Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae)

Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach)

Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.

Usability of biomonitors in monitoring the change of tin concentration in the air

Air pollution, a pressing global issue, encompasses various harmful elements, with heavy metals being particularly significant pollutants affecting all forms of life. Effective monitoring and regulation of heavy metal concentrations, especially in the atmosphere, is pivotal. Employing trees as biomonitors emerges as a potent tool, particularly in retrospectively assessing long-term heavy metal contamination trends. This study aims to furnish insights into both tin (Sn) pollutants and the most suitable species for monitoring and mitigating such pollution. Within this study's ambit, samples were collected from Pinus pinaster, Cupressus arizonica, Picea orientalis, Cedrus atlantica, and Pseudotsuga menziesii species in Duzce Province. This area, ranked as the fourth-most air-polluted in Europe according to the World Air Pollution Report, was examined to discern changes in Sn concentration across species, organs, orientations, and age groups over the last four decades. The findings revealed varying potentials for Sn accumulation among the species. Specifically, Pinus pinaster and Picea orientalis were identified as suitable species for monitoring Sn pollution, while Cupressus arizonica, Cedrus atlantica, and Pseudotsuga menziesii exhibited potential for reducing Sn pollution.

Common microgeographical selection patterns revealed in four European conifers

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

The evolutionary heritage and ecological uniqueness of Scots pine in the Caucasus ecoregion is at risk of climate changes

Scots pine is one of the most widely occurring pines, but future projections suggest a large reduction in its range, mostly at the southern European limits. A significant part of its range is located in the Caucasus, a global hot-spot of diversity. Pine forests are an important reservoir of biodiversity and endemism in this region. We explored demographic and biogeographical processes that shaped the genetic diversity of Scots pine in the Caucasus ecoregion and its probable future distribution under different climate scenarios. We found that the high genetic variability of the Caucasian populations mirrors a complex glacial and postglacial history that had a unique evolutionary trajectory compared to the main range in Europe. Scots pine currently grows under a broad spectrum of climatic conditions in the Caucasus, which implies high adaptive potential in the past. However, the current genetic resources of Scots pine are under high pressure from climate change. From our predictions, over 90% of the current distribution of Scots pine may be lost in this century. By threatening the stability of the forest ecosystems, this would dramatically affect the biodiversity of the Caucasus hot-spot.

The effects of climate change scenarios on Tilia ssp. in Turkey

Global climate change will cause significant changes in climate parameters, especially temperature increases and changes in precipitation regimes worldwide. Since the life of living things is directly related to climate parameters, this process will inevitably affect all living things. The plants will be the most affected living things from this process because they do not have an effective movement and migration mechanism. Therefore, global climate change will cause significant species and population losses in plants. To minimize the potential loss of species and populations, it is necessary to predetermine the potential changes in species' distribution areas and take necessary actions. Therefore, this study was aimed to determine the distribution areas of three Tilia species (Tilia tomentosa, Tilia cordata, and Tilia platyphyllos), which have economic, ecologic, and social value and show the local distribution in Turkey and to determine how they will be affected by global climate change. Within this scope, nineteen bioclimatic variables, Emberger climate classification, aspect, and topographic altitude variable were used in the modeling process. By modeling the scenarios SSP 245 and SSP 585, the projections were made for 2040, 2060, 2080, and 2100 regarding the areas suitable for the growth of these species and how these areas will change compared to their current situation. The results suggest that the distribution areas of all three Tilia species will change due to climate change, and the area of loss will be 43.5 km² (4%) for T. tomentosa, 9953.6 km² (15%) for T. platyphyllos, and 448.0 km² (19%) for T. cordata. Moreover, a more important point here is that increases and decreases will be observed in their distribution areas, and these changes will occur in a short process and at significant levels. In this case, the migration mechanism that these species will require must be provided by humans.

From allozymes to NGS: population genetics of forest trees in Slovakia in the past 40 years

This review summarizes the development of population genetics and population genomics studies of forest trees in Slovakia during the past 40 years. Various protein and DNA markers have been applied during this period to address several topics in evolutionary genetics and biogeography of trees: allozymes, uniparentally inherited chloroplast and mitochondrial markers, simple sequence repeats and single nucleotide polymorphisms. The main object of studies of phylogeny and postglacial migration were Fagus sylvatica s.l. and eastern-Mediterranean firs (Abies Mill. section Abies), where the divergence of genetic lineages (species and subspecific taxa) in time, as well as colonization of the current ranges during the Holocene were reconstructed. The studies on intraspecific gene flow and homoploid hybridization focused on hybrid swarms Pinus sylvestris/P. mugo and firs. Unusual maternal inheritance of chloroplast DNA was revealed in P. mugo × P. sylvestris crosses. Contrasting geographical structures of hybrid zones were revealed in wind-dispersed vs. animal-dispersed trees. Within the studies of adaptation, signals of selection were identified both in field observations and common-garden experiments on Picea abies, F. sylvatica and A. alba. Perspectives of ongoing research employing next-generation sequencing were shortly outlined.

Needle volatiles as chemophenetic markers in differentiation of natural populations of Abies alba, A. x borisii-regis, and A. cephalonica

Seventeen native fir populations from the presumed zones of natural hybridization in the Balkan Peninsula were analyzed using headspace needle volatiles and GC-MS/FID analyses. The multivariate statistical analyses revealed clear differentiation between populations of Abies alba and A. cephalonica, suggesting that Silver and Greek Fir are characterized by distinct volatile profiles. Three populations from northern and central Greece identified as A. x borisii-regis shared the volatile profiles with both of the supposed parent species, whereby profile frequencies changed clinally along the latitudinal gradient connecting the ranges of parent species. Therefore, observed geographical distribution of volatile entities support the hypothesis that studied A. x borisii-regis populations are of secondary origin, formed by hybridization between A. alba and A. cephalonica. All three populations should be included in conservation projects, as the genetic constitution of these polymorphic fir populations may contain useful genetic variation necessary for survival regarding the future environmental challenges in this area.

The possibility of using Scots pine needles as biomonitor in determination of heavy metal accumulation

One of the biggest problems of modern world is the air pollution which causes the death of millions of people every year. The heavy metals included in the component of air pollution occupy an important position in human health since they could remain intact in nature for a long time and build bioaccumulation, and also some of them are toxic or carcinogenic even at some low concentrations. Even the heavy metals functioning as micronutrient element could create toxic effect for human beings at the high concentrations. For this reason, the determination of the heavy metal concentration has an important role in terms of the detection of risky regions and risky level. One of the primary sources of heavy metals is industrial plants where the heavy metal ores are processed. Those regions might have risks at high level in terms of particular heavy metals. Consequently, it is significant to find out in which level they influence the area around these plants and to what extent the heavy metal pollution is effective. In this study, Ba, Zn, Cd, K, and Na concentrations are determined by analyzing the samples which are taken from 1- and 2-year-old needles of Scots pines (Pinus sylvestris L.) growing in 1 km, 3 km, 10 km and 25 km distances around a processing and mining of magnesite ore in Russia. In the end of the study, it is concluded that generally, the concentrations of heavy metals subject to the study are increasing depending upon the distance, and this increase is quite apparent in some elements, and finally in many points, the concentrations determined in 2-year-old needles have higher levels than 1-year-old needles.

Certain soil characteristics and light conditions of enzyme activities and variance conditional to plant type

Soil is one of the most important factors in plant cultivation, and its content affects plant growth significantly. However, soil composition and characteristics vary depending on the environmental conditions in the area where the soil is located. In this study, urease and catalase enzyme activities in plant soils grown under different shade conditions were examined. The Prunus cerasifera, Tilia tomentosa, Gleditsia triacanthos, Euonymus japonica, and Betula pendula species were grown in five different light conditions during one vegetation period, and the urease and catalase enzyme activities and Ph, EC (mS.cm ̄¹), CaCO₃ (%), OM (%), P (ppm), and K (ppm) changes were examined within the scope of the study. As a result, it was found that characteristics other than Ph, which was the subject of the study, changed to a great extent depending on the plant species and light conditions; however, in the areas where different plant species were grown, the soil characters changed at different levels depending on the light. As a result of the study, the highest values in many characteristics were obtained under 45% and 65% light conditions.

Early diversification and permeable species boundaries in the Mediterranean firs

BACKGROUND AND AIMS

Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate.

METHODS

We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status.

KEY RESULTS

Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages.

CONCLUSIONS

Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

Changes in heavy metal accumulation in some edible landscape plants depending on traffic density

Food scarcity is one of global issues that our world faces today. A significant portion of the world's population has no access to adequate food, and it is stated that approximately 830 million people suffer from chronic famine. This predicament is estimated to grow even further. Many attempts have been made to solve the food problem. Some examples are using new resources which have not been used for dietary purposes up to this point, planting new areas to produce food products, and increasing the potential harvest per an area unit. One of the solution proposals, which has come up recently within this scope, is the term of "edible landscaping", which means the use of edible plants in the landscaping works, and thus maximizing the potential for food security. However, edible landscaping poses a considerable risk. Heavy metal accumulation in plants grown in urban centers can reach to high levels, and consuming these plants will allow these heavy metals a direct access into the human body and wreak havoc to the public health. But since this subject has not been sufficiently studied yet, the extent of such a risk is not accurately determined yet. This study aims to determine the changes of Ni, Co and Mn concentrations depending on traffic density in the leaves, branches, barks and fruits of cherry, plum, mulberry and apple trees growing in areas with dense traffic, low-density traffic and no-traffic zones in Kastamonu province. The results showed that the concentrations of Ni and Co elements increased in many organelles depending on traffic density, and that the heavy metal concentrations in fruits could be very high. This situation indicates that fruit and vegetables grown in industrial zones and urban centers, where heavy metal pollution may be high, can be harmful to the public health if consumed as crops.

Determination of Pb and Mg accumulation in some of the landscape plants in shrub forms

Heavy metals have a separate precaution in the air pollution components as they are not easily deteriorated in nature, they tend to bioaccumulate, they are carcinogenic or poisonous, and they can be toxic even at low concentrations. Therefore, monitoring of heavy metal pollution is of great importance. Plants are frequently used as biomonitors to monitor the heavy metal pollution. However, the heavy metal accumulation capacities of plants can vary considerably depending on the plant species, as well as on the organelle basis and the amount of particulate matter in the environment. It is also very important to determine how much of the heavy metal concentrations found in plants are derived from the plant species and how much from the particulate matter on the organ. In this study, it was aimed to determine the change of heavy metal accumulation in some landscape plants grown in the city center of Kastamonu depending on plant type, plant organism, washing status, and traffic density. For this purpose, leaf and branch samples were collected from individuals of Ligustrum vulgare L., Euonymus japonica Thunb., Biota orientalis L., Juniperus sabina L., Berberis thunbergii DC, Mahonia aquifolium (Pursh) Nutt., and Buxus sempervirens L., which are frequently used in urban landscape designs growing in areas with heavy, low dense, and no traffic. Some of the collected samples were washed, and heavy metal analyses were conducted to determine the amount of Pb and Mg concentrations. It was remarkable that Pb concentration was higher in branches than in the leaves for all the species. And the alteration depending on traffic density on the base of the factors studied was in different proportion depending on the metals.

Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae)

The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.