Biology subjects

Bacon, C. D.

Publications and source records attributed to Bacon, C. D..

11 recordsLinked to original sources

bioRxiv2026

Shared genomic signatures of Arctic adaptation among distantly related plant lineages

Extreme environments impose strong selection pressures that can drive convergent adaptation among distantly related species. Arctic plants survive low temperatures, 24-hour light in summer and darkness in winter, short growing seasons, limited precipitation, nutrient-poor soils, and extreme seasonal variation. To test if these conditions are associated with shared genomic signatures, we generated a chromosome-level genome assembly for Oxyria digyna and compared it with existing reference genomes for three distantly related Arctic species (Cochlearia groenlandica, Draba nivalis, Dryas octopetala) and for 16 non-Arctic species from the same families. We identified 214 orthogroups with signatures of positive selection in all Arctic species, 1.6 times the number shared among the non-Arctic species. Although no gene ontology (GO) categories remained significantly enriched after multiple-testing correction, descriptive annotations included genes involved in general functions including protein folding, glycolysis, transcription, and oxidative-stress responses. Orthogroups showing copy number variation were associated with biotic interactions, sexual reproduction, and nutrient acquisition, suggesting that species may respond to biotic and nutrient stresses by shifts in gene copy number. Arctic and alpine genomes contained lower proportions of some repetitive elements, including terminal inverted repeats, and smaller regions of centromeric repeats than non-Arctic genomes. Overall, we see shared genes under positive selection, similar functions of genes with high copy number variation, and lower counts of some repetitive elements in the Arctic plant genomes. Our findings reveal a shared genomic signature of Arctic adaptation across deeply diverged plant lineages, suggesting that evolution in extreme environments repeatedly targets similar genomic features.

genomics↗

bioRxiv2026

A novel mitogenome for Euterpe precatoria (Arecaceae)

Mitochondrial genomes of angiosperms are unusual due to their large size, low gene content, and high structural variation. In the palm family (Arecaceae), mitochondrial architecture is highly dynamic, characterized by expansive sizes, fragmentation, and extensive recombination activity. This biological complexity presents a significant bioinformatic challenge, especially since only three complete palm mitochondrial genomes are publicly available to date. Here, we present the complete mitochondrial genome sequence for the Amazonian palm Euterpe precatoria, assembled de novo using PacBio HiFi long-read sequencing data. The assembly required extensive manual curation and graph tracing to resolve a complex recombination topology. The final resolved sequence spans 1,268,308 base pairs and is supported by a mean read coverage depth estimated at 746X. Annotation revealed a high degree of structural complexity, including 177 total gene features corresponding to 76 unique genes. This gene set includes 41 unique protein-coding genes (56 features), 32 unique tRNA genes (118 features), and three unique rRNA genes, reflecting the characteristic gene duplication and fragmentation documented in Arecaceae. The complete mitochondrial genome sequence is publicly available and provides a high-quality resource for understanding the mechanisms of plant mitochondrial genome expansion and structural evolution.

genomics↗

bioRxiv2025

Environmental Variation Promotes Convergent Evolution and Rapid Diversification of Wing Shape and Color in Skipper Butterflies

Predation is a key driver of speciation and phenotypic diversification, yet how antipredator traits evolve and persist over evolutionary time remains poorly understood. We generated target sequence capture and whole-genome sequencing data for the skipper butterfly subfamily Eudaminae (Hesperiidae) to test whether antipredator defenses, in interaction with environmental variation, promote diversification. We focus on two antipredation wing traits: hindwing tails, which deflect predator attacks, and blue-green coloration, which may enhance motion dazzle and be used as warning coloration. Applying phylogenomics, morphometrics, and comparative methods, we model trait evolution in relation to diel activity and geographic distribution and find that hindwing tails repeatedly evolved at least seven times and blue-green coloration at least fifteen times. Both traits are associated with elevated speciation rates, but evolutionary transitions toward tailless wings and non-iridescent coloration occurred more frequently than trait gains, indicating high evolutionary lability of these antipredator defenses. Trait loss, particularly pronounced in tropical diurnal species, may reflect trade-offs in flight performance, shifts in predation guilds, or the evolution of alternative defensive traits. Our findings highlight rampant convergent evolution of wing traits that are under strong predator-mediated selection. By identifying how antipredator defenses and environmental contexts influence phenotypic and species diversification, this study provides new insights into the ecological and evolutionary processes underlying insect diversity.

evolutionary biology↗

bioRxiv2025

Historical data reveals earlier flowering under environmental change

PremiseGlobal temperatures have risen [~]1.1{degrees}C since the 1800s and the mean annual air temperature in the Arctic has increased nearly four times the global average. Temperature has a significant effect on fundamental life-cycle events of flora and fauna. With temperatures increasing, Arctic plants are expected to shift their active periods accordingly, with a shorter flowering period as later flowering plants converge with flowering timing of early flowering plants. MethodsNearly 120 years of herbarium records and collection data were leveraged to identify flowering shifts in the Arctic-alpine plant Oxyria digyna using climatic data and linear regressions. ResultsWe found that Alpine, Boreal Arctic, and Arctic Tundra populations differed in their flowering time response to increased air temperature. The Boreal Arctic population showed a significant advancement in flowering time as related to mean summer and June temperature increases, while the flowering time of Arctic Tundra and Alpine populations had a shift in flowering timing in response to June temperature change. ConclusionsOur results identify biodiversity response to climate change and determine which populations have greater adaptive potential to respond to rapidly changing abiotic conditions in the Arctic and beyond.

plant biology↗

bioRxiv2023

The evolutionary age-range size relationship is modulated by insularity and dispersal in plants and animals

Earth is home to millions of plant and animal species, with more than 40 thousand species facing extinction worldwide (Diaz et al. 2019). Species range size is particularly important in this context because it influences extinction risk (Purvis et al. 2000, Gaston & Fuller 2009), but the causes underlying the wide natural variation in range size remain poorly known. Here, we investigate how evolutionary age is related to present-day range size for over 25,000 species of mammals, birds, reptiles, amphibians, reef fishes, and plants. We show that, on average, older species have significantly larger ranges, but the effect of age on range size is modulated by clade, geographical context and dispersal ability. Specifically, age does not affect range size for island species, because islands limit dispersal and hence range size, regardless of species age. Furthermore, species from clades with high dispersal capabilities obtain large ranges faster, thereby further neutralizing the relationship between age and range size. Our results can help supporting global conservation priorities, by showing that species that are young, occupy islands, and/or are dispersal limited often have small ranges and therefore increased extinction risk.

ecology↗

bioRxiv2022

Large-scale assessment of habitat quality and quantity change on declining European butterflies

The rapid decline of biodiversity as a consequence of increased environmental impact by human activities requires urgent action against the ongoing crisis. At the heart of conservation policy is the debate on quality versus quantity: should the post-2020 Global Biodiversity Framework focus on maximising total protected area, or pursue instead qualitative targets? To improve conservation practices, we need to both understand the current trend of biodiversity and the factors driving the decline. We address this by: (1) projecting current European butterfly population trends for the next 50 and 100 years, (2) comparing the decline in species richness, phylogenetic diversity and habitat specialization among different habitats, and (3) estimating the relationship between recent trends in habitat quality or quantity and the decline of multiple metrics of European butterfly diversity. We do not find any significant relationship between diversity loss and habitat area loss and conclude that neither long-term nor short-term changes in habitat area are primary predictors of large-scale butterfly decline in Europe. Habitat quality emerges as the most crucial factor in our analyses - both the area affected and the severity of habitat quality reduction. Habitat degradation causes vegetation changes in structure and diversity, which affect butterfly survival. We also estimate a higher decline of habitat specialists than generalist species. We conclude that habitat protection cannot focus solely on the maximization of habitat area but urgently needs to restore high quality ecosystems to provide the full range of ecological requirements for biodiversity.

ecology↗

bioRxiv2021

Fruit colour and range size interact to influence diversification

AimDifferent fruit colours are associated with dispersal by different frugivores, largely based on colour vision type. Frugivore mobility affects overall range size for the plant being dispersed. Here we determine the interaction between different fruit colours, range sizes, and diversification rates by testing two hypotheses: That (1) fruit colours attractive to birds have larger range sizes due to their higher dispersal ability, and that (2) different frugivore disperser groups, bird or mammal, leads to different diversification rate at different range size, where intermediate range size leads to the highest diversification rate. LocationGlobal. Time periodContemporary (or present) Major taxa studiedPalms (Arecaceae) MethodsUsing model selection, we identified three groups of colours with similar diversification rate and likely disperser. Range sizes were estimated and categorized species as small, intermediate, or large-ranged. For model selection and to determine the relationship beween fruit color, range size and diversification rate we used Multi-State Speciation and Extinction (MuSSE) models. ResultsSpecies with intermediate range size had the highest net diversification for all three fruit colour groups. Bird-dispersed palms more likely diversified at small than at large range size while mammal-dispersed palms more likely diversified at larger range size than small. Fruit colours associated with mammal dispersal had more large-ranged species than colours associated with bird dispersal. Main conclusionsThe associated between intermediate range size and higher diversification rate indicates that spatial factors that affect diversification at small and large range sizes result in higher diversification at intermediate ranges. We find striking differences in diversification rate within each range size category between fruit color groups. This suggests that the relationship between diversification rate and range size depends on the specific frugivorous dispersers and their dispersal patterns. This study reveals how fruit traits alter dispersal patterns and how that, in turn, influences diversification.

ecology↗

bioRxiv2021

Temperature predicts leaf shape in palms (Arecaceae)

AimLeaves display a remarkable variety of shapes, each with potential ecological advantages in specific climates. While relations between leaf shape and either climate or height has been relatively well studied in eudicots, the macroecological drivers of shape remain poorly known in monocots. Here, we investigated associations between climate and plant height with the evolution of leaf shape in a clade with high species and morphological diversity. LocationGlobal. Time periodCretaceous to contemporary. Major taxa studiedPalms (Arecaceae). MethodsWe apply a Bayesian phylogenetic mixed model to test for associations between climate and leaf shape (all entire-leaved, pinnate-dissected, palmate-dissected, and costapalmate). We further reconstruct the ancestral leaf shape using multistate speciation and extinction models and compare the frequency of shapes with global temperatures through time. ResultsWe find that plant height associates with dissected leaves and that annual precipitation associates with pinnate shapes. The ancestral leaf shape is unclear but early diversification was dominated by pinnate-dissected palms, which has remained the most species-rich form of leaves throughout palm history. Main conclusionsPalms that are tall and live in humid regions are more likely to have pinnate leaves. Through geological time scales, temperature did not play an obvious role in determining leaf shapes. This study contributes to our understanding of how the diversity of leaf shapes is linked to biological and climatic factors.

evolutionary biology↗

bioRxiv2021

Unbiased clade age estimation using a Bayesian Brownian Bridge

In a recent paper1 we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2 critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.

paleontology↗

bioRxiv2020

Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

ContextAmazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to their clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms such as the small and endemic passerine Elaenia ruficeps. ObjectivesHere, we estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps. MethodsWe sampled individuals of E. ruficeps from three landscapes in Central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimate population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimate genetic isolation by distance and resistance among individuals sampled within landscapes. ResultsWe identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low genetic differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes. ConclusionsOur results uncover population dynamics of E. ruficeps through time. Together with previous studies, this suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds, and that Amazonian landscapes, together with their associated biota, have responded to recent climatic changes.

ecology↗

bioRxiv2020

Unravelling the phylogenomic relationships of the most diverse African palm genus Raphia (Calamoideae, Arecaceae)

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution and other eco-evolutionary aspects of this charismatic, socially and economically important palm genus.

plant biology↗