Biology subjects

Vatanparast, M.

Publications and source records attributed to Vatanparast, M..

8 recordsLinked to original sources

bioRxiv2026

Mapping the distribution of elms in Britain after a century of Dutch elm disease

The establishment of novel pests and pathogens that devastate populations of trees is increasing around the world, giving rise to policy and management decisions about how to restore treescapes. Such decisions may be informed by the example of Dutch elm disease (DED) which caused most mature elms in Europe and North America to be lost in the mid-20th Century. Although affected elms can regenerate, they succumb again after several years. Considerable effort has been made to restore elm through: (1) cloning and breeding of surviving local trees, (2) introduction of resistant Asiatic species, (3) introduction or production of hybrids bred from local and Asiatic species. As trees are planted out into the landscape, it is necessary to record them, and monitor their survival. Here, we compile and map 82,244 elm trees in Britain recorded as 269 distinct elm species, hybrids and cultivars. The vast majority of records are for surviving field elm, English elm and wych elm, which would grow again to maturity if the virulence of the pathogen could be attenuated. The most commonly planted elms were the hybrids: Nanguen (commercial name Lutece), followed by New Horizon, Ademuz, Lobel and Sapporo Autumn Gold, each of which had over 200 occurrences. The current elm-scape of Britain represents much restoration effort and contains considerable genetic diversity.

plant biology↗

bioRxiv2026

Genomic diversity of elm trees for future treescapes

O_LIDutch elm disease has devastated the treescapes of Europe and North America, causing large elm trees to become largely absent. Several decades of work are now coming to fruition with the availability of potentially resistant cultivars for restoration. C_LIO_LIWe analysed genome-wide single-nucleotide polymorphisms derived from whole-genome sequences of more than 200 trees, including elm species, British morphological forms, disease-tolerant Spanish selections and cultivars from several breeding programmes. C_LIO_LIWhile confirming many specimen labels and multigenerational crossing records, our results also revealed unexpected misidentifications and origins of some samples. This included past hybridisation in some resistant selections thought to be pure species. We find that within our samples, field elm (Ulmus minor) is more genetically diverse than wych elm (U. glabra). We show that over ten British elm forms sometimes assigned species epithets fall within the genetic range of U. minor, U. glabra or hybrids. C_LIO_LIWith their exotic parentage, many of the elm cultivars introduced into Britain post-epidemic represent a considerable increase in nucleotide diversity over the still numerically large, native U. minor and U. glabra populations. Currently, the cultivars are being planted mainly as ornamentals. Their long-term arboricultural, adaptive and landscape suitability remains to be demonstrated. C_LI

plant biology↗

bioRxiv2026

Genetic mapping of Dutch elm disease resistance

Dutch elm disease (DED) has killed millions of field elms (Ulmus minor) in Britain and Europe since the 1970s, causing incalculable damage to landscapes and their associated biodiversity. While the species U. minor is highly susceptible to DED, some east Asian and Himalayan species of elm are resistant. These Asiatic species differ in their growth and form to U. minor and cannot fully substitute for it in the landscape. Several breeding programmes have attempted to generate trees that combine DED-resistance with the growth and form of U. minor via hybridisation and back-crossing. These have been partly successful, but further breeding is needed to fully realise these ambitions. Most recently in Britain, a complex resistant hybrid Wingham (FL493) was crossed with a surviving U. minor tree in Tonge Mill, Kent. Sixty progeny from this cross were tested for field resistance to DED and show segregation for this trait. Here, we analyse the genome of these progeny in order to: (1) construct a linkage map of the elm genome, and (2) identify regions of their genome derived from east Asian and Himalayan species that could be associated with DED-resistance. Such knowledge could accelerate future breeding programmes and enhance our understanding of the mechanistic basis of resistance.

genomics↗

bioRxiv2025

European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility

European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by ash dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples, with particular focus on individuals showing low ADB susceptibility. We identified 362,965 structural variants (SVs) present in more than three individuals, including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this reduced the fraction of the genome estimated as dispensable from 35.9% to 8.7%, identifying 3,412 high-confidence dispensable genes, including 141 annotated with gene ontology terms associated with defence response. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This revealed 220 single nucleotide polymorphisms (SNPs) showing allele frequency shifts between healthy and highly damaged pools of individuals that are broadly consistent across the mainly UK seed sources sampled, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

genomics↗

bioRxiv2024

Global distribution of a land plant by means of oceanic dispersal

The geographic range of species is one of the key indicators of their evolutionary success. Unlike animals, most plants are immobile and expand their range primarily through long-distance dispersal (LDD) of seeds. Seeds can be dispersed over very long distances, especially by ocean currents. However, little is understood about the role of ocean currents in LDD and the contribution of land barriers to genetic differentiation on a global scale. To investigate the outermost limits of LDD by ocean currents in land plants, we studied Canavalia rosea (Sw.) DC. (Fabaceae), which is distributed throughout littoral areas of the tropics and subtropics around the world. Our results using DNA sequences from six chloroplast regions and two low-copy nuclear loci from 436 individuals in 37 populations revealed that ocean currents played a crucial role in the species range expansion and maintaining its global distribution despite the constraints by continental barriers. These suggest that the global distribution of C. rosea is the result of recent transoceanic dispersal within and between the Atlantic and Indo-Pacific oceans, while the Isthmus of Panama has prevented gene flow across the American continents. These results highlight the power of oceanic seed dispersal in shaping plant biogeography.

evolutionary biology↗

bioRxiv2023

Comparative Phylogeography of Tree Species in the Hyrcanian Forests, Iran by Genome-wide SNPs

The Hyrcanian forests in Iran are one of the last remaining natural deciduous forests in the world and a UNESCO World Heritage site. We investigated the population genetics of representative indigenous tree species, Acer velutinum Boiss., Fagus orientalis Lipsky, and Quercus castaneifolia C.A. Mey. in northern Iran and also F. orientalis populations in the Euro-Siberian and Colchic sub-regions in northern Turkiye. We used the double-digest RAD-seq method and genotyped 90 populations and 1,589 individuals across the distribution range of the species. Our analyses yielded 1,347, 2,091, and 8,881 genome-wide SNPs from 28 populations of A. velutinum, 32 populations of F. orientalis, and 30 Q. castaneifolia, respectively. Our results revealed higher genetic differentiations among A. velutinum populations than those of F. orientalis and Q. castaneifolia within the Hyrcanian forests. The global FST value was lowest for F. orientalis populations (0.019) and highest for A. velutinum populations (0.12), while the FIS value was negative for A. velutinum (-0.095). Demographic history analysis indicated a bottleneck during the last glacial maximum for the A. velutinum populations with reduced effective population size. The three species showed evidence of population bottlenecks during the Pliocene. Our findings highlight the pronounced genetic divergence among A. velutinum populations in the Hyrcanian forests compared to the other two species, suggesting cryptic speciation. Conversely, F. orientalis and Q. castaneifolia populations demonstrated a reduced level of genetic structure, indicating that species-specific factors, such as pollen production and pollination efficiency, may have influenced the genetic patterns within these species in similar environments. We did not observe significant elevational genetic differentiation within populations of the studied species. Furthermore, the F. orientalis populations from Turkiye exhibited a distinct west-east genetic structure and were highly diverged from the Iranian F. orientalis populations.

evolutionary biology↗

bioRxiv2022

Tracing the origin of Oriental beech stands across Western Europe and reporting hybridization with European beech - implications for assisted gene flow

Human-aided translocation of individuals within the species range, assisted gene flow (AGF), has been suggested as a climate change mitigation strategy, especially for foundational species, such as forest trees. The benefits and risks of AGF largely depend on the genetic divergence between host and donor populations, their rate and direction of hybridization, and the climate distance that the transfer involves. In this study, we explored the use of Oriental beech (Fagus sylvatica subsp. orientalis), growing from Iran to the Balkans, for AGF in populations of European beech (F. sylvatica subsp. sylvatica), which grow throughout Europe and are increasingly affected by climate warming. Using 16 microsatellite loci and samples from 13 and 6 natural populations of Oriental and European beech, respectively, we identified 5 distinct genetic clusters in Oriental beech with a divergence (FST) of 0.15 to 0.25 from European beech. Using this knowledge, we tracked the origin of 11 Oriental beech stands in Western Europe, some established in the early 1900s. In two stands of Greater Caucasus origin, we additionally genotyped offspring and found evidence for extensive hybridization, with 41.3% and 17.8% of the offspring having a hybrid status. Further, climate data revealed a higher degree of seasonality across the Oriental beech growing sites than across the planting sites in Western Europe, with some sites additionally having a warmer and drier climate. Accordingly, in one of these stands, we found evidence that bud burst of Oriental beech occurs four days earlier than in European beech. These results suggest that AGF of Oriental beech could increase the genetic diversity of European beech stands and may even help the introgression of variants that are more adapted to future climatic conditions. Our study showcases an evaluation of the benefits and risks of AGF and calls for similar studies on other native tree species.

evolutionary biology↗

bioRxiv2021

The diversification of Pterocarpus (Leguminosae: Papilionoideae) was influenced by biome-switching and infrequent long-distance dispersal

AimPhenotypes which evolved for dispersal over ecological timescales may lead to significant macroevolutionary consequences, such as infrequent long-distance dispersal and diversification in novel biomes. We aimed to reconstruct the phylogenetic history of Pterocarpus (Leguminosae/ Fabaceae) to assess whether seed dispersal phenotypes and biome switching explain the current biogeographical patterns of this group. LocationPantropical TaxonThe Pterocarpus clade, particularly Pterocarpus (Leguminosae/Fabaceae) MethodsWe sequenced ~300 nuclear loci captured using Angiosperms-353, a genomic bait set for flowering plants, from which we generated a time-calibrated phylogenomic tree. To corroborate this, we also generated a time-calibrated phylogenetic tree from data-mined Sanger-sequencing data. We then collated distribution data and fruit dispersal morphology traits to compare trait-dependent and trait-independent biogeographical models, allowing us to assess whether dispersal traits influenced the spatio-temporal evolution of Pterocarpus. Finally, using the results of these model tests, we estimated the ancestral ranges and biomes of Pterocarpus species to better understand their biogeographical history, and assessed the degree and direction of biome switching over the course of Pterocarpus diversification history. ResultsWe recovered well-supported phylogenetic relationships within Pterocarpus, within which there were two subclades - one Neotropical and the other Palaeotropical. Our divergence date estimates suggested that Pterocarpus largely diversified from around 12 Ma, during the Miocene. Trait-dependent biogeographical models were rejected for both range and biome evolution within Pterocarpus, but models parameterising dispersal were supported. Pterocarpus ancestral node shared a range across the new-world and old-world tropics, followed by divergence into two clades, one palaeotropical and one neotropical. Biome switching occurred most frequently into rainforest and grassland. Main conclusionsOverall, our analyses suggest that Pterocarpus underwent infrequent cross-continental dispersal and establishment into novel biomes. While this was minimally impacted by fruit dispersal syndromes, biome switching precipitated by long-distance dispersal and environmental change have played an important role in diversification within Pterocarpus since the Miocene.

evolutionary biology↗