Biology subjects

Gamba, D.

Publications and source records attributed to Gamba, D..

7 recordsLinked to original sources

bioRxiv2026

Genomic history and ecology of local adaptation in sky-island Arabidopsis thaliana

Adaptation to local environments in isolated habitats may produce independent solutions to similar ecological challenges, yielding insight into the predictability of evolution. Alpine plants on tropical sky-islands, in particular, must cope with extreme diurnal fluctuations in temperature and radiation. These populations may undergo parallel local adaptation to high elevation, or alternatively, distinct local adaptations due to intermountain heterogeneity. For instance, abiotic stress on mountain peaks could select for stress tolerance or stress escape/bet-hedging strategies. We tested these hypotheses in experiments with 163 newly sequenced Arabidopsis thaliana genotypes from East Africa. Genomic history followed geography: Ugandan genotypes were the most divergent, and Ethiopian genotypes more closely related. Effective population size decreased towards the present on all mountains, in concert with declining climatic suitability since the end of the African Humid Period. Genotypes from the colder and seasonally drier mountains showed strong seed dormancy, rapid flowering, short/curved inflorescences. In contrast, genotypes from the milder and less seasonal mountains showed less seed dormancy, delayed flowering, and long/erect inflorescences. Elevational clines found in multiple mountains included seed dormancy-release with short (vs. long) stratification, and shorter inflorescences, at higher elevations. In a genome-wide association study (GWAS) with inflorescence length, we detected the TCP5 transcription factor, but these variants only segregated in some mountains and showed an elevational allele frequency cline at only one mountain. Allele reuse based on GWAS was greater between Ethiopian populations (QTL allele-frequency r > 0.9 for most traits), and generally lower between Uganda and the rest. Results indicate limited evidence of parallel local adaptation along elevation, suggesting that dwarf inflorescences are selected for in multiple mountain tops, while bet-hedging prevails in cold and seasonally dry sky-islands, and divergent selection along elevation in other traits can evolve in mountains with milder climates. Overall these results suggest a long history of isolation and ecological complexity limit the predictability of local adaptation.

evolutionary biology↗

bioRxiv2025

Nonphotochemical quenching changes with abiotic stressor and developmental stages

Nonphotochemical quenching (NPQ) is a critical photoprotective mechanism in plants, safeguarding photosystem II (PSII) and PSI from photodamage under abiotic stress. However, it is unclear if different stressors lead to similar NPQ phenotypes, and the magnitude of natural variation (between and within plant species) in NPQ response to abiotic stress is unknown. Testing a semi-high-throughput leaf-disc approach for examining the NPQ kinetics parameters, we investigated NPQ under chilling, drought and low nitrogen stress across multiple species and/or genotypes. Our results show substantial variation in NPQ phenotypes across species, genotypes and treatments. In C3 crops, tobacco and soybean, multiple NPQ parameters generally increased under chilling and drought, while in C4 crops, maize and sorghum, NPQ traits were more variable including a decrease of multiple NPQ parameters. Low-N stress revealed genotype- and developmental stage-specific effects on NPQ, potentially reflecting distinct adaptive strategies and regulatory changes in NPQ stress response. A significant effect of ecotype and stress treatment was detected on most NPQ kinetics traits in Arabidopsis thaliana, however, the interaction between ecotype and treatment was stronger in drought than in chilling. Differential regulation of NPQ could be associated with a combination of changes in proton motive, ATPase synthase activity, and PSI redox state. Our findings highlight that interpreting relative changes in NPQ under abiotic stress is inherently complex and demands a broader integration of physiological data across multiple regulatory layers.

physiology↗

bioRxiv2025

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

evolutionary biology↗

bioRxiv2024

Local adaptation to climate facilitates a global invasion

Local adaptation may facilitate range expansion during invasions, but the mechanisms underlying successful invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with severe impacts in western North America. We aimed to identify mechanisms and consequences of local adaptation in the North American cheatgrass invasion. We sequenced 307 range-wide genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Nearly half of North American cheatgrass comprises a mosaic of [~]19 locally adapted, near-clonal genotypes, each seemingly very successful in a different part of North America. Additionally, ancestry, phenotype, and allele frequency-environment clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the USA Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Our results indicate that multiple introductions and migration within the invaded range fueled local adaptation and success of cheatgrass in western North America. Understanding how environment and gene flow shape adaptation and invasion is critical for managing ongoing invasions.

evolutionary biology↗

bioRxiv2022

The genomics and physiology of abiotic stressors associated with global elevation gradients in Arabidopsis thaliana

Phenotypic and genetic diversity in Arabidopsis thaliana may be associated with adaptation along its wide elevational range. We took a multi-regional view of elevational adaptation and in a diverse panel of ecotypes measured plant responses to high elevation stressors: low partial CO2 pressure, high light, and night freezing. We conducted genome-wide association studies (GWAS) and found evidence of contrasting locally adaptive clines between regions. Western Mediterranean ecotypes showed low {delta}13C/early flowering at low elevations to high {delta}13C/late flowering at high elevations, while Asian ecotypes showed the opposite pattern. We mapped different candidate genes for each region, and trait-associated SNPs often showed elevational clines likely maintained by selection. Antioxidants and pigmentation showed regional differentiation but rarely elevational clines. GWAS for antioxidants identified an ascorbate transporter PHT4;4 (AT4G00370), which we show alters non-photochemical quenching kinetics under high light and may be involved in local adaptation to Moroccan mountains. The low-antioxidant PHT4;4 GWAS allele was associated with lower PHT4;4 expression and this haplotype was characterized by binding sites of a transcription factor family, DOF, involved in light response. Our results highlight how physiological and genomic elevational clines in different regions can be unique, underlining the complexity of local adaptation in widely distributed species.

evolutionary biology↗

bioRxiv2022

Wavelet characterization of spatial pattern in allele frequency

Characterizing spatial patterns in allele frequencies is fundamental to evolutionary biology because these patterns contain evidence of underlying processes. However, the spatial scales at which gene flow, changing selection, and drift act are often unknown. Many of these processes can operate inconsistently across space, causing non-stationary patterns. We present a wavelet approach to characterize spatial pattern in allele frequency that helps solve these problems. We show how our approach can characterize spatial patterns in relatedness at multiple spatial scales, i.e. a multi-locus wavelet genetic dissimilarity. We also develop wavelet tests of spatial differentiation in allele frequency and quantitative trait loci (QTL). With simulation we illustrate these methods under different scenarios. We also apply our approach to natural populations of Arabidopsis thaliana to characterize population structure and identify locally-adapted loci across scales. We find, for example, that Arabidopsis flowering time QTL show significantly elevated genetic differentiation at 300 to 1300 km scales. Wavelet transforms of allele frequencies offer a flexible way to reveal geographic patterns and underlying evolutionary processes.

evolutionary biology↗

bioRxiv2022

Climate biogeography of Arabidopsis thaliana: linking distribution models, individual performance, and life history

AIMPatterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. However, it is challenging to gather data on individual-level variation at large spatial scales. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATIONGlobal TAXONArabidopsis thaliana ("Arabidopsis") METHODSWe fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on [~]900 natural accessions. RESULTSThe most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONSIntegration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.

ecology↗