Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.

Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

The analysis of mitochondrial and nuclear DNA sequence polymorphisms from modern cattle populations has had a profound impact on our understanding of the events surrounding the domestication of cattle. From these studies, it has been possible to distinguish between pre- and post-domestic genetic differentiation, supporting previous assertions from archaeological studies and, in some cases, revealing novel aspects of the demographic history of cattle. Analyses of genetic material retrieved from the remains of extinct ancestral wild cattle have also added valuable layers of information pertaining to cattle domestic origins; however, information from these investigations have, in general, been limited to small, variable portions of the mitochondrial genome owing to technical challenges associated with the retrieval and amplification of ancient DNA. In recent years, however, new high-throughput, massively parallel genomics technology platforms, such as single-nucleotide polymorphism (SNP) genotyping arrays and next-generation sequencing (NGS), have provided a new impetus to the studies of genetic variation in extant and ancient cattle. Arrays of SNP have facilitated high-resolution genetic surveys of global cattle populations and detection of ancient and recent genomic selective sweeps. Next-generation sequencing analyses of modern and ancient cattle hold great promise for identifying and cataloging of pre- and post-domestication patterns of genomic variation and correlating this with natural and artificial selection processes

Essential Simplices in Persistent Homology and Subtle Admixture Detection

We introduce a robust mathematical definition of the notion of essential elements in a basis of the homology space and prove that these elements are unique. Next we give a novel visualization of the essential elements of the basis of the homology space through a rainfall-like plot (RFL). This plot is data-centric, i.e., is associated with the individual samples of the data, as opposed to the structure-centric barcodes of persistent homology. The proof-of-concept was tested on data generated by SimRA that simulates different admixture scenarios. We show that the barcode analysis can be used not just to detect the presence of admixture but also estimate the number of admixed populations. We also demonstrate that data-centric RFL plots have the potential to further disentangle the common history into admixture events and relative timing of the events, even in very complex scenarios

Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.

Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation

Floquet interface states in illuminated three-dimensional topological insulators

Recent experiments showed that the surface of a three dimensional topological insulator develops gaps in the Floquet-Bloch band spectrum when illuminated with a circularly polarized laser. These Floquet-Bloch bands are characterized by non-trivial Chern numbers which only depend on the helicity of the polarization of the radiation field. Here we propose a setup consisting of a pair of counter-rotating lasers, and show that one-dimensional chiral states emerge at the interface between the two lasers. These interface states turn out to be spin-polarized and may trigger interesting applications in the field of optoelectronics and spintronics.Comment: 5 pages with 3 figures + supplemental materia

Genomics of clownfish adaptive radiation

How species diversify, creating the astonishing biodiversity observed on Earth, has been a central question since Darwin’s On the Origin of Species. Thanks to the sequencing revolution, this question can be approached today from a genomic perspective, examining how intrinsic genomic architecture and extrinsic biological and ecological factors interplay to shape the diversification of organisms. In this sense, clownfishes, which experienced an adaptive radiation following the acquisition of mutualism with sea anemones, represent a fascinating system. Thus, in this thesis, I combine comparative and population genomics approaches to study the genomic architecture underlying the diversification of this group. In the first two sections, I generate genomic resources for ten closely related but ecologically divergent clownfish species and the damselfish Pomacentrus moluccensis. Using this data, I question the genetic mechanisms underlying the acquisition of mutualism. I identify several candidate genes that experienced positive selection at the basis of clownfish radiation and show functions associated with sea anemones toxins discharge, thus likely involved in the evolution of clownfishes' ability to live unharmed within their otherwise-toxic hosts. In the last two sections, I dive into the diversification process of clownfishes. Through comparative genomics approaches, I show that the group experienced bursts of transposable elements, overall accelerated molecular evolution, and ancestral hybridization events, which likely facilitated the radiation of the group by generating the genomic variations necessary for natural selection to act on. I identify genes undergoing differential selective pressures linked with ecological divergence, suggesting that parallel evolution is shaping clownfish diversification, and I pinpoint candidate genes involved in the evolution of the particular size- based hierarchical social structure observed in the group. I finally focus on the mechanisms underlying the evolution of a clownfish clade, the skunk complex. Through population genomics approaches, I demonstrate that gene flow occurred throughout the diversification of the group. Indeed, the species experienced moderate ancestral gene flow, which lessened but still persists in sympatry. Moreover, contrary to what was previously suggested, I demonstrate that A. sandaracinos did not originate from hybrid speciation. I finally pinpoint candidate regions of introgression between species that likely played a role in the diversification of the complex. Overall, my work provides the first insights into the genomic mechanisms underlying clownfish adaptive radiation. -- Comprendre comment les espèces se diversifient et créent l'étonnante biodiversité observée sur Terre sont des questions centrales depuis l’écriture de l’Origine des espèces par Darwin. Grâce à la révolution du séquençage, ces questions peuvent être abordées aujourd'hui en examinant comment l'architecture génomique et les facteurs biologiques et écologiques interagissent et mènent à la diversification des organismes. En ce sens, les poissons-clowns, qui ont connu une radiation adaptative suite à l'acquisition du mutualisme avec les anémones de mer, représentent un système fascinant. Ainsi, dans cette thèse, j’étudie l'architecture génomique qui sous-tend la diversification de ce groupe. Dans les deux premières sections, je génère des ressources génomiques pour dix espèces de poissons-clowns ainsi que pour l’espèce de demoiselle Pomacentrus moluccensis. À partir de ces données, je questionne les mécanismes génétiques qui sous-tendent l'acquisition du mutualisme. J’identifie plusieurs gènes ayant subi une sélection positive à la base du rayonnement des poissons-clowns. Ces gènes ont des fonctions associées à la décharge des toxines des anémones, suggérant donc une implication dans l'évolution de la capacité des poissons-clowns à vivre au sein de leurs hôtes normalement toxiques. Dans les deux dernières sections, je me plonge dans le processus de diversification des poissons-clowns. Grâce à des approches de génomique comparative, je montre non seulement que ce groupe compte une importante quantité d'éléments transposables au sein de son génome, mais qu’il a également subi une évolution moléculaire accélérée ainsi que des événements d'hybridation ancestrale. La combinaison de ces différents éléments a probablement facilité leur diversification en générant les variations génomiques nécessaires à l'action de la sélection naturelle. J’identifie également des gènes ayant subi des pressions de sélection différentielles en lien avec des divergences écologiques, suggérant donc un processus d’évolution parallèle impliquée dans la diversification des poissons-clowns. Finalement, je me suis concentrée sur les mécanismes liés à l'évolution d'un clade de poisson- clown - le clade “skunk”. Je démontre qu’un flux de gènes modéré s'est produit tout au long de la diversification de ce groupe, et - bien que son amplitude ait diminué avec le temps - il persiste encore en sympatrie. De plus, j’identifie des régions candidates d'introgression entre espèces qui ont probablement joué un rôle dans la diversification du complexe. Dans l'ensemble, mon travail fournit les premières informations concernant les mécanismes génomiques impliqués dans la radiation adaptative des poissons-clowns