Author
Rosa Alcazar
Bio: Rosa Alcazar is an academic researcher from Stanford University. The author has contributed to research in topics: Adaptive radiation & Cichlid. The author has an hindex of 7, co-authored 7 publications receiving 1667 citations.
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University of Oxford1, Broad Institute2, Swiss Federal Institute of Aquatic Science and Technology3, University of Bern4, Wellcome Trust Sanger Institute5, Wellcome Trust/Cancer Research UK Gurdon Institute6, University of Konstanz7, Agency for Science, Technology and Research8, Reed College9, Stanford University10, California Institute of Technology11, Benaroya Research Institute12, University of Rennes13, Georgia Institute of Technology14, University of Maryland, College Park15, University of Basel16, University of Texas at Austin17, Tokyo Institute of Technology18, National Museum of Natural History19, University of Stirling20, Carnegie Institution for Science21, National Cheng Kung University22, Science for Life Laboratory23, Norwich University24
TL;DR: This article found an excess of gene duplications in the East African lineage compared to Nile tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
832 citations
Broad Institute1, University of Oxford2, University of Bern3, Swiss Federal Institute of Aquatic Science and Technology4, Wellcome Trust Sanger Institute5, Wellcome Trust/Cancer Research UK Gurdon Institute6, University of Konstanz7, Agency for Science, Technology and Research8, Reed College9, Stanford University10, California Institute of Technology11, Benaroya Research Institute12, University of Rennes13, Georgia Institute of Technology14, University of Maryland, College Park15, University of Basel16, University of Texas at Austin17, Tokyo Institute of Technology18, National Museum of Natural History19, University of Stirling20, Carnegie Institution for Science21, National Cheng Kung University22, Science for Life Laboratory23, Norwich University24
TL;DR: It is concluded that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
666 citations
TL;DR: A systematic pedigree-based analysis of heritable silencing processes resulting from initiation of interference targeted at the C. elegans oocyte maturation factor oma-1 reveals that silencing in the early generations is transmitted independently of the original targeted locus, in a manner indicative of a diffusible epigenetic element.
Abstract: Heritable silencing effects are gene suppression phenomena that can persist for generations after induction In the majority of RNAi experiments conducted in Caenorhabditis elegans, the silencing response results in a hypomorphic phenotype where the effects recede after the F1 generation F2 and subsequent generations revert to the original phenotype Specific examples of transgenerational RNAi in which effects persist to the F2 generation and beyond have been described In this study, we describe a systematic pedigree-based analysis of heritable silencing processes resulting from initiation of interference targeted at the C elegans oocyte maturation factor oma-1 Heritable silencing of oma-1 is a dose-dependent process where the inheritance of the silencing factor is unequally distributed among the population Heritability is not constant over generational time, with silenced populations appearing to undergo a bottleneck three to four generations following microinjection of RNA Transmission of silencing through these generations can be through either maternal or paternal gamete lines and is surprisingly more effective through the male gametic line Genetic linkage tests reveal that silencing in the early generations is transmitted independently of the original targeted locus, in a manner indicative of a diffusible epigenetic element
186 citations
TL;DR: A surprising long-range periodicity that underlies a substantial fraction of C. elegans genomic sequence is described, potentially producing a structure that could resist the assembly of highly ordered nucleosome arrays that have been proposed as a precursor to heterochromatin.
Abstract: We describe a surprising long-range periodicity that underlies a substantial fraction of C. elegans genomic sequence. Extended segments (up to several hundred nucleotides) of the C. elegans genome show a strong bias toward occurrence of AA/TT dinucleotides along one face of the helix while little or no such constraint is evident on the opposite helical face. Segments with this characteristic periodicity are highly overrepresented in intron sequences and are associated with a large fraction of genes with known germline expression in C. elegans. In addition to altering the path and flexibility of DNA in vitro, sequences of this character have been shown by others to constrain DNA::nucleosome interactions, potentially producing a structure that could resist the assembly of highly ordered (phased) nucleosome arrays that have been proposed as a precursor to heterochromatin. We propose a number of ways that the periodic occurrence of An/Tn clusters could reflect evolution and function of genes that express in the germ cell lineage of C. elegans.
65 citations
TL;DR: The data suggest that experience is an advantage during fights for status, and that social learning provides more relevant experience than the physical complexity of the territory.
Abstract: Life experiences can alter cognitive abilities and subsequent behavior. Here we asked whether differences in experience could affect social status. In hierarchical animal societies, high-ranking males that typically win aggressive encounters gain territories and hence access to mates. To understand the relative contributions of social experience and physical environment on status, we used a highly territorial African cichlid fish species, Astatotilapia burtoni, that lives in a dynamic lek-like social hierarchy. Astatotilapia burtoni males are either dominant or submissive and can switch status rapidly depending on the local environment. Although dominant males are innately aggressive, we wondered whether they modulated their aggression based on experience. We hypothesized that as males mature they might hone their fighting tactics based on observation of other males fighting. We compared males of different ages and sizes in distinctly different physical environments and subsequently tested their fighting skills. We found that a size difference previously thought negligible (<10% body length) gave a significant advantage to the larger opponent. In contrast, we found no evidence that increasing environmental complexity affected status outcomes. Surprisingly, we found that males only a few days older than their opponents had a significant advantage during territorial disputes so that being older compensated for the disadvantage of being smaller. Moreover, the slightly older winners exploited a consistent fighting strategy, starting with lower levels of aggression on the first day that significantly increased on the second day, a pattern absent in younger winners. These data suggest that experience is an advantage during fights for status, and that social learning provides more relevant experience than the physical complexity of the territory.
33 citations
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31 Jan 1963
2,885 citations
Max Planck Society1, University of Auckland2, Swiss Institute of Bioinformatics3, ETH Zurich4, University of Melbourne5, University of Technology, Sydney6, University of Otago7, University of Gothenburg8, European Bioinformatics Institute9, University of Basel10, Rice University11, University of Oxford12, University of Edinburgh13, North Carolina State University14, Imperial College London15, University of California, Los Angeles16, Chinese Academy of Sciences17
TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.
Abstract: Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
2,045 citations
TL;DR: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects and generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.
Abstract: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based ann ...
849 citations
TL;DR: It is demonstrated that a germline nuclear small RNA/chromatin pathway can maintain stable inheritance for many generations when triggered by a piRNA-dependent foreign RNA response in C. elegans.
689 citations
TL;DR: These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution and release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.
Abstract: Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.
630 citations