Biology subjects

Carta, A.

Publications and source records attributed to Carta, A..

4 recordsLinked to original sources

bioRxiv2025

Limitations of p50 as a measure of seed longevity and the way forward

PremiseComparative studies of seed longevity assess how environmental conditions, species identity, populations, or genotypes affect seed viability loss in stored seeds. These studies commonly use the time it takes for seed viability to drop to 50% - known as p50, - as a measure of seed longevity. However, p50 is influenced by the initial seed viability. To allow comparisons regardless of the initial seed viability, standard protocols for comparative studies of seed longevity recommend using seed lots with "similar and high" initial viability, typically between 85 and 100%. However, even such range of initial seed viabilities might result in substantial variation in p50. MethodsHere, we use a modelling approach to illustrate how variation in initial viability affects p50 estimates, and to propose alternative, more robust measures of seed longevity in storage. ResultsWe show that for hypothetical accessions with identical rates of seed viability loss, variation in initial viability between 85 and 100% leads to a threefold variation in p50 estimates. Most of the unintended variation is introduced by accessions with very high viability (>95%). Restricting the initial viability to a narrower range (e.g., 85-95%) reduces but does not eliminate this bias. Alternatively, p50 can be recalculated to a standardized value of initial viability (e.g., 90%), which makes it proportional to the rate of probit viability loss without any noise. However, the most straightforward measure of seed longevity for comparative studies is the rate of viability loss itself, represented by {sigma} (sigma) from the viability equation. ConclusionThe common measure of seed longevity, p50, is affected by unintended, substantial variation caused by varying initial viability of the seed lot, and is thus suboptimal for comparative studies of seed longevity among seed accessions. More robust measures of seed longevity include the rate of viability loss, or p50 standardized to a certain initial seed viability.

ecology↗

bioRxiv2024

Phylogenetic and functional compositional shifts associated with selective logging and forest regrowth in tropical rainforests of the Congo Basin

Background and aimsTropical rainforests constitute a globally important biome severely threatened by anthropogenic activities. Accounting for the phylogenetic and functional dimensions can provide insights into how anthropogenic activities affect tree species community assembly. Here, we aimed to assess the effects of selective logging and forest regrowth on the tree composition in the Yangambi region (Democratic Republic of the Congo), as compared to reference undisturbed old-growth forest by incorporating phylogenetic and functional information. MethodsWe measured the phylogenetic and functional alpha-diversity and dissimilarity of undisturbed old-growth, disturbed old-growth, and regrowth rainforests by sampling species abundances and key traits related to usefulness (wood density), vegetative (specific leaf area), and reproductive (fruit type) functions. Then, we evaluated the association between phylogenetic and functional dissimilarity to unravel potential drivers underlying changes in the community composition. Key resultsPhylogenetic and functional dissimilarities resulted in a consistent compositional separation of the disturbed old-growth forests and regrowth forests from the undisturbed old-growth forests, with this separation clearly associated with key functional traits. Compared to undisturbed old-growth forests, disturbed old-growth forests subjected to selective logging did not diverge in terms of both phylogenetic and functional diversity and structure. However, regrowth forests displayed increased levels of phylogenetic diversity and comparable functional diversity as undisturbed old-growth forests. ConclusionsSelective logging and forest regrowth have not led to an overdispersion or clustering of phylogenetic lineages nor functional traits in the tropical rainforests in the Congo Basin, rather, these anthropogenic activities brought an altered phylogenetic and functional community composition which may have serious implications for the stability of these ecosystems.

ecology↗

bioRxiv2021

A global phylogenetic regionalisation of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

Existing global regionalisation schemes for plants consider the compositional affinities among biotas, but these have not considered phylogenetic information explicitly. Incorporating phylogenetic information may substantially advance our understanding of the relationships among regions and the synopsis of biogeographical schemes, because phylogeny captures information on the evolutionary history of taxa. Here, we present the first phytogeographical delineation of the global vascular flora based on the evolutionary relationships of species. We analysed 8,738,520 geographical occurrence records for vascular plant species together with a time-calibrated phylogenetic tree including 67,420 species. We estimated species composition within 200 x 200 km grid cells across the world, and used a metric of phylogenetic beta diversity to generate a phylogenetic delineation of floristic regions. We contrasted these results with a regionalisation generated using a taxonomic beta diversity metric. We identified 16 phylogenetically distinct phytogeographical units, deeply split into two main clusters that broadly correspond to the Laurasia-Gondwana separation. Our regionalisation broadly matches currently recognized phytogeographical classifications, but also highlights that the Gondwanan area is split into a large Holotropical cluster and an Australian-NeoZelandic-Patagonian cluster. In turn, we found that the northernmost and southernmost units have the most evolutionarily distinct vascular plant assemblages. In contrast, taxonomic dissimilarity returned a regionalisation composed of 23 units with a high degree of shared taxa between Laurasian and Gondwanan areas, with no clear split among their biotas. The integration of phylogenetic information provided new insights into the historical relationships among phytogeographical units, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our regionalization scheme provides further evidence for delineating transition zones between the Holarctic and Holotropical kingdoms. The latitudinal patterns of evolutionary distinctiveness of vascular plant assemblages are consistent with recent evidence of higher and more recent diversification of flowering plants outside tropical regions.

evolutionary biology↗

bioRxiv2020

A deep dive into the ancestral chromosome number of flowering plants

O_LIChromosome number and genome variation in flowering plants has stimulated a blossoming number of speculations about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal. C_LIO_LIWe used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 thousands taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5 thousands taxa. C_LIO_LIOur inferences revealed an ancestral haploid chromosome number for angiosperms n = 7, a diploid status, and an ancestral 1C = 1.73 pg. For 160 families, inferred ancestral n are provided for the first time. C_LIO_LIBoth descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, also 1C genome size significantly increases (or decreases) in late-branching lineages. Therefore, no evidence exists for a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes. C_LI

plant biology↗