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Kanzaki N, Ikeda Y, Shinya R. Onthodiplogaster japonica n. gen., n. sp. (Rhabditida: Diplogastridae) isolated from Onthophagus sp. (Coleoptera: Scarabaeidae) from Japan. Sci Rep 2023; 13:6470. [PMID: 37081071 PMCID: PMC10119125 DOI: 10.1038/s41598-023-33586-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
A diplogastrid nematode was isolated from a dung beetle, Onthophagus sp., collected from a rotten mushroom in Kyoto, Japan. The species is characterised by its cheilostomatal shape, separated into 12 narrow plates (rugae), deep stegostom, large ellipsoidal amphids, conical female tail and characteristic receptaculum seminis in the female. Based on its phylogenetic status and stomatal composition, the species is typologically similar to two other diplogastrid genera, Neodiplogaster and Mononchoides. The species can be distinguished from these two genera by the size and shape of the amphid (small pore in Neodiplogaster), female tail shape (long and filiform in Mononchoides) and presence of receptaculum seminis (absence in the two nominal genera), and is described as a monotypic member of a new genus, Onthodiplogaster japonica n. gen., n. sp. Observation of feeding behaviour suggested that O. japonica n. gen., n. sp. does not show clear stomatal dimorphism or polymorphism, which is found in its close relatives, but the species can feed on nematodes (predation), fungi and bacteria. This monomorphic omnivory possibly represents its habitat of dung and other rotten materials, where the environment is biologically divergent, and its condition changes rapidly.
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Affiliation(s)
- Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan.
| | - Yuya Ikeda
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ryoji Shinya
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
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Stracke K, Hejnol A. Marine animal evolutionary developmental biology-Advances through technology development. Evol Appl 2023; 16:580-588. [PMID: 36793684 PMCID: PMC9923486 DOI: 10.1111/eva.13456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 12/01/2022] Open
Abstract
Evolutionary developmental biology, the interdisciplinary effort of illuminating the conserved similarities and differences during animal development across all phylogenetic clades, has gained renewed interest in the past decades. As technology (immunohistochemistry, next-generation sequencing, advanced imaging, and computational resources) has advanced, so has our ability of resolving fundamental hypotheses and overcoming the genotype-phenotype gap. This rapid progress, however, has also exposed gaps in the collective knowledge around the choice and representation of model organisms. It has become clear that evo-devo requires a comparative, large-scale approach including marine invertebrates to resolve some of the most urgent questions about the phylogenetic positioning and character traits of the last common ancestors. Many invertebrates at the base of the tree of life inhabit marine environments and have been used for some years due to their accessibility, husbandry, and morphology. Here, we briefly review the major concepts of evolutionary developmental biology and discuss the suitability of established model organisms to address current research questions, before focussing on the importance, application, and state-of-the-art of marine evo-devo. We highlight novel technical advances that progress evo-devo as a whole.
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Affiliation(s)
- Katharina Stracke
- Department of Biological Sciences, Faculty of Mathematics and Natural Sciences University of Bergen Bergen Norway
| | - Andreas Hejnol
- Department of Biological Sciences, Faculty of Mathematics and Natural Sciences University of Bergen Bergen Norway.,Institute of Systematic Zoology and Evolutionary Biology Friedrich-Schiller-University Jena Jena Germany
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Athanasouli M, Rödelsperger C. Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons. BMC Genomics 2022; 23:523. [PMID: 35854227 PMCID: PMC9297572 DOI: 10.1186/s12864-022-08731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reservoir for molecular innovation. In this study, we aim to add repetitive elements to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation. RESULTS Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences. While retroelements are more frequently found at the chromosome arms, DNA transposons are distributed more evenly. We found multiple DNA transposons, as well as LTR and LINE elements with abundant evidence of expression as single-exon transcripts. When testing whether transposons disproportionately contribute towards new gene formation, we found that roughly 10-20% of genes across all age classes overlap transposable elements with the strongest trend being an enrichment of low complexity regions among the oldest genes. Finally, we characterized a horizontal gene transfer of Zisupton elements into diplogastrid nematodes. These DNA transposons invaded nematodes from eukaryotic donor species and experienced a recent burst of activity in the P. pacificus lineage. CONCLUSIONS The comprehensive annotation of repetitive elements in the P. pacificus genome builds a resource for future functional genomic analyses as well as for more detailed investigations of molecular innovations.
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Affiliation(s)
- Marina Athanasouli
- Max Planck Institute for Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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Harry CJ, Messar SM, Ragsdale EJ. Comparative reconstruction of the predatory feeding structures of the polyphenic nematode Pristionchus pacificus. Evol Dev 2022; 24:16-36. [PMID: 35239990 PMCID: PMC9286642 DOI: 10.1111/ede.12397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/06/2022] [Accepted: 02/01/2022] [Indexed: 12/25/2022]
Abstract
Pristionchus pacificus is a nematode model for the developmental genetics of morphological polyphenism, especially at the level of individual cells. Morphological polyphenism in this species includes an evolutionary novelty, moveable teeth, which have enabled predatory feeding in this species and others in its family (Diplogastridae). From transmission electron micrographs of serial thin sections through an adult hermaphrodite of P. pacificus, we three‐dimensionally reconstructed all epithelial and myoepithelial cells and syncytia, corresponding to 74 nuclei, of its face, mouth, and pharynx. We found that the epithelia that produce the predatory morphology of P. pacificus are identical to Caenorhabditis elegans in the number of cell classes and nuclei. However, differences in cell form, spatial relationships, and nucleus position correlate with gross morphological differences from C. elegans and outgroups. Moreover, we identified fine‐structural features, especially in the anteriormost pharyngeal muscles, that underlie the conspicuous, left‐right asymmetry that characterizes the P. pacificus feeding apparatus. Our reconstruction provides an anatomical map for studying the genetics of polyphenism, feeding behavior, and the development of novel form in a satellite model to C. elegans. All cells making the dimorphic, novel form of an animal with cell constancy were identified. Although the number of cells is fully conserved, divergence in form and connectivity—including fixed asymmetries—sheds light on the origins of this trait.
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Affiliation(s)
- Clayton J Harry
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Sonia M Messar
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Hincapie Agudelo M, Carbonell Medina BA, Arenas Gómez CM, Delgado JP. Ambystoma mexicanum, a model organism in developmental biology and regeneration: a colombian experience. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v27n1.88309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Ambystoma mexicanum is a urodele amphibian endemic to Xochimilco Lake in Mexico, it belongs to the salamander family Ambystomatidae. This species has frequently been used as model organism in developmental biology and regeneration laboratories around the world due to its broad regenerative capacities and adaptability to laboratory conditions. In this review we describe the establishment of the first colony of axolotls in Colombia to study tissue regeneration and our perspectives on the use A. mexicanum as a model organism in Colombia are discussed emphasizing its possible uses in regeneration and developmental biology
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Kruger MS, Kanzaki N, Giblin-Davis RM, Greeff JM. Molecular diversity and relationships of fig associated nematodes from South Africa. PLoS One 2021; 16:e0255451. [PMID: 34375357 PMCID: PMC8354458 DOI: 10.1371/journal.pone.0255451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/16/2021] [Indexed: 12/05/2022] Open
Abstract
Nematodes of figs and fig wasps have received limited attention in Africa since their discovery in 1973. Sixteen of the 25 species of native South African figs were sampled for nematode associates using molecular barcoding with three loci (SSU, LSU D2-D3 and mtCOI) and fourteen (93%) were positive for at least one nematode species. Thirty-three putative species of nematodes were identified and classified according to the loci that were amplified and successfully sequenced. Fourteen putative nematode species were classified as Aphelenchoididae, of which nine were identified as Ficophagus from four species of Ficus from the section Galoglychia (i.e., five ex F. burkei including one shared with F. natalensis, one ex F. glumosa, one ex F. lutea, and one ex F. stuhlmannii) and one species ex F. sur from the section Sycomorus. In addition, there were four nematode species classified as Schistonchus s.s. from section Galoglychia figs (i.e., one ex F. burkei, two ex F. trichopoda, and one ex F. glumosa). There was also one species of Bursaphelenchus nematode recovered from F. sur from the section Sycomorus. Sixteen putative nematode species were classified as Diplogastridae, of which eight occurred in two clades of what is currently called Parasitodiplogaster with one (P. salicifoliae) being recovered from two Ficus species in the section Urostigma (F. salicifolia and F. ingens) and seven diplogastrids being associated with six species of Ficus from the section Galoglychia (i.e., two ex F. burkei including P. sycophilon, one ex F. stuhlmannii, one ex F. burtt-davyi, one ex F. trichopoda, one ex F. abutilifolia and one ex F. sansibarica). Three Acrostichus spp., a Teratodiplogaster and a Pristionchus species were recovered from F. sur and two Teratodiplogaster spp. and Pristionchus sycomori were recovered from F. sycomorus with both Ficus species belonging to the subgenus and section Sycomorus. The identities of the previously described T. martini and Parasitodiplogaster doliostoma (= Pristionchus sp. 35) are discussed. Lastly, there was a panagrolaimid identified from F. petersii.
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Affiliation(s)
- Meike S. Kruger
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Natsumi Kanzaki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Kansai Research Centre, Forestry and Forest Products Research Institute, Kyoto, Japan
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Centre, University of Florida/IFAS, Davie, FL, United States of America
| | - Robin M. Giblin-Davis
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Centre, University of Florida/IFAS, Davie, FL, United States of America
| | - Jaco M. Greeff
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Kanzaki N, Hamaguchi K. Pristionchus trametes n. sp. (Diplogastridae) isolated from the mushroom Trametes orientalis in Kyoto, Japan. J Nematol 2021; 53:e2021-60. [PMID: 34296192 PMCID: PMC8290503 DOI: 10.21307/jofnem-2021-060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Indexed: 12/02/2022] Open
Abstract
A new species of Pristionchus was isolated from fruiting bodies of the wood-decaying fungus Trametes orientalis collected from Kyoto, Japan. Attempts to culture it using bacteria, yeast, and freeze-killed wax moth larvae as food or substrate failed. The eurystomatous form of the species was not found in the collected material, and the species is typologically characterized by: its ‘small’ stoma with thin, membrane-like cheilostomatal plates, a small triangular right subventral tooth, thorn-like dorsal tooth, and small left subventral denticles; a short, blunt male tail spike; and a short, conical female tail. Although the posterior probability support was not high (66%), phylogenetic analysis of both small and large ribosomal RNA gene subunits suggests that the species is closely related to P. elegans and P. bucculentus. The new species can be distinguished from those two by its diagnostic characters comprising the stomatal morphology and male and female tail characters.
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Affiliation(s)
- Natsumi Kanzaki
- Kanzsai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan
| | - Keiko Hamaguchi
- Kanzsai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan
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Pointer MD, Gage MJG, Spurgin LG. Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb) 2021; 126:869-883. [PMID: 33767370 PMCID: PMC8178323 DOI: 10.1038/s41437-021-00420-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023] Open
Abstract
Flour beetles of the genus Tribolium have been utilised as informative study systems for over a century and contributed to major advances across many fields. This review serves to highlight the significant historical contribution that Tribolium study systems have made to the fields of ecology and evolution, and to promote their use as contemporary research models. We review the broad range of studies employing Tribolium to make significant advances in ecology and evolution. We show that research using Tribolium beetles has contributed a substantial amount to evolutionary and ecological understanding, especially in the fields of population dynamics, reproduction and sexual selection, population and quantitative genetics, and behaviour, physiology and life history. We propose a number of future research opportunities using Tribolium, with particular focus on how their amenability to forward and reverse genetic manipulation may provide a valuable complement to other insect models.
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Affiliation(s)
- Michael D Pointer
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Matthew J G Gage
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Kanzaki N. New insight into the tripartite relationship of microbes, nematodes and insects. Environ Microbiol 2021; 23:4856-4858. [PMID: 33684259 DOI: 10.1111/1462-2920.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto, Japan
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10
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Farris SM. The rise to dominance of genetic model organisms and the decline of curiosity-driven organismal research. PLoS One 2020; 15:e0243088. [PMID: 33259560 PMCID: PMC7707607 DOI: 10.1371/journal.pone.0243088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
Curiosity-driven, basic biological research "…performed without thought of practical ends…" establishes fundamental conceptual frameworks for future technological and medical breakthroughs. Traditionally, curiosity-driven research in biological sciences has utilized experimental organisms chosen for their tractability and suitability for studying the question of interest. This approach leverages the diversity of life to uncover working solutions (adaptations) to problems encountered by living things, and evolutionary context as to the extent to which these solutions may be generalized to other species. Despite the well-documented success of this approach, funding portfolios of United States granting agencies are increasingly filled with studies on a few species for which cutting-edge molecular tools are available (genetic model organisms). While this narrow focus may be justified for biomedically-focused funding bodies such as the National Institutes of Health, it is critical that robust federal support for curiosity-driven research using diverse experimental organisms be maintained by agencies such as the National Science Foundation. Using the disciplines of neurobiology and behavioral research as an example, this study finds that NSF grant awards have declined in association with a decrease in the proportion of grants funded for experimental, rather than genetic model organism research. The decline in use of experimental organisms in the literature mirrors but predates the shift grant funding. Today's dominance of genetic model organisms was thus initiated by researchers themselves and/or by publication peer review and editorial preferences, and was further reinforced by pressure from granting agencies, academic employers, and the scientific community.
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Affiliation(s)
- Sarah M. Farris
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
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Athanasouli M, Witte H, Weiler C, Loschko T, Eberhardt G, Sommer RJ, Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 2020; 21:708. [PMID: 33045985 PMCID: PMC7552371 DOI: 10.1186/s12864-020-07100-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.
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Affiliation(s)
- Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Weiler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Gabi Eberhardt
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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Hasoon MSR, Plaistow SJ. Embryogenesis plasticity and the transmission of maternal effects in Daphnia pulex. Evol Dev 2020; 22:345-357. [PMID: 32579775 DOI: 10.1111/ede.12346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding how genetic, nongenetic, and environmental cues are integrated during development may be critical in understanding if, and how, organisms will respond to rapid environmental change. Normally, only post-embryonic studies are possible. But in this study, we developed a real-time, high-throughput confocal microscope assay that allowed us to link Daphnia embryogenesis to offspring life history variation at the individual level. Our assay identified eight clear developmental phenotypes linked by seven developmental stages, the duration of which were correlated with the expression of specific offspring life history traits. Daphnia embryogenesis varied not only between clones reared in the same environment, but also within a single clone when mothers were of different ages or reared in different food environments. Our results support the hypothesis that Daphnia embryogenesis is plastic and can be altered by changes in maternal state or maternal environment. As well as furthering our understanding of the mechanisms underpinning parental effects, our assay may also have an industrial application if it can be used as a rapid ecotoxicological prescreen for testing the effect that pollutant doses have on offspring life histories traditionally assayed with a 21-day Daphnia reproduction test.
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Affiliation(s)
- Megan S R Hasoon
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Biology, University of York, York, UK
| | - Stewart J Plaistow
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Kanzaki N, Liang WR, Chiu CI, Li HF. Acrostichus ziaelasi n. sp. (Nematoda: Diplogastridae) isolated from the beetle Ziaelas formosanus, a tenebrionid symbiont of the termite Odontotermes formosanus with remarks on the genus Acrostichus Rahm, 1928. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Feeding Dimorphism in a Mycophagous Nematode, Bursaphelenchus sinensis. Sci Rep 2019; 9:13956. [PMID: 31562356 PMCID: PMC6765002 DOI: 10.1038/s41598-019-50462-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/09/2019] [Indexed: 02/03/2023] Open
Abstract
Phenotypic plasticity has been widely reported in animals and can drive investment in new biological characters that engender ecological adaptability. The nematode family Diplogastridae, especially Pristionchus pacificus with its dramatic stomatal (feeding) dimorphism, has become an important model system to analyze the evolutionary and developmental aspects of polyphenism. However, this plasticity has not been confirmed in other nematode groups. In the present study, we experimentally examined the feeding dimorphism of a fungal feeding free-living nematode, Bursaphelenchus sinensis. In a laboratory culturing experiment, the nematode expressed dimorphism, i.e., a small proportion of the population manifested as a predatory form. This form only occurred in females and was not clearly influenced by the presence of potential prey species. In addition, the ratio of the predatory form to the mycophagous form varied among different fungal food species grown in monoculture on different culture media. The predatory form of B. sinensis was typologically similar to the monomorphic (specialized) predators belonging to the same family. However, some essential morphological characters were slightly different from the specialized predators, and their behaviours were clearly disparate, suggesting that predation in B. sinensis is derived from a different phylogenetic origin than that of the specialized predators.
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Sanger TJ, Rajakumar R. How a growing organismal perspective is adding new depth to integrative studies of morphological evolution. Biol Rev Camb Philos Soc 2019; 94:184-198. [PMID: 30009397 DOI: 10.1111/brv.12442] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 06/11/2018] [Accepted: 06/14/2018] [Indexed: 01/24/2023]
Abstract
Over the past half century, the field of Evolutionary Developmental Biology, or Evo-devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo-devo to adopt a high-resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro- and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo-devo are integrated more thoroughly with the principles of this organismal framework.
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Affiliation(s)
- Thomas J Sanger
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, U.S.A
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Love AC, Yoshida Y. Reflections on Model Organisms in Evolutionary Developmental Biology. Results Probl Cell Differ 2019; 68:3-20. [PMID: 31598850 DOI: 10.1007/978-3-030-23459-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter reflects on and makes explicit the distinctiveness of reasoning practices associated with model organisms in the context of evolutionary developmental research. Model organisms in evo-devo instantiate a unique synthesis of model systems strategies from developmental biology and comparative strategies from evolutionary biology that negotiate a tension between developmental conservation and evolutionary change to address scientific questions about the evolution of development and the developmental basis of evolutionary change. We review different categories of model systems that have been advanced to understand practices found in the life sciences in order to comprehend how evo-devo model organisms instantiate this synthesis in the context of three examples: the starlet sea anemone and the evolution of bilateral symmetry, leeches and the origins of segmentation in bilaterians, and the corn snake to understand major evolutionary change in axial and appendicular morphology.
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Affiliation(s)
- Alan C Love
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA.
| | - Yoshinari Yoshida
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA
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18
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The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in? Theory Biosci 2018; 137:169-184. [PMID: 30132255 DOI: 10.1007/s12064-018-0269-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2018] [Indexed: 12/23/2022]
Abstract
The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to 'extend' the Modern Synthesis-derived 'standard evolutionary theory' (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES-published by Laland and collaborators in 2015-in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.
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19
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Ponz‐Segrelles G, Bleidorn C, Aguado MT. Expression of
vasa
,
piwi
, and
nanos
during gametogenesis in
Typosyllis antoni
(Annelida, Syllidae). Evol Dev 2018; 20:132-145. [DOI: 10.1111/ede.12263] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guillermo Ponz‐Segrelles
- Departamento de BiologíaFacultad de CienciasUniversidad Autónoma de MadridCantoblancoMadridSpain
| | - Christoph Bleidorn
- Animal Evolution and BiodiversityGeorg‐August‐University GöttingenGöttingenGermany
| | - M. Teresa Aguado
- Departamento de BiologíaFacultad de CienciasUniversidad Autónoma de MadridCantoblancoMadridSpain
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20
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Rödelsperger C, Meyer JM, Prabh N, Lanz C, Bemm F, Sommer RJ. Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus. Cell Rep 2018; 21:834-844. [PMID: 29045848 DOI: 10.1016/j.celrep.2017.09.077] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 09/24/2017] [Indexed: 01/24/2023] Open
Abstract
The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P. pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P. pacificus. Despite widespread conservation of synteny between P. pacificus and C. elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C. elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P. pacificus.
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Affiliation(s)
- Christian Rödelsperger
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
| | - Jan M Meyer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Neel Prabh
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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21
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Namai S, Sugimoto A. Transgenesis by microparticle bombardment for live imaging of fluorescent proteins in Pristionchus pacificus germline and early embryos. Dev Genes Evol 2018; 228:75-82. [DOI: 10.1007/s00427-018-0605-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/09/2018] [Indexed: 01/26/2023]
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22
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Yoshida K, Herrmann M, Kanzaki N, Weiler C, Rödelsperger C, Sommer RJ. Two New Species of Pristionchus (Nematoda: Diplogastridae) from Taiwan and the Definition of the pacificus Species-Complex Sensu Stricto. J Nematol 2018; 50:355-368. [PMID: 30451420 PMCID: PMC6909367 DOI: 10.21307/jofnem-2018-019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/11/2022] Open
Abstract
Pristionchus pacificus Sommer, Carta, Kim, and Sternberg, 1996 is an important model organism in evolutionary biology that aims to integrate developmental biology and evo-devo with population genetics and ecology. Functional studies in P. pacificus are supported by a well-established phylogenetic framework of around 30 species of the genus Pristionchus that have been described in the last decade based on their entomophilic and necromenic association with scarab beetles. Biogeographically, East Asia has emerged as a hotspot of Pristionchus speciation and recent samplings have therefore focused on Islands and mainland settings in East Asia. Here, we describe in a series of three publications the results of our sampling efforts in Taiwan, Japan, and Hongkong in 2016 and 2017. We describe a total of nine new species that cover different phylogenetic species-complexes of the Pristionchus genus. In this first publication, we describe two new species, Pristionchus sikae sp. n. and Pristionchus kurosawai sp. n. that are closely related to P. pacificus . Together with five previously described species they form the " pacificus species-complex sensu stricto" that is characterized by all species forming viable, but sterile F1 hybrids indicating reproductive isolation. P. sikae sp. n. and P. kurosawai sp. n. have a gonochorist mode of reproduction and they are described using morphology, morphometrics, mating experiments, and genome-wide sequence analysis. We discuss the extreme diversification in the pacificus species-complex sensu stricto in East Asia and its potential power to study speciation processes.
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Affiliation(s)
- Kohta Yoshida
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Matthias Herrmann
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto 612-0855, Japan
| | - Christian Weiler
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Christian Rödelsperger
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Ralf J. Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
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23
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Lu Y, Chen M, Reding K, Pick L. Establishment of molecular genetic approaches to study gene expression and function in an invasive hemipteran, Halyomorpha halys. EvoDevo 2017; 8:15. [PMID: 29075432 PMCID: PMC5648497 DOI: 10.1186/s13227-017-0078-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/04/2017] [Indexed: 01/08/2023] Open
Abstract
Hemiptera is a large clade of insects understudied in terms of developmental biology. Halyomorpha halys, the Brown Marmorated Stink Bug (BMSB, referred to throughout as H. halys), is an invasive hemipteran pest of the mid-Atlantic region of the USA that has rapidly spread to other regions in recent years, devastating a wide range of crops using a piercing and sucking mechanism. Its phylogenetic position, polyphagous habits, and rapid spread in the USA suggested that H. halys would be an ideal system to broaden our knowledge of developmental mechanisms in insects. We and others previously generated transcriptome sequences from different life stages of this insect. Here, we describe tools to examine gene expression patterns in whole-mount H. halys embryos and to test the response of H. halys to RNA interference (RNAi). We show that spatial and temporal patterns of gene expression in H. halys can be effectively monitored by both immunostaining and in situ hybridization. We also show that delivery of dsRNA to adult females knocks down gene function in offspring, using the homeotic gene Sex combs reduced (Scr). Knockdown of Hh-Scr resulted in dramatic malformations of the mouthparts, demonstrating for the first time that RNAi is effective in this species. Our results suggest that, despite difficulties with long-term laboratory culture of H. halys, this species shows promise as a developmental system.
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Affiliation(s)
- Yong Lu
- Department of Entomology, University of Maryland, College Park, MD 20742 USA.,Present Address: Department of Anesthesiology, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, NY 11794 USA
| | - Mengyao Chen
- Department of Entomology, University of Maryland, College Park, MD 20742 USA
| | - Katie Reding
- Department of Entomology, University of Maryland, College Park, MD 20742 USA
| | - Leslie Pick
- Department of Entomology, University of Maryland, College Park, MD 20742 USA
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24
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Serobyan V, Sommer RJ. Developmental systems of plasticity and trans-generational epigenetic inheritance in nematodes. Curr Opin Genet Dev 2017; 45:51-57. [DOI: 10.1016/j.gde.2017.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 11/27/2022]
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25
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26
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Chevalier RL. Evolutionary Nephrology. Kidney Int Rep 2017; 2:302-317. [PMID: 28845468 PMCID: PMC5568830 DOI: 10.1016/j.ekir.2017.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 01/05/2023] Open
Abstract
Progressive kidney disease follows nephron loss, hyperfiltration, and incomplete repair, a process described as "maladaptive." In the past 20 years, a new discipline has emerged that expands research horizons: evolutionary medicine. In contrast to physiologic (homeostatic) adaptation, evolutionary adaptation is the result of reproductive success that reflects natural selection. Evolutionary explanations for physiologically maladaptive responses can emerge from mismatch of the phenotype with environment or evolutionary tradeoffs. Evolutionary adaptation to a terrestrial environment resulted in a vulnerable energy-consuming renal tubule and a hypoxic, hyperosmolar microenvironment. Natural selection favors successful energy investment strategy: energy is allocated to maintenance of nephron integrity through reproductive years, but this declines with increasing senescence after ~40 years of age. Risk factors for chronic kidney disease include restricted fetal growth or preterm birth (life history tradeoff resulting in fewer nephrons), evolutionary selection for APOL1 mutations (that provide resistance to trypanosome infection, a tradeoff), and modern life experience (Western diet mismatch leading to diabetes and hypertension). Current advances in genomics, epigenetics, and developmental biology have revealed proximate causes of kidney disease, but attempts to slow kidney disease remain elusive. Evolutionary medicine provides a complementary approach by addressing ultimate causes of kidney disease. Marked variation in nephron number at birth, nephron heterogeneity, and changing susceptibility to kidney injury throughout life history are the result of evolutionary processes. Combined application of molecular genetics, evolutionary developmental biology (evo-devo), developmental programming and life history theory may yield new strategies for prevention and treatment of chronic kidney disease.
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Affiliation(s)
- Robert L. Chevalier
- Department of Pediatrics, The University of Virginia, Charlottesville, Virginia, USA
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27
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Arguello JR, Benton R. Open questions: Tackling Darwin's "instincts": the genetic basis of behavioral evolution. BMC Biol 2017; 15:26. [PMID: 28372547 PMCID: PMC5377514 DOI: 10.1186/s12915-017-0369-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
All of us have marveled at the remarkable diversity of animal behaviors in nature. None of us has much idea of how these have evolved.
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Affiliation(s)
- J Roman Arguello
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland.
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28
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Erick Peirson BR, Kropp H, Damerow J, Laubichler MD. The diversity of experimental organisms in biomedical research may be influenced by biomedical funding. Bioessays 2017; 39. [DOI: 10.1002/bies.201600258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- B. R. Erick Peirson
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempeAZUSA
| | - Heather Kropp
- Department of GeographyColgate UniversityHamiltonNYUSA
| | - Julia Damerow
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempeAZUSA
| | - Manfred D. Laubichler
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempeAZUSA
- Santa Fe InstituteSanta FeNMUSA
- Marine Biological LaboratoryWoods HoleMAUSA
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29
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Meyer JM, Baskaran P, Quast C, Susoy V, Rödelsperger C, Glöckner FO, Sommer RJ. Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island. Environ Microbiol 2017; 19:1476-1489. [PMID: 28198090 DOI: 10.1111/1462-2920.13697] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/20/2016] [Accepted: 01/08/2017] [Indexed: 02/06/2023]
Abstract
Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles´ deaths. Surprisingly, new dauers are seen after 11 days, suggesting that some worms return to the dauer stage after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects.
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Affiliation(s)
- Jan M Meyer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Praveen Baskaran
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Christian Quast
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Vladislav Susoy
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Christian Rödelsperger
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Frank O Glöckner
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
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30
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Two New Pristionchus Species (Nematoda: Diplogastridae) from Taiwan are Part of a Species-cluster Representing the Closest Known Relatives of the Model Organism P. pacificus. Zool Stud 2016; 55:e48. [PMID: 31966193 DOI: 10.6620/zs.2016.55-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/29/2016] [Indexed: 11/18/2022]
Abstract
Matthias Herrmann, Christian Weiler, Christian Rödelsperger, Natsumi Kanzaki, and Ralf J. Sommer (2016) Pristionchus pacificus is an important model organism in evolutionary biology and has been used to establish integrative studies that link developmental biology with ecology and population genetics. This species is part of the P. pacificus species-complex of the genus, many members of which occur in East Asia. While P. pacificus is hermaphroditic, the two most closely related known species are P. exspectatus and P. arcanus from Japan, both of which are gonochorists. P. exspectatus is so far the closest known relative of P. pacificus and thus, considered to represent the sister species. Here, we describe two new species of Pristionchus, P. taiwanensis and P. occultus from Taiwan using morphology, morphometrics, mating experiments and genome- wide sequence analysis. Both species are gonochorists and they are morphologically indistinguishable from P. exspectatus, P. arcanus and P. pacificus. However, reproductive isolation, namely the inability to produce interfertile hybrids, separates all species pairs in the species-complex. Phylogeny inferred from more than 700,000 genome-wide variable sites that were genotyped in all species suggest that P. taiwanensis and P. occultus are the sister species of P. arcanus and P. exspectatus, respectively. P. taiwanensis and P. occultus together with P. exspectatus and P. arcanus form a species-cluster with P. pacificus. The identification of these two novel gonochoristic species is invaluable for studies of population genetics, speciation, and macroevolution in the genus. We discuss the biogeography of Pristionchus in East Asia and the origin of hermaphroditism in the P. pacificus species-complex.
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31
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Sanghvi GV, Baskaran P, Röseler W, Sieriebriennikov B, Rödelsperger C, Sommer RJ. Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts. PLoS One 2016; 11:e0164881. [PMID: 27741297 PMCID: PMC5065204 DOI: 10.1371/journal.pone.0164881] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022] Open
Abstract
Nematodes, the earth's most abundant metazoa are found in all ecosystems. In order to survive in diverse environments, they have evolved distinct feeding strategies and they can use different food sources. While some nematodes are specialists, including parasites of plants and animals, others such as Pristionchus pacificus are omnivorous feeders, which can live on a diet of bacteria, protozoans, fungi or yeast. In the wild, P. pacificus is often found in a necromenic association with beetles and is known to be able to feed on a variety of microbes as well as on nematode prey. However, in laboratory studies Escherichia coli OP50 has been used as standard food source, similar to investigations in Caenorhabditis elegans and it is unclear to what extent this biases the obtained results and how relevant findings are in real nature. To gain first insight into the variation in traits induced by a non-bacterial food source, we study Pristionchus-fungi interactions under laboratory conditions. After screening different yeast strains, we were able to maintain P. pacificus for at least 50-60 generations on Cryptococcus albidus and Cryptococcus curvatus. We describe life history traits of P. pacificus on both yeast strains, including developmental timing, survival and brood size. Despite a slight developmental delay and problems to digest yeast cells, which are both reflected at a transcriptomic level, all analyses support the potential of Cryptococcus strains as food source for P. pacificus. In summary, our work establishes two Cryptococcus strains as alternative food source for P. pacificus and shows change in various developmental, physiological and morphological traits, including the transcriptomic profiles.
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Affiliation(s)
- Gaurav V. Sanghvi
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Praveen Baskaran
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Waltraud Röseler
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
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32
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Marcellini S, González F, Sarrazin AF, Pabón-Mora N, Benítez M, Piñeyro-Nelson A, Rezende GL, Maldonado E, Schneider PN, Grizante MB, Da Fonseca RN, Vergara-Silva F, Suaza-Gaviria V, Zumajo-Cardona C, Zattara EE, Casasa S, Suárez-Baron H, Brown FD. Evolutionary Developmental Biology (Evo-Devo) Research in Latin America. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:5-40. [PMID: 27491339 DOI: 10.1002/jez.b.22687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022]
Abstract
Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.
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Affiliation(s)
- Sylvain Marcellini
- Laboratorio de Desarrollo y Evolución, Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Favio González
- Facultad de Ciencias, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Andres F Sarrazin
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Xochimilco, Ciudad de México, México
| | - Gustavo L Rezende
- Universidade Estadual do Norte Fluminense, CBB, LQFPP, Campos dos Goytacazes, RJ, Brazil
| | - Ernesto Maldonado
- EvoDevo Lab, Unidad de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, México
| | | | | | - Rodrigo Nunes Da Fonseca
- Núcleo em Ecologia e Desenvolvimento SócioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro, Macae, RJ, Brazil
| | | | | | | | | | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Federico D Brown
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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33
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Chevalier RL. The proximal tubule is the primary target of injury and progression of kidney disease: role of the glomerulotubular junction. Am J Physiol Renal Physiol 2016; 311:F145-61. [PMID: 27194714 PMCID: PMC4967168 DOI: 10.1152/ajprenal.00164.2016] [Citation(s) in RCA: 255] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/03/2016] [Indexed: 12/16/2022] Open
Abstract
There is an alarming global increase in the incidence of end-stage kidney disease, for which early biomarkers and effective treatment options are lacking. Largely based on the histology of the end-stage kidney and on the model of unilateral ureteral obstruction, current investigation is focused on the pathogenesis of renal interstitial fibrosis as a central mechanism in the progression of chronic kidney disease (CKD). It is now recognized that cumulative episodes of acute kidney injury (AKI) can lead to CKD, and, conversely, CKD is a risk factor for AKI. Based on recent and historic studies, this review shifts attention from the glomerulus and interstitium to the proximal tubule as the primary sensor and effector in the progression of CKD as well as AKI. Packed with mitochondria and dependent on oxidative phosphorylation, the proximal tubule is particularly vulnerable to injury (obstructive, ischemic, hypoxic, oxidative, metabolic), resulting in cell death and ultimately in the formation of atubular glomeruli. Animal models of human glomerular and tubular disorders have provided evidence for a broad repertoire of morphological and functional responses of the proximal tubule, revealing processes of degeneration and repair that may lead to new therapeutic strategies. Most promising are studies that encompass the entire life cycle from fetus to senescence, recognizing epigenetic factors. The application of techniques in molecular characterization of tubule segments and the development of human kidney organoids may provide new insights into the mammalian kidney subjected to stress or injury, leading to biomarkers of early CKD and new therapies.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
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Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A 2015; 112:15402-7. [PMID: 26621703 PMCID: PMC4687580 DOI: 10.1073/pnas.1518127112] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
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Affiliation(s)
- Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; School of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;
| | - Walker Pett
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Martin Dohrmann
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige 38010, Italy
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany
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35
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Sommer RJ, Mayer MG. Toward a Synthesis of Developmental Biology with Evolutionary Theory and Ecology. Annu Rev Cell Dev Biol 2015; 31:453-71. [DOI: 10.1146/annurev-cellbio-102314-112451] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ralf J. Sommer
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Melanie G. Mayer
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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36
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O'Malley MA, Travisano M, Velicer GJ, Bolker JA. How Do Microbial Populations and Communities Function as Model Systems? QUARTERLY REVIEW OF BIOLOGY 2015; 90:269-93. [DOI: 10.1086/682588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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37
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Mayer MG, Sommer RJ. Nematode orphan genes are adopted by conserved regulatory networks and find a home in ecology. WORM 2015; 4:e1082029. [PMID: 27123366 PMCID: PMC4826153 DOI: 10.1080/21624054.2015.1082029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/06/2015] [Indexed: 11/26/2022]
Abstract
Nematode dauer formation represents an essential survival and dispersal strategy and is one of a few ecologically relevant traits that can be studied in laboratory approaches. Under harsh environmental conditions, the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus arrest their development and induce the formation of stress-resistant dauer larvae in response to dauer pheromones, representing a key example of phenotypic plasticity. Previous studies have indicated that in P. pacificus, many wild isolates show cross-preference of dauer pheromones and compete for access to a limited food source. When investigating the genetic mechanisms underlying this intraspecific competition, we recently discovered that the orphan gene dauerless (dau-1) controls dauer formation by copy number variation. Our results show that dau-1 acts in parallel to or downstream of steroid hormone signaling but upstream of the nuclear hormone receptor daf-12, suggesting that DAU-1 represents a novel inhibitor of DAF-12. Phylogenetic analysis reveals that the observed copy number variation is part of a complex series of gene duplication events that occurred over short evolutionary time scales. Here, we comment on the incorporation of novel or fast-evolving genes into conserved genetic networks as a common principle for the evolution of phenotypic plasticity and intraspecific competition. We discuss the possibility that orphan genes might often function in the regulation and execution of ecologically relevant traits. Given that only few ecological processes can be studied in model organisms, the function of such genes might often go unnoticed, explaining the large number of uncharacterized genes in model system genomes.
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Affiliation(s)
- Melanie G Mayer
- Max Planck Institute for Developmental Biology ; Tübingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology ; Tübingen, Germany
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Abstract
The non-bilaterian animals comprise organisms in the phyla Porifera, Cnidaria, Ctenophora and Placozoa. These early-diverging phyla are pivotal to understanding the evolution of bilaterian animals. After the exponential increase in research in evolutionary development (evo-devo) in the last two decades, these organisms are again in the spotlight of evolutionary biology. In this work, I briefly review some aspects of the developmental biology of nonbilaterians that contribute to understanding the evolution of development and of the metazoans. The evolution of the developmental genetic toolkit, embryonic polarization, the origin of gastrulation and mesodermal cells, and the origin of neural cells are discussed. The possibility that germline and stem cell lineages have the same origin is also examined. Although a considerable number of non-bilaterian species are already being investigated, the use of species belonging to different branches of non-bilaterian lineages and functional experimentation with gene manipulation in the majority of the non-bilaterian lineages will be necessary for further progress in this field.
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Affiliation(s)
- Emilio Lanna
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
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39
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Gilarte P, Kreuzinger-Janik B, Majdi N, Traunspurger W. Life-History Traits of the Model Organism Pristionchus pacificus Recorded Using the Hanging Drop Method: Comparison with Caenorhabditis elegans. PLoS One 2015; 10:e0134105. [PMID: 26247841 PMCID: PMC4527759 DOI: 10.1371/journal.pone.0134105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
The nematode Pristionchus pacificus is of growing interest as a model organism in evolutionary biology. However, despite multiple studies of its genetics, developmental cues, and ecology, the basic life-history traits (LHTs) of P. pacificus remain unknown. In this study, we used the hanging drop method to follow P. pacificus at the individual level and thereby quantify its LHTs. This approach allowed direct comparisons with the LHTs of Caenorhabditis elegans recently determined using this method. When provided with 5×10(9) Escherichia coli cells ml(-1) at 20°C, the intrinsic rate of natural increase of P. pacificus was 1.125 (individually, per day); mean net production was 115 juveniles produced during the life-time of each individual, and each nematode laid an average of 270 eggs (both fertile and unfertile). The mean age of P. pacificus individuals at first reproduction was 65 h, and the average life span was 22 days. The life cycle of P. pacificus is therefore slightly longer than that of C. elegans, with a longer average life span and hatching time and the production of fewer progeny.
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Affiliation(s)
- Patricia Gilarte
- Animal Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany
| | | | - Nabil Majdi
- Animal Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany
| | - Walter Traunspurger
- Animal Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, Germany
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40
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Abstract
In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well developed as standardized, experimental systems and being used by well-organized communities with good networks of exchange and methods of communication.
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41
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Arif S, Kittelmann S, McGregor AP. From shavenbaby to the naked valley: trichome formation as a model for evolutionary developmental biology. Evol Dev 2015; 17:120-6. [PMID: 25627718 DOI: 10.1111/ede.12113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Microtrichia or trichomes are non-sensory actin protrusions produced by the epidermal cells of many insects. Studies of trichome formation in Drosophila have over the last 30 years provided key insights towards our understanding of gene regulation, gene regulatory networks (GRNs), development, the genotype to phenotype map, and the evolution of these processes. Here we review classic studies that have used trichome formation as a model to shed light on Drosophila development as well as recent research on the architecture of the GRN underlying trichome formation. This includes the findings that both small peptides and microRNAs play important roles in the regulation and evolution of this network. In addition, we review research on the evolution of trichome patterns that has provided novel insights into the function and architecture of cis-regulatory modules, and into the genetic basis of morphological change. We conclude that further research on these apparently simple and often functionally enigmatic structures will continue to provide new and important knowledge about development and evolution.
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Affiliation(s)
- Saad Arif
- Friedrich Meischer Laboratory of the Max Planck Society, Spemannstrasse 39, Tuebingen, 72076, Germany
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42
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Santos ME, Berger CS, Refki PN, Khila A. Integrating evo-devo with ecology for a better understanding of phenotypic evolution. Brief Funct Genomics 2015; 14:384-95. [PMID: 25750411 PMCID: PMC4652033 DOI: 10.1093/bfgp/elv003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Evolutionary developmental biology (evo-devo) has provided invaluable contributions to our understanding of the mechanistic relationship between genotypic and phenotypic change. Similarly, evolutionary ecology has greatly advanced our understanding of the relationship between the phenotype and the environment. To fully understand the evolution of organismal diversity, a thorough integration of these two fields is required. This integration remains highly challenging because model systems offering a rich ecological and evolutionary background, together with the availability of developmental genetic tools and genomic resources, are scarce. In this review, we introduce the semi-aquatic bugs (Gerromorpha, Heteroptera) as original models well suited to study why and how organisms diversify. The Gerromorpha invaded water surfaces over 200 mya and diversified into a range of remarkable new forms within this new ecological habitat. We summarize the biology and evolutionary history of this group of insects and highlight a set of characters associated with the habitat change and the diversification that followed. We further discuss the morphological, behavioral, molecular and genomic tools available that together make semi-aquatic bugs a prime model for integration across disciplines. We present case studies showing how the implementation and combination of these approaches can advance our understanding of how the interaction between genotypes, phenotypes and the environment drives the evolution of distinct morphologies. Finally, we explain how the same set of experimental designs can be applied in other systems to address similar biological questions.
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43
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Gene inactivation using the CRISPR/Cas9 system in the nematode Pristionchus pacificus. Dev Genes Evol 2014; 225:55-62. [DOI: 10.1007/s00427-014-0486-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/12/2014] [Indexed: 02/07/2023]
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44
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Sears KE. Quantifying the impact of development on phenotypic variation and evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:643-53. [PMID: 25393554 DOI: 10.1002/jez.b.22592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 08/18/2014] [Indexed: 01/03/2023]
Abstract
A primary goal of evolutionary biology is to identify the factors that shape phenotypic evolution. According to the theory of natural selection, phenotypic evolution occurs through the differential survival and reproduction of individuals whose traits are selectively advantageous relative to other individuals in the population. This implies that evolution by natural selection is contingent upon the distribution and magnitude of phenotypic variation among individuals, which are in turn the products of developmental processes. Development therefore has the potential to affect the trajectory and rate of phenotypic evolution. Recent research in diverse systems (e.g., mammalian teeth, cichlid skulls, butterfly wings, and marsupial limbs) supports the hypothesis that development biases phenotypic variation and evolution, but suggests that these biases might be system-specific.
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Affiliation(s)
- Karen E Sears
- School of Integrative Biology, University of Illinois, Urbana, Illinois; Institute for Genomic Biology, University of Illinois, Urbana, Illinois
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45
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How to become a parasite without sex chromosomes: a hypothesis for the evolution of Strongyloides spp. and related nematodes. Parasitology 2014; 141:1244-54. [PMID: 24829037 DOI: 10.1017/s003118201400064x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Parasitic lifestyles evolved many times independently. Just within the phylum Nematoda animal parasitism must have arisen at least four times. Switching to a parasitic lifestyle is expected to lead to changes in various life history traits including reproductive strategies. Parasitic nematode worms of the genus Strongyloides represent an interesting example to study these processes because they are still capable of forming facultative free-living generations in between parasitic ones. The parasitic generation consists of females only, which reproduce parthenogenetically. The sex in the progeny of the parasitic worms is determined by environmental cues, which control a, presumably ancestral, XX/XO chromosomal sex determining system. In some species the X chromosome is fused with an autosome and one copy of the X-derived sequences is removed by sex-specific chromatin diminution in males. Here I propose a hypothesis for how today's Strongyloides sp. might have evolved from a sexual free-living ancestor through dauer larvae forming free-living and facultative parasitic intermediate stages.
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46
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Sun L, Ye M, Hao H, Wang N, Wang Y, Cheng T, Zhang Q, Wu R. A model framework for identifying genes that guide the evolution of heterochrony. Mol Biol Evol 2014; 31:2238-47. [PMID: 24817546 DOI: 10.1093/molbev/msu156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Heterochrony, the phylogenic change in the time of developmental events or rate of development, has been thought to play an important role in producing phenotypic novelty during evolution. Increasing evidence suggests that specific genes are implicated in heterochrony, guiding the process of developmental divergence, but no quantitative models have been instrumented to map such heterochrony genes. Here, we present a computational framework for genetic mapping by which to characterize and locate quantitative trait loci (QTLs) that govern heterochrony described by four parameters, the timing of the inflection point, the timing of maximum acceleration of growth, the timing of maximum deceleration of growth, and the length of linear growth. The framework was developed from functional mapping, a dynamic model derived to map QTLs for the overall process and pattern of development. By integrating an optimality algorithm, the framework allows the so-called heterochrony QTLs (hQTLs) to be tested and quantified. Specific pipelines are given for testing how hQTLs control the onset and offset of developmental events, the rate of development, and duration of a particular developmental stage. Computer simulation was performed to examine the statistical properties of the model and demonstrate its utility to characterize the effect of hQTLs on population diversification due to heterochrony. By analyzing a genetic mapping data in rice, the framework identified an hQTL that controls the timing of maximum growth rate and duration of linear growth stage in plant height growth. The framework provides a tool to study how genetic variation translates into phenotypic innovation, leading a lineage to evolve, through heterochrony.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Han Hao
- Center for Statistical Genetics, The Pennsylvania State University
| | - Ningtao Wang
- Center for Statistical Genetics, The Pennsylvania State University
| | - Yaqun Wang
- Center for Statistical Genetics, The Pennsylvania State University
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Statistical Genetics, The Pennsylvania State University
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Morgan K, McGaughran A, Ganeshan S, Herrmann M, Sommer RJ. Landscape and oceanic barriers shape dispersal and population structure in the island nematodePristionchus pacificus. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katy Morgan
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | - Angela McGaughran
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | | | - Matthias Herrmann
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | - Ralf J. Sommer
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
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48
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Opposing forces of A/T-biased mutations and G/C-biased gene conversions shape the genome of the nematode Pristionchus pacificus. Genetics 2014; 196:1145-52. [PMID: 24414549 DOI: 10.1534/genetics.113.159863] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation.
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49
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Chopra D, Wolff H, Span J, Schellmann S, Coupland G, Albani MC, Schrader A, Hülskamp M. Analysis of TTG1 function in Arabis alpina. BMC PLANT BIOLOGY 2014; 14:16. [PMID: 24406039 PMCID: PMC3904473 DOI: 10.1186/1471-2229-14-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/07/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND In Arabidopsis thaliana (A. thaliana) the WD40 protein TRANSPARENT TESTA GLABRA1 (TTG1) controls five traits relevant for the adaptation of plants to environmental changes including the production of proanthocyanidin, anthocyanidin, seed coat mucilage, trichomes and root hairs. The analysis of different Brassicaceae species suggests that the function of TTG1 is conserved within the family. RESULTS In this work, we studied the function of TTG1 in Arabis alpina (A. alpina). A comparison of wild type and two Aattg1 alleles revealed that AaTTG1 is involved in the regulation of all five traits. A detailed analysis of the five traits showed striking phenotypic differences between A. alpina and A. thaliana such that trichome formation occurs also at later stages of leaf development and that root hairs form at non-root hair positions. CONCLUSIONS The evolutionary conservation of the regulation of the five traits by TTG1 on the one hand and the striking phenotypic differences make A. alpina a very interesting genetic model system to study the evolution of TTG1-dependent gene regulatory networks at a functional level.
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Affiliation(s)
- Divykriti Chopra
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Heike Wolff
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Johannes Span
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Swen Schellmann
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
| | - Maria C Albani
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
- Max Planck Institute for Plant Breeding, Carl-von-Linne-Weg 10, 50829 Cologne, Germany
| | - Andrea Schrader
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Zülpicher Straße 47b, 50674 Cologne, Germany
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50
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Wotton KR, Jiménez-Guri E, García Matheu B, Jaeger J. A staging scheme for the development of the scuttle fly Megaselia abdita. PLoS One 2014; 9:e84421. [PMID: 24409295 PMCID: PMC3883658 DOI: 10.1371/journal.pone.0084421] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/13/2013] [Indexed: 12/01/2022] Open
Abstract
Model organisms, such as Drosophila melanogaster, provide powerful experimental tools for the study of development. However, approaches using model systems need to be complemented by comparative studies for us to gain a deeper understanding of the functional properties and evolution of developmental processes. New model organisms need to be established to enable such comparative work. The establishment of new model system requires a detailed description of its life cycle and development. The resulting staging scheme is essential for providing morphological context for molecular studies, and allows us to homologise developmental processes between species. In this paper, we provide a staging scheme and morphological characterisation of the life cycle for an emerging non-drosophilid dipteran model system: the scuttle fly Megaselia abdita. We pay particular attention to early embryogenesis (cleavage and blastoderm stages up to gastrulation), the formation and retraction of extraembryonic tissues, and the determination and formation of germ (pole) cells. Despite the large evolutionary distance between the two species (approximately 150 million years), we find that M. abdita development is remarkably similar to D. melanogaster in terms of developmental landmarks and their relative timing.
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Affiliation(s)
- Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Belén García Matheu
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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