Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

Alignment of reference cox1 sequences used in this study. The fragment we used corresponds to positions 6189–6539, Cambridge reference sequence. (TXT 241 kb

Sex chromosomes: how X-Y recombination stops

AbstractSex chromosomes are thought to have evolved from an ordinary autosomal pair in a process involving progressive reduction of recombination between the X and Y chromosomes. A recent study of X-Y locus AMELOGENIN in mammals has provided new insights into how X-Y recombination is suppressed and the consequences of this suppression

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

<p>Abstract</p> <p>Background</p> <p>During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.</p> <p>Results</p> <p>A phylogenetic analysis of cytochrome <it>b </it>third-codon position confirms that the mitochondrial DNA mutation rate is quite variable in birds, passerines being the fastest evolving order. On average, mitochondrial DNA evolves slower in birds than in mammals of similar body size. This result is in agreement with the longevity hypothesis, and contradicts the hypothesis of a metabolic rate-dependent mutation rate. Birds show no footprint of adaptive selection on cytochrome <it>b </it>evolutionary patterns, but no link between direct estimates of population size and cytochrome <it>b </it>diversity. The mutation rate is the best predictor we have of within-species mitochondrial diversity in birds. It partly explains the differences in mitochondrial DNA diversity patterns observed between mammals and birds, previously interpreted as reflecting Hill-Robertson interferences with the W chromosome.</p> <p>Conclusion</p> <p>Mitochondrial DNA diversity patterns in birds are strongly influenced by the wide, unexpected variation of mutation rate across species. From a fundamental point of view, these results are strongly consistent with a relationship between species maximal longevity and mitochondrial mutation rate, in agreement with the mitochondrial theory of ageing. Form an applied point of view, this study reinforces and extends the message of caution previously expressed for mammals: mitochondrial data tell nothing about species population sizes, and strongly depart the molecular clock assumption.</p

Polymorphix: a sequence polymorphism database

Within-species sequence variation data are of special interest since they contain information about recent population/species history, and the molecular evolutionary forces currently in action in natural populations. These data, however, are presently dispersed within generalist databases, and are difficult to access. To solve this problem, we have developed Polymorphix, a database dedicated to sequence polymorphism. It contains within-species homologous sequence families built using EMBL/GenBank under suitable similarity and bibliographic criteria. Polymorphix is an ACNUC structured database allowing both simple and complex queries for population genomic studies. Alignments within families as well as phylogenetic trees can be download. When available, outgroups are included in the alignment. Polymorphix contains sequences from the nuclear, mitochondrial and chloroplastic genomes of every eukaryote species represented in EMBL. It can be accessed by a web interface (http://pbil.univ-lyon1.fr/polymorphix/query.php)

An Algorithm Based on a Cable-Nernst Planck Model Predicting Synaptic Activity throughout the Dendritic Arbor with Micron Specificity

Recent technological advances have enabled the recording of neurons in intact circuits with a high spatial and temporal resolution, creating the need for modeling with the same precision. In particular, the development of ultra-fast two-photon microscopy combined with fluorescence-based genetically-encoded Ca2+-indicators allows capture of full-dendritic arbor and somatic responses associated with synaptic input and action potential output. The complexity of dendritic arbor structures and distributed patterns of activity over time results in the generation of incredibly rich 4D datasets that are challenging to analyze (Sakaki, 2020). Interpreting neural activity from fluorescence-based Ca2+ biosensors is challenging due to non-linear interactions between several factors influencing intracellular calcium ion concentration and its binding to sensors, including the ionic dynamics driven by diffusion, electrical gradients and voltage-gated conductance.To investigate those dynamics, we designed a model based on a Cable-like equation coupled to the Nernst-Planck equations for ionic fluxes in electrolytes. We employ this model to simulate signal propagation and ionic electrodiffusion across a dendritic arbor. Using these simulation results, we then designed an algorithm to detect synapses from Ca2+ imaging datasets. We finally apply this algorithm to experimental Ca2+-indicator datasets from neurons expressing jGCaMP7s (Dana et al., 2019), using full-dendritic arbor sampling in vivo in the Xenopus laevis optic tectum using fast random-access two-photon microscopy.Our model reproduces the dynamics of visual stimulus-evoked jGCaMP7s-mediated calcium signals observed experimentally, and the resulting algorithm allows prediction of the location of synapses across the dendritic arbor.Our study provides a way to predict synaptic activity and location on dendritic arbors, from fluorescence data in the full dendritic arbor of a neuron recorded in the intact and awake developing vertebrate brain