1
|
Omond SET, Lesku JA. Why study sleep in flatworms? J Comp Physiol B 2024; 194:233-239. [PMID: 36899149 PMCID: PMC11233290 DOI: 10.1007/s00360-023-01480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023]
Abstract
The behaviors that characterize sleep have been observed across a broad range of different species. While much attention has been placed on vertebrates (mostly mammals and birds), the grand diversity of invertebrates has gone largely unexplored. Here, we introduce the intrigue and special value in the study of sleeping platyhelminth flatworms. Flatworms are closely related to annelids and mollusks, and yet are comparatively simple. They lack a circulatory system, respiratory system, endocrine glands, a coelom, and an anus. They retain a central and peripheral nervous system, various sensory systems, and an ability to learn. Flatworms sleep, like other animals, a state which is regulated by prior sleep/wake history and by the neurotransmitter GABA. Furthermore, they possess a remarkable ability to regenerate from a mere fragment of the original animal. The regenerative capabilities of flatworms make them a unique bilaterally symmetric animal to study a link between sleep and neurodevelopment. Lastly, the recent applications of tools for probing the flatworm genome, metabolism, and brain activity make their entrance into the field of sleep research all the more timely.
Collapse
Affiliation(s)
- Shauni E T Omond
- School of Agriculture, Biomedicine & Environment, La Trobe University, Melbourne, Australia.
| | - John A Lesku
- School of Agriculture, Biomedicine & Environment, La Trobe University, Melbourne, Australia.
| |
Collapse
|
2
|
Ordoñez JF, Wollesen T. Unfolding the ventral nerve center of chaetognaths. Neural Dev 2024; 19:5. [PMID: 38720353 PMCID: PMC11078758 DOI: 10.1186/s13064-024-00182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Chaetognaths are a clade of marine worm-like invertebrates with a heavily debated phylogenetic position. Their nervous system superficially resembles the protostome type, however, knowledge regarding the molecular processes involved in neurogenesis is lacking. To better understand these processes, we examined the expression profiles of marker genes involved in bilaterian neurogenesis during post-embryonic stages of Spadella cephaloptera. We also investigated whether the transcription factor encoding genes involved in neural patterning are regionally expressed in a staggered fashion along the mediolateral axis of the nerve cord as it has been previously demonstrated in selected vertebrate, insect, and annelid models. METHODS The expression patterns of genes involved in neural differentiation (elav), neural patterning (foxA, nkx2.2, pax6, pax3/7, and msx), and neuronal function (ChAT and VAChT) were examined in S. cephaloptera hatchlings and early juveniles using whole-mount fluorescent in situ hybridization and confocal microscopy. RESULTS The Sce-elav + profile of S. cephaloptera hatchlings reveals that, within 24 h of post-embryonic development, the developing neural territories are not limited to the regions previously ascribed to the cerebral ganglion, the ventral nerve center (VNC), and the sensory organs, but also extend to previously unreported CNS domains that likely contribute to the ventral cephalic ganglia. In general, the neural patterning genes are expressed in distinct neural subpopulations of the cerebral ganglion and the VNC in hatchlings, eventually becoming broadly expressed with reduced intensity throughout the CNS in early juveniles. Neural patterning gene expression domains are also present outside the CNS, including the digestive tract and sensory organs. ChAT and VAChT domains within the CNS are predominantly observed in specific subpopulations of the VNC territory adjacent to the ventral longitudinal muscles in hatchlings. CONCLUSIONS The observed spatial expression domains of bilaterian neural marker gene homologs in S. cephaloptera suggest evolutionarily conserved roles in neurogenesis for these genes among bilaterians. Patterning genes expressed in distinct regions of the VNC do not show a staggered medial-to-lateral expression profile directly superimposable to other bilaterian models. Only when the VNC is conceptually laterally unfolded from the longitudinal muscle into a flat structure, an expression pattern bearing resemblance to the proposed conserved bilaterian mediolateral regionalization becomes noticeable. This finding supports the idea of an ancestral mediolateral patterning of the trunk nervous system in bilaterians.
Collapse
Affiliation(s)
- June F Ordoñez
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, 1030, Vienna, Austria
| | - Tim Wollesen
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, 1030, Vienna, Austria.
| |
Collapse
|
3
|
Thompson JT, Taylor-Burt KR, Kier WM. One size does not fit all: diversity of length-force properties of obliquely striated muscles. J Exp Biol 2023; 226:jeb244949. [PMID: 36633589 PMCID: PMC10658899 DOI: 10.1242/jeb.244949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/28/2022] [Indexed: 01/13/2023]
Abstract
Obliquely striated muscles occur in 17+ phyla, likely evolving repeatedly, yet the implications of oblique striation for muscle function are unknown. Contrary to the belief that oblique striation allows high force output over extraordinary length ranges (i.e. superelongation), recent work suggests diversity in operating length ranges and length-force relationships. We hypothesize oblique striation evolved to increase length-force relationship flexibility. We predict that superelongation is not a general characteristic of obliquely striated muscles and instead that length-force relationships vary with operating length range. To test these predictions, we measured length-force relationships of five obliquely striated muscles from inshore longfin squid, Doryteuthis pealeii: tentacle, funnel retractor and head retractor longitudinal fibers, and arm and fin transverse fibers. Consistent with superelongation, the tentacle length-force relationship had a long descending limb, whereas all others exhibited limited descending limbs. The ascending limb at 0.6P0 was significantly broader (P<0.001) for the tentacle length-force relationship (0.43±0.04L0; where L0 is the preparation length that produced peak isometric stress, P0) than for the arm (0.29±0.03L0), head retractor (0.24±0.06L0), fin (0.20±0.04L0) and funnel retractor (0.27±0.03L0). The fin's narrow ascending limb differed significantly from those of the arm (P=0.004) and funnel retractor (P=0.012). We further characterized the tentacle preparation's maximum isometric stress (315±78 kPa), maximum unloaded shortening velocity (2.97±0.55L0 s-1) and ultrastructural traits (compared with the arm), which may explain its broader length-force relationship. Comparison of obliquely striated muscles across taxa revealed length-force relationship diversity, with only two species exhibiting superelongation.
Collapse
Affiliation(s)
- Joseph T. Thompson
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17604-3003, USA
| | - Kari R. Taylor-Burt
- Department of Biology, Franklin & Marshall College, Lancaster, PA 17604-3003, USA
- Department of Science, Mount St Mary's University, Emmitsburg, MD 21727, USA
| | - William M. Kier
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
4
|
Kutyumov VA, Predeus AV, Starunov VV, Maltseva AL, Ostrovsky AN. Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features. Mitochondrion 2021; 59:96-104. [PMID: 33631347 DOI: 10.1016/j.mito.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.
Collapse
Affiliation(s)
- Vladimir A Kutyumov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander V Predeus
- Bioinformatics Institute, Kantemirovskaya 2A, 197342 Saint Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrew N Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Department of Palaeontology, Faculty of Geography, Geology and Astronomy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria.
| |
Collapse
|
5
|
Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death. Sci Rep 2021; 11:2947. [PMID: 33536473 PMCID: PMC7859237 DOI: 10.1038/s41598-020-80627-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023] Open
Abstract
The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.
Collapse
|
6
|
|
7
|
Borisanova AO, Malakhov VV, Temereva EN. The neuroanatomy of Barentsia discreta (Entoprocta, Coloniales) reveals significant differences between bryozoan and entoproct nervous systems. Front Zool 2019; 16:9. [PMID: 30962810 PMCID: PMC6437902 DOI: 10.1186/s12983-019-0307-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/12/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Entoprocta affinities within Lophotrochozoa remain unclear. In different studies, entoprocts are considered to be related to different groups, including Cycliophora, Bryozoa, Annelida, and Mollusca. The use of modern methods to study the neuroanatomy of Entoprocta should provide new information that may be useful for phylogenetic analysis. RESULTS The anatomy of the nervous system in the colonial Barentsia discreta was studied using immunocytochemistry and transmission electron microscopy. The ganglion gives rise to several main nerves: paired lateral, aboral, and arcuate nerves, and three pairs of tentacular cords that branch out into tentacular nerves. The serotonergic nervous system includes paired esophageal perikarya and two large peripheral perikarya, each with a complex net of neurites. Each tentacle is innervated by one abfrontal and two laterofrontal neurite bundles. Sensory cells occur regularly along the abfrontal side of each tentacle. Star-like nerve cells are scattered in the epidermis of the calyx. The stalk is innervated by paired stalk nerves. CONCLUSIONS The neuroanatomy of the colonial Barentsia discreta is generally similar to that of solitary entoprocts but differs in the anatomy and ultrastructure of the ganglion, the number of neurite bundles in the calyx, and the distribution of serotonin in the nerve elements. A comparison of the organization of the nervous system in the Entoprocta and Bryozoa reveals many differences in tentacle innervations, which may indicate that these groups may not be closely related. Our results can not support with any certainty the homology of nervous system elements in adult entoprocts and adult "basal mollusks".
Collapse
Affiliation(s)
- Anastasia O. Borisanova
- Biological Faculty, Dept. Invertebrate Zoology, Moscow State University, Leninskie Gory, 1-12, 119991 Moscow, Russia
| | - Vladimir V. Malakhov
- Biological Faculty, Dept. Invertebrate Zoology, Moscow State University, Leninskie Gory, 1-12, 119991 Moscow, Russia
- Far Eastern Federal University, 690600 Vladivostok, Russia
| | - Elena N. Temereva
- Biological Faculty, Dept. Invertebrate Zoology, Moscow State University, Leninskie Gory, 1-12, 119991 Moscow, Russia
| |
Collapse
|
8
|
Namigai† EKO, Shimeld SM. Live Imaging of Cleavage Variability and Vesicle Flow Dynamics in Dextral and Sinistral Spiralian Embryos. Zoolog Sci 2019; 36:5-16. [DOI: 10.2108/zs180088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/13/2018] [Indexed: 11/17/2022]
Affiliation(s)
- Erica K. O. Namigai†
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U. K
| | - Sebastian M. Shimeld
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U. K
| |
Collapse
|
9
|
Taylor-Burt KR, Kier WM, Olszewski-Jubelirer J, Thompson JT. Shape, Size, and Structure Affect Obliquely Striated Muscle Function in Squid. Integr Comp Biol 2018; 58:261-275. [PMID: 29873744 DOI: 10.1093/icb/icy053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hollow, cylindrical body plans, and obliquely striated muscles are characteristic of soft-bodied invertebrates, and both affect the biomechanics of movement in these diverse animals. We highlight two different aspects of functional heterogeneity in obliquely striated muscles, one driven by animal shape and size and the other by the intrinsic mechanical properties of the fibers. First, we show how a hollow, cylindrical shape in the mantle of cephalopod molluscs causes a significant difference in muscle strain (defined as the change in length divided by resting length) across the mantle wall, and describe the implications of such "transmural gradients of strain" for the length-tension relationship of the obliquely striated muscles that power movements in these animals. We show that transmural gradients of strain increase in magnitude as mantle wall proportions change during ontogeny, with the relatively thin mantle walls of newly hatched squid experiencing significantly smaller differences in strain than the thicker mantle walls of adults. Second, we describe how the length-tension relationship of obliquely striated mantle muscles varies with position to accommodate the transmural gradient of strain, with the result that circular muscle fibers near the inner and outer surfaces of the mantle are predicted to produce similar force during mantle contraction. The factors that affect the length-tension relationship in obliquely striated muscles are unknown, and thus we have not yet identified the mechanism(s) responsible for the transmural shift in the length-tension properties of the mantle circular fibers. We have, however, developed a mathematical model that predicts small changes in the oblique striation angle (which varies from 4 to 12° in adult squid) have a significant effect on the shape of the length-tension relationship, with lower angles predicted to result in a broader length-tension curve.
Collapse
Affiliation(s)
- Kari R Taylor-Burt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - William M Kier
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Joseph T Thompson
- Department of Biology, Franklin & Marshall College, P.O. Box 3003, Lancaster, PA 17604, USA
| |
Collapse
|
10
|
Mann K, Cerveau N, Gummich M, Fritz M, Mann M, Jackson DJ. In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix. Proteome Sci 2018; 16:11. [PMID: 29983641 PMCID: PMC6003135 DOI: 10.1186/s12953-018-0139-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/25/2018] [Indexed: 01/12/2023] Open
Abstract
Background The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date. Methods The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing. Results We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. Conclusions The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly. Electronic supplementary material The online version of this article (10.1186/s12953-018-0139-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Karlheinz Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nicolas Cerveau
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
| | - Meike Gummich
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Monika Fritz
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Matthias Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Daniel J Jackson
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
| |
Collapse
|
11
|
López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Sci Rep 2018; 8:9106. [PMID: 29904074 PMCID: PMC6002407 DOI: 10.1038/s41598-018-27509-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/05/2018] [Indexed: 11/08/2022] Open
Abstract
Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.
Collapse
Affiliation(s)
- David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain
| | - Jordi Paps
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Colomban de Vargas
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
- UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
- Departament de Genètica, Microbiología i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Javier Del Campo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Catalonia, Spain.
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain.
| |
Collapse
|
12
|
Kocot KM, Struck TH, Merkel J, Waits DS, Todt C, Brannock PM, Weese DA, Cannon JT, Moroz LL, Lieb B, Halanych KM. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Syst Biol 2018; 66:256-282. [PMID: 27664188 DOI: 10.1093/sysbio/syw079] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic data set. [Annelida; Brachiopoda; Bryozoa; Entoprocta; Mollusca; Nemertea; Phoronida; Platyzoa; Polyzoa; Spiralia; Trochozoa.].
Collapse
Affiliation(s)
- Kevin M Kocot
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Biological Sciences and Alabama Museum of Natural History, 307 Mary Harmon Bryant Hall, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Torsten H Struck
- Natural History Museum, Department of Research and Collections, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway
| | - Julia Merkel
- Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany
| | - Damien S Waits
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
| | - Christiane Todt
- University Museum of Bergen, The Natural History Collections, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Pamela M Brannock
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
| | - David A Weese
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Biological and Environmental Sciences, Georgia College and State University, Campus Box 81, Milledgeville, GA 31061 USA
| | - Johanna T Cannon
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Zoology, Naturhistoriska riksmuseet, Box 50007, 104 05 Stockholm, Sweden
| | - Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA
| | - Bernhard Lieb
- Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
13
|
Briggs DE, Caron JB. A Large Cambrian Chaetognath with Supernumerary Grasping Spines. Curr Biol 2017; 27:2536-2543.e1. [DOI: 10.1016/j.cub.2017.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/31/2017] [Accepted: 07/03/2017] [Indexed: 11/16/2022]
|
14
|
Iseto T. Review of the Studies of Japanese Entoprocts (Entoprocta). SPECIES DIVERSITY OF ANIMALS IN JAPAN 2017. [DOI: 10.1007/978-4-431-56432-4_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
15
|
Henne S, Friedrich F, Hammel JU, Sombke A, Schmidt-Rhaesa A. Reconstructing the anterior part of the nervous system ofGordius aquaticus(Nematomorpha, cycloneuralia) by a multimethodological approach. J Morphol 2016; 278:106-118. [DOI: 10.1002/jmor.20623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/23/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Stephan Henne
- Invertebrates I; University of Hamburg, Center of Natural History (CeNak), Zoological Museum Hamburg; Martin-Luther-King-Platz 3 Hamburg 20146 Germany
| | - Frank Friedrich
- Electron Microscopy; University of Hamburg, Biocenter Grindel; Martin-Luther-King-Platz 3 Hamburg 20146 Germany
| | - Jörg U. Hammel
- X-ray Imaging with Synchrotron Radiation, Helmholz-Zentrum Geesthacht; Institute of Materials Research; Max-Planck-Straße 1 Geesthacht 21502 Germany
| | - Andy Sombke
- Cytology and Evolutionary Biology; Ernst-Moritz-Arndt University of Greifswald, Zoological Institute and Museum; Soldmannstrasse 23 Greifswald 17489 Germany
| | - Andreas Schmidt-Rhaesa
- Invertebrates I; University of Hamburg, Center of Natural History (CeNak), Zoological Museum Hamburg; Martin-Luther-King-Platz 3 Hamburg 20146 Germany
| |
Collapse
|
16
|
Greven H, Kaya M, Baran T. The presence of α-chitin in Tardigrada with comments on chitin in the Ecdysozoa. ZOOL ANZ 2016. [DOI: 10.1016/j.jcz.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Oliveira E, Barata C, Piña B. Endocrine Disruption in the Omics Era: New Views, New Hazards, New Approaches. ACTA ACUST UNITED AC 2016. [DOI: 10.2174/1874070701610010020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genome revolution has brought about a complete change on our view of biological systems. The quantitative determination of changes in all the major molecular components of the living cells, the "omics" approach, opened whole new fields for all health sciences, including toxicology. Endocrine disruption,i.e., the capacity of anthropogenic pollutants to alter the hormonal balance of the organisms, is one of the fields of Ecotoxicology in which omics has a relevant role. In the first place, the discovery of scores of potential targets in the genome of almost any Metazoan species studied so far, each of them being a putative candidate for interaction with endocrine disruptors. In addition, the understanding that ligands, receptors, and their physiological functions suffered fundamental variations during animal evolution makes it necessary to assess disruption effects separately for each major taxon. Fortunately, the same deal of knowledge on genes and genomes powered the development of new high-throughput techniques and holistic approaches. Genomics, transcriptomics, proteomics, metabolomics, and others, together with appropriate prediction and modeling tools, will mark the future of endocrine disruption assessment both for wildlife and humans.
Collapse
|
18
|
Barucca M, Canapa A, Biscotti MA. An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality. J Dev Biol 2016; 4:jdb4010012. [PMID: 29615580 PMCID: PMC5831810 DOI: 10.3390/jdb4010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/02/2016] [Accepted: 03/12/2016] [Indexed: 11/29/2022] Open
Abstract
Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca.
Collapse
Affiliation(s)
- Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| |
Collapse
|
19
|
|
20
|
|
21
|
Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
Collapse
Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
| |
Collapse
|
22
|
The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nat Commun 2015; 6:8301. [PMID: 26383154 PMCID: PMC4595640 DOI: 10.1038/ncomms9301] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/07/2015] [Indexed: 12/11/2022] Open
Abstract
The evolutionary origins of lingulid brachiopods and their calcium phosphate shells have been obscure. Here we decode the 425-Mb genome of Lingula anatina to gain insights into brachiopod evolution. Comprehensive phylogenomic analyses place Lingula close to molluscs, but distant from annelids. The Lingula gene number has increased to ∼34,000 by extensive expansion of gene families. Although Lingula and vertebrates have superficially similar hard tissue components, our genomic, transcriptomic and proteomic analyses show that Lingula lacks genes involved in bone formation, indicating an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with EGF domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling and co-option of genes appear to be the genomic background of Lingula's unique biomineralization. This Lingula genome provides resources for further studies of lophotrochozoan evolution. Lingulid brachiopods possess calcium phosphate shells. Here, the authors sequence the genome of Lingula anatine to show that Lingula is evolutionary close to molluscs, but distant from annelids, and identify the genomic background of Lingula's unique biomineralization mechanism.
Collapse
|
23
|
Shen X, Sun S, Zhao FQ, Zhang GT, Tian M, Tsang LM, Wang JF, Chu KH. Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia. ZOOL SCR 2015. [DOI: 10.1111/zsc.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
| | - Song Sun
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Fang Qing Zhao
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Guang Tao Zhang
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
| | - Ling Ming Tsang
- Institute of Marine Biology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Jin Feng Wang
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
| |
Collapse
|
24
|
Temereva EN, Gebruk AA, Malakhov VV. Demonstration of the preoral coelom in the brachiopod Lingula anatina with consideration of its phylogenetic significance. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
25
|
Golombek A, Tobergte S, Struck TH. Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes). Mol Phylogenet Evol 2015; 86:49-63. [DOI: 10.1016/j.ympev.2015.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/18/2015] [Accepted: 02/17/2015] [Indexed: 01/06/2023]
|
26
|
Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, Cavalier-Smith T, Guiry MD, Kirk PM. A higher level classification of all living organisms. PLoS One 2015; 10:e0119248. [PMID: 25923521 PMCID: PMC4418965 DOI: 10.1371/journal.pone.0119248] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/25/2015] [Indexed: 12/28/2022] Open
Abstract
We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists' expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL's database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory "backbone" for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.
Collapse
Affiliation(s)
- Michael A. Ruggiero
- Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Dennis P. Gordon
- National Institute of Water & Atmospheric Research, Wellington, New Zealand
| | - Thomas M. Orrell
- Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | | | - Thierry Bourgoin
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN-CNRS-UPMC-EPHE, Sorbonne Universités, Museum National d'Histoire Naturelle, 57, rue Cuvier, CP 50, F-75005, Paris, France
| | - Richard C. Brusca
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | | | - Michael D. Guiry
- The AlgaeBase Foundation & Irish Seaweed Research Group, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Paul M. Kirk
- Mycology Section, Royal Botanic Gardens, Kew, London, United Kingdom
| |
Collapse
|
27
|
Passamaneck YJ, Hejnol A, Martindale MQ. Mesodermal gene expression during the embryonic and larval development of the articulate brachiopod Terebratalia transversa. EvoDevo 2015; 6:10. [PMID: 25897375 PMCID: PMC4404124 DOI: 10.1186/s13227-015-0004-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background Brachiopods undergo radial cleavage, which is distinct from the stereotyped development of closely related spiralian taxa. The mesoderm has been inferred to derive from the archenteron walls following gastrulation, and the primary mesoderm derivative in the larva is a complex musculature. To investigate the specification and differentiation of the mesoderm in the articulate brachiopod Terebratalia transversa, we have identified orthologs of genes involved in mesoderm development in other taxa and investigated their spatial and temporal expression during the embryonic and larval development of T. transversa. Results Orthologs of 17 developmental regulatory genes with roles in the development of the mesoderm in other bilaterian animals were found to be expressed in the developing mesoderm of T. transversa. Five genes, Tt.twist, Tt.GATA456, Tt.dachshund, Tt.mPrx, and Tt.NK1, were found to have expression throughout the archenteron wall at the radial gastrula stage, shortly after the initiation of gastrulation. Three additional genes, Tt.Pax1/9, Tt.MyoD, and Tt.Six1/2, showed expression at this stage in only a portion of the archenteron wall. Tt.eya, Tt.FoxC, Tt.FoxF, Tt.Mox, Tt.paraxis, Tt.Limpet, and Tt.Mef2 all showed initial mesodermal expression during later gastrula or early larval stages. At the late larval stage, Tt.dachshund, Tt.Limpet, and Tt.Mef2 showed expression in nearly all mesoderm cells, while all other genes were localized to specific regions of the mesoderm. Tt.FoxD and Tt.noggin both showed expression in the ventral mesoderm at the larval stages, with gastrula expression patterns in the archenteron roof and blastopore lip, respectively. Conclusions Expression analyses support conserved roles for developmental regulators in the specification and differentiation of the mesoderm during the development of T. transversa. Expression of multiple mesodermal factors in the archenteron wall during gastrulation supports previous morphological observations that this region gives rise to larval mesoderm. Localized expression domains during gastrulation and larval development evidence early regionalization of the mesoderm and provide a basis for hypotheses regarding the molecular regulation underlying the complex system of musculature observed in the larva. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0004-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yale J Passamaneck
- Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813 USA ; The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate, 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| |
Collapse
|
28
|
Temereva EN. Organization of the coelomic system in
P
horonis australis
(
L
ophotrochozoa:
P
horonida) and consideration of the coelom in the lophophorates. J Zool (1987) 2015. [DOI: 10.1111/jzo.12223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. N. Temereva
- Department of Invertebrate Zoology Biological Faculty Moscow State University Moscow Russia
| |
Collapse
|
29
|
Jékely G, Paps J, Nielsen C. The phylogenetic position of ctenophores and the origin(s) of nervous systems. EvoDevo 2015; 6:1. [PMID: 25905000 PMCID: PMC4406211 DOI: 10.1186/2041-9139-6-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022] Open
Abstract
Ctenophores have traditionally been treated as eumetazoans, but some recent whole genome studies have revived the idea that they are, rather, the sister group to all other metazoans. This deep branching position implies either that nervous systems have evolved twice, in Ctenophora and in Eumetazoa, or that an ancestral metazoan nervous system has been lost in sponges and placozoans. We caution, however, that phylogenetic-tree construction artifacts may have placed ctenophores too deep in the metazoan tree. We discuss nervous system origins under these alternative phylogenies and in light of comparative data of ctenophore and eumetazoan nervous systems. We argue that characters like neuropeptide signaling, ciliary photoreceptors, gap junctions and presynaptic molecules are consistent with a shared ancestry of nervous systems. However, if ctenophores are the sister group to all other metazoans, this ancestral nervous system was likely very simple. Further studies are needed to resolve the deep phylogeny of metazoans and to have a better understanding of the early steps of nervous system evolution.
Collapse
Affiliation(s)
- Gáspár Jékely
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Jordi Paps
- Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX13PS UK
| | - Claus Nielsen
- The Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| |
Collapse
|
30
|
Dunn CW, Giribet G, Edgecombe GD, Hejnol A. Animal Phylogeny and Its Evolutionary Implications. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091627] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912;
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
| | - Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom;
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway;
| |
Collapse
|
31
|
The molecular symplesiomorphies shared by the stem groups of metazoan evolution: can sites as few as 1% have a significant impact on recognizing the phylogenetic position of myzostomida? J Mol Evol 2014; 79:63-74. [PMID: 25128981 DOI: 10.1007/s00239-014-9635-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Although it is clear that taxon sampling, alignments, gene sampling, tree reconstruction methods and the total length of the sequences used are critical to the reconstruction of evolutionary history, weakly supported or misleading nodes exist in phylogenetic studies with no obvious flaw in those aspects. The phylogenetic studies focusing on the basal part of bilaterian evolution are such a case. During the past decade, Myzostomida has appeared in the basal part of Bilateria in several phylogenetic studies of Metazoa. However, most researchers have entertained only two competing hypotheses about the position of Myzostomida-an affinity with Annelida and an affinity with Platyhelminthes. In this study, dozens of symplesiomorphies were discovered by means of ancestral state reconstruction in the complete 18S and 28S rDNAs shared by the stem groups of Metazoa. By contrastive analysis on the datasets with or without such symplesiomorphic sites, we discovered that Myzostomida and other basal groups are basal lineages of Bilateria due to the corresponding symplesiomorphies shared with earlier lineages. As such, symplesiomorphies account for approximately 1-2% of the whole dataset have an essential impact on phylogenetic inference, and this study reminds molecular systematists of the importance of carrying out ancestral state reconstruction at each site in sequence-based phylogenetic studies. In addition, reasons should be explored for the low support of the hypothesis that Myzostomida belongs to Annelida in the results of phylogenomic studies. Future phylogenetic studies concerning Myzostomida should include all of the basal lineages of Bilateria to avoid directly neglecting the stand-alone basal position of Myzostomida as a potential hypothesis.
Collapse
|
32
|
Müller CH, Hylleberg J, Michalik P. Complex epidermal organs ofPhascolion(Sipuncula): insights into the evolution of bimodal secretory cells in annelids. ACTA ZOOL-STOCKHOLM 2014. [DOI: 10.1111/azo.12082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carsten H.G. Müller
- Zoologisches Institut und Museum; Ernst-Moritz-Arndt-Universität Greifswald; Johann-Sebastian-Bach-Str. 11/12 D-17487 Greifswald Germany
- Department of Neuroscience; University of Arizona; 1040 E 4th Street PO Box 210077 Tucson AZ 85721 USA
| | - Jørgen Hylleberg
- Department of Marine Ecology; Institute of Biology; Aarhus University; Bld. 1135 Ole Worms alle 1 8000 Aarhus C Denmark
| | - Peter Michalik
- Zoologisches Institut und Museum; Ernst-Moritz-Arndt-Universität Greifswald; Johann-Sebastian-Bach-Str. 11/12 D-17487 Greifswald Germany
| |
Collapse
|
33
|
Temereva EN, Tsitrin EB. Organization and metamorphic remodeling of the nervous system in juveniles of Phoronopsis harmeri (Phoronida): insights into evolution of the bilaterian nervous system. Front Zool 2014; 11:35. [PMID: 24847374 PMCID: PMC4026883 DOI: 10.1186/1742-9994-11-35] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metamorphic remodeling of the nervous system and its organization in juvenile may shed light on early steps of evolution and can be used as an important criterion for establishing the relationships among large groups of animals. The protostomian affiliation of phoronids does not still have certain morphological and embryological proofs. In addition, the relationship of phoronids and other former "lophophorates" is still uncertain. The resolving of these conflicts requires detailed information from poorly investigated members of phoronids, such as Phoronopsis harmeri. RESULTS During metamorphosis, the juvenile consumes the nerve elements of the larval hood. Two dorsolateral groups of larval perikarya remain and give rise to the dorsal ganglion, which appears as the "commissural brain". The juvenile inherits the main and minor tentacular nerve rings from the larva. Although the larval tentacles are directly inherited by the juvenile in P. harmeri, the ultrastructure and location of the definitive tentacular neurite bundles change greatly. Innervation of the juvenile lophophore exhibits a regular alternation of the intertentacular and abfrontal neurite bundles. The giant nerve fiber appears at early stage of metamorphosis and passes from the right group of dorsolateral perikarya to the left side of the body. DISCUSSION THE METAMORPHIC REMODELING OF THE PHORONID NERVOUS SYSTEM OCCURS IN TWO DIFFERENT WAYS: with complete or incomplete destruction of organ systems. The morphology of the lophophore seems similar to those of the former members of "Lophophorata", but its innervation differs greatly. These findings support the separation of bryozoans from Lophophorata and establish a need for new data on the organization of the brachiopod nervous system. The nervous system of the phoronid juvenile is organized as an epidermal nerve plexus but exhibits a nerve center in the anterior portion of the body. The simultaneous presence of both the apical organ and anlage of the cerebral ganglion in phoronids at the larval stage, and the reduction of the apical organ during metamorphosis support the Trochea theory and allow to suggest the presence of two nervous centers in the last common ancestor of the Bilateria. Phoronids retained some plesiomorphic traits and can be regarded as one of the most primitive groups of lophotrochozoans.
Collapse
Affiliation(s)
- Elena N Temereva
- Department of Invertebrate Zoology, Biological faculty, Lomonosov State University, Leninskie Gory 1/12, Moscow 119992, Russian Federation
| | - Eugeni B Tsitrin
- Institute of Developmental Biology, Russian Academy of Sciences, Moscow 117808, Russia
| |
Collapse
|
34
|
Struck TH, Wey-Fabrizius AR, Golombek A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, Kück P, Herlyn H, Hankeln T. Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia. Mol Biol Evol 2014; 31:1833-49. [PMID: 24748651 DOI: 10.1093/molbev/msu143] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.
Collapse
Affiliation(s)
- Torsten H Struck
- Zoological Research Museum Alexander Koenig, Bonn, GermanyUniversity of Osnabrück, FB05 Biology/Chemistry, AG Zoology, Osnabrück, Germany
| | - Alexandra R Wey-Fabrizius
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Anja Golombek
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Hering
- Animal Evolution and Development, Institute of Biology II, University of Leipzig, Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Sabrina Klebow
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Nataliia Iakovenko
- Department of Biology and Ecology, Ostravian University in Ostrava, Ostrava, Czech RepublicDepartment of Invertebrate Fauna and Systematics, Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
| | | | - Malte Petersen
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Patrick Kück
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
35
|
Wey-Fabrizius AR, Herlyn H, Rieger B, Rosenkranz D, Witek A, Welch DBM, Ebersberger I, Hankeln T. Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage. PLoS One 2014; 9:e88618. [PMID: 24520404 PMCID: PMC3919803 DOI: 10.1371/journal.pone.0088618] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 01/15/2014] [Indexed: 11/25/2022] Open
Abstract
The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparasitism. Here, we report the first phylogenomic analysis that includes all four higher-ranked groups of Syndermata. The analyzed data sets comprise new transcriptome data for Seison spec. (Seisonidea), Brachionus manjavacas (Monogononta), Adineta vaga (Bdelloidea), and Paratenuisentis ambiguus (Acanthocephala). Maximum likelihood and Bayesian trees for a total of 19 metazoan species were reconstructed from up to 410 functionally diverse proteins. The results unanimously place Monogononta basally within Syndermata, and Bdelloidea appear as the sister group to a clade comprising epizoic Seisonidea and endoparasitic Acanthocephala. Our results support monophyly of Syndermata, Hemirotifera (Bdelloidea + Seisonidea + Acanthocephala), and Pararotatoria (Seisonidea + Acanthocephala), rejecting monophyly of traditional Rotifera and Eurotatoria. This serves as an indication that early acanthocephalans lived epizoically or as ectoparasites on arthropods, before their complex lifecycle with arthropod intermediate and vertebrate definite hosts evolved.
Collapse
Affiliation(s)
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Benjamin Rieger
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - David Rosenkranz
- Institute of Anthropology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alexander Witek
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - David B. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Ingo Ebersberger
- Institute for Cell Biology and Neuroscience, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| |
Collapse
|
36
|
Temereva EN, Tsitrin EB. Development and organization of the larval nervous system in Phoronopsis harmeri: new insights into phoronid phylogeny. Front Zool 2014; 11:3. [PMID: 24418063 PMCID: PMC3924620 DOI: 10.1186/1742-9994-11-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The organization and development of the nervous system has traditionally been used as an important character for establishing the relationships among large groups of animals. According to this criterion, phoronids were initially regarded as deuterostomian but have more recently been regarded as protostomian. The resolving of this conflict requires detailed information from poorly investigated members of phoronids, such as Phoronopsis harmeri. RESULTS The serotonin-like immunoreactive part of the P. harmeri nervous system changes during larval development. These changes mostly concern the nervous system of the hood and correlate with the appearance of the median and two marginal neurite bundles, the frontal organ, and the sensory field. The apical organ has bilateral symmetry. The tentacular neurite bundle passes under the tentacles, contains several types of perikarya, and gives rise to intertentacular bundles, which branch in the tentacle base and penetrate into adjacent tentacles by two lateroabfrontal bundles. There are two groups of dorsolateral perikarya, which exhibit serotonin-like immunoreactivity, contact the tentacular neurite bundle, and are located near the youngest tentacles. Larvae have a minor nerve ring, which originates from the posterior marginal neurite bundle of the hood, passes above the tentacle base, and gives rise to the mediofrontal neurite bundle in each tentacle. Paired laterofrontal neurite bundles of tentacles form a continuous nerve tract that conducts to the postoral ciliated band. DISCUSSION The organization of the nervous system differs among the planktotrophic larvae of phoronid species. These differences may correlate with differences in phoronid biology. Data concerning the innervation of tentacles in different phoronid larvae are conflicting and require careful reinvestigation. The overall organization of the nervous system in phoronid larvae has more in common with the deuterostomian than with the protostomian nervous system. Phoronid larvae demonstrate some "deuterostome-like" features, which are, in fact, have to be ancestral bilaterian characters. Our new results and previous data indicate that phoronids have retained some plesiomorphic features, which were inherited from the last common ancestor of all Bilateria. It follows that phoronids should be extracted from the Trochozoan (=Spiralia) clade and placed at the base of the Lophotrochozoan stem.
Collapse
Affiliation(s)
- Elena N Temereva
- Department of Invertebrate Zoology, Biological faculty, Moscow State University, Moscow 119992, Russia.
| | | |
Collapse
|
37
|
O'Malley MA. When integration fails: Prokaryote phylogeny and the tree of life. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:551-62. [PMID: 23137776 DOI: 10.1016/j.shpsc.2012.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.
Collapse
Affiliation(s)
- Maureen A O'Malley
- Department of Philosophy, University of Sydney, Quadrangle A14, NSW 2006, Australia.
| |
Collapse
|
38
|
The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). BIOMED RESEARCH INTERNATIONAL 2013; 2013:407072. [PMID: 24350268 PMCID: PMC3856133 DOI: 10.1155/2013/407072] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 08/08/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022]
Abstract
Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.
Collapse
|
39
|
Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B. New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol 2013; 13:253. [PMID: 24238092 PMCID: PMC4225663 DOI: 10.1186/1471-2148-13-253] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/07/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity. RESULTS The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata. CONCLUSION Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.
Collapse
Affiliation(s)
- Maximilian P Nesnidal
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| | - Martin Helmkampf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Achim Meyer
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Alexander Witek
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str 74, D-20359 Hamburg, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Str 13, D-60438 Frankfurt, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Torsten H Struck
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D-53113 Bonn, Germany
| | - Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| |
Collapse
|
40
|
Sonnleitner B, Schwaha T, Wanninger A. Inter- and intraspecific plasticity in distribution patterns of immunoreactive compounds in actinotroch larvae of Phoronida (Lophotrochozoa). J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Thomas Schwaha
- Department of Integrative Zoology; University of Vienna; Vienna Austria
| | - Andreas Wanninger
- Department of Integrative Zoology; University of Vienna; Vienna Austria
| |
Collapse
|
41
|
Wey-Fabrizius AR, Podsiadlowski L, Herlyn H, Hankeln T. Platyzoan mitochondrial genomes. Mol Phylogenet Evol 2013; 69:365-75. [DOI: 10.1016/j.ympev.2012.12.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 10/16/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
|
42
|
Struck TH. The impact of paralogy on phylogenomic studies - a case study on annelid relationships. PLoS One 2013; 8:e62892. [PMID: 23667537 PMCID: PMC3647064 DOI: 10.1371/journal.pone.0062892] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/26/2013] [Indexed: 12/15/2022] Open
Abstract
Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus) including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1) a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2) blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case of orthology prediction methods like HaMStR it is likewise decreased by using more than one reference taxon.
Collapse
|
43
|
Fischer AH, Arendt D. Mesoteloblast-Like Mesodermal Stem Cells in the Polychaete AnnelidPlatynereis dumerilii(Nereididae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:94-104. [DOI: 10.1002/jez.b.22486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 01/22/2023]
Affiliation(s)
- Antje H.L. Fischer
- Developmental Biology Unit; European Molecular Biology Laboratory; Heidelberg; Germany
| | - Detlev Arendt
- Developmental Biology Unit; European Molecular Biology Laboratory; Heidelberg; Germany
| |
Collapse
|
44
|
A sclerite-bearing stem group entoproct from the early Cambrian and its implications. Sci Rep 2013; 3:1066. [PMID: 23336066 PMCID: PMC3548229 DOI: 10.1038/srep01066] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/16/2012] [Indexed: 12/17/2022] Open
Abstract
The Lophotrochozoa includes disparate tentacle-bearing sessile protostome animals, which apparently appeared in the Cambrian explosion, but lack an uncontested fossil record. Here we describe abundant well preserved material of Cotyledion tylodes Luo et Hu, 1999, from the Cambrian (Series 2) Chengjiang deposits, reinterpreted here as a stem-group entoproct. The entoproct affinity is supported by the sessile body plan and interior soft anatomy. The body consists of an upper calyx and a lower elongate stalk with a distal holdfast. The soft anatomy includes a U-shaped gut with a mouth and aboral anus ringed by retractable marginal tentacles. Cotyledion differs from extant entoprocts in being larger, and having the calyx and the stalk covered by numerous loosely-spaced external sclerites. The description of entoprocts from the Chengjiang biota traces the ancestry of yet another lophotrochozoan phylum back to the Cambrian radiation, and has important implications for the earliest evolution of lophotrochozoans.
Collapse
|
45
|
Cohen BL. Rerooting the rDNA gene tree reveals phoronids to be ‘brachiopods without shells’; dangers of wide taxon samples in metazoan phylogenetics (Phoronida; Brachiopoda). Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00869.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
46
|
Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol 2012; 64:603-17. [DOI: 10.1016/j.ympev.2012.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
|
47
|
Chen HX, Sun SC, Sundberg P, Ren WC, Norenburg JL. A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea. BMC Genomics 2012; 13:139. [PMID: 22507536 PMCID: PMC3368773 DOI: 10.1186/1471-2164-13-139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 04/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens. RESULTS The sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks. CONCLUSION The two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.
Collapse
Affiliation(s)
- Hai-Xia Chen
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Per Sundberg
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
| | - Wei-Cheng Ren
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, PO Box 480, SE-405 30, Sweden
| | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0163, USA
| |
Collapse
|
48
|
Neves RC, Kristensen RM, Funch P. Ultrastructure and morphology of the cycliophoran female. J Morphol 2012; 273:850-69. [PMID: 22505145 DOI: 10.1002/jmor.20025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/20/2012] [Accepted: 03/05/2012] [Indexed: 11/10/2022]
Abstract
Knowledge on the morphology of the cycliophoran female has mostly been based on observations of immature females in brood chambers of feeding stages. With the use of light- and transmission electron microscopy, the morphology and ultrastructure of the free and fully mature female of Cycliophora is described now for the first time. The external morphology is characterized by a ciliation consisting of an anteroventral ciliated field, a posterior ciliated tuft, and four sensory structures extending anteriorly from the anteroventral ciliated field. In addition, a small ciliated structure in the midventral region is interpreted as a round-shaped gonopore. Internally, a bilateral cerebral ganglion is situated in the anterior region and a large oocyte is located medially in the body. Several glands are present anteriorly, while posteriorly a pair of glands is associated with the ciliated tuft. Dorsal and ventral longitudinal muscles, as well as, dorsoventral muscles are identified by electron microscopy. Muscle fibers attach to the endocuticle via the epidermis, by means of attachment fibers. An unknown endosymbiont is present throughout the body of the female. We discuss the functional implications of the morphological and ultrastructural aspects of the cycliophoran female. Finally, we compare this life cycle stage with that fromother phyla, suggested as phylogenetically close.
Collapse
Affiliation(s)
- Ricardo Cardoso Neves
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | | | | |
Collapse
|
49
|
Hartmann S, Helm C, Nickel B, Meyer M, Struck TH, Tiedemann R, Selbig J, Bleidorn C. Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS One 2012; 7:e29843. [PMID: 22276131 PMCID: PMC3262807 DOI: 10.1371/journal.pone.0029843] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 12/06/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms. METHODOLOGY Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. CONCLUSIONS Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.
Collapse
Affiliation(s)
- Stefanie Hartmann
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Conrad Helm
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | | | - Ralph Tiedemann
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Joachim Selbig
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Bleidorn
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| |
Collapse
|
50
|
Paps J, Riutort M. Molecular phylogeny of the phylum Gastrotricha: new data brings together molecules and morphology. Mol Phylogenet Evol 2011; 63:208-12. [PMID: 22198640 DOI: 10.1016/j.ympev.2011.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 11/03/2011] [Accepted: 12/08/2011] [Indexed: 11/29/2022]
Abstract
Gastrotricha is a species-rich phylum of microscopical animals that contains two main orders, Chaetonotida and Macrodasyida. Gastrotrichs are important members of the aquatic environment and significant players in the study of animal evolution. In spite of their ecological and evolutionary importance, their internal relationships are not yet well understood. We have produced new sequences for the 18S rDNA gene to improve both the quality and quantity of taxon sampling for the gastrotrichs. Our phylogeny recovers the monophyly of the two main Gastrotricha clades, in contrast to recent studies with similar sampling, but in agreement with morphology based analyses. However, our topology is not able to resolve the first branches of the macrodasyidans or settle the position of the puzzling Neodasys, a controversial genus classified as a chaetonotidan on morphological grounds but placed within macrodasyidans by molecular studies. This analysis is the most exhaustive molecular phylogeny of the phylum to date, and significantly increases our knowledge of gastrotrich evolution.
Collapse
Affiliation(s)
- Jordi Paps
- Department of Zoology, University of Oxford, Tinbergen Building, Oxford OX13PS, United Kingdom.
| | | |
Collapse
|