| 1. |
- Gauthier, Jérémy, et al.
(författare)
-
First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini) : Comparative models for mimicry genetic studies
- 2023
-
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 23:4, s. 872-885
-
Tidskriftsartikel (refereegranskat)abstract
- The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.
|
|
| 2. |
- Aurelle, Didier, et al.
(författare)
-
On the specific status of eastern Mediterranean Dendrophyllia corals (Cnidaria, Anthozoa): Genetic characterization and speciation scenarios
- 2024
-
Ingår i: Zoologica Scripta. - 0300-3256 .- 1463-6409. ; 53:2, s. 235-247
-
Tidskriftsartikel (refereegranskat)abstract
- The deep-sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to D. ramea but had some morphological differences with other known populations of this species. Here, we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two Caryophyllia species. Both morphological and genetic data confirm that corals found off Cyprus belong to the D. ramea species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species.
|
|
| 3. |
- Bouakaze, Caroline, et al.
(författare)
-
Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex) : Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters
- 2020
-
Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
-
Tidskriftsartikel (refereegranskat)abstract
- We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
|
|
| 4. |
- Saideh, Ibrahim, et al.
(författare)
-
Projection-based adiabatic elimination of bipartite open quantum systems
- 2020
-
Ingår i: Physical Review A. - 2469-9926. ; 102:3
-
Tidskriftsartikel (refereegranskat)abstract
- Adiabatic elimination methods allow the reduction of the space dimension needed to describe systems whose dynamics exhibit separation of timescale. For open quantum systems, it consists in eliminating the fast part assuming it has almost instantaneously reached its steady state and obtaining an approximation of the evolution of the slow part. These methods can be applied to eliminate a linear subspace within the system Hilbert space or, alternatively, to eliminate a fast subsystem in a bipartite quantum system. In this work, we extend an adiabatic elimination method used for removing fast degrees of freedom within a system [Phys. Rev. A 101, 042102 (2020)2469-992610.1103/PhysRevA.101.042102] to eliminate a subsystem from an open bipartite quantum system. As an illustration, we apply our technique to a dispersively coupled two-qubit system and in the case of the open Rabi model.
|
|
