96 research outputs found
On the effect of asymmetric trait inheritance on models of trait evolution
No full textPhyloTraitSimulator
Simulations of intra- and inter-specific trait evolution
This is the code used to simulate phenotypic data for the manuscript: “On the effect of asymmetric trait inheritance on models of trait evolution” by Pablo Duchen, Michael L. Alfaro, Jonathan Rolland, Nicolas Salamin, Daniele Silvestro
The evolution of Cayaponia (Cucurbitaceae)
No full textPremise of the study: The Cucurbitaceae genus Cayaponia comprises ∼60 species that occur from Uruguay to the southern United States and the Caribbean; C. africana occurs in West Africa and on Madagascar. Pollination is by bees or bats, raising the question of the evolutionary direction and frequency of pollinator shifts. Studies that investigated such shifts in other clades have suggested that bat pollination might be an evolutionary end point.
Methods: Plastid and nuclear DNA sequences were obtained for 50 accessions representing 30 species of Cayaponia and close relatives, and analyses were carried out to test monophyly, infer divergence times, and reconstruct ancestral states for habitat preferences and pollination modes.
Key results: The phylogeny shows that Cayaponia is monophyletic as long as Selysia (a genus with four species from Central and South America) is included. The required nomenclatural transfers are made in this paper. African and Madagascan accessions of C. africana form a clade that is part of a polytomy with Caribbean and South American species, and the inferred divergence time of 2–5 Ma implies a transoceanic dispersal event from the New World to Africa. The ancestral state reconstructions suggest that Cayaponia originated in tropical forests from where open savannas were reached several times and that bee pollination arose from bat pollination, roughly concomitant with the shifts from forests to savanna habitats.
Conclusions: Cayaponia provides the first example of evolutionary transitions from bat to bee pollination as well as another instance of transoceanic dispersal from the New World to Africa
Bulk segregant analysis reveals genomic regions associated with imidacloprid resistance in the Colorado potato beetle
No full textEdison A, Narimanov N, Duchen P, Xu S. Bulk segregant analysis reveals genomic regions associated with imidacloprid resistance in the Colorado potato beetle. bioRxiv. 2025.**Abstract**
Given the increased accessibility of genomic techniques, the speed of evolution of resistance, and the large number of genes involved in resistance, investigations into the genetic basis of resistance in more species are pertinent. Despite being an important agricultural pest, only a limited number of genetic mapping studies based on crossed populations have been performed to identify genes involved in resistance in the Colorado potato beetle (
Leptinotarsa decemlineata
, CPB). Here, we performed bulk segregant analysis on a mapping population generated by creating advanced intercross lines from five European strains of CPB. We identified eight peaks across chromosomes 1,8,10, and 16 involved in resistance against the neonicotinoid, imidacloprid. We identified 337 genes within these peaks and shortlisted three candidates based on gene expression and functional annotation. Among the three candidates thus identified, we found that an ABC transporter and a galactosyl transferase are expressed in relatively higher amounts in a relatively more susceptible strain than in a resistant strain. We attempted to validate the role of these two genes in insecticide resistance by knocking them down in a resistant strain using RNA interference (RNAi) and performing toxicity experiments. Surprisingly, our results showed that the activation of RNAi machinery reduced imidacloprid resistance and the effect is not specific to the tested candidate genes, which raised a concern on the suitability of using RNAi for validating insecticide resistance mechanisms in CPB.
</p
Evidence for positive selection at the <i>MtnA</i> locus.
No full text(A) Watterson’s θ of D. melanogaster populations from Zimbabwe (ZK), the Netherlands (NL) and Sweden (SU) calculated in sliding windows of 500 bp with a step size of 250 bp. (B) Fst values for pairwise comparisons of ZK, NL and SU calculated in sliding windows of 500 bp with a step size of 250 bp. (C) Selective sweep (SweepFinder) analysis of the Netherlands population showing the composite likelihood ratio (CLR) statistic in sliding windows of 1000 bp. (D) Selective sweep (SweepFinder) analysis of the Swedish population showing the CLR statistic in sliding windows of 1000 bp. The black line indicates the 5% significance threshold calculated using the demographic model of Duchen et al. [5] for neutral simulations. The red line indicates the 5% significance threshold calculated using the demographic model of Werzner et al. [6] for neutral simulations and the gray dashed line indicates the 5% significance threshold using the model of Thornton and Andolfatto [35]. (E) Gene models for the 6-kb region analyzed. The gray highlighted region indicates the position of the 49-bp indel polymorphism in the MtnA 3’ UTR.</p
Mitochondria and quality control defects in a mouse model of Gaucher Disease-links to Parkinson's Disease
No full textMutations in the glucocerebrosidase (gba) gene cause Gaucher disease (GD), the most common lysosomal storage disorder, and increase susceptibility to Parkinson's disease (PD). While the clinical and pathological features of idiopathic PD and PD related to gba (PD-GBA) mutations are very similar, cellular mechanisms underlying neurodegeneration in each are unclear. Using a mouse model of neuronopathic GD, we show that autophagic machinery and proteasomal machinery are defective in neurons and astrocytes lacking gba. Markers of neurodegeneration-p62/SQSTM1, ubiquitinated proteins, and insoluble α-synuclein-accumulate. Mitochondria were dysfunctional and fragmented, with impaired respiration, reduced respiratory chain complex activities, and a decreased potential maintained by reversal of the ATP synthase. Thus a primary lysosomal defect causes accumulation of dysfunctional mitochondria as a result of impaired autophagy and dysfunctional proteasomal pathways. These data provide conclusive evidence for mitochondrial dysfunction in GD and provide insight into the pathogenesis of PD and PD-GBA
Supplementary Information for: A cautionary note on the use of genotype callers in phylogenomics
No full textNext-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline, and found that it is very sharp in GATK, while ATLAS maintains a high accuracy even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies
The evolution of<i>Cayaponia</i>(Cucurbitaceae): Repeated shifts from bat to bee pollination and long-distance dispersal to Africa 2-5 million years ago
No full text
Inferring the demographic history of the North American firefly Photinus pyralis
No full textThe firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Despite its broad distribution, its demographic history is unknown. In this study, we modelled and inferred different demographic scenarios for North American populations of P. pyralis, which were collected from Texas to New Jersey. We used a combination of ABC techniques (for multi-population/colonization analyses) and likelihood inference (dadi, StairwayPlot2, PoMo) for single-population demographic inference, which proved useful with our RAD data. We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. To estimate the age of divergence between of P. pyralis, which provides deeper insights into the history of the entire species, we assembled a multi-locus phylogenetic data covering the genus Photinus. We uncovered that the phylogenetic node leading to P. pyralis lies at the end of the Miocene. Importantly, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns in a widespread native insect species, which will serve in future studies for the detection of adaptation events in this firefly species, as well as a comparison for future studies of other North American insect taxa
Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture
No full text<p>This "<span>norm_exp_15spe_4tips_new.RData</span>" repository contains all the necessary datasets of this study. </p>
<p>All the required scripts, gene expression data and function file of this study are available on GitHub: <a href="https://github.com/tbegum/phylogenetic-modeling-of-evolutionary_trait_jumps.%20For">https://github.com/tbegum/phylogenetic-modeling-of-evolutionary-trait-jumps.</a></p>
- …
