A burst of segmental duplications in the genome of the African great ape ancestor

It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.

Morphology in phonology : introduction

This fourth volume of Catalan Journal of Linguistics is devoted to a topic discussed at length in the literature but which nevertheless remains a challenge for any view of phonology: the morphology-phonology interaction. The papers collected address two related issues, the role of morphological information in phonology and the role of phonological information in morphology. The first six articles (i.e. McCarthy, Wheeler, Downing, van Oostendorp, José and Auger, and Rice) deal with the former topic; the last three (i.e. Bertinetto and Jetchev, Pérez Saldanya and Vallès, and Viaplana), with the latter. Several papers (Wheeler, van Oostendorp, Rice, Bertinetto and Jetchev, Pérez Saldanya and Vallès, and Viaplana) further discuss the role and concept of paradigms, an old Neogrammarian notion to which renewed attention has been payed both from the phonological perspective (cf. work by Benua 1995, 1997; Burzio 1994 and subsequent work; Kenstowicz 1996, 2002; Steriade 2000, and the articles in the recent volume edited by Downing et al. 2005, among others) and from the morphological perspective (cf. work by Aronoff 1994; Bauer 1997, 2001; Carstairs-McCarthy 1994, 1998; Stump 1991, 1997; van Marle 1985, 1994; Wurzel 1989, and several articles in the recent volume edited by Boucher 2002, among others).

The origins and impact of primate segmental duplications

Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements.Results: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

Loanword Phonology, Lexical Exceptions, Morphologically Driven Underapplication, and the Nature of Positionally Biased Constraints

In this paper we provide a formal account for underapplication of vowel reduction to schwa in Majorcan Catalan loanwords and learned words. On the basis of the comparison of these data with those concerning productive derivation and verbal inflection, which show analogous patterns, in this paper we also explore the existing and not yet acknowledged correlation between those processes that exhibit a particular behaviour in the loanword phonology with respect to the native phonology of the language, those processes that show lexical exceptions and those processes that underapply due to morphological reasons. In light of the analysis of the very same data and taking into account the aforementioned correlation, we show how there might exist a natural diachronic relation between two kinds of Optimality Theory constraints which are commonly used but, in principle, mutually exclusive: positional faithfulness and contextual markedness constraints. Overall, phonological productivity is proven to be crucial in three respects: first, as a context of the grammar, given that «underapplication» is systematically found in what we call the productive phonology of the dialect (including loanwords, learned words, productive derivation and verbal inflection); second, as a trigger or blocker of processes, in that the productivity or the lack of productivity of a specific process or constraint in the language is what explains whether it is challenged or not in any of the depicted situations, and, third, as a guiding principle which can explain the transition from the historical to the synchronic phonology of a linguistic variety.

Leading tone alignment in occitan disapproval statements

L’accent nuclear ascendent-descendent de les oracions expressant desacord en occità consta de tres tons: LH+L*. En comptes de precedir el to asterisc (“starred tone”) a un interval fix en temps normalitzat (Pierrehumbert & Beckman 1989), els tons menadors (“leading tones”) L i H s’alineen amb determinats punts d’ancoratge de la cadena de segments: les fronteres dreta i esquerra de la síl•laba pretònica, respectivament. El model de Grice (1995b) per a l’estructura dels accents tonals permet donar compte d’aquest patró d’alineació incloent els tons menadors en un node diferent que precedeix el que domina to seguidor (“trailing tone”) i to asterisc.

Aspectes fonològics del català de la comarca de la Selva

En aquest treball es presenten alguns dels aspectes més destacats de la fonologia del català parlat a la comarca de la Selva. A partir de 34 entrevistes realitzades a informants de dues generacions diferents de 17 municipis selvatans, el treball descriu els trets observats i planteja també una anàlisi de la variació observada entre els diferents municipis i entre les dues franges d’edat enquestades

Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5′-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters

Background: Hox and ParaHox gene clusters are thought to have resulted from the duplication of a ProtoHox gene cluster early in metazoan evolution. However, the origin and evolution of the other genes belonging to the extended Hox group of homeobox-containing genes, that is, Mox and Evx, remains obscure. We constructed phylogenetic trees with mouse, amphioxus and Drosophila extended Hox and other related Antennapedia-type homeobox gene sequences and analyzed the linkage data available for such genes.Results: We claim that neither Mox nor Evx is a Hox or ParaHox gene. We propose a scenariothat reconciles phylogeny with linkage data, in which an Evx/Mox ancestor gene linked to aProtoHox cluster was involved in a segmental tandem duplication event that generated an arrayof all Hox-like genes, referred to as the `coupled¿ cluster. A chromosomal breakage within thiscluster explains the current composition of the extended Hox cluster (with Evx, Hox and Moxgenes) and the ParaHox cluster.Conclusions: Most studies dealing with the origin and evolution of Hox and ParaHox clustershave not included the Hox-related genes Mox and Evx. Our phylogenetic analyses and theavailable linkage data in mammalian genomes support an evolutionary scenario in which anancestor of Evx and Mox was linked to the ProtoHox cluster, and that a tandem duplication of alarge genomic region early in metazoan evolution generated the Hox and ParaHox clusters, plusthe cluster-neighbors Evx and Mox. The large `coupled¿ Hox-like cluster EvxHox/MoxParaHox wassubsequently broken, thus grouping the Mox and Evx genes to the Hox clusters, and isolating theParaHox cluster.

OCP effects in catalan cliticization

In Catalan, sequences of sibilants are never pronounced as such. In most contexts all varieties coincide in the «strategies» used to avoid these sequences, namely epenthesis or deletion. Variation is only found in the domain of pronominal clitics (but not with other types of clitics). One source of variation is accounted for by decomposing a general constraint into two specific ones, which implies partial constraint reranking. The other source of variation, which involves a case of apparent opacity, is explained through an Output-Output constraint that makes reference to paradigmatic relations.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

El dialecte saxó:Presència escrita i prestigi social

El treball següent ofereix una visió global d'un dels dialectes de la llengua alemanya que menys ha estat objecte de recerca i investigació, el saxó, centrant-se en la presència escrita de què gaudeix aquesta varietat actualment i el seu prestigi social a Alemanya a través dels anys