Biology subjects

Dunning, L. T.

Publications and source records attributed to Dunning, L. T..

18 recordsLinked to original sources

bioRxiv2026

Utilising nuclear encoded plastid DNA to identify donors of grass-to-grass lateral gene transfer

Determining the correct donor species/lineages of grass-to-grass lateral gene transfer (LGT) is vital for deducing specific donor features that could help inform the mechanism of transfer. This requires a dataset spanning a broad range of species to achieve the phylogenetic resolution necessary for precise donor inference. As grass-to-grass LGT often involves the transfer of multi-gene DNA fragments, they can contain additional sequences that allow for accurate orthologous comparisons, such as nuclear DNA of plastid origin (NUPTs). Here we systematically scan for NUPTs in the genomes of four Alloteropsis semialata accessions, whose LGTs have previously been characterised. Using the abundant Panicoideae chloroplast sequences, we reconstruct NUPT phylogenies and infer two lateral acquisitions: one from Paniceae/Digitaria and another from Andropogoneae/Eremochloa adjacent to a previously identified LGT. We then assembled and included an additional 12 Eremochloa chloroplast genomes in the analysis and showed the likely donor was Eremochloa attenuata. Subsequent short-read mapping from E. attenuata to the nuclear region flanking this NUPT showed consistent coverage across the region, including the previously identified LGT, supporting co-transfer. Overall this study highlights the potential for NUPTs to better identify the donors of grass-to-grass LGT.

evolutionary biology↗

bioRxiv2026

Horizontal gene transfer fuels metabolic innovation in the grass Zuloagaea bulbosa

Horizontal gene transfer (HGT) allows the movement of DNA across broad evolutionary distances without sexual reproduction. In grasses, HGT is widespread and although a few horizontally transferred genes (HTG) are adaptive, most are purged over time. Within the adaptive HTG, biosynthetic genes encoding enzymes that act together in the same pathway and physically co-localise in clusters have been reported multiple times. The aims of this study are to test whether HGT is bidirectional in a pair of grass species, maize and Zuloagaea bulbosa, and if HTGs are found more than expected by chance in biosynthetic genes organised in clusters. To achieve this, we firstly generated a phased reference genome for Z. bulbosa. Then we identified 56 candidate horizontally transferred genes, of which 45% were from Andropogoneae, including two likely to be of maize origin. Since transfers from Z. bulbosa to maize were previously described, our results show that HGT is bidirectional, although the balance might not be even. After predicting all biosynthetic gene clusters in the Z. bulbosa genome, we found that HTGs are enriched in biosynthetic genes organised in clusters. This correlation between HGT and gene clustering is likely to be a consequence of selection due to the immediate adaptive benefit a whole pathway can provide. Two of the HTGs from Andropogoneae belong to the benzoxazinoid BGC, which previously underwent an ancestral transfer from Panicoideae into Pooideae. The dynamism of biosynthetic gene clusters, including recurrent horizontal gene transfers, contributes to the extraordinary metabolic diversity present in plants. Significance statementHorizontal gene transfer (HGT) is a significant driver of evolution that is widespread in grasses. In this study, we show for the first time reciprocal transfer of DNA between maize and another Mexican grass, Zuloagaea bulbosa. This result represents a proof of concept of bidirectional HGT which allows for limited, recurrent gene flow among distant species. Furthermore, we show that horizontally transferred genes are enriched for biosynthetic genes organised in biosynthetic gene clusters, regions of the genome that encode for multiple enzymes that act in the same biosynthetic pathway. We hypothesise that the transfer of a complete multi-genic pathway, ready to be used and potentially offering an evolutionary advantage, might promote a predominant retention of gene clusters in comparison with background HGT.

genomics↗

bioRxiv2026

Adaptation to free-living drives loss of beneficial endosymbiosis through metabolic trade-offs

Symbioses are widespread (1) and underpin the function of diverse ecosystems (2-6), but their evolutionary stability is challenging to explain (7,8). Fitness trade-offs between contrasting intracellular and extracellular niches could act to stabilise endosymbioses because adaptation to either niche is predicted to reduce fitness in the alternate niche, thus reinforcing symbiosis (8,9). Here, we experimentally evolved four diverse Chlorella green algal endosymbionts of Paramecium bursaria to free-living conditions supplying either an amino acid, as provisioned by hosts (10,11), or nitrate, as available in freshwater (12), as the sole nitrogen source. Experimental algal populations adapted to free-living environments, generally increasing in population density and cellular chlorophyll content over time. In one of the four endosymbiont strains, adaptation to the nitrate free-living environment, but not the amino acid environments, drove the loss of fitness benefits to the host in reconstituted symbioses. This loss was not associated with reduced ability to grow on host-provisioned amino acids, nor lost ability to release the sugars provisioned to the host (10,13). Genome sequencing of evolved algal lines revealed genomic divergence between nitrate-adapted and amino acid-adapted lines, affecting genes involved with metabolic organisation and intracellular resource transport. Untargeted metabolomic profiling further showed extensive changes to membrane remodelling and turnover in N-evolved lines. Together, our data support a role for metabolic trade-offs driving divergence between contrasting intracellular and extracellular niches, with nitrogen as a key environmental axis driving divergence. Fitness trade-offs may, therefore, be a general, simple mechanism acting to reinforce symbiosis, contributing to evolutionary stability.

evolutionary biology↗

bioRxiv2025

Intracellular niche specialisation drives evolutionary entrapment of endosymbiotic algae

Endosymbiosis underpins the evolution of complex life and the function of diverse ecosystems, but the mechanisms driving the origin and stability of endosymbiosis remain unclear. Fitness trade-offs between intracellular and extracellular niches could drive the emergence of stable endosymbiosis if adaptation to the intracellular niche reduces fitness in the extracellular niche, reinforcing endosymbiosis through niche specialisation by the endosymbiont. We tested this hypothesis by quantifying phenotypic divergence between endosymbiotic and free-living populations of a facultative algal endosymbiont along trait axes predicted to contrast between its intracellular and extracellular lifestyles. Consistent with endosymbiont specialisation, we observed strong divergence involving multiple traits between endosymbiotic and free-living populations. Specifically, endosymbionts showed convergent losses of multiple nitrogen metabolism pathways, increased export of maltose and glucose, increased sensitivity to acidification, higher and less variable photosynthetic efficiency, and reduced free-living growth rate. Intracellular environments are stable, safe from natural enemies, and come with a reliable supply of specific nutrients, but are acidic and place demands upon endosymbionts to provision their hosts; our data suggest that adapting to this niche is likely to reduce free-living growth and survival of endosymbionts. Our findings support fitness trade-offs between contrasting intracellular and extracellular environments as a mechanism stabilising endosymbiosis by driving evolutionary entrapment of niche-specialist endosymbionts.

evolutionary biology↗

bioRxiv2025

Regulatory features determine the evolutionary fate of laterally acquired genes in plants

Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis, putatively functional laterally acquired genes had expression levels significantly more similar to their donor xenolog than to their vertically inherited homolog. This pattern suggests that transferred genes may carry cis-regulatory elements encoded on the fragment of DNA that moves between species, facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor and recipient orthologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation. Significance StatementLateral gene transfer (LGT) can introduce novel traits into plant genomes, yet most transferred genes are only transient residents and are degenerating, with reduced expression, truncation, and elevated DNA methylation. However, a minority persist and are more likely to resemble their donor counterparts in expression, suggesting co-transfer of cis-regulatory elements. These findings indicate that regulatory compatibility is key to their long-term survival.

evolutionary biology↗

bioRxiv2025

Gene turnover and contingency facilitated the repeated evolution of C4 photosynthesis in grasses

SummaryO_LIIn grasses, almost all species belong to two evenly sized clades (BOP and PACMAD), yet the >20 independent origins of C4 photosynthesis in this family only occur in the PACMAD lineage. Here, we identify potential genetic precursors for C4 photosynthesis that were present at the base of the PACMAD clade, representing the last common ancestor of all C4 grasses. C_LIO_LIWe generated the first reference genomes for Aristidoideae species (Aristida adscensionis and Stipagrostis hirtigluma), the sister lineage of all other PACMAD grasses. In combination with 34 other Poales genomes, we identify gene gains at the base of the PACMAD clade, and genes lost in the sister BOP lineage. C_LIO_LICandidate C4 precursors include {beta}-carbonic anhydrase, as well as genes involved in amino acid and nitrate transport, carbon metabolism, oxidative stress management and transcription regulation. C_LIO_LIGene turnover created the necessary genetic contingency, facilitating the independent recruitment and refinement of C4 genes in multiple independent origins. Our results support the idea that the repeated evolution of C4 photosynthesis in PACMAD grasses was not driven by a single genetic event but was instead underwritten by chance genetic changes that originated long before there was selection for the trait itself. C_LI

evolutionary biology↗

bioRxiv2025

Dietary restriction is evolutionary conserved on the phenotypic and mechanistic level

The anti-ageing response of Dietary Restriction (DR) is thought to be an ancient mechanistic response, reasoning from its phenotypic conservation in a wide range of organisms. However, DR is implemented using different diets and methods across species, and evidence for conservation at the mechanistic level remains limited. Here we tested the longevity and fecundity response to DR across eight different species of Drosophila using the same diets in a reaction norm framework. We confirm that DR is phenotypically conserved across Drosophila. Next, we used comparative transcriptomics across six species and found strongly concordant differential expression in response to DR (rs > 0.28, < 0.72, P < 0.0001). We studied the evolutionary history of the top concordantly differentially expressed orthologous genes and identified that the large majority of these genes are "young" genes and are Diptera specific. Our results indicate that large parts of the DR response are likely to be taxonomic specific, suggesting that the genetic basis of DR is not widely conserved. To validate this hypothesis we tested whether the 15 most conserved genes that change in transcription in response to DR using conditional in vivo RNAi. Surprisingly, we found that 12 out of 15 genes tested had a lifespan phenotype, with 9 extending lifespan. Five of these genes are related to cysteine metabolism implicating it in the mechanisms of DR, further suggesting physiological compensation to DR is ubiquitous and providing a possible biomedical target. Our findings suggest that while large parts of the DR response are taxonomically specific, some core mechanisms are conserved across divergent species. The comparative approaches we used here hold promise to identify shared mechanisms relevant to our own species and therefore ultimately anti-ageing interventions.

evolutionary biology↗

bioRxiv2024

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

evolutionary biology↗

bioRxiv2024

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗

bioRxiv2024

Plastic responses to past environments shape adaptation to novel selection pressures

Phenotypic plasticity may pave the way for rapid adaptation to newly encountered environments. Although it is often contested, there is growing evidence that initial plastic responses of ancestral populations to new environmental cues may promote subsequent adaptation. However, we do not know whether plasticity to cues present in the ancestral habitat (past-cue plasticity) can facilitate adaptation to novel cues. Conceivably, this could occur if plastic responses are coincidentally optimal to both past and novel cues (i.e., are pre-adaptive) or if they are transferred to novel cues during adaptation. Past plastic phenotype values could also become fixed and genetically co-opted during adaptation to the new environment. To uncover the role of past-cue plasticity in adaptation, we tested gene expression plasticity responses of two parallel mine-waste adapted Silene uniflora populations and their closest coastal relatives. Plants were exposed to the past and novel-cues of salt and zinc, which revealed that during adaptation to mine-waste plasticity to salt diminishes. Despite this, our results show that ancestral plasticity to salt has a substantial impact on subsequent adaptation to zinc. For a third of genes that have evolved zinc plasticity in mine populations, salt plasticity has been transferred to the zinc response. Furthermore, a quarter of fixed expression differences between mine and coastal populations were similar to ancestral salt responses. Alongside evidence that ancestral plasticity to novel cues can facilitate adaptation, our results provide a clear indication that ancestral past-cue plasticity can also play a key role in rapid, parallel adaptation to novel habitats. Significance StatementThe role of phenotypic plasticity in promoting adaptation is hotly debated, with conflicting evidence for the benefits of ancestral plasticity in newly encountered environments. Here, we present an alternative mode by which ancestral plasticity can promote adaptation. We investigated whether phenotypic plasticity towards environmental cues that are experienced only in ancestral habitats (past-cue plasticity) can significantly contribute towards rapid adaptation to completely distinct cues. We show that, in the maritime plant species, Silene uniflora, past-cue plasticity to salt has made a substantial contribution to rapid adaptation to heavy-metal pollution in newly encountered habitats. This phenomenon has broad implications for the capacity and predictability of species to persist in the face of anthropogenic environmental change.

evolutionary biology↗

bioRxiv2024

Identifying leaf anatomy and metabolic regulators that underpin C4 photosynthesis in Alloteropsis semialata

O_LIC4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species. C_LIO_LIHere, we perform a genome wide association study (GWAS) using the grass Alloteropsis semialata, the only known species to have C3, intermediate, and C4 accessions. We aimed to identify genomic regions associated with the strength of the C4 cycle (measured using {delta}13C), and the development of C4 leaf anatomy. C_LIO_LIGenomic regions correlated with {delta}13C include regulators of C4 decarboxylation enzymes (RIPK), non-photochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW-LIKE). Regions associated with the development of C4 leaf anatomy in the intermediate accessions contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GRF1). C_LIO_LIThe detection of highly correlated genomic regions with a modest sample size indicates that the emergence of C4 photosynthesis in A. semialata required a few loci of large effect. The candidate genes could prove to be relevant for engineering C4 leaf anatomy in C3 species. C_LI

plant biology↗

bioRxiv2022

Variation in the rate lateral gene transfers accumulate in a grass lineage

Lateral gene transfer (LGT) has been reported in multiple eukaryotes. This process seems particularly widespread in the grass family, although we know very little about the underlying dynamics and how it impacts gene content variation within a species. Alloteropsis semialata is a tropical grass, and multiple LGT were detected in a reference genome assembled from an Australian individual. As part of this study we assemble three additional de novo genomes for A. semialata and one for its sister species Alloteropsis angusta. In total we detect 168 LGT across the five reference genomes. Using whole-genome resequencing data for a further 40 individuals we establish the distribution of these transfers and map their origin along the species phylogeny. This shows that many LGTs were acquired relatively recently, with numerous secondary losses. Exponential decay models indicate that the rate of LGT acquisitions varied significantly among lineages [6-28 per Ma], with a high rate of subsequent LGT losses [11-24% per Ma] that largely exceeds that of native loci [0.02-0.8% per Ma]. This high turnover creates large intraspecific structural variants, with a preponderance of LGT occurring as accessory genes in the Alloteropsis pangenome. The acquired genes represent unparalleled genetic novelties, having independently evolved for tens of millions of years before they were transferred. Ultimately, the rapid LGT turnover generates standing variation that can fuel local adaptation.

evolutionary biology↗

bioRxiv2021

Genetic assimilation of ancestral plasticity during parallel adaptation

Phenotypic plasticity in ancestral populations is hypothesised to facilitate adaptation, but evidence supporting its contribution is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel genetic and phenotypic adaptive changes has not been explored. The most general finding is that nearly all ancestral gene expression plasticity is reversed following adaptation, but this is usually examined transcriptome-wide rather than focused on the genes directly involved in adaptation. We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared to ancestral, zinc-sensitive plants. Our experiments show that reinforcement of ancestral plasticity plays an influential role in the evolution of plasticity in derived populations and, surprisingly, one third of constitutive differences between ecotypes are the result of genetic assimilation of ancestral plasticity. Ancestral plasticity also increases the chance that genes are recruited repeatedly during adaptation. However, despite a high degree of convergence in gene expression levels between independently adapted lineages, genes with ancestral plasticity are as likely to have similar expression levels in adapted populations as genes without. Overall, these results demonstrate that ancestral plasticity does play an important role in adaptive parallel evolution, particularly via genetic assimilation across evolutionary replicates.

evolutionary biology↗

bioRxiv2021

Hybridisation and chloroplast capture between ancient Themeda triandra ecotypes in Australia

Ecotypes are distinct populations within a species which are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. A chloroplast phylogeny confirms that Australia was colonised by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of gene-flow among the ecotypes, largely restricted to two geographic areas. In northern Queensland there appears to be a hybrid zone with admixed nuclear genomes and shared plastid haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal plastid and interior clade nuclear genomes. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. A stable hybrid zone in the east, and the displacement of one ecotype in the west, highlights the unpredictable nature of hybrid zones, with repeated contacts between the same ecotypes producing different outcomes.

evolutionary biology↗

bioRxiv2021

Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass

C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4, and C3+C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4-like photosynthetic efficiency in C3+C4 x C4, but not in C3 x C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3+C4 species providing an essential step for C4 evolution.

plant biology↗

bioRxiv2020

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. Here, we found that rapid parallel adaptation to anthropogenic pollution has taken place without geneflow spreading adaptive alleles between populations of the mine ecotype. Across replicate ecotype pairs, we identified shared targets of selection with functions linked to physiological differences between the ecotypes, although the genetic response is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

evolutionary biology↗

bioRxiv2020

Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

O_LIC4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C4 and non-C4 populations. C_LIO_LIUsing phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence in A. semialata. We further establish the genetic origins of polyploids in this species. C_LIO_LIOrganelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated [~] 2-3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4 trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. C_LIO_LILimited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4 physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species. C_LI

evolutionary biology↗

bioRxiv2020

Phylogenetic relatedness, co-occurrence, and rhizomes increase lateral gene transfer among grasses

O_LILateral gene transfer (LGT) has been documented in a broad range of prokaryotes and eukaryotes, and it can promote adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT in the group. C_LIO_LIWe scan the genomes of a diverse set of 17 grass species that span more than 50 million years of divergence and include major crops to identify grass-to-grass protein-coding LGT. C_LIO_LIWe identify LGT in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility amongst close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species with overlapping distributions also occur, pointing to an additional role of biogeography. C_LIO_LIOverall, we show that LGT is a widespread phenomenon in grasses, which has moved functional genes across the entire grass family into domesticated and wild species alike. The dynamics of successful LGT appears to be dependent on both opportunity (co-occurrence and rhizomes) and compatibility (phylogenetic distance). C_LI

evolutionary biology↗