Biology subjects

Allaby, R. G.

Publications and source records attributed to Allaby, R. G..

11 recordsLinked to original sources

bioRxiv2026

Reticulate evolution and climate driven diversification shaped the origin and geographic structure of Linum bienne

[vrecto] Hybridization, incomplete lineage sorting and climatic oscillations can interact across evolutionary timescales, but their combined effects on plant diversification remain difficult to resolve. We investigated how these processes shaped the origin and geographic structure of Linum bienne, the putative progenitor of cultivated flax. [vrecto]We integrated genus-level Angiosperms353 phylogenomics across Linum with plastome analyses, low-depth nuclear resequencing, demographic inference and environmental niche modelling across the range of L. bienne. This framework allowed us to assess phylogenetic discordance, test for reticulation and reconstruct lineage history through time. [vrecto]Phylogenetic discordance was widespread across our genus-level sampling and largely consistent with incomplete lineage sorting. However, branch-length and maximum-likelihood network analyses detected additional signal of gene flow at the node including L. bienne, cultivated flax and the closest relatives. Within L. bienne, plastid and nuclear data recovered four geographically structured lineages across the species range, with cytonuclear discordance and demographic analyses supporting repeated secondary contact. [vrecto]Our results show that the evolutionary history of L. bienne reflects the interaction between deep reticulation, incomplete lineage sorting and Pleistocene range dynamics. This multiscale perspective highlights L. bienne as a genetically complex species and illustrates how reticulate evolution and climatic change can jointly shape plant diversification.

evolutionary biology↗

bioRxiv2025

A depositional taphonomy model for sedimentary ancient DNA based on biotic profiles of contrasting sedimentation regimes

Sedimentary ancient DNA (sedaDNA) has become an important tool in Quaternary Science, but still little is understood of its taphonomy and whether sedaDNA represents the local vicinity or originates from distant sources. Here we show key insights can be made about the origins of sedaDNA by integrating sedimentological and sedaDNA data into a sediment influx depositional model. We reconstruct contrasting taphonomic regimes of lacustrine, alluvial, terrestrial and permafrost systems. Lacustrine systems show signals of regional catchment sources of sedaDNA, while alluvial, terrestrial and permafrost systems show a greater influence of DNA from the immediate local environment. However, there is a prevalence of mixed ecosystem signals which may span a broad temporal timeframe if sediment reworking has occurred. The ability to distinguish between local and distal sources of sedaDNA is of major importance in the interpretation of taxonomic profiles to reconstruct palaeoenvironments.

ecology↗

bioRxiv2021

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Asian rice (Oryza sativa L.) is consumed by more than half of the worlds population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering. Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.

plant biology↗

bioRxiv2021

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for designing new approaches in crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

evolutionary biology↗

bioRxiv2020

A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication

Most models of selection incorporate some notion of environmental degradation where the majority of the population becomes less fit with respect to a character resulting in pressure to adapt. Such models have been variously associated with an adaptation cost, the substitution load. Conversely, adaptative mutations that represent an improvement in fitness in the absence of environmental change have generally been assumed to be associated with negligible cost. However, such adaptations could represent a competitive advantage that diminishes resource availability for others and so induces a cost. This type of adaptation in the form of seedling competition has been suggested as a mechanism for increases in seed size during domestication, a trait associated with the standard stabilizing selection model. We present a novel cost framework for competitive selection that demonstrates significant differences in behaviour to environmental based selection in intensity, intensity over time and directly contrasts to the expectations of the standard model. Grain metrics of nine archaeological crops fit a mixed model in which episodes of competitive selection often emerge from shifting optimum episodes of stabilizing selection, highlighting the potential prevalence of the mechanism outlined here and providing a fundamental insight into the factors driving domestication.

evolutionary biology↗

bioRxiv2020

Multi-proxy evidence for the impact of the Storegga Slide Tsunami on the early Holocene landscapes of the southern North Sea

Doggerland was a land mass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British land mass from the rest of Europe. The Storegga Slide, which triggered a tsunami reflected in sediment deposits in the Northern North Sea, North East coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed because to date no direct evidence for the event has been recovered from the southern North Sea. We present evidence that Storegga associated deposits occur in the southern North Sea. Palaeo-river systems have been identified using seismic survey in the southwestern North Sea and sedimentary cores extracted to track the Mid Holocene inundation. At the head of one palaeo-river system near the Outer Dowsing Deep, the Southern River, we observed an abrupt and catastrophic inundation stratum. Based on lithostratigraphic, macro and microfossils and sedimentary ancient DNA (sedaDNA) evidence, supported by optical stimulation luminescence (OSL) and radiocarbon dating, we conclude these deposits were a result of the Storegga event. Seismic identification of this stratum to adjacent cores indicated diminished traces of the tsunami, largely removed by subsequent erosional processes. Our results demonstrate the catastrophic impact of Storegga within this area of the Southern North Sea, but indicate that these effects were temporary and likely localized and mitigated by the dense woodland and topography of the area. We conclude clear physical remnants of the wave are likely to be restricted to inland basins and incised river valley systems.

paleontology↗

bioRxiv2020

Habitat selection drives dietary specialisation in Sorex minutus

To meet their demand for food, Eurasian pygmy shrews (Sorex minutus) require large territories, normally in fields, woodlands, and meadows. Their high metabolism and food requirement often leads to high mortality during winter. However, evidence of shrews in the roof voids of residential buildings has recently been observed, contrary to ecological expectations. Here, five faecal samples collected from different locations were studied by metagenomic analysis to gain information about the shrews diets and environments. Two of the samples were collected from novel indoor locations, while the other three were from outdoors in traditional habitats. Distinct differences were observed between the diets of the two populations, suggesting a commensal niche expansion has occurred in S. minutus. We found that S. minutus exploit man-made spaces for foraging, potentially at the cost of a greater parasite burden.

ecology↗

bioRxiv2019

Guano morphology reveals ecological information in British bats

1.0.Bats are primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystems health, however four of the seventeen Great British species are listed as declining. In this study we aim to investigate the link between bat guano morphology and diet, specifically looking at the ability to predict 1) species, 2) dietary guild and 3) bat size, using guano morphology alone. It was found that guano morphology overlapped too much to make predictions on species however, in some cases, it could be used to predict dietary guild or size.

ecology↗

bioRxiv2018

A domestication history of dynamic adaptation and genomic deterioration in sorghum

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated introgressions. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck but instead suggest a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially on architectural and nutritional domestication traits, and adaptation to the local environment. Later introgression between sorghum races allowed exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration was not focused on the initial stages of domestication but occurred throughout the history of cultivation.

evolutionary biology↗

bioRxiv2017

Adaptation to European latitudes through assimilation of wild diversity at the LuTFL1 locus altered architecture and promoted fiber production in flax.

After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2, vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A. thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.

evolutionary biology↗

bioRxiv2017

A new model for ancient DNA decay based on paleogenomic meta-analysis

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation.

genomics↗