Biology subjects

van den Berg, C.

Publications and source records attributed to van den Berg, C..

6 recordsLinked to original sources

bioRxiv2025

SAND-MEDIATED DNA EXTRACTION FROM ORCHIDS FOR GENOMIC APPLICATIONS

DNA extraction is an essential routine procedure for downstream applications in genetics and molecular biology. Since DNA was extracted for the first time, countless protocols have been developed yielding excellent results; however, the diversity of plant families and the distribution in remote areas represent a challenge for these protocols. Orchidaceae, one of the most species-rich plant families in the world, is a group with abundant polyphenols and polysaccharides in its tissues. In addition, sample collection in remote areas represents a challenge, consequently, conventional protocols can be inappropriate for obtaining DNA. In this way, CTAB-based gel preservation has emerged as an excellent alternative to easily collect, store and transport samples, moreover, alternatives such as sterile sand and DNA stabilization solutions during grinding allow a suitable DNA extraction. Here, we combined saturated NaCI-CTAB gels, sterile sand, sucrose-based DNA stabilization buffer, and conventional CTAB solution for obtaining DNA from fresh and stored samples for up to 32 days at room temperature, and described, from sample collection to spectrophotometer-obtained quantification, a non-organic method for obtaining DNA from orchids species for genomic applications. This protocol allows not only the extraction of suitable quantities of high molecular weight DNA of adequate purity and integrity from different orchid species without the use of expensive equipment and cumbersome reagents such as liquid nitrogen and toxic phenols, and/or time-consuming procedures, but also, the use of this DNA in downstream applications such as PCR-based genotyping, restriction enzyme analysis, and most genomic applications.

genetics↗

bioRxiv2023

The Origin And Speciation Of Orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and [~]7% (1,921) of the currently 29,524 accepted species. We then use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distribution data through the World Checklist of Vascular Plants. Orchids most recent common ancestor is traced back to the Late Cretaceous in Laurasia. The modern Southeast Asian range of subfamily Apostasioideae is interpreted as relictual, matching the history of numerous clades that went extinct at higher latitudes following the global climate cooled during the Oligocene. Despite their ancient origins, modern orchid species diversity mainly originated over the last 5 Ma, with the fastest speciation rates found in south-eastern Central America. Our results substantially alter our understanding of the geographic origin of orchids, previously proposed as Australian, and further pinpoint the role of Central American as a region of recent and explosive speciation.

evolutionary biology↗

bioRxiv2023

Colour patterns are less variable in highly unpalatable nudibranchs

The selective factors that shape phenotypic diversity in prey communities with aposematic animals are diverse and coincide with similar diversity in the strength of underlying secondary defences. However, quantitative assessments of colour pattern variation and the strength of chemical defences in assemblages of aposematic species are lacking. We quantified colour pattern diversity using Quantitative Colour Pattern Analysis (QCPA) in 13 Dorid nudibranch species (Infraorder: Doridoidei) that varied in the strength of their chemical defences. We accounted for the physiological properties of a potential predators visual system (a triggerfish, Rhinecanthus aculeatus) and modelled the appearance of nudibranchs from multiple viewing distances (2cm and 10cm). We identified distinct colour pattern properties associated with the presence and strength of chemical defences. Colour patterns were also less variable among species with chemical defences when compared to undefended species. This confirms correlations between secondary defences and diverse, bold colouration while showing that chemical defences coincide with decreased colour pattern variability among species. Our study suggests that complex spatiochromatic properties of colour patterns perceived by potential predators can be used to make inferences on the presence and strength of chemical defences.

animal behavior and cognition↗

bioRxiv2022

Highly defended nudibranchs do not 'escape' to visually diverse background habitats

The escape and radiate hypothesis predicts that once species have evolved aposematism, defended species can utilise more visually diverse visual backgrounds as they escape the need to be well camouflaged. This enables species to explore new ecological niches, resulting in increased diversification rates. To test this hypothesis escape component, we examined whether the background habitats of 12 nudibranch mollusc species differed among species depending on the presence and strength of chemical defences. We obtained a rich array of colour pattern statistics using Quantitative Colour Pattern Analysis (QCPA) to analyse backgrounds viewed through the eyes of a potential predator (triggerfish, Rhinecanthus aculeatus). Colour pattern analysis was done at viewing distances simulating an escalating predation sequence. We identified four latent factors comprising 17 non-correlated colour pattern parameters, which captured the among-species variability associated with differences in chemical defences. We found that chemically defended species, indeed, were found on visually distinct backgrounds with increased colour and luminance contrast, independent of viewing distance. However, we found no evidence for increased among-species background diversity coinciding with the presence and strength of chemical defences. Our results agree with the escape and radiate hypothesis, suggesting that potent chemical defences in Dorid nudibranchs coincide with spatiochromatic differences of visual background habitats perceived by potential predators. Lay SummaryAccording to the escape and radiate hypothesis, the ability to store potent chemical defences as protection from predators enables animals to be minimally dependent on matching visual backgrounds for camouflage. We found evidence supporting this hypothesis in 12 species of nudibranch molluscs. Aposematic species were found on visual backgrounds that differed consistently in appearance from the visual background of undefended cryptic species. However, we found no difference in the variability of visual backgrounds between species with or without chemical defences. This suggests that warning colouration in eastern Australian Dorid nudibranchs coincides with broadly generalisable spatiochromatic properties of visual backgrounds.

ecology↗

bioRxiv2022

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleraceae and E. precatoria) from different Brazilian biomes

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, but overexploitation requires conservation strategies to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

evolutionary biology↗

bioRxiv2020

More than noise: context-dependant luminance contrast discrimination in a coral reef fish (Rhinecanthus aculeatus)

Achromatic (luminance) vision is used by animals to perceive motion, pattern, space and texture. Luminance contrast sensitivity thresholds are often poorly characterised for individual species and are applied across a diverse range of perceptual contexts using over-simplified assumptions of an animal’s visual system. Such thresholds are often estimated using the Receptor Noise Limited model (RNL) using quantum catch values and estimated noise levels of photoreceptors. However, the suitability of the RNL model to describe luminance contrast perception remains poorly tested.Here, we investigated context-dependent luminance discrimination using triggerfish (Rhinecanthus aculeatus) presented with large achromatic stimuli (spots) against uniform achromatic backgrounds of varying absolute and relative contrasts. ‘Dark’ and ‘bright’ spots were presented against relatively dark and bright backgrounds. We found significant differences in luminance discrimination thresholds across treatments. When measured using Michelson contrast, thresholds for bright spots on a bright background were significantly higher than for other scenarios, and the lowest threshold was found when dark spots were presented on dark backgrounds. Thresholds expressed in Weber contrast revealed increased contrast sensitivity for stimuli darker than their backgrounds, which is consistent with the literature. The RNL model was unable to estimate threshold scaling across scenarios as predicted by the Weber-Fechner law, highlighting limitations in the current use of the RNL model to quantify luminance contrast perception. Our study confirms that luminance contrast discrimination thresholds are context-dependent and should therefore be interpreted with caution.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗