Biology subjects

Gamba, D.

Publications and source records attributed to Gamba, D..

3 recordsLinked to original sources

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↗