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Marie-anne Félix - One of the best experts on this subject based on the ideXlab platform.
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Comparative genomics of 10 new Caenorhabditis species.
Evolution letters, 2019Co-Authors: Lewis Stevens, Marie-anne Félix, Lise Frézal, David H A Fitch, Christian Braendle, Toni Beltran, Carlos Caurcel, Sarah Fausett, Charlie Gosse, Taniya KaurAbstract:The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Comparative genomics of ten new Caenorhabditis species
2018Co-Authors: Lewis Stevens, Marie-anne Félix, Lise Frézal, David H A Fitch, Christian Braendle, Toni Beltran, Carlos Caurcel, Sarah Fausett, Taniya Kaur, Karin KiontkeAbstract:The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species.
PLoS ONE, 2014Co-Authors: Marie-anne Félix, Asher D Cutter, Christian Braendle, Bob GoldsteinAbstract:The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence. With the aim of expediting species designations, here we propose and apply a revised framework for species diagnosis and description in this group. Our solution prioritizes reproductive isolation over traditional morphological characters as the key feature in delineating and diagnosing new species, reflecting both practical considerations and conceptual justifications. DNA sequence divergence criteria help prioritize crosses for establishing patterns of reproductive isolation among the many species of Caenorhabditis known to science, such as with the ribosomal internal transcribed spacer-2 (ITS2) DNA barcode. By adopting this approach, we provide new species name designations for 15 distinct biological species, thus increasing the number of named Caenorhabditis species in laboratory culture by nearly 3-fold. We anticipate that the improved accessibility of these species to the research community will expand the opportunities for study and accelerate our understanding of diverse biological phenomena.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes.
Virology, 2013Co-Authors: Carl J. Franz, Marie-anne Félix, Hilary Renshaw, Lise Frézal, Yanfang Jiang, David WangAbstract:Abstract The discoveries of Orsay, Santeuil and Le Blanc viruses, three viruses infecting either Caenorhabditis elegans or its relative Caenorhabditis briggsae, enable the study of virus–host interactions using natural pathogens of these two well-established model organisms. We characterized the tissue tropism of infection in Caenorhabditis nematodes by these viruses. Using immunofluorescence assays targeting proteins from each of the viruses, and in situ hybridization, we demonstrate viral proteins and RNAs localize to intestinal cells in larval stage Caenorhabditis nematodes. Viral proteins were detected in one to six of the 20 intestinal cells present in Caenorhabditis nematodes. In Orsay virus-infected C. elegans, viral proteins were detected as early as 6 h post-infection. The RNA-dependent RNA polymerase and capsid proteins of Orsay virus exhibited different subcellular localization patterns. Collectively, these observations provide the first experimental insights into viral protein expression in any nematode host, and broaden our understanding of viral infection in Caenorhabditis nematodes.
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Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest.
BMC Evolutionary Biology, 2013Co-Authors: Marie-anne Félix, Richard Jovelin, Celine Ferrari, Shery Han, Young Ran Cho, Erik Andersen, Asher Cutter, Christian BraendleAbstract:UNLABELLED: ABSTRACT: BACKGROUND: In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. METHODS: Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. RESULTS: Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. CONCLUSIONS: The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species.
Asher D Cutter - One of the best experts on this subject based on the ideXlab platform.
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X exceptionalism in Caenorhabditis speciation
Molecular ecology, 2017Co-Authors: Asher D CutterAbstract:Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis. Studies to date implicate improper chromatin regulation of the X-chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self-fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y-chromosome, sex chromosome-dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation.
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Ephemeral-Habitat Colonization And Neotropical Species Richness Of Caenorhabditis Nematodes
2017Co-Authors: Celine Ferrari, Richard Jovelin, Asher D Cutter, Romain Salle, Nicolas Callemeyn-torre, Christian BraendleAbstract:Background: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar outward morphology despite deep genomic divergence. Methods: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats. Results: We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity. Discussion: Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.
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Caenorhabditis evolution in the wild
BioEssays : news and reviews in molecular cellular and developmental biology, 2015Co-Authors: Asher D CutterAbstract:Recent research has filled many gaps about Caenorhabditis natural history, simultaneously exposing how much remains to be discovered. This awareness now provides means of connecting ecological and evolutionary theory with diverse biological patterns within and among species in terms of adaptation, sexual selection, breeding systems, speciation, and other phenomena. Moreover, the heralded laboratory tractability of C. elegans, and Caenorhabditis species generally, provides a powerful case study for experimental hypothesis testing about evolutionary and ecological processes to levels of detail unparalleled by most study systems. Here, I synthesize pertinent theory with what we know and suspect about Caenorhabditis natural history for salient features of biodiversity, phenotypes, population dynamics, and interactions within and between species. I identify topics of pressing concern to advance Caenorhabditis biology and to study general evolutionary processes, including the key opportunities to tackle problems in dispersal dynamics, competition, and the dimensionality of niche space.
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Mainstreaming Caenorhabditis elegans in experimental evolution
Proceedings. Biological sciences, 2014Co-Authors: Jeremy C. Gray, Asher D CutterAbstract:Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host–pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.
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Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes
Proceedings. Biological sciences, 2014Co-Authors: Richard Jovelin, Toyoshi Yoshiga, Ryusei Tanaka, Asher D CutterAbstract:Species with broad ecological amplitudes with respect to a key focal resource, niche generalists, should maintain larger and more connected populations than niche specialists, leading to the prediction that nucleotide diversity will be lower and more subdivided in specialists relative to their generalist relatives. This logic describes the specialist-generalist variation hypothesis (SGVH). Some outbreeding species of Caenorhabditis nematodes use a variety of invertebrate dispersal vectors and have high molecular diversity. By contrast, Caenorhabditis japonica lives in a strict association and synchronized life cycle with its dispersal host, the shield bug Parastrachia japonensis, itself a diet specialist. Here, we characterize sequence variation for 20 nuclear loci to investigate how C. japonica's life history shapes nucleotide diversity. We find that C. japonica has more than threefold lower polymorphism than other outbreeding Caenorhabditis species, but that local populations are not genetically disconnected. Coupled with its restricted range, we propose that its specialist host association contributes to a smaller effective population size and lower genetic variation than host generalist Caenorhabditis species with outbreeding reproductive modes. A literature survey of diverse organisms provides broader support for the SGVH. These findings encourage further testing of ecological and evolutionary hypotheses with comparative population genetics in Caenorhabditis and other taxa.
Christian Braendle - One of the best experts on this subject based on the ideXlab platform.
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Comparative genomics of 10 new Caenorhabditis species.
Evolution letters, 2019Co-Authors: Lewis Stevens, Marie-anne Félix, Lise Frézal, David H A Fitch, Christian Braendle, Toni Beltran, Carlos Caurcel, Sarah Fausett, Charlie Gosse, Taniya KaurAbstract:The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Comparative genomics of ten new Caenorhabditis species
2018Co-Authors: Lewis Stevens, Marie-anne Félix, Lise Frézal, David H A Fitch, Christian Braendle, Toni Beltran, Carlos Caurcel, Sarah Fausett, Taniya Kaur, Karin KiontkeAbstract:The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Ephemeral-Habitat Colonization And Neotropical Species Richness Of Caenorhabditis Nematodes
2017Co-Authors: Celine Ferrari, Richard Jovelin, Asher D Cutter, Romain Salle, Nicolas Callemeyn-torre, Christian BraendleAbstract:Background: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar outward morphology despite deep genomic divergence. Methods: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats. Results: We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity. Discussion: Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.
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Workshop report: Caenorhabditis nematodes as model organisms to study trait variation and its evolution.
Worm, 2015Co-Authors: Christian Braendle, Henrique TeotonioAbstract:A fundamental problem in biology is to understand how genome expression translates into variation in molecular, cellular, developmental, physiological, behavioral, or life-history traits. During the summer of 2014, worm biologists with a keen interest in evolutionary biology and natural ecology met in Les Treilles (France) to define the problems of trait variation better and to discuss empirical approaches using Caenorhabditis species to address these problems. Compared with other model organisms, Caenorhabditis has several advantages, such as well-defined traits that can be subjected to highly controlled environmental and genetic manipulation and the possibility for long-term experimental evolution that can be coupled with genome-wide mapping of trait variation. The Les Treilles workshop brought together researchers studying the evolution of phenotypic plasticity, gene-networks, genome structure and population genetics, sex-determination and development in the laboratory, behavior and the life-history of natural Caenorhabditis populations. Here, we outline the key aims of this workshop and summarize the contributions of each participant.
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A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species.
PLoS ONE, 2014Co-Authors: Marie-anne Félix, Asher D Cutter, Christian Braendle, Bob GoldsteinAbstract:The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence. With the aim of expediting species designations, here we propose and apply a revised framework for species diagnosis and description in this group. Our solution prioritizes reproductive isolation over traditional morphological characters as the key feature in delineating and diagnosing new species, reflecting both practical considerations and conceptual justifications. DNA sequence divergence criteria help prioritize crosses for establishing patterns of reproductive isolation among the many species of Caenorhabditis known to science, such as with the ribosomal internal transcribed spacer-2 (ITS2) DNA barcode. By adopting this approach, we provide new species name designations for 15 distinct biological species, thus increasing the number of named Caenorhabditis species in laboratory culture by nearly 3-fold. We anticipate that the improved accessibility of these species to the research community will expand the opportunities for study and accelerate our understanding of diverse biological phenomena.
Richard Jovelin - One of the best experts on this subject based on the ideXlab platform.
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Ephemeral-Habitat Colonization And Neotropical Species Richness Of Caenorhabditis Nematodes
2017Co-Authors: Celine Ferrari, Richard Jovelin, Asher D Cutter, Romain Salle, Nicolas Callemeyn-torre, Christian BraendleAbstract:Background: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar outward morphology despite deep genomic divergence. Methods: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe. This effort provides the first in-depth quantitative analysis of substrate specificity for Caenorhabditis in natural, unperturbed habitats. Results: We amassed a total of 626 strain isolates from nine species of Caenorhabditis among 2865 substrate samples. With the two new species described here (C. astrocarya and C. dolens), we estimate that our sampling procedures will discover few additional species of these microbivorous animals in this tropical rainforest system. We demonstrate experimentally that the two most prevalent species (C. nouraguensis and C. tropicalis) rapidly colonize fresh resource patches, whereas at least one rarer species shows specialist micro-habitat fidelity. Discussion: Despite the potential to colonize rapidly, these ephemeral patchy resources of rotting fruits and flowers are likely to often remain uncolonized by Caenorhabditis prior to their complete decay, implying dispersal-limited resource exploitation. We hypothesize that a combination of rapid colonization, high ephemerality of resource patches, and species heterogeneity in degree of specialization on micro-habitats and life histories enables dynamic co-existence of so many morphologically cryptic species of Caenorhabditis.
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Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes
Proceedings. Biological sciences, 2014Co-Authors: Richard Jovelin, Toyoshi Yoshiga, Ryusei Tanaka, Asher D CutterAbstract:Species with broad ecological amplitudes with respect to a key focal resource, niche generalists, should maintain larger and more connected populations than niche specialists, leading to the prediction that nucleotide diversity will be lower and more subdivided in specialists relative to their generalist relatives. This logic describes the specialist-generalist variation hypothesis (SGVH). Some outbreeding species of Caenorhabditis nematodes use a variety of invertebrate dispersal vectors and have high molecular diversity. By contrast, Caenorhabditis japonica lives in a strict association and synchronized life cycle with its dispersal host, the shield bug Parastrachia japonensis, itself a diet specialist. Here, we characterize sequence variation for 20 nuclear loci to investigate how C. japonica's life history shapes nucleotide diversity. We find that C. japonica has more than threefold lower polymorphism than other outbreeding Caenorhabditis species, but that local populations are not genetically disconnected. Coupled with its restricted range, we propose that its specialist host association contributes to a smaller effective population size and lower genetic variation than host generalist Caenorhabditis species with outbreeding reproductive modes. A literature survey of diverse organisms provides broader support for the SGVH. These findings encourage further testing of ecological and evolutionary hypotheses with comparative population genetics in Caenorhabditis and other taxa.
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eLS - Fifteen Years of Evolutionary Genomics in Caenorhabditis elegans
eLS, 2013Co-Authors: Richard Jovelin, Alivia Dey, Asher D CutterAbstract:The nematode worm Caenorhabditis elegans, introduced by Sydney Brenner for the genetic analysis of nervous system formation, is now a powerful model organism for studying nearly all aspects of biology, from development to diseases to evolution. Sequencing and analysis of the worm genome revealed intriguing nonrandom patterns of genome organisation and unusual features such as abundant operons. Surprising upon first discovery, worms and humans have a similar number of genes that are comprised of a similar proportion of transcription factors to regulate their genomes. However, differences in small ribonucleic acid content may contribute to differences in organismal complexity. In nature, the bacterivorous C. elegans is found primarily on rotting vegetation in temperate regions across the world. Natural selection, combined with the low effective recombination rate associated with selfing, strongly reduces nucleotide variation across the genome, yielding similarly low polymorphism to other selfing hermaphrodite species of Caenorhabditis. The genus Caenorhabditis provides a superb model system for ecological and evolutionary genetics, benefiting from C. elegans tools and information when applied to investigations of species with a higher polymorphism and better known ecological context. Key Concepts: The nematode Caenorhabditis elegans, introduced by Sydney Brenner for the genetic analysis of nervous system development, was the first metazoan to have a complete sequenced genome and is now a model organism for nearly all fields of biology. Many genomic features are not randomly distributed along C. elegans chromosomes and are prevalent either in the chromosome arms or in its centre. An unusually large fraction of protein-coding genes is organised in operons, possibly optimising transcriptional resources during recovery from developmental arrest. Gene duplication and alternative splicing contribute to extensive diversification of gene function, with 10.5% of protein-coding genes having paralogs and 25% of genes being alternatively spliced. The ratio of transcription factors to protein-coding genes is similar in worms and humans but the two species differ greatly in their microRNA content. The differences in chromatin states contribute to phenotypic variation and the transgenerational epigenetic inheritance suggests a role for epigenetic information in evolution. The rate of duplication is two orders of magnitude greater than the nucleotide mutation rate, highlighting the role of gene duplication in the evolution of the C. elegans genome. Caenorhabditis is not a soil nematode but instead proliferates and feeds on bacteria in rotting vegetation. Population genetic variation is strongly affected by the mating system of Caenorhabditis, with very low polymorphism in selfing hermaphroditic species relative to outcrossing gonochoristic species. Keywords: Caenorhabditis; genome evolution; operons; gene regulation; mating systems; epigenetics; polymorphism
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Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest.
BMC Evolutionary Biology, 2013Co-Authors: Marie-anne Félix, Richard Jovelin, Celine Ferrari, Shery Han, Young Ran Cho, Erik Andersen, Asher Cutter, Christian BraendleAbstract:UNLABELLED: ABSTRACT: BACKGROUND: In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. METHODS: Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. RESULTS: Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. CONCLUSIONS: The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species.
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Functional constraint and divergence in the G protein family in Caenorhabditis elegans and Caenorhabditis briggsae
Molecular Genetics and Genomics, 2005Co-Authors: Richard Jovelin, Patrick C. PhillipsAbstract:Part of the challenge of the post-genomic world is to identify functional elements within the wide array of information generated by genome sequencing. Although cross-species comparisons and investigation of rates of sequence divergence are an efficient approach, the relationship between sequence divergence and functional conservation is not clear. Here, we use a comparative approach to examine questions of evolutionary rates and conserved function within the guanine nucleotide-binding protein (G protein) gene family in nematodes of the genus Caenorhabditis . In particular, we show that, in cases where the Caenorhabditis elegans ortholog shows a loss-of-function phenotype, G protein genes of C. elegans and Caenorhabditis briggsae diverge on average three times more slowly than G protein genes that do not exhibit any phenotype when mutated in C. elegans , suggesting that genes with loss of function phenotypes are subject to stronger selective constraints in relation to their function in both species. Our results also indicate that selection is as strong on G proteins involved in environmental perception as it is on those controlling other important processes. Finally, using phylogenetic footprinting, we identify a conserved non-coding motif present in multiple copies in the genomes of four species of Caenorhabditis . The presence of this motif in the same intron in the gpa-1 genes of C. elegans , C. briggsae and Caenorhabditis remanei suggests that it plays a role in the regulation of gpa-1 , as well as other loci.
Lau Chow - One of the best experts on this subject based on the ideXlab platform.
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The species, sex, and stage specificity of a Caenorhabditis sex pheromone
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Jeffrey Robert Chasnov, Chun Man Chan, Lau ChowAbstract:Four species in the ELEGANS group of subgenus the Caenorhabditis are distinguished by two very different mating systems: androdioecy in C. elegans and Caenorhabditis briggsae with males and self-fertilizing hermaphrodites and dioecy in Caenorhabditis remanei and Caenorhabditis sp. strain CB5161 with males and females. Using chemotaxis assays, we demonstrate that females secrete a potent sex pheromone that attracts males from a distance, whereas hermaphrodites do not. The female sex pheromone is not species-specific, with males of all four species attracted to both the C. remanei and Caenorhabditis sp. female sex pheromones. The pheromone is, however, sex-specific, with only females secreting the pheromone and attracting only males. Furthermore, the sex pheromone is stage-specific, with female secretion and male detection of the pheromone beginning near adulthood. Females lose their attractiveness immediately after mating but regain it several hours after mating ceases. Finally, the female somatic gonad is required for sex-pheromone production, and the male-specific cephalic neurons (CEM) are required for male response.
