout most of its geographic range in Europe. We found that the damage caused by chewing insect herbivores as well as the incidence of leaf-mining and gall-inducing herbivores consistently decreased with increasing impervious surface around focal oaks. Herbivory by chewing herbivores increased with increasing forest cover, regardless of impervious surface. In contrast, an increase in local canopy cover buffered the negative effect of impervious surface on leaf miners and strengthened its effect on gall inducers. These results show that-just like in non-urban areas-plant-herbivore interactions in cities are structured by a complex set of interacting factors. This highlights that local habitat characteristics within cities have the potential to attenuate or modify the effect of impervious surfaces on biotic interactions.

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

Forest microclimates and climate change: Importance, drivers and future research agenda

Forest microclimates contrast strongly with the climate outside forests. To fully understand and better predict how forests' biodiversity and functions relate to climate and climate change, microclimates need to be integrated into ecological research. Despite the potentially broad impact of microclimates on the response of forest ecosystems to global change, our understanding of how microclimates within and below tree canopies modulate biotic responses to global change at the species, community and ecosystem level is still limited. Here, we review how spatial and temporal variation in forest microclimates result from an interplay of forest features, local water balance, topography and landscape composition. We first stress and exemplify the importance of considering forest microclimates to understand variation in biodiversity and ecosystem functions across forest landscapes. Next, we explain how macroclimate warming (of the free atmosphere) can affect microclimates, and vice versa, via interactions with land-use changes across different biomes. Finally, we perform a priority ranking of future research avenues at the interface of microclimate ecology and global change biology, with a specific focus on three key themes: (1) disentangling the abiotic and biotic drivers and feedbacks of forest microclimates; (2) global and regional mapping and predictions of forest microclimates; and (3) the impacts of microclimate on forest biodiversity and ecosystem functioning in the face of climate change. The availability of microclimatic data will significantly increase in the coming decades, characterizing climate variability at unprecedented spatial and temporal scales relevant to biological processes in forests. This will revolutionize our understanding of the dynamics, drivers and implications of forest microclimates on biodiversity and ecological functions, and the impacts of global changes. In order to support the sustainable use of forests and to secure their biodiversity and ecosystem services for future generations, microclimates cannot be ignored.

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.

WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees

Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.

Leaf chemical defences and insect herbivory in oak: accounting for canopy position unravels marked genetic relatedness effects

BACKGROUND AND AIMS

Highly controlled experiments document that plant genetic diversity and relatedness can shape herbivore communities and patterns of herbivory. Evidence from the field is, however, scarce and inconsistent. We assessed whether a genetic signal underlying herbivory can be detected in oak woodlands when accounting for variation at smaller (within-tree) and larger (among-stand) scales.

METHODS

We tested relationships between tree genetic relatedness, leaf chemical defences and insect herbivory for different canopy layers in 240 trees from 15 pedunculate oak (Quercus robur) forest stands. We partitioned sources of variability in herbivory and defences among stands, individuals and branches.

KEY RESULTS

Leaf defences, insect herbivory and their relationship differed systematically between the upper and the lower tree canopy. When accounting for this canopy effect, the variation explained by tree genetic relatedness rose from 2.8 to 34.1 % for herbivory and from 7.1 to 13.8 % for leaf defences. The effect was driven by markedly stronger relationships in the upper canopy.

CONCLUSIONS

Our findings illustrate that considerable effects of the host plant genotype on levels of leaf chemical defences and associated insect herbivory can be detected in natural tree populations when within-individual variation is properly accounted for.

Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: Weak differentiation yet distinct associations with water availability

Populations residing near species' low-latitude range margins (LLMs) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographical range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at single nucleotide polymorphisms (SNPs) located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographical structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive F_ST -outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.

ΔTraitSDMs: species distribution models that account for local adaptation and phenotypic plasticity

Improving our understanding of species ranges under rapid climate change requires application of our knowledge of the tolerance and adaptive capacity of populations to changing environmental conditions. Here, we describe an emerging modelling approach, ΔTraitSDM, which attempts to achieve this by explaining species distribution ranges based on phenotypic plasticity and local adaptation of fitness-related traits measured across large geographical gradients. The collection of intraspecific trait data measured in common gardens spanning broad environmental clines has promoted the development of these new models - first in trees but now rapidly expanding to other organisms. We review, explain and harmonize the main findings from this new generation of models that, by including trait variation over geographical scales, are able to provide new insights into future species ranges. Overall, ΔTraitSDM predictions generally deliver a less alarming message than previous models of species distribution under new climates, indicating that phenotypic plasticity should help, to a considerable degree, some plant populations to persist under climate change. The development of ΔTraitSDMs offers a new perspective to analyse intraspecific variation in single and multiple traits, with the rationale that trait (co)variation and consequently fitness can significantly change across geographical gradients and new climates.

Drivers of tree fecundity in pedunculate oak (Quercus robur) refugial populations at the species' southwestern range margin

The current low latitudinal range margins of many extra-tropical plant species consist of small and scattered populations that persist locally in microrefugia. It remains poorly understood how their refugial distribution affects mating patterns and reproductive success. Here we examine flower and acorn production and their determinants in refugial populations of the widespread European forest tree pedunculate oak (Quercus robur). We monitored male flower, female flower and acorn production in 159 adult trees from 12 oak stands over 2 years. We related these and derived parameters to a series of ecological and genetic predictor variables extrinsic (stand size, density and isolation as well as elevation, topography and forest cover) or intrinsic (size, phenology and several genotypic measures) to the target tree. Tree fertility was unrelated to extrinsic factors but determined by tree size, although we detected size-independent variation in reproductive investment. Female flower number accurately predicted acorn crop size. Fruit set differed between years, evidencing the existence of pollen limitation at the landscape but not at the local scale. Fruit set also tended to increase with the number of mates of the target tree. We detected no other evidence for genetic constraints on mating. Reproduction was triggered by a combination of small-scale and landscape-scale drivers. Although short-distance mating prevailed, limited pollen flow did not appear to significantly constrain reproductive success. The high intrinsic ability of populations to maintain their reproductive capacity may help explain their successful long-term persistence in an adverse broader environment.

Climate refugia: joint inference from fossil records, species distribution models and phylogeography

Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.

Efficient mitigation of founder effects during the establishment of a leading-edge oak population

Numerous plant species are shifting their range polewards in response to ongoing climate change. Range shifts typically involve the repeated establishment and growth of leading-edge populations well ahead of the main species range. How these populations recover from founder events and associated diversity loss remains poorly understood. To help fill this gap, we exhaustively investigated a newly established population of holm oak (Quercus ilex) growing more than 30 km ahead of the nearest larger stands. Pedigree reconstructions showed that plants belong to two non-overlapping generations and that the whole population originates from only two founder trees. The four first-generation trees that have reached maturity showed disparate mating patterns despite being full-sibs. Long-distance pollen immigration was notable despite the strong isolation of the stand: 6 per cent gene flow events in acorns collected on the trees (n = 255), and as much as 27 per cent among their established offspring (n = 33). Our results show that isolated leading-edge populations of wind-pollinated forest trees can rapidly restore their genetic diversity through the interacting effects of efficient long-distance pollen flow and purging of inbred individuals during recruitment. They imply that range expansions of these species are primarily constrained by initial propagule arrival rather than by subsequent gene flow.

Conserving biodiversity under climate change: the rear edge matters

Modern climate change is producing poleward range shifts of numerous taxa, communities and ecosystems worldwide. The response of species to changing environments is likely to be determined largely by population responses at range margins. In contrast to the expanding edge, the low-latitude limit (rear edge) of species ranges remains understudied, and the critical importance of rear edge populations as long-term stores of species' genetic diversity and foci of speciation has been little acknowledged. We review recent findings from the fossil record, phylogeography and ecology to illustrate that rear edge populations are often disproportionately important for the survival and evolution of biota. Their ecological features, dynamics and conservation requirements differ from those of populations in other parts of the range, and some commonly recommended conservation practices might therefore be of little use or even counterproductive for rear edge populations.

Isolation and characterization of 20 microsatellite loci for laurel species (Laurus, Lauraceae)

PREMISE OF THE STUDY

Microsatellite primers were developed for the evergreen tree Laurus to investigate population genetic structure and patterns of gene flow via animal-dispersed pollen and seeds.

METHODS AND RESULTS

Twenty polymorphic nuclear microsatellite markers were developed using CA, GA, AAC, and ATG n-enriched genomic libraries. Given the tetraploidy of the sampled populations, we analyzed our data both as dominant loci and as codominant genotypic data to calculate allele frequencies and genetic diversity. A total of 196 and 222 alleles were found in 37 Mediterranean (L. nobilis) and 26 Macaronesian islands (L. azorica) individuals, respectively.

CONCLUSIONS

Levels of polymorphism of the reported markers are adequate for studies of diversity and parentage in natural populations of this Tertiary relict tree.

Isolation and characterization of 16 polymorphic microsatellite loci for Frangula alnus (Rhamnaceae)

We report the first 16 polymorphic nuclear microsatellite markers developed for Frangula alnus (Rhamnaceae). Markers were tested on all three subspecies as well as on three local populations, including analyses of both leaf and seed endocarps. A total of 87 alleles were found (mean number of alleles per locus was 5.44) for 72 individuals genotyped. Observed and expected heterozygosities ranged from 0.097 to 0.792 and from 0.093 to 0.794, respectively. The levels of polymorphism and exclusionary power of the developed markers render them applicable for parentage analyses and measurements of seed dispersal through direct comparison of endocarps and adult tree genotypes.

Phylogeography of North African Atlas cedar (Cedrus atlantica, Pinaceae): Combined molecular and fossil data reveal a complex Quaternary history

Northwest Africa is a major hotspot of plant biodiversity, but very little is known about the Quaternary range dynamics of plant species in this region. Here we investigate the range-wide population structure and phylogeography of Atlas cedar (Cedrus atlantica), an emblematic forest tree endemic to Morocco and Algeria. We genotyped 261 individuals from 11 populations using AFLP markers. Data were analyzed using both conventional F(ST)-based techniques and Bayesian clustering. Overall population differentiation was high (F(ST) = 0.25). Two major groups of populations were identified, one distributed through the Rif and Middle Atlas mountains in Morocco and the other through the Algerian Tell Atlas and Aurès mountains as well as the Middle Atlas. Combined molecular and fossil data indicate that C. atlantica survived the Last Glacial Maximum in at least three disjunct refugia along the coast of the Mediterranean Sea, whereas the Middle Atlas, today the core of the species range, has been colonized relatively recently (<10000 yr BP). The colonization history of individual populations has left clear imprints in their present-day diversity, which may vary greatly even between nearby stands. Our study illustrates how integrating different data sources and analytical approaches can help elucidate complex range dynamics that would otherwise remain undeciphered.

Ever deeper phylogeographies: trees retain the genetic imprint of Tertiary plate tectonics

Changes in species distributions after the last glacial maximum (c. 18 000 years bp) are beginning to be understood, but information diminishes quickly as one moves further back in time. In this issue of Molecular Ecology, Magri et al. (2007) present the fascinating case of a Mediterranean tree species whose populations preserve the genetic imprints of plate tectonic events that took place between 25 million years and 15 million years ago. The study provides a unique insight into the pace of evolution of trees, which, despite interspecific gene flow, can retain a cohesive species identity over timescales long enough to allow the diversification of entire plant and animal genera.

Can population genetic structure be predicted from life-history traits?

Population genetic structure is a key parameter in evolutionary biology. Earlier comparative studies have shown that genetic structure depends on species ecological attributes and life-history traits, but species phylogenetic relatedness had not been accounted for. Here we reevaluate the relationships between genetic structure and species traits in seed plants. Each species is characterized by a set of life-history and ecological features as well as by its geographic range size, its heterozygote deficit, and its genetic structure at nuclear and organelle markers to distinguish between pollen- and seed-mediated gene flow. We use both a conventional regression approach and a method that controls for phylogenetic relationships. Once phylogenetic conservatism and covariation among traits are taken into account, genetic structure is shown to be related with only a few synthetic traits, such as mating system for nuclear markers and seed dispersal mode or geographic range size for organelle markers. Along with other studies on invasiveness or rarity, our work illustrates the fact that predicting the fate of species across a broad taxonomic assemblage on the basis of simple traits is rarely possible, a testimony of the highly contingent nature of evolution.

Can Population Genetic Structure Be Predicted from Life‐History Traits?

Population genetic structure is a key parameter in evolutionary biology. Earlier comparative studies have shown that genetic structure depends on species ecological attributes and life-history traits, but species phylogenetic relatedness had not been accounted for. Here we reevaluate the relationships between genetic structure and species traits in seed plants. Each species is characterized by a set of life-history and ecological features as well as by its geographic range size, its heterozygote deficit, and its genetic structure at nuclear and organelle markers to distinguish between pollen- and seed-mediated gene flow. We use both a conventional regression approach and a method that controls for phylogenetic relationships. Once phylogenetic conservatism and covariation among traits are taken into account, genetic structure is shown to be related with only a few synthetic traits, such as mating system for nuclear markers and seed dispersal mode or geographic range size for organelle markers. Along with other studies on invasiveness or rarity, our work illustrates the fact that predicting the fate of species across a broad taxonomic assemblage on the basis of simple traits is rarely possible, a testimony of the highly contingent nature of evolution.

Fecundity limits in Frangula alnus (Rhamnaceae) relict populations at the species? southern range margin

The geographic range of many temperate plant species is constrained by climate, but it remains little known how climate affects population performance at low-latitude range margins. This study investigated the reproduction of the Eurasian tree Frangula alnus in relict populations near its southwestern range limit in southern Spain. The aim was to identify the principal stages and causes of ovule loss experienced by these marginal populations. More than 6,800 flowers were monitored over 2 years, insect observations and different experiments were carried out to assess levels of pollen and resource limitation, as well as the influence of flowering phenology on seed production. Most ovule losses occurred during flower anthesis and were due to strong cross-pollen limitation. Fruit set was affected by tree size, light regime and flowering phenology, probably through their effects on pollinator behaviour. Fruit set was almost zero throughout the first half of the flowering season. Then it increased paralleling changes in pollinator abundance but was soon overridden by increasing ovule desiccation due to summer drought. Successful seed production was mostly confined to a brief period near the end of the flowering season. Adverse weather during this period in the second study year resulted in a threefold bud and flower mortality and a 50% decrease of fruit production. Spring rainfalls in southwestern Spain have diminished more than 30% through past decades leading to an earlier onset of summer drought. This trend and its adverse effects on seed production may contribute to explaining the recent decline of F. alnus at its southwestern range limit.

INVITED REVIEW: Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations

Plants offer excellent models to investigate how gene flow shapes the organization of genetic diversity. Their three genomes can have different modes of transmission and will hence experience varying levels of gene flow. We have compiled studies of genetic structure based on chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear markers in seed plants. Based on a data set of 183 species belonging to 103 genera and 52 families, we show that the precision of estimates of genetic differentiation (G(ST)) used to infer gene flow is mostly constrained by the sampling of populations. Mode of inheritance appears to have a major effect on G(ST). Maternally inherited genomes experience considerably more subdivision (median value of 0.67) than paternally or biparentally inherited genomes (approximately 0.10). G(ST) at cpDNA and mtDNA markers covary narrowly when both genomes are maternally inherited, whereas G(ST) at paternally and biparentally inherited markers also covary positively but more loosely and G(ST) at maternally inherited markers are largely independent of values based on nuclear markers. A model-based gross estimate suggests that, at the rangewide scale, historical levels of pollen flow are generally at least an order of magnitude larger than levels of seed flow (median of the pollen-to-seed migration ratio: 17) and that pollen and seed gene flow vary independently across species. Finally, we show that measures of subdivision that take into account the degree of similarity between haplotypes (N(ST) or R(ST)) make better use of the information inherent in haplotype data than standard measures based on allele frequencies only.

Rangewide phylogeography of a bird‐dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical structure, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and temperate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long-term historical continuity has allowed them to maintain a unique store of genetic variation.

Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a dense and complex structure of five genes

Performed within the framework of the sequencing of the 356-kb MHC class I distal region, systematic bioinformatic annotation and preliminary experiments conducted on the whole sequence indicate a high level and a complex pattern of expression. In this paper, we analyze a particular stretch of 69 kb centromeric to the HLA-J gene, in which we identify 21 different mRNAs mainly expressed in testis, and characterize five different transcription units, HZFw, HZFc, HCGV, HTEX6, and HTEX4. These tightly linked genes form a cluster conserved between human and mouse and displaying a high gene density of about one every 14 kb. Alternative splicing processes are observed for all the genes, together with an alternative polyadenylation event for gene HTEX4, sense/antisense mRNA overlaps for HZFw and HZFc, for HZFw and HCGV at their 3' end, and for HTEX6 and HTEX4 at their 5' end. This complex genomic structure suggests a mechanism of coregulation by cis-interaction in gene expression.

A 356-Kb sequence of the subtelomeric part of the MHC Class I region

The subtelomeric part of the MHC Class I region contains 11 of the 21 genes described on chromosome 6 at position 6p21.3. The general organization of those and other genes resident in the region was revealed by determining a 356,376 bp sequence. Potential exons for new genes were identified by computer analysis and a large number of ESTs were selected by testing the sequence by the BLAST algorithm against the GenBank nonredundant and EST databases. Most of the ESTs are clustered in two regions. In contrast, the whole HLA-gene region is crammed with LINE and SINE repeats, fragments of genes and microsatellites, which tends to hinder the identification of new genes.

Sequence analysis of two genomic regions containing the KIT and the FMS receptor tyrosine kinase genes

The KIT and FMS tyrosine kinase receptors, which are implicated in the control of cell growth and differentiation, stem through duplications from a common ancestor. We have conducted a detailed structural analysis of the two loci containing the KIT and FMS genes. The sequence of the approximately 90-kb KIT locus reveals the position and size of the 21 introns and of the 5' regulatory region of the KIT gene. The introns and the 3'-untranslated parts of KIT and FMS have been analyzed in parallel. Comparison of the two sequences shows that, while introns of both genes have extensively diverged in size and sequence, this divergence is, at least in part, due to intron expansion through internal duplications, as suggested by the discrete extant analogies. Repetitive elements as well as exon predictions obtained using the GRAIL and GENEFINDER programs are described in detail. These programs led us to identify a novel gene, designated SMF, immediately downstream of FMS, in the opposite orientation. This finding emphasizes the gene-rich characteristic of this genomic region.

Systematic sequencing of the human HLA-A/HLA-F region: establishment of a cosmid contig and identification of a new gene cluster within 37 kb of sequence

The class I region of the human histocompatibility complex is characterized by a high density of genes and pseudogenes and a complex structural organization. To elucidate the complete structure of the HLA-A/HLA-F region with a view to defining its contents in genes and pseudogenes, we developed a strategy of systematic sequencing. This report describes the establishment of a cosmid contig spanning most of the region and the analysis of a 37-kb sequence from one of the cosmids. Four new genes, organized with the HCG-V gene in a clustered structure, have been identified. Two of these contain a zinc finger motif characteristic of DNA-binding proteins. The former, a member of the C3HC4 protein family, is highly expressed in prostate and contains a B30-2-like sequence identified in several genes mapped within the class I region. The latter, which is ubiquitously expressed, is the human equivalent of the yeast polymerase IA12.2 subunit and of the murine tctex6 gene. Of the two other genes, one remains an anonymous gene with no particular feature, while the fourth, specifically expressed in testis, is the human equivalent of the murine tctex4 gene. This cluster, located in a region corresponding to a syntenic unit between mouse and human, appears to be highly conserved.