Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution

Dynamics of Genome Rearrangement in Bacterial Populations

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes

Greeks and the Peoples of the Black Sea Region. Beyond Ethnicity and Identity: an Archaeology of Commonalities

This paper presents a new theoretical framework for analyzing cultural interactions which focuses on mapping tangible changes in the material culture, and consequently the customs of the studied people, without making assumptions about self-professed identities. By doing so, this framework deemphasizes the issue of ethnicity and limits the role of modern ethno-cultural biases in the study of ancient societies. The applicability of this theoretical framework, termed “archaeology of commonalities”, is demonstrated in relation to the cemeteries of Nymphaion, a settlement situated on the eastern shores of the Crimean Peninsula.Les Grecs et les peuples de la région de la mer Noire. Au-delà de l’ethnicité et de l’identité : une archéologie des traits partagés Cet article présente un nouveau cadre théorique pour l’analyse des interactions culturelles, centré sur l’enregistrement des changements tangibles dans la culture matérielle et, par conséquent des habitudes des populations étudiées, sans préjuger d’éventuelles identités auto-assignées. De cette manière, ce cadre limite l’importance de la question de l’ethnicité et le rôle des biais ethno-culturels modernes dans l’étude des sociétés anciennes. La démonstration de l’applicabilité de ce cadre théorique, appelé «archéologie des traits partagés [“communalités”] » , s’appuie ici sur l’analyse des nécropoles de Nymphaion, un établissement situé sur les rives orientales de la Crimée.K. Szamalek Jakub. Greeks and the Peoples of the Black Sea Region. Beyond Ethnicity and Identity: an Archaeology of Commonalities . In: Dialogues d'histoire ancienne. Supplément n°10, 2014. pp. 53-80

Greeks and the Peoples of the Black Sea Region. Beyond Ethnicity and Identity: an Archaeology of Commonalities

This paper presents a new theoretical framework for analyzing cultural interactions which focuses on mapping tangible changes in the material culture, and consequently the customs of the studied people, without making assumptions about self-professed identities. By doing so, this framework deemphasizes the issue of ethnicity and limits the role of modern ethno-cultural biases in the study of ancient societies. The applicability of this theoretical framework, termed “archaeology of commonalities”, is demonstrated in relation to the cemeteries of Nymphaion, a settlement situated on the eastern shores of the Crimean Peninsula.Les Grecs et les peuples de la région de la mer Noire. Au-delà de l’ethnicité et de l’identité : une archéologie des traits partagés Cet article présente un nouveau cadre théorique pour l’analyse des interactions culturelles, centré sur l’enregistrement des changements tangibles dans la culture matérielle et, par conséquent des habitudes des populations étudiées, sans préjuger d’éventuelles identités auto-assignées. De cette manière, ce cadre limite l’importance de la question de l’ethnicité et le rôle des biais ethno-culturels modernes dans l’étude des sociétés anciennes. La démonstration de l’applicabilité de ce cadre théorique, appelé «archéologie des traits partagés [“communalités”] » , s’appuie ici sur l’analyse des nécropoles de Nymphaion, un établissement situé sur les rives orientales de la Crimée.K. Szamalek Jakub. Greeks and the Peoples of the Black Sea Region. Beyond Ethnicity and Identity: an Archaeology of Commonalities . In: Dialogues d'histoire ancienne. Supplément n°10, 2014. pp. 53-80

Recurrent inversion toggling and great ape genome evolution

Inversions play an important role in disease and evolution but are difficult to characterize because their breakpoints map to large repeats. We increased by sixfold the number (n = 1,069) of previously reported great ape inversions by using single-cell DNA template strand and long-read sequencing. We find that the X chromosome is most enriched (2.5-fold) for inversions, on the basis of its size and duplication content. There is an excess of differentially expressed primate genes near the breakpoints of large (>100 kilobases (kb)) inversions but not smaller events. We show that when great ape lineage-specific duplications emerge, they preferentially (approximately 75%) occur in an inverted orientation compared to that at their ancestral locus. We construct megabase-pair scale haplotypes for individual chromosomes and identify 23 genomic regions that have recurrently toggled between a direct and an inverted state over 15 million years. The direct orientation is most frequently the derived state for human polymorphisms that predispose to recurrent copy number variants associated with neurodevelopmental disease