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Yadav K, Bhat AH, Abolafia J, Machado RA, Wani SM, Chaubey AK. Redescription and molecular characterisation of Panagrolaimus labiatus (Kreis, 1929) Andrássy, 1960 (Rhabditida, Panagrolaimidae) from India and proposal of P. burdwanensis Chaturvedi & Khera, 1979 as a junior synonym of P. labiatus. NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Summary
Two populations of bacterial-feeding nematodes belonging to the genus Panagrolaimus were recovered from infected slugs collected from gardens, agricultural areas and nurseries of the Baghpat district (India). Initial morphological characterisation of these populations show that they resemble Panagrolaimus labiatus from China and Bulgaria, P. burdwanensis from India, and P. cf. labiatus from Iran. To clarify taxonomical affiliations, we morphologically compared these two new populations to those recovered from China, Bulgaria, India and Iran. In addition, we sequenced several taxonomically relevant genes and used them to reconstruct phylogenetic relationships. Our results show that the two Indian populations do not significantly differ morphologically from the specimens used to describe the species P. labiatus, and also do not differ among them. We only observed small variations in the size of males and females. In addition, morphologically, the nematodes used to describe P. burdwanensis are very similar to the nematodes used to describe P. labiatus and to the two populations described in this study. Therefore, we propose P. burdwanensis as a junior synonym of P. labiatus and that the two populations recovered from India belong to the P. labiatus species. Phylogenetic analyses using the nucleotide sequences of the internal transcribed spacer (ITS), 18S and 28S rRNA gene sequences support our morphological conclusions. Our study therefore provides a detailed morphological description and molecular marker 18S and 28S gene sequences that can support future taxonomical studies of this species and highlights the importance of using both molecular and morphological data for the proper description of soil microfauna.
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Affiliation(s)
- Kajol Yadav
- Nematology Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, 250004, Uttar Pradesh, India
| | - Aashaq Hussain Bhat
- Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus ‘Las Lagunillas’ s/n, Edificio B3, 23071 Jaén, Spain
| | - Ricardo A.R. Machado
- Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Shaheen Majeed Wani
- Nematode Biodiversity and Genomics Research Laboratory, Baba Ghulam Shah Badshah University Rajouri, 185234, Jammu and Kashmir, India
| | - Ashok Kumar Chaubey
- Nematology Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, 250004, Uttar Pradesh, India
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Dulovic A, Renahan T, Röseler W, Rödelsperger C, Rose AM, Streit A. Rhabditophanes diutinus a parthenogenetic clade IV nematode with dauer larvae. PLoS Pathog 2020; 16:e1009113. [PMID: 33270811 PMCID: PMC7738172 DOI: 10.1371/journal.ppat.1009113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/15/2020] [Accepted: 10/30/2020] [Indexed: 01/13/2023] Open
Abstract
Comparative studies using non-parasitic model species such as Caenorhabditis elegans, have been very helpful in investigating the basic biology and evolution of parasitic nematodes. However, as phylogenetic distance increases, these comparisons become more difficult, particularly when outside of the nematode clade to which C. elegans belongs (V). One of the reasons C. elegans has nevertheless been used for these comparisons, is that closely related well characterized free-living species that can serve as models for parasites of interest are frequently not available. The Clade IV parasitic nematodes Strongyloides are of great research interest due to their life cycle and other unique biological features, as well as their medical and veterinary importance. Rhabditophanes, a closely related free-living genus, forms part of the Strongyloidoidea nematode superfamily. Rhabditophanes diutinus (= R. sp. KR3021) was included in the recent comparative genomic analysis of the Strongyloididae, providing some insight into the genomic nature of parasitism. However, very little is known about this species, limiting its usefulness as a research model. Here we provide a species description, name the species as R. diutinus and investigate its life cycle and subsequently gene expression in multiple life stages. We identified two previously unreported starvation induced life stages: dauer larvae and arrested J2 (J2A) larvae. The dauer larvae are morphologically similar to and are the same developmental stage as dauers in C. elegans and infective larvae in Strongyloides. As in C. elegans and Strongyloides, dauer formation is inhibited by treatment with dafachronic acid, indicating some genetic control mechanisms are conserved. Similarly, the expression patterns of putative dauer/infective larva control genes resemble each other, in particular between R. diutinus and Strongyloides spp. These findings illustrate and increase the usefulness of R. diutinus as a non-parasitic, easy to work with model species for the Strongyloididae for studying the evolution of parasitism as well as many aspects of the biology of Strongyloides spp, in particular the formation of infective larvae. Parasitic worms are an issue of great medical, veterinary, agricultural and economic importance, yet little is known about how worms become parasites. Comparative studies with non-parasitic model species like C. elegans have been useful, however, this usefulness decreases as the evolutionary distance between the species increases. One way to combat this is by having more well-studied closely related species to parasites of interest. To address this, we provide information about Rhabditophanes diutinus, a free-living nematode that is part of the same superfamily as the medically and veterinary important Strongyloides parasites. We provide analysis on its life cycle, in particular on two starvation induced life stages, along with gene expression data. Overall, this important information illustrates and improves the use of R. diutinus, as a non-parasitic model species for studying parasite evolution and basic biology within Strongyloides.
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Affiliation(s)
- Alex Dulovic
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Tess Renahan
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Waltraud Röseler
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Christian Rödelsperger
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
| | - Ann M. Rose
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany
- * E-mail:
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Ewe CK, Torres Cleuren YN, Rothman JH. Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network of Caenorhabditis and Other Nematodes. Front Cell Dev Biol 2020; 8:170. [PMID: 32258041 PMCID: PMC7093329 DOI: 10.3389/fcell.2020.00170] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/02/2020] [Indexed: 01/17/2023] Open
Abstract
Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis elegans has been a central model for advancing many important discoveries in fundamental mechanistic biology and, more recently, has provided a strong base from which to explore the evolutionary diversification of GRN architecture and developmental processes in other species. In this short review, we will focus on evolutionary diversification of the GRN for the most ancient of the embryonic germ layers, the endoderm. Early embryogenesis diverges considerably across the phylum Nematoda. Notably, while some species deploy regulative development, more derived species, such as C. elegans, exhibit largely mosaic modes of embryogenesis. Despite the relatively similar morphology of the nematode gut across species, widespread variation has been observed in the signaling inputs that initiate the endoderm GRN, an exemplar of developmental system drift (DSD). We will explore how genetic variation in the endoderm GRN helps to drive DSD at both inter- and intraspecies levels, thereby resulting in a robust developmental system. Comparative studies using divergent nematodes promise to unveil the genetic mechanisms controlling developmental plasticity and provide a paradigm for the principles governing evolutionary modification of an embryonic GRN.
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Affiliation(s)
- Chee Kiang Ewe
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | | | - Joel H. Rothman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
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Kalay G, Atallah J, Sierra NC, Tang AM, Crofton AE, Murugesan MK, Wykoff-Clary S, Lott SE. Evolution of larval segment position across 12 Drosophila species. Evolution 2019; 74:1409-1422. [PMID: 31886902 PMCID: PMC7496318 DOI: 10.1111/evo.13911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/25/2022]
Abstract
Many developmental traits that are critical to the survival of the organism are also robust. These robust traits are resistant to phenotypic change in the face of variation. This presents a challenge to evolution. In this article, we asked whether and how a well‐established robust trait, Drosophila segment patterning, changed over the evolutionary history of the genus. We compared segment position scaled to body length at the first‐instar larval stage among 12 Drosophila species. We found that relative segment position has changed many times across the phylogeny. Changes were frequent, but primarily small in magnitude. Phylogenetic analysis demonstrated that rates of change in segment position are variable along the Drosophila phylogenetic tree, and that these changes can occur in short evolutionary timescales. Correlation between position shifts of segments decreased as the distance between two segments increased, suggesting local control of segment position. The posterior‐most abdominal segment showed the highest magnitude of change on average, had the highest rate of evolution between species, and appeared to be evolving more independently as compared to the rest of the segments. This segment was exceptionally elongated in the cactophilic species in our dataset, raising questions as to whether this change may be adaptive.
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Affiliation(s)
- Gizem Kalay
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Joel Atallah
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616.,current address: Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148
| | - Noemie C Sierra
- Earth and Planetary Sciences Department, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Austin M Tang
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Amanda E Crofton
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Mohan K Murugesan
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Sherri Wykoff-Clary
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
| | - Susan E Lott
- Department of Evolution and Ecology, University of California, Davis, One Shields Avenue, Davis, California, 95616
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Necessity and Contingency in Developmental Genetic Screens: EGF, Wnt, and Semaphorin Pathways in Vulval Induction of the Nematode Oscheius tipulae. Genetics 2019; 211:1315-1330. [PMID: 30700527 PMCID: PMC6456316 DOI: 10.1534/genetics.119.301970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023] Open
Abstract
Genetic screens in the nematode Caenorhabditis elegans have identified EGF and Notch pathways as key for vulval precursor cell fate patterning. Here, Vargas-Velazquez, Besnard, and Félix report on the molecular identification of... Genetic screens in the nematode Caenorhabditis elegans identified the EGF/Ras and Notch pathways as central for vulval precursor cell fate patterning. Schematically, the anchor cell secretes EGF, inducing the P6.p cell to a primary (1°) vulval fate; P6.p in turn induces its neighbors to a secondary (2°) fate through Delta-Notch signaling and represses Ras signaling. In the nematode Oscheius tipulae, the anchor cell successively induces 2° then 1° vulval fates. Here, we report on the molecular identification of mutations affecting vulval induction in O. tipulae. A single Induction Vulvaless mutation was found, which we identify as a cis-regulatory deletion in a tissue-specific enhancer of the O. tipulae lin-3 homolog, confirmed by clustered regularly interspaced short palindromic repeats/Cas9 mutation. In contrast to this predictable Vulvaless mutation, mutations resulting in an excess of 2° fates unexpectedly correspond to the plexin/semaphorin pathway. Hyperinduction of P4.p and P8.p in these mutants likely results from mispositioning of these cells due to a lack of contact inhibition. The third signaling pathway found by forward genetics in O. tipulae is the Wnt pathway; a decrease in Wnt pathway activity results in loss of vulval precursor competence and induction, and 1° fate miscentering on P5.p. Our results suggest that the EGF and Wnt pathways have qualitatively similar activities in vulval induction in C. elegans and O. tipulae, albeit with quantitative differences in the effects of mutation. Thus, the derived induction process in C. elegans with an early induction of the 1° fate appeared during evolution, after the recruitment of the EGF pathway for vulval induction.
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Abolafia J, Peña-Santiago R. Morphology, taxonomy and phylogeny of the enigmatic genus Aulolaimus de Man, 1880 (Nematoda, Aulolaimidae). ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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Pristionchus nematodes occur frequently in diverse rotting vegetal substrates and are not exclusively necromenic, while Panagrellus redivivoides is found specifically in rotting fruits. PLoS One 2018; 13:e0200851. [PMID: 30074986 PMCID: PMC6075748 DOI: 10.1371/journal.pone.0200851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/05/2018] [Indexed: 01/31/2023] Open
Abstract
The lifestyle and feeding habits of nematodes are highly diverse. Several species of Pristionchus (Nematoda: Diplogastridae), including Pristionchus pacificus, have been reported to be necromenic, i.e. to associate with beetles in their dauer diapause stage and wait until the death of their host to resume development and feed on microbes in the decomposing beetle corpse. We review the literature and suggest that the association of Pristionchus to beetles may be phoretic and not necessarily necromenic. The view that Pristionchus nematodes have a necromenic lifestyle is based on studies that have sought Pristionchus only by sampling live beetles. By surveying for nematode genera in different types of rotting vegetal matter, we found Pristionchus spp. at a similar high frequency as Caenorhabditis, often in large numbers and in feeding stages. Thus, these Pristionchus species may feed in decomposing vegetal matter. In addition, we report that one species of Panagrellus (Nematoda: Panagrolaimidae), Panagrellus redivivoides, is found in rotting fruits but not in rotting stems, with a likely association with Drosophila fruitflies. Based on our sampling and the observed distribution of feeding and dauer stages, we propose a life cycle for Pristionchus nematodes and Panagrellus redivivoides that is similar to that of C. elegans, whereby they feed on the microbial blooms on decomposing vegetal matter and are transported between food patches by coleopterans for Pristionchus spp., fruitflies for Panagrellus redivivoides and isopods and terrestrial molluscs for C. elegans.
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Huelsz-Prince G, van Zon JS. Canalization of C. elegans Vulva Induction against Anatomical Variability. Cell Syst 2017; 4:219-230.e6. [PMID: 28215526 PMCID: PMC5330807 DOI: 10.1016/j.cels.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 09/29/2016] [Accepted: 01/11/2017] [Indexed: 11/24/2022]
Abstract
It is a fundamental open question as to how embryos develop into complex adult organisms with astounding reproducibility, particularly because cells are inherently variable on the molecular level. During C. elegans vulva induction, the anchor cell induces cell fate in the vulva precursor cells in a distance-dependent manner. Surprisingly, we found that initial anchor cell position was highly variable and caused variability in cell fate induction. However, we observed that vulva induction was "canalized," i.e., the variability in anchor cell position and cell fate was progressively reduced, resulting in an invariant spatial pattern of cell fates at the end of induction. To understand the mechanism of canalization, we quantified induction dynamics as a function of anchor cell position during the canalization process. Our experiments, combined with mathematical modeling, showed that canalization required a specific combination of long-range induction, lateral inhibition, and cell migration that is also found in other developmental systems.
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Grimbert S, Tietze K, Barkoulas M, Sternberg PW, Félix MA, Braendle C. Anchor cell signaling and vulval precursor cell positioning establish a reproducible spatial context during C. elegans vulval induction. Dev Biol 2016; 416:123-135. [PMID: 27288708 DOI: 10.1016/j.ydbio.2016.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/05/2016] [Accepted: 05/31/2016] [Indexed: 01/26/2023]
Abstract
How cells coordinate their spatial positioning through intercellular signaling events is poorly understood. Here we address this topic using Caenorhabditis elegans vulval patterning during which hypodermal vulval precursor cells (VPCs) adopt distinct cell fates determined by their relative positions to the gonadal anchor cell (AC). LIN-3/EGF signaling by the AC induces the central VPC, P6.p, to adopt a 1° vulval fate. Exact alignment of AC and VPCs is thus critical for correct fate patterning, yet, as we show here, the initial AC-VPC positioning is both highly variable and asymmetric among individuals, with AC and P6.p only becoming aligned at the early L3 stage. Cell ablations and mutant analysis indicate that VPCs, most prominently 1° cells, move towards the AC. We identify AC-released LIN-3/EGF as a major attractive signal, which therefore plays a dual role in vulval patterning (cell alignment and fate induction). Additionally, compromising Wnt pathway components also induces AC-VPC alignment errors, with loss of posterior Wnt signaling increasing stochastic vulval centering on P5.p. Our results illustrate how intercellular signaling reduces initial spatial variability in cell positioning to generate reproducible interactions across tissues.
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Affiliation(s)
- Stéphanie Grimbert
- Centre National de la Recherche Scientifique (CNRS) UMR7277 - Institut National de la Santé et de la Recherche Médicale (INSERM) U1091, Université Nice Sophia Antipolis, 06108 Nice cedex 02, France
| | - Kyria Tietze
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Michalis Barkoulas
- Institute of Biology of the Ecole Normale Supérieure, CNRS UMR 8197 and INSERM U1024, 46 rue d'Ulm, 75230 Paris cedex 05, France
| | - Paul W Sternberg
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, CNRS UMR 8197 and INSERM U1024, 46 rue d'Ulm, 75230 Paris cedex 05, France
| | - Christian Braendle
- Centre National de la Recherche Scientifique (CNRS) UMR7277 - Institut National de la Santé et de la Recherche Médicale (INSERM) U1091, Université Nice Sophia Antipolis, 06108 Nice cedex 02, France.
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Peterson T, Müller GB. Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory. Evol Biol 2016; 43:314-335. [PMID: 27512237 PMCID: PMC4960286 DOI: 10.1007/s11692-016-9372-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/29/2016] [Indexed: 10/25/2022]
Abstract
The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.
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Affiliation(s)
- Tim Peterson
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Gerd B. Müller
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- The KLI Institute, Martinstrasse 12, 3400 Klosterneuburg, Austria
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12
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Han Z, Boas S, Schroeder NE. Unexpected Variation in Neuroanatomy among Diverse Nematode Species. Front Neuroanat 2016; 9:162. [PMID: 26778973 PMCID: PMC4700257 DOI: 10.3389/fnana.2015.00162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/30/2015] [Indexed: 12/31/2022] Open
Abstract
Nematodes are considered excellent models for understanding fundamental aspects of neuron function. However, nematodes are less frequently used as models for examining the evolution of nervous systems. While the habitats and behaviors of nematodes are diverse, the neuroanatomy of nematodes is often considered highly conserved. A small number of nematode species greatly influences our understanding of nematode neurobiology. The free-living species Caenorhabditis elegans and, to a lesser extent, the mammalian gastrointestinal parasite Ascaris suum are, historically, the primary sources of knowledge regarding nematode neurobiology. Despite differences in size and habitat, C. elegans and A. suum share a surprisingly similar neuroanatomy. Here, we examined species across several clades in the phylum Nematoda and show that there is a surprising degree of neuroanatomical variation both within and among nematode clades when compared to C. elegans and Ascaris. We found variation in the numbers of neurons in the ventral nerve cord and dye-filling pattern of sensory neurons. For example, we found that Pristionchus pacificus, a bacterial feeding species used for comparative developmental research had 20% fewer ventral cord neurons compared to C. elegans. Steinernema carpocapsae, an insect-parasitic nematode capable of jumping behavior, had 40% more ventral cord neurons than C. elegans. Interestingly, the non-jumping congeneric nematode, S. glaseri showed an identical number of ventral cord neurons as S. carpocapsae. There was also variability in the timing of neurodevelopment of the ventral cord with two of five species that hatch as second-stage juveniles showing delayed neurodevelopment. We also found unexpected variation in the dye-filling of sensory neurons among examined species. Again, sensory neuron dye-filling pattern did not strictly correlate with phylogeny. Our results demonstrate that variation in nematode neuroanatomy is more prevalent than previously assumed and recommend this diverse phylum for future "evo-devo-neuro" studies.
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Affiliation(s)
- Ziduan Han
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - Stephanie Boas
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - Nathan E Schroeder
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, UrbanaIL, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, UrbanaIL, USA
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Abstract
The phenotype of many regulatory circuits in which mutations can cause complex, polygenic diseases is to some extent robust to DNA mutations that affect circuit components. Here I demonstrate how such mutational robustness can prevent the discovery of genetic disease determinants. To make my case, I use a mathematical model of the insulin signaling pathway implicated in type 2 diabetes, whose signaling output is governed by 15 genetically determined parameters. Using multiple complementary measures of a parameter's importance for this phenotype, I show that any one disease determinant that is crucial in one genetic background will be virtually irrelevant in other backgrounds. In an evolving population that drifts through the parameter space of this or other robust circuits through DNA mutations, the genetic changes that can cause disease will vary randomly over time. I call this phenomenon causal drift. It means that mutations causing disease in one (human or non-human) population may have no effect in another population, and vice versa. Causal drift casts doubt on our ability to infer the molecular mechanisms of complex diseases from non-human model organisms.
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Affiliation(s)
- Andreas Wagner
- University of Zurich, Institute for Evolutionary Biology and Environmental Studies, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico
- * E-mail:
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Koshel EI, Aleshin VV, Eroshenko GA, Kutyrev VV. Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague. BIOMED RESEARCH INTERNATIONAL 2014; 2014:135218. [PMID: 24804197 PMCID: PMC3996313 DOI: 10.1155/2014/135218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/05/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.
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Affiliation(s)
- E. I. Koshel
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Aleshin
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- National Research Institute of Physiology, Biochemistry, and Nutrition of Farm Animals, Russian Academy of Agricultural Sciences, Kaluga Region, Borovsk 249013, Russia
| | - G. A. Eroshenko
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
| | - V. V. Kutyrev
- Russian Research Anti-Plague Institute “Microbe”, Saratov 410005, Russia
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Sharanya D, Thillainathan B, Marri S, Bojanala N, Taylor J, Flibotte S, Moerman DG, Waterston RH, Gupta BP. Genetic control of vulval development in Caenorhabditis briggsae. G3 (BETHESDA, MD.) 2012; 2:1625-41. [PMID: 23275885 PMCID: PMC3516484 DOI: 10.1534/g3.112.004598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/19/2012] [Indexed: 01/23/2023]
Abstract
The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause the egg-laying defective (Egl) phenotype. Here, we report the characterization of 13 genes, including three that are orthologs of Caenorhabditis elegans unc-84 (SUN domain), lin-39 (Dfd/Scr-related homeobox), and lin-11 (LIM homeobox). Based on the morphology and cell fate changes, the mutants were placed into four different categories. Class 1 animals have normal-looking vulva and vulva-uterine connections, indicating defects in other components of the egg-laying system. Class 2 animals frequently lack some or all of the vulval precursor cells (VPCs) due to defects in the migration of P-cell nuclei into the ventral hypodermal region. Class 3 animals show inappropriate fusion of VPCs to the hypodermal syncytium, leading to a reduced number of vulval progeny. Finally, class 4 animals exhibit abnormal vulval invagination and morphology. Interestingly, we did not find mutations that affect VPC induction and fates. Our work is the first study involving the characterization of genes in C. briggsae vulva formation, and it offers a basis for future investigations of these genes in C. elegans.
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Affiliation(s)
- Devika Sharanya
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Sujatha Marri
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Jon Taylor
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephane Flibotte
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Donald G. Moerman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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18
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Félix MA, Barkoulas M. Robustness and flexibility in nematode vulva development. Trends Genet 2012; 28:185-95. [DOI: 10.1016/j.tig.2012.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/09/2012] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
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Avinoam O, Podbilewicz B. Eukaryotic cell-cell fusion families. CURRENT TOPICS IN MEMBRANES 2012; 68:209-34. [PMID: 21771501 DOI: 10.1016/b978-0-12-385891-7.00009-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ori Avinoam
- Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
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Pénigault JB, Félix MA. High sensitivity of C. elegans vulval precursor cells to the dose of posterior Wnts. Dev Biol 2011; 357:428-38. [DOI: 10.1016/j.ydbio.2011.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/02/2011] [Accepted: 06/04/2011] [Indexed: 10/18/2022]
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Ragsdale EJ, Baldwin JG. Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda. Proc Biol Sci 2010; 277:1299-307. [PMID: 20106846 PMCID: PMC2871949 DOI: 10.1098/rspb.2009.2195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 01/06/2010] [Indexed: 11/12/2022] Open
Abstract
Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.
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Affiliation(s)
- Erik J Ragsdale
- Department of Nematology, University of California, Riverside, CA 92521, USA.
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HERRMANN MATTHIAS, KIENLE SIMONE, ROCHAT JACQUES, MAYER WERNERE, SOMMER RALFJ. Haplotype diversity of the nematode Pristionchus pacificus on Réunion in the Indian Ocean suggests multiple independent invasions. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01410.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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YANG JP, ZHENG JJ. The Effect of Emotion on the Quality of Crisis Decision-making. ACTA PSYCHOLOGICA SINICA 2009. [DOI: 10.3724/sp.j.1041.2009.00481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lewis SC, Dyal LA, Hilburn CF, Weitz S, Liau WS, Lamunyon CW, Denver DR. Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi. BMC Evol Biol 2009; 9:15. [PMID: 19149894 PMCID: PMC2632994 DOI: 10.1186/1471-2148-9-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 01/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As exemplified by the famously successful model organism Caenorhabditis elegans, nematodes offer outstanding animal systems for investigating diverse biological phenomena due to their small genome sizes, short generation times and ease of laboratory maintenance. Nematodes in the genus Panagrolaimus have served in comparative development and anhydrobiosis studies, and the Antarctic species P. davidi offers a powerful paradigm for understanding the biological mechanisms of extreme cold tolerance. Panagrolaimus nematodes are also unique in that examples of gonochoristic, hermaphroditic and parthenogenetic reproductive modes have been reported for members of this genus. The evolutionary origins of these varying reproductive modes and the Antarctic species P. davidi, however, remain enigmatic. RESULTS We collected nuclear ribosomal RNA gene and mitochondrial protein-coding gene sequences from diverse Panagrolaimus species and strains, including newly discovered isolates from Oregon, to investigate phylogenetic relationships in this nematode genus. Nuclear phylogenies showed that the species and strains historically identified as members of Panagrolaimus constitute a paraphyletic group, suggesting that taxonomic revision is required for Panagrolaimus and related nematode lineages. Strain-specific reproductive modes were mapped onto the molecular phylogeny to show a single origin of parthenogenesis from a presumably gonochoristic ancestor. The hermaphroditic strains were all placed outside a major monophyletic clade that contained the majority of other Panagrolaimus nematodes. Phylogenetic analyses of mitochondrial sequences showed that substantial molecular and geographic diversity exists within the clade of parthenogenetic strains. The Antarctic species P. davidi was found to be very closely related to two Panagrolaimus strains from southern California. Phylogenetic and molecular clock analyses suggested that P. davidi and the California strain PS1579 shared a common ancestor in the very recent evolutionary past. CONCLUSION Our study provides a phylogenetic framework for understanding the evolutionary origins and diversification patterns of varying reproductive modes within Panagrolaimus and important insights into the origin of the Antarctic species P. davidi. Panagrolaimus offers a powerful nematode model for understanding diverse evolutionary phenomena including the evolution of asexuality and the adaptive evolution of extreme cold tolerance.
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Affiliation(s)
- Samantha C Lewis
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA.
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Abstract
The efficiency of RNA interference varies between different organisms, even among nematodes. A recent report of successful RNA interference in the nematode Panagrolaimus superbus in BMC Molecular Biology has implications for the comparative study of the functional genomics of nematode species, and prompts reflections on the choice of Caenorhabditis elegans as a model organism.
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Affiliation(s)
- Marie-Anne Félix
- Institut Jacques Monod, CNRS - Universities of Paris 7 and 6, Tour 43, 2 place Jussieu, 75251 Paris cedex 05, France.
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Milloz J, Duveau F, Nuez I, Félix MA. Intraspecific evolution of the intercellular signaling network underlying a robust developmental system. Genes Dev 2008; 22:3064-75. [PMID: 18981482 PMCID: PMC2577794 DOI: 10.1101/gad.495308] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 08/29/2008] [Indexed: 11/25/2022]
Abstract
Many biological systems produce an invariant output when faced with stochastic or environmental variation. This robustness of system output to variation affecting the underlying process may allow for "cryptic" genetic evolution within the system without change in output. We studied variation of cell fate patterning of Caenorhabditis elegans vulva precursors, a developmental system that relies on a simple intercellular signaling network and yields an invariant output of cell fates and lineages among C. elegans wild isolates. We first investigated the system's genetic variation in C. elegans by means of genetic tools and cell ablation to break down its buffering mechanisms. We uncovered distinct architectures of quantitative variation along the Ras signaling cascade, including compensatory variation, and differences in cell sensitivity to induction along the anteroposterior axis. In the unperturbed system, we further found variation between isolates in spatio-temporal dynamics of Ras pathway activity, which can explain the phenotypic differences revealed upon perturbation. Finally, the variation mostly affects the signaling pathways in a tissue-specific manner. We thus demonstrate and characterize microevolution of a developmental signaling network. In addition, our results suggest that the vulva genetic screens would have yielded a different mutation spectrum, especially for Wnt pathway mutations, had they been performed in another C. elegans genetic background.
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Affiliation(s)
- Josselin Milloz
- Institut Jacques Monod, CNRS-University Denis Diderot-Paris 7-UPMC, 75251 Paris cedex 05, France
| | - Fabien Duveau
- Institut Jacques Monod, CNRS-University Denis Diderot-Paris 7-UPMC, 75251 Paris cedex 05, France
| | - Isabelle Nuez
- Institut Jacques Monod, CNRS-University Denis Diderot-Paris 7-UPMC, 75251 Paris cedex 05, France
| | - Marie-Anne Félix
- Institut Jacques Monod, CNRS-University Denis Diderot-Paris 7-UPMC, 75251 Paris cedex 05, France
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27
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Bert W, Leliaert F, Vierstraete AR, Vanfleteren JR, Borgonie G. Molecular phylogeny of the Tylenchina and evolution of the female gonoduct (Nematoda: Rhabditida). Mol Phylogenet Evol 2008; 48:728-44. [DOI: 10.1016/j.ympev.2008.04.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 03/31/2008] [Accepted: 04/01/2008] [Indexed: 11/25/2022]
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Shannon AJ, Tyson T, Dix I, Boyd J, Burnell AM. Systemic RNAi mediated gene silencing in the anhydrobiotic nematode Panagrolaimus superbus. BMC Mol Biol 2008; 9:58. [PMID: 18565215 PMCID: PMC2453295 DOI: 10.1186/1471-2199-9-58] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2008] [Accepted: 06/19/2008] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Gene silencing by RNA interference (RNAi) is a powerful tool for functional genomics. Although RNAi was first described in Caenorhabditis elegans, several nematode species are unable to mount an RNAi response when exposed to exogenous double stranded RNA (dsRNA). These include the satellite model organisms Pristionchus pacificus and Oscheius tipulae. Available data also suggest that the RNAi pathway targeting exogenous dsRNA may not be fully functional in some animal parasitic nematodes. The genus Panagrolaimus contains bacterial feeding nematodes which occupy a diversity of niches ranging from polar, temperate and semi-arid soils to terrestrial mosses. Thus many Panagrolaimus species are adapted to tolerate freezing and desiccation and are excellent systems to study the molecular basis of environmental stress tolerance. We investigated whether Panagrolaimus is susceptible to RNAi to determine whether this nematode could be used in large scale RNAi studies in functional genomics. RESULTS We studied two species: Panagrolaimus sp. PS1159 and Panagrolaimus superbus. Both nematode species displayed embryonic lethal RNAi phenotypes following ingestion of Escherichia coli expressing dsRNA for the C. elegans embryonic lethal genes Ce-lmn-1 and Ce-ran-4. Embryonic lethal RNAi phenotypes were also obtained in both species upon ingestion of dsRNA for the Panagrolaimus genes ef1b and rps-2. Single nematode RT-PCR showed that a significant reduction in mRNA transcript levels occurred for the target ef1b and rps-2 genes in RNAi treated Panagrolaimus sp. 1159 nematodes. Visible RNAi phenotypes were also observed when P. superbus was exposed to dsRNA for structural genes encoding contractile proteins. All RNAi phenotypes were highly penetrant, particularly in P. superbus. CONCLUSION This demonstration that Panagrolaimus is amenable to RNAi by feeding will allow the development of high throughput methods of RNAi screening for P. superbus. This greatly enhances the utility of this nematode as a model system for the study of the molecular biology of anhydrobiosis and cryobiosis and as a possible satellite model nematode for comparative and functional genomics. Our data also identify another nematode infraorder which is amenable to RNAi and provide additional information on the diversity of RNAi phenotypes in nematodes.
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Affiliation(s)
- Adam J Shannon
- Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Trevor Tyson
- Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Ilona Dix
- Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Jacqueline Boyd
- Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham Rd., Southwell, NG25 0QF, UK
| | - Ann M Burnell
- Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland
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29
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Trends, Stasis, and Drift in the Evolution of Nematode Vulva Development. Curr Biol 2007; 17:1925-37. [DOI: 10.1016/j.cub.2007.10.061] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/19/2007] [Accepted: 10/22/2007] [Indexed: 11/22/2022]
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30
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Loer CM, Rivard L. Evolution of neuronal patterning in free-living rhabditid nematodes I: Sex-specific serotonin-containing neurons. J Comp Neurol 2007; 502:736-67. [PMID: 17436291 DOI: 10.1002/cne.21288] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As a first step toward understanding the evolution of neuronal patterning and function in a group of simple animals, we have examined serotonin-containing neurons in 17 species of free-living rhabditid nematodes and compared them with identified neurons of Caenorhabditis elegans. We found many serotonin-immunoreactive (serotonin-IR) neurons that are likely homologs of those in C. elegans; this paper focuses on sex-specific neurons such as the egg laying hermaphrodite-specific neurons (HSNs), VCs, and male CAs, CPs, and ray sensory neurons known to function in mating. These cells vary in number and position in the species examined but are consistent with a current molecularly based phylogeny. Two groups (Oscheius and Pristionchus) appear independently to have lost a serotonin-IR HSN. Oscheius furthermore has no serotonin-IR innervation of the vulval region, in contrast to every other species we examined. We also saw variation in the location of somas of putative HSN, consistent with evolutionary changes in HSN migration. In C. elegans, the HSN soma migrates during embryogenesis from the tail to the central body, where it innervates its major postsynaptic targets, the vulval muscles. For other species, we observed putative HSN homologs along the anterior-posterior axis from the head to the tail, but typically HSNs were located near the vulva, which also varies in anterior-posterior position among the species we examined. The varying positions of the HSN somas in other species are reminiscent of phenotypes seen in various C. elegans mutants with altered HSN migration, suggesting possible mechanisms for the evolutionary differences we observed.
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Affiliation(s)
- Curtis M Loer
- Department of Biology, University of San Diego, California 92110, USA.
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31
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Félix MA. Cryptic quantitative evolution of the vulva intercellular signaling network in Caenorhabditis. Curr Biol 2007; 17:103-14. [PMID: 17240335 DOI: 10.1016/j.cub.2006.12.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 11/22/2006] [Accepted: 11/23/2006] [Indexed: 10/23/2022]
Abstract
BACKGROUND The Caenorhabditis vulva is formed from a row of Pn.p precursor cells, which adopt a spatial cell-fate pattern-3 degrees 3 degrees 2 degrees 1 degrees 2 degrees 3 degrees -centered on the gonadal anchor cell. This pattern is robustly specified by an intercellular signaling network including EGF/Ras induction from the anchor cell and Delta/Notch signaling between the precursor cells. It is unknown how the roles and quantitative contributions of these signaling pathways have evolved in closely related Caenorhabditis species. RESULTS Cryptic evolution in the network is uncovered by quantification of cell-fate-pattern frequencies obtained after displacement of the system out of its normal range, either by anchor-cell ablations or through LIN-3/EGF overexpression. Silent evolution in the Caenorhabditis genus covers a large neutral space of cell-fate patterns. Direct induction of the 1 degrees fate as in C. elegans appeared within the genus. C. briggsae displays a graded induction of 1 degrees and 2 degrees fates, with 1 degrees fate induction requiring a longer time than in C. elegans, and a reduced lateral inhibition of adjacent 1 degrees fates. C. remanei displays a strong lateral induction of 2 degrees fates relative to vulval-fate activation in the central cell. This evolution in cell-fate pattern space can be experimentally reconstituted by mild variations of Ras, Wnt, and Notch pathway activities in C. elegans and C. briggsae. CONCLUSIONS Quantitative evolution in the roles of graded induction by LIN-3/EGF and Notch signaling is demonstrated for the Caenorhabditis vulva signaling network. This evolutionary system biology approach provides a quantitative view of the variational properties of this biological system.
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Affiliation(s)
- Marie-Anne Félix
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Universities of Paris 6 and 7, Tour 43, 2 place Jussieu , 75251 Paris cedex 05, France.
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32
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Bumbarger DJ, Crum J, Ellisman MH, Baldwin JG. Three-dimensional reconstruction of the nose epidermal cells in the microbial feeding nematode, Acrobeles complexus (Nematoda: Rhabditida). J Morphol 2007; 267:1257-72. [PMID: 16710857 DOI: 10.1002/jmor.10456] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The epidermis of the anterior end (nose) plays an important role in the evolution, development, and functional feeding morphology in nematodes, but information on this complex organ system is limited. Here, we produce a 3D model of 13 of the cells making up this organ system reconstructed from serial transmission electron micrographs of the microbial feeding nematode, Acrobeles complexus. Nose epidermal cells were found to be broadly similar to those of the distantly related model organism Caenorhabditis elegans in the number and arrangement of nuclei in these largely syncytial cells; this similarity demonstrates striking evolutionary conservation that allows for robust statements of homology between the taxa. Examining details of cell shape, however, revealed surprisingly complex subcellular specialization, which differed markedly from C. elegans in the number and arrangement of cell processes. Anterior toroid processes of the anterior arcade, posterior arcade, and HypB syncytia form a nested complex at the base of the labial probolae. Anterior toroid processes of HypC and the inner labial socket cells are associated with the base of the cephalic probolae and radial ridge processes. Extracellular filaments (tendon organs) and radiating cytoskeletal filaments of the posterior arcade syncytium form a connection between the body wall muscle cells and the pharynx. An epidermal cell with no known homolog in other nematodes is identified. Findings provide a basis to propose hypotheses related to the development and evolutionary origin of specialized feeding appendages (probolae) in the Cephalobinae (including Acrobeles), and hypotheses of homology are revised for epidermal cells in the nose of the closely related and primarily plant parasitic group, Tylenchida.
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Affiliation(s)
- Daniel J Bumbarger
- Department of Nematology, University of California, Riverside, California 92521, USA.
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33
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Nadler SA, De Ley P, Mundo-Ocampo M, Smythe AB, Patricia Stock S, Bumbarger D, Adams BJ, De Ley IT, Holovachov O, Baldwin JG. Phylogeny of Cephalobina (Nematoda): Molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications. Mol Phylogenet Evol 2006; 40:696-711. [PMID: 16750400 DOI: 10.1016/j.ympev.2006.04.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 02/02/2006] [Accepted: 04/06/2006] [Indexed: 11/17/2022]
Abstract
Nematodes of the suborder Cephalobina include an ecologically and morphologically diverse array of species that range from soil-dwelling microbivores to parasites of vertebrates and invertebrates. Despite a long history of study, certain of these microbivores (Cephaloboidea) present some of the most intractable problems in nematode systematics; the lack of an evolutionary framework for these taxa has prevented the identification of natural groups and inhibited understanding of soil biodiversity and nematode ecology. Phylogenetic analyses of ribosomal (LSU) sequence data from 53 taxa revealed strong support for monophyly of taxa representing the Cephaloboidea, but do not support the monophyly of most genera within this superfamily. Historically these genera have primarily been recognized based on variation in labial morphology, but molecular phylogenies show the same general labial (probolae) morphotype often results from recurrent similarity, a result consistent with the phenotypic plasticity of probolae previously observed for some species in ecological time. Phylogenetic analyses of LSU rDNA also recovered strong support for some other groups of cephalobs, including taxa representing most (but not all) Panagrolaimoidea. In addition to revealing homoplasy of probolae, molecular trees also imply other unexpected patterns of character evolution or polarity, including recurrent similarity of offset spermatheca presence, and representation of complex probolae as the ancestral condition within Cephaloboidea. For Cephalobidae, molecular trees do not support traditional genera as natural groups, but it remains untested if deconstructing probolae morphotypes or other structural features into finer component characters may reveal homologies that help delimit evolutionary lineages.
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Affiliation(s)
- Steven A Nadler
- Department of Nematology, University of California, Davis, 95616, USA.
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34
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Schlager B, Röseler W, Zheng M, Gutierrez A, Sommer RJ. HAIRY-like Transcription Factors and the Evolution of the Nematode Vulva Equivalence Group. Curr Biol 2006; 16:1386-94. [PMID: 16860737 DOI: 10.1016/j.cub.2006.06.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 06/02/2006] [Accepted: 06/06/2006] [Indexed: 11/21/2022]
Abstract
BACKGROUND Nematode vulva formation provides a paradigm to study the evolution of pattern formation and cell-fate specification. The Caenorhabditis elegans vulva is generated from three of six equipotent cells that form the so-called vulva equivalence group. During evolution, the size of the vulva equivalence group has changed: Panagrellus redivivus has eight, C. elegans six, and Pristionchus pacificus only three cells that are competent to form vulval tissue. In P. pacificus, programmed cell death of individual vulval precursor cells alters the size of the vulva equivalence group. RESULTS We have identified the genes controlling this cell-death event and the molecular mechanism of the reduction of the vulva equivalence group. Mutations in Ppa-hairy, a gene that is unknown from C. elegans, result in the survival of two precursor cells, which expands the vulva equivalence group. Mutations in Ppa-groucho cause a similar phenotype. Ppa-HAIRY and Ppa-GROUCHO form a molecular module that represses the Hox gene Ppa-lin-39 and thereby reduces the size of the vulva equivalence group. The C. elegans genome does not encode a similar hairy-like gene, and no typical HAIRY/GROUCHO module exists. CONCLUSIONS We conclude that the vulva equivalence group in Pristionchus is patterned by a HAIRY/GROUCHO module, which is absent in Caenorhabditis. Thus, changes in the number, structure, and function of nematode hairy-like transcription factors are involved in the evolutionary alteration of this equivalence group.
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Affiliation(s)
- Benjamin Schlager
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
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Chiang JTA, Steciuk M, Shtonda B, Avery L. Evolution of pharyngeal behaviors and neuronal functions in free-living soil nematodes. J Exp Biol 2006; 209:1859-73. [PMID: 16651552 DOI: 10.1242/jeb.02165] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYTo explore the use of Caenorhabditis elegans and related nematodes for studying behavioral evolution, we conducted a comparative study of pharyngeal behaviors and neuronal regulation in free-living soil nematodes. The pharynx is divided into three parts: corpus, isthmus and terminal bulb,and pharyngeal behaviors consist of stereotyped patterns of two motions:pumping and peristalsis. Based on an outgroup species, Teratocephalus lirellus, the ancestral pattern of pharyngeal behaviors consisted of corpus pumping, isthmus peristalsis and terminal bulb pumping, each occurring independently. Whereas corpus pumping remained largely conserved, isthmus and terminal bulb behaviors evolved extensively from the ancestral pattern in the four major free-living soil nematode families. In the Rhabditidae family,which includes Caenorhabditis elegans, the anterior isthmus switched from peristalsis to pumping, and anterior isthmus and terminal bulb pumping became coupled to corpus pumping. In the Diplogasteridae family, the terminal bulb switched from pumping to peristalsis, and isthmus and terminal bulb became coupled for peristalsis. In the Cephalobidae family, isthmus peristalsis and terminal bulb pumping became coupled. And in the Panagrolaimidae family, the posterior isthmus switched from peristalsis to pumping. Along with these behavioral changes, we also found differences in the neuronal regulation of isthmus and terminal bulb behaviors. M2, a neuron that has no detectable function in C. elegans, stimulated anterior isthmus peristalsis in the Panagrolaimidae. Further, M4 was an important excitatory neuron in each family, but its exact downstream function varied between stimulation of posterior isthmus peristalsis in the Rhabditidae,isthmus/terminal bulb peristalsis in the Diplogasteridae, isthmus peristalsis and terminal bulb pumping in the Cephalobidae, and posterior isthmus/terminal bulb pumping in the Panagrolaimidae. In the Rhabditidae family, although M4 normally has no effect on the terminal bulb, we found that M4 can stimulate the terminal bulb in C. elegans if the Ca2+-activated K+ channel SLO-1 is inactivated. C. elegans slo-1 mutants have generally increased neurotransmission, and in slo-1 mutants we found novel electropharyngeogram signals and increased pumping rates that suggested activation of M4-terminal bulb synapses. Thus, we suggest that the lack of M4-terminal bulb stimulations in C. elegans and the Rhabditidae family evolved by changes in synaptic transmission. Altogether, we found behavioral and neuronal differences in the isthmus and terminal bulb of free-living soil nematodes, and we examined potential underlying mechanisms of one aspect of M4 evolution. Our results suggest the utility of Caenorhabditis elegans and related nematodes for studying behavioral evolution.
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Affiliation(s)
- Jing-Tzyh Alan Chiang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA.
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De Ley P, De Ley IT, Morris K, Abebe E, Mundo-Ocampo M, Yoder M, Heras J, Waumann D, Rocha-Olivares A, Jay Burr AH, Baldwin JG, Thomas WK. An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philos Trans R Soc Lond B Biol Sci 2006; 360:1945-58. [PMID: 16214752 PMCID: PMC1609217 DOI: 10.1098/rstb.2005.1726] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.
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Affiliation(s)
- Paul De Ley
- Department of Nematology, University of California, Riverside, CA 92521, USA.
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Abstract
Nematodes pervade Earth's biosphere and occupy innumerable ecological niches. The role of Caenorhabditis elegans as a model for developmental processes has encouraged us to cultivate a second nematode, Pristionchus pacificus, as a comparative counterpoint to address questions in development, behavior and ecology in nematode evolution. We hope that this endeavor, now more than a decade underway, will allow us to project findings onto other comparative models for biological processes. To this end, our laboratory has made an extensive genetic map and mutant screens to understand changes in developmental programs. Recently, we have been capitalizing on the whole genome sequence of P. pacificus to describe more thoroughly the molecular basis for these changes, as well as to better integrate our molecular knowledge with the biodiversity of Pristionchus species.
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Affiliation(s)
- Ray L Hong
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
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Scholtz G. Homology and ontogeny: pattern and process in comparative developmental biology. Theory Biosci 2005; 124:121-43. [PMID: 17046352 DOI: 10.1007/bf02814480] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Accepted: 09/08/2005] [Indexed: 10/22/2022]
Abstract
In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologized. These two approaches must not be con-flated. This distinction leads to the conclusion that there is no ontogenetic homology "criterion".
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Affiliation(s)
- Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie/Vergleichende Zoologie, Philippstr. 13, DE-10115 Berlin, Germany.
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Hong RL, Villwock A, Sommer RJ. Cultivation of the rhabditid Poikilolaimus oxycercus as a laboratory nematode for genetic analyses. ACTA ACUST UNITED AC 2005; 303:742-60. [PMID: 16106407 DOI: 10.1002/jez.a.200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vulva formation is a paradigm for evolutionary developmental biology in nematodes. Not only do the number of vulval precursor cells (VPCs) differ between members in the Rhabditidae and Diplogastridae, they are also sculpted via different developmental mechanisms, either by cell fusion in most Rhabditidae or by programmed cell death in the Diplogastridae. In this context, the species Poikilolaimus oxycercus is the only known species in the family Rhabditidae to have a subset of the Pn.p cells commit programmed cell death during the patterning of the VPCs. Our current study introduces P. oxycercus as a new laboratory organism. There are discrete laboratory strains that are genetically polymorphic from each other as well as heterogeneous within each strain. In order to cultivate this gonochoristic nematode into an experimental model with a tractable genetic system, we produced two inbreeding tolerant, near-isogenic strains capable of producing viable progeny with each other. We also described P. oxycera's morphology by scanning electron microscopy (SEM), basic life history traits, hybrid viability, and mating behavior. P. oxycercus females have no preference for inter- or intra-strain matings, and can mate with multiple males in a relatively short time period, suggesting a propensity for maintaining heterozygosity through promiscuity. Interestingly, all sexes from three species in the genus Poikilolaimus show five 4',6-diamidino-2-phenylindole (DAPI) staining bodies in their germ line cells. This could indicate that Poikilolaimus species possess five bivalent chromosomes in their germ lines, in contrast to the hermaphroditic Caenorhabditis elegans or Pristionchus pacificus, which have six chromosomes.
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Affiliation(s)
- Ray L Hong
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076 Tuebingen, Germany.
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40
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Félix MA. An inversion in the wiring of an intercellular signal: evolution of Wnt signaling in the nematode vulva. Bioessays 2005; 27:765-9. [PMID: 16015606 DOI: 10.1002/bies.20275] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Signal transduction pathways are largely conserved throughout the animal kingdom. The repertoire of pathways is limited and each pathway is used in different intercellular signaling events during the development of a given animal. For example, Wnt signaling is recruited, sometimes redundantly with other molecular pathways, in four cell specification events during Caenorhabditis elegans vulva development, including the activation of vulval differentiation. Strikingly,a recent study finds that Wnts act to repress vulval differentiation in the nematode Pristionchus pacificus,1 demonstrating evolutionary flexibility in the use of intercellular signaling pathways.
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Affiliation(s)
- Marie-Anne Félix
- Institut Jacques Monod, CNRS-University of Paris 6-7, Tour 43, 2 place Jussieu, 75251 Paris cedex 05, France.
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41
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Félix MA, Barrière A. Evolvability of cell specification mechanisms. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2005; 304:536-47. [PMID: 15887244 DOI: 10.1002/jez.b.21045] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The architecture of gene action during development is relevant to phenotypic evolution as it links genotype to morphological phenotype. Analysis of development at the level of cell fate specification mechanisms illuminates some of the properties of developmental evolution. In this article, we first review examples of evolutionary change in mechanisms of cell fate specification, with an emphasis on evolution in the dependence on inductive signaling and on evolution of the mechanisms that result in spatial asymmetries. We then focus on properties of development that bias possible phenotypic change and present how the distribution of phenotypes that are available by mutational change of the starting genotype can be experimentally tested by systematic mutagenesis. We finally discuss ways in which selection pressures on phenotypes can be inferred from a comparison of the phenotypic spectrum found on mutation with that found in the wild.
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Affiliation(s)
- Marie-Anne Félix
- Institut Jacques Monod, CNRS-Universités Paris 6 & 7, 75251 Paris cedex 05, France.
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42
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Dutt A, Canevascini S, Froehli-Hoier E, Hajnal A. EGF signal propagation during C. elegans vulval development mediated by ROM-1 rhomboid. PLoS Biol 2004; 2:e334. [PMID: 15455032 PMCID: PMC519001 DOI: 10.1371/journal.pbio.0020334] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Accepted: 08/03/2004] [Indexed: 02/05/2023] Open
Abstract
During Caenorhabditis elegans vulval development, the anchor cell (AC) in the somatic gonad secretes an epidermal growth factor (EGF) to activate the EGF receptor (EGFR) signaling pathway in the adjacent vulval precursor cells (VPCs). The inductive AC signal specifies the vulval fates of the three proximal VPCs P5.p, P6.p, and P7.p. The C. elegans Rhomboid homolog ROM-1 increases the range of EGF, allowing the inductive signal to reach the distal VPCs P3.p, P4.p and P8.p, which are further away from the AC. Surprisingly, ROM-1 functions in the signal-receiving VPCs rather than the signal-sending AC. This observation led to the discovery of an AC-independent activity of EGF in the VPCs that promotes vulval cell fate specification and depends on ROM-1. Of the two previously reported EGF splice variants, the longer one requires ROM-1 for its activity, while the shorter form acts independently of ROM-1. We present a model in which ROM-1 relays the inductive AC signal from the proximal to the distal VPCs by allowing the secretion of the LIN-3L splice variant. These results indicate that, in spite of their structural diversity, Rhomboid proteins play a conserved role in activating EGFR signaling in C. elegans, Drosophila, and possibly also in mammals.
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Affiliation(s)
- Amit Dutt
- 1Zoologisches Institut, Universität ZurichZurichSwitzerland
| | | | | | - Alex Hajnal
- 1Zoologisches Institut, Universität ZurichZurichSwitzerland
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43
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Boldogköi Z. Gene Network Polymorphism Is the Raw Material of Natural Selection: The Selfish Gene Network Hypothesis. J Mol Evol 2004; 59:340-57. [PMID: 15553089 DOI: 10.1007/s00239-004-2629-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.
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Affiliation(s)
- Zsolt Boldogköi
- Laboratory of Neuromorphology, Department of Anatomy, Faculty of Medicine, University of Budapest, Budapest, Hungary.
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44
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Kolotuev I, Podbilewicz B. Pristionchus pacificus vulva formation: polarized division, cell migration, cell fusion, and evolution of invagination. Dev Biol 2004; 266:322-33. [PMID: 14738880 DOI: 10.1016/j.ydbio.2003.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tube formation is a widespread process during organogenesis. Specific cellular behaviors participate in the invagination of epithelial monolayers that form tubes. However, little is known about the evolutionary mechanisms of cell assembly into tubes during development. In Caenorhabditis elegans, the detailed step-to-step process of vulva formation has been studied in wild type and in several mutants. Here we show that cellular processes during vulva development, which involve toroidal cell formation and stacking of rings, are conserved between C. elegans and Pristionchus pacificus, two species of nematodes that diverged approximately 100 million years ago. These cellular behaviors are divided into phases of cell proliferation, short-range migration, and cell fusion that are temporally distinct in C. elegans but not in P. pacificus. Thus, we identify heterochronic changes in the cellular events of vulva development between these two species. We find that alterations in the division axes of two equivalent vulval cells from Left-Right cleavage in C. elegans to Anterior-Posterior division in P. pacificus can cause the formation of an additional eighth ring. Thus, orthogonal changes in cell division axes with alterations in the number and sequence of cell fusion events result in dramatic differences in vulval shape and in the number of rings in the species studied. Our characterization of vulva formation in P. pacificus compared to C. elegans provides an evolutionary-developmental foundation for molecular genetic analyses of organogenesis in different species within the phylum Nematoda.
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Affiliation(s)
- Irina Kolotuev
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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45
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Félix MA. Alternative morphs and plasticity of vulval development in a rhabditid nematode species. Dev Genes Evol 2004; 214:55-63. [PMID: 14730447 DOI: 10.1007/s00427-003-0376-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2003] [Accepted: 11/27/2003] [Indexed: 10/26/2022]
Abstract
The nematode species Rhabditis sp. SB347 (Family Rhabditidae) in standard culture conditions displays two developmental morphs with distinct modes of sexual reproduction: (1). females and males that develop through four feeding juvenile ("larval") stages; (2). self-fertile protandric hermaphrodites that develop through an obligatory non-feeding third juvenile stage, the "dauer" larva. In females and males, somatic gonad development begins in the first larval stage, whereas in hermaphrodites it is delayed to the second larval stage. Vulval development also differs between females and hermaphrodites: (1). the P8.p cell divides in females but stays undivided in hermaphrodites; (2). the number, timing, and source of inductive signals from the gonad to the vulval precursor cells differ between the two morphs. These results show that discrete vulva developmental routes can be adopted by animals of the same genotype.
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Affiliation(s)
- Marie-Anne Félix
- Institut Jacques Monod, CNRS, Universités Paris 6 et 7, Tour 43, 2 place Jussieu, 75251, Paris cedex 05, France.
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46
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Dichtel-Danjoy ML, Félix MA. The two steps of vulval induction in Oscheius tipulae CEW1 recruit common regulators including a MEK kinase. Dev Biol 2004; 265:113-26. [PMID: 14697357 DOI: 10.1016/j.ydbio.2003.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The cell interactions that specify the spatial pattern of vulval precursor cell (VPC) fates differ between the nematodes Oscheius tipulae CEW1 and Caenorhabditis elegans. In the former, the centered pattern of fates is obtained by two successive inductions from the gonadal anchor cell, whereas in the latter, a single inductive step by the anchor cell (EGF-Ras-MAP kinase pathway) can act as a morphogen and is reinforced by lateral signaling between the vulval precursors (Notch pathway). We performed a genetic screen for vulva mutants in O. tipulae CEW1. Here we present the mutants that specifically affect the vulval induction mechanisms. Phenotypic and epistatic analyses of these mutants show that both vulval induction steps share common components, one of which appears to be MEK kinase(s). Moreover, the inductive pathway (including MEK kinase) influences the competence of the vulval precursor cells and more strikingly their division pattern as well, irrespective of their vulval fate. Finally, a comparison of vulval mutant phenotypes obtained in C. elegans and O. tipulae CEW1 highlights the evolution of vulval induction mechanisms between the two species.
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47
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Abstract
Over the past two to three decades, developmental biology has demonstrated that all multicellular organisms in the animal kingdom share many of the same molecular building blocks and many of the same regulatory genetic pathways. Yet we still do not understand how the various organisms use these molecules and pathways to assume all the forms we know today. Evolutionary developmental biology tackles this problem by comparing the development of one organism to another and comparing the genes involved and gene functions to understand what makes one organism different from another. In this review, we revisit a set of seven concepts defined by Lewis Wolpert (fate maps, asymmetric division, induction, competence, positional information, determination, and lateral inhibition) that describe the characters of many developmental systems and supplement them with three additional concepts (developmental genomics, genetic redundancy, and genetic networks). We will discuss examples of comparative developmental studies where these concepts have guided observations on the advent of a developmental novelty. Finally, we identify a set of evolutionary frameworks, such as developmental constraints, cooption, duplication, parallel and convergent evolution, and homoplasy, to adequately describe the evolutionary properties of developmental systems.
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Affiliation(s)
- David Rudel
- Max-Planck Institut für Entwicklungsbiologie, Abteilung Evolutionsbiologie, Spemannstrasse 37-39, D-72076 Tübingen, Germany
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48
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Brakefield PM, French V, Zwaan BJ. Development and the Genetics of Evolutionary Change Within Insect Species. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2003. [DOI: 10.1146/annurev.ecolsys.34.011802.132425] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
▪ Abstract Changes in genes and in developmental processes generate the phenotypic variation that is sorted by natural selection in adaptive evolution. We review several case studies in which artificial selection experiments in insects have led to divergent morphologies, and where further work has revealed information about the underlying changes at both the genetic and developmental levels. In addition, we examine several studies of phenotypic plasticity where multidisciplinary approaches are also beginning to reveal more about how developmental processes are modulated. Such integrated research will lead to a richer understanding of the changes in development that occur during evolutionary responses to natural selection, and it will also more rigorously examine how developmental processes can influence the tempo and direction of evolutionary change.
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Affiliation(s)
- Paul M. Brakefield
- Institute of Biology, Leiden University, Leiden, 2300 RA The Netherlands
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Vernon French
- Institute of Biology, Leiden University, Leiden, 2300 RA The Netherlands
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Bas J. Zwaan
- Institute of Biology, Leiden University, Leiden, 2300 RA The Netherlands
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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49
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Srinivasan J, Sinz W, Jesse T, Wiggers-Perebolte L, Jansen K, Buntjer J, van der Meulen M, Sommer RJ. An integrated physical and genetic map of the nematode Pristionchus pacificus. Mol Genet Genomics 2003; 269:715-22. [PMID: 12884007 DOI: 10.1007/s00438-003-0881-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 06/06/2003] [Indexed: 11/26/2022]
Abstract
The free-living nematode Pristionchus pacificus is one of several species that have recently been developed as a satellite system for comparative functional studies in evolutionary developmental biology. Comparisons of developmental processes between P. pacificus and the well established model organism Caenorhabditis elegans at the cellular and genetic levels provide detailed insight into the molecular changes that shape evolutionary transitions. To facilitate genetic analysis and cloning of mutations in P. pacificus, we previously generated a BAC-based genetic linkage map for this organism. Here, we describe the construction of a physical map of the P. pacificus genome based on AFLP fingerprint analysis of 7747 BAC clones. Most of the SSCP markers used to generate the genetic linkage map were derived from BAC ends, so that the physical genome map and the genetic map can be integrated. The contigs that make up the physical map are evenly distributed over the genetic linkage map and no clustering is observed, indicating that the physical map provides a valid representation of the P. pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes.
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Affiliation(s)
- J Srinivasan
- Abteilung für Evolutionsbiologie, Max-Planck Institut für Entwicklungsbiologie, Spemannstrasse 37, 72076 Tübingen, Germany
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50
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Perlman SJ, Spicer GS, Shoemaker DD, Jaenike J. Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle. Mol Ecol 2003; 12:237-49. [PMID: 12492892 DOI: 10.1046/j.1365-294x.2003.01721.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Little is known about what determines patterns of host association of horizontally transmitted parasites over evolutionary timescales. We examine the evolution of associations between mushroom-feeding Drosophila flies (Diptera: Drosophilidae), particularly in the quinaria and testacea species groups, and their horizontally transmitted Howardula nematode parasites (Tylenchida: Allantonematidae). Howardula species were identified by molecular characterization of nematodes collected from wild-caught flies. In addition, DNA sequence data is used to infer the phylogenetic relationships of both host Drosophila (mtDNA: COI, II, III) and their Howardula parasites (rDNA: 18S, ITS1; mtDNA: COI). Host and parasite phylogenies are not congruent, with patterns of host association resulting from frequent and sometimes rapid host colonizations. Drosophila-parasitic Howardula are not monophyletic, and host switches have occurred between Drosophila and distantly related mycophagous sphaerocerid flies. There is evidence for some phylogenetic association between parasites and hosts, with some nematode clades associated with certain host lineages. Overall, these host associations are highly dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared breeding sites and large potential host ranges of the nematodes.
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Affiliation(s)
- Steve J Perlman
- Department of Ecology and Evolutionary Biology, Biological Sciences West, University of Arizona, Tucson, AZ 85721, USA.
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